Nucleic acid sequence Maximum Likelihood method, version 3.573c

Data set # 1:


Empirical Base Frequencies:

   A       0.24654
   C       0.24065
   G       0.29411
  T(U)     0.21869

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.494041)


  +B-clarridg
  !  
  !     +B-spp-Deer
  !  +-10  
  !  !  +B--weissii
  !  !  
  !  !  +B-arupensi
--5--3  !  
  !  !  !        +B-quintana
  !  !  !     +--9  
  !  !  !     !  +B-bacillif
  !  !  !     !  
  !  +--8  +-11     +B-elizabet
  !     !  !  !  +--6  
  !     !  !  !  !  +B-grahamii
  !     !  !  +--7  
  !     !  !     !  +B-birtlesi
  !     !  !     !  !  
  !     +--2     +-12     +B-vinsonii
  !        !        !  +--4  
  !        !        +--1  +B-henselae
  !        !           !  
  !        !           +B--doshiae
  !        !  
  !        +B-berhoffi
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2957.34621

Examined  956 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   5          B-clarridg        0.01193     (  0.00595,     0.01795) **
   5             3              0.00459     (  0.00076,     0.00846) **
   3            10              0.00680     (  0.00231,     0.01123) **
  10          B-spp-Deer        0.00003     (     zero,    infinity)
  10          B--weissii        0.00003     (     zero,    infinity)
   3             8              0.00276     (     zero,     0.00567) **
   8          B-arupensi        0.00076     (     zero,     0.00223) **
   8             2              0.00150     (     zero,     0.00354) **
   2            11              0.00151     (     zero,     0.00355) **
  11             9              0.00220     (     zero,     0.00471) **
   9          B-quintana        0.01111     (  0.00548,     0.01673) **
   9          B-bacillif        0.00817     (  0.00331,     0.01298) **
  11             7              0.00221     (     zero,     0.00470) **
   7             6              0.00219     (     zero,     0.00467) **
   6          B-elizabet        0.00661     (  0.00227,     0.01091) **
   6          B-grahamii        0.00006     (     zero,    infinity)
   7            12              0.00141     (     zero,     0.00342) **
  12          B-birtlesi        0.00363     (  0.00046,     0.00684) **
  12             1              0.00006     (     zero,     0.00218)
   1             4              0.00070     (     zero,     0.00211) **
   4          B-vinsonii        0.00006     (     zero,    infinity)
   4          B-henselae        0.00298     (  0.00001,     0.00584) **
   1          B--doshiae        0.00003     (     zero,    infinity)
   2          B-berhoffi        0.00149     (     zero,     0.00352) **
   5          A-tumefaci        0.05453     (  0.04175,     0.06740) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 2:


Empirical Base Frequencies:

   A       0.24261
   C       0.23236
   G       0.31201
  T(U)     0.21302

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.489540)


  +B-clarridg
  !  
  !                    +B-bacillif
  !                 +--2  
  !                 !  !  +B--weissii
  !              +--6  +-10  
  !              !  !     +B-spp-Deer
  !           +--1  !  
  !           !  !  +B-henselae
  !           !  !  
  !           !  +B-quintana
  !        +--3  
  !        !  !     +B-grahamii
  !        !  !  +-12  
  !        !  !  !  !  +B-birtlesi
  !     +--9  +--8  +-11  
  !     !  !     !     +B--doshiae
  !     !  !     !  
  !  +--4  !     +B-vinsonii
  !  !  !  !  
  !  !  !  +B-arupensi
--5--7  !  
  !  !  +B-berhoffi
  !  !  
  !  +B-elizabet
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3091.90401

Examined  868 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   5          B-clarridg        0.00987     (  0.00439,     0.01537) **
   5             7              0.00522     (  0.00115,     0.00928) **
   7             4              0.00206     (     zero,     0.00463) **
   4             9              0.00070     (     zero,     0.00211) **
   9             3              0.00003     (     zero,    infinity)
   3             1              0.00218     (     zero,     0.00468) **
   1             6              0.00248     (     zero,     0.00526) **
   6             2              0.00645     (  0.00203,     0.01093) **
   2          B-bacillif        0.01468     (  0.00810,     0.02132) **
   2            10              0.00851     (  0.00345,     0.01356) **
  10          B--weissii        0.00222     (     zero,     0.00470) **
  10          B-spp-Deer        0.00006     (     zero,     0.00201)
   6          B-henselae        0.00569     (  0.00156,     0.00976) **
   1          B-quintana        0.00888     (  0.00386,     0.01391) **
   3             8              0.00293     (  0.00007,     0.00580) **
   8            12              0.00006     (     zero,     0.00151)
  12          B-grahamii        0.00143     (     zero,     0.00344) **
  12            11              0.00006     (     zero,    infinity)
  11          B-birtlesi        0.00146     (     zero,     0.00349) **
  11          B--doshiae        0.00146     (     zero,     0.00349) **
   8          B-vinsonii        0.00146     (     zero,     0.00349) **
   9          B-arupensi        0.00365     (  0.00049,     0.00688) **
   4          B-berhoffi        0.00003     (     zero,    infinity)
   7          B-elizabet        0.00597     (  0.00181,     0.01017) **
   5          A-tumefaci        0.06049     (  0.04711,     0.07429) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 3:


Empirical Base Frequencies:

   A       0.23843
   C       0.24073
   G       0.32726
  T(U)     0.19357

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.495474)


  +B-clarridg
  !  
  !           +B-arupensi
  !           !  
  !           !     +B-elizabet
  !           !     !  
  !        +-12  +--9  +B-grahamii
  !        !  !  !  !  !  
  !        !  !  !  +--8     +B--doshiae
  !        !  !  !     !  +-10  
  !        !  +--4     +-11  +B-birtlesi
  !     +--1     !        !  
  !     !  !     !        +B-vinsonii
  !     !  !     !  
  !  +--2  !     +B-henselae
  !  !  !  !  
  !  !  !  +B-berhoffi
--7--5  !  
  !  !  +B-quintana
  !  !  
  !  !  +B-bacillif
  !  +--3  
  !     !  +B--weissii
  !     +--6  
  !        +B-spp-Deer
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3162.01819

Examined  876 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7          B-clarridg        0.00817     (  0.00310,     0.01326) **
   7             5              0.00636     (  0.00157,     0.01105) **
   5             2              0.00373     (  0.00018,     0.00722) **
   2             1              0.00333     (     zero,     0.00660) **
   1            12              0.00003     (     zero,     0.00213)
  12          B-arupensi        0.00077     (     zero,     0.00224) **
  12             4              0.00354     (  0.00011,     0.00697) **
   4             9              0.00003     (     zero,     0.00214)
   9          B-elizabet        0.01030     (  0.00491,     0.01570) **
   9             8              0.00229     (     zero,     0.00517) **
   8          B-grahamii        0.00068     (     zero,     0.00208) *
   8            11              0.00006     (     zero,     0.00171)
  11            10              0.00003     (     zero,    infinity)
  10          B--doshiae        0.00003     (     zero,    infinity)
  10          B-birtlesi        0.00291     (  0.00007,     0.00577) **
  11          B-vinsonii        0.00220     (     zero,     0.00468) **
   4          B-henselae        0.00657     (  0.00224,     0.01087) **
   1          B-berhoffi        0.00221     (     zero,     0.00470) **
   2          B-quintana        0.00860     (  0.00355,     0.01365) **
   5             3              0.00626     (  0.00176,     0.01074) **
   3          B-bacillif        0.01051     (  0.00476,     0.01627) **
   3             6              0.00734     (  0.00258,     0.01211) **
   6          B--weissii        0.00112     (     zero,     0.00320) **
   6          B-spp-Deer        0.00325     (  0.00008,     0.00642) **
   7          A-tumefaci        0.07362     (  0.05883,     0.08909) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 4:


Empirical Base Frequencies:

   A       0.22877
   C       0.24720
   G       0.31061
  T(U)     0.21342

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.514892)


  +B-berhoffi
  !  
  !           +B-birtlesi
  !        +-12  
  !        !  +B--doshiae
  !        !  
  !        !        +B-bacillif
  !     +--5     +-10  
  !     !  !     !  !  +B-spp-Deer
  !     !  !  +--8  +-11  
  !     !  !  !  !     +B--weissii
  !     !  +--4  !  
  !  +--1     !  +B-henselae
  !  !  !     !  
  !  !  !     +B-vinsonii
  !  !  !  
  !  !  !  +B-grahamii
--3--2  +--7  
  !  !     +B-elizabet
  !  !  
  !  !     +B-quintana
  !  !  +--6  
  !  +--9  +B-clarridg
  !     !  
  !     +B-arupensi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3132.91573

Examined  544 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   3          B-berhoffi        0.00006     (     zero,     0.00152)
   3             2              0.00075     (     zero,     0.00221) **
   2             1              0.00367     (  0.00046,     0.00689) **
   1             5              0.00150     (     zero,     0.00355) **
   5            12              0.00003     (     zero,    infinity)
  12          B-birtlesi        0.00436     (  0.00092,     0.00788) **
  12          B--doshiae        0.00003     (     zero,    infinity)
   5             4              0.00069     (     zero,     0.00209) **
   4             8              0.00593     (  0.00180,     0.01001) **
   8            10              0.00591     (  0.00180,     0.01002) **
  10          B-bacillif        0.01188     (  0.00605,     0.01771) **
  10            11              0.00370     (  0.00045,     0.00695) **
  11          B-spp-Deer        0.00074     (     zero,     0.00218) **
  11          B--weissii        0.00072     (     zero,     0.00214) **
   8          B-henselae        0.00218     (     zero,     0.00468) **
   4          B-vinsonii        0.00151     (     zero,     0.00357) **
   1             7              0.00064     (     zero,     0.00209)
   7          B-grahamii        0.00011     (     zero,     0.00155)
   7          B-elizabet        0.00959     (  0.00438,     0.01480) **
   2             9              0.00003     (     zero,     0.00217)
   9             6              0.00645     (  0.00202,     0.01089) **
   6          B-quintana        0.01138     (  0.00559,     0.01721) **
   6          B-clarridg        0.01248     (  0.00653,     0.01854) **
   9          B-arupensi        0.00364     (  0.00048,     0.00687) **
   3          A-tumefaci        0.06496     (  0.05105,     0.07924) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 5:


Empirical Base Frequencies:

   A       0.24379
   C       0.24394
   G       0.29232
  T(U)     0.21996

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.498334)


  +B-clarridg
  !  
  !     +B-arupensi
  !  +--4  
  !  !  +B-berhoffi
  !  !  
  !  !              +B-elizabet
  !  !           +--8  
  !  !        +--2  +B-grahamii
--9--5        !  !  
  !  !     +-10  +B-birtlesi
  !  !     !  !  
  !  !  +--6  +B-vinsonii
  !  !  !  !  
  !  !  !  +B--doshiae
  !  +--3  
  !     !     +B-bacillif
  !     !  +-12  
  !     !  !  +B-quintana
  !     +--7  
  !        !     +B--weissii
  !        !  +-11  
  !        +--1  +B-spp-Deer
  !           !  
  !           +B-henselae
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3088.38505

Examined  828 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   9          B-clarridg        0.00808     (  0.00304,     0.01315) **
   9             5              0.00811     (  0.00304,     0.01318) **
   5             4              0.00006     (     zero,    infinity)
   4          B-arupensi        0.00220     (     zero,     0.00468) **
   4          B-berhoffi        0.00220     (     zero,     0.00469) **
   5             3              0.00073     (     zero,     0.00217) **
   3             6              0.00145     (     zero,     0.00349) **
   6            10              0.00006     (     zero,     0.00181)
  10             2              0.00003     (     zero,     0.00188)
   2             8              0.00146     (     zero,     0.00350) **
   8          B-elizabet        0.01174     (  0.00601,     0.01752) **
   8          B-grahamii        0.00006     (     zero,     0.00181)
   2          B-birtlesi        0.00292     (  0.00007,     0.00578) **
  10          B-vinsonii        0.00146     (     zero,     0.00347) **
   6          B--doshiae        0.00006     (     zero,    infinity)
   3             7              0.00293     (  0.00006,     0.00580) **
   7            12              0.00512     (  0.00131,     0.00895) **
  12          B-bacillif        0.01256     (  0.00660,     0.01857) **
  12          B-quintana        0.00516     (  0.00131,     0.00900) **
   7             1              0.00072     (     zero,     0.00218) *
   1            11              0.00807     (  0.00331,     0.01286) **
  11          B--weissii        0.00149     (     zero,     0.00352) **
  11          B-spp-Deer        0.00076     (     zero,     0.00222) **
   1          B-henselae        0.00372     (  0.00042,     0.00694) **
   9          A-tumefaci        0.07167     (  0.05706,     0.08669) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 6:


Empirical Base Frequencies:

   A       0.25343
   C       0.22562
   G       0.31730
  T(U)     0.20364

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.466659)


  +B-elizabet
  !  
  !  +B-berhoffi
  !  !  
  !  !        +B-grahamii
  !  !        !  
  !  !        !        +B-henselae
  !  !     +--9     +--5  
  !  !     !  !  +--3  +B-vinsonii
--7--4     !  !  !  !  
  !  !  +--8  +-12  +B-birtlesi
  !  !  !  !     !  
  !  !  !  !     +B--doshiae
  !  !  !  !  
  !  !  !  +B-arupensi
  !  !  !  
  !  +--6           +B--weissii
  !     !        +-10  
  !     !     +--1  +B-spp-Deer
  !     !     !  !  
  !     !  +--2  +B-clarridg
  !     !  !  !  
  !     +-11  +B-bacillif
  !        !  
  !        +B-quintana
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3021.72187

Examined  840 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7          B-elizabet        0.00557     (  0.00140,     0.00980) **
   7             4              0.00573     (  0.00150,     0.00994) **
   4          B-berhoffi        0.00050     (     zero,     0.00192)
   4             6              0.00168     (     zero,     0.00396) **
   6             8              0.00003     (     zero,     0.00168)
   8             9              0.00219     (     zero,     0.00467) **
   9          B-grahamii        0.00070     (     zero,     0.00211) **
   9            12              0.00068     (     zero,     0.00205) **
  12             3              0.00003     (     zero,    infinity)
   3             5              0.00145     (     zero,     0.00348) **
   5          B-henselae        0.00659     (  0.00230,     0.01091) **
   5          B-vinsonii        0.00147     (     zero,     0.00351) **
   3          B-birtlesi        0.00219     (     zero,     0.00466) **
  12          B--doshiae        0.00071     (     zero,     0.00211) **
   8          B-arupensi        0.00513     (  0.00134,     0.00895) **
   6            11              0.00374     (  0.00025,     0.00726) **
  11             2              0.00381     (  0.00050,     0.00720) **
   2             1              0.00158     (     zero,     0.00431) **
   1            10              0.00788     (  0.00313,     0.01266) **
  10          B--weissii        0.00165     (     zero,     0.00387) **
  10          B-spp-Deer        0.00130     (     zero,     0.00331) **
   1          B-clarridg        0.00893     (  0.00380,     0.01404) **
   2          B-bacillif        0.00942     (  0.00406,     0.01479) **
  11          B-quintana        0.00951     (  0.00417,     0.01485) **
   7          A-tumefaci        0.04898     (  0.03715,     0.06135) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 7:


Empirical Base Frequencies:

   A       0.23713
   C       0.22719
   G       0.32986
  T(U)     0.20582

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.488316)


        +B-spp-Deer
     +--9  
     !  +B--weissii
     !  
  +--6  +B-berhoffi
  !  !  !  
  !  !  !     +B-quintana
  !  !  !  +--8  
  !  +--1  !  +B-arupensi
  !     !  !  
  !     !  !        +B-vinsonii
  !     !  !     +-11  
  !     +--3     !  !  +B-birtlesi
  !        !     !  +--2  
  !        !  +--5     +B--doshiae
  !        !  !  !  
  !        !  !  !     +B-elizabet
  !        !  !  !  +-12  
  !        +-10  +--4  +B-grahamii
  !           !     !  
  !           !     +B-henselae
  !           !  
  !           +B-bacillif
  !  
--7-B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3034.79178

Examined 1012 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7             6              0.00488     (  0.00089,     0.00886) **
   6             9              0.01043     (  0.00496,     0.01594) **
   9          B-spp-Deer        0.00121     (     zero,     0.00337) **
   9          B--weissii        0.00243     (     zero,     0.00525) **
   6             1              0.00450     (  0.00073,     0.00831) **
   1          B-berhoffi        0.00146     (     zero,     0.00348) **
   1             3              0.00006     (     zero,    infinity)
   3             8              0.00076     (     zero,     0.00221) **
   8          B-quintana        0.01176     (  0.00601,     0.01754) **
   8          B-arupensi        0.00006     (     zero,    infinity)
   3            10              0.00221     (     zero,     0.00470) **
  10             5              0.00151     (     zero,     0.00356) **
   5            11              0.00006     (     zero,    infinity)
  11          B-vinsonii        0.00292     (  0.00007,     0.00579) **
  11             2              0.00006     (     zero,    infinity)
   2          B-birtlesi        0.00223     (     zero,     0.00471) **
   2          B--doshiae        0.00003     (     zero,    infinity)
   5             4              0.00076     (     zero,     0.00222) **
   4            12              0.00075     (     zero,     0.00219) **
  12          B-elizabet        0.00882     (  0.00382,     0.01380) **
  12          B-grahamii        0.00006     (     zero,    infinity)
   4          B-henselae        0.00586     (  0.00181,     0.00992) **
  10          B-bacillif        0.01330     (  0.00714,     0.01944) **
   7          B-clarridg        0.00465     (  0.00081,     0.00848) **
   7          A-tumefaci        0.06761     (  0.05321,     0.08199) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 8:


Empirical Base Frequencies:

   A       0.22968
   C       0.24170
   G       0.31401
  T(U)     0.21461

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.510947)


  +B-clarridg
  !  
  !              +B-arupensi
  !           +-10  
  !           !  +B-vinsonii
  !        +--4  
  !        !  !     +B-grahamii
  !        !  !  +--2  
  !        !  +-12  +B-birtlesi
  !     +--8     !  
  !     !  !     +B--doshiae
  !     !  !  
  !     !  !  +B-henselae
  !     !  !  !  
  !     !  +--5  +B-quintana
  !  +--1     !  !  
  !  !  !     +--9     +B--weissii
  !  !  !        !  +-11  
  !  !  !        +--3  +B-spp-Deer
--7--6  !           !  
  !  !  !           +B-bacillif
  !  !  !  
  !  !  +B-elizabet
  !  !  
  !  +B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3081.90701

Examined  542 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7          B-clarridg        0.00954     (  0.00426,     0.01494) **
   7             6              0.00587     (  0.00164,     0.01020) **
   6             1              0.00225     (     zero,     0.00477) **
   1             8              0.00223     (     zero,     0.00475) **
   8             4              0.00018     (     zero,     0.00219)
   4            10              0.00150     (     zero,     0.00354) **
  10          B-arupensi        0.00294     (  0.00007,     0.00582) **
  10          B-vinsonii        0.00215     (     zero,     0.00462) **
   4            12              0.00059     (     zero,     0.00260)
  12             2              0.00059     (     zero,     0.00260)
   2          B-grahamii        0.00144     (     zero,     0.00344) **
   2          B-birtlesi        0.00074     (     zero,     0.00218) **
  12          B--doshiae        0.00006     (     zero,    infinity)
   8             5              0.00357     (  0.00034,     0.00679) **
   5          B-henselae        0.00229     (     zero,     0.00491) **
   5             9              0.00260     (     zero,     0.00552) **
   9          B-quintana        0.01582     (  0.00902,     0.02266) **
   9             3              0.00446     (  0.00073,     0.00826) **
   3            11              0.00508     (  0.00112,     0.00908) **
  11          B--weissii        0.00076     (     zero,     0.00222) **
  11          B-spp-Deer        0.00221     (     zero,     0.00470) **
   3          B-bacillif        0.00598     (  0.00160,     0.01036) **
   1          B-elizabet        0.00807     (  0.00331,     0.01285) **
   6          B-berhoffi        0.00003     (     zero,    infinity)
   7          A-tumefaci        0.06420     (  0.05043,     0.07848) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 9:


Empirical Base Frequencies:

   A       0.25233
   C       0.21850
   G       0.31746
  T(U)     0.21171

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.466666)


  +B-bacillif
  !  
  !     +B--weissii
  !  +-10  
  !  !  +B-spp-Deer
  !  !  
  !  !        +B-henselae
  !  !     +--9  
  !  !     !  +B--doshiae
--3--6  +--4  
  !  !  !  !  +B-vinsonii
  !  !  !  !  !  
  !  !  !  +--8     +B-grahamii
  !  !  !     !  +--7  
  !  !  !     +--2  +B-elizabet
  !  +--5        !  
  !     !        +B-birtlesi
  !     !  
  !     !        +B-clarridg
  !     !     +-11  
  !     !  +-12  +B-quintana
  !     !  !  !  
  !     +--1  +B-berhoffi
  !        !  
  !        +B-arupensi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3120.62511

Examined 1204 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   3          B-bacillif        0.00636     (  0.00175,     0.01099) **
   3             6              0.00554     (  0.00109,     0.01001) **
   6            10              0.01041     (  0.00484,     0.01598) **
  10          B--weissii        0.00003     (     zero,    infinity)
  10          B-spp-Deer        0.00365     (  0.00046,     0.00684) **
   6             5              0.00602     (  0.00157,     0.01054) **
   5             4              0.00337     (  0.00015,     0.00650) **
   4             9              0.00218     (     zero,     0.00465) **
   9          B-henselae        0.00364     (  0.00047,     0.00683) **
   9          B--doshiae        0.00006     (     zero,    infinity)
   4             8              0.00003     (     zero,     0.00168)
   8          B-vinsonii        0.00219     (     zero,     0.00466) **
   8             2              0.00006     (     zero,     0.00279)
   2             7              0.00213     (     zero,     0.00459) **
   7          B-grahamii        0.00006     (     zero,    infinity)
   7          B-elizabet        0.01175     (  0.00599,     0.01751) **
   2          B-birtlesi        0.00359     (  0.00044,     0.00679) **
   5             1              0.00006     (     zero,     0.00163)
   1            12              0.00250     (     zero,     0.00525) **
  12            11              0.00587     (  0.00177,     0.00997) **
  11          B-clarridg        0.01778     (  0.01065,     0.02492) **
  11          B-quintana        0.00438     (  0.00084,     0.00795) **
  12          B-berhoffi        0.00070     (     zero,     0.00211) *
   1          B-arupensi        0.00070     (     zero,     0.00210) **
   3          A-tumefaci        0.06094     (  0.04734,     0.07462) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 10:


Empirical Base Frequencies:

   A       0.24740
   C       0.23132
   G       0.32259
  T(U)     0.19869

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.476025)


  +B-berhoffi
  !  
  !        +B-quintana
  !        !  
  !     +--7     +B-bacillif
  !     !  !  +-12  
  !     !  !  !  !  +B--weissii
  !     !  +--4  +--8  
  !  +--1     !     +B-spp-Deer
  !  !  !     !  
  !  !  !     +B-clarridg
  !  !  !  
  !  !  +B-arupensi
  !  !  
-11--3        +B-henselae
  !  !     +--5  
  !  !     !  !  +B-elizabet
  !  !     !  +--2  
  !  !  +-10     +B-grahamii
  !  !  !  !  
  !  !  !  !  +B-birtlesi
  !  +--9  +--6  
  !     !     +B--doshiae
  !     !  
  !     +B-vinsonii
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2981.88858

Examined  690 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  11          B-berhoffi        0.00006     (     zero,     0.00152)
  11             3              0.00149     (     zero,     0.00357) **
   3             1              0.00003     (     zero,    infinity)
   1             7              0.00296     (  0.00008,     0.00591) **
   7          B-quintana        0.00662     (  0.00230,     0.01097) **
   7             4              0.00090     (     zero,     0.00269) *
   4            12              0.00589     (  0.00177,     0.01003) **
  12          B-bacillif        0.00893     (  0.00379,     0.01407) **
  12             8              0.01114     (  0.00543,     0.01686) **
   8          B--weissii        0.00223     (     zero,     0.00473) **
   8          B-spp-Deer        0.00003     (     zero,     0.00185)
   4          B-clarridg        0.00574     (  0.00156,     0.00982) **
   1          B-arupensi        0.00291     (  0.00010,     0.00580) **
   3             9              0.00439     (  0.00088,     0.00792) **
   9            10              0.00003     (     zero,     0.00174)
  10             5              0.00150     (     zero,     0.00355) **
   5          B-henselae        0.00807     (  0.00333,     0.01287) **
   5             2              0.00077     (     zero,     0.00224) **
   2          B-elizabet        0.00586     (  0.00183,     0.00994) **
   2          B-grahamii        0.00003     (     zero,    infinity)
  10             6              0.00003     (     zero,    infinity)
   6          B-birtlesi        0.00146     (     zero,     0.00349) **
   6          B--doshiae        0.00074     (     zero,     0.00219) **
   9          B-vinsonii        0.00220     (     zero,     0.00468) **
  11          A-tumefaci        0.06421     (  0.05048,     0.07835) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 11:


Empirical Base Frequencies:

   A       0.25287
   C       0.21950
   G       0.31945
  T(U)     0.20818

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.464027)


  +B-clarridg
  !  
  !     +B-quintana
  !     !  
  !  +--7  +B-berhoffi
  !  !  !  !  
  !  !  !  !  +B-arupensi
  !  !  +--1  !  
  !  !     !  !              +B-vinsonii
  !  !     !  !           +--6  
  !  !     !  !        +-12  +B-birtlesi
  !  !     +-10        !  !  
  !  !        !     +--4  +B-grahamii
-11--8        !     !  !  
  !  !        !  +--2  +B--doshiae
  !  !        !  !  !  
  !  !        +--5  +B-henselae
  !  !           !  
  !  !           +B-elizabet
  !  !  
  !  !     +B--weissii
  !  !  +--3  
  !  +--9  +B-spp-Deer
  !     !  
  !     +B-bacillif
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3222.94988

Examined  796 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  11          B-clarridg        0.00845     (  0.00325,     0.01369) **
  11             8              0.00636     (  0.00166,     0.01113) **
   8             7              0.00343     (     zero,     0.00702) **
   7          B-quintana        0.00874     (  0.00358,     0.01379) **
   7             1              0.00463     (  0.00078,     0.00842) **
   1          B-berhoffi        0.00143     (     zero,     0.00344) **
   1            10              0.00003     (     zero,     0.00188)
  10          B-arupensi        0.00661     (  0.00230,     0.01093) **
  10             5              0.00390     (  0.00042,     0.00734) **
   5             2              0.00003     (     zero,     0.00189)
   2             4              0.00191     (     zero,     0.00445) **
   4            12              0.00006     (     zero,     0.00182)
  12             6              0.00006     (     zero,    infinity)
   6          B-vinsonii        0.00292     (  0.00007,     0.00578) **
   6          B-birtlesi        0.00069     (     zero,     0.00208) **
  12          B-grahamii        0.00144     (     zero,     0.00345) **
   4          B--doshiae        0.00003     (     zero,    infinity)
   2          B-henselae        0.00586     (  0.00180,     0.00991) **
   5          B-elizabet        0.01031     (  0.00490,     0.01570) **
   8             9              0.00762     (  0.00260,     0.01270) **
   9             3              0.00962     (  0.00413,     0.01508) **
   3          B--weissii        0.00113     (     zero,     0.00318) **
   3          B-spp-Deer        0.00327     (  0.00010,     0.00645) **
   9          B-bacillif        0.01074     (  0.00490,     0.01669) **
  11          A-tumefaci        0.06617     (  0.05232,     0.08082) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 12:


Empirical Base Frequencies:

   A       0.24647
   C       0.22937
   G       0.32030
  T(U)     0.20387

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.477960)


           +B-quintana
           !  
        +--4  +B-arupensi
        !  !  !  
        !  !  !  +B-berhoffi
        !  +-11  !  
        !     !  !        +B-elizabet
        !     !  !     +--7  
        !     +--2     !  +B-grahamii
        !        !  +--6  
     +--9        !  !  !  +B-henselae
     !  !        !  !  +--1  
     !  !        +-10     +B-vinsonii
     !  !           !  
     !  !           !  +B--doshiae
  +-12  !           +--8  
  !  !  !              +B-birtlesi
  !  !  !  
  !  !  +B-clarridg
  !  !  
  !  +B-bacillif
  !  
  !  +B--weissii
--3--5  
  !  +B-spp-Deer
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2914.47974

Examined  586 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   3            12              0.00491     (  0.00101,     0.00876) **
  12             9              0.00231     (     zero,     0.00500) **
   9             4              0.00348     (  0.00028,     0.00669) **
   4          B-quintana        0.00815     (  0.00324,     0.01303) **
   4            11              0.00289     (     zero,     0.00590) **
  11          B-arupensi        0.00146     (     zero,     0.00348) **
  11             2              0.00003     (     zero,    infinity)
   2          B-berhoffi        0.00150     (     zero,     0.00353) **
   2            10              0.00146     (     zero,     0.00348) **
  10             6              0.00003     (     zero,     0.00162)
   6             7              0.00219     (     zero,     0.00467) **
   7          B-elizabet        0.01169     (  0.00603,     0.01749) **
   7          B-grahamii        0.00006     (     zero,     0.00181)
   6             1              0.00146     (     zero,     0.00348) **
   1          B-henselae        0.00371     (  0.00041,     0.00690) **
   1          B-vinsonii        0.00075     (     zero,     0.00220) **
  10             8              0.00006     (     zero,    infinity)
   8          B--doshiae        0.00071     (     zero,     0.00211) **
   8          B-birtlesi        0.00074     (     zero,     0.00218) **
   9          B-clarridg        0.00684     (  0.00230,     0.01138) **
  12          B-bacillif        0.00739     (  0.00267,     0.01207) **
   3             5              0.00247     (     zero,     0.00554) **
   5          B--weissii        0.00076     (     zero,     0.00222) **
   5          B-spp-Deer        0.00072     (     zero,     0.00213) **
   3          A-tumefaci        0.05826     (  0.04517,     0.07178) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 13:


Empirical Base Frequencies:

   A       0.25067
   C       0.23017
   G       0.29985
  T(U)     0.21931

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.483923)


  +B-bacillif
  !  
  !     +B-spp-Deer
  !  +--6  
  !  !  +B--weissii
--5--1  
  !  !  +B-clarridg
  !  !  !  
  !  +--2  +B-quintana
  !     !  !  
  !     !  !  +B-arupensi
  !     +--4  !  
  !        !  !     +B-elizabet
  !        !  !     !  
  !        +--3  +-10  +B-grahamii
  !           !  !  !  !  
  !           !  !  +--7     +B--doshiae
  !           !  !     !  +-12  
  !           !  !     !  !  !  +B-henselae
  !           +--8     +--9  +-11  
  !              !        !     +B-vinsonii
  !              !        !  
  !              !        +B-birtlesi
  !              !  
  !              +B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3084.53615

Examined  722 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   5          B-bacillif        0.00537     (  0.00128,     0.00946) **
   5             1              0.00467     (  0.00073,     0.00862) **
   1             6              0.00486     (  0.00096,     0.00876) **
   6          B-spp-Deer        0.00146     (     zero,     0.00350) **
   6          B--weissii        0.00003     (     zero,     0.00224)
   1             2              0.00521     (  0.00131,     0.00919) **
   2          B-clarridg        0.00989     (  0.00441,     0.01530) **
   2             4              0.00459     (  0.00076,     0.00845) **
   4          B-quintana        0.00906     (  0.00387,     0.01427) **
   4             3              0.00438     (  0.00059,     0.00812) **
   3          B-arupensi        0.00515     (  0.00134,     0.00897) **
   3             8              0.00006     (     zero,     0.00179)
   8            10              0.00217     (     zero,     0.00466) **
  10          B-elizabet        0.00592     (  0.00180,     0.01001) **
  10             7              0.00143     (     zero,     0.00346) **
   7          B-grahamii        0.00003     (     zero,     0.00183)
   7             9              0.00220     (     zero,     0.00469) **
   9            12              0.00003     (     zero,     0.00222)
  12          B--doshiae        0.00006     (     zero,    infinity)
  12            11              0.00069     (     zero,     0.00209) **
  11          B-henselae        0.00368     (  0.00045,     0.00689) **
  11          B-vinsonii        0.00295     (  0.00005,     0.00583) **
   9          B-birtlesi        0.00365     (  0.00044,     0.00685) **
   8          B-berhoffi        0.00145     (     zero,     0.00347) **
   5          A-tumefaci        0.06774     (  0.05361,     0.08240) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 14:


Empirical Base Frequencies:

   A       0.25278
   C       0.23624
   G       0.31552
  T(U)     0.19546

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.474839)


                    +B-birtlesi
                 +--2  
                 !  !  +B-elizabet
                 !  +--4  
              +--5     +B-grahamii
              !  !  
              !  !  +B-vinsonii
              !  +--8  
           +-10     !  +B--doshiae
           !  !     +--6  
           !  !        +B-henselae
           !  !  
           !  !  +B-arupensi
        +--1  +--7  
        !  !     !  +B--weissii
        !  !     +-12  
     +--9  !        +B-spp-Deer
     !  !  !  
     !  !  +B-berhoffi
  +-11  !  
  !  !  +B-quintana
  !  !  
  !  +B-bacillif
  !  
--3-B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3042.41039

Examined 1092 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   3            11              0.00376     (  0.00034,     0.00717) **
  11             9              0.00509     (  0.00125,     0.00896) **
   9             1              0.00077     (     zero,     0.00236) *
   1            10              0.00292     (  0.00007,     0.00578) **
  10             5              0.00365     (  0.00046,     0.00685) **
   5             2              0.00003     (     zero,     0.00266)
   2          B-birtlesi        0.00656     (  0.00227,     0.01086) **
   2             4              0.00435     (  0.00086,     0.00786) **
   4          B-elizabet        0.00585     (  0.00180,     0.00990) **
   4          B-grahamii        0.00006     (     zero,     0.00201)
   5             8              0.00003     (     zero,    infinity)
   8          B-vinsonii        0.00149     (     zero,     0.00352) **
   8             6              0.00151     (     zero,     0.00354) **
   6          B--doshiae        0.00006     (     zero,    infinity)
   6          B-henselae        0.00364     (  0.00046,     0.00684) **
  10             7              0.00006     (     zero,    infinity)
   7          B-arupensi        0.00219     (     zero,     0.00467) **
   7            12              0.01100     (  0.00542,     0.01656) **
  12          B--weissii        0.00146     (     zero,     0.00348) **
  12          B-spp-Deer        0.00003     (     zero,    infinity)
   1          B-berhoffi        0.00149     (     zero,     0.00352) **
   9          B-quintana        0.01020     (  0.00484,     0.01561) **
  11          B-bacillif        0.01176     (  0.00599,     0.01764) **
   3          B-clarridg        0.00447     (  0.00080,     0.00819) **
   3          A-tumefaci        0.05842     (  0.04510,     0.07178) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 15:


Empirical Base Frequencies:

   A       0.22974
   C       0.23222
   G       0.33428
  T(U)     0.20376

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.502655)


           +B-berhoffi
        +--5  
        !  !  +B-arupensi
        !  +--1  
        !     +B-quintana
     +--2  
     !  !  +B-bacillif
     !  !  !  
     !  !  !     +B-birtlesi
     !  +--8  +--7  
     !     !  !  !  +B-henselae
     !     !  !  +--3  
     !     !  !     !  +B-elizabet
  +--6     +--9     +-10  
  !  !        !        +B-grahamii
  !  !        !  
  !  !        !  +B-vinsonii
  !  !        +-11  
  !  !           +B--doshiae
  !  !  
  !  !  +B-spp-Deer
  !  +-12  
  !     +B--weissii
  !  
--4-B-clarridg
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2972.16668

Examined 1976 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   4             6              0.00358     (     zero,     0.00713) **
   6             2              0.00353     (  0.00026,     0.00680) **
   2             5              0.00003     (     zero,     0.00208)
   5          B-berhoffi        0.00217     (     zero,     0.00465) **
   5             1              0.00074     (     zero,     0.00218) **
   1          B-arupensi        0.00220     (     zero,     0.00468) **
   1          B-quintana        0.01175     (  0.00598,     0.01750) **
   2             8              0.00308     (     zero,     0.00618) **
   8          B-bacillif        0.00876     (  0.00385,     0.01376) **
   8             9              0.00202     (     zero,     0.00464) **
   9             7              0.00006     (     zero,     0.00187)
   7          B-birtlesi        0.00145     (     zero,     0.00346) **
   7             3              0.00147     (     zero,     0.00350) **
   3          B-henselae        0.00365     (  0.00046,     0.00685) **
   3            10              0.00070     (     zero,     0.00209) **
  10          B-elizabet        0.00877     (  0.00382,     0.01375) **
  10          B-grahamii        0.00006     (     zero,     0.00149)
   9            11              0.00004     (     zero,    infinity)
  11          B-vinsonii        0.00146     (     zero,     0.00347) **
  11          B--doshiae        0.00070     (     zero,     0.00209) **
   6            12              0.00746     (  0.00278,     0.01212) **
  12          B-spp-Deer        0.00003     (     zero,     0.00181)
  12          B--weissii        0.00290     (  0.00007,     0.00576) **
   4          B-clarridg        0.00782     (  0.00285,     0.01281) **
   4          A-tumefaci        0.05829     (  0.04521,     0.07176) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 16:


Empirical Base Frequencies:

   A       0.23552
   C       0.23264
   G       0.34362
  T(U)     0.18822

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.488020)


     +B-elizabet
     !  
     !  +B-berhoffi
     !  !  
     !  !              +B-grahamii
  +--3  !           +--9  
  !  !  !           !  +B-birtlesi
  !  !  !           !  
  !  !  !           !        +B-bacillif
  !  !  !        +--5     +--4  
  !  +--6        !  !     !  !  +B-spp-Deer
  !     !        !  !  +--2  +-11  
  !     !        !  !  !  !     +B--weissii
  !     !     +--7  +--8  !  
  !     !     !  !     !  +B-henselae
  !     !     !  !     !  
  !     !  +--1  !     +B--doshiae
  !     !  !  !  !  
  !     !  !  !  +B-vinsonii
  !     +-12  !  
  !        !  +B-arupensi
  !        !  
  !        +B-quintana
  !  
-10-B-clarridg
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2896.02821

Examined  978 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10             3              0.00780     (  0.00293,     0.01271) **
   3          B-elizabet        0.00907     (  0.00391,     0.01419) **
   3             6              0.00125     (     zero,     0.00333) *
   6          B-berhoffi        0.00003     (     zero,    infinity)
   6            12              0.00216     (     zero,     0.00463) **
  12             1              0.00098     (     zero,     0.00284) **
   1             7              0.00294     (     zero,     0.00600) **
   7             5              0.00098     (     zero,     0.00284) **
   5             9              0.00097     (     zero,     0.00287)
   9          B-grahamii        0.00219     (     zero,     0.00466) **
   9          B-birtlesi        0.00006     (     zero,     0.00164)
   5             8              0.00072     (     zero,     0.00214) **
   8             2              0.00145     (     zero,     0.00348) **
   2             4              0.00556     (  0.00153,     0.00961) **
   4          B-bacillif        0.00508     (  0.00119,     0.00906) **
   4            11              0.00546     (  0.00144,     0.00951) **
  11          B-spp-Deer        0.00142     (     zero,     0.00343) **
  11          B--weissii        0.00076     (     zero,     0.00222) **
   2          B-henselae        0.00293     (  0.00006,     0.00581) **
   8          B--doshiae        0.00003     (     zero,    infinity)
   7          B-vinsonii        0.00003     (     zero,    infinity)
   1          B-arupensi        0.00221     (     zero,     0.00470) **
  12          B-quintana        0.00735     (  0.00277,     0.01188) **
  10          B-clarridg        0.00651     (  0.00187,     0.01106) **
  10          A-tumefaci        0.05245     (  0.04011,     0.06529) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 17:


Empirical Base Frequencies:

   A       0.23934
   C       0.24327
   G       0.28623
  T(U)     0.23116

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.502557)


  +B-berhoffi
  !  
  !     +B-quintana
  !  +-10  
  !  !  +B-arupensi
  !  !  
  !  !  +B-clarridg
--1--5  !  
  !  !  !        +B-henselae
  !  !  !        !  
  !  !  !        !        +B-birtlesi
  !  !  !     +--4     +-11  
  !  +--6     !  !     !  !  +B-elizabet
  !     !     !  !  +--8  +-12  
  !     !     !  !  !  !     +B-grahamii
  !     !  +--3  +--9  !  
  !     !  !  !     !  +B--doshiae
  !     !  !  !     !  
  !     !  !  !     +B-vinsonii
  !     +--2  !  
  !        !  +B-bacillif
  !        !  
  !        !  +B-spp-Deer
  !        +--7  
  !           +B--weissii
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2933.46923

Examined  896 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   1          B-berhoffi        0.00003     (     zero,     0.00180)
   1             5              0.00311     (  0.00012,     0.00617) **
   5            10              0.00146     (     zero,     0.00349) **
  10          B-quintana        0.00643     (  0.00209,     0.01071) **
  10          B-arupensi        0.00095     (     zero,     0.00272) **
   5             6              0.00138     (     zero,     0.00359) **
   6          B-clarridg        0.01259     (  0.00660,     0.01859) **
   6             2              0.00342     (     zero,     0.00686) **
   2             3              0.00372     (  0.00028,     0.00717) **
   3             4              0.00505     (  0.00097,     0.00910) **
   4          B-henselae        0.00410     (  0.00064,     0.00760) **
   4             9              0.00348     (  0.00014,     0.00682) **
   9             8              0.00003     (     zero,     0.00242)
   8            11              0.00006     (     zero,     0.00158)
  11          B-birtlesi        0.00003     (     zero,    infinity)
  11            12              0.00144     (     zero,     0.00346) **
  12          B-elizabet        0.00807     (  0.00331,     0.01285) **
  12          B-grahamii        0.00006     (     zero,     0.00181)
   8          B--doshiae        0.00003     (     zero,    infinity)
   9          B-vinsonii        0.00292     (  0.00002,     0.00579) **
   3          B-bacillif        0.00301     (     zero,     0.00624) **
   2             7              0.00349     (  0.00017,     0.00680) **
   7          B-spp-Deer        0.00003     (     zero,     0.00187)
   7          B--weissii        0.00141     (     zero,     0.00342) **
   1          A-tumefaci        0.06099     (  0.04763,     0.07473) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 18:


Empirical Base Frequencies:

   A       0.25185
   C       0.23545
   G       0.30252
  T(U)     0.21019

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.482640)


        +B-quintana
     +-12  
     !  !  +B-clarridg
     !  +--7  
     !     !  +B--weissii
     !     +--6  
     !        +B-spp-Deer
     !  
  +--3     +B-elizabet
  !  !     !  
  !  !     !     +B--doshiae
  !  !  +--2     !  
  !  !  !  !  +--5     +B-grahamii
  !  !  !  !  !  !  +--9  
  !  !  !  !  !  +--8  +B-henselae
  !  !  !  +-11     !  
  !  +--4     !     +B-birtlesi
  !     !     !  
  !     !     +B-vinsonii
  !     !  
  !     !  +B-arupensi
  !     +--1  
  !        +B-berhoffi
  !  
-10-B-bacillif
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2948.63046

Examined 1250 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10             3              0.00441     (  0.00034,     0.00852) **
   3            12              0.00442     (  0.00086,     0.00794) **
  12          B-quintana        0.00589     (  0.00166,     0.01011) **
  12             7              0.00233     (     zero,     0.00529) **
   7          B-clarridg        0.00644     (  0.00211,     0.01075) **
   7             6              0.00805     (  0.00328,     0.01282) **
   6          B--weissii        0.00166     (     zero,     0.00390) **
   6          B-spp-Deer        0.00202     (     zero,     0.00448) **
   3             4              0.00144     (     zero,     0.00383) *
   4             2              0.00219     (     zero,     0.00467) **
   2          B-elizabet        0.00657     (  0.00229,     0.01087) **
   2            11              0.00069     (     zero,     0.00210) **
  11             5              0.00006     (     zero,    infinity)
   5          B--doshiae        0.00075     (     zero,     0.00220) **
   5             8              0.00006     (     zero,    infinity)
   8             9              0.00069     (     zero,     0.00208) **
   9          B-grahamii        0.00006     (     zero,    infinity)
   9          B-henselae        0.00364     (  0.00046,     0.00683) **
   8          B-birtlesi        0.00006     (     zero,    infinity)
  11          B-vinsonii        0.00507     (  0.00136,     0.00886) **
   4             1              0.00006     (     zero,     0.00156)
   1          B-arupensi        0.00292     (  0.00007,     0.00579) **
   1          B-berhoffi        0.00218     (     zero,     0.00465) **
  10          B-bacillif        0.00733     (  0.00249,     0.01218) **
  10          A-tumefaci        0.05956     (  0.04633,     0.07313) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 19:


Empirical Base Frequencies:

   A       0.25599
   C       0.23661
   G       0.30080
  T(U)     0.20659

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.478992)


                 +B-birtlesi
              +--9  
              !  !  +B-grahamii
              !  +--3  
           +--1     !  +B-vinsonii
           !  !     +--7  
           !  !        +B--doshiae
        +-12  !  
        !  !  +B-henselae
        !  !  
        !  +B-elizabet
        !  
     +-11     +B-quintana
     !  !     !  
     !  !  +--8     +B--weissii
     !  !  !  !  +--6  
     !  !  !  +--5  +B-spp-Deer
  +--2  +--4     !  
  !  !     !     +B-bacillif
  !  !     !  
  !  !     +B-clarridg
  !  !  
  !  +B-arupensi
  !  
-10-B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3122.56967

Examined 1772 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10             2              0.00219     (     zero,     0.00467) **
   2            11              0.00003     (     zero,    infinity)
  11            12              0.00548     (  0.00147,     0.00953) **
  12             1              0.00003     (     zero,     0.00183)
   1             9              0.00181     (     zero,     0.00425) **
   9          B-birtlesi        0.00075     (     zero,     0.00220) **
   9             3              0.00003     (     zero,    infinity)
   3          B-grahamii        0.00075     (     zero,     0.00220) **
   3             7              0.00003     (     zero,    infinity)
   7          B-vinsonii        0.00146     (     zero,     0.00348) **
   7          B--doshiae        0.00076     (     zero,     0.00222) **
   1          B-henselae        0.00513     (  0.00135,     0.00893) **
  12          B-elizabet        0.01032     (  0.00491,     0.01572) **
  11             4              0.00644     (  0.00205,     0.01085) **
   4             8              0.00167     (     zero,     0.00402) **
   8          B-quintana        0.00627     (  0.00186,     0.01070) **
   8             5              0.00731     (  0.00247,     0.01218) **
   5             6              0.01118     (  0.00545,     0.01697) **
   6          B--weissii        0.00003     (     zero,     0.00223)
   6          B-spp-Deer        0.00440     (  0.00085,     0.00791) **
   5          B-bacillif        0.01503     (  0.00833,     0.02176) **
   4          B-clarridg        0.00979     (  0.00440,     0.01517) **
   2          B-arupensi        0.00149     (     zero,     0.00353) **
  10          B-berhoffi        0.00003     (     zero,     0.00169)
  10          A-tumefaci        0.06113     (  0.04771,     0.07486) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 20:


Empirical Base Frequencies:

   A       0.23495
   C       0.22751
   G       0.30562
  T(U)     0.23192

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.502501)


  +B-arupensi
  !  
  !     +B-clarridg
  !  +-10  
  !  !  +B-quintana
  !  !  
--3--7  +B-berhoffi
  !  !  !  
  !  !  !     +B-elizabet
  !  +-11     !  
  !     !  +--4     +B-spp-Deer
  !     !  !  !  +--1  
  !     !  !  +--2  +B--weissii
  !     +--5     !  
  !        !     +B-bacillif
  !        !  
  !        !  +B-grahamii
  !        +-12  
  !           !  +B-birtlesi
  !           +--8  
  !              !  +B-vinsonii
  !              +--6  
  !                 !  +B-henselae
  !                 +--9  
  !                    +B--doshiae
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3158.84951

Examined 1762 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   3          B-arupensi        0.00231     (     zero,     0.00518) **
   3             7              0.00361     (  0.00020,     0.00705) **
   7            10              0.00480     (  0.00095,     0.00867) **
  10          B-clarridg        0.01247     (  0.00655,     0.01852) **
  10          B-quintana        0.01221     (  0.00622,     0.01819) **
   7            11              0.00003     (     zero,     0.00171)
  11          B-berhoffi        0.00141     (     zero,     0.00341) **
  11             5              0.00137     (     zero,     0.00374) **
   5             4              0.00289     (  0.00004,     0.00577) **
   4          B-elizabet        0.00737     (  0.00264,     0.01208) **
   4             2              0.00281     (     zero,     0.00601) **
   2             1              0.01103     (  0.00546,     0.01667) **
   1          B-spp-Deer        0.00114     (     zero,     0.00308) **
   1          B--weissii        0.00105     (     zero,     0.00292) **
   2          B-bacillif        0.00754     (  0.00277,     0.01227) **
   5            12              0.00235     (     zero,     0.00519) **
  12          B-grahamii        0.00070     (     zero,     0.00210) **
  12             8              0.00070     (     zero,     0.00211) *
   8          B-birtlesi        0.00291     (  0.00005,     0.00577) **
   8             6              0.00006     (     zero,     0.00181)
   6          B-vinsonii        0.00219     (     zero,     0.00467) **
   6             9              0.00217     (     zero,     0.00464) **
   9          B-henselae        0.00516     (  0.00130,     0.00893) **
   9          B--doshiae        0.00006     (     zero,    infinity)
   3          A-tumefaci        0.06651     (  0.05249,     0.08090) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 21:


Empirical Base Frequencies:

   A       0.26857
   C       0.21955
   G       0.30449
  T(U)     0.20739

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.451832)


           +B--weissii
        +--6  
     +--4  +B-spp-Deer
     !  !  
     !  +B-bacillif
     !  
  +--5  +B-quintana
  !  !  !  
  !  !  !     +B-arupensi
  !  !  !     !  
  !  !  !     !           +B-henselae
  !  +--8     !        +--9  
  !     !  +-12     +--3  +B--doshiae
  !     !  !  !     !  !  
  !     !  !  !  +-10  +B-vinsonii
  !     !  !  !  !  !  
  !     !  !  +--2  +B-birtlesi
  !     +--1     !  
  !        !     !  +B-elizabet
  !        !     +--7  
  !        !        +B-grahamii
  !        !  
  !        +B-berhoffi
  !  
-11-B-clarridg
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3041.59493

Examined  570 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  11             5              0.00664     (  0.00207,     0.01129) **
   5             4              0.00627     (  0.00185,     0.01070) **
   4             6              0.00597     (  0.00164,     0.01037) **
   6          B--weissii        0.00003     (     zero,    infinity)
   6          B-spp-Deer        0.00368     (  0.00046,     0.00690) **
   4          B-bacillif        0.00770     (  0.00277,     0.01267) **
   5             8              0.00215     (     zero,     0.00490) **
   8          B-quintana        0.00837     (  0.00328,     0.01343) **
   8             1              0.00350     (  0.00000,     0.00701) **
   1            12              0.00003     (     zero,     0.00187)
  12          B-arupensi        0.00512     (  0.00138,     0.00897) **
  12             2              0.00294     (  0.00007,     0.00582) **
   2            10              0.00139     (     zero,     0.00340) **
  10             3              0.00006     (     zero,     0.00219)
   3             9              0.00075     (     zero,     0.00219) **
   9          B-henselae        0.00587     (  0.00183,     0.00995) **
   9          B--doshiae        0.00006     (     zero,    infinity)
   3          B-vinsonii        0.00294     (  0.00007,     0.00581) **
  10          B-birtlesi        0.00290     (  0.00004,     0.00578) **
   2             7              0.00148     (     zero,     0.00352) **
   7          B-elizabet        0.00366     (  0.00047,     0.00688) **
   7          B-grahamii        0.00003     (     zero,    infinity)
   1          B-berhoffi        0.00075     (     zero,     0.00220) **
  11          B-clarridg        0.00809     (  0.00299,     0.01319) **
  11          A-tumefaci        0.05703     (  0.04410,     0.07054) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 22:


Empirical Base Frequencies:

   A       0.24096
   C       0.24001
   G       0.30651
  T(U)     0.21253

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.496767)


  +B-clarridg
  !  
  !           +B-arupensi
  !           !  
  !           !        +B-elizabet
  !           !     +-11  
  !        +--5     !  +B-grahamii
  !        !  !  +-10  
  !        !  !  !  !  +B-birtlesi
  !        !  !  !  +--6  
  !        !  !  !     !  +B--doshiae
  !        !  +--1     +--9  
  !     +--7     !        !  +B-henselae
  !     !  !     !        +--8  
  !     !  !     !           +B-vinsonii
  !     !  !     !  
  !  +--2  !     +B-berhoffi
  !  !  !  !  
  !  !  !  +B-quintana
  !  !  !  
-12--4  !  +B--weissii
  !  !  +--3  
  !  !     +B-spp-Deer
  !  !  
  !  +B-bacillif
  !  
  +----A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3107.57576

Examined  582 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  12          B-clarridg        0.00641     (  0.00190,     0.01095) **
  12             4              0.00636     (  0.00184,     0.01094) **
   4             2              0.00243     (     zero,     0.00533) **
   2             7              0.00148     (     zero,     0.00401) **
   7             5              0.00210     (     zero,     0.00457) **
   5          B-arupensi        0.00439     (  0.00086,     0.00791) **
   5             1              0.00006     (     zero,     0.00162)
   1            10              0.00291     (  0.00007,     0.00576) **
  10            11              0.00076     (     zero,     0.00224) **
  11          B-elizabet        0.00730     (  0.00278,     0.01183) **
  11          B-grahamii        0.00003     (     zero,     0.00157)
  10             6              0.00133     (     zero,     0.00335) **
   6          B-birtlesi        0.00088     (     zero,     0.00289)
   6             9              0.00067     (     zero,     0.00268)
   9          B--doshiae        0.00006     (     zero,    infinity)
   9             8              0.00291     (  0.00006,     0.00576) **
   8          B-henselae        0.00657     (  0.00229,     0.01087) **
   8          B-vinsonii        0.00150     (     zero,     0.00354) **
   1          B-berhoffi        0.00220     (     zero,     0.00470) **
   7          B-quintana        0.00812     (  0.00332,     0.01292) **
   2             3              0.00932     (  0.00414,     0.01451) **
   3          B--weissii        0.00074     (     zero,     0.00218) **
   3          B-spp-Deer        0.00003     (     zero,     0.00155)
   4          B-bacillif        0.00936     (  0.00415,     0.01461) **
  12          A-tumefaci        0.07798     (  0.06288,     0.09393) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 23:


Empirical Base Frequencies:

   A       0.26489
   C       0.21167
   G       0.31752
  T(U)     0.20591

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.441858)


        +B-clarridg
        !  
     +--8     +B--weissii
     !  !  +-12  
     !  +-11  +B-spp-Deer
     !     !  
     !     +B-quintana
     !  
     !     +B-berhoffi
  +--4     !  
  !  !     !     +B-grahamii
  !  !     !     !  
  !  !  +--6  +-10     +B-vinsonii
  !  !  !  !  !  !  +--5  
  !  !  !  !  !  !  !  !  +B--doshiae
  !  !  !  !  !  +--3  +--9  
  !  !  !  +--1     !     +B-henselae
  !  +--7     !     !  
  !     !     !     +B-birtlesi
  !     !     !  
  !     !     +B-elizabet
  !     !  
  !     +B-arupensi
  !  
--2-B-bacillif
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3029.34688

Examined 1248 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   2             4              0.00547     (  0.00127,     0.00963) **
   4             8              0.00294     (  0.00002,     0.00589) **
   8          B-clarridg        0.01280     (  0.00667,     0.01895) **
   8            11              0.00218     (     zero,     0.00488) **
  11            12              0.00679     (  0.00237,     0.01126) **
  12          B--weissii        0.00139     (     zero,     0.00343) **
  12          B-spp-Deer        0.00084     (     zero,     0.00246) **
  11          B-quintana        0.00644     (  0.00201,     0.01081) **
   4             7              0.00140     (     zero,     0.00383) *
   7             6              0.00003     (     zero,     0.00183)
   6          B-berhoffi        0.00219     (     zero,     0.00467) **
   6             1              0.00274     (     zero,     0.00559) **
   1            10              0.00088     (     zero,     0.00260) **
  10          B-grahamii        0.00075     (     zero,     0.00220) **
  10             3              0.00069     (     zero,     0.00209) *
   3             5              0.00006     (     zero,     0.00176)
   5          B-vinsonii        0.00219     (     zero,     0.00466) **
   5             9              0.00141     (     zero,     0.00340) **
   9          B--doshiae        0.00003     (     zero,    infinity)
   9          B-henselae        0.00731     (  0.00279,     0.01185) **
   3          B-birtlesi        0.00216     (     zero,     0.00463) **
   1          B-elizabet        0.00659     (  0.00228,     0.01090) **
   7          B-arupensi        0.00293     (  0.00007,     0.00580) **
   2          B-bacillif        0.00410     (  0.00036,     0.00791) **
   2          A-tumefaci        0.06740     (  0.05341,     0.08211) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 24:


Empirical Base Frequencies:

   A       0.23716
   C       0.24456
   G       0.30560
  T(U)     0.21268

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.503736)


  +B-elizabet
  !  
  !           +B-birtlesi
  !        +--5  
  !        !  !  +B-vinsonii
  !        !  +-11  
  !        !     +B--doshiae
  !        !  
  !        !           +B--weissii
  !        !        +--1  
  !     +--2        !  +B-spp-Deer
  !     !  !     +--8  
  !     !  !     !  !     +B-quintana
  !     !  !     !  !  +-12  
  !     !  !  +--4  +-10  +B-bacillif
  !     !  !  !  !     !  
  !  +--6  !  !  !     +B-clarridg
  !  !  !  +--3  !  
  !  !  !     !  +B-henselae
  !  !  !     !  
--7--9  !     +B-arupensi
  !  !  !  
  !  !  +B-berhoffi
  !  !  
  !  +B-grahamii
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2926.07664

Examined  826 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7          B-elizabet        0.00336     (  0.00004,     0.00669) **
   7             9              0.00478     (  0.00099,     0.00862) **
   9             6              0.00156     (     zero,     0.00372) **
   6             2              0.00076     (     zero,     0.00222) **
   2             5              0.00072     (     zero,     0.00214) *
   5          B-birtlesi        0.00146     (     zero,     0.00347) **
   5            11              0.00003     (     zero,    infinity)
  11          B-vinsonii        0.00074     (     zero,     0.00218) **
  11          B--doshiae        0.00003     (     zero,    infinity)
   2             3              0.00003     (     zero,     0.00182)
   3             4              0.00145     (     zero,     0.00348) **
   4             8              0.00215     (     zero,     0.00464) **
   8             1              0.00519     (  0.00131,     0.00899) **
   1          B--weissii        0.00145     (     zero,     0.00348) **
   1          B-spp-Deer        0.00146     (     zero,     0.00348) **
   8            10              0.00075     (     zero,     0.00221) **
  10            12              0.00290     (  0.00000,     0.00580) **
  12          B-quintana        0.01039     (  0.00490,     0.01581) **
  12          B-bacillif        0.00736     (  0.00280,     0.01197) **
  10          B-clarridg        0.00959     (  0.00437,     0.01479) **
   4          B-henselae        0.00294     (  0.00005,     0.00581) **
   3          B-arupensi        0.00147     (     zero,     0.00351) **
   6          B-berhoffi        0.00222     (     zero,     0.00471) **
   9          B-grahamii        0.00066     (     zero,     0.00215)
   7          A-tumefaci        0.06460     (  0.05069,     0.07877) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 25:


Empirical Base Frequencies:

   A       0.23961
   C       0.22926
   G       0.31940
  T(U)     0.21173

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.489850)


           +B-berhoffi
           !  
           !           +B-arupensi
           !        +--8  
           !        !  +B-vinsonii
           !     +-12  
        +--1     !  !  +B-birtlesi
        !  !     !  +--9  
        !  !  +--5     +B--doshiae
        !  !  !  !  
        !  !  !  !  +B-henselae
        !  !  !  +--4  
        !  +--2     !  +B--weissii
     +--3     !     +-11  
     !  !     !        +B-spp-Deer
     !  !     !  
     !  !     !  +B-grahamii
  +--7  !     +-10  
  !  !  !        +B-elizabet
  !  !  !  
  !  !  +B-quintana
  !  !  
  !  +B-clarridg
  !  
--6-B-bacillif
  !  
  +----A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3195.32822

Examined 1228 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   6             7              0.00804     (  0.00289,     0.01320) **
   7             3              0.00368     (  0.00038,     0.00698) **
   3             1              0.00303     (  0.00006,     0.00601) **
   1          B-berhoffi        0.00218     (     zero,     0.00465) **
   1             2              0.00076     (     zero,     0.00224) **
   2             5              0.00222     (     zero,     0.00470) **
   5            12              0.00142     (     zero,     0.00344) **
  12             8              0.00145     (     zero,     0.00347) **
   8          B-arupensi        0.00364     (  0.00045,     0.00684) **
   8          B-vinsonii        0.00144     (     zero,     0.00345) **
  12             9              0.00003     (     zero,     0.00194)
   9          B-birtlesi        0.00290     (  0.00007,     0.00575) **
   9          B--doshiae        0.00075     (     zero,     0.00220) **
   5             4              0.00437     (  0.00091,     0.00792) **
   4          B-henselae        0.00144     (     zero,     0.00348) **
   4            11              0.01027     (  0.00491,     0.01567) **
  11          B--weissii        0.00149     (     zero,     0.00352) **
  11          B-spp-Deer        0.00072     (     zero,     0.00215) **
   2            10              0.00148     (     zero,     0.00352) **
  10          B-grahamii        0.00144     (     zero,     0.00346) **
  10          B-elizabet        0.01099     (  0.00545,     0.01657) **
   3          B-quintana        0.00794     (  0.00317,     0.01270) **
   7          B-clarridg        0.01235     (  0.00638,     0.01832) **
   6          B-bacillif        0.00618     (  0.00151,     0.01075) **
   6          A-tumefaci        0.07620     (  0.06118,     0.09179) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 26:


Empirical Base Frequencies:

   A       0.25403
   C       0.23026
   G       0.30384
  T(U)     0.21188

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.477031)


  +B-clarridg
  !  
  !           +B-quintana
  !        +-12  
  !     +--5  +B-arupensi
  !     !  !  
  !     !  +B-berhoffi
  !     !  
  !     !        +B--doshiae
  !  +--8     +-10  
  !  !  !     !  !  +B-vinsonii
  !  !  !  +--6  +--1  
  !  !  !  !  !     +B-henselae
  !  !  !  !  !  
  !  !  +-11  +B-birtlesi
--4--3     !  
  !  !     !  +B-grahamii
  !  !     +--2  
  !  !        +B-elizabet
  !  !  
  !  !     +B-spp-Deer
  !  !  +--9  
  !  +--7  +B--weissii
  !     !  
  !     +B-bacillif
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3032.25317

Examined 1242 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   4          B-clarridg        0.00357     (  0.00027,     0.00688) **
   4             3              0.00526     (  0.00130,     0.00924) **
   3             8              0.00140     (     zero,     0.00344) **
   8             5              0.00006     (     zero,     0.00189)
   5            12              0.00146     (     zero,     0.00349) **
  12          B-quintana        0.00955     (  0.00436,     0.01475) **
  12          B-arupensi        0.00220     (     zero,     0.00470) **
   5          B-berhoffi        0.00151     (     zero,     0.00356) **
   8            11              0.00512     (  0.00131,     0.00892) **
  11             6              0.00075     (     zero,     0.00221) *
   6            10              0.00006     (     zero,     0.00181)
  10          B--doshiae        0.00003     (     zero,    infinity)
  10             1              0.00074     (     zero,     0.00219) **
   1          B-vinsonii        0.00219     (     zero,     0.00468) **
   1          B-henselae        0.00588     (  0.00182,     0.00995) **
   6          B-birtlesi        0.00291     (  0.00005,     0.00577) **
  11             2              0.00042     (     zero,     0.00185)
   2          B-grahamii        0.00031     (     zero,     0.00174)
   2          B-elizabet        0.01031     (  0.00490,     0.01570) **
   3             7              0.00467     (  0.00095,     0.00841) **
   7             9              0.00580     (  0.00170,     0.00990) **
   9          B-spp-Deer        0.00076     (     zero,     0.00222) **
   9          B--weissii        0.00075     (     zero,     0.00219) **
   7          B-bacillif        0.01097     (  0.00533,     0.01663) **
   4          A-tumefaci        0.06405     (  0.05026,     0.07822) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 27:


Empirical Base Frequencies:

   A       0.23427
   C       0.23570
   G       0.30056
  T(U)     0.22947

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.504786)


  +B-clarridg
  !  
  !  +B-elizabet
  !  !  
-11-10  +B-grahamii
  !  !  !  
  !  !  !     +B-quintana
  !  +--5  +-12  
  !     !  !  +B-berhoffi
  !     !  !  
  !     +--4  +B-arupensi
  !        !  !  
  !        !  !     +B-vinsonii
  !        !  !     !  
  !        +--1  +--8  +B--doshiae
  !           !  !  !  !  
  !           !  !  +--9  +B-henselae
  !           !  !     !  !  
  !           !  !     +--3     +B--weissii
  !           +--7        !  +--6  
  !              !        +--2  +B-spp-Deer
  !              !           !  
  !              !           +B-bacillif
  !              !  
  !              +B-birtlesi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2942.78728

Examined  674 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  11          B-clarridg        0.00580     (  0.00166,     0.00995) **
  11            10              0.00443     (  0.00084,     0.00812) **
  10          B-elizabet        0.00296     (  0.00002,     0.00583) **
  10             5              0.00220     (     zero,     0.00470) **
   5          B-grahamii        0.00072     (     zero,     0.00215) *
   5             4              0.00072     (     zero,     0.00215) **
   4            12              0.00221     (     zero,     0.00471) **
  12          B-quintana        0.00952     (  0.00436,     0.01471) **
  12          B-berhoffi        0.00075     (     zero,     0.00221) *
   4             1              0.00072     (     zero,     0.00213) **
   1          B-arupensi        0.00220     (     zero,     0.00470) **
   1             7              0.00068     (     zero,     0.00209) *
   7             8              0.00003     (     zero,    infinity)
   8          B-vinsonii        0.00070     (     zero,     0.00210) **
   8             9              0.00218     (     zero,     0.00466) **
   9          B--doshiae        0.00003     (     zero,    infinity)
   9             3              0.00352     (  0.00034,     0.00673) **
   3          B-henselae        0.00307     (  0.00006,     0.00606) **
   3             2              0.00515     (  0.00132,     0.00898) **
   2             6              0.00237     (     zero,     0.00500) **
   6          B--weissii        0.00003     (     zero,    infinity)
   6          B-spp-Deer        0.00141     (     zero,     0.00341) **
   2          B-bacillif        0.01237     (  0.00648,     0.01837) **
   7          B-birtlesi        0.00292     (  0.00007,     0.00577) **
  11          A-tumefaci        0.06213     (  0.04872,     0.07616) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 28:


Empirical Base Frequencies:

   A       0.25002
   C       0.22249
   G       0.32482
  T(U)     0.20267

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.465594)


  +B-berhoffi
  !  
  !        +B-birtlesi
  !     +--2  
  !     !  !  +B-grahamii
  !     !  +--8  
  !  +--7     +B-elizabet
  !  !  !  
  !  !  !  +B-vinsonii
  !  !  +-12  
  !  !     +B--doshiae
-10--1  
  !  !  +B-arupensi
  !  !  !  
  !  !  !        +B-clarridg
  !  !  !     +--4  
  !  +--5     !  !  +B-bacillif
  !     !     !  +-11  
  !     !  +--6     !  +B-spp-Deer
  !     !  !  !     +--9  
  !     !  !  !        +B--weissii
  !     +--3  !  
  !        !  +B-quintana
  !        !  
  !        +B-henselae
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3115.26022

Examined 1030 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10          B-berhoffi        0.00003     (     zero,     0.00181)
  10             1              0.00220     (     zero,     0.00468) **
   1             7              0.00584     (  0.00179,     0.00990) **
   7             2              0.00003     (     zero,     0.00188)
   2          B-birtlesi        0.00146     (     zero,     0.00348) **
   2             8              0.00142     (     zero,     0.00342) **
   8          B-grahamii        0.00006     (     zero,    infinity)
   8          B-elizabet        0.01100     (  0.00548,     0.01661) **
   7            12              0.00003     (     zero,    infinity)
  12          B-vinsonii        0.00142     (     zero,     0.00342) **
  12          B--doshiae        0.00220     (     zero,     0.00468) **
   1             5              0.00003     (     zero,    infinity)
   5          B-arupensi        0.00371     (  0.00045,     0.00693) **
   5             3              0.00438     (  0.00088,     0.00789) **
   3             6              0.00003     (     zero,     0.00158)
   6             4              0.00302     (  0.00004,     0.00600) **
   4          B-clarridg        0.00952     (  0.00428,     0.01474) **
   4            11              0.00549     (  0.00143,     0.00955) **
  11          B-bacillif        0.00853     (  0.00355,     0.01356) **
  11             9              0.00517     (  0.00124,     0.00906) **
   9          B-spp-Deer        0.00363     (  0.00041,     0.00683) **
   9          B--weissii        0.00003     (     zero,     0.00256)
   6          B-quintana        0.01251     (  0.00658,     0.01849) **
   3          B-henselae        0.00293     (  0.00007,     0.00580) **
  10          A-tumefaci        0.07156     (  0.05699,     0.08655) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 29:


Empirical Base Frequencies:

   A       0.22737
   C       0.23526
   G       0.32005
  T(U)     0.21732

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.511209)


     +B-arupensi
     !  
     !        +B-clarridg
     !     +--8  
     !     !  !  +B-bacillif
     !     !  +-11  
  +--6  +--3     +B-quintana
  !  !  !  !  
  !  !  !  !  +B-spp-Deer
  !  !  !  +-10  
  !  !  !     +B--weissii
  !  !  !  
  !  +--2        +B-vinsonii
  !     !     +-12  
  !     !     !  !  +B-birtlesi
  !     !     !  +--5  
  !     !  +--1     !  +B-grahamii
  !     !  !  !     +--7  
  !     !  !  !        +B-elizabet
  !     +--4  !  
  !        !  +B--doshiae
  !        !  
  !        +B-henselae
  !  
--9-B-berhoffi
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2882.00959

Examined  542 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   9             6              0.00150     (     zero,     0.00358) **
   6          B-arupensi        0.00070     (     zero,     0.00210) **
   6             2              0.00076     (     zero,     0.00225) **
   2             3              0.00169     (     zero,     0.00402) **
   3             8              0.00173     (     zero,     0.00416) **
   8          B-clarridg        0.01179     (  0.00591,     0.01772) **
   8            11              0.00452     (  0.00072,     0.00826) **
  11          B-bacillif        0.01066     (  0.00507,     0.01627) **
  11          B-quintana        0.00522     (  0.00120,     0.00927) **
   3            10              0.00565     (  0.00154,     0.00969) **
  10          B-spp-Deer        0.00075     (     zero,     0.00220) **
  10          B--weissii        0.00076     (     zero,     0.00222) **
   2             4              0.00501     (  0.00113,     0.00879) **
   4             1              0.00087     (     zero,     0.00255) **
   1            12              0.00084     (     zero,     0.00245) **
  12          B-vinsonii        0.00141     (     zero,     0.00342) **
  12             5              0.00003     (     zero,     0.00166)
   5          B-birtlesi        0.00147     (     zero,     0.00349) **
   5             7              0.00142     (     zero,     0.00342) **
   7          B-grahamii        0.00003     (     zero,    infinity)
   7          B-elizabet        0.00808     (  0.00331,     0.01285) **
   1          B--doshiae        0.00003     (     zero,    infinity)
   4          B-henselae        0.00222     (     zero,     0.00472) **
   9          B-berhoffi        0.00003     (     zero,     0.00176)
   9          A-tumefaci        0.05300     (  0.04070,     0.06584) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 30:


Empirical Base Frequencies:

   A       0.24205
   C       0.24266
   G       0.29780
  T(U)     0.21748

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.498546)


  +B-bacillif
  !  
  !     +B-spp-Deer
  !  +--4  
  !  !  +B--weissii
  !  !  
  !  !           +B-arupensi
  !  !           !  
  !  !           !  +B-elizabet
  !  !        +--3  !  
  !  !        !  !  !           +B--doshiae
  !  !        !  !  !        +-12  
-11--9        !  +--5     +--1  +B-henselae
  !  !        !     !     !  !  
  !  !     +--2     !  +--7  +B-vinsonii
  !  !     !  !     !  !  !  
  !  !     !  !     +-10  +B-birtlesi
  !  !     !  !        !  
  !  !  +--8  !        +B-grahamii
  !  !  !  !  !  
  !  !  !  !  +B-berhoffi
  !  +--6  !  
  !     !  +B-quintana
  !     !  
  !     +B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3102.58353

Examined 2124 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  11          B-bacillif        0.00694     (  0.00233,     0.01157) **
  11             9              0.00428     (  0.00041,     0.00812) **
   9             4              0.00664     (  0.00215,     0.01108) **
   4          B-spp-Deer        0.00290     (  0.00006,     0.00576) **
   4          B--weissii        0.00006     (     zero,     0.00211)
   9             6              0.00461     (  0.00064,     0.00859) **
   6             8              0.00511     (  0.00121,     0.00894) **
   8             2              0.00260     (     zero,     0.00557) **
   2             3              0.00006     (     zero,    infinity)
   3          B-arupensi        0.00292     (  0.00009,     0.00579) **
   3             5              0.00161     (     zero,     0.00382) **
   5          B-elizabet        0.01315     (  0.00698,     0.01926) **
   5            10              0.00147     (     zero,     0.00350) **
  10             7              0.00083     (     zero,     0.00248) **
   7             1              0.00006     (     zero,     0.00180)
   1            12              0.00147     (     zero,     0.00349) **
  12          B--doshiae        0.00006     (     zero,    infinity)
  12          B-henselae        0.00511     (  0.00134,     0.00890) **
   1          B-vinsonii        0.00219     (     zero,     0.00466) **
   7          B-birtlesi        0.00219     (     zero,     0.00466) **
  10          B-grahamii        0.00059     (     zero,     0.00202)
   2          B-berhoffi        0.00144     (     zero,     0.00345) **
   8          B-quintana        0.00550     (  0.00140,     0.00959) **
   6          B-clarridg        0.01092     (  0.00529,     0.01657) **
  11          A-tumefaci        0.06610     (  0.05222,     0.08067) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 31:


Empirical Base Frequencies:

   A       0.25167
   C       0.22161
   G       0.31744
  T(U)     0.20928

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.468390)


  +B-clarridg
  !  
  !     +B-bacillif
  !  +--8  
  !  !  !  +B-spp-Deer
  !  !  +--4  
  !  !     +B--weissii
  !  !  
  !  !        +B-elizabet
-11--3     +--6  
  !  !     !  +B-grahamii
  !  !     !  
  !  !  +--5     +B-vinsonii
  !  !  !  !  +--9  
  !  !  !  !  !  !  +B--doshiae
  !  !  !  +--7  +-12  
  !  +--1     !     +B-henselae
  !     !     !  
  !     !     +B-birtlesi
  !     !  
  !     !  +B-arupensi
  !     +--2  
  !        !  +B-quintana
  !        +-10  
  !           +B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3025.94482

Examined 1866 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  11          B-clarridg        0.00649     (  0.00210,     0.01097) **
  11             3              0.00381     (  0.00021,     0.00743) **
   3             8              0.00478     (  0.00096,     0.00859) **
   8          B-bacillif        0.00884     (  0.00361,     0.01402) **
   8             4              0.00722     (  0.00257,     0.01191) **
   4          B-spp-Deer        0.00138     (     zero,     0.00340) **
   4          B--weissii        0.00082     (     zero,     0.00242) **
   3             1              0.00274     (     zero,     0.00575) **
   1             5              0.00518     (  0.00118,     0.00908) **
   5             6              0.00223     (     zero,     0.00473) **
   6          B-elizabet        0.00955     (  0.00437,     0.01476) **
   6          B-grahamii        0.00006     (     zero,     0.00181)
   5             7              0.00067     (     zero,     0.00206) *
   7             9              0.00003     (     zero,     0.00188)
   9          B-vinsonii        0.00003     (     zero,    infinity)
   9            12              0.00075     (     zero,     0.00220) **
  12          B--doshiae        0.00003     (     zero,    infinity)
  12          B-henselae        0.00512     (  0.00134,     0.00892) **
   7          B-birtlesi        0.00365     (  0.00045,     0.00685) **
   1             2              0.00072     (     zero,     0.00256)
   2          B-arupensi        0.00291     (  0.00007,     0.00578) **
   2            10              0.00003     (     zero,     0.00232)
  10          B-quintana        0.00953     (  0.00436,     0.01473) **
  10          B-berhoffi        0.00003     (     zero,    infinity)
  11          A-tumefaci        0.06580     (  0.05192,     0.08031) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 32:


Empirical Base Frequencies:

   A       0.24941
   C       0.23018
   G       0.31742
  T(U)     0.20299

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.475259)


              +B-clarridg
           +-11  
        +--8  +B-quintana
        !  !  
     +--2  +B-bacillif
     !  !  
     !  !  +B-spp-Deer
     !  +--4  
  +--3     +B--weissii
  !  !  
  !  !  +B-arupensi
  !  !  !  
  !  +--5  +B--doshiae
  !     !  !  
  !     !  !        +B-elizabet
  !     +--6     +--9  
  !        !     !  +B-grahamii
  !        !  +-12  
  !        !  !  !  +B-vinsonii
  !        +--7  +--1  
  !           !     +B-henselae
  !           !  
  !           +B-birtlesi
  !  
-10-B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3043.83026

Examined  810 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10             3              0.00151     (     zero,     0.00359) **
   3             2              0.00327     (     zero,     0.00659) **
   2             8              0.00270     (     zero,     0.00571) **
   8            11              0.00311     (     zero,     0.00648) **
  11          B-clarridg        0.01416     (  0.00777,     0.02068) **
  11          B-quintana        0.00841     (  0.00336,     0.01349) **
   8          B-bacillif        0.01133     (  0.00537,     0.01723) **
   2             4              0.00699     (  0.00238,     0.01162) **
   4          B-spp-Deer        0.00222     (     zero,     0.00469) **
   4          B--weissii        0.00072     (     zero,     0.00215) **
   3             5              0.00003     (     zero,     0.00181)
   5          B-arupensi        0.00293     (  0.00007,     0.00581) **
   5             6              0.00287     (  0.00007,     0.00572) **
   6          B--doshiae        0.00075     (     zero,     0.00219) **
   6             7              0.00003     (     zero,     0.00180)
   7            12              0.00003     (     zero,     0.00187)
  12             9              0.00138     (     zero,     0.00337) **
   9          B-elizabet        0.00582     (  0.00181,     0.00987) **
   9          B-grahamii        0.00003     (     zero,     0.00186)
  12             1              0.00138     (     zero,     0.00337) **
   1          B-vinsonii        0.00144     (     zero,     0.00346) **
   1          B-henselae        0.00221     (     zero,     0.00469) **
   7          B-birtlesi        0.00146     (     zero,     0.00348) **
  10          B-berhoffi        0.00006     (     zero,     0.00166)
  10          A-tumefaci        0.07201     (  0.05757,     0.08718) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 33:


Empirical Base Frequencies:

   A       0.25062
   C       0.21818
   G       0.30556
  T(U)     0.22564

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.479731)


  +B-clarridg
  !  
  !     +B-berhoffi
  !     !  
  !     !        +B-grahamii
  !     !        !  
  !     !     +--8     +B--weissii
  !     !     !  !  +--7  
  !     !     !  +--1  +B-spp-Deer
  !  +--6     !     !  
  !  !  !  +--2     +B-bacillif
  !  !  !  !  !  
  !  !  !  !  !     +B-vinsonii
  !  !  !  !  !  +--5  
  !  !  !  !  !  !  +B-birtlesi
  !  !  !  !  +-12  
-11--3  +--4     !     +B-quintana
  !  !     !     !  +--9  
  !  !     !     +-10  +B-henselae
  !  !     !        !  
  !  !     !        +B--doshiae
  !  !     !  
  !  !     +B-elizabet
  !  !  
  !  +B-arupensi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3104.97804

Examined 2026 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  11          B-clarridg        0.00924     (  0.00388,     0.01461) **
  11             3              0.01000     (  0.00441,     0.01559) **
   3             6              0.00003     (     zero,     0.00182)
   6          B-berhoffi        0.00003     (     zero,     0.00163)
   6             4              0.00366     (  0.00045,     0.00687) **
   4             2              0.00364     (  0.00045,     0.00683) **
   2             8              0.00006     (     zero,    infinity)
   8          B-grahamii        0.00003     (     zero,    infinity)
   8             1              0.00691     (  0.00249,     0.01143) **
   1             7              0.00952     (  0.00430,     0.01473) **
   7          B--weissii        0.00003     (     zero,    infinity)
   7          B-spp-Deer        0.00438     (  0.00088,     0.00787) **
   1          B-bacillif        0.00774     (  0.00300,     0.01249) **
   2            12              0.00006     (     zero,    infinity)
  12             5              0.00006     (     zero,    infinity)
   5          B-vinsonii        0.00141     (     zero,     0.00341) **
   5          B-birtlesi        0.00006     (     zero,    infinity)
  12            10              0.00218     (     zero,     0.00464) **
  10             9              0.00295     (     zero,     0.00582) **
   9          B-quintana        0.01032     (  0.00491,     0.01572) **
   9          B-henselae        0.00361     (  0.00048,     0.00683) **
  10          B--doshiae        0.00006     (     zero,    infinity)
   4          B-elizabet        0.00511     (  0.00133,     0.00890) **
   3          B-arupensi        0.00512     (  0.00133,     0.00893) **
  11          A-tumefaci        0.06430     (  0.05070,     0.07869) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 34:


Empirical Base Frequencies:

   A       0.25472
   C       0.21724
   G       0.31314
  T(U)     0.21490

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.466190)


  +B-arupensi
  !  
  !           +B-henselae
  !        +--3  
  !        !  !  +B-spp-Deer
  !        !  +--5  
  !     +--1     +B--weissii
  !     !  !  
  !     !  !  +B-quintana
  !  +-11  +--7  
  !  !  !     +B-bacillif
  !  !  !  
  !  !  +B-clarridg
--8--4  
  !  !  +B-berhoffi
  !  !  !  
  !  !  !     +B-birtlesi
  !  +--2  +-10  
  !     !  !  !  +B--doshiae
  !     !  !  +-12  
  !     +--9     +B-vinsonii
  !        !  
  !        !  +B-elizabet
  !        +--6  
  !           +B-grahamii
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2964.70792

Examined  558 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   8          B-arupensi        0.00264     (     zero,     0.00551) **
   8             4              0.00332     (  0.00009,     0.00653) **
   4            11              0.00324     (     zero,     0.00661) **
  11             1              0.00227     (     zero,     0.00481) **
   1             3              0.00214     (     zero,     0.00463) **
   3          B-henselae        0.00599     (  0.00175,     0.01033) **
   3             5              0.00352     (  0.00008,     0.00694) **
   5          B-spp-Deer        0.00223     (     zero,     0.00472) **
   5          B--weissii        0.00142     (     zero,     0.00343) **
   1             7              0.00316     (  0.00006,     0.00626) **
   7          B-quintana        0.00905     (  0.00377,     0.01440) **
   7          B-bacillif        0.00692     (  0.00221,     0.01163) **
  11          B-clarridg        0.00823     (  0.00315,     0.01324) **
   4             2              0.00031     (     zero,     0.00176)
   2          B-berhoffi        0.00079     (     zero,     0.00229) **
   2             9              0.00218     (     zero,     0.00466) **
   9            10              0.00070     (     zero,     0.00212) *
  10          B-birtlesi        0.00147     (     zero,     0.00349) **
  10            12              0.00003     (     zero,     0.00178)
  12          B--doshiae        0.00073     (     zero,     0.00215) **
  12          B-vinsonii        0.00365     (  0.00046,     0.00685) **
   9             6              0.00149     (     zero,     0.00355) **
   6          B-elizabet        0.00952     (  0.00437,     0.01472) **
   6          B-grahamii        0.00003     (     zero,     0.00191)
   8          A-tumefaci        0.04967     (  0.03749,     0.06188) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 35:


Empirical Base Frequencies:

   A       0.24897
   C       0.25383
   G       0.29660
  T(U)     0.20060

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.499922)


  +B-clarridg
  !  
  !     +B-quintana
  !  +-10  
  !  !  !  +B--weissii
  !  !  +--6  
  !  !     +B-spp-Deer
  !  !  
  !  !        +B-birtlesi
  !  !        !  
  !  !     +--9  +B-vinsonii
--8--4     !  !  !  
  !  !     !  +--1     +B-elizabet
  !  !     !     !  +--7  
  !  !     !     !  !  +B-grahamii
  !  !  +--5     +--3  
  !  !  !  !        !  +B-henselae
  !  !  !  !        +-11  
  !  !  !  !           +B--doshiae
  !  +--2  !  
  !     !  +B-bacillif
  !     !  
  !     !  +B-arupensi
  !     +-12  
  !        +B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3006.01687

Examined  590 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   8          B-clarridg        0.00827     (  0.00320,     0.01341) **
   8             4              0.00647     (  0.00192,     0.01103) **
   4            10              0.00231     (     zero,     0.00497) **
  10          B-quintana        0.00725     (  0.00267,     0.01184) **
  10             6              0.00610     (  0.00182,     0.01027) **
   6          B--weissii        0.00003     (     zero,     0.00185)
   6          B-spp-Deer        0.00362     (  0.00046,     0.00683) **
   4             2              0.00141     (     zero,     0.00363) **
   2             5              0.00224     (     zero,     0.00473) **
   5             9              0.00293     (  0.00006,     0.00581) **
   9          B-birtlesi        0.00075     (     zero,     0.00219) **
   9             1              0.00006     (     zero,    infinity)
   1          B-vinsonii        0.00220     (     zero,     0.00468) **
   1             3              0.00006     (     zero,    infinity)
   3             7              0.00218     (     zero,     0.00466) **
   7          B-elizabet        0.00807     (  0.00332,     0.01285) **
   7          B-grahamii        0.00006     (     zero,     0.00182)
   3            11              0.00069     (     zero,     0.00209) **
  11          B-henselae        0.00443     (  0.00085,     0.00793) **
  11          B--doshiae        0.00006     (     zero,    infinity)
   5          B-bacillif        0.01177     (  0.00602,     0.01757) **
   2            12              0.00003     (     zero,     0.00156)
  12          B-arupensi        0.00298     (  0.00003,     0.00586) **
  12          B-berhoffi        0.00146     (     zero,     0.00349) **
   8          A-tumefaci        0.05946     (  0.04631,     0.07313) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 36:


Empirical Base Frequencies:

   A       0.23852
   C       0.22069
   G       0.32701
  T(U)     0.21378

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.485665)


     +B-quintana
     !  
  +--4  +B-berhoffi
  !  !  !  
  !  !  !  +B-arupensi
  !  +--7  !  
  !     !  !        +B--weissii
  !     !  !     +-12  
  !     +--2  +--3  +B-spp-Deer
  !        !  !  !  
  !        !  !  +B-bacillif
  !        !  !  
  !        +-11     +B--doshiae
  !           !  +-10  
  !           !  !  !  +B-birtlesi
  !           !  !  +--8  
  !           !  !     !  +B-vinsonii
  !           +--1     +--9  
  !              !        +B-henselae
  !              !  
  !              !  +B-grahamii
  !              +--6  
  !                 +B-elizabet
  !  
--5-B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2938.25701

Examined 1042 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   5             4              0.00848     (  0.00338,     0.01359) **
   4          B-quintana        0.00763     (  0.00283,     0.01252) **
   4             7              0.00191     (     zero,     0.00483)
   7          B-berhoffi        0.00006     (     zero,    infinity)
   7             2              0.00146     (     zero,     0.00349) **
   2          B-arupensi        0.00515     (  0.00134,     0.00896) **
   2            11              0.00095     (     zero,     0.00274) **
  11             3              0.00360     (  0.00022,     0.00695) **
   3            12              0.00599     (  0.00180,     0.01020) **
  12          B--weissii        0.00006     (     zero,    infinity)
  12          B-spp-Deer        0.00217     (     zero,     0.00464) **
   3          B-bacillif        0.00508     (  0.00111,     0.00909) **
  11             1              0.00270     (     zero,     0.00553) **
   1            10              0.00003     (     zero,    infinity)
  10          B--doshiae        0.00006     (     zero,    infinity)
  10             8              0.00006     (     zero,    infinity)
   8          B-birtlesi        0.00292     (  0.00007,     0.00578) **
   8             9              0.00073     (     zero,     0.00217) **
   9          B-vinsonii        0.00072     (     zero,     0.00213) **
   9          B-henselae        0.00365     (  0.00046,     0.00685) **
   1             6              0.00292     (  0.00007,     0.00578) **
   6          B-grahamii        0.00003     (     zero,    infinity)
   6          B-elizabet        0.00506     (  0.00137,     0.00887) **
   5          B-clarridg        0.00549     (  0.00110,     0.00981) **
   5          A-tumefaci        0.05841     (  0.04508,     0.07183) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 37:


Empirical Base Frequencies:

   A       0.24860
   C       0.23722
   G       0.30489
  T(U)     0.20930

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.486448)


     +B-grahamii
     !  
  +--6  +B--doshiae
  !  !  !  
  !  !  !     +B-bacillif
  !  +--1  +--8  
  !     !  !  !  +B-quintana
  !     !  !  +-12  
  !     !  !     +B-birtlesi
  !     +-10  
  !        !     +B-arupensi
  !        !  +--7  
  !        !  !  +B-vinsonii
  !        +--2  
  !           !  +B-berhoffi
  !           +--3  
  !              !  +B-elizabet
  !              +--9  
  !                 !  +B-clarridg
  !                 +--4  
  !                    !  +B--weissii
  !                    +--5  
  !                       +B-spp-Deer
  !  
-11-B-henselae
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3062.04693

Examined  624 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  11             6              0.00051     (     zero,     0.00202)
   6          B-grahamii        0.00006     (     zero,    infinity)
   6             1              0.00292     (  0.00007,     0.00578) **
   1          B--doshiae        0.00076     (     zero,     0.00222) **
   1            10              0.00006     (     zero,    infinity)
  10             8              0.00294     (  0.00006,     0.00582) **
   8          B-bacillif        0.00966     (  0.00437,     0.01487) **
   8            12              0.00075     (     zero,     0.00221) *
  12          B-quintana        0.01399     (  0.00773,     0.02032) **
  12          B-birtlesi        0.00003     (     zero,     0.00156)
  10             2              0.00006     (     zero,     0.00179)
   2             7              0.00151     (     zero,     0.00356) **
   7          B-arupensi        0.00365     (  0.00045,     0.00686) **
   7          B-vinsonii        0.00149     (     zero,     0.00354) **
   2             3              0.00218     (     zero,     0.00466) **
   3          B-berhoffi        0.00006     (     zero,     0.00152)
   3             9              0.00081     (     zero,     0.00240) **
   9          B-elizabet        0.00651     (  0.00225,     0.01084) **
   9             4              0.00309     (  0.00007,     0.00617) **
   4          B-clarridg        0.01021     (  0.00481,     0.01568) **
   4             5              0.00950     (  0.00427,     0.01473) **
   5          B--weissii        0.00440     (  0.00089,     0.00792) **
   5          B-spp-Deer        0.00070     (     zero,     0.00212) **
  11          B-henselae        0.00536     (  0.00142,     0.00932) **
  11          A-tumefaci        0.06677     (  0.05281,     0.08128) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 38:


Empirical Base Frequencies:

   A       0.24798
   C       0.22838
   G       0.32320
  T(U)     0.20044

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.473042)


     +B-bacillif
     !  
  +--5     +B--weissii
  !  !  +--1  
  !  !  !  +B-spp-Deer
  !  +--2  
  !     !  +B-henselae
  !     !  !  
  !     +--6  +B--doshiae
  !        !  !  
  !        +--4     +B-arupensi
  !           !  +-12  
  !           !  !  +B-vinsonii
  !           +-11  
  !              !  +B-birtlesi
  !              !  !  
  !              +--3     +B-grahamii
  !                 !  +-10  
  !                 !  !  +B-elizabet
  !                 +--8  
  !                    !  +B-berhoffi
  !                    +--9  
  !                       +B-quintana
  !  
--7-B-clarridg
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2920.76444

Examined  562 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7             5              0.00541     (  0.00120,     0.00970) **
   5          B-bacillif        0.00763     (  0.00276,     0.01255) **
   5             2              0.00329     (  0.00009,     0.00650) **
   2             1              0.00299     (     zero,     0.00630) **
   1          B--weissii        0.00076     (     zero,     0.00223) **
   1          B-spp-Deer        0.00218     (     zero,     0.00466) **
   2             6              0.00340     (     zero,     0.00677) **
   6          B-henselae        0.00342     (  0.00022,     0.00660) **
   6             4              0.00171     (     zero,     0.00403) **
   4          B--doshiae        0.00006     (     zero,    infinity)
   4            11              0.00074     (     zero,     0.00218) **
  11            12              0.00073     (     zero,     0.00216) **
  12          B-arupensi        0.00596     (  0.00177,     0.01003) **
  12          B-vinsonii        0.00073     (     zero,     0.00216) **
  11             3              0.00006     (     zero,     0.00218)
   3          B-birtlesi        0.00289     (  0.00004,     0.00575) **
   3             8              0.00145     (     zero,     0.00347) **
   8            10              0.00145     (     zero,     0.00347) **
  10          B-grahamii        0.00003     (     zero,     0.00194)
  10          B-elizabet        0.00880     (  0.00384,     0.01379) **
   8             9              0.00223     (     zero,     0.00472) **
   9          B-berhoffi        0.00151     (     zero,     0.00356) **
   9          B-quintana        0.00732     (  0.00280,     0.01188) **
   7          B-clarridg        0.00759     (  0.00285,     0.01242) **
   7          A-tumefaci        0.04764     (  0.03591,     0.05980) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 39:


Empirical Base Frequencies:

   A       0.24649
   C       0.23051
   G       0.31957
  T(U)     0.20342

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.478880)


  +B-arupensi
  !  
  !           +B-clarridg
  !        +--2  
  !        !  !  +B--weissii
  !     +--1  +-11  
  !     !  !     +B-spp-Deer
  !  +-10  !  
  !  !  !  +B-quintana
  !  !  !  
-12--8  +B-bacillif
  !  !  
  !  !  +B-berhoffi
  !  !  !  
  !  +--6  +B-elizabet
  !     !  !  
  !     !  !        +B-grahamii
  !     +--3     +--9  
  !        !     !  +B-birtlesi
  !        !  +--5  
  !        !  !  !  +B-henselae
  !        +--7  +--4  
  !           !     +B--doshiae
  !           !  
  !           +B-vinsonii
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3002.79954

Examined 1966 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  12          B-arupensi        0.00369     (  0.00044,     0.00693) **
  12             8              0.00146     (     zero,     0.00353) **
   8            10              0.00356     (  0.00025,     0.00677) **
  10             1              0.00423     (  0.00069,     0.00774) **
   1             2              0.00033     (     zero,     0.00229)
   2          B-clarridg        0.00734     (  0.00278,     0.01191) **
   2            11              0.00809     (  0.00330,     0.01288) **
  11          B--weissii        0.00146     (     zero,     0.00347) **
  11          B-spp-Deer        0.00006     (     zero,    infinity)
   1          B-quintana        0.01093     (  0.00527,     0.01650) **
  10          B-bacillif        0.01046     (  0.00499,     0.01595) **
   8             6              0.00003     (     zero,     0.00186)
   6          B-berhoffi        0.00070     (     zero,     0.00210) **
   6             3              0.00307     (     zero,     0.00619) **
   3          B-elizabet        0.00658     (  0.00227,     0.01089) **
   3             7              0.00200     (     zero,     0.00463) **
   7             5              0.00003     (     zero,     0.00193)
   5             9              0.00006     (     zero,     0.00187)
   9          B-grahamii        0.00003     (     zero,    infinity)
   9          B-birtlesi        0.00074     (     zero,     0.00218) **
   5             4              0.00291     (  0.00007,     0.00577) **
   4          B-henselae        0.00958     (  0.00437,     0.01478) **
   4          B--doshiae        0.00003     (     zero,    infinity)
   7          B-vinsonii        0.00220     (     zero,     0.00468) **
  12          A-tumefaci        0.05561     (  0.04289,     0.06872) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 40:


Empirical Base Frequencies:

   A       0.26686
   C       0.23557
   G       0.30164
  T(U)     0.19593

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.464304)


  +B-berhoffi
  !  
  !           +B-grahamii
  !        +--5  
  !        !  !  +B-bacillif
  !        !  +-11  
  !     +--2     +B-elizabet
  !     !  !  
  !     !  !  +B-birtlesi
  !     !  !  !  
  !     !  +--4     +B--doshiae
  !  +--3     !  +--1  
  !  !  !     +--9  +B-henselae
  !  !  !        !  
  !  !  !        +B-vinsonii
  !  !  !  
--6--7  +B-arupensi
  !  !  
  !  !     +B-quintana
  !  !  +-12  
  !  !  !  +B-clarridg
  !  +--8  
  !     !  +B-spp-Deer
  !     +-10  
  !        +B--weissii
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3120.60226

Examined 1706 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   6          B-berhoffi        0.00003     (     zero,     0.00157)
   6             7              0.00073     (     zero,     0.00216) **
   7             3              0.00003     (     zero,     0.00178)
   3             2              0.00360     (  0.00048,     0.00680) **
   2             5              0.00003     (     zero,     0.00186)
   5          B-grahamii        0.00287     (  0.00006,     0.00573) **
   5            11              0.00288     (  0.00002,     0.00576) **
  11          B-bacillif        0.01111     (  0.00548,     0.01673) **
  11          B-elizabet        0.00584     (  0.00183,     0.00995) **
   2             4              0.00073     (     zero,     0.00217) *
   4          B-birtlesi        0.00212     (     zero,     0.00458) **
   4             9              0.00006     (     zero,     0.00177)
   9             1              0.00218     (     zero,     0.00465) **
   1          B--doshiae        0.00003     (     zero,    infinity)
   1          B-henselae        0.00511     (  0.00133,     0.00890) **
   9          B-vinsonii        0.00142     (     zero,     0.00342) **
   3          B-arupensi        0.00513     (  0.00135,     0.00894) **
   7             8              0.00401     (  0.00055,     0.00754) **
   8            12              0.00214     (     zero,     0.00467) **
  12          B-quintana        0.01192     (  0.00595,     0.01780) **
  12          B-clarridg        0.01334     (  0.00710,     0.01959) **
   8            10              0.01069     (  0.00508,     0.01627) **
  10          B-spp-Deer        0.00218     (     zero,     0.00466) **
  10          B--weissii        0.00220     (     zero,     0.00470) **
   6          A-tumefaci        0.05860     (  0.04550,     0.07201) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 41:


Empirical Base Frequencies:

   A       0.23963
   C       0.22602
   G       0.32051
  T(U)     0.21385

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.488408)


  +B-clarridg
  !  
  !        +B-arupensi
  !     +--2  
  !     !  !  +B-quintana
  !     !  +-12  
  !  +--1     +B-berhoffi
  !  !  !  
  !  !  !  +B-bacillif
  !  !  +-11  
  !  !     !  +B-birtlesi
  !  !     +--9  
  !  !        !  +B-vinsonii
  !  !        +--7  
--5--4           !  +B--doshiae
  !  !           +--3  
  !  !              !  +B-henselae
  !  !              +--8  
  !  !                 !  +B-elizabet
  !  !                 +-10  
  !  !                    +B-grahamii
  !  !  
  !  !  +B-spp-Deer
  !  +--6  
  !     +B--weissii
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3155.29908

Examined  694 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   5          B-clarridg        0.01019     (  0.00460,     0.01584) **
   5             4              0.00416     (  0.00035,     0.00798) **
   4             1              0.00269     (     zero,     0.00554) **
   1             2              0.00003     (     zero,     0.00194)
   2          B-arupensi        0.00366     (  0.00046,     0.00687) **
   2            12              0.00080     (     zero,     0.00237) **
  12          B-quintana        0.01248     (  0.00654,     0.01841) **
  12          B-berhoffi        0.00071     (     zero,     0.00213) **
   1            11              0.00323     (  0.00013,     0.00633) **
  11          B-bacillif        0.01326     (  0.00713,     0.01940) **
  11             9              0.00326     (  0.00013,     0.00637) **
   9          B-birtlesi        0.00222     (     zero,     0.00469) **
   9             7              0.00003     (     zero,    infinity)
   7          B-vinsonii        0.00145     (     zero,     0.00346) **
   7             3              0.00006     (     zero,     0.00179)
   3          B--doshiae        0.00074     (     zero,     0.00218) *
   3             8              0.00218     (     zero,     0.00465) **
   8          B-henselae        0.00656     (  0.00226,     0.01085) **
   8            10              0.00294     (  0.00006,     0.00582) **
  10          B-elizabet        0.01248     (  0.00654,     0.01841) **
  10          B-grahamii        0.00003     (     zero,     0.00156)
   4             6              0.00761     (  0.00288,     0.01229) **
   6          B-spp-Deer        0.00146     (     zero,     0.00349) **
   6          B--weissii        0.00365     (  0.00045,     0.00685) **
   5          A-tumefaci        0.05510     (  0.04244,     0.06821) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 42:


Empirical Base Frequencies:

   A       0.26927
   C       0.21826
   G       0.31179
  T(U)     0.20069

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.441966)


  +B-elizabet
  !  
  !        +B--weissii
  !     +-10  
  !  +--5  +B-spp-Deer
  !  !  !  
  !  !  +B-bacillif
  !  !  
  !  !     +B-berhoffi
  !  !     !  
  !  !     !        +B-vinsonii
--7-11     !        !  
  !  !     !     +--2     +B-henselae
  !  !  +--9     !  !  +--8  
  !  !  !  !     !  !  !  !  +B-grahamii
  !  !  !  !     !  +--6  +--4  
  !  !  !  !  +--1     !     +B-birtlesi
  !  !  !  !  !  !     !  
  !  +-12  !  !  !     +B--doshiae
  !     !  +--3  !  
  !     !     !  +B-arupensi
  !     !     !  
  !     !     +B-quintana
  !     !  
  !     +B-clarridg
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2875.73795

Examined  596 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7          B-elizabet        0.00672     (  0.00226,     0.01115) **
   7            11              0.00225     (     zero,     0.00495) **
  11             5              0.00423     (  0.00066,     0.00780) **
   5            10              0.00887     (  0.00385,     0.01389) **
  10          B--weissii        0.00006     (     zero,     0.00173)
  10          B-spp-Deer        0.00145     (     zero,     0.00347) **
   5          B-bacillif        0.00220     (     zero,     0.00475) **
  11            12              0.00229     (     zero,     0.00485) **
  12             9              0.00304     (     zero,     0.00606) **
   9          B-berhoffi        0.00367     (  0.00048,     0.00691) **
   9             3              0.00151     (     zero,     0.00356) **
   3             1              0.00084     (     zero,     0.00248) **
   1             2              0.00333     (  0.00014,     0.00646) **
   2          B-vinsonii        0.00073     (     zero,     0.00216) **
   2             6              0.00169     (     zero,     0.00394) **
   6             8              0.00003     (     zero,     0.00167)
   8          B-henselae        0.00512     (  0.00134,     0.00892) **
   8             4              0.00070     (     zero,     0.00229)
   4          B-grahamii        0.00144     (     zero,     0.00347) **
   4          B-birtlesi        0.00013     (     zero,     0.00158)
   6          B--doshiae        0.00003     (     zero,    infinity)
   1          B-arupensi        0.00146     (     zero,     0.00348) **
   3          B-quintana        0.00661     (  0.00224,     0.01091) **
  12          B-clarridg        0.00798     (  0.00317,     0.01279) **
   7          A-tumefaci        0.05061     (  0.03852,     0.06304) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 43:


Empirical Base Frequencies:

   A       0.23837
   C       0.24661
   G       0.32550
  T(U)     0.18952

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.501489)


              +B-arupensi
           +-12  
        +--8  +B-quintana
        !  !  
        !  +B-berhoffi
        !  
     +--2     +B-grahamii
     !  !  +--9  
     !  !  !  +B-elizabet
     !  !  !  
     !  +--4     +B-birtlesi
     !     !  +--6  
  +--1     !  !  +B--doshiae
  !  !     +-10  
  !  !        !  +B-vinsonii
  !  !        +--7  
  !  !           +B-henselae
  !  !  
  !  !  +B-bacillif
  !  +-11  
  !     !  +B-spp-Deer
  !     +--5  
  !        +B--weissii
  !  
--3-B-clarridg
  !  
  +----A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2973.68719

Examined  706 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   3             1              0.00671     (  0.00211,     0.01134) **
   1             2              0.00447     (  0.00080,     0.00815) **
   2             8              0.00006     (     zero,     0.00181)
   8            12              0.00151     (     zero,     0.00356) **
  12          B-arupensi        0.00227     (     zero,     0.00477) **
  12          B-quintana        0.00659     (  0.00229,     0.01090) **
   8          B-berhoffi        0.00071     (     zero,     0.00213) **
   2             4              0.00217     (     zero,     0.00464) **
   4             9              0.00074     (     zero,     0.00219) **
   9          B-grahamii        0.00006     (     zero,    infinity)
   9          B-elizabet        0.00733     (  0.00279,     0.01187) **
   4            10              0.00074     (     zero,     0.00218) **
  10             6              0.00003     (     zero,    infinity)
   6          B-birtlesi        0.00149     (     zero,     0.00352) **
   6          B--doshiae        0.00003     (     zero,    infinity)
  10             7              0.00075     (     zero,     0.00220) **
   7          B-vinsonii        0.00222     (     zero,     0.00471) **
   7          B-henselae        0.00219     (     zero,     0.00467) **
   1            11              0.00373     (  0.00047,     0.00708) **
  11          B-bacillif        0.00655     (  0.00216,     0.01090) **
  11             5              0.00374     (  0.00045,     0.00709) **
   5          B-spp-Deer        0.00363     (  0.00048,     0.00684) **
   5          B--weissii        0.00003     (     zero,    infinity)
   3          B-clarridg        0.00726     (  0.00248,     0.01204) **
   3          A-tumefaci        0.07568     (  0.06084,     0.09143) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 44:


Empirical Base Frequencies:

   A       0.25702
   C       0.22212
   G       0.31295
  T(U)     0.20790

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.463081)


                 +B-henselae
              +-12  
              !  !  +B-spp-Deer
              !  +--9  
           +--4     +B--weissii
           !  !  
           !  !  +B-quintana
        +--3  +--6  
        !  !     +B-bacillif
        !  !  
        !  !  +B-grahamii
        !  +--8  
        !     !  +B--doshiae
     +--2     +-11  
     !  !        !  +B-birtlesi
     !  !        +--7  
     !  !           !  +B-arupensi
  +-10  !           +--1  
  !  !  !              +B-vinsonii
  !  !  !  
  !  !  +B-elizabet
  !  !  
  !  +B-berhoffi
  !  
--5-B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3261.81975

Examined  768 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   5            10              0.00726     (  0.00244,     0.01215) **
  10             2              0.00072     (     zero,     0.00214) **
   2             3              0.00077     (     zero,     0.00225) **
   3             4              0.00369     (  0.00042,     0.00690) **
   4            12              0.00224     (     zero,     0.00476) **
  12          B-henselae        0.00440     (  0.00087,     0.00794) **
  12             9              0.01032     (  0.00491,     0.01574) **
   9          B-spp-Deer        0.00293     (  0.00006,     0.00581) **
   9          B--weissii        0.00214     (     zero,     0.00462) **
   4             6              0.00505     (  0.00122,     0.00890) **
   6          B-quintana        0.01186     (  0.00610,     0.01776) **
   6          B-bacillif        0.01638     (  0.00951,     0.02326) **
   3             8              0.00217     (     zero,     0.00464) **
   8          B-grahamii        0.00219     (     zero,     0.00467) **
   8            11              0.00075     (     zero,     0.00220) **
  11          B--doshiae        0.00003     (     zero,    infinity)
  11             7              0.00006     (     zero,    infinity)
   7          B-birtlesi        0.00364     (  0.00047,     0.00683) **
   7             1              0.00219     (     zero,     0.00468) **
   1          B-arupensi        0.00364     (  0.00048,     0.00686) **
   1          B-vinsonii        0.00293     (  0.00005,     0.00579) **
   2          B-elizabet        0.00954     (  0.00436,     0.01473) **
  10          B-berhoffi        0.00006     (     zero,     0.00150)
   5          B-clarridg        0.01043     (  0.00477,     0.01615) **
   5          A-tumefaci        0.06079     (  0.04734,     0.07456) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 45:


Empirical Base Frequencies:

   A       0.22719
   C       0.22712
   G       0.32330
  T(U)     0.22239

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.509164)


  +B-berhoffi
  !  
  !                 +B-vinsonii
  !              +--2  
  !              !  !  +B--doshiae
  !           +-11  +--1  
  !           !  !     +B-henselae
  !        +--8  !  
  !        !  !  +B-birtlesi
  !     +--4  !  
  !     !  !  +B-grahamii
  !  +--3  !  
  !  !  !  +B-elizabet
  !  !  !  
  !  !  +B-arupensi
  !  !  
--6--7        +B-bacillif
  !  !     +-12  
  !  !     !  !  +B-spp-Deer
  !  !  +--9  +-10  
  !  !  !  !     +B--weissii
  !  +--5  !  
  !     !  +B-quintana
  !     !  
  !     +B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2969.00114

Examined  876 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   6          B-berhoffi        0.00003     (     zero,     0.00158)
   6             7              0.00221     (     zero,     0.00471) **
   7             3              0.00006     (     zero,    infinity)
   3             4              0.00294     (  0.00007,     0.00582) **
   4             8              0.00072     (     zero,     0.00216) *
   8            11              0.00075     (     zero,     0.00221) *
  11             2              0.00006     (     zero,     0.00167)
   2          B-vinsonii        0.00074     (     zero,     0.00218) **
   2             1              0.00076     (     zero,     0.00221) **
   1          B--doshiae        0.00003     (     zero,    infinity)
   1          B-henselae        0.00732     (  0.00280,     0.01187) **
  11          B-birtlesi        0.00139     (     zero,     0.00339) **
   8          B-grahamii        0.00072     (     zero,     0.00214) **
   4          B-elizabet        0.00660     (  0.00230,     0.01091) **
   3          B-arupensi        0.00293     (  0.00007,     0.00581) **
   7             5              0.00338     (  0.00013,     0.00665) **
   5             9              0.00193     (     zero,     0.00457) **
   9            12              0.00472     (  0.00062,     0.00880) **
  12          B-bacillif        0.00784     (  0.00274,     0.01296) **
  12            10              0.00769     (  0.00275,     0.01254) **
  10          B-spp-Deer        0.00191     (     zero,     0.00434) **
  10          B--weissii        0.00099     (     zero,     0.00282) **
   9          B-quintana        0.00655     (  0.00203,     0.01111) **
   5          B-clarridg        0.00913     (  0.00393,     0.01430) **
   6          A-tumefaci        0.06246     (  0.04909,     0.07652) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 46:


Empirical Base Frequencies:

   A       0.25545
   C       0.22330
   G       0.30683
  T(U)     0.21443

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.471111)


  +B-clarridg
  !  
  !     +B-bacillif
  !  +--6  
  !  !  !  +B-spp-Deer
  !  !  +-11  
  !  !     +B--weissii
  !  !  
--8--5  +B-quintana
  !  !  !  
  !  !  !           +B--doshiae
  !  !  !        +--3  
  !  !  !        !  !  +B-birtlesi
  !  !  !        !  +--1  
  !  +--4     +--7     +B-grahamii
  !     !     !  !  
  !     !     !  !  +B-vinsonii
  !     !  +-12  +--9  
  !     !  !  !     +B-henselae
  !     !  !  !  
  !     +-10  +B-arupensi
  !        !  
  !        !  +B-elizabet
  !        +--2  
  !           +B-berhoffi
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2877.56285

Examined 1498 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   8          B-clarridg        0.00302     (     zero,     0.00607) **
   8             5              0.00427     (  0.00035,     0.00815) **
   5             6              0.00361     (  0.00022,     0.00701) **
   6          B-bacillif        0.00707     (  0.00239,     0.01181) **
   6            11              0.00515     (  0.00113,     0.00918) **
  11          B-spp-Deer        0.00096     (     zero,     0.00277) **
  11          B--weissii        0.00126     (     zero,     0.00326) **
   5             4              0.00405     (  0.00041,     0.00772) **
   4          B-quintana        0.00374     (  0.00020,     0.00721) **
   4            10              0.00289     (     zero,     0.00607) **
  10            12              0.00003     (     zero,     0.00217)
  12             7              0.00283     (  0.00005,     0.00568) **
   7             3              0.00003     (     zero,     0.00224)
   3          B--doshiae        0.00003     (     zero,    infinity)
   3             1              0.00003     (     zero,     0.00216)
   1          B-birtlesi        0.00218     (     zero,     0.00465) **
   1          B-grahamii        0.00076     (     zero,     0.00221) **
   7             9              0.00146     (     zero,     0.00348) **
   9          B-vinsonii        0.00076     (     zero,     0.00222) **
   9          B-henselae        0.00517     (  0.00129,     0.00895) **
  12          B-arupensi        0.00366     (  0.00046,     0.00687) **
  10             2              0.00075     (     zero,     0.00219) **
   2          B-elizabet        0.00952     (  0.00435,     0.01470) **
   2          B-berhoffi        0.00074     (     zero,     0.00218) **
   8          A-tumefaci        0.05523     (  0.04266,     0.06836) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 47:


Empirical Base Frequencies:

   A       0.24712
   C       0.24005
   G       0.29097
  T(U)     0.22185

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.494151)


  +B-bacillif
  !  
  !              +B-vinsonii
  !           +--8  
  !           !  +B-arupensi
  !           !  
  !        +--1  +B--doshiae
  !        !  !  !  
  !        !  !  !     +B-quintana
  !        !  +--7  +--3  
  !        !     !  !  !  +B-clarridg
  !        !     !  !  +--9  
  !     +-11     +--6     !  +B-spp-Deer
  !     !  !        !     +--5  
  !     !  !        !        +B--weissii
  !     !  !        !  
  !     !  !        +B-henselae
  !  +--4  !  
  !  !  !  !  +B-grahamii
  !  !  !  +-12  
-10--2  !     +B-birtlesi
  !  !  !  
  !  !  +B-berhoffi
  !  !  
  !  +B-elizabet
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3182.38093

Examined  576 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10          B-bacillif        0.00871     (  0.00353,     0.01398) **
  10             2              0.00500     (  0.00104,     0.00904) **
   2             4              0.00458     (  0.00088,     0.00824) **
   4            11              0.00032     (     zero,     0.00178)
  11             1              0.00150     (     zero,     0.00355) **
   1             8              0.00220     (     zero,     0.00469) **
   8          B-vinsonii        0.00142     (     zero,     0.00344) **
   8          B-arupensi        0.00368     (  0.00046,     0.00691) **
   1             7              0.00143     (     zero,     0.00344) **
   7          B--doshiae        0.00006     (     zero,    infinity)
   7             6              0.00220     (     zero,     0.00469) **
   6             3              0.00158     (     zero,     0.00403) **
   3          B-quintana        0.01300     (  0.00688,     0.01917) **
   3             9              0.00236     (     zero,     0.00513) **
   9          B-clarridg        0.01092     (  0.00535,     0.01655) **
   9             5              0.00977     (  0.00443,     0.01506) **
   5          B-spp-Deer        0.00074     (     zero,     0.00219) **
   5          B--weissii        0.00151     (     zero,     0.00356) **
   6          B-henselae        0.00440     (  0.00088,     0.00791) **
  11            12              0.00138     (     zero,     0.00339) **
  12          B-grahamii        0.00150     (     zero,     0.00354) **
  12          B-birtlesi        0.00366     (  0.00046,     0.00686) **
   4          B-berhoffi        0.00339     (  0.00020,     0.00658) **
   2          B-elizabet        0.00546     (  0.00133,     0.00950) **
  10          A-tumefaci        0.06781     (  0.05372,     0.08257) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 48:


Empirical Base Frequencies:

   A       0.22938
   C       0.25025
   G       0.30458
  T(U)     0.21578

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.515216)


  +B-elizabet
  !  
  !     +B-clarridg
  !     !  
  !     !     +B-henselae
  !     !     !  
  !  +--9     !        +B-birtlesi
  !  !  !  +--6     +--7  
  !  !  !  !  !  +--3  +B-grahamii
  !  !  !  !  !  !  !  
  !  !  !  !  +-12  +B-vinsonii
  !  !  +--2     !  
  !  !     !     +B--doshiae
  !  !     !  
--8--1     !  +B-berhoffi
  !  !     +-10  
  !  !        !  +B-arupensi
  !  !        +-11  
  !  !           +B-quintana
  !  !  
  !  !     +B-spp-Deer
  !  !  +--4  
  !  +--5  +B--weissii
  !     !  
  !     +B-bacillif
  !  
  +----A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3354.09612

Examined 2550 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   8          B-elizabet        0.00877     (  0.00357,     0.01400) **
   8             1              0.00411     (  0.00030,     0.00795) **
   1             9              0.00372     (  0.00035,     0.00701) **
   9          B-clarridg        0.01382     (  0.00755,     0.02018) **
   9             2              0.00388     (  0.00049,     0.00728) **
   2             6              0.00258     (     zero,     0.00561) **
   6          B-henselae        0.00660     (  0.00228,     0.01091) **
   6            12              0.00250     (     zero,     0.00551) **
  12             3              0.00006     (     zero,     0.00263)
   3             7              0.00006     (     zero,     0.00216)
   7          B-birtlesi        0.00219     (     zero,     0.00466) **
   7          B-grahamii        0.00366     (  0.00046,     0.00686) **
   3          B-vinsonii        0.00292     (  0.00007,     0.00579) **
  12          B--doshiae        0.00073     (     zero,     0.00217) *
   2            10              0.00003     (     zero,     0.00228)
  10          B-berhoffi        0.00006     (     zero,    infinity)
  10            11              0.00151     (     zero,     0.00356) **
  11          B-arupensi        0.00221     (     zero,     0.00471) **
  11          B-quintana        0.01847     (  0.01123,     0.02574) **
   1             5              0.00461     (  0.00076,     0.00846) **
   5             4              0.00813     (  0.00328,     0.01296) **
   4          B-spp-Deer        0.00186     (     zero,     0.00438) **
   4          B--weissii        0.00251     (     zero,     0.00534) **
   5          B-bacillif        0.01223     (  0.00621,     0.01823) **
   8          A-tumefaci        0.08178     (  0.06607,     0.09803) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 49:


Empirical Base Frequencies:

   A       0.25872
   C       0.21430
   G       0.31667
  T(U)     0.21031

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.455080)


  +B-clarridg
  !  
  !     +B-quintana
  !     !  
  !     !  +B-berhoffi
  !  +--9  !  
  !  !  !  !     +B-grahamii
  !  !  !  !  +-12  
  !  !  +--4  !  +B-elizabet
  !  !     !  !  
  !  !     !  !     +B-arupensi
  !  !     !  !     !  
  !  !     +--2     !     +B-vinsonii
  !  !        !  +--8  +--1  
--6-10        !  !  !  !  !  +B-spp-Deer
  !  !        !  !  !  !  +-11  
  !  !        !  !  +--3     +B--weissii
  !  !        +--5     !  
  !  !           !     !  +B-henselae
  !  !           !     +--7  
  !  !           !        +B--doshiae
  !  !           !  
  !  !           +B-birtlesi
  !  !  
  !  +B-bacillif
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3033.94033

Examined 1998 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   6          B-clarridg        0.00816     (  0.00322,     0.01310) **
   6            10              0.00602     (  0.00172,     0.01033) **
  10             9              0.00373     (  0.00045,     0.00703) **
   9          B-quintana        0.00867     (  0.00367,     0.01366) **
   9             4              0.00235     (     zero,     0.00501) **
   4          B-berhoffi        0.00151     (     zero,     0.00355) **
   4             2              0.00145     (     zero,     0.00347) **
   2            12              0.00291     (  0.00002,     0.00577) **
  12          B-grahamii        0.00006     (     zero,     0.00214)
  12          B-elizabet        0.01175     (  0.00601,     0.01752) **
   2             5              0.00139     (     zero,     0.00339) **
   5             8              0.00006     (     zero,     0.00211)
   8          B-arupensi        0.00363     (  0.00049,     0.00685) **
   8             3              0.00003     (     zero,    infinity)
   3             1              0.00150     (     zero,     0.00353) **
   1          B-vinsonii        0.00003     (     zero,    infinity)
   1            11              0.00805     (  0.00331,     0.01282) **
  11          B-spp-Deer        0.00292     (  0.00006,     0.00579) **
  11          B--weissii        0.00143     (     zero,     0.00344) **
   3             7              0.00076     (     zero,     0.00222) **
   7          B-henselae        0.00658     (  0.00229,     0.01088) **
   7          B--doshiae        0.00006     (     zero,    infinity)
   5          B-birtlesi        0.00217     (     zero,     0.00465) **
  10          B-bacillif        0.00567     (  0.00160,     0.00977) **
   6          A-tumefaci        0.05499     (  0.04227,     0.06802) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 50:


Empirical Base Frequencies:

   A       0.25715
   C       0.23403
   G       0.30584
  T(U)     0.20298

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.473113)


        +B-berhoffi
     +--7  
     !  +B-elizabet
     !  
     !        +B--doshiae
     !     +--5  
     !     !  !  +B-vinsonii
     !     !  +-10  
  +--2     !     +B-arupensi
  !  !     !  
  !  !  +--6     +B-henselae
  !  !  !  !     !  
  !  !  !  !  +--8     +B-spp-Deer
  !  !  !  !  !  !  +-12  
  !  !  !  !  !  +-11  +B--weissii
  !  +--1  +--3     !  
  !     !     !     +B-bacillif
  !     !     !  
  !     !     +B-quintana
  !     !  
  !     !  +B-birtlesi
  !     +--9  
  !        +B-grahamii
  !  
--4-B-clarridg
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3008.73056

Examined  618 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   4             2              0.00430     (  0.00063,     0.00798) **
   2             7              0.00003     (     zero,     0.00191)
   7          B-berhoffi        0.00071     (     zero,     0.00212) **
   7          B-elizabet        0.00808     (  0.00331,     0.01286) **
   2             1              0.00076     (     zero,     0.00223) **
   1             6              0.00076     (     zero,     0.00222) **
   6             5              0.00006     (     zero,     0.00156)
   5          B--doshiae        0.00006     (     zero,    infinity)
   5            10              0.00073     (     zero,     0.00217) **
  10          B-vinsonii        0.00146     (     zero,     0.00348) **
  10          B-arupensi        0.00216     (     zero,     0.00464) **
   6             3              0.00298     (  0.00003,     0.00587) **
   3             8              0.00073     (     zero,     0.00221) *
   8          B-henselae        0.00226     (     zero,     0.00476) **
   8            11              0.00470     (  0.00095,     0.00845) **
  11            12              0.01033     (  0.00489,     0.01577) **
  12          B-spp-Deer        0.00293     (  0.00006,     0.00581) **
  12          B--weissii        0.00075     (     zero,     0.00221) **
  11          B-bacillif        0.00788     (  0.00307,     0.01267) **
   3          B-quintana        0.01332     (  0.00716,     0.01949) **
   1             9              0.00071     (     zero,     0.00213) *
   9          B-birtlesi        0.00292     (  0.00007,     0.00579) **
   9          B-grahamii        0.00075     (     zero,     0.00221) **
   4          B-clarridg        0.01036     (  0.00490,     0.01592) **
   4          A-tumefaci        0.05825     (  0.04527,     0.07181) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 51:


Empirical Base Frequencies:

   A       0.26509
   C       0.21506
   G       0.30048
  T(U)     0.21937

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.461571)


  +B-clarridg
  !  
  !           +B-quintana
  !        +-11  
  !        !  +B-henselae
  !     +--7  
  !     !  !  +B-bacillif
  !     !  +--8  
  !     !     !  +B--weissii
  !  +--1     +-10  
  !  !  !        +B-spp-Deer
  !  !  !  
  !  !  !  +B-birtlesi
  !  !  +--9  
  !  !     !  +B-berhoffi
  !  !     +--6  
-12--3        !  +B--doshiae
  !  !        +--2  
  !  !           !  +B-arupensi
  !  !           +--5  
  !  !              +B-vinsonii
  !  !  
  !  !  +B-elizabet
  !  +--4  
  !     +B-grahamii
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2893.73501

Examined 2426 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  12          B-clarridg        0.00740     (  0.00265,     0.01215) **
  12             3              0.00448     (  0.00083,     0.00826) **
   3             1              0.00067     (     zero,     0.00222)
   1             7              0.00511     (  0.00134,     0.00890) **
   7            11              0.00006     (     zero,     0.00208)
  11          B-quintana        0.00954     (  0.00435,     0.01472) **
  11          B-henselae        0.00363     (  0.00043,     0.00683) **
   7             8              0.00216     (     zero,     0.00464) **
   8          B-bacillif        0.00366     (  0.00045,     0.00688) **
   8            10              0.00735     (  0.00279,     0.01191) **
  10          B--weissii        0.00143     (     zero,     0.00344) **
  10          B-spp-Deer        0.00070     (     zero,     0.00210) **
   1             9              0.00003     (     zero,     0.00160)
   9          B-birtlesi        0.00218     (     zero,     0.00465) **
   9             6              0.00003     (     zero,    infinity)
   6          B-berhoffi        0.00006     (     zero,    infinity)
   6             2              0.00004     (     zero,    infinity)
   2          B--doshiae        0.00006     (     zero,    infinity)
   2             5              0.00070     (     zero,     0.00209) **
   5          B-arupensi        0.00146     (     zero,     0.00348) **
   5          B-vinsonii        0.00003     (     zero,    infinity)
   3             4              0.00140     (     zero,     0.00355) **
   4          B-elizabet        0.00585     (  0.00180,     0.00990) **
   4          B-grahamii        0.00006     (     zero,     0.00208)
  12          A-tumefaci        0.06828     (  0.05428,     0.08320) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 52:


Empirical Base Frequencies:

   A       0.26830
   C       0.23066
   G       0.29083
  T(U)     0.21021

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.468688)


  +B-arupensi
  !  
  !              +B-henselae
  !           +--5  
  !        +--4  +B--doshiae
  !        !  !  
  !     +--1  +B-vinsonii
  !     !  !  
  !  +-12  +B-birtlesi
  !  !  !  
  !  !  !  +B-grahamii
  !  !  +--2  
  !  !     +B-elizabet
  !  !  
--8-10        +B-clarridg
  !  !     +--9  
  !  !     !  !  +B-bacillif
  !  !     !  +--7  
  !  !  +--6     !  +B--weissii
  !  !  !  !     +-11  
  !  !  !  !        +B-spp-Deer
  !  +--3  !  
  !     !  +B-quintana
  !     !  
  !     +B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3168.73163

Examined 1842 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   8          B-arupensi        0.00511     (  0.00120,     0.00897) **
   8            10              0.00087     (     zero,     0.00266)
  10            12              0.00585     (  0.00181,     0.00993) **
  12             1              0.00074     (     zero,     0.00220) *
   1             4              0.00003     (     zero,     0.00186)
   4             5              0.00220     (     zero,     0.00468) **
   5          B-henselae        0.00440     (  0.00089,     0.00793) **
   5          B--doshiae        0.00006     (     zero,    infinity)
   4          B-vinsonii        0.00367     (  0.00046,     0.00689) **
   1          B-birtlesi        0.00217     (     zero,     0.00466) **
  12             2              0.00218     (     zero,     0.00467) **
   2          B-grahamii        0.00003     (     zero,     0.00189)
   2          B-elizabet        0.01032     (  0.00492,     0.01573) **
  10             3              0.00006     (     zero,     0.00201)
   3             6              0.00375     (  0.00044,     0.00706) **
   6             9              0.00221     (     zero,     0.00480) **
   9          B-clarridg        0.00954     (  0.00427,     0.01480) **
   9             7              0.00392     (  0.00047,     0.00738) **
   7          B-bacillif        0.01163     (  0.00590,     0.01752) **
   7            11              0.00450     (  0.00088,     0.00812) **
  11          B--weissii        0.00130     (     zero,     0.00330) **
  11          B-spp-Deer        0.00088     (     zero,     0.00256) **
   6          B-quintana        0.01030     (  0.00485,     0.01573) **
   3          B-berhoffi        0.00076     (     zero,     0.00222) **
   8          A-tumefaci        0.07328     (  0.05819,     0.08834) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 53:


Empirical Base Frequencies:

   A       0.24305
   C       0.24290
   G       0.31743
  T(U)     0.19662

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.493115)


  +B-berhoffi
  !  
  !           +B--doshiae
  !        +--4  
  !        !  !  +B-birtlesi
  !        !  +--9  
  !        !     !  +B-henselae
  !        !     +-12  
  !     +--1        +B-grahamii
  !     !  !  
  !     !  !  +B-vinsonii
  !     !  !  !  
  !     !  !  !     +B-clarridg
  !     !  +--6  +--8  
  !     !     !  !  !  +B-bacillif
  !  +--3     !  !  +-11  
  !  !  !     +--7     +B-quintana
  !  !  !        !  
  !  !  !        !  +B--weissii
-10--5  !        +--2  
  !  !  !           +B-spp-Deer
  !  !  !  
  !  !  +B-arupensi
  !  !  
  !  +B-elizabet
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3003.15672

Examined  550 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10          B-berhoffi        0.00006     (     zero,     0.00153)
  10             5              0.00154     (     zero,     0.00368) **
   5             3              0.00148     (     zero,     0.00353) **
   3             1              0.00003     (     zero,     0.00186)
   1             4              0.00210     (     zero,     0.00458) **
   4          B--doshiae        0.00006     (     zero,    infinity)
   4             9              0.00006     (     zero,     0.00219)
   9          B-birtlesi        0.00295     (  0.00003,     0.00581) **
   9            12              0.00067     (     zero,     0.00204) **
  12          B-henselae        0.00223     (     zero,     0.00471) **
  12          B-grahamii        0.00003     (     zero,    infinity)
   1             6              0.00161     (     zero,     0.00377) **
   6          B-vinsonii        0.00128     (     zero,     0.00330) *
   6             7              0.00159     (     zero,     0.00383) **
   7             8              0.00253     (     zero,     0.00540) **
   8          B-clarridg        0.01084     (  0.00520,     0.01645) **
   8            11              0.00369     (  0.00042,     0.00698) **
  11          B-bacillif        0.00828     (  0.00333,     0.01322) **
  11          B-quintana        0.00652     (  0.00212,     0.01092) **
   7             2              0.01541     (  0.00876,     0.02208) **
   2          B--weissii        0.00072     (     zero,     0.00214) **
   2          B-spp-Deer        0.00152     (     zero,     0.00358) **
   3          B-arupensi        0.00157     (     zero,     0.00370) **
   5          B-elizabet        0.00877     (  0.00378,     0.01377) **
  10          A-tumefaci        0.06517     (  0.05139,     0.07952) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 54:


Empirical Base Frequencies:

   A       0.24613
   C       0.22422
   G       0.32192
  T(U)     0.20773

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.475550)


     +B-berhoffi
     !  
     !        +B-grahamii
     !     +--4  
     !     !  +B-elizabet
     !     !  
  +--8  +--3     +B-birtlesi
  !  !  !  !  +--1  
  !  !  !  !  !  !  +B-henselae
  !  !  !  !  !  +--9  
  !  !  !  +--7     +B--doshiae
  !  !  !     !  
  !  +--6     !  +B-arupensi
  !     !     +-10  
  !     !        +B-vinsonii
  !     !  
  !     !     +B-bacillif
  !     !  +-12  
  !     !  !  !  +B--weissii
  !     +--5  +-11  
  !        !     +B-spp-Deer
  !        !  
  !        +B-quintana
  !  
--2-B-clarridg
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2967.60871

Examined 1148 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   2             8              0.00661     (  0.00205,     0.01119) **
   8          B-berhoffi        0.00006     (     zero,     0.00208)
   8             6              0.00148     (     zero,     0.00353) **
   6             3              0.00224     (     zero,     0.00472) **
   3             4              0.00290     (  0.00009,     0.00577) **
   4          B-grahamii        0.00003     (     zero,    infinity)
   4          B-elizabet        0.01029     (  0.00490,     0.01569) **
   3             7              0.00149     (     zero,     0.00353) **
   7             1              0.00003     (     zero,    infinity)
   1          B-birtlesi        0.00150     (     zero,     0.00354) **
   1             9              0.00075     (     zero,     0.00219) **
   9          B-henselae        0.00222     (     zero,     0.00470) **
   9          B--doshiae        0.00006     (     zero,    infinity)
   7            10              0.00074     (     zero,     0.00219) **
  10          B-arupensi        0.00222     (     zero,     0.00471) **
  10          B-vinsonii        0.00074     (     zero,     0.00218) **
   6             5              0.00199     (     zero,     0.00471) **
   5            12              0.00427     (  0.00058,     0.00792) **
  12          B-bacillif        0.00843     (  0.00327,     0.01357) **
  12            11              0.00650     (  0.00200,     0.01101) **
  11          B--weissii        0.00006     (     zero,    infinity)
  11          B-spp-Deer        0.00292     (  0.00007,     0.00579) **
   5          B-quintana        0.01052     (  0.00494,     0.01611) **
   2          B-clarridg        0.01335     (  0.00702,     0.01969) **
   2          A-tumefaci        0.04730     (  0.03556,     0.05936) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 55:


Empirical Base Frequencies:

   A       0.25450
   C       0.22510
   G       0.32436
  T(U)     0.19605

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.458765)


     +B-berhoffi
     !  
     !  +B-elizabet
     !  !  
  +--5  !           +B-arupensi
  !  !  !        +--9  
  !  !  !        !  +B-vinsonii
  !  !  !     +--6  
  !  !  !     !  !  +B--doshiae
  !  +--7     !  !  !  
  !     !     !  +-11     +B-spp-Deer
  !     !     !     !  +--8  
  !     !  +--2     +--4  +B--weissii
  !     !  !  !        !  
  !     !  !  !        +B-henselae
  !     !  !  !  
  !     !  !  !  +B-birtlesi
  !     +-10  +--1  
  !        !     !  +B-bacillif
  !        !     +--3  
  !        !        +B-quintana
  !        !  
  !        +B-grahamii
  !  
-12-B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3045.43116

Examined  612 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  12             5              0.00914     (  0.00380,     0.01443) **
   5          B-berhoffi        0.00066     (     zero,     0.00228)
   5             7              0.00184     (     zero,     0.00431) **
   7          B-elizabet        0.00737     (  0.00281,     0.01194) **
   7            10              0.00255     (     zero,     0.00534) **
  10             2              0.00075     (     zero,     0.00221) **
   2             6              0.00146     (     zero,     0.00348) **
   6             9              0.00150     (     zero,     0.00355) **
   9          B-arupensi        0.00368     (  0.00046,     0.00690) **
   9          B-vinsonii        0.00219     (     zero,     0.00467) **
   6            11              0.00076     (     zero,     0.00222) **
  11          B--doshiae        0.00003     (     zero,    infinity)
  11             4              0.00294     (  0.00005,     0.00583) **
   4             8              0.00813     (  0.00331,     0.01292) **
   8          B-spp-Deer        0.00366     (  0.00045,     0.00686) **
   8          B--weissii        0.00003     (     zero,     0.00179)
   4          B-henselae        0.00216     (     zero,     0.00465) **
   2             1              0.00146     (     zero,     0.00349) **
   1          B-birtlesi        0.00148     (     zero,     0.00351) **
   1             3              0.00228     (     zero,     0.00494) **
   3          B-bacillif        0.01039     (  0.00494,     0.01585) **
   3          B-quintana        0.00947     (  0.00426,     0.01471) **
  10          B-grahamii        0.00006     (     zero,     0.00185)
  12          B-clarridg        0.00732     (  0.00247,     0.01213) **
  12          A-tumefaci        0.06089     (  0.04751,     0.07484) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 56:


Empirical Base Frequencies:

   A       0.25616
   C       0.23839
   G       0.29942
  T(U)     0.20603

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.480499)


              +B-grahamii
           +--6  
           !  +B-elizabet
           !  
        +--2     +B-vinsonii
        !  !  +-10  
        !  !  !  !  +B--doshiae
        !  +--5  +--8  
     +-12     !     +B-henselae
     !  !     !  
     !  !     +B-birtlesi
     !  !  
     !  +B-bacillif
  +--3  
  !  !     +B-quintana
  !  !  +--9  
  !  !  !  !  +B-clarridg
  !  !  !  +--7  
  !  +--4     !  +B--weissii
  !     !     +--1  
  !     !        +B-spp-Deer
  !     !  
  !     +B-berhoffi
  !  
-11-B-arupensi
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3052.99446

Examined  798 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  11             3              0.00168     (     zero,     0.00396) **
   3            12              0.00180     (     zero,     0.00417) **
  12             2              0.00180     (     zero,     0.00418) **
   2             6              0.00292     (  0.00002,     0.00578) **
   6          B-grahamii        0.00003     (     zero,     0.00258)
   6          B-elizabet        0.01100     (  0.00545,     0.01658) **
   2             5              0.00069     (     zero,     0.00211) *
   5            10              0.00006     (     zero,     0.00180)
  10          B-vinsonii        0.00070     (     zero,     0.00210) **
  10             8              0.00291     (  0.00007,     0.00576) **
   8          B--doshiae        0.00006     (     zero,    infinity)
   8          B-henselae        0.00730     (  0.00279,     0.01183) **
   5          B-birtlesi        0.00289     (  0.00006,     0.00575) **
  12          B-bacillif        0.01256     (  0.00655,     0.01850) **
   3             4              0.00006     (     zero,     0.00189)
   4             9              0.00396     (  0.00054,     0.00739) **
   9          B-quintana        0.00940     (  0.00420,     0.01459) **
   9             7              0.00279     (     zero,     0.00601) **
   7          B-clarridg        0.00805     (  0.00318,     0.01300) **
   7             1              0.00879     (  0.00379,     0.01380) **
   1          B--weissii        0.00350     (  0.00015,     0.00678) **
   1          B-spp-Deer        0.00240     (     zero,     0.00519) **
   4          B-berhoffi        0.00003     (     zero,    infinity)
  11          B-arupensi        0.00128     (     zero,     0.00330) **
  11          A-tumefaci        0.05353     (  0.04113,     0.06634) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 57:


Empirical Base Frequencies:

   A       0.25698
   C       0.23017
   G       0.30821
  T(U)     0.20464

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.469812)


  +B-grahamii
  !  
  !     +B--doshiae
  !     !  
  !  +--5  +B-vinsonii
  !  !  !  !  
  !  !  +--2  +B-arupensi
  !  !     !  !  
  !  !     !  !     +B-berhoffi
  !  !     +--8  +-11  
  !  !        !  !  +B-elizabet
  !  !        !  !  
  !  !        !  !     +B-quintana
  !  !        +--4     !  
-12--1           !  +--3  +B-clarridg
  !  !           !  !  !  !  
  !  !           !  !  +-10     +B--weissii
  !  !           !  !     !  +--9  
  !  !           +--6     +--7  +B-spp-Deer
  !  !              !        !  
  !  !              !        +B-bacillif
  !  !              !  
  !  !              +B-henselae
  !  !  
  !  +B-birtlesi
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2844.71236

Examined  870 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  12          B-grahamii        0.00003     (     zero,     0.00156)
  12             1              0.00145     (     zero,     0.00347) **
   1             5              0.00006     (     zero,     0.00181)
   5          B--doshiae        0.00003     (     zero,    infinity)
   5             2              0.00006     (     zero,     0.00181)
   2          B-vinsonii        0.00003     (     zero,    infinity)
   2             8              0.00137     (     zero,     0.00338) **
   8          B-arupensi        0.00073     (     zero,     0.00217) **
   8             4              0.00003     (     zero,     0.00188)
   4            11              0.00004     (     zero,    infinity)
  11          B-berhoffi        0.00006     (     zero,    infinity)
  11          B-elizabet        0.00953     (  0.00436,     0.01473) **
   4             6              0.00293     (  0.00006,     0.00580) **
   6             3              0.00059     (     zero,     0.00211)
   3          B-quintana        0.00969     (  0.00442,     0.01497) **
   3            10              0.00296     (     zero,     0.00587) **
  10          B-clarridg        0.01266     (  0.00662,     0.01870) **
  10             7              0.00479     (  0.00100,     0.00859) **
   7             9              0.00277     (     zero,     0.00564) **
   9          B--weissii        0.00183     (     zero,     0.00422) **
   9          B-spp-Deer        0.00181     (     zero,     0.00418) **
   7          B-bacillif        0.00638     (  0.00208,     0.01076) **
   6          B-henselae        0.00439     (  0.00088,     0.00792) **
   1          B-birtlesi        0.00074     (     zero,     0.00218) **
  12          A-tumefaci        0.05160     (  0.03918,     0.06398) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 58:


Empirical Base Frequencies:

   A       0.23155
   C       0.23578
   G       0.31480
  T(U)     0.21787

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.505939)


  +B-bacillif
  !  
  !     +B-elizabet
  !     !  
  !     !           +B-quintana
  !     !        +--4  
  !     !     +--2  +B-arupensi
  !     !     !  !  
  !  +-11     !  +B-berhoffi
  !  !  !     !  
  !  !  !  +--1     +B-vinsonii
  !  !  !  !  !  +--6  
  !  !  !  !  !  !  !  +B-birtlesi
  !  !  !  !  !  !  +--3  
  !  !  !  !  +--7     !  +B-grahamii
--5-12  +--8     !     +-10  
  !  !     !     !        +B--doshiae
  !  !     !     !  
  !  !     !     +B-henselae
  !  !     !  
  !  !     +B-clarridg
  !  !  
  !  !  +B--weissii
  !  +--9  
  !     +B-spp-Deer
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2934.41474

Examined 2424 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   5          B-bacillif        0.00688     (  0.00216,     0.01161) **
   5            12              0.00467     (  0.00075,     0.00853) **
  12            11              0.00469     (  0.00083,     0.00854) **
  11          B-elizabet        0.00597     (  0.00184,     0.01011) **
  11             8              0.00291     (  0.00003,     0.00580) **
   8             1              0.00083     (     zero,     0.00244) *
   1             2              0.00006     (     zero,     0.00175)
   2             4              0.00150     (     zero,     0.00354) **
   4          B-quintana        0.01248     (  0.00657,     0.01844) **
   4          B-arupensi        0.00076     (     zero,     0.00223) **
   2          B-berhoffi        0.00140     (     zero,     0.00340) **
   1             7              0.00094     (     zero,     0.00272) **
   7             6              0.00194     (     zero,     0.00438) **
   6          B-vinsonii        0.00292     (  0.00007,     0.00578) **
   6             3              0.00003     (     zero,     0.00190)
   3          B-birtlesi        0.00070     (     zero,     0.00210) **
   3            10              0.00006     (     zero,    infinity)
  10          B-grahamii        0.00003     (     zero,    infinity)
  10          B--doshiae        0.00003     (     zero,    infinity)
   7          B-henselae        0.00370     (  0.00041,     0.00690) **
   8          B-clarridg        0.01092     (  0.00539,     0.01652) **
  12             9              0.00553     (  0.00137,     0.00961) **
   9          B--weissii        0.00006     (     zero,     0.00213)
   9          B-spp-Deer        0.00216     (     zero,     0.00464) **
   5          A-tumefaci        0.05759     (  0.04458,     0.07101) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 59:


Empirical Base Frequencies:

   A       0.22504
   C       0.23068
   G       0.34143
  T(U)     0.20285

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.508925)


  +B-clarridg
  !  
  !     +B-birtlesi
  !     !  
  !     !     +B-vinsonii
  !  +--4  +--3  
  !  !  !  !  !  +B-henselae
  !  !  !  !  +-11  
  !  !  !  !     !  +B--weissii
  !  !  +--1     +--5  
  !  !     !        +B-spp-Deer
  !  !     !  
  !  !     !  +B--doshiae
  !  !     !  !  
--6--9     +--8  +B-arupensi
  !  !        !  !  
  !  !        +-10  +B-berhoffi
  !  !           !  !  
  !  !           +--7     +B-grahamii
  !  !              !  +-12  
  !  !              +--2  +B-elizabet
  !  !                 !  
  !  !                 +B-quintana
  !  !  
  !  +B-bacillif
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2972.33765

Examined  584 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   6          B-clarridg        0.01012     (  0.00457,     0.01566) **
   6             9              0.00290     (     zero,     0.00595) **
   9             4              0.00456     (  0.00082,     0.00831) **
   4          B-birtlesi        0.00290     (  0.00007,     0.00577) **
   4             1              0.00003     (     zero,     0.00240)
   1             3              0.00146     (     zero,     0.00349) **
   3          B-vinsonii        0.00006     (     zero,    infinity)
   3            11              0.00085     (     zero,     0.00250) *
  11          B-henselae        0.00505     (  0.00124,     0.00887) **
  11             5              0.00516     (  0.00135,     0.00900) **
   5          B--weissii        0.00310     (  0.00003,     0.00607) **
   5          B-spp-Deer        0.00211     (     zero,     0.00459) **
   1             8              0.00003     (     zero,    infinity)
   8          B--doshiae        0.00003     (     zero,    infinity)
   8            10              0.00074     (     zero,     0.00218) **
  10          B-arupensi        0.00226     (     zero,     0.00477) **
  10             7              0.00153     (     zero,     0.00358) **
   7          B-berhoffi        0.00151     (     zero,     0.00356) **
   7             2              0.00292     (  0.00003,     0.00581) **
   2            12              0.00221     (     zero,     0.00472) **
  12          B-grahamii        0.00368     (  0.00041,     0.00690) **
  12          B-elizabet        0.00298     (  0.00006,     0.00590) **
   2          B-quintana        0.00963     (  0.00441,     0.01488) **
   9          B-bacillif        0.00723     (  0.00258,     0.01189) **
   6          A-tumefaci        0.05488     (  0.04202,     0.06789) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 60:


Empirical Base Frequencies:

   A       0.23324
   C       0.22206
   G       0.30473
  T(U)     0.23996

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.506366)


                    +B--doshiae
                    !  
                 +--8     +B--weissii
                 !  !  +-12  
                 !  +--9  +B-spp-Deer
              +--1     !  
              !  !     +B-henselae
              !  !  
           +--2  +B-vinsonii
           !  !  
           !  !  +B-birtlesi
           !  +--5  
        +-11     !  +B-grahamii
        !  !     +--4  
        !  !        +B-elizabet
     +--3  !  
     !  !  +B-arupensi
     !  !  
  +--7  +B-berhoffi
  !  !  
  !  !  +B-quintana
  !  +-10  
  !     +B-bacillif
  !  
--6-B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2836.85539

Examined 1952 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   6             7              0.00639     (  0.00199,     0.01085) **
   7             3              0.00390     (  0.00047,     0.00734) **
   3            11              0.00003     (     zero,     0.00186)
  11             2              0.00214     (     zero,     0.00461) **
   2             1              0.00003     (     zero,    infinity)
   1             8              0.00140     (     zero,     0.00339) **
   8          B--doshiae        0.00003     (     zero,    infinity)
   8             9              0.00218     (     zero,     0.00465) **
   9            12              0.00733     (  0.00279,     0.01186) **
  12          B--weissii        0.00003     (     zero,    infinity)
  12          B-spp-Deer        0.00148     (     zero,     0.00351) **
   9          B-henselae        0.00003     (     zero,    infinity)
   1          B-vinsonii        0.00003     (     zero,    infinity)
   2             5              0.00003     (     zero,     0.00185)
   5          B-birtlesi        0.00218     (     zero,     0.00465) **
   5             4              0.00074     (     zero,     0.00218) **
   4          B-grahamii        0.00006     (     zero,    infinity)
   4          B-elizabet        0.00513     (  0.00132,     0.00892) **
  11          B-arupensi        0.00074     (     zero,     0.00219) **
   3          B-berhoffi        0.00070     (     zero,     0.00211) **
   7            10              0.00298     (  0.00003,     0.00594) **
  10          B-quintana        0.00613     (  0.00190,     0.01036) **
  10          B-bacillif        0.00708     (  0.00257,     0.01165) **
   6          B-clarridg        0.00657     (  0.00211,     0.01102) **
   6          A-tumefaci        0.05885     (  0.04584,     0.07251) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 61:


Empirical Base Frequencies:

   A       0.24040
   C       0.23249
   G       0.31976
  T(U)     0.20735

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.489628)


     +B--weissii
  +-12  
  !  +B-spp-Deer
  !  
  !     +B-bacillif
  !     !  
  !     !           +B-vinsonii
  !     !           !  
  !     !        +--2     +B-henselae
  !     !        !  !  +--6  
  !     !        !  !  !  +B--doshiae
  !  +--5        !  +--8  
  !  !  !        !     !  +B-birtlesi
  !  !  !     +--1     +--7  
  !  !  !     !  !        !  +B-grahamii
  !  !  !     !  !        +-10  
  !  !  !  +--3  !           +B-elizabet
--4--9  !  !  !  !  
  !  !  !  !  !  +B-arupensi
  !  !  +-11  !  
  !  !     !  +B-quintana
  !  !     !  
  !  !     +B-berhoffi
  !  !  
  !  +B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2888.63591

Examined  798 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   4            12              0.00402     (  0.00037,     0.00767) **
  12          B--weissii        0.00073     (     zero,     0.00216) **
  12          B-spp-Deer        0.00003     (     zero,     0.00160)
   4             9              0.00321     (     zero,     0.00650) **
   9             5              0.00287     (     zero,     0.00578) **
   5          B-bacillif        0.00861     (  0.00363,     0.01361) **
   5            11              0.00381     (  0.00043,     0.00719) **
  11             3              0.00146     (     zero,     0.00348) **
   3             1              0.00089     (     zero,     0.00260) **
   1             2              0.00334     (  0.00019,     0.00648) **
   2          B-vinsonii        0.00146     (     zero,     0.00348) **
   2             8              0.00166     (     zero,     0.00391) **
   8             6              0.00006     (     zero,    infinity)
   6          B-henselae        0.00435     (  0.00091,     0.00786) **
   6          B--doshiae        0.00003     (     zero,    infinity)
   8             7              0.00006     (     zero,     0.00202)
   7          B-birtlesi        0.00288     (  0.00007,     0.00573) **
   7            10              0.00145     (     zero,     0.00347) **
  10          B-grahamii        0.00006     (     zero,    infinity)
  10          B-elizabet        0.00657     (  0.00229,     0.01086) **
   1          B-arupensi        0.00146     (     zero,     0.00349) **
   3          B-quintana        0.00584     (  0.00172,     0.00987) **
  11          B-berhoffi        0.00154     (     zero,     0.00363) **
   9          B-clarridg        0.00537     (  0.00140,     0.00936) **
   4          A-tumefaci        0.06008     (  0.04692,     0.07384) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 62:


Empirical Base Frequencies:

   A       0.25077
   C       0.23007
   G       0.29018
  T(U)     0.22898

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.489072)


  +B-berhoffi
  !  
  !     +B-arupensi
  !  +--9  
  !  !  !  +B-vinsonii
  !  !  +-12  
  !  !     !  +B-clarridg
  !  !     +-10  
  !  !        +B-quintana
--4-11  
  !  !     +B-henselae
  !  !  +--5  
  !  !  !  !  +B-bacillif
  !  !  !  +--3  
  !  !  !     !  +B-spp-Deer
  !  +--6     +--2  
  !     !        +B--weissii
  !     !  
  !     !  +B--doshiae
  !     +--8  
  !        !  +B-birtlesi
  !        +--1  
  !           !  +B-elizabet
  !           +--7  
  !              +B-grahamii
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3052.93906

Examined  714 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   4          B-berhoffi        0.00006     (     zero,     0.00161)
   4            11              0.00220     (     zero,     0.00468) **
  11             9              0.00219     (     zero,     0.00467) **
   9          B-arupensi        0.00071     (     zero,     0.00213) **
   9            12              0.00366     (  0.00046,     0.00687) **
  12          B-vinsonii        0.00223     (     zero,     0.00473) **
  12            10              0.00436     (  0.00088,     0.00792) **
  10          B-clarridg        0.01109     (  0.00549,     0.01672) **
  10          B-quintana        0.00439     (  0.00086,     0.00793) **
  11             6              0.00097     (     zero,     0.00278) **
   6             5              0.00659     (  0.00229,     0.01089) **
   5          B-henselae        0.00003     (     zero,     0.00167)
   5             3              0.00918     (  0.00404,     0.01439) **
   3          B-bacillif        0.01005     (  0.00468,     0.01550) **
   3             2              0.00652     (  0.00215,     0.01087) **
   2          B-spp-Deer        0.00144     (     zero,     0.00347) **
   2          B--weissii        0.00003     (     zero,     0.00219)
   6             8              0.00189     (     zero,     0.00431) **
   8          B--doshiae        0.00003     (     zero,    infinity)
   8             1              0.00003     (     zero,     0.00181)
   1          B-birtlesi        0.00076     (     zero,     0.00222) **
   1             7              0.00150     (     zero,     0.00353) **
   7          B-elizabet        0.01027     (  0.00489,     0.01565) **
   7          B-grahamii        0.00006     (     zero,    infinity)
   4          A-tumefaci        0.06496     (  0.05118,     0.07920) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 63:


Empirical Base Frequencies:

   A       0.22850
   C       0.23243
   G       0.33105
  T(U)     0.20801

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.505987)


  +B-elizabet
  !  
  !  +B-berhoffi
  !  !  
  !  !     +B-arupensi
  !  !     !  
--7-12  +--3     +B-spp-Deer
  !  !  !  !  +-11  
  !  !  !  !  !  +B--weissii
  !  !  !  +-10  
  !  !  !     !  +B-clarridg
  !  +--1     +--2  
  !     !        +B-quintana
  !     !  
  !     !  +B-bacillif
  !     !  !  
  !     !  !        +B-birtlesi
  !     +--5     +--8  
  !        !     !  +B--doshiae
  !        !  +--6  
  !        !  !  !  +B-henselae
  !        +--9  +--4  
  !           !     +B-grahamii
  !           !  
  !           +B-vinsonii
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3097.94789

Examined 1140 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7          B-elizabet        0.00844     (  0.00336,     0.01353) **
   7            12              0.00238     (     zero,     0.00533) **
  12          B-berhoffi        0.00027     (     zero,     0.00174)
  12             1              0.00339     (  0.00024,     0.00655) **
   1             3              0.00003     (     zero,    infinity)
   3          B-arupensi        0.00442     (  0.00088,     0.00794) **
   3            10              0.00361     (  0.00019,     0.00704) **
  10            11              0.00740     (  0.00264,     0.01211) **
  11          B-spp-Deer        0.00072     (     zero,     0.00214) **
  11          B--weissii        0.00366     (  0.00046,     0.00687) **
  10             2              0.00213     (     zero,     0.00464) **
   2          B-clarridg        0.01048     (  0.00492,     0.01609) **
   2          B-quintana        0.00873     (  0.00360,     0.01385) **
   1             5              0.00219     (     zero,     0.00467) **
   5          B-bacillif        0.01025     (  0.00488,     0.01563) **
   5             9              0.00147     (     zero,     0.00352) **
   9             6              0.00003     (     zero,    infinity)
   6             8              0.00003     (     zero,    infinity)
   8          B-birtlesi        0.00006     (     zero,    infinity)
   8          B--doshiae        0.00149     (     zero,     0.00352) **
   6             4              0.00218     (     zero,     0.00464) **
   4          B-henselae        0.00731     (  0.00279,     0.01184) **
   4          B-grahamii        0.00003     (     zero,    infinity)
   9          B-vinsonii        0.00291     (  0.00007,     0.00576) **
   7          A-tumefaci        0.06706     (  0.05273,     0.08136) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 64:


Empirical Base Frequencies:

   A       0.22876
   C       0.25110
   G       0.29597
  T(U)     0.22418

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.514477)


  +B-clarridg
  !  
  !           +B-arupensi
  !        +--9  
  !     +--3  +B-quintana
  !     !  !  
  !     !  +B-berhoffi
  !     !  
  !     !           +B--doshiae
  !     !        +-10  
  !  +-12        !  !  +B-vinsonii
  !  !  !        !  +--6  
  !  !  !     +--5     !  +B-bacillif
  !  !  !     !  !     +-11  
  !  !  !     !  !        +B-birtlesi
  !  !  !  +--1  !  
--2--7  !  !  !  +B-grahamii
  !  !  +--8  !  
  !  !     !  +B-henselae
  !  !     !  
  !  !     +B-elizabet
  !  !  
  !  !  +B--weissii
  !  +--4  
  !     +B-spp-Deer
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3050.30177

Examined  700 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   2          B-clarridg        0.00631     (  0.00178,     0.01084) **
   2             7              0.00415     (  0.00041,     0.00789) **
   7            12              0.00281     (     zero,     0.00572) **
  12             3              0.00003     (     zero,    infinity)
   3             9              0.00219     (     zero,     0.00467) **
   9          B-arupensi        0.00146     (     zero,     0.00349) **
   9          B-quintana        0.01097     (  0.00545,     0.01656) **
   3          B-berhoffi        0.00140     (     zero,     0.00339) **
  12             8              0.00434     (  0.00086,     0.00784) **
   8             1              0.00003     (     zero,     0.00205)
   1             5              0.00291     (  0.00007,     0.00576) **
   5            10              0.00144     (     zero,     0.00345) **
  10          B--doshiae        0.00072     (     zero,     0.00213) **
  10             6              0.00003     (     zero,    infinity)
   6          B-vinsonii        0.00292     (  0.00006,     0.00577) **
   6            11              0.00070     (     zero,     0.00212) **
  11          B-bacillif        0.01246     (  0.00656,     0.01841) **
  11          B-birtlesi        0.00070     (     zero,     0.00212) **
   5          B-grahamii        0.00006     (     zero,     0.00216)
   1          B-henselae        0.00296     (  0.00004,     0.00583) **
   8          B-elizabet        0.01026     (  0.00489,     0.01564) **
   7             4              0.00595     (  0.00181,     0.01011) **
   4          B--weissii        0.00440     (  0.00086,     0.00790) **
   4          B-spp-Deer        0.00003     (     zero,    infinity)
   2          A-tumefaci        0.06258     (  0.04891,     0.07647) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 65:


Empirical Base Frequencies:

   A       0.24834
   C       0.22464
   G       0.31642
  T(U)     0.21060

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.475682)


     +B-spp-Deer
  +--7  
  !  +B--weissii
  !  
  !  +B-bacillif
  !  !  
  !  !           +B-grahamii
  !  !        +--8  
  !  !        !  +B-henselae
  !  !        !  
  !  !     +--5     +B-arupensi
--1--3     !  !  +--2  
  !  !     !  !  !  !  +B-quintana
  !  !     !  +-12  +-11  
  !  !  +-10     !     +B-clarridg
  !  !  !  !     !  
  !  !  !  !     +B-berhoffi
  !  !  !  !  
  !  !  !  !  +B--doshiae
  !  +--9  +--6  
  !     !     !  +B-vinsonii
  !     !     +--4  
  !     !        +B-birtlesi
  !     !  
  !     +B-elizabet
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2959.40209

Examined 1380 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   1             7              0.00719     (  0.00246,     0.01193) **
   7          B-spp-Deer        0.00003     (     zero,    infinity)
   7          B--weissii        0.00140     (     zero,     0.00339) **
   1             3              0.00499     (  0.00109,     0.00886) **
   3          B-bacillif        0.00738     (  0.00269,     0.01210) **
   3             9              0.00432     (  0.00059,     0.00800) **
   9            10              0.00436     (  0.00087,     0.00785) **
  10             5              0.00003     (     zero,    infinity)
   5             8              0.00144     (     zero,     0.00344) **
   8          B-grahamii        0.00003     (     zero,    infinity)
   8          B-henselae        0.00290     (  0.00007,     0.00574) **
   5            12              0.00220     (     zero,     0.00466) **
  12             2              0.00003     (     zero,     0.00177)
   2          B-arupensi        0.00435     (  0.00089,     0.00786) **
   2            11              0.00389     (  0.00050,     0.00729) **
  11          B-quintana        0.00780     (  0.00309,     0.01256) **
  11          B-clarridg        0.00801     (  0.00323,     0.01278) **
  12          B-berhoffi        0.00218     (     zero,     0.00464) **
  10             6              0.00074     (     zero,     0.00217) **
   6          B--doshiae        0.00006     (     zero,    infinity)
   6             4              0.00006     (     zero,    infinity)
   4          B-vinsonii        0.00222     (     zero,     0.00469) **
   4          B-birtlesi        0.00218     (     zero,     0.00464) **
   9          B-elizabet        0.00218     (     zero,     0.00465) **
   1          A-tumefaci        0.05740     (  0.04451,     0.07086) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 66:


Empirical Base Frequencies:

   A       0.25438
   C       0.24990
   G       0.31766
  T(U)     0.17805

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.485577)


  +B-clarridg
  !  
  !                 +B-vinsonii
  !              +--2  
  !              !  !  +B-arupensi
  !              !  +--1  
  !           +--5     +B-quintana
  !           !  !  
  !           !  !  +B-berhoffi
  !        +--3  +-11  
  !        !  !     +B-elizabet
  !        !  !  
  !        !  !  +B--doshiae
  !     +--8  +--4  
  !     !  !     !  +B-birtlesi
  !     !  !     +--6  
  !     !  !        +B-grahamii
  !  +--9  !  
  !  !  !  +B-henselae
  !  !  !  
-10--7  !  +B-spp-Deer
  !  !  +-12  
  !  !     +B--weissii
  !  !  
  !  +B-bacillif
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2790.33991

Examined 1170 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10          B-clarridg        0.00500     (  0.00091,     0.00910) **
  10             7              0.00406     (  0.00042,     0.00769) **
   7             9              0.00218     (     zero,     0.00480) **
   9             8              0.00362     (  0.00032,     0.00696) **
   8             3              0.00292     (  0.00006,     0.00580) **
   3             5              0.00003     (     zero,     0.00289)
   5             2              0.00147     (     zero,     0.00350) **
   2          B-vinsonii        0.00152     (     zero,     0.00358) **
   2             1              0.00073     (     zero,     0.00217) **
   1          B-arupensi        0.00149     (     zero,     0.00354) **
   1          B-quintana        0.01033     (  0.00493,     0.01575) **
   5            11              0.00074     (     zero,     0.00220) **
  11          B-berhoffi        0.00154     (     zero,     0.00361) **
  11          B-elizabet        0.00589     (  0.00182,     0.00997) **
   3             4              0.00358     (  0.00036,     0.00679) **
   4          B--doshiae        0.00003     (     zero,    infinity)
   4             6              0.00006     (     zero,     0.00283)
   6          B-birtlesi        0.00074     (     zero,     0.00217) **
   6          B-grahamii        0.00006     (     zero,    infinity)
   8          B-henselae        0.00003     (     zero,     0.00189)
   9            12              0.00248     (     zero,     0.00521) **
  12          B-spp-Deer        0.00164     (     zero,     0.00388) **
  12          B--weissii        0.00057     (     zero,     0.00203)
   7          B-bacillif        0.00450     (  0.00068,     0.00827) **
  10          A-tumefaci        0.05762     (  0.04466,     0.07108) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 67:


Empirical Base Frequencies:

   A       0.27182
   C       0.22475
   G       0.30716
  T(U)     0.19628

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.445591)


  +B-elizabet
  !  
  !  +B-berhoffi
  !  !  
  !  !     +B-quintana
-10--5  +--7  
  !  !  !  +B-clarridg
  !  !  !  
  !  !  !  +B-grahamii
  !  +--1  !  
  !     !  !        +B-arupensi
  !     !  !     +-11  
  !     !  !     !  +B-vinsonii
  !     +-12     !  
  !        !     !     +B-henselae
  !        !  +--2     !  
  !        !  !  !  +--3     +B--weissii
  !        !  !  !  !  !  +--8  
  !        !  !  !  !  +--4  +B-spp-Deer
  !        +--9  +--6     !  
  !           !     !     +B-bacillif
  !           !     !  
  !           !     +B--doshiae
  !           !  
  !           +B-birtlesi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2923.58614

Examined  598 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10          B-elizabet        0.00385     (  0.00041,     0.00734) **
  10             5              0.00199     (     zero,     0.00464) **
   5          B-berhoffi        0.00003     (     zero,    infinity)
   5             1              0.00070     (     zero,     0.00212) *
   1             7              0.00701     (  0.00248,     0.01154) **
   7          B-quintana        0.00706     (  0.00250,     0.01161) **
   7          B-clarridg        0.00879     (  0.00376,     0.01381) **
   1            12              0.00221     (     zero,     0.00472) **
  12          B-grahamii        0.00003     (     zero,    infinity)
  12             9              0.00072     (     zero,     0.00215) *
   9             2              0.00006     (     zero,     0.00177)
   2            11              0.00145     (     zero,     0.00347) **
  11          B-arupensi        0.00220     (     zero,     0.00469) **
  11          B-vinsonii        0.00074     (     zero,     0.00219) **
   2             6              0.00219     (     zero,     0.00467) **
   6             3              0.00214     (     zero,     0.00461) **
   3          B-henselae        0.00142     (     zero,     0.00343) **
   3             4              0.00366     (  0.00045,     0.00689) **
   4             8              0.00293     (  0.00005,     0.00582) **
   8          B--weissii        0.00003     (     zero,    infinity)
   8          B-spp-Deer        0.00366     (  0.00046,     0.00686) **
   4          B-bacillif        0.00960     (  0.00436,     0.01480) **
   6          B--doshiae        0.00003     (     zero,    infinity)
   9          B-birtlesi        0.00217     (     zero,     0.00465) **
  10          A-tumefaci        0.06352     (  0.04974,     0.07746) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 68:


Empirical Base Frequencies:

   A       0.24245
   C       0.23686
   G       0.31458
  T(U)     0.20611

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.490728)


     +B-spp-Deer
  +-11  
  !  +B--weissii
  !  
  !  +B-clarridg
  !  !  
  !  !        +B-berhoffi
  !  !     +--5  
  !  !     !  !  +B-quintana
  !  !     !  +-10  
  !  !     !     +B-arupensi
--6--9     !  
  !  !  +--1     +B-elizabet
  !  !  !  !     !  
  !  !  !  !  +-12     +B-birtlesi
  !  !  !  !  !  !  +--2  
  !  !  !  !  !  !  !  !  +B-grahamii
  !  !  !  !  !  +--4  +--8  
  !  +--3  +--7     !     +B-henselae
  !     !     !     !  
  !     !     !     +B-vinsonii
  !     !     !  
  !     !     +B--doshiae
  !     !  
  !     +B-bacillif
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2719.98999

Examined  558 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   6            11              0.00646     (  0.00195,     0.01098) **
  11          B-spp-Deer        0.00147     (     zero,     0.00349) **
  11          B--weissii        0.00076     (     zero,     0.00222) **
   6             9              0.00155     (     zero,     0.00404) *
   9          B-clarridg        0.00659     (  0.00215,     0.01103) **
   9             3              0.00223     (     zero,     0.00476) **
   3             1              0.00122     (     zero,     0.00343) **
   1             5              0.00006     (     zero,     0.00175)
   5          B-berhoffi        0.00003     (     zero,    infinity)
   5            10              0.00074     (     zero,     0.00218) **
  10          B-quintana        0.00438     (  0.00088,     0.00789) **
  10          B-arupensi        0.00367     (  0.00046,     0.00688) **
   1             7              0.00286     (  0.00005,     0.00571) **
   7            12              0.00003     (     zero,     0.00180)
  12          B-elizabet        0.00438     (  0.00088,     0.00788) **
  12             4              0.00003     (     zero,     0.00180)
   4             2              0.00003     (     zero,     0.00180)
   2          B-birtlesi        0.00219     (     zero,     0.00466) **
   2             8              0.00074     (     zero,     0.00218) **
   8          B-grahamii        0.00006     (     zero,    infinity)
   8          B-henselae        0.00364     (  0.00046,     0.00683) **
   4          B-vinsonii        0.00146     (     zero,     0.00347) **
   7          B--doshiae        0.00003     (     zero,    infinity)
   3          B-bacillif        0.00391     (  0.00043,     0.00739) **
   6          A-tumefaci        0.04802     (  0.03605,     0.06002) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 69:


Empirical Base Frequencies:

   A       0.25778
   C       0.23072
   G       0.30774
  T(U)     0.20376

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.469242)


  +B-bacillif
  !  
  !     +B-grahamii
  !  +-11  
  !  !  +B-elizabet
  !  !  
  !  !     +B-vinsonii
  !  !     !  
  !  !  +--3  +B--doshiae
-12--4  !  !  !  
  !  !  !  +--1  +B-henselae
  !  !  !     !  !  
  !  !  !     !  !     +B-arupensi
  !  !  !     +--5  +-10  
  !  !  !        !  !  +B-berhoffi
  !  !  !        !  !  
  !  +--2        +--6     +B--weissii
  !     !           !  +--8  
  !     !           !  !  +B-spp-Deer
  !     !           +--7  
  !     !              !  +B-quintana
  !     !              +--9  
  !     !                 +B-clarridg
  !     !  
  !     +B-birtlesi
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2936.14280

Examined  778 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  12          B-bacillif        0.00464     (  0.00065,     0.00859) **
  12             4              0.00559     (  0.00124,     0.00987) **
   4            11              0.00267     (     zero,     0.00550) **
  11          B-grahamii        0.00003     (     zero,     0.00185)
  11          B-elizabet        0.00808     (  0.00329,     0.01284) **
   4             2              0.00030     (     zero,     0.00174)
   2             3              0.00006     (     zero,     0.00180)
   3          B-vinsonii        0.00140     (     zero,     0.00340) **
   3             1              0.00146     (     zero,     0.00347) **
   1          B--doshiae        0.00006     (     zero,    infinity)
   1             5              0.00151     (     zero,     0.00359) **
   5          B-henselae        0.00287     (  0.00002,     0.00573) **
   5             6              0.00142     (     zero,     0.00343) **
   6            10              0.00144     (     zero,     0.00351) **
  10          B-arupensi        0.00151     (     zero,     0.00361) **
  10          B-berhoffi        0.00289     (     zero,     0.00575) **
   6             7              0.00339     (  0.00012,     0.00668) **
   7             8              0.00612     (  0.00181,     0.01041) **
   8          B--weissii        0.00220     (     zero,     0.00468) **
   8          B-spp-Deer        0.00069     (     zero,     0.00209) **
   7             9              0.00349     (  0.00028,     0.00672) **
   9          B-quintana        0.00697     (  0.00229,     0.01158) **
   9          B-clarridg        0.00944     (  0.00410,     0.01477) **
   2          B-birtlesi        0.00291     (  0.00004,     0.00577) **
  12          A-tumefaci        0.04841     (  0.03665,     0.06064) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 70:


Empirical Base Frequencies:

   A       0.26093
   C       0.23614
   G       0.31040
  T(U)     0.19253

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.466254)


        +B-arupensi
        !  
        !        +B--doshiae
        !        !  
        !        !        +B-bacillif
        !     +--7     +--1  
     +--2     !  !     !  !  +B--weissii
     !  !     !  !  +--6  +--8  
     !  !     !  !  !  !     +B-spp-Deer
     !  !  +--3  +-11  !  
     !  !  !  !     !  +B-henselae
     !  !  !  !     !  
     !  !  !  !     +B-vinsonii
  +--9  +-10  !  
  !  !     !  +B-grahamii
  !  !     !  
  !  !     !  +B-quintana
  !  !     +--5  
  !  !        +B-birtlesi
  !  !  
  !  !  +B-berhoffi
  !  +-12  
  !     +B-elizabet
  !  
--4-B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2958.98669

Examined 1006 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   4             9              0.00581     (  0.00156,     0.01009) **
   9             2              0.00070     (     zero,     0.00210) **
   2          B-arupensi        0.00445     (  0.00086,     0.00797) **
   2            10              0.00145     (     zero,     0.00347) **
  10             3              0.00003     (     zero,     0.00164)
   3             7              0.00073     (     zero,     0.00215) **
   7          B--doshiae        0.00003     (     zero,    infinity)
   7            11              0.00145     (     zero,     0.00347) **
  11             6              0.00293     (  0.00006,     0.00579) **
   6             1              0.00292     (  0.00003,     0.00581) **
   1          B-bacillif        0.01258     (  0.00660,     0.01858) **
   1             8              0.00441     (  0.00088,     0.00795) **
   8          B--weissii        0.00003     (     zero,    infinity)
   8          B-spp-Deer        0.00364     (  0.00048,     0.00684) **
   6          B-henselae        0.00220     (     zero,     0.00468) **
  11          B-vinsonii        0.00071     (     zero,     0.00212) **
   3          B-grahamii        0.00006     (     zero,    infinity)
  10             5              0.00585     (  0.00180,     0.00990) **
   5          B-quintana        0.00660     (  0.00229,     0.01091) **
   5          B-birtlesi        0.00072     (     zero,     0.00215) **
   9            12              0.00003     (     zero,     0.00188)
  12          B-berhoffi        0.00071     (     zero,     0.00211) **
  12          B-elizabet        0.00734     (  0.00279,     0.01188) **
   4          B-clarridg        0.00451     (  0.00067,     0.00831) **
   4          A-tumefaci        0.06118     (  0.04761,     0.07482) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 71:


Empirical Base Frequencies:

   A       0.23673
   C       0.23239
   G       0.31383
  T(U)     0.21704

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.497573)


  +B-clarridg
  !  
  !        +B--weissii
  !     +--6  
  !  +--4  +B-spp-Deer
  !  !  !  
  !  !  +B-bacillif
  !  !  
-10--8        +B-quintana
  !  !     +--5  
  !  !  +--9  +B-arupensi
  !  !  !  !  
  !  !  !  +B-berhoffi
  !  +--3  
  !     !  +B-elizabet
  !     !  !  
  !     +--2     +B-grahamii
  !        !  +-12  
  !        !  !  +B-henselae
  !        +--1  
  !           !  +B-birtlesi
  !           +-11  
  !              !  +B-vinsonii
  !              +--7  
  !                 +B--doshiae
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3067.31879

Examined  844 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10          B-clarridg        0.00215     (     zero,     0.00478) **
  10             8              0.00767     (  0.00275,     0.01252) **
   8             4              0.00327     (  0.00004,     0.00650) **
   4             6              0.00572     (  0.00152,     0.00995) **
   6          B--weissii        0.00356     (  0.00033,     0.00679) **
   6          B-spp-Deer        0.00086     (     zero,     0.00257) *
   4          B-bacillif        0.01167     (  0.00580,     0.01766) **
   8             3              0.00428     (  0.00058,     0.00798) **
   3             9              0.00003     (     zero,     0.00212)
   9             5              0.00220     (     zero,     0.00469) **
   5          B-quintana        0.01181     (  0.00601,     0.01759) **
   5          B-arupensi        0.00370     (  0.00045,     0.00693) **
   9          B-berhoffi        0.00147     (     zero,     0.00350) **
   3             2              0.00391     (  0.00046,     0.00740) **
   2          B-elizabet        0.01035     (  0.00489,     0.01575) **
   2             1              0.00195     (     zero,     0.00457) **
   1            12              0.00223     (     zero,     0.00471) **
  12          B-grahamii        0.00006     (     zero,     0.00201)
  12          B-henselae        0.00363     (  0.00043,     0.00684) **
   1            11              0.00072     (     zero,     0.00218) *
  11          B-birtlesi        0.00220     (     zero,     0.00467) **
  11             7              0.00003     (     zero,     0.00186)
   7          B-vinsonii        0.00290     (  0.00010,     0.00577) **
   7          B--doshiae        0.00003     (     zero,    infinity)
  10          A-tumefaci        0.05160     (  0.03943,     0.06426) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 72:


Empirical Base Frequencies:

   A       0.22994
   C       0.24568
   G       0.31307
  T(U)     0.21131

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.512756)


  +B-arupensi
  !  
  !     +B-berhoffi
  !     !  
  !     !     +B-clarridg
  !  +--1     !  
  !  !  !  +--6     +B--weissii
  !  !  !  !  !  +--5  
  !  !  !  !  +--4  +B-spp-Deer
  !  !  +--3     !  
  !  !     !     +B-bacillif
--2--7     !  
  !  !     +B-quintana
  !  !  
  !  !     +B-grahamii
  !  !  +-11  
  !  !  !  +B-elizabet
  !  +--8  
  !     !  +B-birtlesi
  !     +--9  
  !        !  +B-vinsonii
  !        +-10  
  !           !  +B-henselae
  !           +-12  
  !              +B--doshiae
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3135.64270

Examined  832 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   2          B-arupensi        0.00277     (     zero,     0.00566) **
   2             7              0.00317     (  0.00007,     0.00628) **
   7             1              0.00003     (     zero,     0.00226)
   1          B-berhoffi        0.00145     (     zero,     0.00347) **
   1             3              0.00274     (     zero,     0.00579) **
   3             6              0.00342     (  0.00014,     0.00675) **
   6          B-clarridg        0.01066     (  0.00496,     0.01632) **
   6             4              0.00529     (  0.00123,     0.00937) **
   4             5              0.00592     (  0.00169,     0.01022) **
   5          B--weissii        0.00072     (     zero,     0.00215) **
   5          B-spp-Deer        0.00146     (     zero,     0.00348) **
   4          B-bacillif        0.00922     (  0.00396,     0.01453) **
   3          B-quintana        0.00759     (  0.00284,     0.01235) **
   7             8              0.00438     (  0.00086,     0.00788) **
   8            11              0.00215     (     zero,     0.00462) **
  11          B-grahamii        0.00003     (     zero,     0.00187)
  11          B-elizabet        0.01173     (  0.00601,     0.01751) **
   8             9              0.00073     (     zero,     0.00218) *
   9          B-birtlesi        0.00218     (     zero,     0.00465) **
   9            10              0.00006     (     zero,     0.00179)
  10          B-vinsonii        0.00075     (     zero,     0.00220) **
  10            12              0.00076     (     zero,     0.00221) **
  12          B-henselae        0.00586     (  0.00180,     0.00991) **
  12          B--doshiae        0.00003     (     zero,    infinity)
   2          A-tumefaci        0.07272     (  0.05787,     0.08781) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 73:


Empirical Base Frequencies:

   A       0.27267
   C       0.23162
   G       0.29812
  T(U)     0.19759

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.457281)


                 +B-elizabet
              +-12  
              !  +B-grahamii
              !  
           +--7  +B-arupensi
           !  !  !  
           !  !  !        +B-vinsonii
           !  !  !     +-11  
           !  +--2     !  !  +B-henselae
           !     !     !  +--5  
           !     !  +--4     !  +B--weissii
        +--3     !  !  !     +--6  
        !  !     !  !  !        +B-spp-Deer
        !  !     +-10  !  
        !  !        !  +B-birtlesi
     +--9  !        !  
     !  !  !        +B--doshiae
     !  !  !  
  +--1  !  +B-berhoffi
  !  !  !  
  !  !  +B-quintana
  !  !  
  !  +B-bacillif
  !  
--8-B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3036.63968

Examined 1268 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   8             1              0.00320     (     zero,     0.00644) **
   1             9              0.00299     (  0.00003,     0.00595) **
   9             3              0.00310     (  0.00006,     0.00615) **
   3             7              0.00215     (     zero,     0.00462) **
   7            12              0.00290     (  0.00005,     0.00578) **
  12          B-elizabet        0.00662     (  0.00227,     0.01092) **
  12          B-grahamii        0.00006     (     zero,     0.00215)
   7             2              0.00217     (     zero,     0.00464) **
   2          B-arupensi        0.00289     (  0.00006,     0.00576) **
   2            10              0.00003     (     zero,     0.00221)
  10             4              0.00003     (     zero,    infinity)
   4            11              0.00142     (     zero,     0.00343) **
  11          B-vinsonii        0.00003     (     zero,     0.00184)
  11             5              0.00291     (  0.00004,     0.00579) **
   5          B-henselae        0.00510     (  0.00133,     0.00892) **
   5             6              0.00741     (  0.00280,     0.01199) **
   6          B--weissii        0.00145     (     zero,     0.00347) **
   6          B-spp-Deer        0.00072     (     zero,     0.00214) **
   4          B-birtlesi        0.00438     (  0.00088,     0.00788) **
  10          B--doshiae        0.00006     (     zero,    infinity)
   3          B-berhoffi        0.00006     (     zero,    infinity)
   9          B-quintana        0.01009     (  0.00474,     0.01550) **
   1          B-bacillif        0.00785     (  0.00310,     0.01266) **
   8          B-clarridg        0.00584     (  0.00168,     0.01004) **
   8          A-tumefaci        0.06780     (  0.05339,     0.08221) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 74:


Empirical Base Frequencies:

   A       0.26032
   C       0.21914
   G       0.30760
  T(U)     0.21293

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.462017)


     +B-elizabet
     !  
     !  +B-berhoffi
     !  !  
  +--7  !           +B-bacillif
  !  !  !        +--8  
  !  !  !        !  !  +B--weissii
  !  !  !        !  +-10  
  !  !  !     +--4     +B-spp-Deer
  !  +-12     !  !  
  !     !     !  !  +B--doshiae
  !     !     !  +--1  
  !     !     !     !  +B-vinsonii
  !     !  +--5     +-11  
  !     !  !  !        !  +B-birtlesi
  !     !  !  !        +--9  
  !     !  !  !           +B-grahamii
  !     +--2  !  
  !        !  !  +B-henselae
  !        !  +--6  
  !        !     +B-quintana
  !        !  
  !        +B-arupensi
  !  
--3-B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3327.28556

Examined 2462 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   3             7              0.00976     (  0.00420,     0.01535) **
   7          B-elizabet        0.01005     (  0.00458,     0.01551) **
   7            12              0.00237     (     zero,     0.00530) **
  12          B-berhoffi        0.00003     (     zero,    infinity)
  12             2              0.00217     (     zero,     0.00463) **
   2             5              0.00003     (     zero,     0.00173)
   5             4              0.00417     (  0.00066,     0.00764) **
   4             8              0.00730     (  0.00274,     0.01187) **
   8          B-bacillif        0.01031     (  0.00489,     0.01574) **
   8            10              0.00884     (  0.00382,     0.01386) **
  10          B--weissii        0.00003     (     zero,    infinity)
  10          B-spp-Deer        0.00505     (  0.00136,     0.00884) **
   4             1              0.00165     (     zero,     0.00392) **
   1          B--doshiae        0.00073     (     zero,     0.00216) **
   1            11              0.00003     (     zero,     0.00170)
  11          B-vinsonii        0.00290     (  0.00007,     0.00575) **
  11             9              0.00003     (     zero,     0.00206)
   9          B-birtlesi        0.00290     (  0.00006,     0.00575) **
   9          B-grahamii        0.00290     (  0.00007,     0.00575) **
   5             6              0.00218     (     zero,     0.00467) **
   6          B-henselae        0.00657     (  0.00232,     0.01091) **
   6          B-quintana        0.01255     (  0.00655,     0.01849) **
   2          B-arupensi        0.00365     (  0.00046,     0.00685) **
   3          B-clarridg        0.00943     (  0.00381,     0.01505) **
   3          A-tumefaci        0.07401     (  0.05934,     0.08965) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 75:


Empirical Base Frequencies:

   A       0.24267
   C       0.23238
   G       0.30340
  T(U)     0.22155

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.493052)


        +B-quintana
        !  
        !  +B-berhoffi
        !  !  
     +-11  !           +B--weissii
     !  !  !        +--6  
     !  !  !     +--5  +B-spp-Deer
     !  !  !     !  !  
     !  +--3     !  +B-henselae
     !     !     !  
     !     !     !           +B-elizabet
     !     !  +--1        +--4  
     !     !  !  !     +--9  +B-grahamii
  +--7     !  !  !     !  !  
  !  !     !  !  !  +--8  +B-birtlesi
  !  !     +--2  !  !  !  
  !  !        !  +-10  +B-vinsonii
  !  !        !     !  
  !  !        !     +B--doshiae
  !  !        !  
  !  !        +B-arupensi
  !  !  
  !  +B-clarridg
  !  
-12-B-bacillif
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3111.49689

Examined  684 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  12             7              0.00642     (  0.00178,     0.01112) **
   7            11              0.00677     (  0.00218,     0.01138) **
  11          B-quintana        0.00771     (  0.00294,     0.01250) **
  11             3              0.00180     (     zero,     0.00435) **
   3          B-berhoffi        0.00075     (     zero,     0.00220) **
   3             2              0.00303     (     zero,     0.00625) **
   2             1              0.00140     (     zero,     0.00415)
   1             5              0.00364     (  0.00043,     0.00687) **
   5             6              0.00985     (  0.00446,     0.01524) **
   6          B--weissii        0.00143     (     zero,     0.00345) **
   6          B-spp-Deer        0.00141     (     zero,     0.00344) **
   5          B-henselae        0.00272     (     zero,     0.00570) **
   1            10              0.00274     (     zero,     0.00607) **
  10             8              0.00003     (     zero,     0.00243)
   8             9              0.00049     (     zero,     0.00371)
   9             4              0.00283     (     zero,     0.00570) **
   4          B-elizabet        0.01033     (  0.00490,     0.01572) **
   4          B-grahamii        0.00006     (     zero,    infinity)
   9          B-birtlesi        0.00335     (  0.00023,     0.00655) **
   8          B-vinsonii        0.00074     (     zero,     0.00217) **
  10          B--doshiae        0.00073     (     zero,     0.00217) **
   2          B-arupensi        0.00151     (     zero,     0.00355) **
   7          B-clarridg        0.00985     (  0.00432,     0.01544) **
  12          B-bacillif        0.01015     (  0.00434,     0.01587) **
  12          A-tumefaci        0.05965     (  0.04635,     0.07347) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 76:


Empirical Base Frequencies:

   A       0.26665
   C       0.23786
   G       0.30688
  T(U)     0.18861

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.462425)


  +B-arupensi
  !  
  !        +B--doshiae
  !        !  
  !     +-12  +B-vinsonii
  !     !  !  !  
  !     !  +--4     +B-grahamii
  !     !     !  +--6  
  !     !     +--3  +B-elizabet
  !     !        !  
  !     !        +B-birtlesi
  !     !  
  !  +--2              +B-spp-Deer
  !  !  !           +-10  
  !  !  !        +--9  +B--weissii
  !  !  !        !  !  
  !  !  !     +--8  +B-bacillif
  !  !  !     !  !  
--5-11  !  +--7  +B-clarridg
  !  !  !  !  !  
  !  !  +--1  +B-quintana
  !  !     !  
  !  !     +B-henselae
  !  !  
  !  +B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2963.31846

Examined 1064 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   5          B-arupensi        0.00219     (     zero,     0.00472) **
   5            11              0.00383     (  0.00046,     0.00720) **
  11             2              0.00006     (     zero,     0.00216)
   2            12              0.00361     (  0.00043,     0.00682) **
  12          B--doshiae        0.00076     (     zero,     0.00222) **
  12             4              0.00003     (     zero,     0.00180)
   4          B-vinsonii        0.00074     (     zero,     0.00219) **
   4             3              0.00003     (     zero,     0.00177)
   3             6              0.00150     (     zero,     0.00354) **
   6          B-grahamii        0.00006     (     zero,    infinity)
   6          B-elizabet        0.01033     (  0.00491,     0.01573) **
   3          B-birtlesi        0.00003     (     zero,    infinity)
   2             1              0.00367     (  0.00046,     0.00689) **
   1             7              0.00071     (     zero,     0.00219)
   7             8              0.00404     (  0.00047,     0.00751) **
   8             9              0.00382     (  0.00025,     0.00740) **
   9            10              0.00461     (  0.00083,     0.00838) **
  10          B-spp-Deer        0.00136     (     zero,     0.00364) **
  10          B--weissii        0.00082     (     zero,     0.00283)
   9          B-bacillif        0.01003     (  0.00447,     0.01560) **
   8          B-clarridg        0.00635     (  0.00205,     0.01072) **
   7          B-quintana        0.00517     (  0.00135,     0.00900) **
   1          B-henselae        0.00291     (  0.00007,     0.00579) **
  11          B-berhoffi        0.00151     (     zero,     0.00355) **
   5          A-tumefaci        0.06518     (  0.05135,     0.07953) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 77:


Empirical Base Frequencies:

   A       0.23966
   C       0.23836
   G       0.32664
  T(U)     0.19534

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.491762)


  +B-clarridg
  !  
  !     +B--weissii
  !  +--9  
  !  !  +B-spp-Deer
  !  !  
  !  !                 +B-grahamii
  !  !              +-12  
  !  !              !  +B-henselae
  !  !           +--1  
  !  !           !  !     +B-birtlesi
  !  !           !  !  +--7  
--6--3        +--8  +--2  +B--doshiae
  !  !        !  !     !  
  !  !        !  !     +B-vinsonii
  !  !     +--4  !  
  !  !     !  !  +B-elizabet
  !  !     !  !  
  !  !  +-11  !  +B-quintana
  !  !  !  !  +--5  
  !  !  !  !     +B-bacillif
  !  +-10  !  
  !     !  +B-berhoffi
  !     !  
  !     +B-arupensi
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3006.03551

Examined  610 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   6          B-clarridg        0.00435     (  0.00055,     0.00809) **
   6             3              0.00524     (  0.00116,     0.00932) **
   3             9              0.00735     (  0.00280,     0.01191) **
   9          B--weissii        0.00367     (  0.00046,     0.00687) **
   9          B-spp-Deer        0.00006     (     zero,    infinity)
   3            10              0.00145     (     zero,     0.00349) **
  10            11              0.00069     (     zero,     0.00208) **
  11             4              0.00292     (  0.00003,     0.00581) **
   4             8              0.00273     (     zero,     0.00585) **
   8             1              0.00213     (     zero,     0.00515) **
   1            12              0.00294     (  0.00005,     0.00580) **
  12          B-grahamii        0.00123     (     zero,     0.00325) **
  12          B-henselae        0.00388     (  0.00050,     0.00726) **
   1             2              0.00026     (     zero,     0.00183)
   2             7              0.00003     (     zero,    infinity)
   7          B-birtlesi        0.00292     (  0.00007,     0.00578) **
   7          B--doshiae        0.00003     (     zero,    infinity)
   2          B-vinsonii        0.00003     (     zero,    infinity)
   8          B-elizabet        0.00884     (  0.00385,     0.01385) **
   4             5              0.00361     (  0.00034,     0.00685) **
   5          B-quintana        0.01045     (  0.00495,     0.01592) **
   5          B-bacillif        0.01414     (  0.00776,     0.02052) **
  11          B-berhoffi        0.00003     (     zero,    infinity)
  10          B-arupensi        0.00071     (     zero,     0.00212) **
   6          A-tumefaci        0.05576     (  0.04290,     0.06881) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 78:


Empirical Base Frequencies:

   A       0.24093
   C       0.23728
   G       0.30489
  T(U)     0.21690

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.496086)


  +B-elizabet
  !  
  !  +B-grahamii
  !  !  
--7--2  +B-birtlesi
  !  !  !  
  !  !  !  +B--doshiae
  !  +--5  !  
  !     !  !     +B-vinsonii
  !     !  !     !  
  !     +-10  +--1  +B-henselae
  !        !  !  !  !  
  !        !  !  +-11     +B-spp-Deer
  !        !  !     !  +-12  
  !        !  !     +--6  +B--weissii
  !        +--3        !  
  !           !        +B-bacillif
  !           !  
  !           !  +B-arupensi
  !           !  !  
  !           +--9     +B-quintana
  !              !  +--8  
  !              +--4  +B-clarridg
  !                 !  
  !                 +B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2982.08746

Examined 1604 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7          B-elizabet        0.00067     (     zero,     0.00250)
   7             2              0.00663     (  0.00227,     0.01108) **
   2          B-grahamii        0.00003     (     zero,    infinity)
   2             5              0.00075     (     zero,     0.00220) **
   5          B-birtlesi        0.00149     (     zero,     0.00352) **
   5            10              0.00006     (     zero,     0.00291)
  10          B--doshiae        0.00006     (     zero,    infinity)
  10             3              0.00006     (     zero,     0.00292)
   3             1              0.00073     (     zero,     0.00217) **
   1          B-vinsonii        0.00216     (     zero,     0.00464) **
   1            11              0.00366     (  0.00046,     0.00687) **
  11          B-henselae        0.00003     (     zero,    infinity)
  11             6              0.00289     (     zero,     0.00609) **
   6            12              0.01101     (  0.00535,     0.01665) **
  12          B-spp-Deer        0.00221     (     zero,     0.00469) **
  12          B--weissii        0.00006     (     zero,    infinity)
   6          B-bacillif        0.01127     (  0.00551,     0.01710) **
   3             9              0.00499     (  0.00129,     0.00878) **
   9          B-arupensi        0.00220     (     zero,     0.00468) **
   9             4              0.00003     (     zero,     0.00298)
   4             8              0.00465     (  0.00094,     0.00837) **
   8          B-quintana        0.00859     (  0.00361,     0.01358) **
   8          B-clarridg        0.00955     (  0.00433,     0.01479) **
   4          B-berhoffi        0.00076     (     zero,     0.00222) **
   7          A-tumefaci        0.06222     (  0.04880,     0.07627) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 79:


Empirical Base Frequencies:

   A       0.25354
   C       0.22037
   G       0.31998
  T(U)     0.20612

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.462526)


  +B-clarridg
  !  
  !           +B-arupensi
  !           !  
  !           !        +B-birtlesi
  !           !     +--6  
  !        +--1     !  +B--doshiae
  !        !  !  +--5  
  !        !  !  !  !  +B-henselae
  !        !  !  !  +--4  
  !        !  +--7     +B-vinsonii
  !     +-10     !  
  !     !  !     !  +B-elizabet
  !     !  !     +-11  
  !  +--2  !        +B-grahamii
  !  !  !  !  
  !  !  !  +B-berhoffi
  !  !  !  
-12--3  +B-quintana
  !  !  
  !  !     +B-spp-Deer
  !  !  +--9  
  !  +--8  +B--weissii
  !     !  
  !     +B-bacillif
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3252.58423

Examined 1012 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  12          B-clarridg        0.00451     (  0.00072,     0.00829) **
  12             3              0.00690     (  0.00224,     0.01156) **
   3             2              0.00454     (  0.00081,     0.00822) **
   2            10              0.00379     (  0.00039,     0.00722) **
  10             1              0.00003     (     zero,     0.00192)
   1          B-arupensi        0.00588     (  0.00181,     0.00996) **
   1             7              0.00433     (  0.00091,     0.00785) **
   7             5              0.00217     (     zero,     0.00464) **
   5             6              0.00006     (     zero,    infinity)
   6          B-birtlesi        0.00213     (     zero,     0.00459) **
   6          B--doshiae        0.00006     (     zero,    infinity)
   5             4              0.00151     (     zero,     0.00355) **
   4          B-henselae        0.00370     (  0.00042,     0.00689) **
   4          B-vinsonii        0.00296     (  0.00002,     0.00583) **
   7            11              0.00071     (     zero,     0.00212) **
  11          B-elizabet        0.01471     (  0.00826,     0.02117) **
  11          B-grahamii        0.00003     (     zero,    infinity)
  10          B-berhoffi        0.00147     (     zero,     0.00349) **
   2          B-quintana        0.00643     (  0.00207,     0.01080) **
   3             8              0.00469     (  0.00070,     0.00868) **
   8             9              0.00974     (  0.00430,     0.01512) **
   9          B-spp-Deer        0.00144     (     zero,     0.00345) **
   9          B--weissii        0.00006     (     zero,    infinity)
   8          B-bacillif        0.01632     (  0.00936,     0.02333) **
  12          A-tumefaci        0.07425     (  0.05912,     0.08942) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 80:


Empirical Base Frequencies:

   A       0.23564
   C       0.22152
   G       0.33509
  T(U)     0.20775

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.486468)


                 +B-elizabet
              +-11  
              !  +B-grahamii
              !  
           +--4     +B-birtlesi
           !  !  +--5  
           !  !  !  !  +B-henselae
           !  +--7  +-10  
        +--1     !     +B--doshiae
        !  !     !  
        !  !     +B-vinsonii
     +--6  !  
     !  !  +B-berhoffi
     !  !  
     !  !  +B-arupensi
  +--8  +--2  
  !  !     +B-quintana
  !  !  
  !  !  +B-clarridg
  !  +--9  
  !     !  +B--weissii
  !     +-12  
  !        +B-spp-Deer
  !  
--3-B-bacillif
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3115.91583

Examined  646 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   3             8              0.00448     (  0.00073,     0.00829) **
   8             6              0.00399     (  0.00045,     0.00755) **
   6             1              0.00003     (     zero,     0.00167)
   1             4              0.00292     (  0.00007,     0.00579) **
   4            11              0.00215     (     zero,     0.00462) **
  11          B-elizabet        0.00807     (  0.00331,     0.01284) **
  11          B-grahamii        0.00006     (     zero,     0.00219)
   4             7              0.00147     (     zero,     0.00349) **
   7             5              0.00006     (     zero,    infinity)
   5          B-birtlesi        0.00364     (  0.00048,     0.00684) **
   5            10              0.00074     (     zero,     0.00218) **
  10          B-henselae        0.00508     (  0.00136,     0.00888) **
  10          B--doshiae        0.00006     (     zero,    infinity)
   7          B-vinsonii        0.00217     (     zero,     0.00464) **
   1          B-berhoffi        0.00006     (     zero,    infinity)
   6             2              0.00143     (     zero,     0.00345) **
   2          B-arupensi        0.00443     (  0.00089,     0.00797) **
   2          B-quintana        0.01697     (  0.01004,     0.02395) **
   8             9              0.00229     (     zero,     0.00504) **
   9          B-clarridg        0.01272     (  0.00660,     0.01881) **
   9            12              0.00558     (  0.00153,     0.00965) **
  12          B--weissii        0.00160     (     zero,     0.00382) **
  12          B-spp-Deer        0.00129     (     zero,     0.00329) **
   3          B-bacillif        0.00721     (  0.00242,     0.01201) **
   3          A-tumefaci        0.06145     (  0.04799,     0.07541) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 81:


Empirical Base Frequencies:

   A       0.25544
   C       0.23462
   G       0.29851
  T(U)     0.21143

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.480026)


  +B-bacillif
  !  
  !        +B-arupensi
  !        !  
  !     +--5  +B-vinsonii
  !     !  !  !  
  !     !  +--6     +B-henselae
  !     !     !  +--4  
  !     !     !  !  +B--doshiae
  !     !     +-11  
  !  +--2        !     +B-elizabet
  !  !  !        !  +-12  
  !  !  !        +--3  +B-grahamii
  !  !  !           !  
  !  !  !           +B-birtlesi
-10--1  !  
  !  !  +B-berhoffi
  !  !  
  !  !     +B-clarridg
  !  !  +--9  
  !  !  !  +B-quintana
  !  +--8  
  !     !  +B-spp-Deer
  !     +--7  
  !        +B--weissii
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3115.32237

Examined 1778 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10          B-bacillif        0.00501     (  0.00055,     0.00940) **
  10             1              0.00786     (  0.00273,     0.01301) **
   1             2              0.00406     (  0.00033,     0.00788) **
   2             5              0.00073     (     zero,     0.00253)
   5          B-arupensi        0.00293     (  0.00006,     0.00580) **
   5             6              0.00195     (     zero,     0.00438) **
   6          B-vinsonii        0.00217     (     zero,     0.00463) **
   6            11              0.00003     (     zero,     0.00200)
  11             4              0.00145     (     zero,     0.00347) **
   4          B-henselae        0.00215     (     zero,     0.00462) **
   4          B--doshiae        0.00006     (     zero,    infinity)
  11             3              0.00003     (     zero,     0.00215)
   3            12              0.00364     (  0.00047,     0.00684) **
  12          B-elizabet        0.01025     (  0.00490,     0.01563) **
  12          B-grahamii        0.00003     (     zero,    infinity)
   3          B-birtlesi        0.00147     (     zero,     0.00349) **
   2          B-berhoffi        0.00169     (     zero,     0.00399) **
   1             8              0.00377     (  0.00040,     0.00715) **
   8             9              0.00180     (     zero,     0.00436) **
   9          B-clarridg        0.01224     (  0.00625,     0.01827) **
   9          B-quintana        0.01151     (  0.00567,     0.01733) **
   8             7              0.01011     (  0.00460,     0.01562) **
   7          B-spp-Deer        0.00150     (     zero,     0.00354) **
   7          B--weissii        0.00003     (     zero,    infinity)
  10          A-tumefaci        0.06403     (  0.05036,     0.07835) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 82:


Empirical Base Frequencies:

   A       0.25767
   C       0.21850
   G       0.30886
  T(U)     0.21497

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.465186)


  +B-berhoffi
  !  
  !     +B-arupensi
  !     !  
  !     !        +B-birtlesi
  !     !        !  
  !     !     +--9     +B-elizabet
  !     !     !  !  +--7  
  !  +-10     !  !  !  +B-grahamii
  !  !  !     !  +--6  
  !  !  !  +--4     !  +B-henselae
  !  !  !  !  !     +--8  
  !  !  !  !  !        +B--doshiae
  !  !  !  !  !  
  !  !  +--5  +B-vinsonii
--3-11     !  
  !  !     !     +B--weissii
  !  !     !  +--1  
  !  !     +--2  +B-spp-Deer
  !  !        !  
  !  !        +B-bacillif
  !  !  
  !  !  +B-clarridg
  !  +-12  
  !     +B-quintana
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3036.69808

Examined  638 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   3          B-berhoffi        0.00006     (     zero,     0.00174)
   3            11              0.00295     (  0.00006,     0.00586) **
  11            10              0.00082     (     zero,     0.00245) **
  10          B-arupensi        0.00368     (  0.00046,     0.00690) **
  10             5              0.00083     (     zero,     0.00247) **
   5             4              0.00345     (  0.00022,     0.00663) **
   4             9              0.00003     (     zero,     0.00171)
   9          B-birtlesi        0.00291     (  0.00007,     0.00577) **
   9             6              0.00003     (     zero,    infinity)
   6             7              0.00144     (     zero,     0.00347) **
   7          B-elizabet        0.01109     (  0.00544,     0.01667) **
   7          B-grahamii        0.00006     (     zero,     0.00181)
   6             8              0.00152     (     zero,     0.00356) **
   8          B-henselae        0.00591     (  0.00177,     0.00995) **
   8          B--doshiae        0.00003     (     zero,    infinity)
   4          B-vinsonii        0.00146     (     zero,     0.00348) **
   5             2              0.00403     (  0.00057,     0.00749) **
   2             1              0.00509     (  0.00127,     0.00890) **
   1          B--weissii        0.00070     (     zero,     0.00211) **
   1          B-spp-Deer        0.00439     (  0.00089,     0.00791) **
   2          B-bacillif        0.00485     (  0.00108,     0.00863) **
  11            12              0.00501     (  0.00109,     0.00894) **
  12          B-clarridg        0.01024     (  0.00482,     0.01567) **
  12          B-quintana        0.00764     (  0.00279,     0.01238) **
   3          A-tumefaci        0.05869     (  0.04564,     0.07221) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 83:


Empirical Base Frequencies:

   A       0.25616
   C       0.22405
   G       0.30967
  T(U)     0.21012

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.467810)


  +B-bacillif
  !  
  !        +B-vinsonii
  !     +-10  
  !     !  +B-birtlesi
  !  +-12  
  !  !  !  +B-grahamii
  !  !  +-11  
  !  !     +B-elizabet
  !  !  
  !  !              +B-clarridg
  !  !           +--9  
  !  !           !  !  +B--weissii
--7--6        +--1  +--2  
  !  !        !  !     +B-spp-Deer
  !  !        !  !  
  !  !     +--3  +B-quintana
  !  !     !  !  
  !  !     !  !  +B--doshiae
  !  !  +--5  +--4  
  !  !  !  !     +B-henselae
  !  +--8  !  
  !     !  +B-arupensi
  !     !  
  !     +B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2909.13915

Examined  870 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7          B-bacillif        0.00686     (  0.00221,     0.01150) **
   7             6              0.00272     (     zero,     0.00593) **
   6            12              0.00217     (     zero,     0.00519) **
  12            10              0.00051     (     zero,     0.00194)
  10          B-vinsonii        0.00354     (  0.00035,     0.00674) **
  10          B-birtlesi        0.00102     (     zero,     0.00289) **
  12            11              0.00141     (     zero,     0.00342) **
  11          B-grahamii        0.00003     (     zero,     0.00187)
  11          B-elizabet        0.00586     (  0.00181,     0.00993) **
   6             8              0.00223     (     zero,     0.00527) **
   8             5              0.00075     (     zero,     0.00220) **
   5             3              0.00235     (     zero,     0.00494) **
   3             1              0.00211     (     zero,     0.00459) **
   1             9              0.00072     (     zero,     0.00217) *
   9          B-clarridg        0.00589     (  0.00182,     0.00998) **
   9             2              0.00664     (  0.00230,     0.01098) **
   2          B--weissii        0.00140     (     zero,     0.00341) **
   2          B-spp-Deer        0.00151     (     zero,     0.00356) **
   1          B-quintana        0.00661     (  0.00228,     0.01092) **
   3             4              0.00076     (     zero,     0.00222) **
   4          B--doshiae        0.00086     (     zero,     0.00251) **
   4          B-henselae        0.00581     (  0.00167,     0.00985) **
   5          B-arupensi        0.00146     (     zero,     0.00349) **
   8          B-berhoffi        0.00006     (     zero,     0.00157)
   7          A-tumefaci        0.05850     (  0.04531,     0.07197) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 84:


Empirical Base Frequencies:

   A       0.24964
   C       0.24407
   G       0.31091
  T(U)     0.19538

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.487455)


  +B-clarridg
  !  
  !     +B-berhoffi
  !     !  
  !  +-10  +B-arupensi
  !  !  !  !  
  !  !  +--7  +B-henselae
  !  !     !  !  
  !  !     !  !     +B-vinsonii
  !  !     +--9  +-12  
  !  !        !  !  !  +B-birtlesi
  !  !        !  !  +--2  
  !  !        +--5     !  +B-elizabet
--8--3           !     +--4  
  !  !           !        +B-grahamii
  !  !           !  
  !  !           +B--doshiae
  !  !  
  !  !        +B-spp-Deer
  !  !     +-11  
  !  !  +--6  +B--weissii
  !  !  !  !  
  !  +--1  +B-bacillif
  !     !  
  !     +B-quintana
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3277.23503

Examined  472 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   8          B-clarridg        0.00918     (  0.00374,     0.01458) **
   8             3              0.00856     (  0.00325,     0.01381) **
   3            10              0.00377     (  0.00014,     0.00743) **
  10          B-berhoffi        0.00087     (     zero,     0.00256) **
  10             7              0.00153     (     zero,     0.00373) **
   7          B-arupensi        0.00293     (  0.00008,     0.00581) **
   7             9              0.00487     (  0.00104,     0.00865) **
   9          B-henselae        0.00665     (  0.00230,     0.01099) **
   9             5              0.00238     (     zero,     0.00506) **
   5            12              0.00003     (     zero,     0.00163)
  12          B-vinsonii        0.00217     (     zero,     0.00466) **
  12             2              0.00003     (     zero,     0.00240)
   2          B-birtlesi        0.00214     (     zero,     0.00462) **
   2             4              0.00508     (  0.00136,     0.00890) **
   4          B-elizabet        0.00957     (  0.00437,     0.01478) **
   4          B-grahamii        0.00003     (     zero,     0.00200)
   5          B--doshiae        0.00003     (     zero,    infinity)
   3             1              0.00309     (  0.00005,     0.00621) **
   1             6              0.00397     (     zero,     0.00790) **
   6            11              0.00862     (  0.00349,     0.01374) **
  11          B-spp-Deer        0.00096     (     zero,     0.00280) **
  11          B--weissii        0.00349     (  0.00024,     0.00670) **
   6          B-bacillif        0.01365     (  0.00707,     0.02019) **
   1          B-quintana        0.01404     (  0.00763,     0.02056) **
   8          A-tumefaci        0.06099     (  0.04736,     0.07480) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 85:


Empirical Base Frequencies:

   A       0.23490
   C       0.24631
   G       0.30122
  T(U)     0.21757

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.507224)


  +B-bacillif
  !  
  !        +B-spp-Deer
  !     +-11  
  !     !  +B--weissii
  !  +-10  
  !  !  !  +B-henselae
  !  !  !  !  
  !  !  +--1  +B--doshiae
  !  !     !  !  
  !  !     !  !     +B-arupensi
  !  !     +--2  +-12  
  !  !        !  !  +B-vinsonii
  !  !        !  !  
--8--4        +--3     +B-grahamii
  !  !           !  +--7  
  !  !           !  !  !  +B-elizabet
  !  !           +--5  +--6  
  !  !              !     +B-berhoffi
  !  !              !  
  !  !              +B-birtlesi
  !  !  
  !  !  +B-clarridg
  !  +--9  
  !     +B-quintana
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3075.03005

Examined  530 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   8          B-bacillif        0.00763     (  0.00258,     0.01270) **
   8             4              0.00858     (  0.00329,     0.01387) **
   4            10              0.00260     (     zero,     0.00546) **
  10            11              0.00309     (     zero,     0.00624) **
  11          B-spp-Deer        0.00301     (  0.00008,     0.00597) **
  11          B--weissii        0.00134     (     zero,     0.00336) **
  10             1              0.00374     (  0.00027,     0.00717) **
   1          B-henselae        0.00086     (     zero,     0.00257) **
   1             2              0.00441     (  0.00077,     0.00804) **
   2          B--doshiae        0.00003     (     zero,    infinity)
   2             3              0.00077     (     zero,     0.00227) **
   3            12              0.00070     (     zero,     0.00210) **
  12          B-arupensi        0.00374     (  0.00042,     0.00697) **
  12          B-vinsonii        0.00142     (     zero,     0.00343) **
   3             5              0.00003     (     zero,     0.00232)
   5             7              0.00145     (     zero,     0.00348) **
   7          B-grahamii        0.00075     (     zero,     0.00222) **
   7             6              0.00175     (     zero,     0.00410) **
   6          B-elizabet        0.00959     (  0.00438,     0.01481) **
   6          B-berhoffi        0.00266     (     zero,     0.00550) **
   5          B-birtlesi        0.00292     (  0.00006,     0.00581) **
   4             9              0.00151     (     zero,     0.00427)
   9          B-clarridg        0.00746     (  0.00283,     0.01208) **
   9          B-quintana        0.00842     (  0.00343,     0.01336) **
   8          A-tumefaci        0.06607     (  0.05174,     0.08041) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 86:


Empirical Base Frequencies:

   A       0.23351
   C       0.23837
   G       0.31494
  T(U)     0.21318

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.504097)


  +B-bacillif
  !  
  !     +B--weissii
  !  +--8  
  !  !  +B-spp-Deer
  !  !  
  !  !        +B-grahamii
  !  !     +--6  
  !  !     !  +B-elizabet
-10--7     !  
  !  !  +--3        +B-henselae
  !  !  !  !     +-11  
  !  !  !  !  +--1  +B--doshiae
  !  !  !  !  !  !  
  !  !  !  +--2  +B-birtlesi
  !  +--5     !  
  !     !     +B-vinsonii
  !     !  
  !     !  +B-arupensi
  !     !  !  
  !     +--9     +B-quintana
  !        !  +-12  
  !        +--4  +B-clarridg
  !           !  
  !           +B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3137.91770

Examined  730 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10          B-bacillif        0.00859     (  0.00322,     0.01399) **
  10             7              0.00616     (  0.00143,     0.01084) **
   7             8              0.00754     (  0.00273,     0.01235) **
   8          B--weissii        0.00076     (     zero,     0.00223) **
   8          B-spp-Deer        0.00289     (  0.00009,     0.00576) **
   7             5              0.00478     (  0.00076,     0.00885) **
   5             3              0.00365     (  0.00048,     0.00687) **
   3             6              0.00218     (     zero,     0.00465) **
   6          B-grahamii        0.00006     (     zero,     0.00181)
   6          B-elizabet        0.00729     (  0.00281,     0.01184) **
   3             2              0.00003     (     zero,    infinity)
   2             1              0.00003     (     zero,    infinity)
   1            11              0.00146     (     zero,     0.00347) **
  11          B-henselae        0.00439     (  0.00089,     0.00789) **
  11          B--doshiae        0.00003     (     zero,    infinity)
   1          B-birtlesi        0.00292     (  0.00007,     0.00578) **
   2          B-vinsonii        0.00219     (     zero,     0.00467) **
   5             9              0.00069     (     zero,     0.00210) *
   9          B-arupensi        0.00368     (  0.00046,     0.00690) **
   9             4              0.00075     (     zero,     0.00221) **
   4            12              0.00435     (  0.00082,     0.00789) **
  12          B-quintana        0.00888     (  0.00385,     0.01391) **
  12          B-clarridg        0.01112     (  0.00548,     0.01676) **
   4          B-berhoffi        0.00069     (     zero,     0.00210) **
  10          A-tumefaci        0.06811     (  0.05389,     0.08286) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 87:


Empirical Base Frequencies:

   A       0.26101
   C       0.23549
   G       0.29644
  T(U)     0.20706

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.475070)


     +B-clarridg
     !  
     !           +B-elizabet
     !           !  
     !        +-11  +B-grahamii
     !        !  !  !  
     !        !  !  !        +B-arupensi
     !        !  +--6     +--4  
  +--9        !     !     !  +B-vinsonii
  !  !        !     !  +-12  
  !  !     +--2     !  !  !  +B-henselae
  !  !     !  !     +--8  +-10  
  !  !     !  !        !     +B--doshiae
  !  !     !  !        !  
  !  !  +--3  !        +B-birtlesi
  !  !  !  !  !  
  !  !  !  !  +B-berhoffi
  !  +--5  !  
  !     !  +B-quintana
  !     !  
  !     +B-bacillif
  !  
  !  +B-spp-Deer
--1--7  
  !  +B--weissii
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3044.04792

Examined 1050 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   1             9              0.00261     (     zero,     0.00557) **
   9          B-clarridg        0.00520     (  0.00124,     0.00917) **
   9             5              0.00367     (  0.00032,     0.00705) **
   5             3              0.00508     (  0.00127,     0.00890) **
   3             2              0.00006     (     zero,     0.00201)
   2            11              0.00220     (     zero,     0.00469) **
  11          B-elizabet        0.00657     (  0.00231,     0.01089) **
  11             6              0.00073     (     zero,     0.00216) **
   6          B-grahamii        0.00073     (     zero,     0.00217) **
   6             8              0.00223     (     zero,     0.00471) **
   8            12              0.00006     (     zero,     0.00245)
  12             4              0.00222     (     zero,     0.00471) **
   4          B-arupensi        0.00366     (  0.00046,     0.00687) **
   4          B-vinsonii        0.00071     (     zero,     0.00212) **
  12            10              0.00075     (     zero,     0.00219) **
  10          B-henselae        0.00437     (  0.00089,     0.00787) **
  10          B--doshiae        0.00006     (     zero,    infinity)
   8          B-birtlesi        0.00586     (  0.00177,     0.00991) **
   2          B-berhoffi        0.00076     (     zero,     0.00222) **
   3          B-quintana        0.01322     (  0.00711,     0.01935) **
   5          B-bacillif        0.00888     (  0.00385,     0.01394) **
   1             7              0.01090     (  0.00515,     0.01668) **
   7          B-spp-Deer        0.00006     (     zero,     0.00154)
   7          B--weissii        0.00291     (  0.00006,     0.00577) **
   1          A-tumefaci        0.05634     (  0.04326,     0.06940) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 88:


Empirical Base Frequencies:

   A       0.25709
   C       0.22081
   G       0.31849
  T(U)     0.20361

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.457499)


                 +B-vinsonii
                 !  
              +--8     +B-henselae
              !  !  +-10  
              !  !  !  !  +B-grahamii
              !  +--2  +--9  
           +--4     !     +B-elizabet
           !  !     !  
           !  !     +B--doshiae
        +--1  !  
        !  !  +B-birtlesi
        !  !  
        !  !  +B-bacillif
     +--5  +-12  
     !  !     !  +B-spp-Deer
     !  !     +--3  
     !  !        +B--weissii
  +--7  !  
  !  !  +B-arupensi
  !  !  
  !  !  +B-clarridg
  !  +-11  
  !     +B-quintana
  !  
--6-B-berhoffi
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3035.37169

Examined  984 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   6             7              0.00074     (     zero,     0.00221) **
   7             5              0.00220     (     zero,     0.00468) **
   5             1              0.00006     (     zero,    infinity)
   1             4              0.00292     (  0.00007,     0.00578) **
   4             8              0.00003     (     zero,    infinity)
   8          B-vinsonii        0.00150     (     zero,     0.00353) **
   8             2              0.00003     (     zero,     0.00187)
   2            10              0.00145     (     zero,     0.00347) **
  10          B-henselae        0.00438     (  0.00090,     0.00789) **
  10             9              0.00295     (  0.00005,     0.00583) **
   9          B-grahamii        0.00006     (     zero,    infinity)
   9          B-elizabet        0.00438     (  0.00089,     0.00789) **
   2          B--doshiae        0.00073     (     zero,     0.00219) *
   4          B-birtlesi        0.00362     (  0.00049,     0.00683) **
   1            12              0.00726     (  0.00259,     0.01193) **
  12          B-bacillif        0.01211     (  0.00615,     0.01808) **
  12             3              0.00722     (  0.00260,     0.01181) **
   3          B-spp-Deer        0.00075     (     zero,     0.00221) **
   3          B--weissii        0.00151     (     zero,     0.00355) **
   5          B-arupensi        0.00220     (     zero,     0.00469) **
   7            11              0.00357     (  0.00041,     0.00681) **
  11          B-clarridg        0.01412     (  0.00771,     0.02044) **
  11          B-quintana        0.00895     (  0.00383,     0.01397) **
   6          B-berhoffi        0.00006     (     zero,     0.00154)
   6          A-tumefaci        0.05619     (  0.04353,     0.06946) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 89:


Empirical Base Frequencies:

   A       0.22888
   C       0.22810
   G       0.32472
  T(U)     0.21831

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.505867)


  +B-clarridg
  !  
  !        +B-berhoffi
  !        !  
  !     +--5  +B-bacillif
  !     !  !  !  
  !     !  !  !        +B--doshiae
  !     !  +--3     +-10  
  !     !     !  +--6  +B-vinsonii
  !     !     !  !  !  
  !     !     +--1  +B-birtlesi
  !  +--4        !  
  !  !  !        !  +B-henselae
  !  !  !        +--7  
  !  !  !           !  +B-elizabet
  !  !  !           +--2  
  !  !  !              +B-grahamii
--9--8  !  
  !  !  !  +B-arupensi
  !  !  +-12  
  !  !     +B-quintana
  !  !  
  !  !  +B-spp-Deer
  !  +-11  
  !     +B--weissii
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3197.85732

Examined 1260 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   9          B-clarridg        0.00837     (  0.00320,     0.01355) **
   9             8              0.00752     (  0.00262,     0.01246) **
   8             4              0.00202     (     zero,     0.00453) **
   4             5              0.00003     (     zero,    infinity)
   5          B-berhoffi        0.00439     (  0.00089,     0.00790) **
   5             3              0.00493     (  0.00116,     0.00871) **
   3          B-bacillif        0.01550     (  0.00885,     0.02213) **
   3             1              0.00168     (     zero,     0.00394) **
   1             6              0.00003     (     zero,    infinity)
   6            10              0.00006     (     zero,    infinity)
  10          B--doshiae        0.00006     (     zero,    infinity)
  10          B-vinsonii        0.00291     (  0.00007,     0.00577) **
   6          B-birtlesi        0.00362     (  0.00047,     0.00681) **
   1             7              0.00219     (     zero,     0.00466) **
   7          B-henselae        0.00439     (  0.00087,     0.00789) **
   7             2              0.00150     (     zero,     0.00353) **
   2          B-elizabet        0.01026     (  0.00489,     0.01565) **
   2          B-grahamii        0.00003     (     zero,     0.00155)
   4            12              0.00219     (     zero,     0.00467) **
  12          B-arupensi        0.00075     (     zero,     0.00221) **
  12          B-quintana        0.01694     (  0.01001,     0.02388) **
   8            11              0.00746     (  0.00283,     0.01211) **
  11          B-spp-Deer        0.00070     (     zero,     0.00211) **
  11          B--weissii        0.00292     (  0.00007,     0.00577) **
   9          A-tumefaci        0.05764     (  0.04461,     0.07107) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 90:


Empirical Base Frequencies:

   A       0.25853
   C       0.24056
   G       0.31803
  T(U)     0.18288

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.468807)


  +B-clarridg
  !  
  !     +B-berhoffi
  !     !  
  !     !  +B-arupensi
  !     !  !  
  !  +-11  !        +B-grahamii
  !  !  !  !     +--4  
  !  !  !  !     !  !  +B-henselae
  !  !  !  !     !  +--9  
  !  !  +--6  +--1     +B--doshiae
  !  !     !  !  !  
  !  !     !  !  !  +B-birtlesi
  !  !     !  !  !  !  
  !  !     !  !  +--2     +B-bacillif
--5-12     !  !     !  +--8  
  !  !     +--7     !  !  !  +B--weissii
  !  !        !     +--3  +-10  
  !  !        !        !     +B-spp-Deer
  !  !        !        !  
  !  !        !        +B-elizabet
  !  !        !  
  !  !        +B-vinsonii
  !  !  
  !  +B-quintana
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2891.30528

Examined  834 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   5          B-clarridg        0.00297     (     zero,     0.00614) **
   5            12              0.00823     (  0.00331,     0.01317) **
  12            11              0.00297     (     zero,     0.00607) **
  11          B-berhoffi        0.00293     (  0.00007,     0.00581) **
  11             6              0.00003     (     zero,    infinity)
   6          B-arupensi        0.00142     (     zero,     0.00343) **
   6             7              0.00076     (     zero,     0.00221) **
   7             1              0.00003     (     zero,    infinity)
   1             4              0.00003     (     zero,    infinity)
   4          B-grahamii        0.00074     (     zero,     0.00218) **
   4             9              0.00073     (     zero,     0.00216) **
   9          B-henselae        0.00363     (  0.00048,     0.00683) **
   9          B--doshiae        0.00003     (     zero,    infinity)
   1             2              0.00003     (     zero,    infinity)
   2          B-birtlesi        0.00074     (     zero,     0.00218) **
   2             3              0.00445     (  0.00082,     0.00798) **
   3             8              0.00138     (     zero,     0.00341) **
   8          B-bacillif        0.00591     (  0.00182,     0.01000) **
   8            10              0.00737     (  0.00280,     0.01194) **
  10          B--weissii        0.00003     (     zero,    infinity)
  10          B-spp-Deer        0.00146     (     zero,     0.00348) **
   3          B-elizabet        0.01104     (  0.00552,     0.01670) **
   7          B-vinsonii        0.00146     (     zero,     0.00347) **
  12          B-quintana        0.00585     (  0.00169,     0.01007) **
   5          A-tumefaci        0.05699     (  0.04407,     0.07029) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 91:


Empirical Base Frequencies:

   A       0.22947
   C       0.24224
   G       0.32595
  T(U)     0.20234

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.510910)


     +B-berhoffi
     !  
     !        +B-birtlesi
     !     +--4  
     !     !  +B-grahamii
     !     !  
  +--8  +--1  +B-vinsonii
  !  !  !  !  !  
  !  !  !  !  !     +B-henselae
  !  !  !  +--3     !  
  !  !  !     !  +--7     +B-spp-Deer
  !  !  !     !  !  !  +--6  
  !  !  !     !  !  +--2  +B--weissii
  !  +-12     +--5     !  
  !     !        !     +B-bacillif
  !     !        !  
  !     !        +B--doshiae
  !     !  
  !     !     +B-clarridg
  !     !  +-11  
  !     +--9  +B-quintana
  !        !  
  !        +B-arupensi
  !  
-10-B-elizabet
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3132.50847

Examined  952 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10             8              0.00295     (     zero,     0.00628) **
   8          B-berhoffi        0.00003     (     zero,    infinity)
   8            12              0.00292     (  0.00007,     0.00577) **
  12             1              0.00437     (  0.00089,     0.00787) **
   1             4              0.00003     (     zero,    infinity)
   4          B-birtlesi        0.00070     (     zero,     0.00209) **
   4          B-grahamii        0.00149     (     zero,     0.00351) **
   1             3              0.00003     (     zero,    infinity)
   3          B-vinsonii        0.00291     (  0.00007,     0.00577) **
   3             5              0.00149     (     zero,     0.00351) **
   5             7              0.00404     (  0.00065,     0.00752) **
   7          B-henselae        0.00469     (  0.00097,     0.00840) **
   7             2              0.00476     (  0.00102,     0.00851) **
   2             6              0.00309     (     zero,     0.00619) **
   6          B-spp-Deer        0.00291     (  0.00006,     0.00577) **
   6          B--weissii        0.00143     (     zero,     0.00344) **
   2          B-bacillif        0.00753     (  0.00285,     0.01227) **
   5          B--doshiae        0.00006     (     zero,    infinity)
  12             9              0.00003     (     zero,     0.00223)
   9            11              0.00506     (  0.00126,     0.00887) **
  11          B-clarridg        0.01113     (  0.00549,     0.01678) **
  11          B-quintana        0.01033     (  0.00490,     0.01576) **
   9          B-arupensi        0.00289     (  0.00007,     0.00576) **
  10          B-elizabet        0.00737     (  0.00261,     0.01218) **
  10          A-tumefaci        0.07084     (  0.05636,     0.08582) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 92:


Empirical Base Frequencies:

   A       0.23539
   C       0.23168
   G       0.30147
  T(U)     0.23147

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.503010)


  +B-elizabet
  !  
  !  +B-berhoffi
  !  !  
  !  !        +B-quintana
  !  !     +--8  
  !  !     !  +B-clarridg
  !  !     !  
  !  !  +--3  +B-henselae
-12-10  !  !  !  
  !  !  !  !  !     +B--doshiae
  !  !  !  +--2  +--7  
  !  !  !     !  !  !  +B-vinsonii
  !  !  !     !  !  +-11  
  !  !  !     !  !     !  +B-birtlesi
  !  !  !     +--1     +--5  
  !  +--6        !        +B-grahamii
  !     !        !  
  !     !        !     +B-spp-Deer
  !     !        !  +--9  
  !     !        +--4  +B--weissii
  !     !           !  
  !     !           +B-bacillif
  !     !  
  !     +B-arupensi
  !  
  +----A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3205.45735

Examined  974 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  12          B-elizabet        0.00498     (  0.00089,     0.00905) **
  12            10              0.00609     (  0.00165,     0.01053) **
  10          B-berhoffi        0.00003     (     zero,    infinity)
  10             6              0.00122     (     zero,     0.00321) **
   6             3              0.00224     (     zero,     0.00473) **
   3             8              0.00197     (     zero,     0.00468) **
   8          B-quintana        0.00965     (  0.00432,     0.01500) **
   8          B-clarridg        0.01391     (  0.00758,     0.02024) **
   3             2              0.00162     (     zero,     0.00415) **
   2          B-henselae        0.00309     (     zero,     0.00620) **
   2             1              0.00437     (  0.00089,     0.00790) **
   1             7              0.00266     (     zero,     0.00559) **
   7          B--doshiae        0.00003     (     zero,    infinity)
   7            11              0.00003     (     zero,    infinity)
  11          B-vinsonii        0.00219     (     zero,     0.00466) **
  11             5              0.00003     (     zero,     0.00187)
   5          B-birtlesi        0.00290     (  0.00007,     0.00575) **
   5          B-grahamii        0.00145     (     zero,     0.00347) **
   1             4              0.00494     (  0.00096,     0.00889) **
   4             9              0.00805     (  0.00326,     0.01287) **
   9          B-spp-Deer        0.00588     (  0.00179,     0.00994) **
   9          B--weissii        0.00070     (     zero,     0.00210) **
   4          B-bacillif        0.01012     (  0.00471,     0.01554) **
   6          B-arupensi        0.00253     (     zero,     0.00526) **
  12          A-tumefaci        0.07629     (  0.06136,     0.09197) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 93:


Empirical Base Frequencies:

   A       0.24282
   C       0.23230
   G       0.33836
  T(U)     0.18652

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.475882)


  +B-elizabet
  !  
  !     +B-bacillif
  !  +--3  
  !  !  !  +B-spp-Deer
  !  !  +--9  
  !  !     +B--weissii
  !  !  
  !  !           +B-clarridg
-12--2        +--7  
  !  !     +--4  +B-grahamii
  !  !     !  !  
  !  !  +--1  +B-birtlesi
  !  !  !  !  
  !  !  !  !  +B-henselae
  !  !  !  +-11  
  !  +--8     +B--doshiae
  !     !  
  !     !  +B-berhoffi
  !     !  !  
  !     +--6     +B-arupensi
  !        !  +--5  
  !        +-10  +B-quintana
  !           !  
  !           +B-vinsonii
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2904.45713

Examined 1360 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  12          B-elizabet        0.00390     (  0.00039,     0.00733) **
  12             2              0.00360     (  0.00028,     0.00691) **
   2             3              0.00219     (     zero,     0.00472) **
   3          B-bacillif        0.00376     (  0.00042,     0.00703) **
   3             9              0.00817     (  0.00331,     0.01300) **
   9          B-spp-Deer        0.00077     (     zero,     0.00223) **
   9          B--weissii        0.00003     (     zero,    infinity)
   2             8              0.00367     (  0.00045,     0.00691) **
   8             1              0.00187     (     zero,     0.00463) **
   1             4              0.00006     (     zero,     0.00243)
   4             7              0.00143     (     zero,     0.00344) **
   7          B-clarridg        0.01561     (  0.00891,     0.02228) **
   7          B-grahamii        0.00006     (     zero,    infinity)
   4          B-birtlesi        0.00150     (     zero,     0.00354) **
   1            11              0.00076     (     zero,     0.00222) **
  11          B-henselae        0.00366     (  0.00048,     0.00688) **
  11          B--doshiae        0.00003     (     zero,    infinity)
   8             6              0.00171     (     zero,     0.00448)
   6          B-berhoffi        0.00152     (     zero,     0.00365) **
   6            10              0.00147     (     zero,     0.00350) **
  10             5              0.00006     (     zero,     0.00181)
   5          B-arupensi        0.00077     (     zero,     0.00230) **
   5          B-quintana        0.00883     (  0.00386,     0.01385) **
  10          B-vinsonii        0.00216     (     zero,     0.00466) **
  12          A-tumefaci        0.05823     (  0.04532,     0.07188) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 94:


Empirical Base Frequencies:

   A       0.24216
   C       0.23730
   G       0.30937
  T(U)     0.21116

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.493145)


  +B-bacillif
  !  
  !        +B-clarridg
  !     +-11  
  !     !  +B-quintana
  !     !  
  !     !        +B--doshiae
  !     !     +--9  
  !  +--5     !  +B-henselae
  !  !  !     !  
  !  !  !  +--4     +B-grahamii
  !  !  !  !  !  +--3  
  !  !  !  !  !  !  !  +B-vinsonii
  !  !  !  !  +--7  +-12  
  !  !  +--2     !     +B-birtlesi
-10--6     !     !  
  !  !     !     +B-elizabet
  !  !     !  
  !  !     !  +B-berhoffi
  !  !     +--1  
  !  !        +B-arupensi
  !  !  
  !  !  +B-spp-Deer
  !  +--8  
  !     +B--weissii
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2922.18803

Examined  632 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  10          B-bacillif        0.00439     (  0.00063,     0.00815) **
  10             6              0.00229     (     zero,     0.00546) **
   6             5              0.00677     (  0.00220,     0.01134) **
   5            11              0.00555     (  0.00151,     0.00959) **
  11          B-clarridg        0.00728     (  0.00274,     0.01186) **
  11          B-quintana        0.00404     (  0.00056,     0.00751) **
   5             2              0.00006     (     zero,     0.00258)
   2             4              0.00367     (  0.00046,     0.00688) **
   4             9              0.00292     (  0.00007,     0.00579) **
   9          B--doshiae        0.00003     (     zero,    infinity)
   9          B-henselae        0.00293     (  0.00007,     0.00579) **
   4             7              0.00003     (     zero,    infinity)
   7             3              0.00003     (     zero,    infinity)
   3          B-grahamii        0.00006     (     zero,    infinity)
   3            12              0.00003     (     zero,    infinity)
  12          B-vinsonii        0.00006     (     zero,    infinity)
  12          B-birtlesi        0.00075     (     zero,     0.00220) **
   7          B-elizabet        0.01176     (  0.00602,     0.01755) **
   2             1              0.00006     (     zero,    infinity)
   1          B-berhoffi        0.00006     (     zero,    infinity)
   1          B-arupensi        0.00076     (     zero,     0.00221) **
   6             8              0.00951     (  0.00426,     0.01479) **
   8          B-spp-Deer        0.00221     (     zero,     0.00469) **
   8          B--weissii        0.00003     (     zero,    infinity)
  10          A-tumefaci        0.06568     (  0.05165,     0.08005) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 95:


Empirical Base Frequencies:

   A       0.24437
   C       0.23316
   G       0.30101
  T(U)     0.22146

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.491981)


  +B-bacillif
  !  
  !     +B-arupensi
  !  +--3  
  !  !  +B-berhoffi
  !  !  
  !  !        +B-henselae
  !  !     +--6  
--7--8     !  +B--doshiae
  !  !  +--1  
  !  !  !  !     +B-grahamii
  !  !  !  !  +-12  
  !  !  !  +--5  +B-elizabet
  !  +--4     !  
  !     !     +B-birtlesi
  !     !  
  !     !  +B-vinsonii
  !     +-10  
  !        !  +B-quintana
  !        +--2  
  !           !  +B-clarridg
  !           +--9  
  !              !  +B--weissii
  !              +-11  
  !                 +B-spp-Deer
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3004.93300

Examined 1508 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7          B-bacillif        0.00509     (  0.00116,     0.00903) **
   7             8              0.00589     (  0.00175,     0.01013) **
   8             3              0.00074     (     zero,     0.00219) **
   3          B-arupensi        0.00441     (  0.00089,     0.00795) **
   3          B-berhoffi        0.00227     (     zero,     0.00479) **
   8             4              0.00075     (     zero,     0.00221) **
   4             1              0.00006     (     zero,     0.00159)
   1             6              0.00076     (     zero,     0.00221) **
   6          B-henselae        0.00443     (  0.00085,     0.00794) **
   6          B--doshiae        0.00003     (     zero,    infinity)
   1             5              0.00073     (     zero,     0.00237)
   5            12              0.00365     (  0.00040,     0.00686) **
  12          B-grahamii        0.00003     (     zero,     0.00180)
  12          B-elizabet        0.00882     (  0.00383,     0.01381) **
   5          B-birtlesi        0.00432     (  0.00078,     0.00783) **
   4            10              0.00225     (     zero,     0.00473) **
  10          B-vinsonii        0.00003     (     zero,     0.00155)
  10             2              0.00351     (  0.00015,     0.00683) **
   2          B-quintana        0.00850     (  0.00350,     0.01350) **
   2             9              0.00374     (  0.00031,     0.00718) **
   9          B-clarridg        0.01014     (  0.00466,     0.01552) **
   9            11              0.00293     (  0.00003,     0.00581) **
  11          B--weissii        0.00171     (     zero,     0.00403) **
  11          B-spp-Deer        0.00121     (     zero,     0.00321) **
   7          A-tumefaci        0.05669     (  0.04380,     0.06996) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 96:


Empirical Base Frequencies:

   A       0.25533
   C       0.23144
   G       0.32262
  T(U)     0.19060

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.462665)


  +B-bacillif
  !  
  !        +B--weissii
  !     +--7  
  !     !  +B-spp-Deer
  !     !  
  !     !     +B-berhoffi
  !  +--5  +--4  
  !  !  !  !  !  +B-quintana
  !  !  !  !  +--1  
  !  !  !  !     !  +B-elizabet
  !  !  +--3     +--6  
  !  !     !        +B-grahamii
  !  !     !  
  !  !     !  +B-arupensi
-12--9     +--8  
  !  !        !  +B-birtlesi
  !  !        +-10  
  !  !           !  +B-vinsonii
  !  !           +-11  
  !  !              !  +B--doshiae
  !  !              +--2  
  !  !                 +B-henselae
  !  !  
  !  +B-clarridg
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3152.03746

Examined 1036 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

  12          B-bacillif        0.00466     (  0.00077,     0.00852) **
  12             9              0.00472     (  0.00083,     0.00862) **
   9             5              0.00373     (  0.00046,     0.00703) **
   5             7              0.01217     (  0.00622,     0.01814) **
   7          B--weissii        0.00145     (     zero,     0.00346) **
   7          B-spp-Deer        0.00003     (     zero,    infinity)
   5             3              0.00394     (  0.00043,     0.00746) **
   3             4              0.00364     (  0.00047,     0.00683) **
   4          B-berhoffi        0.00003     (     zero,    infinity)
   4             1              0.00037     (     zero,     0.00206)
   1          B-quintana        0.01430     (  0.00797,     0.02076) **
   1             6              0.00542     (  0.00150,     0.00944) **
   6          B-elizabet        0.00776     (  0.00304,     0.01250) **
   6          B-grahamii        0.00107     (     zero,     0.00299) *
   3             8              0.00006     (     zero,    infinity)
   8          B-arupensi        0.00073     (     zero,     0.00215) **
   8            10              0.00364     (  0.00046,     0.00684) **
  10          B-birtlesi        0.00438     (  0.00087,     0.00787) **
  10            11              0.00006     (     zero,    infinity)
  11          B-vinsonii        0.00215     (     zero,     0.00462) **
  11             2              0.00074     (     zero,     0.00217) **
   2          B--doshiae        0.00006     (     zero,    infinity)
   2          B-henselae        0.00584     (  0.00180,     0.00989) **
   9          B-clarridg        0.01411     (  0.00772,     0.02058) **
  12          A-tumefaci        0.05876     (  0.04583,     0.07246) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 97:


Empirical Base Frequencies:

   A       0.25666
   C       0.24017
   G       0.31000
  T(U)     0.19317

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.475541)


     +B-arupensi
     !  
     !     +B-clarridg
     !     !  
     !  +--5     +B-bacillif
  +--2  !  !  +-11  
  !  !  !  !  !  !  +B--weissii
  !  !  !  +--4  +-10  
  !  !  !     !     +B-spp-Deer
  !  !  !     !  
  !  !  !     +B-quintana
  !  +--1  
  !     !        +B-vinsonii
  !     !        !  
  !     !     +-12     +B-elizabet
  !     !     !  !  +--9  
  !     !     !  +--8  +B-grahamii
  !     !  +--7     !  
  !     !  !  !     +B-birtlesi
  !     +--6  !  
  !        !  +B--doshiae
  !        !  
  !        +B-henselae
  !  
--3-B-berhoffi
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3122.39468

Examined 1004 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   3             2              0.00224     (     zero,     0.00477) **
   2          B-arupensi        0.00366     (  0.00047,     0.00688) **
   2             1              0.00078     (     zero,     0.00236) *
   1             5              0.00473     (  0.00087,     0.00853) **
   5          B-clarridg        0.01289     (  0.00678,     0.01902) **
   5             4              0.00181     (     zero,     0.00431) **
   4            11              0.00651     (  0.00203,     0.01100) **
  11          B-bacillif        0.01122     (  0.00544,     0.01703) **
  11            10              0.00765     (  0.00286,     0.01244) **
  10          B--weissii        0.00003     (     zero,     0.00221)
  10          B-spp-Deer        0.00365     (  0.00042,     0.00684) **
   4          B-quintana        0.00516     (  0.00111,     0.00921) **
   1             6              0.00461     (  0.00084,     0.00835) **
   6             7              0.00186     (     zero,     0.00440) **
   7            12              0.00090     (     zero,     0.00264) **
  12          B-vinsonii        0.00439     (  0.00087,     0.00789) **
  12             8              0.00003     (     zero,     0.00181)
   8             9              0.00145     (     zero,     0.00346) **
   9          B-elizabet        0.00882     (  0.00380,     0.01378) **
   9          B-grahamii        0.00003     (     zero,    infinity)
   8          B-birtlesi        0.00074     (     zero,     0.00218) **
   7          B--doshiae        0.00006     (     zero,     0.00150)
   6          B-henselae        0.00726     (  0.00272,     0.01180) **
   3          B-berhoffi        0.00006     (     zero,     0.00176)
   3          A-tumefaci        0.06005     (  0.04680,     0.07366) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 98:


Empirical Base Frequencies:

   A       0.24057
   C       0.23276
   G       0.32071
  T(U)     0.20597

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.489068)


  +B-clarridg
  !  
  !           +B-quintana
  !        +-11  
  !        !  +B-bacillif
  !        !  
  !        !           +B-grahamii
  !        !        +--6  
  !        !        !  +B-birtlesi
  !     +--2     +--3  
  !     !  !     !  !  +B--doshiae
  !     !  !     !  +--8  
  !     !  !  +--4     +B-vinsonii
  !     !  !  !  !  
  !     !  !  !  !  +B-henselae
  !  +--9  !  !  +--5  
  !  !  !  +--1     !  +B-spp-Deer
  !  !  !     !     +-12  
  !  !  !     !        +B--weissii
--7-10  !     !  
  !  !  !     +B-arupensi
  !  !  !  
  !  !  +B-elizabet
  !  !  
  !  +B-berhoffi
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3023.77755

Examined  878 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   7          B-clarridg        0.00891     (  0.00375,     0.01411) **
   7            10              0.00732     (  0.00259,     0.01205) **
  10             9              0.00003     (     zero,    infinity)
   9             2              0.00150     (     zero,     0.00355) **
   2            11              0.00663     (  0.00228,     0.01099) **
  11          B-quintana        0.00518     (  0.00130,     0.00903) **
  11          B-bacillif        0.01193     (  0.00607,     0.01779) **
   2             1              0.00151     (     zero,     0.00356) **
   1             4              0.00003     (     zero,     0.00251)
   4             3              0.00438     (  0.00087,     0.00790) **
   3             6              0.00006     (     zero,     0.00218)
   6          B-grahamii        0.00142     (     zero,     0.00344) **
   6          B-birtlesi        0.00290     (  0.00003,     0.00577) **
   3             8              0.00003     (     zero,    infinity)
   8          B--doshiae        0.00074     (     zero,     0.00219) **
   8          B-vinsonii        0.00070     (     zero,     0.00209) **
   4             5              0.00439     (  0.00086,     0.00793) **
   5          B-henselae        0.00585     (  0.00182,     0.00997) **
   5            12              0.00894     (  0.00385,     0.01398) **
  12          B-spp-Deer        0.00076     (     zero,     0.00223) **
  12          B--weissii        0.00220     (     zero,     0.00470) **
   1          B-arupensi        0.00074     (     zero,     0.00219) **
   9          B-elizabet        0.00663     (  0.00230,     0.01095) **
  10          B-berhoffi        0.00003     (     zero,    infinity)
   7          A-tumefaci        0.05766     (  0.04472,     0.07117) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 99:


Empirical Base Frequencies:

   A       0.23477
   C       0.22048
   G       0.35036
  T(U)     0.19439

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.477742)


  +B-berhoffi
  !  
  !     +B-quintana
  !     !  
  !  +--7  +B-clarridg
  !  !  !  !  
  !  !  +--8     +B--weissii
  !  !     !  +--6  
  !  !     +--5  +B-spp-Deer
  !  !        !  
--2--3        +B-bacillif
  !  !  
  !  !  +B-arupensi
  !  !  !  
  !  !  !        +B--doshiae
  !  !  !     +--9  
  !  +--1     !  !  +B-vinsonii
  !     !  +-11  +-12  
  !     !  !  !     +B-henselae
  !     !  !  !  
  !     +--4  +B-birtlesi
  !        !  
  !        !  +B-grahamii
  !        +-10  
  !           +B-elizabet
  !  
  +---A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3035.51898

Examined  742 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   2          B-berhoffi        0.00003     (     zero,     0.00170)
   2             3              0.00150     (     zero,     0.00355) **
   3             7              0.00602     (  0.00170,     0.01035) **
   7          B-quintana        0.00721     (  0.00256,     0.01191) **
   7             8              0.00330     (  0.00008,     0.00650) **
   8          B-clarridg        0.00985     (  0.00437,     0.01530) **
   8             5              0.00563     (  0.00143,     0.00985) **
   5             6              0.00555     (  0.00147,     0.00963) **
   6          B--weissii        0.00094     (     zero,     0.00271) **
   6          B-spp-Deer        0.00273     (     zero,     0.00556) **
   5          B-bacillif        0.01012     (  0.00464,     0.01562) **
   3             1              0.00003     (     zero,    infinity)
   1          B-arupensi        0.00221     (     zero,     0.00469) **
   1             4              0.00437     (  0.00088,     0.00787) **
   4            11              0.00003     (     zero,    infinity)
  11             9              0.00006     (     zero,     0.00173)
   9          B--doshiae        0.00074     (     zero,     0.00218) *
   9            12              0.00150     (     zero,     0.00354) **
  12          B-vinsonii        0.00225     (     zero,     0.00475) **
  12          B-henselae        0.00657     (  0.00227,     0.01086) **
  11          B-birtlesi        0.00145     (     zero,     0.00346) **
   4            10              0.00217     (     zero,     0.00463) **
  10          B-grahamii        0.00006     (     zero,     0.00181)
  10          B-elizabet        0.00729     (  0.00278,     0.01181) **
   2          A-tumefaci        0.06097     (  0.04763,     0.07473) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Data set # 100:


Empirical Base Frequencies:

   A       0.25722
   C       0.23390
   G       0.31403
  T(U)     0.19485

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.467497)


  +B-berhoffi
  !  
  !  +B-arupensi
  !  !  
  !  !        +B--doshiae
  !  !        !  
  !  !     +--1  +B-henselae
  !  !     !  !  !  
  !  !     !  +--5     +B-spp-Deer
  !  !     !     !  +--9  
--6-12     !     !  !  +B--weissii
  !  !     !     +--3  
  !  !     !        !  +B-bacillif
  !  !  +-10        +--4  
  !  !  !  !           !  +B-quintana
  !  !  !  !           +--7  
  !  !  !  !              +B-clarridg
  !  !  !  !  
  !  +-11  !     +B-elizabet
  !     !  !  +--8  
  !     !  +--2  +B-grahamii
  !     !     !  
  !     !     +B-birtlesi
  !     !  
  !     +B-vinsonii
  !  
  +--A-tumefaci


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -2925.28345

Examined  530 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   6          B-berhoffi        0.00006     (     zero,     0.00184)
   6            12              0.00454     (  0.00091,     0.00819) **
  12          B-arupensi        0.00071     (     zero,     0.00212) **
  12            11              0.00293     (  0.00006,     0.00579) **
  11            10              0.00073     (     zero,     0.00216) **
  10             1              0.00074     (     zero,     0.00218) **
   1          B--doshiae        0.00006     (     zero,    infinity)
   1             5              0.00434     (  0.00085,     0.00786) **
   5          B-henselae        0.00075     (     zero,     0.00224) **
   5             3              0.00239     (     zero,     0.00507) **
   3             9              0.00495     (  0.00118,     0.00876) **
   9          B-spp-Deer        0.00078     (     zero,     0.00229) **
   9          B--weissii        0.00144     (     zero,     0.00348) **
   3             4              0.00323     (  0.00015,     0.00636) **
   4          B-bacillif        0.00500     (  0.00109,     0.00892) **
   4             7              0.00209     (     zero,     0.00490) **
   7          B-quintana        0.00954     (  0.00419,     0.01492) **
   7          B-clarridg        0.01332     (  0.00701,     0.01956) **
  10             2              0.00003     (     zero,     0.00224)
   2             8              0.00288     (  0.00007,     0.00574) **
   8          B-elizabet        0.00513     (  0.00134,     0.00893) **
   8          B-grahamii        0.00006     (     zero,     0.00178)
   2          B-birtlesi        0.00290     (  0.00005,     0.00576) **
  11          B-vinsonii        0.00006     (     zero,     0.00162)
   6          A-tumefaci        0.05532     (  0.04258,     0.06834) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01