Nucleic acid sequence Maximum Likelihood method, version 3.573c

Data set # 1:


Empirical Base Frequencies:

   A       0.26696
   C       0.21719
   G       0.29948
  T(U)     0.21637

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.459645)


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


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

Ln Likelihood = -1295.90638

Examined  596 trees

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

   2             7              0.01788     (  0.00138,     0.03450) **
   7             3              0.01820     (  0.00156,     0.03483) **
   3          B-clarridg        0.06234     (  0.03222,     0.09266) **
   3             8              0.01537     (     zero,     0.03109) **
   8            10              0.00641     (     zero,     0.01638) *
  10          B-spp-Deer        0.02098     (  0.00373,     0.03825) **
  10          B-bacillif        0.04971     (  0.02341,     0.07630) **
   8          B--weissii        0.01008     (     zero,     0.02202) **
   7             5              0.01354     (     zero,     0.02804) **
   5             1              0.00003     (     zero,     0.00982)
   1          B-henselae        0.01043     (     zero,     0.02233) **
   1             9              0.00691     (     zero,     0.01662) **
   9             6              0.03520     (  0.01318,     0.05744) **
   6          B-elizabet        0.00340     (     zero,     0.01041) *
   6            12              0.00688     (     zero,     0.01671) **
  12          B-birtlesi        0.05902     (  0.03008,     0.08857) **
  12          B-grahamii        0.00003     (     zero,    infinity)
   9          B-quintana        0.00369     (     zero,     0.01102) **
   5             4              0.00982     (     zero,     0.02151) **
   4          B-vinsonii        0.00362     (     zero,     0.01071) **
   4            11              0.00328     (     zero,     0.01011) *
  11          B-arupensi        0.00708     (     zero,     0.01703) **
  11          B-berhoffi        0.03804     (  0.01545,     0.06101) **
   2          B--doshiae        0.00003     (     zero,     0.01474)
   2          A-tumefaci        0.32762     (  0.24560,     0.41259) **

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


Data set # 2:


Empirical Base Frequencies:

   A       0.29758
   C       0.22920
   G       0.29116
  T(U)     0.18206

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.431346)


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


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

Ln Likelihood = -1107.50213

Examined 1894 trees

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

  11             5              0.02550     (  0.00656,     0.04445) **
   5             4              0.00358     (     zero,     0.01059) **
   4             9              0.01091     (     zero,     0.02330) **
   9            12              0.00719     (     zero,     0.01724) **
  12          B-grahamii        0.00003     (     zero,     0.00848)
  12          B-birtlesi        0.02945     (  0.00899,     0.04994) **
   9          B-elizabet        0.01033     (     zero,     0.02209) **
   4             7              0.00003     (     zero,    infinity)
   7          B-arupensi        0.00003     (     zero,    infinity)
   7          B-bacillif        0.04184     (  0.01809,     0.06582) **
   5             8              0.00003     (     zero,    infinity)
   8             2              0.01028     (     zero,     0.02194) **
   2            10              0.02061     (  0.00420,     0.03727) **
  10          B--weissii        0.00006     (     zero,     0.00735)
  10             3              0.01439     (  0.00016,     0.02866) **
   3          B-clarridg        0.05040     (  0.02379,     0.07724) **
   3          B-spp-Deer        0.01015     (     zero,     0.02218) **
   2             1              0.00003     (     zero,     0.00729)
   1          B-henselae        0.00688     (     zero,     0.01643) **
   1             6              0.00346     (     zero,     0.01027) **
   6          B-berhoffi        0.02446     (  0.00631,     0.04271) **
   6          B-quintana        0.00349     (     zero,     0.01034) **
   8          B-vinsonii        0.00342     (     zero,     0.01010) **
  11          B--doshiae        0.00003     (     zero,     0.00947)
  11          A-tumefaci        0.31032     (  0.23027,     0.39259) **

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


Data set # 3:


Empirical Base Frequencies:

   A       0.32251
   C       0.23271
   G       0.26523
  T(U)     0.17955

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.447117)


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


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

Ln Likelihood = -1371.78717

Examined 1380 trees

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

   8             2              0.04282     (  0.01449,     0.07130) **
   2             1              0.03213     (  0.00915,     0.05534) **
   1             7              0.01352     (     zero,     0.02712) **
   7          B-vinsonii        0.00348     (     zero,     0.01061) *
   7             4              0.01478     (  0.00037,     0.02920) **
   4             9              0.00006     (     zero,     0.00747)
   9            10              0.02039     (  0.00387,     0.03692) **
  10          B--doshiae        0.03225     (  0.01128,     0.05337) **
  10             6              0.01012     (     zero,     0.02212) **
   6          B--weissii        0.00485     (     zero,     0.01359) **
   6             3              0.01026     (     zero,     0.02234) **
   3          B-bacillif        0.07380     (  0.04218,     0.10611) **
   3             5              0.01007     (     zero,     0.02194) **
   5          B-spp-Deer        0.00003     (     zero,    infinity)
   5          B-clarridg        0.05818     (  0.03046,     0.08647) **
   9            12              0.00915     (     zero,     0.02092) **
  12          B-berhoffi        0.02949     (  0.00978,     0.04946) **
  12          B-henselae        0.00003     (     zero,     0.00817)
   4          B-quintana        0.01003     (     zero,     0.02140) **
   1          B-arupensi        0.00695     (     zero,     0.01706) **
   2            11              0.02565     (  0.00587,     0.04574) **
  11          B-grahamii        0.00763     (     zero,     0.02029)
  11          B-elizabet        0.02957     (  0.00914,     0.05032) **
   8          B-birtlesi        0.04336     (  0.01313,     0.07361) **
   8          A-tumefaci        0.25307     (  0.18413,     0.32410) **

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


Data set # 4:


Empirical Base Frequencies:

   A       0.28039
   C       0.19671
   G       0.34382
  T(U)     0.17908

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.359943)


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


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

Ln Likelihood = -1283.32901

Examined  642 trees

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

   5             6              0.03518     (  0.01312,     0.05758) **
   6             4              0.00998     (     zero,     0.02208) **
   4             2              0.01323     (     zero,     0.02653) **
   2             9              0.01010     (     zero,     0.02157) **
   9          B-arupensi        0.00006     (     zero,    infinity)
   9          B-berhoffi        0.03719     (  0.01525,     0.05952) **
   2          B-vinsonii        0.00329     (     zero,     0.00990) *
   4             3              0.00003     (     zero,     0.00956)
   3             1              0.00679     (     zero,     0.01651) **
   1             7              0.05250     (  0.02575,     0.07963) **
   7          B-grahamii        0.00003     (     zero,    infinity)
   7            12              0.01007     (     zero,     0.02203) **
  12          B-birtlesi        0.06148     (  0.03209,     0.09131) **
  12          B-elizabet        0.01363     (  0.00011,     0.02732) **
   1          B-quintana        0.00698     (     zero,     0.01682) **
   3          B-henselae        0.01044     (     zero,     0.02224) **
   6             8              0.02803     (  0.00829,     0.04782) **
   8          B--weissii        0.00665     (     zero,     0.01625) **
   8            10              0.01383     (  0.00002,     0.02759) **
  10            11              0.00310     (     zero,     0.01016)
  11          B-spp-Deer        0.00681     (     zero,     0.01640) **
  11          B-bacillif        0.04459     (  0.02008,     0.06904) **
  10          B-clarridg        0.03406     (  0.01294,     0.05554) **
   5          B--doshiae        0.00003     (     zero,     0.01383)
   5          A-tumefaci        0.30153     (  0.22538,     0.38046) **

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


Data set # 5:


Empirical Base Frequencies:

   A       0.27842
   C       0.21538
   G       0.30400
  T(U)     0.20220

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.435101)


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


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

Ln Likelihood = -1235.11084

Examined 1752 trees

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

  10             1              0.02364     (  0.00496,     0.04234) **
   1             6              0.04283     (  0.01857,     0.06747) **
   6          B-grahamii        0.00003     (     zero,     0.01038)
   6             8              0.01396     (     zero,     0.02812) **
   8          B-elizabet        0.01340     (     zero,     0.02710) **
   8          B-birtlesi        0.05869     (  0.02979,     0.08801) **
   1             7              0.00617     (     zero,     0.01580) *
   7          B-henselae        0.00337     (     zero,     0.00996) **
   7             9              0.00003     (     zero,     0.00700)
   9             3              0.00329     (     zero,     0.00978) **
   3             2              0.00769     (     zero,     0.01833) **
   2             4              0.01015     (     zero,     0.02184) **
   4          B-arupensi        0.01272     (     zero,     0.02603) **
   4          B-vinsonii        0.00752     (     zero,     0.01801) **
   2          B-berhoffi        0.03350     (  0.01206,     0.05494) **
   3          B-quintana        0.00003     (     zero,     0.00695)
   9             5              0.02739     (  0.00831,     0.04656) **
   5          B--weissii        0.00653     (     zero,     0.01608) **
   5            12              0.01890     (  0.00241,     0.03533) **
  12          B-bacillif        0.03321     (  0.01191,     0.05452) **
  12            11              0.00955     (     zero,     0.02129) **
  11          B-spp-Deer        0.00006     (     zero,     0.00744)
  11          B-clarridg        0.03800     (  0.01539,     0.06063) **
  10          B--doshiae        0.00143     (     zero,     0.01216)
  10          A-tumefaci        0.27726     (  0.20413,     0.35217) **

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


Data set # 6:


Empirical Base Frequencies:

   A       0.27932
   C       0.21224
   G       0.33404
  T(U)     0.17441

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.387844)


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


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

Ln Likelihood = -1303.67347

Examined  838 trees

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

   7          B--doshiae        0.00003     (     zero,     0.01521)
   7             5              0.04613     (  0.02093,     0.07153) **
   5             4              0.00348     (     zero,     0.01031) **
   4             8              0.00333     (     zero,     0.01005) *
   8          B-arupensi        0.00678     (     zero,     0.01628) **
   8          B-berhoffi        0.02731     (  0.00846,     0.04649) **
   4          B-vinsonii        0.00003     (     zero,    infinity)
   5             2              0.00288     (     zero,     0.00970)
   2          B-henselae        0.02112     (  0.00424,     0.03808) **
   2             3              0.00003     (     zero,     0.00764)
   3            10              0.01433     (  0.00009,     0.02857) **
  10             6              0.01026     (     zero,     0.02298) **
   6          B-bacillif        0.04182     (  0.01756,     0.06629) **
   6             1              0.00668     (     zero,     0.01703) **
   1          B-spp-Deer        0.00652     (     zero,     0.01712) *
   1          B-clarridg        0.05578     (  0.02806,     0.08412) **
  10          B--weissii        0.00650     (     zero,     0.01691) **
   3            11              0.00677     (     zero,     0.01662) **
  11          B-quintana        0.01386     (  0.00016,     0.02755) **
  11             9              0.03856     (  0.01485,     0.06232) **
   9            12              0.00852     (     zero,     0.02112) *
  12          B-birtlesi        0.06848     (  0.03754,     0.09995) **
  12          B-grahamii        0.00006     (     zero,     0.00819)
   9          B-elizabet        0.03040     (  0.00984,     0.05101) **
   7          A-tumefaci        0.31896     (  0.23786,     0.40236) **

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


Data set # 7:


Empirical Base Frequencies:

   A       0.25875
   C       0.24324
   G       0.32340
  T(U)     0.17461

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.468493)


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


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

Ln Likelihood = -1197.47176

Examined 1010 trees

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

   7          B-birtlesi        0.01449     (     zero,     0.03613)
   7             5              0.05414     (  0.02456,     0.08410) **
   5            12              0.00777     (     zero,     0.01888) **
  12          B-elizabet        0.01194     (     zero,     0.02481) **
  12          B-grahamii        0.00130     (     zero,     0.00817)
   5             8              0.01785     (  0.00171,     0.03418) **
   8             1              0.00666     (     zero,     0.01590) **
   1             2              0.00993     (     zero,     0.02164) **
   2             6              0.02395     (  0.00601,     0.04187) **
   6            10              0.00611     (     zero,     0.01551) **
  10             9              0.00347     (     zero,     0.01044) *
   9          B-clarridg        0.06886     (  0.03809,     0.10002) **
   9          B-spp-Deer        0.00392     (     zero,     0.01182) *
  10          B-bacillif        0.03427     (  0.01299,     0.05580) **
   6          B--weissii        0.00003     (     zero,    infinity)
   2          B--doshiae        0.02421     (  0.00606,     0.04229) **
   1             4              0.00005     (     zero,    infinity)
   4             3              0.00678     (     zero,     0.01619) **
   3            11              0.00669     (     zero,     0.01612) **
  11          B-vinsonii        0.00673     (     zero,     0.01611) **
  11          B-arupensi        0.01014     (     zero,     0.02165) **
   3          B-berhoffi        0.01686     (  0.00204,     0.03171) **
   4          B-henselae        0.01348     (  0.00027,     0.02672) **
   8          B-quintana        0.00003     (     zero,     0.00735)
   7          A-tumefaci        0.27125     (  0.19950,     0.34500) **

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


Data set # 8:


Empirical Base Frequencies:

   A       0.25683
   C       0.23677
   G       0.31572
  T(U)     0.19068

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.469155)


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


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

Ln Likelihood = -1142.38045

Examined  570 trees

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

   7             4              0.02657     (  0.00552,     0.04772) **
   4             1              0.00730     (     zero,     0.01737) **
   1          B-grahamii        0.00996     (     zero,     0.02138) **
   1          B-elizabet        0.00337     (     zero,     0.01010) **
   4            10              0.00293     (     zero,     0.00972)
  10          B-arupensi        0.00006     (     zero,    infinity)
  10             9              0.01342     (  0.00026,     0.02658) **
   9          B-vinsonii        0.01003     (     zero,     0.02142) **
   9             8              0.00003     (     zero,    infinity)
   8             5              0.00006     (     zero,     0.00819)
   5             6              0.01202     (     zero,     0.02529) **
   6          B-berhoffi        0.02866     (  0.00877,     0.04872) **
   6          B-henselae        0.00006     (     zero,     0.00829)
   5          B-quintana        0.01015     (     zero,     0.02166) **
   8            12              0.00987     (     zero,     0.02164) **
  12          B--doshiae        0.02428     (  0.00608,     0.04242) **
  12             2              0.02770     (  0.00844,     0.04725) **
   2            11              0.00006     (     zero,     0.01236)
  11          B--weissii        0.00980     (     zero,     0.02125) **
  11             3              0.01033     (     zero,     0.02209) **
   3          B-spp-Deer        0.00661     (     zero,     0.01602) **
   3          B-clarridg        0.02055     (  0.00415,     0.03719) **
   2          B-bacillif        0.04820     (  0.02266,     0.07378) **
   7          B-birtlesi        0.02050     (  0.00088,     0.04007) **
   7          A-tumefaci        0.28437     (  0.21185,     0.36056) **

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


Data set # 9:


Empirical Base Frequencies:

   A       0.28211
   C       0.19138
   G       0.33296
  T(U)     0.19355

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.375984)


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


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

Ln Likelihood = -1096.38595

Examined  750 trees

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

  11          B-birtlesi        0.03091     (  0.00608,     0.05591) **
  11             1              0.03136     (  0.00675,     0.05625) **
   1             8              0.00336     (     zero,     0.01031) *
   8             7              0.02418     (  0.00586,     0.04251) **
   7          B-grahamii        0.00417     (     zero,     0.01233) *
   7          B-elizabet        0.00656     (     zero,     0.01617) **
   8          B--doshiae        0.01046     (     zero,     0.02239) **
   1             4              0.00003     (     zero,     0.00979)
   4             5              0.01050     (     zero,     0.02241) **
   5          B-berhoffi        0.02075     (  0.00400,     0.03751) **
   5             2              0.00695     (     zero,     0.01677) **
   2          B-vinsonii        0.01030     (     zero,     0.02201) **
   2          B-arupensi        0.00338     (     zero,     0.01012) **
   4            12              0.00331     (     zero,     0.00998) *
  12             9              0.00004     (     zero,    infinity)
   9          B-henselae        0.00684     (     zero,     0.01631) **
   9             6              0.01362     (  0.00034,     0.02706) **
   6          B-bacillif        0.02747     (  0.00849,     0.04674) **
   6            10              0.00006     (     zero,    infinity)
  10          B--weissii        0.00006     (     zero,    infinity)
  10             3              0.00704     (     zero,     0.01684) **
   3          B-spp-Deer        0.00668     (     zero,     0.01621) **
   3          B-clarridg        0.03534     (  0.01340,     0.05752) **
  12          B-quintana        0.01031     (     zero,     0.02198) **
  11          A-tumefaci        0.26621     (  0.19458,     0.34028) **

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


Data set # 10:


Empirical Base Frequencies:

   A       0.25245
   C       0.23261
   G       0.30318
  T(U)     0.21175

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.480362)


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


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

Ln Likelihood = -1165.41483

Examined  514 trees

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

  10          B--doshiae        0.00003     (     zero,     0.01188)
  10             3              0.03643     (  0.01361,     0.05930) **
   3             9              0.00707     (     zero,     0.01695) **
   9          B-vinsonii        0.00364     (     zero,     0.01083) **
   9          B-arupensi        0.01017     (     zero,     0.02194) **
   3             1              0.00352     (     zero,     0.01123)
   1             5              0.00698     (     zero,     0.01674) **
   5          B-henselae        0.01059     (     zero,     0.02257) **
   5             7              0.00342     (     zero,     0.01023) *
   7          B-quintana        0.00691     (     zero,     0.01649) **
   7            11              0.00308     (     zero,     0.01025)
  11          B-berhoffi        0.02467     (  0.00639,     0.04324) **
  11            12              0.03172     (  0.01063,     0.05313) **
  12          B-bacillif        0.03228     (  0.01110,     0.05377) **
  12             4              0.00655     (     zero,     0.01686) *
   4             8              0.00752     (     zero,     0.01813) **
   8          B--weissii        0.00343     (     zero,     0.01014) **
   8          B-spp-Deer        0.00003     (     zero,    infinity)
   4          B-clarridg        0.04203     (  0.01796,     0.06658) **
   1             6              0.01729     (  0.00106,     0.03354) **
   6          B-birtlesi        0.04485     (  0.01920,     0.07049) **
   6             2              0.00805     (     zero,     0.01929) **
   2          B-elizabet        0.01033     (     zero,     0.02203) **
   2          B-grahamii        0.00006     (     zero,     0.00704)
  10          A-tumefaci        0.27421     (  0.20162,     0.34867) **

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


Data set # 11:


Empirical Base Frequencies:

   A       0.33390
   C       0.22109
   G       0.27203
  T(U)     0.17298

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.411128)


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


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

Ln Likelihood = -1153.48674

Examined  550 trees

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

  11          B-birtlesi        0.02336     (     zero,     0.04714) **
  11             4              0.02527     (  0.00233,     0.04842) **
   4            12              0.01803     (  0.00201,     0.03407) **
  12          B-grahamii        0.00294     (     zero,     0.01017)
  12          B-elizabet        0.01094     (     zero,     0.02343) **
   4            10              0.01071     (     zero,     0.02359) **
  10             5              0.00699     (     zero,     0.01675) **
   5             1              0.00340     (     zero,     0.01031) *
   1             7              0.00003     (     zero,     0.00718)
   7          B-quintana        0.01045     (     zero,     0.02228) **
   7             6              0.00006     (     zero,    infinity)
   6          B-vinsonii        0.01037     (     zero,     0.02212) **
   6             2              0.00308     (     zero,     0.01010)
   2          B--doshiae        0.02514     (  0.00641,     0.04388) **
   2             3              0.03583     (  0.01344,     0.05819) **
   3          B--weissii        0.00348     (     zero,     0.01044) *
   3             9              0.00350     (     zero,     0.01056) *
   9          B-bacillif        0.02444     (  0.00630,     0.04267) **
   9             8              0.00362     (     zero,     0.01079) **
   8          B-clarridg        0.05772     (  0.02930,     0.08659) **
   8          B-spp-Deer        0.00336     (     zero,     0.01021) *
   1          B-henselae        0.01046     (     zero,     0.02230) **
   5          B-berhoffi        0.03161     (  0.01101,     0.05256) **
  10          B-arupensi        0.00006     (     zero,    infinity)
  11          A-tumefaci        0.28650     (  0.21078,     0.36414) **

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


Data set # 12:


Empirical Base Frequencies:

   A       0.29363
   C       0.21905
   G       0.28628
  T(U)     0.20104

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.437766)


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


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

Ln Likelihood = -1275.40023

Examined 1280 trees

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

   2          B-henselae        0.00003     (     zero,    infinity)
   2             3              0.01056     (     zero,     0.02252) **
   3             8              0.00003     (     zero,    infinity)
   8            11              0.00003     (     zero,    infinity)
  11          B-berhoffi        0.02403     (  0.00631,     0.04205) **
  11             4              0.00697     (     zero,     0.01663) **
   4             1              0.00003     (     zero,    infinity)
   1          B-vinsonii        0.00682     (     zero,     0.01628) **
   1            10              0.00003     (     zero,     0.01134)
  10          B-birtlesi        0.08045     (  0.04678,     0.11514) **
  10             6              0.01020     (     zero,     0.02217) **
   6          B--doshiae        0.03903     (  0.01590,     0.06249) **
   6             7              0.01396     (  0.00003,     0.02789) **
   7          B-elizabet        0.02055     (  0.00414,     0.03712) **
   7          B-grahamii        0.00003     (     zero,    infinity)
   4          B-arupensi        0.00003     (     zero,    infinity)
   8             5              0.04216     (  0.01803,     0.06633) **
   5          B--weissii        0.01040     (     zero,     0.02254) **
   5            12              0.01037     (     zero,     0.02264) **
  12          B-bacillif        0.08589     (  0.05099,     0.12120) **
  12             9              0.00354     (     zero,     0.01084) *
   9          B-clarridg        0.06433     (  0.03440,     0.09471) **
   9          B-spp-Deer        0.00003     (     zero,     0.00845)
   3          B-quintana        0.00341     (     zero,     0.01008) **
   2          A-tumefaci        0.32548     (  0.24377,     0.40958) **

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


Data set # 13:


Empirical Base Frequencies:

   A       0.27323
   C       0.25288
   G       0.30176
  T(U)     0.17213

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.475842)


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


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

Ln Likelihood = -1105.28295

Examined  616 trees

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

   5          B-birtlesi        0.02068     (  0.00128,     0.04008) **
   5            12              0.01522     (     zero,     0.03257) **
  12          B-arupensi        0.01027     (     zero,     0.02193) **
  12             9              0.00006     (     zero,     0.01012)
   9             8              0.00686     (     zero,     0.01641) **
   8             7              0.01030     (     zero,     0.02228) **
   7            10              0.01978     (  0.00280,     0.03676) **
  10          B-elizabet        0.01347     (     zero,     0.02711) **
  10          B-grahamii        0.00501     (     zero,     0.01463) *
   7          B--doshiae        0.01752     (  0.00203,     0.03303) **
   8             4              0.00687     (     zero,     0.01644) **
   4             1              0.00003     (     zero,    infinity)
   1          B-quintana        0.00685     (     zero,     0.01633) **
   1             2              0.00683     (     zero,     0.01628) **
   2             3              0.00003     (     zero,    infinity)
   3          B-bacillif        0.03459     (  0.01312,     0.05626) **
   3             6              0.00341     (     zero,     0.01015) **
   6          B-spp-Deer        0.00342     (     zero,     0.01015) **
   6          B--weissii        0.01031     (     zero,     0.02201) **
   2          B-clarridg        0.03497     (  0.01319,     0.05682) **
   4            11              0.00467     (     zero,     0.01372) *
  11          B-henselae        0.01048     (     zero,     0.02238) **
  11          B-berhoffi        0.01939     (  0.00284,     0.03599) **
   9          B-vinsonii        0.00006     (     zero,    infinity)
   5          A-tumefaci        0.29472     (  0.21718,     0.37434) **

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


Data set # 14:


Empirical Base Frequencies:

   A       0.32908
   C       0.18789
   G       0.28843
  T(U)     0.19460

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.367436)


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


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

Ln Likelihood = -1230.10342

Examined  582 trees

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

   4          B--doshiae        0.00006     (     zero,     0.01249)
   4             5              0.02499     (  0.00587,     0.04412) **
   5            12              0.02486     (  0.00623,     0.04368) **
  12          B--weissii        0.00006     (     zero,     0.00838)
  12            11              0.00350     (     zero,     0.01113)
  11          B-bacillif        0.04553     (  0.02060,     0.07086) **
  11             6              0.01455     (  0.00011,     0.02901) **
   6          B-spp-Deer        0.00308     (     zero,     0.00991)
   6          B-clarridg        0.04257     (  0.01839,     0.06698) **
   5             3              0.02161     (  0.00397,     0.03932) **
   3             1              0.00251     (     zero,     0.00951)
   1          B-quintana        0.01489     (  0.00043,     0.02937) **
   1             9              0.00405     (     zero,     0.01218) *
   9            10              0.01743     (  0.00164,     0.03337) **
  10          B-vinsonii        0.00679     (     zero,     0.01646) **
  10             7              0.01430     (  0.00024,     0.02844) **
   7          B-arupensi        0.00006     (     zero,     0.00770)
   7             8              0.01790     (  0.00193,     0.03390) **
   8          B-birtlesi        0.03346     (  0.01147,     0.05554) **
   8             2              0.01379     (  0.00002,     0.02768) **
   2          B-elizabet        0.01379     (  0.00024,     0.02734) **
   2          B-grahamii        0.00006     (     zero,     0.00932)
   9          B-berhoffi        0.03234     (  0.01088,     0.05377) **
   3          B-henselae        0.01073     (     zero,     0.02291) **
   4          A-tumefaci        0.29285     (  0.21721,     0.37133) **

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


Data set # 15:


Empirical Base Frequencies:

   A       0.30061
   C       0.19152
   G       0.31373
  T(U)     0.19414

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.369850)


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


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

Ln Likelihood = -1139.22205

Examined 1524 trees

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

  11             1              0.02157     (  0.00426,     0.03899) **
   1             8              0.01740     (  0.00197,     0.03282) **
   8             5              0.00659     (     zero,     0.01624) **
   5          B-bacillif        0.02396     (  0.00609,     0.04200) **
   5            12              0.01398     (  0.00022,     0.02773) **
  12          B-spp-Deer        0.00003     (     zero,     0.00954)
  12          B-clarridg        0.04105     (  0.01780,     0.06464) **
   8          B--weissii        0.01371     (  0.00010,     0.02731) **
   1             2              0.00680     (     zero,     0.01677) **
   2             3              0.00003     (     zero,    infinity)
   3          B-quintana        0.01017     (     zero,     0.02167) **
   3          B-vinsonii        0.00674     (     zero,     0.01608) **
   2             9              0.00003     (     zero,    infinity)
   9             4              0.00349     (     zero,     0.01034) **
   4             6              0.00003     (     zero,    infinity)
   6          B-berhoffi        0.03062     (  0.01067,     0.05088) **
   6          B-arupensi        0.00337     (     zero,     0.00998) **
   4             7              0.02151     (  0.00400,     0.03895) **
   7          B-birtlesi        0.04044     (  0.01645,     0.06462) **
   7            10              0.01003     (     zero,     0.02190) **
  10          B-elizabet        0.02046     (  0.00405,     0.03690) **
  10          B-grahamii        0.00006     (     zero,     0.01093)
   9          B-henselae        0.02063     (  0.00418,     0.03729) **
  11          B--doshiae        0.00003     (     zero,     0.01479)
  11          A-tumefaci        0.21545     (  0.15469,     0.27791) **

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


Data set # 16:


Empirical Base Frequencies:

   A       0.28923
   C       0.17618
   G       0.36793
  T(U)     0.16666

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.271639)


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


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

Ln Likelihood = -1119.20528

Examined 1422 trees

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

   3          B-henselae        0.00006     (     zero,     0.00769)
   3             8              0.01070     (     zero,     0.02284) **
   8          B-berhoffi        0.03118     (  0.01082,     0.05182) **
   8             1              0.00329     (     zero,     0.01015)
   1             2              0.00003     (     zero,    infinity)
   2            12              0.00339     (     zero,     0.01028) *
  12          B-quintana        0.01040     (     zero,     0.02217) **
  12             7              0.01979     (  0.00286,     0.03670) **
   7             9              0.00570     (     zero,     0.01597) **
   9          B-grahamii        0.00006     (     zero,    infinity)
   9          B-birtlesi        0.03935     (  0.01611,     0.06292) **
   7          B-elizabet        0.00592     (     zero,     0.01543) *
   2             6              0.00339     (     zero,     0.01007) **
   6          B-vinsonii        0.00342     (     zero,     0.01013) **
   6          B-arupensi        0.01026     (     zero,     0.02187) **
   1             5              0.02066     (  0.00409,     0.03750) **
   5             4              0.01015     (     zero,     0.02203) **
   4            11              0.00006     (     zero,     0.00940)
  11          B-spp-Deer        0.01367     (  0.00027,     0.02709) **
  11          B--weissii        0.00003     (     zero,    infinity)
   4            10              0.01714     (  0.00173,     0.03267) **
  10          B-clarridg        0.03900     (  0.01581,     0.06250) **
  10          B--doshiae        0.01741     (  0.00174,     0.03309) **
   5          B-bacillif        0.02424     (  0.00613,     0.04240) **
   3          A-tumefaci        0.29706     (  0.22093,     0.37679) **

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


Data set # 17:


Empirical Base Frequencies:

   A       0.31271
   C       0.20186
   G       0.32940
  T(U)     0.15602

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.308660)


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


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

Ln Likelihood = -1116.72190

Examined 1308 trees

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

   8             1              0.01652     (  0.00091,     0.03211) **
   1          B-arupensi        0.00976     (     zero,     0.02134) **
   1             5              0.01182     (     zero,     0.02498) **
   5          B-vinsonii        0.02338     (  0.00574,     0.04102) **
   5             9              0.00003     (     zero,     0.00910)
   9             3              0.00710     (     zero,     0.01688) **
   3            10              0.00003     (     zero,    infinity)
  10             4              0.00660     (     zero,     0.01590) **
   4          B-berhoffi        0.01701     (  0.00206,     0.03198) **
   4          B-henselae        0.00679     (     zero,     0.01622) **
  10             2              0.02022     (  0.00401,     0.03647) **
   2             6              0.00003     (     zero,    infinity)
   6             7              0.01003     (     zero,     0.02143) **
   7          B-spp-Deer        0.01012     (     zero,     0.02157) **
   7          B--weissii        0.00006     (     zero,    infinity)
   6          B-bacillif        0.04430     (  0.02007,     0.06867) **
   2          B-clarridg        0.04917     (  0.02331,     0.07536) **
   3          B-quintana        0.01358     (  0.00021,     0.02684) **
   9            11              0.00863     (     zero,     0.02011) **
  11            12              0.00871     (     zero,     0.02025) **
  12          B-elizabet        0.00668     (     zero,     0.01593) **
  12          B-grahamii        0.00006     (     zero,    infinity)
  11          B-birtlesi        0.02435     (  0.00609,     0.04283) **
   8          B--doshiae        0.00003     (     zero,     0.01380)
   8          A-tumefaci        0.23984     (  0.17441,     0.30797) **

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


Data set # 18:


Empirical Base Frequencies:

   A       0.24489
   C       0.21223
   G       0.35337
  T(U)     0.18952

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.446038)


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


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

Ln Likelihood = -1065.29089

Examined 1120 trees

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

  11             4              0.01498     (     zero,     0.03290) **
   4             3              0.00145     (     zero,     0.00800)
   3          B-vinsonii        0.00339     (     zero,     0.01001) **
   3             2              0.01012     (     zero,     0.02157) **
   2             8              0.00006     (     zero,     0.00978)
   8          B-henselae        0.00998     (     zero,     0.02138) **
   8            12              0.00674     (     zero,     0.01610) **
  12          B-quintana        0.00677     (     zero,     0.01612) **
  12             1              0.00313     (     zero,     0.00993)
   1          B-berhoffi        0.01365     (  0.00017,     0.02711) **
   1             7              0.03757     (  0.01536,     0.06010) **
   7            10              0.00581     (     zero,     0.01522) *
  10          B-bacillif        0.02610     (  0.00733,     0.04497) **
  10          B--weissii        0.00523     (     zero,     0.01484) **
   7             6              0.00003     (     zero,    infinity)
   6          B-spp-Deer        0.00333     (     zero,     0.00985) **
   6          B-clarridg        0.03429     (  0.01292,     0.05569) **
   2             5              0.00670     (     zero,     0.01615) **
   5             9              0.01013     (     zero,     0.02168) **
   9          B-elizabet        0.00003     (     zero,    infinity)
   9          B-grahamii        0.00668     (     zero,     0.01593) **
   5          B--doshiae        0.01363     (  0.00023,     0.02704) **
   4          B-arupensi        0.00182     (     zero,     0.00834)
  11          B-birtlesi        0.02721     (  0.00552,     0.04897) **
  11          A-tumefaci        0.28029     (  0.20582,     0.35674) **

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


Data set # 19:


Empirical Base Frequencies:

   A       0.31855
   C       0.17815
   G       0.28506
  T(U)     0.21825

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.403686)


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


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

Ln Likelihood = -1248.76929

Examined  564 trees

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

  10          B--doshiae        0.00003     (     zero,     0.01317)
  10             9              0.03938     (  0.01595,     0.06298) **
   9            11              0.01062     (     zero,     0.02279) **
  11          B-arupensi        0.02080     (  0.00408,     0.03769) **
  11          B-vinsonii        0.00350     (     zero,     0.01060) *
   9             2              0.00235     (     zero,     0.00974)
   2             8              0.00326     (     zero,     0.01000) *
   8             1              0.00003     (     zero,     0.00717)
   1          B-quintana        0.00348     (     zero,     0.01027) **
   1          B-berhoffi        0.04254     (  0.01833,     0.06687) **
   8             5              0.01765     (  0.00199,     0.03337) **
   5             4              0.00663     (     zero,     0.01697) *
   4          B-bacillif        0.04257     (  0.01851,     0.06715) **
   4             6              0.01046     (     zero,     0.02262) **
   6          B--weissii        0.01041     (     zero,     0.02226) **
   6          B-spp-Deer        0.00700     (     zero,     0.01679) **
   5          B-clarridg        0.05104     (  0.02413,     0.07828) **
   2            12              0.00124     (     zero,     0.00814)
  12          B-henselae        0.00347     (     zero,     0.01031) **
  12             7              0.02476     (  0.00499,     0.04464) **
   7          B-birtlesi        0.04385     (  0.01863,     0.06925) **
   7             3              0.01471     (     zero,     0.03064) **
   3          B-elizabet        0.01388     (  0.00028,     0.02752) **
   3          B-grahamii        0.00006     (     zero,    infinity)
  10          A-tumefaci        0.33408     (  0.25178,     0.42026) **

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


Data set # 20:


Empirical Base Frequencies:

   A       0.32619
   C       0.20353
   G       0.29598
  T(U)     0.17430

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.357573)


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


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

Ln Likelihood = -1174.71531

Examined 1330 trees

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

   2          B--doshiae        0.00003     (     zero,     0.01018)
   2            11              0.03528     (  0.01339,     0.05738) **
  11             7              0.00003     (     zero,    infinity)
   7          B-quintana        0.00673     (     zero,     0.01608) **
   7             5              0.00346     (     zero,     0.01026) **
   5          B-vinsonii        0.01022     (     zero,     0.02177) **
   5             6              0.00346     (     zero,     0.01026) **
   6          B-arupensi        0.00003     (     zero,    infinity)
   6             4              0.02084     (  0.00295,     0.03869) **
   4          B-birtlesi        0.03965     (  0.01563,     0.06391) **
   4            12              0.01366     (     zero,     0.02753) **
  12          B-grahamii        0.00370     (     zero,     0.01311)
  12          B-elizabet        0.00644     (     zero,     0.01708) **
  11             8              0.00003     (     zero,    infinity)
   8             9              0.00003     (     zero,    infinity)
   9          B-berhoffi        0.04148     (  0.01797,     0.06529) **
   9             1              0.03461     (  0.01308,     0.05631) **
   1          B-bacillif        0.00674     (     zero,     0.01642) **
   1             3              0.01032     (     zero,     0.02221) **
   3            10              0.00711     (     zero,     0.01711) **
  10          B-clarridg        0.06719     (  0.03683,     0.09821) **
  10          B-spp-Deer        0.00997     (     zero,     0.02163) **
   3          B--weissii        0.00333     (     zero,     0.00996) **
   8          B-henselae        0.00680     (     zero,     0.01622) **
   2          A-tumefaci        0.29929     (  0.22232,     0.37841) **

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


Data set # 21:


Empirical Base Frequencies:

   A       0.25482
   C       0.21414
   G       0.35976
  T(U)     0.17129

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.413636)


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


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

Ln Likelihood = -1218.60801

Examined  572 trees

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

   2             1              0.02213     (  0.00434,     0.04012) **
   1             6              0.02422     (  0.00614,     0.04245) **
   6          B--weissii        0.00003     (     zero,    infinity)
   6            11              0.02114     (  0.00415,     0.03816) **
  11          B-clarridg        0.03864     (  0.01561,     0.06168) **
  11          B-spp-Deer        0.00630     (     zero,     0.01583) **
   1            12              0.01088     (     zero,     0.02370) **
  12          B-arupensi        0.01025     (     zero,     0.02199) **
  12             5              0.01085     (     zero,     0.02325) **
   5             8              0.00339     (     zero,     0.01006) **
   8          B-quintana        0.01018     (     zero,     0.02173) **
   8             9              0.00336     (     zero,     0.01007) **
   9          B-henselae        0.00342     (     zero,     0.01013) **
   9          B-berhoffi        0.01699     (  0.00207,     0.03192) **
   5            10              0.00003     (     zero,    infinity)
  10          B-vinsonii        0.00679     (     zero,     0.01618) **
  10             4              0.01457     (     zero,     0.03025) **
   4          B-bacillif        0.05633     (  0.02800,     0.08474) **
   4             3              0.01546     (     zero,     0.03313) **
   3             7              0.01179     (     zero,     0.02676) **
   7          B-elizabet        0.01629     (  0.00088,     0.03181) **
   7          B-grahamii        0.00750     (     zero,     0.01886) *
   3          B-birtlesi        0.03934     (  0.01472,     0.06425) **
   2          B--doshiae        0.00006     (     zero,     0.01098)
   2          A-tumefaci        0.32341     (  0.24163,     0.40879) **

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


Data set # 22:


Empirical Base Frequencies:

   A       0.30823
   C       0.21058
   G       0.32782
  T(U)     0.15337

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.331345)


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


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

Ln Likelihood = -1147.65283

Examined  494 trees

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

  12          B--doshiae        0.00006     (     zero,     0.00972)
  12            10              0.03662     (  0.01378,     0.05964) **
  10             9              0.01032     (     zero,     0.02277) **
   9             8              0.01411     (  0.00021,     0.02793) **
   8          B-henselae        0.00340     (     zero,     0.01011) **
   8             7              0.00003     (     zero,    infinity)
   7          B-quintana        0.00349     (     zero,     0.01027) **
   7             1              0.00672     (     zero,     0.01663) **
   1          B-berhoffi        0.02839     (  0.00862,     0.04834) **
   1             4              0.02869     (  0.00871,     0.04903) **
   4          B-bacillif        0.03909     (  0.01597,     0.06263) **
   4             3              0.00638     (     zero,     0.01633) *
   3          B--weissii        0.00333     (     zero,     0.01003) *
   3             2              0.00702     (     zero,     0.01672) **
   2          B-spp-Deer        0.00006     (     zero,    infinity)
   2          B-clarridg        0.04956     (  0.02353,     0.07599) **
   9             5              0.00339     (     zero,     0.01040) *
   5          B-birtlesi        0.03605     (  0.01367,     0.05864) **
   5             6              0.00361     (     zero,     0.01067) **
   6          B-vinsonii        0.01058     (     zero,     0.02255) **
   6          B-arupensi        0.00325     (     zero,     0.01003)
  10            11              0.02430     (  0.00573,     0.04313) **
  11          B-elizabet        0.00657     (     zero,     0.01623) **
  11          B-grahamii        0.00419     (     zero,     0.01238) *
  12          A-tumefaci        0.23960     (  0.17363,     0.30807) **

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


Data set # 23:


Empirical Base Frequencies:

   A       0.31722
   C       0.19065
   G       0.28073
  T(U)     0.21140

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.410473)


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


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

Ln Likelihood = -1319.70465

Examined 1348 trees

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

   2          B-birtlesi        0.03914     (  0.01168,     0.06664) **
   2             5              0.03351     (  0.00798,     0.05910) **
   5             3              0.00508     (     zero,     0.01417) *
   3             7              0.00958     (     zero,     0.02113) **
   7             1              0.00003     (     zero,     0.00722)
   1          B-berhoffi        0.02576     (  0.00686,     0.04468) **
   1             8              0.02805     (  0.00825,     0.04813) **
   8          B-bacillif        0.02954     (  0.00892,     0.05054) **
   8            11              0.02319     (  0.00372,     0.04268) **
  11             9              0.01700     (  0.00116,     0.03294) **
   9          B--doshiae        0.04453     (  0.01955,     0.06986) **
   9            12              0.00718     (     zero,     0.01899) *
  12          B--weissii        0.00006     (     zero,     0.00802)
  12          B-spp-Deer        0.01016     (     zero,     0.02166) **
  11          B-clarridg        0.05027     (  0.02331,     0.07756) **
   7            10              0.02250     (  0.00488,     0.04013) **
  10          B-grahamii        0.00334     (     zero,     0.00992) **
  10          B-elizabet        0.00006     (     zero,     0.00807)
   3             4              0.00248     (     zero,     0.01277)
   4          B-henselae        0.01301     (     zero,     0.02638) **
   4          B-quintana        0.01001     (     zero,     0.02157) **
   5             6              0.00719     (     zero,     0.01737) **
   6          B-arupensi        0.02723     (  0.00831,     0.04640) **
   6          B-vinsonii        0.01702     (  0.00193,     0.03208) **
   2          A-tumefaci        0.30476     (  0.22649,     0.38536) **

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


Data set # 24:


Empirical Base Frequencies:

   A       0.28090
   C       0.19893
   G       0.33959
  T(U)     0.18058

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.367410)


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


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

Ln Likelihood = -1242.70857

Examined  590 trees

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

   7          B--doshiae        0.00312     (     zero,     0.01590)
   7             3              0.02145     (  0.00334,     0.03960) **
   3             4              0.01716     (  0.00217,     0.03231) **
   4            12              0.00005     (     zero,    infinity)
  12             1              0.01665     (  0.00177,     0.03170) **
   1          B--weissii        0.01410     (  0.00028,     0.02797) **
   1             8              0.00323     (     zero,     0.01022)
   8          B-clarridg        0.04506     (  0.02012,     0.06997) **
   8          B-spp-Deer        0.00726     (     zero,     0.01741) **
  12          B-quintana        0.00336     (     zero,     0.00998) **
   4             6              0.00782     (     zero,     0.01898) **
   6          B-berhoffi        0.03343     (  0.01194,     0.05524) **
   6          B-henselae        0.01757     (  0.00210,     0.03307) **
   3             2              0.00003     (     zero,     0.00816)
   2             9              0.01743     (  0.00187,     0.03306) **
   9            11              0.01749     (  0.00200,     0.03302) **
  11          B-birtlesi        0.05690     (  0.02905,     0.08542) **
  11          B-grahamii        0.00006     (     zero,     0.00774)
   9            10              0.01362     (  0.00002,     0.02719) **
  10          B-bacillif        0.05217     (  0.02548,     0.07887) **
  10          B-elizabet        0.00003     (     zero,     0.00819)
   2             5              0.00687     (     zero,     0.01637) **
   5          B-vinsonii        0.01046     (     zero,     0.02227) **
   5          B-arupensi        0.00313     (     zero,     0.00976)
   7          A-tumefaci        0.30962     (  0.23024,     0.39077) **

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


Data set # 25:


Empirical Base Frequencies:

   A       0.27868
   C       0.20693
   G       0.32867
  T(U)     0.18572

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.395038)


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


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

Ln Likelihood = -1089.22552

Examined  618 trees

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

   9             4              0.02242     (  0.00242,     0.04236) **
   4          B--doshiae        0.01366     (  0.00005,     0.02721) **
   4             8              0.00309     (     zero,     0.01011)
   8             5              0.00336     (     zero,     0.00991) **
   5          B-quintana        0.00667     (     zero,     0.01590) **
   5             2              0.00003     (     zero,     0.00789)
   2          B-henselae        0.00333     (     zero,     0.00986) **
   2             1              0.01337     (  0.00004,     0.02672) **
   1          B-berhoffi        0.01356     (  0.00018,     0.02704) **
   1            11              0.02361     (  0.00605,     0.04133) **
  11          B--weissii        0.00003     (     zero,     0.00825)
  11             6              0.01026     (     zero,     0.02194) **
   6             7              0.00308     (     zero,     0.00980)
   7          B-spp-Deer        0.00003     (     zero,    infinity)
   7          B-bacillif        0.02002     (  0.00399,     0.03611) **
   6          B-clarridg        0.05190     (  0.02546,     0.07857) **
   8            12              0.00335     (     zero,     0.00996) **
  12             3              0.01338     (  0.00025,     0.02651) **
   3            10              0.03379     (  0.01261,     0.05515) **
  10          B-grahamii        0.00356     (     zero,     0.01112)
  10          B-elizabet        0.01340     (  0.00007,     0.02679) **
   3          B-arupensi        0.00006     (     zero,     0.00765)
  12          B-vinsonii        0.00332     (     zero,     0.00988) **
   9          B-birtlesi        0.03822     (  0.01334,     0.06327) **
   9          A-tumefaci        0.19278     (  0.13557,     0.25162) **

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


Data set # 26:


Empirical Base Frequencies:

   A       0.30039
   C       0.19237
   G       0.34745
  T(U)     0.15979

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.293048)


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


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

Ln Likelihood = -1082.11718

Examined  840 trees

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

   6             7              0.01426     (  0.00001,     0.02851) **
   7             2              0.01045     (     zero,     0.02264) **
   2             9              0.00003     (     zero,     0.00903)
   9             3              0.00703     (     zero,     0.01684) **
   3          B-spp-Deer        0.00675     (     zero,     0.01640) **
   3          B-clarridg        0.04561     (  0.02054,     0.07073) **
   9          B--weissii        0.00349     (     zero,     0.01033) **
   2             4              0.01030     (     zero,     0.02212) **
   4          B-henselae        0.01025     (     zero,     0.02185) **
   4            11              0.00003     (     zero,    infinity)
  11            12              0.00536     (     zero,     0.01506)
  12          B-quintana        0.00839     (     zero,     0.01972) **
  12            10              0.01633     (  0.00083,     0.03189) **
  10          B-birtlesi        0.04601     (  0.02021,     0.07227) **
  10             1              0.00954     (     zero,     0.02244) **
   1          B-elizabet        0.02042     (  0.00410,     0.03692) **
   1          B-grahamii        0.00003     (     zero,     0.00851)
  11             8              0.00675     (     zero,     0.01615) **
   8             5              0.00006     (     zero,     0.00821)
   5          B-vinsonii        0.00338     (     zero,     0.01000) **
   5          B-arupensi        0.00679     (     zero,     0.01621) **
   8          B-berhoffi        0.02407     (  0.00617,     0.04197) **
   7          B-bacillif        0.03108     (  0.01056,     0.05168) **
   6          B--doshiae        0.00003     (     zero,     0.01091)
   6          A-tumefaci        0.21825     (  0.15616,     0.28191) **

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


Data set # 27:


Empirical Base Frequencies:

   A       0.28197
   C       0.19440
   G       0.32775
  T(U)     0.19589

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.386504)


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


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

Ln Likelihood = -1283.03839

Examined  840 trees

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

  11          B--doshiae        0.00006     (     zero,     0.01248)
  11             3              0.03894     (  0.01593,     0.06227) **
   3             9              0.00003     (     zero,     0.00721)
   9            12              0.00491     (     zero,     0.01455)
  12          B-quintana        0.02752     (  0.00821,     0.04684) **
  12          B-henselae        0.01578     (  0.00058,     0.03092) **
   9             7              0.00696     (     zero,     0.01664) **
   7          B-berhoffi        0.04873     (  0.02305,     0.07470) **
   7             8              0.00326     (     zero,     0.01007)
   8          B-vinsonii        0.00006     (     zero,    infinity)
   8          B-arupensi        0.01017     (     zero,     0.02169) **
   3             1              0.01768     (  0.00191,     0.03344) **
   1             2              0.01722     (  0.00148,     0.03296) **
   2             6              0.02784     (  0.00839,     0.04749) **
   6            10              0.00978     (     zero,     0.02163) **
  10          B-clarridg        0.05704     (  0.02899,     0.08569) **
  10          B--weissii        0.02101     (  0.00407,     0.03815) **
   6          B-spp-Deer        0.00003     (     zero,     0.00950)
   2          B-bacillif        0.02404     (  0.00601,     0.04225) **
   1             5              0.02062     (  0.00337,     0.03786) **
   5             4              0.01324     (     zero,     0.02720) **
   4          B-birtlesi        0.04765     (  0.02165,     0.07388) **
   4          B-grahamii        0.00303     (     zero,     0.00984)
   5          B-elizabet        0.00176     (     zero,     0.00872)
  11          A-tumefaci        0.25222     (  0.18451,     0.32334) **

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


Data set # 28:


Empirical Base Frequencies:

   A       0.28474
   C       0.19232
   G       0.31079
  T(U)     0.21214

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.412789)


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


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

Ln Likelihood = -1260.12576

Examined  892 trees

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

  12            10              0.00006     (     zero,     0.01165)
  10          B-vinsonii        0.00006     (     zero,    infinity)
  10             1              0.00661     (     zero,     0.01614) **
   1          B--doshiae        0.02396     (  0.00619,     0.04191) **
   1             3              0.01710     (  0.00198,     0.03223) **
   3          B-henselae        0.00006     (     zero,     0.00991)
   3             5              0.00674     (     zero,     0.01623) **
   5             6              0.00307     (     zero,     0.01075)
   6             9              0.03165     (  0.01054,     0.05281) **
   9             4              0.00702     (     zero,     0.01746) **
   4          B-clarridg        0.03467     (  0.01285,     0.05674) **
   4            11              0.00736     (     zero,     0.01795) **
  11          B-bacillif        0.03852     (  0.01573,     0.06156) **
  11          B-spp-Deer        0.00618     (     zero,     0.01580) **
   9          B--weissii        0.02019     (  0.00319,     0.03733) **
   6          B-berhoffi        0.03105     (  0.01054,     0.05183) **
   5          B-quintana        0.02400     (  0.00626,     0.04196) **
  12             7              0.01051     (     zero,     0.02255) **
   7             2              0.01603     (     zero,     0.03352) **
   2             8              0.02408     (  0.00584,     0.04241) **
   8          B-grahamii        0.00709     (     zero,     0.02041)
   8          B-elizabet        0.01315     (     zero,     0.02838) **
   2          B-birtlesi        0.04277     (  0.01666,     0.06892) **
   7          B-arupensi        0.00340     (     zero,     0.01023) *
  12          A-tumefaci        0.30155     (  0.22455,     0.38088) **

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


Data set # 29:


Empirical Base Frequencies:

   A       0.28344
   C       0.24633
   G       0.29157
  T(U)     0.17866

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.464325)


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


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

Ln Likelihood = -1314.31073

Examined  564 trees

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

   9          B-birtlesi        0.03210     (  0.00510,     0.05934) **
   9             7              0.04288     (  0.01421,     0.07153) **
   7             6              0.01160     (     zero,     0.02525) **
   6            12              0.01420     (  0.00025,     0.02821) **
  12             1              0.00331     (     zero,     0.01048)
   1          B--doshiae        0.01062     (     zero,     0.02270) **
   1             5              0.02132     (  0.00411,     0.03851) **
   5             3              0.00710     (     zero,     0.01710) **
   3          B-berhoffi        0.03932     (  0.01573,     0.06281) **
   3          B-quintana        0.01434     (  0.00018,     0.02852) **
   5             2              0.00006     (     zero,     0.01036)
   2          B-henselae        0.01048     (     zero,     0.02247) **
   2             8              0.03195     (  0.01099,     0.05300) **
   8            10              0.02616     (  0.00673,     0.04584) **
  10          B-spp-Deer        0.00953     (     zero,     0.02183) **
  10          B-clarridg        0.07113     (  0.03888,     0.10396) **
   8          B--weissii        0.00006     (     zero,    infinity)
  12          B-vinsonii        0.02138     (  0.00422,     0.03858) **
   6          B-arupensi        0.00006     (     zero,     0.00751)
   7             4              0.01084     (     zero,     0.02351) **
   4            11              0.01497     (  0.00007,     0.02977) **
  11          B-bacillif        0.06105     (  0.03186,     0.09068) **
  11          B-elizabet        0.00003     (     zero,    infinity)
   4          B-grahamii        0.00605     (     zero,     0.01613)
   9          A-tumefaci        0.25979     (  0.18763,     0.33382) **

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


Data set # 30:


Empirical Base Frequencies:

   A       0.29555
   C       0.21466
   G       0.30958
  T(U)     0.18022

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.395521)


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


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

Ln Likelihood = -1121.63896

Examined 1146 trees

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

  11          B-henselae        0.00003     (     zero,    infinity)
  11             2              0.00670     (     zero,     0.01600) **
   2            12              0.00004     (     zero,    infinity)
  12            10              0.02858     (  0.00844,     0.04863) **
  10             7              0.01238     (     zero,     0.02615) **
   7          B-elizabet        0.01670     (  0.00203,     0.03136) **
   7          B-grahamii        0.00003     (     zero,    infinity)
  10          B-birtlesi        0.03812     (  0.01539,     0.06115) **
  12             4              0.01993     (  0.00403,     0.03600) **
   4             9              0.00006     (     zero,     0.00755)
   9          B-bacillif        0.04382     (  0.01996,     0.06802) **
   9             6              0.00686     (     zero,     0.01639) **
   6          B-clarridg        0.04480     (  0.02036,     0.06951) **
   6          B-spp-Deer        0.00313     (     zero,     0.00969)
   4          B--weissii        0.00006     (     zero,    infinity)
   2             3              0.00006     (     zero,     0.00750)
   3             1              0.00657     (     zero,     0.01588) **
   1             5              0.00678     (     zero,     0.01627) **
   5          B-arupensi        0.00668     (     zero,     0.01597) **
   5          B-vinsonii        0.00671     (     zero,     0.01600) **
   1          B--doshiae        0.02698     (  0.00829,     0.04590) **
   3             8              0.00330     (     zero,     0.00980) **
   8          B-quintana        0.00006     (     zero,    infinity)
   8          B-berhoffi        0.02011     (  0.00400,     0.03627) **
  11          A-tumefaci        0.24347     (  0.17810,     0.31047) **

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


Data set # 31:


Empirical Base Frequencies:

   A       0.25504
   C       0.24347
   G       0.30887
  T(U)     0.19263

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.481029)


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


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

Ln Likelihood = -1118.31785

Examined  524 trees

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

  11          B-henselae        0.00003     (     zero,     0.00691)
  11            10              0.00349     (     zero,     0.01033) **
  10             9              0.00003     (     zero,    infinity)
   9             7              0.00003     (     zero,    infinity)
   7          B-vinsonii        0.00676     (     zero,     0.01614) **
   7             2              0.01062     (     zero,     0.02271) **
   2          B-berhoffi        0.01358     (  0.00029,     0.02704) **
   2             1              0.00698     (     zero,     0.01680) **
   1             5              0.02471     (  0.00634,     0.04306) **
   5             6              0.01045     (     zero,     0.02227) **
   6          B-birtlesi        0.06321     (  0.03299,     0.09375) **
   6          B-elizabet        0.00006     (     zero,    infinity)
   5          B-grahamii        0.00006     (     zero,    infinity)
   1          B-arupensi        0.00006     (     zero,     0.00754)
   9          B-quintana        0.00006     (     zero,    infinity)
  10            12              0.02071     (  0.00394,     0.03753) **
  12          B--doshiae        0.02075     (  0.00393,     0.03757) **
  12             3              0.01711     (  0.00182,     0.03240) **
   3             4              0.01305     (     zero,     0.02669) **
   4             8              0.00664     (     zero,     0.01663) **
   8          B-bacillif        0.05517     (  0.02743,     0.08289) **
   8          B-spp-Deer        0.00746     (     zero,     0.01810) **
   4          B-clarridg        0.03569     (  0.01349,     0.05801) **
   3          B--weissii        0.00003     (     zero,    infinity)
  11          A-tumefaci        0.24678     (  0.17956,     0.31608) **

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


Data set # 32:


Empirical Base Frequencies:

   A       0.25600
   C       0.19630
   G       0.33126
  T(U)     0.21643

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.445282)


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


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

Ln Likelihood = -1115.32003

Examined  876 trees

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

   6            12              0.02685     (  0.00487,     0.04891) **
  12             5              0.00637     (     zero,     0.01852)
   5             1              0.00401     (     zero,     0.01549)
   1             8              0.00006     (     zero,    infinity)
   8             3              0.00004     (     zero,    infinity)
   3          B-quintana        0.01015     (     zero,     0.02163) **
   3          B-vinsonii        0.01015     (     zero,     0.02165) **
   8             7              0.00336     (     zero,     0.00995) **
   7             9              0.02736     (  0.00803,     0.04667) **
   9          B-elizabet        0.01361     (  0.00008,     0.02721) **
   9          B-grahamii        0.00374     (     zero,     0.01155)
   7          B-arupensi        0.00003     (     zero,    infinity)
   1            10              0.00418     (     zero,     0.01288)
  10          B-berhoffi        0.02658     (  0.00754,     0.04588) **
  10             2              0.02073     (  0.00409,     0.03751) **
   2             4              0.00773     (     zero,     0.01856) **
   4            11              0.00687     (     zero,     0.01643) **
  11          B-clarridg        0.03128     (  0.01073,     0.05183) **
  11          B-spp-Deer        0.00003     (     zero,    infinity)
   4          B-bacillif        0.02398     (  0.00615,     0.04186) **
   2          B--weissii        0.00576     (     zero,     0.01523) *
   5          B-henselae        0.01325     (     zero,     0.02674) **
  12          B--doshiae        0.01394     (     zero,     0.02794) **
   6          B-birtlesi        0.02781     (  0.00519,     0.05049) **
   6          A-tumefaci        0.25364     (  0.18485,     0.32540) **

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


Data set # 33:


Empirical Base Frequencies:

   A       0.29655
   C       0.25514
   G       0.24219
  T(U)     0.20613

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.506466)


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


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

Ln Likelihood = -1176.57316

Examined  638 trees

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

  12             4              0.02180     (  0.00092,     0.04265) **
   4          B-arupensi        0.01023     (     zero,     0.02185) **
   4            11              0.00006     (     zero,     0.01018)
  11          B-vinsonii        0.00006     (     zero,    infinity)
  11             3              0.01691     (  0.00200,     0.03186) **
   3             2              0.00006     (     zero,     0.00722)
   2             6              0.00670     (     zero,     0.01621) **
   6          B-quintana        0.00703     (     zero,     0.01685) **
   6             5              0.02746     (  0.00826,     0.04667) **
   5          B-grahamii        0.00003     (     zero,    infinity)
   5          B-elizabet        0.01019     (     zero,     0.02169) **
   2            10              0.00340     (     zero,     0.01023) *
  10          B-henselae        0.00346     (     zero,     0.01027) **
  10          B-berhoffi        0.03461     (  0.01313,     0.05632) **
   3             8              0.01370     (     zero,     0.02750) **
   8             7              0.01374     (     zero,     0.02759) **
   7             1              0.01008     (     zero,     0.02167) **
   1             9              0.00694     (     zero,     0.01664) **
   9          B-clarridg        0.05572     (  0.02809,     0.08336) **
   9          B-spp-Deer        0.00003     (     zero,     0.00787)
   1          B-bacillif        0.03445     (  0.01294,     0.05597) **
   7          B--weissii        0.00006     (     zero,    infinity)
   8          B--doshiae        0.04198     (  0.01805,     0.06620) **
  12          B-birtlesi        0.03352     (  0.00901,     0.05803) **
  12          A-tumefaci        0.26367     (  0.19243,     0.33676) **

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


Data set # 34:


Empirical Base Frequencies:

   A       0.28259
   C       0.19613
   G       0.32705
  T(U)     0.19423

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.386276)


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


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

Ln Likelihood = -1236.45427

Examined  876 trees

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

  12             8              0.02077     (  0.00405,     0.03749) **
   8             4              0.00313     (     zero,     0.01003)
   4            10              0.02267     (  0.00414,     0.04117) **
  10          B-birtlesi        0.03923     (  0.01572,     0.06287) **
  10             6              0.02950     (  0.00907,     0.05007) **
   6          B-elizabet        0.02360     (  0.00607,     0.04117) **
   6          B-grahamii        0.00006     (     zero,     0.01065)
   4             1              0.01025     (     zero,     0.02196) **
   1             7              0.00328     (     zero,     0.00992) *
   7          B-quintana        0.00672     (     zero,     0.01604) **
   7             2              0.00691     (     zero,     0.01720) **
   2             3              0.02759     (  0.00829,     0.04692) **
   3          B--weissii        0.00966     (     zero,     0.02121) **
   3            11              0.00374     (     zero,     0.01135) *
  11             5              0.00003     (     zero,     0.00716)
   5          B-clarridg        0.05217     (  0.02578,     0.07917) **
   5          B-spp-Deer        0.00003     (     zero,    infinity)
  11          B-bacillif        0.05480     (  0.02788,     0.08221) **
   2          B-berhoffi        0.03051     (  0.01009,     0.05096) **
   1          B-henselae        0.00687     (     zero,     0.01644) **
   8             9              0.00687     (     zero,     0.01641) **
   9          B-vinsonii        0.01012     (     zero,     0.02158) **
   9          B-arupensi        0.00327     (     zero,     0.00983) *
  12          B--doshiae        0.00006     (     zero,     0.01166)
  12          A-tumefaci        0.27523     (  0.20359,     0.34873) **

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


Data set # 35:


Empirical Base Frequencies:

   A       0.30891
   C       0.23216
   G       0.29735
  T(U)     0.16159

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.410371)


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


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

Ln Likelihood = -1257.08713

Examined 2038 trees

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

   8          B--doshiae        0.00006     (     zero,     0.01430)
   8             4              0.05018     (  0.02363,     0.07679) **
   4            12              0.01759     (  0.00215,     0.03314) **
  12             7              0.01560     (     zero,     0.03181) **
   7             1              0.01355     (     zero,     0.02746) **
   1          B-elizabet        0.01064     (     zero,     0.02373) **
   1          B-grahamii        0.00305     (     zero,     0.01370)
   7          B-birtlesi        0.05054     (  0.02298,     0.07839) **
  12          B-arupensi        0.00331     (     zero,     0.01024)
   4             5              0.00003     (     zero,     0.00878)
   5          B-vinsonii        0.01033     (     zero,     0.02201) **
   5            11              0.00595     (     zero,     0.01638) **
  11          B-henselae        0.01577     (  0.00051,     0.03093) **
  11            10              0.00595     (     zero,     0.01557) *
  10          B-quintana        0.00351     (     zero,     0.01035) **
  10             9              0.00716     (     zero,     0.01756) **
   9          B-berhoffi        0.03470     (  0.01290,     0.05678) **
   9             3              0.01785     (  0.00183,     0.03389) **
   3             2              0.00458     (     zero,     0.01384)
   2          B-bacillif        0.05932     (  0.03038,     0.08853) **
   2             6              0.00376     (     zero,     0.01138) *
   6          B-spp-Deer        0.01235     (     zero,     0.02580) **
   6          B-clarridg        0.03994     (  0.01640,     0.06382) **
   3          B--weissii        0.01662     (  0.00130,     0.03215) **
   8          A-tumefaci        0.27442     (  0.20128,     0.35088) **

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


Data set # 36:


Empirical Base Frequencies:

   A       0.27177
   C       0.24093
   G       0.26857
  T(U)     0.21873

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.485852)


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


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

Ln Likelihood = -1222.07712

Examined  614 trees

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

   8          B--doshiae        0.00006     (     zero,     0.01747)
   8            10              0.03889     (  0.01528,     0.06248) **
  10             3              0.01365     (     zero,     0.02775) **
   3          B-clarridg        0.04477     (  0.02002,     0.06999) **
   3            12              0.01416     (     zero,     0.02851) **
  12          B--weissii        0.00006     (     zero,     0.00773)
  12             5              0.01350     (     zero,     0.02706) **
   5          B-spp-Deer        0.01010     (     zero,     0.02192) **
   5          B-bacillif        0.04848     (  0.02303,     0.07441) **
  10             7              0.01120     (     zero,     0.02426) **
   7            11              0.00003     (     zero,     0.00736)
  11             2              0.00356     (     zero,     0.01057) **
   2          B-berhoffi        0.02706     (  0.00836,     0.04606) **
   2             9              0.00703     (     zero,     0.01683) **
   9             6              0.00704     (     zero,     0.01677) **
   6             4              0.02907     (  0.00880,     0.04958) **
   4          B-birtlesi        0.05249     (  0.02499,     0.08057) **
   4             1              0.00946     (     zero,     0.02135) **
   1          B-grahamii        0.00003     (     zero,     0.01035)
   1          B-elizabet        0.01681     (  0.00205,     0.03160) **
   6          B-arupensi        0.00006     (     zero,    infinity)
   9          B-vinsonii        0.00332     (     zero,     0.00991) **
  11          B-quintana        0.01007     (     zero,     0.02149) **
   7          B-henselae        0.01696     (  0.00207,     0.03186) **
   8          A-tumefaci        0.23034     (  0.16664,     0.29668) **

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


Data set # 37:


Empirical Base Frequencies:

   A       0.29297
   C       0.22408
   G       0.31435
  T(U)     0.16860

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.400396)


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


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

Ln Likelihood = -1335.45810

Examined 1038 trees

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

   7          B-henselae        0.00631     (     zero,     0.01674) *
   7            11              0.01475     (     zero,     0.02970) **
  11             3              0.00006     (     zero,     0.00756)
   3             2              0.01429     (  0.00017,     0.02846) **
   2            10              0.00854     (     zero,     0.02025) **
  10          B--doshiae        0.03359     (  0.01182,     0.05548) **
  10             6              0.00695     (     zero,     0.01696) **
   6          B-arupensi        0.00512     (     zero,     0.01443) *
   6          B-vinsonii        0.01916     (  0.00275,     0.03570) **
   2             1              0.01993     (  0.00240,     0.03747) **
   1          B-birtlesi        0.06283     (  0.03271,     0.09345) **
   1             9              0.01522     (     zero,     0.03055) **
   9          B-elizabet        0.02759     (  0.00851,     0.04693) **
   9          B-grahamii        0.00006     (     zero,     0.00960)
   3             5              0.01914     (  0.00272,     0.03559) **
   5          B--weissii        0.00506     (     zero,     0.01427) *
   5             8              0.01376     (     zero,     0.02954) **
   8          B-bacillif        0.05931     (  0.02983,     0.08924) **
   8             4              0.01735     (  0.00125,     0.03363) **
   4          B-clarridg        0.05336     (  0.02559,     0.08159) **
   4          B-spp-Deer        0.00671     (     zero,     0.01878)
  11            12              0.00695     (     zero,     0.01663) **
  12          B-berhoffi        0.02078     (  0.00413,     0.03754) **
  12          B-quintana        0.00689     (     zero,     0.01651) **
   7          A-tumefaci        0.33134     (  0.24811,     0.41725) **

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


Data set # 38:


Empirical Base Frequencies:

   A       0.31355
   C       0.21918
   G       0.26673
  T(U)     0.20055

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.444754)


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


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

Ln Likelihood = -1278.84199

Examined  578 trees

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

   5          B--doshiae        0.00003     (     zero,     0.01399)
   5             4              0.04256     (  0.01717,     0.06835) **
   4             6              0.02684     (  0.00636,     0.04731) **
   6            11              0.01110     (     zero,     0.02550) **
  11            12              0.00782     (     zero,     0.01963) **
  12          B-arupensi        0.00981     (     zero,     0.02175) **
  12          B-vinsonii        0.01122     (     zero,     0.02389) **
  11             9              0.02039     (  0.00219,     0.03862) **
   9            10              0.02198     (  0.00316,     0.04094) **
  10          B-grahamii        0.00006     (     zero,     0.00826)
  10          B-elizabet        0.00693     (     zero,     0.01655) **
   9          B-birtlesi        0.04410     (  0.01744,     0.07078) **
   6             3              0.00006     (     zero,     0.00996)
   3             8              0.00380     (     zero,     0.01122) **
   8          B-berhoffi        0.03882     (  0.01575,     0.06234) **
   8          B-henselae        0.00003     (     zero,    infinity)
   3          B-quintana        0.02111     (  0.00426,     0.03813) **
   4             1              0.02481     (  0.00586,     0.04403) **
   1          B--weissii        0.00351     (     zero,     0.01063) *
   1             7              0.00588     (     zero,     0.01598) *
   7             2              0.00699     (     zero,     0.01719) **
   2          B-spp-Deer        0.00491     (     zero,     0.01429) *
   2          B-bacillif        0.05250     (  0.02499,     0.08005) **
   7          B-clarridg        0.04781     (  0.02160,     0.07408) **
   5          A-tumefaci        0.31470     (  0.23516,     0.39740) **

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


Data set # 39:


Empirical Base Frequencies:

   A       0.27861
   C       0.24050
   G       0.32960
  T(U)     0.15128

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.428581)


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


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

Ln Likelihood = -1308.36666

Examined  928 trees

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

  12          B--doshiae        0.01051     (     zero,     0.03033)
  12             9              0.03480     (  0.01046,     0.05915) **
   9          B-vinsonii        0.00003     (     zero,    infinity)
   9             5              0.00006     (     zero,    infinity)
   5             6              0.01029     (     zero,     0.02192) **
   6            10              0.01125     (     zero,     0.02501) **
  10          B-bacillif        0.07195     (  0.04048,     0.10427) **
  10             7              0.02340     (  0.00488,     0.04206) **
   7             3              0.02153     (  0.00368,     0.03940) **
   3          B-birtlesi        0.05791     (  0.02939,     0.08679) **
   3          B-grahamii        0.00249     (     zero,     0.00957)
   7          B-elizabet        0.00451     (     zero,     0.01513)
   6          B-arupensi        0.00003     (     zero,    infinity)
   5             2              0.01332     (  0.00019,     0.02652) **
   2             4              0.00006     (     zero,     0.01002)
   4          B-henselae        0.02042     (  0.00408,     0.03689) **
   4             1              0.01689     (  0.00206,     0.03172) **
   1          B--weissii        0.00003     (     zero,     0.00809)
   1            11              0.01394     (  0.00006,     0.02789) **
  11          B-spp-Deer        0.01645     (  0.00155,     0.03151) **
  11          B-clarridg        0.05555     (  0.02799,     0.08326) **
   2             8              0.00675     (     zero,     0.01629) **
   8          B-berhoffi        0.02700     (  0.00828,     0.04602) **
   8          B-quintana        0.01697     (  0.00200,     0.03197) **
  12          A-tumefaci        0.28110     (  0.20694,     0.35748) **

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


Data set # 40:


Empirical Base Frequencies:

   A       0.30165
   C       0.23248
   G       0.28474
  T(U)     0.18113

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.438153)


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


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

Ln Likelihood = -1131.28933

Examined  558 trees

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

   7          B-birtlesi        0.02223     (  0.00252,     0.04205) **
   7             9              0.01661     (     zero,     0.03417) **
   9             5              0.02040     (  0.00401,     0.03686) **
   5          B-grahamii        0.00332     (     zero,     0.01031)
   5          B-elizabet        0.00332     (     zero,     0.01031)
   9             3              0.00694     (     zero,     0.01688) **
   3             4              0.01000     (     zero,     0.02132) **
   4             6              0.00475     (     zero,     0.01335) **
   6            12              0.00463     (     zero,     0.01391)
  12             1              0.00764     (     zero,     0.01834) **
   1          B-henselae        0.00624     (     zero,     0.01570) **
   1          B-berhoffi        0.03108     (  0.01026,     0.05183) **
  12          B-quintana        0.01785     (  0.00228,     0.03348) **
   6             2              0.00661     (     zero,     0.01604) **
   2          B--doshiae        0.01501     (  0.00056,     0.02953) **
   2             8              0.01909     (  0.00287,     0.03553) **
   8            11              0.00327     (     zero,     0.01000) *
  11          B-bacillif        0.03388     (  0.01286,     0.05520) **
  11            10              0.00339     (     zero,     0.01022) *
  10          B-spp-Deer        0.00003     (     zero,    infinity)
  10          B-clarridg        0.04115     (  0.01785,     0.06478) **
   8          B--weissii        0.00649     (     zero,     0.01593) **
   4          B-vinsonii        0.00006     (     zero,    infinity)
   3          B-arupensi        0.00006     (     zero,    infinity)
   7          A-tumefaci        0.26580     (  0.19612,     0.33883) **

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


Data set # 41:


Empirical Base Frequencies:

   A       0.25200
   C       0.23382
   G       0.34971
  T(U)     0.16447

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.451462)


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


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

Ln Likelihood = -1126.05622

Examined  780 trees

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

   5          B--doshiae        0.00006     (     zero,     0.01031)
   5             3              0.00544     (     zero,     0.01657)
   3             4              0.01012     (     zero,     0.02213) **
   4             6              0.01366     (     zero,     0.02840) **
   6          B-spp-Deer        0.01356     (  0.00026,     0.02688) **
   6          B--weissii        0.00006     (     zero,     0.00781)
   4          B-clarridg        0.04213     (  0.01751,     0.06675) **
   3             7              0.02063     (  0.00247,     0.03868) **
   7            12              0.00006     (     zero,    infinity)
  12             2              0.00003     (     zero,     0.00788)
   2          B-henselae        0.01708     (  0.00204,     0.03205) **
   2             8              0.00743     (     zero,     0.01776) **
   8          B-berhoffi        0.02056     (  0.00407,     0.03709) **
   8            10              0.00297     (     zero,     0.01055)
  10            11              0.01015     (     zero,     0.02180) **
  11          B-bacillif        0.04733     (  0.02215,     0.07288) **
  11          B-elizabet        0.00403     (     zero,     0.01198) *
  10             9              0.01168     (     zero,     0.02489) **
   9          B-birtlesi        0.07284     (  0.04012,     0.10610) **
   9          B-grahamii        0.00003     (     zero,    infinity)
  12             1              0.00679     (     zero,     0.01622) **
   1          B-arupensi        0.01018     (     zero,     0.02173) **
   1          B-vinsonii        0.00336     (     zero,     0.01002) **
   7          B-quintana        0.00677     (     zero,     0.01616) **
   5          A-tumefaci        0.21308     (  0.15128,     0.27629) **

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


Data set # 42:


Empirical Base Frequencies:

   A       0.27477
   C       0.25144
   G       0.30257
  T(U)     0.17121

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.471769)


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


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

Ln Likelihood = -1190.38145

Examined  650 trees

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

   9          B--doshiae        0.00382     (     zero,     0.01869)
   9             1              0.02760     (  0.00714,     0.04818) **
   1             8              0.00003     (     zero,     0.01080)
   8             2              0.01023     (     zero,     0.02178) **
   2          B-vinsonii        0.00006     (     zero,    infinity)
   2          B-arupensi        0.00336     (     zero,     0.00996) **
   8             6              0.00678     (     zero,     0.01615) **
   6          B-quintana        0.00341     (     zero,     0.01008) **
   6             3              0.00003     (     zero,    infinity)
   3             7              0.00739     (     zero,     0.01768) **
   7          B-berhoffi        0.02700     (  0.00783,     0.04640) **
   7          B-henselae        0.00688     (     zero,     0.01644) **
   3            12              0.02751     (  0.00806,     0.04726) **
  12          B-clarridg        0.04329     (  0.01854,     0.06822) **
  12             5              0.01713     (  0.00126,     0.03302) **
   5            10              0.00292     (     zero,     0.00976)
  10          B--weissii        0.00663     (     zero,     0.01602) **
  10          B-spp-Deer        0.01384     (  0.00025,     0.02744) **
   5          B-bacillif        0.04157     (  0.01785,     0.06529) **
   1             4              0.01768     (  0.00191,     0.03348) **
   4            11              0.01334     (     zero,     0.02696) **
  11          B-elizabet        0.02374     (  0.00613,     0.04146) **
  11          B-grahamii        0.00003     (     zero,     0.00908)
   4          B-birtlesi        0.03946     (  0.01598,     0.06310) **
   9          A-tumefaci        0.25420     (  0.18621,     0.32466) **

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


Data set # 43:


Empirical Base Frequencies:

   A       0.27031
   C       0.19794
   G       0.37006
  T(U)     0.16169

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.339935)


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


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

Ln Likelihood = -1167.33347

Examined  532 trees

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

   2             4              0.00003     (     zero,     0.01109)
   4             8              0.00003     (     zero,    infinity)
   8             7              0.01068     (     zero,     0.02278) **
   7          B-vinsonii        0.01403     (  0.00024,     0.02777) **
   7             6              0.00004     (     zero,    infinity)
   6            10              0.00713     (     zero,     0.01728) **
  10          B-birtlesi        0.03686     (  0.01407,     0.06007) **
  10          B--doshiae        0.01051     (     zero,     0.02258) **
   6            12              0.01390     (  0.00026,     0.02764) **
  12          B-arupensi        0.00706     (     zero,     0.01688) **
  12             9              0.01388     (  0.00019,     0.02758) **
   9          B-grahamii        0.00003     (     zero,    infinity)
   9          B-elizabet        0.00689     (     zero,     0.01645) **
   8             3              0.00655     (     zero,     0.01630) **
   3          B-henselae        0.01808     (  0.00215,     0.03399) **
   3          B-berhoffi        0.04341     (  0.01883,     0.06845) **
   4          B-quintana        0.01411     (  0.00023,     0.02792) **
   2             1              0.02792     (  0.00850,     0.04741) **
   1          B--weissii        0.00003     (     zero,    infinity)
   1            11              0.00341     (     zero,     0.01024) *
  11             5              0.00355     (     zero,     0.01057) **
   5          B-clarridg        0.05390     (  0.02655,     0.08174) **
   5          B-spp-Deer        0.00006     (     zero,    infinity)
  11          B-bacillif        0.04231     (  0.01829,     0.06659) **
   2          A-tumefaci        0.30759     (  0.22934,     0.38949) **

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


Data set # 44:


Empirical Base Frequencies:

   A       0.27013
   C       0.22091
   G       0.34990
  T(U)     0.15906

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.394470)


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


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

Ln Likelihood = -1054.80898

Examined 1002 trees

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

  12          B--doshiae        0.00006     (     zero,     0.01193)
  12             7              0.02219     (  0.00441,     0.04017) **
   7          B-clarridg        0.01066     (     zero,     0.02304) **
   7             9              0.01711     (  0.00159,     0.03264) **
   9             5              0.00342     (     zero,     0.01012) **
   5          B-spp-Deer        0.00003     (     zero,     0.00721)
   5             4              0.01031     (     zero,     0.02229) **
   4          B-bacillif        0.02391     (  0.00612,     0.04185) **
   4             3              0.01783     (  0.00193,     0.03361) **
   3          B-birtlesi        0.03531     (  0.01346,     0.05750) **
   3             2              0.00302     (     zero,     0.00982)
   2             6              0.00670     (     zero,     0.01606) **
   6          B-quintana        0.00699     (     zero,     0.01663) **
   6             8              0.01344     (  0.00020,     0.02682) **
   8          B-elizabet        0.00674     (     zero,     0.01614) **
   8          B-grahamii        0.00336     (     zero,     0.01003) *
   2            11              0.00006     (     zero,     0.00766)
  11          B-henselae        0.01693     (  0.00212,     0.03186) **
  11             1              0.00683     (     zero,     0.01627) **
   1            10              0.00003     (     zero,    infinity)
  10          B-arupensi        0.00333     (     zero,     0.00987) **
  10          B-berhoffi        0.01708     (  0.00209,     0.03209) **
   1          B-vinsonii        0.01010     (     zero,     0.02155) **
   9          B--weissii        0.00006     (     zero,    infinity)
  12          A-tumefaci        0.27369     (  0.20188,     0.34742) **

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


Data set # 45:


Empirical Base Frequencies:

   A       0.30464
   C       0.22318
   G       0.29439
  T(U)     0.17779

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.411600)


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


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

Ln Likelihood = -1155.66658

Examined  608 trees

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

   6             4              0.03683     (  0.01411,     0.05997) **
   4             1              0.00003     (     zero,    infinity)
   1             8              0.00365     (     zero,     0.01107) *
   8            11              0.01828     (  0.00216,     0.03445) **
  11          B-birtlesi        0.03367     (  0.01176,     0.05590) **
  11          B-grahamii        0.00006     (     zero,    infinity)
   8            12              0.01369     (     zero,     0.02750) **
  12          B-bacillif        0.03480     (  0.01324,     0.05682) **
  12          B-elizabet        0.01418     (  0.00019,     0.02819) **
   1             5              0.01031     (     zero,     0.02195) **
   5             3              0.00006     (     zero,    infinity)
   3             2              0.00394     (     zero,     0.01165) **
   2          B-berhoffi        0.02013     (  0.00363,     0.03678) **
   2          B-henselae        0.00344     (     zero,     0.01022) **
   3          B-quintana        0.01724     (  0.00216,     0.03245) **
   5             9              0.02828     (  0.00860,     0.04817) **
   9          B-clarridg        0.04268     (  0.01844,     0.06723) **
   9            10              0.00629     (     zero,     0.01619) *
  10          B-spp-Deer        0.00003     (     zero,    infinity)
  10          B--weissii        0.00683     (     zero,     0.01630) **
   4             7              0.00684     (     zero,     0.01631) **
   7          B-arupensi        0.00684     (     zero,     0.01633) **
   7          B-vinsonii        0.00003     (     zero,     0.00699)
   6          B--doshiae        0.00003     (     zero,     0.01080)
   6          A-tumefaci        0.30046     (  0.22324,     0.37991) **

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


Data set # 46:


Empirical Base Frequencies:

   A       0.29993
   C       0.19840
   G       0.29874
  T(U)     0.20293

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.402745)


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


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

Ln Likelihood = -1178.22838

Examined 1002 trees

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

   8          B--doshiae        0.00003     (     zero,     0.01158)
   8             2              0.02145     (  0.00425,     0.03866) **
   2             3              0.00674     (     zero,     0.01607) **
   3             4              0.00006     (     zero,    infinity)
   4             5              0.03050     (  0.01040,     0.05076) **
   5            11              0.00697     (     zero,     0.01687) **
  11          B-spp-Deer        0.01037     (     zero,     0.02231) **
  11          B-clarridg        0.03824     (  0.01547,     0.06128) **
   5          B--weissii        0.00345     (     zero,     0.01051) *
   4          B-henselae        0.01358     (  0.00026,     0.02691) **
   3          B-quintana        0.01359     (  0.00026,     0.02693) **
   2             9              0.00003     (     zero,     0.00820)
   9            12              0.00677     (     zero,     0.01615) **
  12            10              0.00335     (     zero,     0.01014) *
  10          B-berhoffi        0.04145     (  0.01787,     0.06516) **
  10          B-arupensi        0.00335     (     zero,     0.01010) *
  12          B-vinsonii        0.00337     (     zero,     0.01000) **
   9             1              0.00997     (     zero,     0.02336) **
   1             6              0.00898     (     zero,     0.02158) **
   6          B-bacillif        0.04229     (  0.01782,     0.06684) **
   6             7              0.01963     (  0.00300,     0.03643) **
   7          B-grahamii        0.00388     (     zero,     0.01191)
   7          B-elizabet        0.00280     (     zero,     0.01003)
   1          B-birtlesi        0.04413     (  0.01845,     0.06996) **
   8          A-tumefaci        0.26285     (  0.19380,     0.33414) **

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


Data set # 47:


Empirical Base Frequencies:

   A       0.30676
   C       0.19642
   G       0.32493
  T(U)     0.17189

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.330375)


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


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

Ln Likelihood = -1233.11731

Examined  584 trees

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

  10          B--doshiae        0.00003     (     zero,     0.01145)
  10             1              0.02062     (  0.00411,     0.03723) **
   1             8              0.01012     (     zero,     0.02153) **
   8             4              0.00006     (     zero,    infinity)
   4          B-vinsonii        0.01343     (  0.00020,     0.02655) **
   4          B-berhoffi        0.03387     (  0.01292,     0.05517) **
   8          B-arupensi        0.01007     (     zero,     0.02142) **
   1             7              0.00003     (     zero,    infinity)
   7             3              0.01725     (  0.00138,     0.03311) **
   3          B-bacillif        0.03430     (  0.01272,     0.05608) **
   3            11              0.03909     (  0.01571,     0.06265) **
  11            12              0.01366     (  0.00024,     0.02709) **
  12          B-grahamii        0.00006     (     zero,    infinity)
  12          B-birtlesi        0.04605     (  0.02105,     0.07150) **
  11          B-elizabet        0.00006     (     zero,     0.00826)
   7             2              0.00991     (     zero,     0.02123) **
   2          B-quintana        0.02018     (  0.00388,     0.03641) **
   2             6              0.00003     (     zero,     0.01000)
   6          B-henselae        0.00684     (     zero,     0.01631) **
   6             5              0.01547     (  0.00070,     0.03024) **
   5             9              0.01378     (  0.00011,     0.02758) **
   9          B-clarridg        0.03281     (  0.01161,     0.05434) **
   9          B-spp-Deer        0.01798     (  0.00209,     0.03405) **
   5          B--weissii        0.00467     (     zero,     0.01388) *
  10          A-tumefaci        0.26876     (  0.19759,     0.34274) **

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


Data set # 48:


Empirical Base Frequencies:

   A       0.28302
   C       0.26316
   G       0.25919
  T(U)     0.19463

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.504452)


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


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

Ln Likelihood = -1140.34336

Examined  922 trees

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

  12             3              0.01977     (  0.00099,     0.03861) **
   3          B-henselae        0.01702     (  0.00204,     0.03198) **
   3             8              0.00003     (     zero,     0.00839)
   8             2              0.00336     (     zero,     0.00997) **
   2          B-quintana        0.00337     (     zero,     0.01001) **
   2            11              0.00874     (     zero,     0.02025) **
  11             4              0.02070     (  0.00391,     0.03743) **
   4             5              0.01555     (  0.00082,     0.03033) **
   5             9              0.00343     (     zero,     0.01033) *
   9          B-spp-Deer        0.00003     (     zero,     0.00743)
   9          B-clarridg        0.04120     (  0.01782,     0.06482) **
   5          B-bacillif        0.03417     (  0.01282,     0.05552) **
   4          B--weissii        0.00469     (     zero,     0.01347) *
  11          B-berhoffi        0.02194     (  0.00459,     0.03950) **
   8             6              0.00006     (     zero,    infinity)
   6          B-vinsonii        0.00671     (     zero,     0.01602) **
   6            10              0.00679     (     zero,     0.01619) **
  10          B-arupensi        0.00006     (     zero,    infinity)
  10             7              0.01931     (  0.00097,     0.03762) **
   7          B-birtlesi        0.04804     (  0.02089,     0.07520) **
   7             1              0.02062     (  0.00371,     0.03766) **
   1          B-elizabet        0.01055     (     zero,     0.02487) *
   1          B-grahamii        0.00626     (     zero,     0.01985)
  12          B--doshiae        0.01110     (     zero,     0.02747)
  12          A-tumefaci        0.20787     (  0.14791,     0.26936) **

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


Data set # 49:


Empirical Base Frequencies:

   A       0.28434
   C       0.23404
   G       0.28461
  T(U)     0.19702

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.458471)


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


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

Ln Likelihood = -1184.73822

Examined 1798 trees

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

   7          B--doshiae        0.00295     (     zero,     0.01388)
   7             1              0.01860     (  0.00153,     0.03567) **
   1             8              0.00003     (     zero,    infinity)
   8             5              0.00707     (     zero,     0.01692) **
   5          B-arupensi        0.00003     (     zero,    infinity)
   5             3              0.02817     (  0.00802,     0.04841) **
   3            12              0.01231     (     zero,     0.02604) **
  12          B-grahamii        0.00003     (     zero,     0.00880)
  12          B-birtlesi        0.06007     (  0.03042,     0.08981) **
   3          B-elizabet        0.00965     (     zero,     0.02143) **
   8          B-vinsonii        0.00678     (     zero,     0.01617) **
   1             6              0.00718     (     zero,     0.01825) **
   6             4              0.00598     (     zero,     0.01544) *
   4             2              0.00003     (     zero,    infinity)
   2            11              0.02057     (  0.00416,     0.03723) **
  11             9              0.00324     (     zero,     0.01026)
   9            10              0.00700     (     zero,     0.01692) **
  10          B-spp-Deer        0.00330     (     zero,     0.01014)
  10          B-bacillif        0.04201     (  0.01809,     0.06604) **
   9          B-clarridg        0.03859     (  0.01581,     0.06178) **
  11          B--weissii        0.01381     (  0.00025,     0.02745) **
   2          B-berhoffi        0.03826     (  0.01546,     0.06101) **
   4          B-quintana        0.01369     (  0.00026,     0.02712) **
   6          B-henselae        0.00726     (     zero,     0.01843) **
   7          A-tumefaci        0.24016     (  0.17370,     0.31007) **

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


Data set # 50:


Empirical Base Frequencies:

   A       0.29603
   C       0.19018
   G       0.28595
  T(U)     0.22784

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.439454)


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


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

Ln Likelihood = -1187.57047

Examined 1168 trees

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

   6             5              0.01985     (  0.00257,     0.03725) **
   5             7              0.03515     (  0.01244,     0.05791) **
   7          B-elizabet        0.00466     (     zero,     0.01440)
   7             9              0.01435     (     zero,     0.02939) **
   9          B-birtlesi        0.05883     (  0.02993,     0.08818) **
   9          B-grahamii        0.00003     (     zero,    infinity)
   5             1              0.00297     (     zero,     0.00982)
   1             4              0.00006     (     zero,     0.00987)
   4          B-henselae        0.01032     (     zero,     0.02204) **
   4             2              0.00684     (     zero,     0.01634) **
   2             8              0.00003     (     zero,     0.00736)
   8             3              0.02453     (  0.00622,     0.04307) **
   3          B-clarridg        0.04247     (  0.01829,     0.06691) **
   3            11              0.00930     (     zero,     0.02153) **
  11          B--weissii        0.01469     (  0.00032,     0.02907) **
  11            12              0.00684     (     zero,     0.01669) **
  12          B-spp-Deer        0.00775     (     zero,     0.01858) **
  12          B-bacillif        0.03420     (  0.01245,     0.05612) **
   8          B-berhoffi        0.02753     (  0.00848,     0.04680) **
   2          B-quintana        0.00338     (     zero,     0.01002) **
   1            10              0.00340     (     zero,     0.01014) **
  10          B-vinsonii        0.00687     (     zero,     0.01639) **
  10          B-arupensi        0.00685     (     zero,     0.01636) **
   6          B--doshiae        0.00193     (     zero,     0.01127)
   6          A-tumefaci        0.25334     (  0.18539,     0.32435) **

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


Data set # 51:


Empirical Base Frequencies:

   A       0.32578
   C       0.19240
   G       0.28255
  T(U)     0.19928

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.389006)


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


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

Ln Likelihood = -1237.55050

Examined  890 trees

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

   6             3              0.02925     (  0.00882,     0.04969) **
   3            10              0.01381     (  0.00006,     0.02756) **
  10             7              0.01435     (  0.00017,     0.02851) **
   7          B-clarridg        0.06754     (  0.03712,     0.09881) **
   7          B-spp-Deer        0.00642     (     zero,     0.01613) **
  10          B--weissii        0.00006     (     zero,    infinity)
   3             8              0.01073     (     zero,     0.02321) **
   8            11              0.00006     (     zero,     0.00819)
  11          B-henselae        0.00682     (     zero,     0.01627) **
  11          B-quintana        0.01373     (  0.00027,     0.02720) **
   8             4              0.00706     (     zero,     0.01700) **
   4             1              0.00307     (     zero,     0.01129)
   1          B-bacillif        0.07111     (  0.03981,     0.10333) **
   1            12              0.02430     (  0.00497,     0.04387) **
  12          B-elizabet        0.01650     (  0.00121,     0.03187) **
  12             2              0.00992     (     zero,     0.02319) **
   2          B-birtlesi        0.05224     (  0.02492,     0.08008) **
   2          B-grahamii        0.00006     (     zero,     0.00903)
   4             5              0.01036     (     zero,     0.02210) **
   5             9              0.00003     (     zero,     0.00784)
   9          B-berhoffi        0.03467     (  0.01311,     0.05635) **
   9          B-arupensi        0.00342     (     zero,     0.01014) **
   5          B-vinsonii        0.01365     (  0.00025,     0.02705) **
   6          B--doshiae        0.00003     (     zero,     0.01211)
   6          A-tumefaci        0.24866     (  0.18117,     0.31802) **

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


Data set # 52:


Empirical Base Frequencies:

   A       0.26381
   C       0.20858
   G       0.30729
  T(U)     0.22032

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.456771)


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


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

Ln Likelihood = -1235.93924

Examined  702 trees

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

   3          B--doshiae        0.00006     (     zero,     0.01110)
   3             9              0.03156     (  0.01036,     0.05277) **
   9             7              0.01370     (     zero,     0.02763) **
   7            11              0.01090     (     zero,     0.02337) **
  11          B--weissii        0.00003     (     zero,     0.00858)
  11          B-spp-Deer        0.01678     (  0.00212,     0.03160) **
   7          B-clarridg        0.04117     (  0.01725,     0.06500) **
   9             4              0.01111     (     zero,     0.02401) **
   4             1              0.00006     (     zero,     0.00720)
   1          B-quintana        0.00003     (     zero,    infinity)
   1             5              0.00342     (     zero,     0.01027) *
   5          B-vinsonii        0.00676     (     zero,     0.01613) **
   5            10              0.01050     (     zero,     0.02239) **
  10          B-arupensi        0.00006     (     zero,     0.00796)
  10             8              0.01044     (     zero,     0.02239) **
   8          B-berhoffi        0.01359     (  0.00025,     0.02696) **
   8             6              0.00295     (     zero,     0.01032)
   6          B-bacillif        0.05933     (  0.03109,     0.08824) **
   6            12              0.01836     (  0.00190,     0.03487) **
  12          B-birtlesi        0.08213     (  0.04760,     0.11742) **
  12             2              0.00659     (     zero,     0.01655) **
   2          B-grahamii        0.00006     (     zero,     0.00895)
   2          B-elizabet        0.02016     (  0.00405,     0.03647) **
   4          B-henselae        0.01688     (  0.00214,     0.03179) **
   3          A-tumefaci        0.28760     (  0.21412,     0.36355) **

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


Data set # 53:


Empirical Base Frequencies:

   A       0.25976
   C       0.22907
   G       0.28659
  T(U)     0.22459

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.481281)


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


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

Ln Likelihood = -1342.43355

Examined 1008 trees

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

   3          B-birtlesi        0.03490     (  0.01045,     0.05964) **
   3             5              0.01600     (     zero,     0.03616) *
   5             9              0.01257     (     zero,     0.02799) **
   9          B-elizabet        0.02714     (  0.00826,     0.04604) **
   9          B-grahamii        0.00006     (     zero,     0.00729)
   5             1              0.01728     (  0.00095,     0.03359) **
   1            12              0.01252     (     zero,     0.02631) **
  12          B-henselae        0.00343     (     zero,     0.01011) **
  12             6              0.00333     (     zero,     0.01017) *
   6          B-quintana        0.01688     (  0.00209,     0.03189) **
   6          B-berhoffi        0.04471     (  0.02035,     0.06944) **
   1             7              0.00975     (     zero,     0.02284) **
   7            10              0.01355     (  0.00017,     0.02704) **
  10             4              0.01926     (  0.00251,     0.03590) **
   4            11              0.01371     (     zero,     0.02773) **
  11             2              0.01351     (     zero,     0.02730) **
   2          B--weissii        0.00003     (     zero,     0.00884)
   2             8              0.02045     (  0.00404,     0.03685) **
   8          B-clarridg        0.09145     (  0.05583,     0.12764) **
   8          B-spp-Deer        0.00003     (     zero,    infinity)
  11          B-bacillif        0.05547     (  0.02821,     0.08335) **
   4          B--doshiae        0.00676     (     zero,     0.01628) **
  10          B-arupensi        0.00810     (     zero,     0.01949) **
   7          B-vinsonii        0.00480     (     zero,     0.01405) **
   3          A-tumefaci        0.32892     (  0.24699,     0.41339) **

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


Data set # 54:


Empirical Base Frequencies:

   A       0.26089
   C       0.23016
   G       0.31440
  T(U)     0.19454

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.459060)


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


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

Ln Likelihood = -1297.64185

Examined  544 trees

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

   8          B--doshiae        0.00434     (     zero,     0.02134)
   8             7              0.04161     (  0.01670,     0.06689) **
   7             9              0.00006     (     zero,     0.00880)
   9          B-vinsonii        0.01012     (     zero,     0.02165) **
   9            10              0.01392     (  0.00017,     0.02768) **
  10          B-arupensi        0.00688     (     zero,     0.01656) **
  10             2              0.01404     (     zero,     0.02918) **
   2             4              0.01011     (     zero,     0.02205) **
   4          B-grahamii        0.00346     (     zero,     0.01283)
   4          B-elizabet        0.01002     (     zero,     0.02251) **
   2          B-birtlesi        0.05183     (  0.02403,     0.07985) **
   7             1              0.00566     (     zero,     0.01577) **
   1          B-henselae        0.01908     (  0.00283,     0.03550) **
   1             6              0.00585     (     zero,     0.01536) *
   6          B-quintana        0.00687     (     zero,     0.01637) **
   6             3              0.00437     (     zero,     0.01397)
   3          B-berhoffi        0.02648     (  0.00711,     0.04600) **
   3             5              0.04230     (  0.01841,     0.06681) **
   5            11              0.00395     (     zero,     0.01499)
  11          B--weissii        0.01073     (     zero,     0.02286) **
  11            12              0.00682     (     zero,     0.01652) **
  12          B-bacillif        0.04799     (  0.02237,     0.07370) **
  12          B-spp-Deer        0.00383     (     zero,     0.01170)
   5          B-clarridg        0.05526     (  0.02729,     0.08364) **
   8          A-tumefaci        0.32516     (  0.24262,     0.41216) **

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


Data set # 55:


Empirical Base Frequencies:

   A       0.29534
   C       0.19207
   G       0.34067
  T(U)     0.17192

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.323214)


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


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

Ln Likelihood = -1216.33849

Examined 1374 trees

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

  11             4              0.02949     (  0.00906,     0.05010) **
   4             7              0.00744     (     zero,     0.01820) **
   7          B-birtlesi        0.08643     (  0.05004,     0.12331) **
   7             2              0.00674     (     zero,     0.01674) **
   2             3              0.00003     (     zero,    infinity)
   3             8              0.02429     (  0.00622,     0.04251) **
   8            12              0.01092     (     zero,     0.02339) **
  12          B-clarridg        0.04591     (  0.02079,     0.07135) **
  12          B-spp-Deer        0.01021     (     zero,     0.02219) **
   8          B--weissii        0.00341     (     zero,     0.01043) *
   3          B-henselae        0.00692     (     zero,     0.01651) **
   2             1              0.00707     (     zero,     0.01692) **
   1          B-berhoffi        0.03859     (  0.01565,     0.06162) **
   1          B-quintana        0.00328     (     zero,     0.01009)
   4             6              0.00003     (     zero,    infinity)
   6             5              0.01053     (     zero,     0.02261) **
   5             9              0.00676     (     zero,     0.01654) **
   9          B-arupensi        0.00003     (     zero,     0.00718)
   9            10              0.01794     (  0.00163,     0.03434) **
  10          B-grahamii        0.01782     (  0.00166,     0.03420) **
  10          B-elizabet        0.00920     (     zero,     0.02108) **
   5          B-bacillif        0.03868     (  0.01581,     0.06192) **
   6          B-vinsonii        0.00343     (     zero,     0.01014) **
  11          B--doshiae        0.00003     (     zero,     0.00916)
  11          A-tumefaci        0.27381     (  0.20095,     0.34993) **

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


Data set # 56:


Empirical Base Frequencies:

   A       0.29763
   C       0.25017
   G       0.26934
  T(U)     0.18287

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.478033)


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


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

Ln Likelihood = -1184.50275

Examined  620 trees

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

   8            11              0.03686     (  0.01424,     0.05945) **
  11            10              0.00447     (     zero,     0.01314) **
  10             3              0.01025     (     zero,     0.02194) **
   3             9              0.00325     (     zero,     0.00981) *
   9             5              0.00675     (     zero,     0.01607) **
   5             2              0.00003     (     zero,     0.01013)
   2          B-berhoffi        0.04090     (  0.01756,     0.06425) **
   2             1              0.01416     (     zero,     0.02854) **
   1             7              0.02374     (  0.00581,     0.04175) **
   7          B-spp-Deer        0.00909     (     zero,     0.02039) **
   7            12              0.00761     (     zero,     0.01805) **
  12          B-bacillif        0.05069     (  0.02490,     0.07675) **
  12          B--weissii        0.00006     (     zero,     0.00890)
   1          B-clarridg        0.03434     (  0.01227,     0.05635) **
   5          B-quintana        0.01005     (     zero,     0.02143) **
   9          B-henselae        0.00670     (     zero,     0.01598) **
   3             4              0.01006     (     zero,     0.02214) **
   4          B-birtlesi        0.05009     (  0.02353,     0.07658) **
   4             6              0.01696     (  0.00187,     0.03218) **
   6          B-grahamii        0.00003     (     zero,    infinity)
   6          B-elizabet        0.00995     (     zero,     0.02124) **
  10          B-vinsonii        0.00330     (     zero,     0.00984) **
  11          B-arupensi        0.00006     (     zero,     0.00684)
   8          B--doshiae        0.00006     (     zero,     0.01106)
   8          A-tumefaci        0.21674     (  0.15613,     0.28029) **

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


Data set # 57:


Empirical Base Frequencies:

   A       0.30166
   C       0.20019
   G       0.25850
  T(U)     0.23966

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.477381)


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


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

Ln Likelihood = -1252.75252

Examined 1082 trees

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

  12          B-henselae        0.00648     (     zero,     0.01677) *
  12             2              0.01095     (     zero,     0.02391) **
   2             6              0.00003     (     zero,    infinity)
   6             3              0.00346     (     zero,     0.01031) **
   3             1              0.00674     (     zero,     0.01668) **
   1          B--doshiae        0.03135     (  0.01084,     0.05215) **
   1             4              0.02063     (  0.00328,     0.03795) **
   4          B-elizabet        0.00985     (     zero,     0.02154) **
   4             8              0.00822     (     zero,     0.01942) **
   8          B-grahamii        0.00003     (     zero,     0.00727)
   8          B-birtlesi        0.06548     (  0.03504,     0.09633) **
   3             5              0.00686     (     zero,     0.01639) **
   5          B-vinsonii        0.01020     (     zero,     0.02178) **
   5            11              0.00335     (     zero,     0.01015) *
  11          B-berhoffi        0.02760     (  0.00851,     0.04695) **
  11          B-arupensi        0.00338     (     zero,     0.01014) *
   6            10              0.01737     (  0.00192,     0.03281) **
  10          B-clarridg        0.05370     (  0.02643,     0.08145) **
  10             7              0.00663     (     zero,     0.01669) **
   7             9              0.00327     (     zero,     0.01009)
   9          B--weissii        0.00006     (     zero,    infinity)
   9          B-spp-Deer        0.00339     (     zero,     0.01003) **
   7          B-bacillif        0.03811     (  0.01555,     0.06094) **
   2          B-quintana        0.01364     (  0.00027,     0.02702) **
  12          A-tumefaci        0.36474     (  0.27658,     0.45593) **

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


Data set # 58:


Empirical Base Frequencies:

   A       0.29449
   C       0.18728
   G       0.31523
  T(U)     0.20300

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.382142)


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


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

Ln Likelihood = -1200.34570

Examined  538 trees

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

   1             6              0.02768     (  0.00798,     0.04751) **
   6          B-arupensi        0.00330     (     zero,     0.01005) *
   6             2              0.00787     (     zero,     0.01878) **
   2          B-vinsonii        0.00677     (     zero,     0.01620) **
   2             3              0.00517     (     zero,     0.01449) **
   3            12              0.00369     (     zero,     0.01097) **
  12          B-henselae        0.00974     (     zero,     0.02122) **
  12             4              0.00003     (     zero,     0.00763)
   4             5              0.00696     (     zero,     0.01675) **
   5            11              0.02641     (  0.00706,     0.04602) **
  11          B-elizabet        0.01130     (     zero,     0.02410) **
  11            10              0.00939     (     zero,     0.02137) **
  10          B-grahamii        0.00003     (     zero,     0.00867)
  10          B-birtlesi        0.05855     (  0.02967,     0.08763) **
   5          B-quintana        0.00548     (     zero,     0.01478) **
   4             7              0.02766     (  0.00805,     0.04723) **
   7             8              0.00817     (     zero,     0.02001) *
   8             9              0.00675     (     zero,     0.01650) **
   9          B--weissii        0.00965     (     zero,     0.02135) **
   9          B-spp-Deer        0.01079     (     zero,     0.02317) **
   8          B-clarridg        0.03543     (  0.01353,     0.05776) **
   7          B-bacillif        0.04054     (  0.01659,     0.06458) **
   3          B-berhoffi        0.02605     (  0.00705,     0.04498) **
   1          B--doshiae        0.00003     (     zero,     0.00938)
   1          A-tumefaci        0.25658     (  0.18767,     0.32752) **

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


Data set # 59:


Empirical Base Frequencies:

   A       0.25216
   C       0.24464
   G       0.27873
  T(U)     0.22447

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.494858)


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


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

Ln Likelihood = -1262.36760

Examined 1182 trees

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

   6          B-henselae        0.01255     (     zero,     0.02698) **
   6            11              0.01254     (     zero,     0.02749) **
  11             3              0.00003     (     zero,     0.00748)
   3             1              0.01040     (     zero,     0.02218) **
   1          B-quintana        0.00351     (     zero,     0.01034) **
   1             7              0.00003     (     zero,     0.00948)
   7          B-berhoffi        0.02796     (  0.00861,     0.04758) **
   7             4              0.02254     (  0.00419,     0.04097) **
   4             5              0.01520     (     zero,     0.03079) **
   5             9              0.00997     (     zero,     0.02345) *
   9          B-bacillif        0.03450     (  0.01210,     0.05726) **
   9          B--weissii        0.01252     (     zero,     0.02778) **
   5          B-spp-Deer        0.00753     (     zero,     0.01899) **
   4          B-clarridg        0.06078     (  0.03109,     0.09092) **
   3             2              0.00003     (     zero,     0.00742)
   2            10              0.00344     (     zero,     0.01018) **
  10          B-arupensi        0.00006     (     zero,    infinity)
  10          B-vinsonii        0.01032     (     zero,     0.02202) **
   2          B--doshiae        0.03864     (  0.01569,     0.06168) **
  11            12              0.02087     (  0.00327,     0.03865) **
  12             8              0.01675     (  0.00078,     0.03275) **
   8          B-grahamii        0.00006     (     zero,    infinity)
   8          B-birtlesi        0.05729     (  0.02824,     0.08670) **
  12          B-elizabet        0.00971     (     zero,     0.02161) **
   6          A-tumefaci        0.31790     (  0.23774,     0.40221) **

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


Data set # 60:


Empirical Base Frequencies:

   A       0.31926
   C       0.20588
   G       0.28016
  T(U)     0.19470

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.406844)


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


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

Ln Likelihood = -1330.12711

Examined  550 trees

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

   1          B-birtlesi        0.04234     (  0.01505,     0.06987) **
   1             3              0.02253     (  0.00097,     0.04427) **
   3             5              0.00683     (     zero,     0.01637) **
   5             6              0.00003     (     zero,     0.01049)
   6             8              0.01432     (     zero,     0.02954) **
   8          B--doshiae        0.03405     (  0.01206,     0.05647) **
   8             9              0.03786     (  0.01451,     0.06132) **
   9          B-bacillif        0.03342     (  0.01111,     0.05563) **
   9            12              0.00857     (     zero,     0.02276)
  12          B--weissii        0.01380     (     zero,     0.02875) **
  12             7              0.00703     (     zero,     0.01832) *
   7          B-spp-Deer        0.01395     (  0.00006,     0.02790) **
   7          B-clarridg        0.05598     (  0.02818,     0.08413) **
   6            10              0.00582     (     zero,     0.01627) **
  10            11              0.00594     (     zero,     0.01563) *
  11          B-berhoffi        0.03087     (  0.01038,     0.05126) **
  11          B-quintana        0.00694     (     zero,     0.01671) **
  10          B-henselae        0.01897     (  0.00246,     0.03549) **
   5             4              0.02649     (  0.00762,     0.04567) **
   4          B-grahamii        0.01158     (     zero,     0.02455) **
   4          B-elizabet        0.00619     (     zero,     0.01592) **
   3             2              0.00362     (     zero,     0.01079) **
   2          B-arupensi        0.01000     (     zero,     0.02154) **
   2          B-vinsonii        0.02049     (  0.00410,     0.03701) **
   1          A-tumefaci        0.28623     (  0.21125,     0.36330) **

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


Data set # 61:


Empirical Base Frequencies:

   A       0.25800
   C       0.22124
   G       0.32063
  T(U)     0.20013

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.453941)


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


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

Ln Likelihood = -1163.27494

Examined  552 trees

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

   4          B--doshiae        0.00123     (     zero,     0.01126)
   4             6              0.02712     (  0.00750,     0.04700) **
   6             3              0.01030     (     zero,     0.02235) **
   3             8              0.00006     (     zero,     0.00838)
   8             7              0.00671     (     zero,     0.01601) **
   7             2              0.00006     (     zero,    infinity)
   2             9              0.03122     (  0.01080,     0.05179) **
   9          B-clarridg        0.04242     (  0.01841,     0.06673) **
   9            12              0.00260     (     zero,     0.00947)
  12          B--weissii        0.01012     (     zero,     0.02158) **
  12             5              0.00337     (     zero,     0.01018) *
   5          B-spp-Deer        0.00334     (     zero,     0.01011) *
   5          B-bacillif        0.04471     (  0.02034,     0.06940) **
   2          B-quintana        0.00335     (     zero,     0.00992) **
   7            11              0.01247     (     zero,     0.02570) **
  11             1              0.01373     (  0.00016,     0.02729) **
   1          B-vinsonii        0.01241     (     zero,     0.02558) **
   1          B-arupensi        0.00782     (     zero,     0.01856) **
  11          B-berhoffi        0.01126     (     zero,     0.02390) **
   8          B-henselae        0.00334     (     zero,     0.00988) **
   3          B-birtlesi        0.05833     (  0.02958,     0.08733) **
   6            10              0.01701     (  0.00188,     0.03215) **
  10          B-grahamii        0.00003     (     zero,     0.01008)
  10          B-elizabet        0.00999     (     zero,     0.02137) **
   4          A-tumefaci        0.22239     (  0.16091,     0.28713) **

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


Data set # 62:


Empirical Base Frequencies:

   A       0.29343
   C       0.15358
   G       0.34658
  T(U)     0.20641

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.325716)


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


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

Ln Likelihood = -1184.15921

Examined  774 trees

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

   4          B--doshiae        0.00003     (     zero,     0.01484)
   4             2              0.02662     (  0.00665,     0.04674) **
   2            11              0.01876     (  0.00193,     0.03560) **
  11             9              0.00003     (     zero,     0.00763)
   9             3              0.01065     (     zero,     0.02275) **
   3            12              0.00681     (     zero,     0.01668) **
  12          B-vinsonii        0.01045     (     zero,     0.02232) **
  12          B-arupensi        0.01049     (     zero,     0.02241) **
   3          B-berhoffi        0.02497     (  0.00649,     0.04370) **
   9          B-quintana        0.01781     (  0.00218,     0.03346) **
  11             6              0.00003     (     zero,    infinity)
   6          B-henselae        0.01384     (  0.00022,     0.02753) **
   6             7              0.01412     (     zero,     0.02910) **
   7          B-bacillif        0.03270     (  0.01128,     0.05430) **
   7             5              0.01359     (     zero,     0.02843) **
   5          B-elizabet        0.00296     (     zero,     0.01176)
   5             8              0.02064     (  0.00277,     0.03848) **
   8          B-birtlesi        0.02661     (  0.00686,     0.04638) **
   8          B-grahamii        0.00006     (     zero,    infinity)
   2             1              0.02114     (  0.00389,     0.03849) **
   1          B--weissii        0.00006     (     zero,     0.01057)
   1            10              0.00715     (     zero,     0.01719) **
  10          B-clarridg        0.04017     (  0.01636,     0.06427) **
  10          B-spp-Deer        0.01048     (     zero,     0.02256) **
   4          A-tumefaci        0.31969     (  0.23857,     0.40322) **

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


Data set # 63:


Empirical Base Frequencies:

   A       0.26565
   C       0.23474
   G       0.34333
  T(U)     0.15627

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.430113)


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


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

Ln Likelihood = -1158.39689

Examined 1042 trees

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

   9            10              0.02995     (  0.00930,     0.05083) **
  10             1              0.00325     (     zero,     0.01052)
   1             7              0.00836     (     zero,     0.01978) **
   7          B-quintana        0.01358     (  0.00027,     0.02690) **
   7             4              0.00003     (     zero,    infinity)
   4          B-henselae        0.00678     (     zero,     0.01617) **
   4             2              0.01065     (     zero,     0.02277) **
   2             5              0.00505     (     zero,     0.01477) *
   5          B-bacillif        0.03262     (  0.01162,     0.05398) **
   5             6              0.00642     (     zero,     0.01668) *
   6          B-birtlesi        0.05737     (  0.02813,     0.08685) **
   6            12              0.02360     (  0.00522,     0.04211) **
  12          B-elizabet        0.00003     (     zero,     0.00756)
  12          B-grahamii        0.00335     (     zero,     0.00992) **
   2             8              0.01382     (  0.00027,     0.02739) **
   8             3              0.00003     (     zero,     0.00912)
   3          B-vinsonii        0.01360     (  0.00027,     0.02696) **
   3          B-arupensi        0.00335     (     zero,     0.00998) **
   8          B-berhoffi        0.01694     (  0.00207,     0.03186) **
   1          B-clarridg        0.04428     (  0.01955,     0.06924) **
  10            11              0.00922     (     zero,     0.02083) **
  11          B-spp-Deer        0.01008     (     zero,     0.02155) **
  11          B--weissii        0.00003     (     zero,    infinity)
   9          B--doshiae        0.00006     (     zero,     0.01484)
   9          A-tumefaci        0.29962     (  0.22178,     0.38029) **

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


Data set # 64:


Empirical Base Frequencies:

   A       0.30169
   C       0.21201
   G       0.30455
  T(U)     0.18175

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.391304)


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


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

Ln Likelihood = -1272.21119

Examined  624 trees

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

   6          B-birtlesi        0.03015     (  0.00201,     0.05845) **
   6            10              0.05252     (  0.02145,     0.08386) **
  10             2              0.00669     (     zero,     0.01615) **
   2            11              0.01703     (  0.00194,     0.03227) **
  11          B-bacillif        0.01361     (  0.00003,     0.02720) **
  11             5              0.02047     (  0.00402,     0.03713) **
   5          B-grahamii        0.01005     (     zero,     0.02148) **
   5          B-elizabet        0.00006     (     zero,     0.00806)
   2             1              0.00006     (     zero,     0.00850)
   1             8              0.00990     (     zero,     0.02244) **
   8          B-henselae        0.02259     (  0.00467,     0.04048) **
   8             7              0.00529     (     zero,     0.01479)
   7          B-quintana        0.00676     (     zero,     0.01613) **
   7             3              0.00003     (     zero,     0.00877)
   3            12              0.00355     (     zero,     0.01098)
  12          B-berhoffi        0.04144     (  0.01770,     0.06534) **
  12             4              0.01027     (     zero,     0.02210) **
   4          B--weissii        0.01338     (     zero,     0.02683) **
   4          B-spp-Deer        0.00708     (     zero,     0.01699) **
   3          B-clarridg        0.07090     (  0.03954,     0.10270) **
   1          B--doshiae        0.02733     (  0.00839,     0.04645) **
  10             9              0.00351     (     zero,     0.01051) *
   9          B-arupensi        0.01356     (  0.00017,     0.02698) **
   9          B-vinsonii        0.00682     (     zero,     0.01639) **
   6          A-tumefaci        0.30473     (  0.22648,     0.38548) **

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


Data set # 65:


Empirical Base Frequencies:

   A       0.27502
   C       0.23504
   G       0.31620
  T(U)     0.17374

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.439600)


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


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

Ln Likelihood = -1217.82216

Examined 1352 trees

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

   4             3              0.02867     (  0.00868,     0.04867) **
   3          B-arupensi        0.00339     (     zero,     0.01017) *
   3             5              0.00354     (     zero,     0.01059) *
   5          B-vinsonii        0.00006     (     zero,     0.00694)
   5             6              0.01052     (     zero,     0.02248) **
   6            12              0.00354     (     zero,     0.01053) **
  12             2              0.00313     (     zero,     0.01036)
   2          B-berhoffi        0.04268     (  0.01832,     0.06703) **
   2             9              0.02151     (  0.00433,     0.03894) **
   9            10              0.00710     (     zero,     0.01721) **
  10          B-birtlesi        0.05920     (  0.03016,     0.08883) **
  10             7              0.00671     (     zero,     0.01638) **
   7          B-bacillif        0.04812     (  0.02290,     0.07381) **
   7          B-elizabet        0.00003     (     zero,    infinity)
   9          B-grahamii        0.00006     (     zero,    infinity)
  12             1              0.02060     (  0.00404,     0.03711) **
   1            11              0.02139     (  0.00425,     0.03854) **
  11          B-clarridg        0.04233     (  0.01836,     0.06665) **
  11          B-spp-Deer        0.00283     (     zero,     0.00965)
   1          B--weissii        0.00003     (     zero,    infinity)
   6             8              0.00003     (     zero,    infinity)
   8          B-henselae        0.01027     (     zero,     0.02189) **
   8          B-quintana        0.01030     (     zero,     0.02192) **
   4          B--doshiae        0.00006     (     zero,     0.01265)
   4          A-tumefaci        0.35454     (  0.26771,     0.44551) **

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


Data set # 66:


Empirical Base Frequencies:

   A       0.30070
   C       0.21723
   G       0.30074
  T(U)     0.18134

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.402927)


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


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

Ln Likelihood = -1211.33898

Examined  670 trees

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

  10          B--doshiae        0.00006     (     zero,     0.01540)
  10             8              0.04898     (  0.02231,     0.07621) **
   8             5              0.01364     (     zero,     0.02812) **
   5          B-clarridg        0.06683     (  0.03592,     0.09859) **
   5             9              0.01917     (  0.00188,     0.03657) **
   9          B--weissii        0.00006     (     zero,    infinity)
   9            12              0.00677     (     zero,     0.01639) **
  12          B-spp-Deer        0.00690     (     zero,     0.01660) **
  12          B-bacillif        0.03458     (  0.01319,     0.05638) **
   8             3              0.00572     (     zero,     0.01674)
   3             1              0.00344     (     zero,     0.01018) **
   1          B-vinsonii        0.01026     (     zero,     0.02191) **
   1            11              0.00335     (     zero,     0.01027) *
  11          B-berhoffi        0.04197     (  0.01816,     0.06606) **
  11          B-arupensi        0.00697     (     zero,     0.01674) **
   3             2              0.00006     (     zero,    infinity)
   2          B-henselae        0.01027     (     zero,     0.02194) **
   2             7              0.00264     (     zero,     0.00962)
   7             4              0.02454     (  0.00536,     0.04388) **
   4          B-birtlesi        0.05990     (  0.03003,     0.09035) **
   4             6              0.01194     (     zero,     0.02610) **
   6          B-elizabet        0.00680     (     zero,     0.01626) **
   6          B-grahamii        0.00006     (     zero,    infinity)
   7          B-quintana        0.00427     (     zero,     0.01242) **
  10          A-tumefaci        0.24953     (  0.18137,     0.31936) **

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


Data set # 67:


Empirical Base Frequencies:

   A       0.28778
   C       0.21470
   G       0.30082
  T(U)     0.19671

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.423530)


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


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

Ln Likelihood = -1191.33076

Examined 1238 trees

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

   1             3              0.00004     (     zero,     0.00954)
   3            10              0.00326     (     zero,     0.00985) *
  10             2              0.01017     (     zero,     0.02171) **
   2             7              0.00003     (     zero,    infinity)
   7          B-quintana        0.01009     (     zero,     0.02151) **
   7             9              0.00731     (     zero,     0.01757) **
   9          B-henselae        0.01028     (     zero,     0.02196) **
   9          B-berhoffi        0.02642     (  0.00766,     0.04541) **
   2             5              0.02752     (  0.00811,     0.04694) **
   5          B-clarridg        0.04232     (  0.01827,     0.06674) **
   5             8              0.01312     (     zero,     0.02695) **
   8          B--weissii        0.01034     (     zero,     0.02205) **
   8             4              0.00323     (     zero,     0.01000)
   4          B-spp-Deer        0.00359     (     zero,     0.01080) *
   4          B-bacillif        0.05146     (  0.02526,     0.07811) **
  10          B--doshiae        0.01685     (  0.00213,     0.03176) **
   3          B-vinsonii        0.00003     (     zero,    infinity)
   1            11              0.00680     (     zero,     0.01644) **
  11          B-arupensi        0.00341     (     zero,     0.01021) *
  11             6              0.01737     (  0.00172,     0.03299) **
   6          B-birtlesi        0.02498     (  0.00634,     0.04377) **
   6            12              0.02419     (  0.00607,     0.04230) **
  12          B-grahamii        0.00006     (     zero,     0.01152)
  12          B-elizabet        0.01673     (  0.00200,     0.03146) **
   1          A-tumefaci        0.25516     (  0.18722,     0.32473) **

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


Data set # 68:


Empirical Base Frequencies:

   A       0.24107
   C       0.21629
   G       0.35874
  T(U)     0.18390

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.452609)


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


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

Ln Likelihood = -1180.50862

Examined  752 trees

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

   9          B--doshiae        0.00437     (     zero,     0.01795)
   9             4              0.02352     (  0.00447,     0.04271) **
   4             7              0.00345     (     zero,     0.01038) *
   7            10              0.00340     (     zero,     0.01020) **
  10             1              0.00003     (     zero,     0.00800)
   1          B-quintana        0.01023     (     zero,     0.02187) **
   1            11              0.02918     (  0.00922,     0.04938) **
  11             3              0.00686     (     zero,     0.01688) **
   3             6              0.00683     (     zero,     0.01688) **
   6          B-spp-Deer        0.00521     (     zero,     0.01469) *
   6          B-bacillif        0.03984     (  0.01641,     0.06342) **
   3          B-clarridg        0.05897     (  0.02999,     0.08822) **
  11          B--weissii        0.00514     (     zero,     0.01434) **
  10          B-henselae        0.01034     (     zero,     0.02202) **
   7             8              0.01936     (  0.00164,     0.03708) **
   8            12              0.01934     (  0.00189,     0.03701) **
  12          B-elizabet        0.01018     (     zero,     0.02176) **
  12          B-grahamii        0.00006     (     zero,     0.00790)
   8          B-birtlesi        0.03919     (  0.01550,     0.06283) **
   4             2              0.00346     (     zero,     0.01031) **
   2          B-vinsonii        0.01032     (     zero,     0.02203) **
   2             5              0.00686     (     zero,     0.01658) **
   5          B-arupensi        0.00683     (     zero,     0.01649) **
   5          B-berhoffi        0.02803     (  0.00849,     0.04757) **
   9          A-tumefaci        0.22502     (  0.16075,     0.29173) **

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


Data set # 69:


Empirical Base Frequencies:

   A       0.33639
   C       0.21311
   G       0.26955
  T(U)     0.18095

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.407335)


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


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

Ln Likelihood = -1211.79193

Examined  670 trees

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

  12          B--doshiae        0.00006     (     zero,     0.01277)
  12             3              0.01520     (  0.00017,     0.03025) **
   3             2              0.00725     (     zero,     0.01790) **
   2            10              0.01084     (     zero,     0.02317) **
  10          B-arupensi        0.00006     (     zero,     0.00798)
  10          B-vinsonii        0.01743     (  0.00216,     0.03279) **
   2             6              0.02273     (  0.00436,     0.04121) **
   6             4              0.00315     (     zero,     0.01016)
   4          B-henselae        0.00352     (     zero,     0.01044) **
   4             9              0.01075     (     zero,     0.02299) **
   9          B-quintana        0.01777     (  0.00210,     0.03342) **
   9             7              0.01035     (     zero,     0.02271) **
   7          B-clarridg        0.02548     (  0.00641,     0.04455) **
   7          B-berhoffi        0.02514     (  0.00641,     0.04401) **
   6             5              0.02317     (  0.00429,     0.04219) **
   5          B-birtlesi        0.03463     (  0.01196,     0.05775) **
   5            11              0.02120     (  0.00380,     0.03863) **
  11          B-grahamii        0.00003     (     zero,     0.01026)
  11          B-elizabet        0.02811     (  0.00862,     0.04778) **
   3             1              0.02023     (  0.00292,     0.03762) **
   1          B--weissii        0.01864     (  0.00210,     0.03528) **
   1             8              0.01044     (     zero,     0.02283) **
   8          B-spp-Deer        0.01561     (  0.00052,     0.03085) **
   8          B-bacillif        0.02707     (  0.00747,     0.04694) **
  12          A-tumefaci        0.24296     (  0.17569,     0.31288) **

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


Data set # 70:


Empirical Base Frequencies:

   A       0.29990
   C       0.18888
   G       0.30585
  T(U)     0.20537

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.389514)


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


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

Ln Likelihood = -1133.61114

Examined  646 trees

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

   3          B--doshiae        0.00003     (     zero,     0.00866)
   3             9              0.02760     (  0.00798,     0.04725) **
   9            11              0.00386     (     zero,     0.01192)
  11             6              0.00003     (     zero,    infinity)
   6             5              0.00685     (     zero,     0.01635) **
   5             7              0.02087     (  0.00421,     0.03774) **
   7          B-elizabet        0.00327     (     zero,     0.01006)
   7            10              0.01396     (  0.00025,     0.02771) **
  10          B-grahamii        0.00006     (     zero,    infinity)
  10          B-birtlesi        0.05347     (  0.02638,     0.08106) **
   5          B-arupensi        0.00006     (     zero,    infinity)
   6          B-vinsonii        0.00336     (     zero,     0.00994) **
  11             2              0.01018     (     zero,     0.02181) **
   2          B-quintana        0.00348     (     zero,     0.01040) **
   2            12              0.00657     (     zero,     0.01618) **
  12          B-berhoffi        0.02794     (  0.00858,     0.04755) **
  12          B-henselae        0.01738     (  0.00212,     0.03281) **
   9             1              0.01741     (  0.00191,     0.03291) **
   1          B-bacillif        0.02135     (  0.00411,     0.03851) **
   1             4              0.01298     (     zero,     0.02656) **
   4          B--weissii        0.00003     (     zero,     0.01014)
   4             8              0.00693     (     zero,     0.01658) **
   8          B-spp-Deer        0.00326     (     zero,     0.00996) *
   8          B-clarridg        0.03811     (  0.01550,     0.06088) **
   3          A-tumefaci        0.26253     (  0.19352,     0.33453) **

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


Data set # 71:


Empirical Base Frequencies:

   A       0.25859
   C       0.20875
   G       0.33803
  T(U)     0.19462

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.428959)


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


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

Ln Likelihood = -1160.74581

Examined 2524 trees

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

  11          B--doshiae        0.00006     (     zero,     0.01256)
  11             2              0.03207     (  0.01106,     0.05323) **
   2             7              0.00669     (     zero,     0.01625) **
   7          B-vinsonii        0.00006     (     zero,    infinity)
   7          B-arupensi        0.00337     (     zero,     0.00998) **
   2             1              0.01046     (     zero,     0.02255) **
   1             9              0.00003     (     zero,     0.01041)
   9             5              0.00695     (     zero,     0.01659) **
   5             3              0.00003     (     zero,     0.00795)
   3            12              0.02102     (  0.00414,     0.03785) **
  12          B-elizabet        0.01343     (  0.00026,     0.02661) **
  12            10              0.00003     (     zero,     0.00739)
  10          B-birtlesi        0.05844     (  0.02974,     0.08757) **
  10          B-grahamii        0.00003     (     zero,    infinity)
   3             4              0.02078     (  0.00391,     0.03756) **
   4             6              0.00650     (     zero,     0.01633) **
   6          B--weissii        0.00336     (     zero,     0.01008) **
   6             8              0.01411     (  0.00014,     0.02803) **
   8          B-clarridg        0.03790     (  0.01548,     0.06073) **
   8          B-spp-Deer        0.01321     (     zero,     0.02660) **
   4          B-bacillif        0.04517     (  0.02035,     0.07004) **
   5          B-berhoffi        0.02368     (  0.00614,     0.04139) **
   9          B-henselae        0.00681     (     zero,     0.01623) **
   1          B-quintana        0.01350     (  0.00026,     0.02681) **
  11          A-tumefaci        0.22567     (  0.16202,     0.29088) **

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


Data set # 72:


Empirical Base Frequencies:

   A       0.29984
   C       0.20759
   G       0.29085
  T(U)     0.20172

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.418183)


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


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

Ln Likelihood = -1182.82233

Examined 1376 trees

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

   1             6              0.01414     (  0.00021,     0.02804) **
   6             9              0.00336     (     zero,     0.01030) *
   9             8              0.00699     (     zero,     0.01670) **
   8             4              0.01471     (  0.00003,     0.02937) **
   4          B-bacillif        0.04501     (  0.02015,     0.07012) **
   4            10              0.00426     (     zero,     0.01476)
  10          B-birtlesi        0.06325     (  0.03295,     0.09431) **
  10            11              0.02025     (  0.00292,     0.03760) **
  11          B-grahamii        0.01012     (     zero,     0.02195) **
  11          B-elizabet        0.00345     (     zero,     0.01077)
   8             3              0.00003     (     zero,    infinity)
   3          B-vinsonii        0.00339     (     zero,     0.01002) **
   3             7              0.00338     (     zero,     0.01000) **
   7             2              0.00003     (     zero,     0.00711)
   2          B-clarridg        0.06334     (  0.03388,     0.09321) **
   2            12              0.00336     (     zero,     0.01002) **
  12          B-henselae        0.00342     (     zero,     0.01013) **
  12          B-berhoffi        0.01369     (  0.00026,     0.02713) **
   7          B-quintana        0.02051     (  0.00416,     0.03707) **
   9          B-arupensi        0.00681     (     zero,     0.01627) **
   6             5              0.01368     (  0.00028,     0.02718) **
   5          B--weissii        0.00003     (     zero,    infinity)
   5          B-spp-Deer        0.01710     (  0.00209,     0.03212) **
   1          B--doshiae        0.00006     (     zero,     0.00970)
   1          A-tumefaci        0.34334     (  0.25943,     0.43005) **

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


Data set # 73:


Empirical Base Frequencies:

   A       0.31876
   C       0.22334
   G       0.25240
  T(U)     0.20551

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.466486)


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


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

Ln Likelihood = -1344.19921

Examined  688 trees

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

   7          B--doshiae        0.00003     (     zero,     0.01339)
   7             2              0.02916     (  0.00846,     0.04988) **
   2             1              0.02548     (  0.00623,     0.04494) **
   1             9              0.00003     (     zero,    infinity)
   9          B-quintana        0.01031     (     zero,     0.02204) **
   9             3              0.00764     (     zero,     0.01883) **
   3             4              0.01213     (     zero,     0.02564) **
   4            10              0.02237     (  0.00415,     0.04067) **
  10          B-vinsonii        0.01710     (  0.00161,     0.03252) **
  10          B-arupensi        0.01404     (  0.00000,     0.02811) **
   4          B-berhoffi        0.02178     (  0.00410,     0.03955) **
   3            11              0.02460     (  0.00552,     0.04386) **
  11          B-birtlesi        0.04855     (  0.02200,     0.07532) **
  11            12              0.00699     (     zero,     0.01705) **
  12          B-elizabet        0.01363     (  0.00026,     0.02704) **
  12          B-grahamii        0.00006     (     zero,     0.00804)
   1          B-henselae        0.01040     (     zero,     0.02216) **
   2             5              0.03169     (  0.01062,     0.05297) **
   5          B--weissii        0.00336     (     zero,     0.01030) *
   5             8              0.00715     (     zero,     0.01737) **
   8          B-clarridg        0.06485     (  0.03464,     0.09552) **
   8             6              0.01017     (     zero,     0.02204) **
   6          B-spp-Deer        0.00006     (     zero,     0.00926)
   6          B-bacillif        0.05973     (  0.03126,     0.08882) **
   7          A-tumefaci        0.34288     (  0.25999,     0.43008) **

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


Data set # 74:


Empirical Base Frequencies:

   A       0.28281
   C       0.22519
   G       0.30657
  T(U)     0.18542

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.429118)


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


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

Ln Likelihood = -1182.52936

Examined 1412 trees

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

   2             3              0.02208     (  0.00006,     0.04409) **
   3             1              0.00003     (     zero,    infinity)
   1          B-arupensi        0.00336     (     zero,     0.00995) **
   1             4              0.01345     (  0.00028,     0.02668) **
   4             5              0.00003     (     zero,     0.00786)
   5            11              0.00676     (     zero,     0.01612) **
  11             9              0.00004     (     zero,    infinity)
   9            12              0.02723     (  0.00840,     0.04636) **
  12          B-elizabet        0.00671     (     zero,     0.01620) **
  12          B-grahamii        0.00673     (     zero,     0.01622) **
   9          B-berhoffi        0.02701     (  0.00832,     0.04597) **
  11            10              0.01006     (     zero,     0.02157) **
  10          B--weissii        0.00341     (     zero,     0.01027) *
  10             7              0.01023     (     zero,     0.02193) **
   7          B-bacillif        0.04782     (  0.02278,     0.07349) **
   7          B-spp-Deer        0.00345     (     zero,     0.01040) *
   5             6              0.00003     (     zero,    infinity)
   6          B-quintana        0.01010     (     zero,     0.02156) **
   6          B-henselae        0.00335     (     zero,     0.00992) **
   4             8              0.01673     (  0.00129,     0.03217) **
   8          B-clarridg        0.03141     (  0.01071,     0.05245) **
   8          B--doshiae        0.03513     (  0.01312,     0.05737) **
   3          B-vinsonii        0.00333     (     zero,     0.00987) **
   2          B-birtlesi        0.04772     (  0.01864,     0.07692) **
   2          A-tumefaci        0.31090     (  0.23196,     0.39254) **

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


Data set # 75:


Empirical Base Frequencies:

   A       0.27953
   C       0.21978
   G       0.33049
  T(U)     0.17021

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.398792)


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


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

Ln Likelihood = -1219.43035

Examined  786 trees

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

   7          B-arupensi        0.00003     (     zero,     0.00969)
   7            10              0.00701     (     zero,     0.01687) **
  10             2              0.00864     (     zero,     0.02042) **
   2             1              0.00215     (     zero,     0.01184)
   1            11              0.00674     (     zero,     0.01639) **
  11          B-quintana        0.01030     (     zero,     0.02202) **
  11          B-berhoffi        0.01711     (  0.00207,     0.03222) **
   1             3              0.00328     (     zero,     0.01302)
   3             4              0.02584     (  0.00583,     0.04583) **
   4             9              0.01666     (  0.00050,     0.03290) **
   9          B-grahamii        0.00006     (     zero,     0.01142)
   9          B-elizabet        0.02715     (  0.00835,     0.04620) **
   4          B-birtlesi        0.06342     (  0.03288,     0.09431) **
   3          B-henselae        0.01042     (     zero,     0.02223) **
   2             8              0.01036     (     zero,     0.02223) **
   8             6              0.01059     (     zero,     0.02280) **
   6            12              0.00929     (     zero,     0.02147) **
  12             5              0.01048     (     zero,     0.02279) **
   5          B-clarridg        0.03718     (  0.01461,     0.06011) **
   5          B-spp-Deer        0.00440     (     zero,     0.01304)
  12          B-bacillif        0.05540     (  0.02733,     0.08370) **
   6          B--weissii        0.00837     (     zero,     0.01987) **
   8          B--doshiae        0.02569     (  0.00675,     0.04481) **
  10          B-vinsonii        0.00678     (     zero,     0.01626) **
   7          A-tumefaci        0.24284     (  0.17722,     0.31140) **

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


Data set # 76:


Empirical Base Frequencies:

   A       0.30528
   C       0.19652
   G       0.30812
  T(U)     0.19009

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.371624)


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


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

Ln Likelihood = -1226.89443

Examined  908 trees

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

   5             3              0.01445     (     zero,     0.03238) **
   3            12              0.00006     (     zero,     0.00825)
  12          B-vinsonii        0.01041     (     zero,     0.02219) **
  12          B-arupensi        0.01384     (  0.00021,     0.02747) **
   3             1              0.01447     (  0.00033,     0.02862) **
   1             4              0.00003     (     zero,     0.00841)
   4             2              0.00662     (     zero,     0.01633) **
   2             6              0.03845     (  0.01532,     0.06191) **
   6          B-grahamii        0.01104     (     zero,     0.02419) **
   6          B-elizabet        0.00683     (     zero,     0.01750) *
   2          B-quintana        0.01434     (  0.00028,     0.02852) **
   4            11              0.00674     (     zero,     0.01694) **
  11          B-berhoffi        0.03832     (  0.01524,     0.06145) **
  11          B-henselae        0.00003     (     zero,     0.00864)
   1             8              0.01563     (     zero,     0.03156) **
   8          B-bacillif        0.04903     (  0.02223,     0.07611) **
   8             9              0.01393     (     zero,     0.02818) **
   9             7              0.00355     (     zero,     0.01770)
   7            10              0.00683     (     zero,     0.01651) **
  10          B-spp-Deer        0.00003     (     zero,    infinity)
  10          B-clarridg        0.03878     (  0.01585,     0.06203) **
   7          B--weissii        0.00513     (     zero,     0.01416) **
   9          B--doshiae        0.04408     (  0.01894,     0.06961) **
   5          B-birtlesi        0.04830     (  0.02038,     0.07622) **
   5          A-tumefaci        0.26012     (  0.18963,     0.33226) **

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


Data set # 77:


Empirical Base Frequencies:

   A       0.27570
   C       0.24350
   G       0.30510
  T(U)     0.17571

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.458346)


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


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

Ln Likelihood = -1156.75260

Examined 1064 trees

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

   6          B--doshiae        0.00003     (     zero,     0.01218)
   6             9              0.02030     (  0.00400,     0.03670) **
   9             7              0.00006     (     zero,     0.00960)
   7          B--weissii        0.00332     (     zero,     0.00985) **
   7             3              0.01013     (     zero,     0.02159) **
   3          B-clarridg        0.05866     (  0.03062,     0.08709) **
   3          B-spp-Deer        0.00006     (     zero,    infinity)
   9             4              0.01372     (  0.00006,     0.02729) **
   4             8              0.01003     (     zero,     0.02175) **
   8            10              0.00677     (     zero,     0.01616) **
  10          B-vinsonii        0.01676     (  0.00213,     0.03158) **
  10            11              0.00318     (     zero,     0.00983)
  11          B-berhoffi        0.02388     (  0.00612,     0.04165) **
  11          B-arupensi        0.00669     (     zero,     0.01604) **
   8             5              0.00003     (     zero,    infinity)
   5          B-henselae        0.00669     (     zero,     0.01598) **
   5             1              0.00331     (     zero,     0.01000) *
   1            12              0.02352     (  0.00568,     0.04136) **
  12             2              0.00413     (     zero,     0.01218) *
   2          B-birtlesi        0.04477     (  0.02037,     0.06946) **
   2          B-grahamii        0.00006     (     zero,     0.00845)
  12          B-elizabet        0.00632     (     zero,     0.01566) **
   1          B-quintana        0.00675     (     zero,     0.01621) **
   4          B-bacillif        0.02386     (  0.00609,     0.04172) **
   6          A-tumefaci        0.32909     (  0.24758,     0.41308) **

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


Data set # 78:


Empirical Base Frequencies:

   A       0.30539
   C       0.20502
   G       0.32409
  T(U)     0.16551

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.340663)


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


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

Ln Likelihood = -1172.06548

Examined  588 trees

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

   4          B-birtlesi        0.03497     (  0.01046,     0.05959) **
   4             1              0.01934     (     zero,     0.03907) **
   1             9              0.00348     (     zero,     0.01031) **
   9          B-arupensi        0.01006     (     zero,     0.02153) **
   9          B-vinsonii        0.00677     (     zero,     0.01620) **
   1             2              0.00677     (     zero,     0.01628) **
   2             8              0.01354     (     zero,     0.02717) **
   8             5              0.02042     (  0.00390,     0.03704) **
   5          B-grahamii        0.00003     (     zero,    infinity)
   5          B-elizabet        0.01339     (  0.00028,     0.02654) **
   8          B-quintana        0.02059     (  0.00405,     0.03735) **
   2             3              0.00537     (     zero,     0.01510) *
   3          B--doshiae        0.01495     (  0.00038,     0.02964) **
   3            10              0.01714     (  0.00178,     0.03254) **
  10          B-bacillif        0.03572     (  0.01351,     0.05815) **
  10             6              0.01206     (     zero,     0.02565) **
   6            12              0.00006     (     zero,     0.00998)
  12          B-spp-Deer        0.00006     (     zero,    infinity)
  12          B-clarridg        0.04135     (  0.01794,     0.06512) **
   6             7              0.01678     (  0.00200,     0.03155) **
   7          B--weissii        0.00003     (     zero,    infinity)
   7            11              0.01679     (  0.00194,     0.03176) **
  11          B-henselae        0.01378     (  0.00026,     0.02748) **
  11          B-berhoffi        0.02046     (  0.00403,     0.03705) **
   4          A-tumefaci        0.19780     (  0.13933,     0.25792) **

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


Data set # 79:


Empirical Base Frequencies:

   A       0.30244
   C       0.22472
   G       0.27864
  T(U)     0.19421

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.440370)


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


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

Ln Likelihood = -1157.51392

Examined  712 trees

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

  12          B-birtlesi        0.01365     (     zero,     0.03111) *
  12             5              0.01857     (     zero,     0.03725) **
   5             2              0.00341     (     zero,     0.01029) *
   2             4              0.00003     (     zero,    infinity)
   4             6              0.01271     (     zero,     0.02697) **
   6          B--doshiae        0.01838     (  0.00173,     0.03508) **
   6             3              0.01118     (     zero,     0.02445) **
   3             8              0.01233     (     zero,     0.02660) **
   8          B--weissii        0.00823     (     zero,     0.01950) **
   8             9              0.00700     (     zero,     0.01790) **
   9          B-spp-Deer        0.00632     (     zero,     0.01620) **
   9          B-bacillif        0.04131     (  0.01728,     0.06530) **
   3          B-clarridg        0.05420     (  0.02609,     0.08270) **
   4          B-henselae        0.01393     (  0.00029,     0.02761) **
   2             7              0.00338     (     zero,     0.01012) *
   7            11              0.01379     (  0.00026,     0.02735) **
  11          B-elizabet        0.01024     (     zero,     0.02185) **
  11          B-grahamii        0.00003     (     zero,     0.00835)
   7          B-quintana        0.00690     (     zero,     0.01650) **
   5             1              0.00686     (     zero,     0.01655) **
   1            10              0.00338     (     zero,     0.01024) *
  10          B-arupensi        0.00691     (     zero,     0.01656) **
  10          B-berhoffi        0.02427     (  0.00625,     0.04238) **
   1          B-vinsonii        0.00344     (     zero,     0.01022) **
  12          A-tumefaci        0.31378     (  0.23530,     0.39576) **

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


Data set # 80:


Empirical Base Frequencies:

   A       0.25918
   C       0.21289
   G       0.33919
  T(U)     0.18874

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.427556)


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


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

Ln Likelihood = -1181.32656

Examined  586 trees

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

   7             1              0.02184     (  0.00432,     0.03944) **
   1            12              0.01046     (     zero,     0.02252) **
  12          B--weissii        0.02060     (  0.00405,     0.03731) **
  12             8              0.00661     (     zero,     0.01636) **
   8             9              0.01411     (  0.00018,     0.02797) **
   9          B-clarridg        0.03127     (  0.01072,     0.05181) **
   9          B-spp-Deer        0.00006     (     zero,     0.00839)
   8          B-bacillif        0.03137     (  0.01074,     0.05204) **
   1             4              0.00712     (     zero,     0.01717) **
   4             3              0.00003     (     zero,    infinity)
   3            10              0.00003     (     zero,     0.01132)
  10          B-henselae        0.01381     (  0.00030,     0.02743) **
  10             6              0.00696     (     zero,     0.01677) **
   6          B-quintana        0.01718     (  0.00204,     0.03247) **
   6          B-berhoffi        0.03469     (  0.01321,     0.05660) **
   3             2              0.00355     (     zero,     0.01051) **
   2          B-arupensi        0.00003     (     zero,    infinity)
   2             5              0.03040     (  0.00925,     0.05185) **
   5          B-elizabet        0.01263     (     zero,     0.02635) **
   5            11              0.01775     (  0.00100,     0.03453) **
  11          B-grahamii        0.00006     (     zero,     0.00842)
  11          B-birtlesi        0.05931     (  0.03009,     0.08878) **
   4          B-vinsonii        0.01022     (     zero,     0.02180) **
   7          B--doshiae        0.00006     (     zero,     0.01103)
   7          A-tumefaci        0.25985     (  0.18992,     0.33244) **

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


Data set # 81:


Empirical Base Frequencies:

   A       0.25706
   C       0.20214
   G       0.34828
  T(U)     0.19253

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.417279)


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


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

Ln Likelihood = -1195.24641

Examined  748 trees

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

   2          B--doshiae        0.00498     (     zero,     0.01802)
   2             3              0.01628     (     zero,     0.03295) **
   3             1              0.00004     (     zero,    infinity)
   1             6              0.00706     (     zero,     0.01684) **
   6            11              0.01795     (  0.00207,     0.03401) **
  11            12              0.01013     (     zero,     0.02202) **
  12          B-elizabet        0.01698     (  0.00206,     0.03196) **
  12          B-grahamii        0.00003     (     zero,     0.01091)
  11          B-birtlesi        0.03721     (  0.01397,     0.06045) **
   6          B-arupensi        0.00006     (     zero,    infinity)
   1             8              0.01367     (  0.00026,     0.02710) **
   8             4              0.00006     (     zero,    infinity)
   4             9              0.03041     (  0.00989,     0.05117) **
   9          B-clarridg        0.03278     (  0.01140,     0.05449) **
   9             7              0.00993     (     zero,     0.02196) **
   7            10              0.00434     (     zero,     0.01287) *
  10          B-bacillif        0.04889     (  0.02317,     0.07493) **
  10          B-spp-Deer        0.00336     (     zero,     0.01027) *
   7          B--weissii        0.01281     (     zero,     0.02620) **
   4          B-quintana        0.01378     (  0.00023,     0.02727) **
   8             5              0.01098     (     zero,     0.02357) **
   5          B-berhoffi        0.03034     (  0.00996,     0.05100) **
   5          B-henselae        0.01400     (  0.00021,     0.02781) **
   3          B-vinsonii        0.00338     (     zero,     0.01001) **
   2          A-tumefaci        0.28938     (  0.21399,     0.36713) **

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


Data set # 82:


Empirical Base Frequencies:

   A       0.28408
   C       0.21185
   G       0.33336
  T(U)     0.17071

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.377714)


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


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

Ln Likelihood = -1203.69295

Examined 1056 trees

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

   6            11              0.00988     (     zero,     0.02340) *
  11            10              0.00815     (     zero,     0.01956) **
  10          B-berhoffi        0.04173     (  0.01726,     0.06625) **
  10          B-henselae        0.00733     (     zero,     0.01758) **
  11             8              0.00003     (     zero,     0.00854)
   8          B-quintana        0.01747     (  0.00218,     0.03296) **
   8             4              0.00619     (     zero,     0.01567) **
   4             5              0.00362     (     zero,     0.01071) **
   5          B-arupensi        0.00006     (     zero,     0.00784)
   5          B-vinsonii        0.01377     (  0.00021,     0.02730) **
   4             3              0.01397     (  0.00011,     0.02789) **
   3             1              0.01752     (  0.00205,     0.03317) **
   1             2              0.00003     (     zero,     0.00962)
   2            12              0.01077     (     zero,     0.02301) **
  12          B-spp-Deer        0.00672     (     zero,     0.01647) **
  12          B-clarridg        0.03574     (  0.01349,     0.05817) **
   2          B--weissii        0.00999     (     zero,     0.02170) **
   1          B-bacillif        0.05620     (  0.02856,     0.08434) **
   3          B--doshiae        0.01762     (  0.00199,     0.03321) **
   6             9              0.01653     (     zero,     0.03434) **
   9          B-birtlesi        0.05940     (  0.02932,     0.08983) **
   9             7              0.01021     (     zero,     0.02240) **
   7          B-elizabet        0.02063     (  0.00413,     0.03724) **
   7          B-grahamii        0.00003     (     zero,     0.00720)
   6          A-tumefaci        0.22347     (  0.15982,     0.28914) **

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


Data set # 83:


Empirical Base Frequencies:

   A       0.28746
   C       0.21995
   G       0.30726
  T(U)     0.18532

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.416983)


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


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

Ln Likelihood = -1065.24345

Examined  520 trees

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

   7          B--doshiae        0.00003     (     zero,     0.00787)
   7             3              0.00353     (     zero,     0.01049) **
   3             2              0.00914     (     zero,     0.02058) **
   2          B--weissii        0.00470     (     zero,     0.01334) **
   2             9              0.00669     (     zero,     0.01642) **
   9          B-clarridg        0.03493     (  0.01319,     0.05678) **
   9          B-spp-Deer        0.00325     (     zero,     0.00994) *
   3             5              0.01056     (     zero,     0.02253) **
   5             6              0.00366     (     zero,     0.01119) *
   6          B-bacillif        0.03090     (  0.01040,     0.05132) **
   6            10              0.01067     (     zero,     0.02292) **
  10          B-arupensi        0.00702     (     zero,     0.01684) **
  10            11              0.01398     (     zero,     0.02797) **
  11            12              0.00703     (     zero,     0.01683) **
  12          B-birtlesi        0.04018     (  0.01640,     0.06414) **
  12          B-grahamii        0.00014     (     zero,    infinity)
  11          B-elizabet        0.00333     (     zero,     0.01000) *
   5             4              0.00003     (     zero,    infinity)
   4          B-vinsonii        0.01706     (  0.00206,     0.03202) **
   4             1              0.00321     (     zero,     0.00986) *
   1          B-quintana        0.00708     (     zero,     0.01683) **
   1             8              0.00389     (     zero,     0.01168) *
   8          B-henselae        0.01024     (     zero,     0.02199) **
   8          B-berhoffi        0.02029     (  0.00360,     0.03703) **
   7          A-tumefaci        0.24512     (  0.17859,     0.31368) **

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


Data set # 84:


Empirical Base Frequencies:

   A       0.30468
   C       0.23190
   G       0.31368
  T(U)     0.14975

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.391543)


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


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

Ln Likelihood = -1212.80710

Examined  734 trees

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

   8          B--doshiae        0.00003     (     zero,     0.01378)
   8             7              0.02117     (  0.00417,     0.03823) **
   7             2              0.00006     (     zero,     0.01133)
   2            12              0.00680     (     zero,     0.01625) **
  12          B-vinsonii        0.00006     (     zero,    infinity)
  12          B-arupensi        0.00338     (     zero,     0.01001) **
   2             9              0.01023     (     zero,     0.02181) **
   9          B-quintana        0.01023     (     zero,     0.02180) **
   9             1              0.00003     (     zero,    infinity)
   1            10              0.01307     (     zero,     0.02760) **
  10          B-berhoffi        0.04922     (  0.02295,     0.07609) **
  10          B-henselae        0.00342     (     zero,     0.01035) *
   1             3              0.02689     (  0.00748,     0.04654) **
   3            11              0.00994     (     zero,     0.02210) **
  11             6              0.00780     (     zero,     0.01878) **
   6          B-spp-Deer        0.01021     (     zero,     0.02196) **
   6          B-bacillif        0.03473     (  0.01305,     0.05644) **
  11          B--weissii        0.01614     (  0.00109,     0.03113) **
   3          B-clarridg        0.03637     (  0.01375,     0.05916) **
   7             4              0.03074     (  0.00971,     0.05216) **
   4             5              0.02201     (  0.00413,     0.03991) **
   5          B-grahamii        0.00006     (     zero,     0.01128)
   5          B-elizabet        0.01340     (  0.00026,     0.02665) **
   4          B-birtlesi        0.02923     (  0.00858,     0.04987) **
   8          A-tumefaci        0.28435     (  0.21048,     0.36049) **

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


Data set # 85:


Empirical Base Frequencies:

   A       0.32426
   C       0.22584
   G       0.28769
  T(U)     0.16221

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.397685)


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


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

Ln Likelihood = -1163.97474

Examined  714 trees

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

   8          B--doshiae        0.00469     (     zero,     0.01681)
   8             2              0.01337     (     zero,     0.02888) **
   2             3              0.00334     (     zero,     0.01063)
   3          B-vinsonii        0.01426     (  0.00033,     0.02831) **
   3            12              0.00369     (     zero,     0.01114) *
  12          B-arupensi        0.00340     (     zero,     0.01067)
  12             6              0.03402     (  0.01178,     0.05660) **
   6             7              0.01018     (     zero,     0.02238) **
   7          B-grahamii        0.00003     (     zero,     0.00769)
   7          B-elizabet        0.01389     (  0.00026,     0.02752) **
   6          B-birtlesi        0.02657     (  0.00680,     0.04657) **
   2             9              0.01085     (     zero,     0.02318) **
   9             4              0.02517     (  0.00612,     0.04430) **
   4          B-clarridg        0.05468     (  0.02673,     0.08295) **
   4            10              0.01375     (     zero,     0.02839) **
  10          B--weissii        0.00352     (     zero,     0.01074) *
  10            11              0.01420     (  0.00010,     0.02828) **
  11          B-spp-Deer        0.00705     (     zero,     0.01727) **
  11          B-bacillif        0.03550     (  0.01322,     0.05782) **
   9             1              0.00003     (     zero,     0.00767)
   1          B-quintana        0.00006     (     zero,    infinity)
   1             5              0.01750     (  0.00198,     0.03305) **
   5          B-berhoffi        0.01753     (  0.00197,     0.03309) **
   5          B-henselae        0.01436     (  0.00021,     0.02851) **
   8          A-tumefaci        0.24903     (  0.18020,     0.31944) **

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


Data set # 86:


Empirical Base Frequencies:

   A       0.25373
   C       0.22622
   G       0.30814
  T(U)     0.21191

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.473334)


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


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

Ln Likelihood = -1210.12859

Examined 1018 trees

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

  10          B--doshiae        0.00003     (     zero,     0.01234)
  10            12              0.02893     (  0.00890,     0.04913) **
  12             3              0.01063     (     zero,     0.02268) **
   3             9              0.00351     (     zero,     0.01089)
   9          B-vinsonii        0.01025     (     zero,     0.02193) **
   9          B-arupensi        0.01379     (  0.00026,     0.02738) **
   3          B-berhoffi        0.02755     (  0.00821,     0.04690) **
  12             2              0.00025     (     zero,     0.00719)
   2          B-quintana        0.01003     (     zero,     0.02164) **
   2            11              0.00301     (     zero,     0.00987)
  11          B-henselae        0.00340     (     zero,     0.01004) **
  11             4              0.00006     (     zero,     0.00893)
   4             6              0.03970     (  0.01512,     0.06447) **
   6          B-birtlesi        0.04101     (  0.01665,     0.06574) **
   6             1              0.01361     (     zero,     0.02922) **
   1          B-grahamii        0.00006     (     zero,     0.00771)
   1          B-elizabet        0.01699     (  0.00209,     0.03195) **
   4             7              0.03875     (  0.01586,     0.06194) **
   7          B-bacillif        0.04243     (  0.01834,     0.06667) **
   7             8              0.00255     (     zero,     0.00954)
   8          B--weissii        0.00003     (     zero,    infinity)
   8             5              0.00703     (     zero,     0.01690) **
   5          B-clarridg        0.05719     (  0.02893,     0.08570) **
   5          B-spp-Deer        0.01007     (     zero,     0.02178) **
  10          A-tumefaci        0.24035     (  0.17458,     0.30951) **

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


Data set # 87:


Empirical Base Frequencies:

   A       0.28482
   C       0.20647
   G       0.29471
  T(U)     0.21400

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.437342)


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


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

Ln Likelihood = -1102.71954

Examined 2418 trees

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

   5          B--doshiae        0.00006     (     zero,     0.00899)
   5             8              0.00676     (     zero,     0.01666) **
   8             4              0.01408     (  0.00011,     0.02805) **
   4            10              0.00005     (     zero,    infinity)
  10          B-quintana        0.01344     (  0.00026,     0.02662) **
  10             3              0.00344     (     zero,     0.01022) **
   3            12              0.00346     (     zero,     0.01025) **
  12             6              0.01022     (     zero,     0.02224) **
   6            11              0.01707     (  0.00194,     0.03218) **
  11          B-elizabet        0.02001     (  0.00399,     0.03613) **
  11          B-grahamii        0.00006     (     zero,     0.00854)
   6          B-birtlesi        0.03204     (  0.01099,     0.05313) **
  12          B-arupensi        0.00003     (     zero,    infinity)
   3          B-vinsonii        0.01000     (     zero,     0.02135) **
   4             2              0.00328     (     zero,     0.00973) **
   2          B-berhoffi        0.01682     (  0.00207,     0.03160) **
   2          B-henselae        0.00003     (     zero,    infinity)
   8             1              0.03748     (  0.01527,     0.05995) **
   1          B--weissii        0.00003     (     zero,    infinity)
   1             7              0.00331     (     zero,     0.00979) **
   7             9              0.00003     (     zero,    infinity)
   9          B-clarridg        0.04131     (  0.01778,     0.06490) **
   9          B-bacillif        0.04044     (  0.01755,     0.06366) **
   7          B-spp-Deer        0.00003     (     zero,    infinity)
   5          A-tumefaci        0.26022     (  0.19267,     0.33166) **

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


Data set # 88:


Empirical Base Frequencies:

   A       0.26619
   C       0.23475
   G       0.30178
  T(U)     0.19728

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.464502)


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


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

Ln Likelihood = -1178.03537

Examined  550 trees

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

   2             1              0.00730     (     zero,     0.01834) *
   1             9              0.01345     (  0.00004,     0.02680) **
   9          B-grahamii        0.00006     (     zero,     0.00777)
   9          B-elizabet        0.00327     (     zero,     0.00969) **
   1          B-birtlesi        0.03582     (  0.01355,     0.05831) **
   2             5              0.00280     (     zero,     0.01051)
   5          B-arupensi        0.00003     (     zero,    infinity)
   5             4              0.01002     (     zero,     0.02133) **
   4          B-vinsonii        0.00665     (     zero,     0.01589) **
   4             6              0.00329     (     zero,     0.00981) **
   6          B-quintana        0.01670     (  0.00210,     0.03142) **
   6             7              0.00003     (     zero,    infinity)
   7          B-henselae        0.01001     (     zero,     0.02134) **
   7            10              0.00006     (     zero,     0.00827)
  10          B-berhoffi        0.03006     (  0.01042,     0.04992) **
  10             8              0.01288     (     zero,     0.02653) **
   8          B--doshiae        0.03797     (  0.01531,     0.06086) **
   8             3              0.04128     (  0.01771,     0.06517) **
   3            12              0.00319     (     zero,     0.00988)
  12          B-bacillif        0.03013     (  0.01043,     0.05004) **
  12            11              0.00676     (     zero,     0.01614) **
  11          B-clarridg        0.06514     (  0.03575,     0.09518) **
  11          B-spp-Deer        0.00006     (     zero,    infinity)
   3          B--weissii        0.00331     (     zero,     0.00996) *
   2          A-tumefaci        0.25800     (  0.18871,     0.32903) **

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


Data set # 89:


Empirical Base Frequencies:

   A       0.27426
   C       0.27798
   G       0.29768
  T(U)     0.15008

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.524888)


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


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

Ln Likelihood = -1114.84091

Examined  518 trees

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

   9          B--doshiae        0.00003     (     zero,     0.00948)
   9             6              0.02549     (  0.00648,     0.04448) **
   6             4              0.01412     (  0.00007,     0.02825) **
   4             1              0.00338     (     zero,     0.00999) **
   1          B-quintana        0.00006     (     zero,    infinity)
   1             5              0.00686     (     zero,     0.01646) **
   5            12              0.01386     (  0.00014,     0.02759) **
  12          B-arupensi        0.01379     (  0.00025,     0.02743) **
  12          B-vinsonii        0.00685     (     zero,     0.01649) **
   5          B-berhoffi        0.02401     (  0.00623,     0.04202) **
   4             2              0.00003     (     zero,    infinity)
   2          B-henselae        0.00006     (     zero,    infinity)
   2            10              0.00849     (     zero,     0.02163) **
  10          B-birtlesi        0.04584     (  0.01998,     0.07177) **
  10             7              0.01062     (     zero,     0.02369) **
   7          B-elizabet        0.00851     (     zero,     0.01959) **
   7          B-grahamii        0.00162     (     zero,     0.00826)
   6             3              0.01360     (  0.00002,     0.02720) **
   3            11              0.00003     (     zero,     0.01202)
  11             8              0.01428     (  0.00029,     0.02827) **
   8          B-spp-Deer        0.00284     (     zero,     0.00958)
   8          B-clarridg        0.05653     (  0.02882,     0.08490) **
  11          B--weissii        0.00003     (     zero,    infinity)
   3          B-bacillif        0.03771     (  0.01540,     0.06032) **
   9          A-tumefaci        0.24076     (  0.17318,     0.30997) **

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


Data set # 90:


Empirical Base Frequencies:

   A       0.28467
   C       0.19986
   G       0.32184
  T(U)     0.19363

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.391283)


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


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

Ln Likelihood = -1327.69313

Examined 1262 trees

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

   5          B--doshiae        0.00003     (     zero,     0.01242)
   5             8              0.03251     (  0.01125,     0.05420) **
   8             3              0.01408     (     zero,     0.02837) **
   3            12              0.00006     (     zero,    infinity)
  12          B-quintana        0.02070     (  0.00418,     0.03740) **
  12             4              0.01832     (  0.00216,     0.03442) **
   4             9              0.00003     (     zero,     0.01005)
   9             7              0.01631     (  0.00051,     0.03203) **
   7          B-birtlesi        0.06847     (  0.03663,     0.10066) **
   7             1              0.01103     (     zero,     0.02435) **
   1          B-grahamii        0.00003     (     zero,     0.00895)
   1          B-elizabet        0.02374     (  0.00621,     0.04153) **
   9          B-bacillif        0.06899     (  0.03837,     0.10038) **
   4             2              0.00690     (     zero,     0.01649) **
   2             6              0.00405     (     zero,     0.01219) *
   6          B-arupensi        0.01372     (  0.00023,     0.02720) **
   6          B-vinsonii        0.01018     (     zero,     0.02180) **
   2          B-berhoffi        0.02692     (  0.00769,     0.04617) **
   3          B-henselae        0.01721     (  0.00211,     0.03233) **
   8            10              0.01727     (  0.00184,     0.03271) **
  10          B--weissii        0.00006     (     zero,    infinity)
  10            11              0.01066     (     zero,     0.02278) **
  11          B-clarridg        0.06035     (  0.03164,     0.08977) **
  11          B-spp-Deer        0.00303     (     zero,     0.00990)
   5          A-tumefaci        0.29676     (  0.22065,     0.37497) **

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


Data set # 91:


Empirical Base Frequencies:

   A       0.28232
   C       0.25439
   G       0.27460
  T(U)     0.18869

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.486622)


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


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

Ln Likelihood = -1267.74521

Examined  574 trees

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

   8          B-birtlesi        0.03740     (  0.01033,     0.06439) **
   8             4              0.03268     (  0.00678,     0.05864) **
   4             5              0.00679     (     zero,     0.01641) **
   5             1              0.01269     (     zero,     0.02614) **
   1             7              0.00185     (     zero,     0.00872)
   7          B-quintana        0.02433     (  0.00635,     0.04253) **
   7             9              0.00326     (     zero,     0.01033)
   9          B-berhoffi        0.02089     (  0.00400,     0.03779) **
   9             2              0.02052     (  0.00318,     0.03782) **
   2            11              0.00650     (     zero,     0.01686) *
  11          B-clarridg        0.04843     (  0.02264,     0.07476) **
  11             6              0.00777     (     zero,     0.01871) **
   6          B-spp-Deer        0.00345     (     zero,     0.01029) **
   6          B--weissii        0.00677     (     zero,     0.01627) **
   2          B-bacillif        0.05032     (  0.02388,     0.07724) **
   1          B-henselae        0.01635     (  0.00129,     0.03142) **
   5             3              0.00668     (     zero,     0.01655) **
   3          B--doshiae        0.03152     (  0.01083,     0.05235) **
   3            10              0.01741     (  0.00208,     0.03294) **
  10          B-elizabet        0.00337     (     zero,     0.01016) *
  10          B-grahamii        0.00684     (     zero,     0.01641) **
   4            12              0.00354     (     zero,     0.01052) **
  12          B-vinsonii        0.00006     (     zero,    infinity)
  12          B-arupensi        0.01360     (  0.00033,     0.02702) **
   8          A-tumefaci        0.32742     (  0.24450,     0.41305) **

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


Data set # 92:


Empirical Base Frequencies:

   A       0.27891
   C       0.19615
   G       0.32109
  T(U)     0.20385

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.406218)


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


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

Ln Likelihood = -1325.32731

Examined 1036 trees

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

  12             6              0.02101     (  0.00280,     0.03920) **
   6            11              0.00354     (     zero,     0.01057) *
  11          B-vinsonii        0.01454     (  0.00044,     0.02880) **
  11          B-arupensi        0.01284     (     zero,     0.02624) **
   6             7              0.00805     (     zero,     0.01944) **
   7          B-birtlesi        0.05945     (  0.02992,     0.08889) **
   7             1              0.00678     (     zero,     0.01669) **
   1             3              0.00006     (     zero,    infinity)
   3             2              0.01655     (  0.00091,     0.03218) **
   2             4              0.01756     (  0.00189,     0.03344) **
   4             9              0.00955     (     zero,     0.02275) **
   9             8              0.01788     (  0.00208,     0.03381) **
   8          B-clarridg        0.05741     (  0.02923,     0.08621) **
   8          B-spp-Deer        0.00279     (     zero,     0.00976)
   9          B--weissii        0.00362     (     zero,     0.01093) *
   4          B-bacillif        0.05346     (  0.02592,     0.08152) **
   2             5              0.00318     (     zero,     0.01323)
   5            10              0.03561     (  0.01351,     0.05801) **
  10          B-elizabet        0.02058     (  0.00407,     0.03709) **
  10          B-grahamii        0.00003     (     zero,     0.00773)
   5          B-berhoffi        0.04660     (  0.02103,     0.07219) **
   3          B-henselae        0.00685     (     zero,     0.01634) **
   1          B-quintana        0.01710     (  0.00216,     0.03220) **
  12          B--doshiae        0.00275     (     zero,     0.01473)
  12          A-tumefaci        0.30522     (  0.22744,     0.38655) **

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


Data set # 93:


Empirical Base Frequencies:

   A       0.22944
   C       0.21711
   G       0.34670
  T(U)     0.20675

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.491855)


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


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

Ln Likelihood = -1124.93502

Examined  950 trees

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

  12          B--doshiae        0.00006     (     zero,     0.00953)
  12             8              0.01120     (     zero,     0.02419) **
   8             5              0.01481     (  0.00010,     0.02966) **
   5            10              0.00341     (     zero,     0.01008) **
  10          B-arupensi        0.00006     (     zero,    infinity)
  10          B-vinsonii        0.00686     (     zero,     0.01633) **
   5             1              0.00004     (     zero,    infinity)
   1             2              0.00740     (     zero,     0.01770) **
   2             4              0.01106     (     zero,     0.02362) **
   4          B-birtlesi        0.04528     (  0.01966,     0.07115) **
   4          B-grahamii        0.00003     (     zero,     0.00806)
   2          B-elizabet        0.00682     (     zero,     0.01637) **
   1             6              0.00679     (     zero,     0.01630) **
   6            11              0.00385     (     zero,     0.01150) **
  11          B-henselae        0.00336     (     zero,     0.01015) *
  11          B-berhoffi        0.02362     (  0.00581,     0.04163) **
   6          B-quintana        0.00353     (     zero,     0.01047) **
   8             3              0.02846     (  0.00856,     0.04859) **
   3          B--weissii        0.00649     (     zero,     0.01640) **
   3             7              0.01017     (     zero,     0.02232) **
   7          B-bacillif        0.04607     (  0.02074,     0.07158) **
   7             9              0.01430     (  0.00010,     0.02850) **
   9          B-spp-Deer        0.00003     (     zero,     0.00809)
   9          B-clarridg        0.06036     (  0.03150,     0.08966) **
  12          A-tumefaci        0.25885     (  0.18867,     0.33085) **

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


Data set # 94:


Empirical Base Frequencies:

   A       0.32454
   C       0.19319
   G       0.28639
  T(U)     0.19588

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.381722)


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


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

Ln Likelihood = -1213.62879

Examined  680 trees

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

  10          B-henselae        0.00006     (     zero,     0.00744)
  10             2              0.01763     (  0.00209,     0.03318) **
   2             1              0.00689     (     zero,     0.01652) **
   1          B-berhoffi        0.01718     (  0.00202,     0.03234) **
   1            12              0.01723     (  0.00205,     0.03246) **
  12          B-vinsonii        0.00335     (     zero,     0.01009) *
  12          B-arupensi        0.00685     (     zero,     0.01641) **
   2             9              0.00006     (     zero,     0.00795)
   9             3              0.00697     (     zero,     0.01666) **
   3             7              0.00700     (     zero,     0.01679) **
   7          B-grahamii        0.00682     (     zero,     0.01632) **
   7             4              0.00701     (     zero,     0.01675) **
   4          B-birtlesi        0.08085     (  0.04674,     0.11541) **
   4          B-elizabet        0.00006     (     zero,     0.00747)
   3          B-quintana        0.00341     (     zero,     0.01012) **
   9             6              0.01366     (     zero,     0.02740) **
   6          B--doshiae        0.02453     (  0.00628,     0.04298) **
   6             8              0.01729     (  0.00195,     0.03280) **
   8            11              0.00947     (     zero,     0.02120) **
  11             5              0.00593     (     zero,     0.01596)
   5          B-bacillif        0.02572     (  0.00665,     0.04499) **
   5          B-clarridg        0.06381     (  0.03365,     0.09419) **
  11          B-spp-Deer        0.00772     (     zero,     0.01829) **
   8          B--weissii        0.00682     (     zero,     0.01644) **
  10          A-tumefaci        0.32333     (  0.24327,     0.40634) **

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


Data set # 95:


Empirical Base Frequencies:

   A       0.32123
   C       0.20474
   G       0.27643
  T(U)     0.19759

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.411587)


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


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

Ln Likelihood = -1327.56491

Examined 1044 trees

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

   8             2              0.00263     (     zero,     0.00942)
   2             7              0.02411     (  0.00498,     0.04347) **
   7          B-birtlesi        0.03933     (  0.01568,     0.06321) **
   7            12              0.02834     (  0.00777,     0.04887) **
  12          B-grahamii        0.00006     (     zero,     0.01141)
  12          B-elizabet        0.02375     (  0.00609,     0.04146) **
   2          B-henselae        0.01742     (  0.00209,     0.03271) **
   8             3              0.00006     (     zero,     0.00800)
   3             5              0.02066     (  0.00386,     0.03750) **
   5          B--doshiae        0.01403     (     zero,     0.02822) **
   5            11              0.03394     (  0.01212,     0.05583) **
  11          B--weissii        0.00744     (     zero,     0.01796) **
  11             1              0.00991     (     zero,     0.02166) **
   1             9              0.00878     (     zero,     0.02078) *
   9          B-clarridg        0.07281     (  0.04077,     0.10567) **
   9          B-bacillif        0.03240     (  0.01099,     0.05383) **
   1          B-spp-Deer        0.00003     (     zero,     0.00893)
   3             6              0.00006     (     zero,     0.00712)
   6          B-quintana        0.00672     (     zero,     0.01604) **
   6            10              0.00732     (     zero,     0.01739) **
  10             4              0.00315     (     zero,     0.00998)
   4          B-arupensi        0.01382     (  0.00017,     0.02743) **
   4          B-berhoffi        0.03797     (  0.01559,     0.06081) **
  10          B-vinsonii        0.00335     (     zero,     0.00995) **
   8          A-tumefaci        0.35869     (  0.27103,     0.44916) **

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


Data set # 96:


Empirical Base Frequencies:

   A       0.28788
   C       0.18941
   G       0.34831
  T(U)     0.17439

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.326836)


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


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

Ln Likelihood = -1300.15811

Examined  826 trees

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

  12          B-arupensi        0.00006     (     zero,     0.00953)
  12            11              0.00591     (     zero,     0.01579) *
  11            10              0.01091     (     zero,     0.02355) **
  10             2              0.00843     (     zero,     0.02022) **
   2             1              0.02394     (  0.00481,     0.04316) **
   1             6              0.01882     (  0.00217,     0.03559) **
   6          B-elizabet        0.02745     (  0.00848,     0.04672) **
   6          B-grahamii        0.00003     (     zero,     0.00816)
   1          B-birtlesi        0.04946     (  0.02218,     0.07664) **
   2             4              0.00334     (     zero,     0.01024) *
   4             3              0.00006     (     zero,     0.00789)
   3          B-quintana        0.01033     (     zero,     0.02202) **
   3             8              0.01022     (     zero,     0.02186) **
   8          B-berhoffi        0.02777     (  0.00853,     0.04724) **
   8          B-henselae        0.00346     (     zero,     0.01028) **
   4             5              0.02114     (  0.00411,     0.03836) **
   5          B-bacillif        0.06412     (  0.03408,     0.09424) **
   5             7              0.00627     (     zero,     0.01621) *
   7          B--weissii        0.00003     (     zero,     0.00729)
   7             9              0.00706     (     zero,     0.01696) **
   9          B-clarridg        0.05709     (  0.02894,     0.08562) **
   9          B-spp-Deer        0.00664     (     zero,     0.01623) **
  10          B--doshiae        0.03753     (  0.01478,     0.06069) **
  11          B-vinsonii        0.01492     (  0.00043,     0.02942) **
  12          A-tumefaci        0.34992     (  0.26374,     0.43999) **

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


Data set # 97:


Empirical Base Frequencies:

   A       0.29876
   C       0.20765
   G       0.27072
  T(U)     0.22287

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.455530)


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


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

Ln Likelihood = -1160.53535

Examined  588 trees

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

   6            12              0.03790     (  0.01281,     0.06325) **
  12             3              0.00399     (     zero,     0.01285)
   3             1              0.00345     (     zero,     0.01026) **
   1             4              0.00680     (     zero,     0.01652) **
   4             5              0.01040     (     zero,     0.02226) **
   5          B-clarridg        0.05403     (  0.02639,     0.08173) **
   5            10              0.00003     (     zero,     0.01024)
  10          B--weissii        0.00343     (     zero,     0.01015) **
  10            11              0.00694     (     zero,     0.01664) **
  11          B-bacillif        0.02806     (  0.00850,     0.04759) **
  11          B-spp-Deer        0.00342     (     zero,     0.01036) *
   4          B-berhoffi        0.02134     (  0.00428,     0.03857) **
   1          B-quintana        0.01400     (  0.00024,     0.02773) **
   3             2              0.00003     (     zero,     0.00729)
   2             7              0.00350     (     zero,     0.01033) **
   7          B-vinsonii        0.00687     (     zero,     0.01638) **
   7          B-arupensi        0.00342     (     zero,     0.01015) **
   2             8              0.01035     (     zero,     0.02237) **
   8          B--doshiae        0.01046     (     zero,     0.02257) **
   8             9              0.03905     (  0.01593,     0.06250) **
   9          B-elizabet        0.00350     (     zero,     0.01045) *
   9          B-grahamii        0.00337     (     zero,     0.01019) *
  12          B-henselae        0.00988     (     zero,     0.02215) **
   6          B-birtlesi        0.01667     (     zero,     0.03689) *
   6          A-tumefaci        0.29988     (  0.22235,     0.38083) **

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


Data set # 98:


Empirical Base Frequencies:

   A       0.30232
   C       0.27038
   G       0.26796
  T(U)     0.15934

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.510588)


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


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

Ln Likelihood = -1144.27537

Examined 1666 trees

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

   7          B--doshiae        0.00003     (     zero,     0.01254)
   7             8              0.01776     (  0.00211,     0.03353) **
   8             2              0.00692     (     zero,     0.01689) **
   2            10              0.01052     (     zero,     0.02243) **
  10          B-berhoffi        0.01694     (  0.00207,     0.03183) **
  10             3              0.00003     (     zero,     0.00842)
   3             6              0.02133     (  0.00387,     0.03870) **
   6             9              0.01691     (  0.00169,     0.03217) **
   9          B-grahamii        0.00006     (     zero,    infinity)
   9          B-elizabet        0.00668     (     zero,     0.01595) **
   6          B-birtlesi        0.04005     (  0.01634,     0.06417) **
   3          B-arupensi        0.00336     (     zero,     0.00994) **
   2            11              0.00003     (     zero,    infinity)
  11          B-quintana        0.00673     (     zero,     0.01606) **
  11             1              0.00003     (     zero,    infinity)
   1          B-vinsonii        0.01343     (  0.00029,     0.02664) **
   1          B-henselae        0.00675     (     zero,     0.01610) **
   8            12              0.02745     (  0.00840,     0.04672) **
  12             5              0.00194     (     zero,     0.00871)
   5             4              0.00345     (     zero,     0.01037) *
   4          B-spp-Deer        0.00468     (     zero,     0.01342) *
   4          B-clarridg        0.06516     (  0.03508,     0.09559) **
   5          B-bacillif        0.03197     (  0.01121,     0.05287) **
  12          B--weissii        0.00336     (     zero,     0.01005) **
   7          A-tumefaci        0.25867     (  0.19010,     0.32945) **

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


Data set # 99:


Empirical Base Frequencies:

   A       0.26227
   C       0.23104
   G       0.29168
  T(U)     0.21501

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.475168)


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


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

Ln Likelihood = -1311.52703

Examined  608 trees

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

   9             4              0.03271     (  0.01094,     0.05448) **
   4             1              0.01350     (     zero,     0.02801) **
   1             2              0.01051     (     zero,     0.02254) **
   2            11              0.00726     (     zero,     0.01836) *
  11          B-birtlesi        0.04377     (  0.01901,     0.06903) **
  11            10              0.02679     (  0.00773,     0.04619) **
  10          B-grahamii        0.00006     (     zero,     0.00793)
  10          B-elizabet        0.02347     (  0.00608,     0.04103) **
   2             5              0.00675     (     zero,     0.01619) **
   5             3              0.00003     (     zero,     0.00707)
   3             7              0.01028     (     zero,     0.02202) **
   7          B-quintana        0.01678     (  0.00198,     0.03174) **
   7          B-berhoffi        0.02737     (  0.00827,     0.04651) **
   3             6              0.03375     (  0.01285,     0.05496) **
   6          B--weissii        0.00003     (     zero,    infinity)
   6             8              0.01785     (  0.00232,     0.03350) **
   8          B-clarridg        0.07744     (  0.04503,     0.11081) **
   8          B-spp-Deer        0.00245     (     zero,     0.00919)
   5          B-henselae        0.01012     (     zero,     0.02158) **
   1            12              0.00328     (     zero,     0.00998) *
  12          B-arupensi        0.00673     (     zero,     0.01610) **
  12          B-vinsonii        0.00337     (     zero,     0.01001) **
   4          B-bacillif        0.05642     (  0.02837,     0.08459) **
   9          B--doshiae        0.00003     (     zero,     0.01535)
   9          A-tumefaci        0.28955     (  0.21580,     0.36761) **

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


Data set # 100:


Empirical Base Frequencies:

   A       0.27984
   C       0.23168
   G       0.31080
  T(U)     0.17768

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.434256)


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


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

Ln Likelihood = -1260.38193

Examined  588 trees

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

   6          B--doshiae        0.00003     (     zero,     0.01279)
   6             2              0.01761     (  0.00212,     0.03311) **
   2            11              0.00340     (     zero,     0.01041) *
  11            10              0.00701     (     zero,     0.01677) **
  10             8              0.01868     (  0.00132,     0.03617) **
   8          B-birtlesi        0.08184     (  0.04666,     0.11745) **
   8             1              0.02439     (  0.00555,     0.04327) **
   1          B-elizabet        0.00441     (     zero,     0.01336) *
   1          B-grahamii        0.01247     (     zero,     0.02588) **
  10          B-arupensi        0.00006     (     zero,     0.00702)
  11          B-vinsonii        0.01704     (  0.00210,     0.03204) **
   2             5              0.00881     (     zero,     0.02016) **
   5             7              0.00195     (     zero,     0.00868)
   7            12              0.00691     (     zero,     0.01664) **
  12          B-berhoffi        0.02411     (  0.00600,     0.04211) **
  12             3              0.01045     (     zero,     0.02252) **
   3          B-bacillif        0.04843     (  0.02306,     0.07444) **
   3             4              0.00325     (     zero,     0.01031)
   4          B--weissii        0.01007     (     zero,     0.02159) **
   4             9              0.00352     (     zero,     0.01043) **
   9          B-spp-Deer        0.00003     (     zero,    infinity)
   9          B-clarridg        0.04160     (  0.01802,     0.06547) **
   7          B-quintana        0.01382     (  0.00023,     0.02737) **
   5          B-henselae        0.01987     (  0.00352,     0.03642) **
   6          A-tumefaci        0.34024     (  0.25681,     0.42688) **

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