Nucleic acid sequence Maximum Likelihood method, version 3.573c

Data set # 1:


Empirical Base Frequencies:

   A       0.26125
   C       0.22134
   G       0.31128
  T(U)     0.20612

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.457281)


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


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

Ln Likelihood = -11203.68102

Examined  704 trees

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

   5          B-clarridg        0.01139     (  0.00787,     0.01502) **
   5             8              0.00784     (  0.00471,     0.01094) **
   8             3              0.00405     (  0.00196,     0.00617) **
   3            10              0.01105     (  0.00758,     0.01446) **
  10          B-spp-Deer        0.00846     (  0.00560,     0.01137) **
  10          B--weissii        0.00254     (  0.00088,     0.00421) **
   3             2              0.00865     (  0.00552,     0.01176) **
   2             9              0.00390     (  0.00192,     0.00591) **
   9          B-quintana        0.01199     (  0.00855,     0.01542) **
   9          B-henselae        0.00625     (  0.00377,     0.00880) **
   2             1              0.00119     (     zero,     0.00240) **
   1             4              0.00062     (     zero,     0.00149) **
   4          B--doshiae        0.00335     (  0.00155,     0.00517) **
   4            12              0.00263     (  0.00088,     0.00443) **
  12             6              0.00280     (  0.00107,     0.00449) **
   6          B-elizabet        0.01123     (  0.00792,     0.01453) **
   6          B-grahamii        0.00493     (  0.00273,     0.00714) **
  12          B-birtlesi        0.01302     (  0.00941,     0.01658) **
   1            11              0.00208     (  0.00054,     0.00364) **
  11             7              0.00178     (  0.00033,     0.00318) **
   7          B-arupensi        0.00470     (  0.00247,     0.00694) **
   7          B-berhoffi        0.00594     (  0.00351,     0.00839) **
  11          B-vinsonii        0.00424     (  0.00212,     0.00633) **
   8          B-bacillif        0.01065     (  0.00720,     0.01401) **
   5          A-tumefaci        0.09984     (  0.08973,     0.11069) **

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


Data set # 2:


Empirical Base Frequencies:

   A       0.26270
   C       0.21732
   G       0.30329
  T(U)     0.21669

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.462355)


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


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

Ln Likelihood = -11201.13254

Examined  838 trees

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

   8             2              0.00737     (  0.00443,     0.01042) **
   2          B-bacillif        0.00859     (  0.00562,     0.01166) **
   2             3              0.00428     (  0.00204,     0.00652) **
   3          B-clarridg        0.01395     (  0.01011,     0.01777) **
   3            10              0.01240     (  0.00886,     0.01599) **
  10          B--weissii        0.00602     (  0.00352,     0.00857) **
  10          B-spp-Deer        0.00667     (  0.00400,     0.00930) **
   8             4              0.00505     (  0.00240,     0.00772) **
   4             1              0.00109     (  0.00001,     0.00220) **
   1            11              0.00070     (     zero,     0.00165) **
  11            12              0.00159     (  0.00031,     0.00284) **
  12          B-grahamii        0.00792     (  0.00517,     0.01077) **
  12          B--doshiae        0.00315     (  0.00135,     0.00494) **
  11          B-birtlesi        0.01041     (  0.00725,     0.01360) **
   1             6              0.00325     (  0.00135,     0.00518) **
   6          B-elizabet        0.00978     (  0.00663,     0.01294) **
   6             7              0.00236     (  0.00075,     0.00395) **
   7          B-henselae        0.00591     (  0.00339,     0.00840) **
   7          B-quintana        0.01179     (  0.00832,     0.01526) **
   4             5              0.00189     (  0.00048,     0.00339) **
   5          B-vinsonii        0.00406     (  0.00198,     0.00613) **
   5             9              0.00363     (  0.00164,     0.00554) **
   9          B-arupensi        0.00422     (  0.00207,     0.00632) **
   9          B-berhoffi        0.00482     (  0.00256,     0.00702) **
   8          A-tumefaci        0.10833     (  0.09780,     0.11970) **

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


Data set # 3:


Empirical Base Frequencies:

   A       0.25791
   C       0.21465
   G       0.30197
  T(U)     0.22547

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.471700)


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


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

Ln Likelihood = -11092.61019

Examined  566 trees

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

   7          B-clarridg        0.01160     (  0.00799,     0.01522) **
   7             3              0.00631     (  0.00337,     0.00917) **
   3             2              0.00774     (  0.00467,     0.01079) **
   2             8              0.00338     (  0.00145,     0.00535) **
   8          B-birtlesi        0.00750     (  0.00473,     0.01026) **
   8             4              0.00143     (  0.00016,     0.00274) **
   4            10              0.00086     (     zero,     0.00199) **
  10          B--doshiae        0.00472     (  0.00258,     0.00690) **
  10             9              0.00113     (  0.00000,     0.00228) **
   9          B-henselae        0.00892     (  0.00595,     0.01188) **
   9            11              0.00348     (  0.00164,     0.00538) **
  11          B-grahamii        0.00770     (  0.00492,     0.01052) **
  11          B-elizabet        0.00954     (  0.00645,     0.01262) **
   4             1              0.00283     (  0.00110,     0.00456) **
   1          B-vinsonii        0.00352     (  0.00164,     0.00541) **
   1            12              0.00193     (  0.00045,     0.00329) **
  12          B-berhoffi        0.00473     (  0.00256,     0.00692) **
  12          B-arupensi        0.00326     (  0.00135,     0.00505) **
   2          B-quintana        0.01254     (  0.00900,     0.01612) **
   3             5              0.00758     (  0.00469,     0.01047) **
   5             6              0.00878     (  0.00568,     0.01194) **
   6          B--weissii        0.00451     (  0.00235,     0.00666) **
   6          B-spp-Deer        0.00827     (  0.00542,     0.01115) **
   5          B-bacillif        0.01147     (  0.00795,     0.01503) **
   7          A-tumefaci        0.09372     (  0.08359,     0.10388) **

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


Data set # 4:


Empirical Base Frequencies:

   A       0.26303
   C       0.22785
   G       0.29900
  T(U)     0.21012

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.467561)


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


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

Ln Likelihood = -11117.55232

Examined  620 trees

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

   6             8              0.00675     (  0.00377,     0.00973) **
   8             5              0.00758     (  0.00453,     0.01070) **
   5          B-quintana        0.01093     (  0.00755,     0.01426) **
   5             4              0.00386     (  0.00181,     0.00591) **
   4          B-henselae        0.00673     (  0.00408,     0.00931) **
   4             3              0.00175     (  0.00031,     0.00326) **
   3             7              0.00218     (  0.00031,     0.00398) **
   7            12              0.00253     (  0.00085,     0.00421) **
  12          B-birtlesi        0.00784     (  0.00495,     0.01076) **
  12          B-grahamii        0.00537     (  0.00293,     0.00781) **
   7          B--doshiae        0.00520     (  0.00276,     0.00759) **
   3             2              0.00225     (  0.00066,     0.00383) **
   2             1              0.00176     (  0.00046,     0.00309) **
   1             9              0.00434     (  0.00227,     0.00641) **
   9          B-arupensi        0.00383     (  0.00186,     0.00582) **
   9          B-berhoffi        0.00248     (  0.00092,     0.00412) **
   1          B-vinsonii        0.00278     (  0.00115,     0.00444) **
   2          B-elizabet        0.01269     (  0.00913,     0.01622) **
   8            10              0.00448     (  0.00217,     0.00675) **
  10          B-bacillif        0.01439     (  0.01054,     0.01833) **
  10            11              0.00855     (  0.00550,     0.01160) **
  11          B-spp-Deer        0.00765     (  0.00488,     0.01044) **
  11          B--weissii        0.00510     (  0.00282,     0.00741) **
   6          B-clarridg        0.01209     (  0.00848,     0.01582) **
   6          A-tumefaci        0.09429     (  0.08432,     0.10472) **

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


Data set # 5:


Empirical Base Frequencies:

   A       0.27088
   C       0.21931
   G       0.30388
  T(U)     0.20594

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.448734)


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


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

Ln Likelihood = -11061.71435

Examined  730 trees

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

   9             7              0.00711     (  0.00409,     0.01013) **
   7             1              0.00324     (  0.00139,     0.00510) **
   1             4              0.00375     (  0.00164,     0.00577) **
   4            10              0.00077     (     zero,     0.00174) **
  10             6              0.00204     (  0.00052,     0.00360) **
   6             8              0.00179     (  0.00039,     0.00320) **
   8          B-elizabet        0.00900     (  0.00600,     0.01195) **
   8          B-grahamii        0.00847     (  0.00561,     0.01137) **
   6          B-birtlesi        0.00772     (  0.00498,     0.01050) **
  10             3              0.00192     (  0.00049,     0.00331) **
   3          B-vinsonii        0.00460     (  0.00247,     0.00673) **
   3             2              0.00205     (  0.00054,     0.00346) **
   2          B-arupensi        0.00318     (  0.00139,     0.00497) **
   2          B-berhoffi        0.00390     (  0.00196,     0.00586) **
   4          B--doshiae        0.00356     (  0.00169,     0.00542) **
   1          B-henselae        0.00622     (  0.00366,     0.00877) **
   7          B-quintana        0.00956     (  0.00639,     0.01273) **
   9             5              0.00729     (  0.00432,     0.01029) **
   5            12              0.00281     (  0.00094,     0.00467) **
  12            11              0.00934     (  0.00625,     0.01247) **
  11          B--weissii        0.00658     (  0.00399,     0.00915) **
  11          B-spp-Deer        0.00641     (  0.00386,     0.00896) **
  12          B-bacillif        0.01191     (  0.00838,     0.01542) **
   5          B-clarridg        0.01485     (  0.01099,     0.01884) **
   9          A-tumefaci        0.10245     (  0.09213,     0.11342) **

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


Data set # 6:


Empirical Base Frequencies:

   A       0.26110
   C       0.22814
   G       0.30105
  T(U)     0.20971

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.468619)


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


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

Ln Likelihood = -10812.91426

Examined  588 trees

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

   7            11              0.00402     (  0.00176,     0.00626) **
  11          B-quintana        0.01126     (  0.00782,     0.01470) **
  11             5              0.00507     (  0.00277,     0.00746) **
   5          B-henselae        0.00914     (  0.00609,     0.01219) **
   5             3              0.00158     (     zero,     0.00307) **
   3             4              0.00191     (  0.00042,     0.00336) **
   4          B-elizabet        0.00996     (  0.00687,     0.01305) **
   4             6              0.00114     (     zero,     0.00221) **
   6             8              0.00112     (  0.00001,     0.00216) **
   8          B-arupensi        0.00178     (  0.00043,     0.00313) **
   8          B-berhoffi        0.00384     (  0.00191,     0.00576) **
   6          B-vinsonii        0.00415     (  0.00210,     0.00612) **
   3             9              0.00147     (     zero,     0.00298) **
   9            12              0.00288     (  0.00107,     0.00464) **
  12          B-birtlesi        0.00673     (  0.00414,     0.00941) **
  12          B-grahamii        0.00771     (  0.00490,     0.01052) **
   9          B--doshiae        0.00573     (  0.00324,     0.00823) **
   7             2              0.00477     (  0.00233,     0.00712) **
   2          B-clarridg        0.01329     (  0.00966,     0.01708) **
   2             1              0.00237     (  0.00074,     0.00408) **
   1          B-bacillif        0.01336     (  0.00960,     0.01711) **
   1            10              0.00771     (  0.00483,     0.01060) **
  10          B--weissii        0.00539     (  0.00300,     0.00781) **
  10          B-spp-Deer        0.00752     (  0.00473,     0.01034) **
   7          A-tumefaci        0.09091     (  0.08122,     0.10112) **

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


Data set # 7:


Empirical Base Frequencies:

   A       0.26585
   C       0.22297
   G       0.30855
  T(U)     0.20263

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.452911)


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


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

Ln Likelihood = -10580.53040

Examined  528 trees

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

   7             6              0.00698     (  0.00394,     0.01005) **
   6            10              0.00559     (  0.00305,     0.00816) **
  10          B-bacillif        0.00993     (  0.00660,     0.01326) **
  10             9              0.00994     (  0.00658,     0.01325) **
   9          B-spp-Deer        0.00692     (  0.00430,     0.00956) **
   9          B--weissii        0.00474     (  0.00251,     0.00695) **
   6             5              0.00682     (  0.00382,     0.00977) **
   5          B-birtlesi        0.00511     (  0.00284,     0.00739) **
   5             1              0.00157     (  0.00023,     0.00287) **
   1             3              0.00120     (  0.00001,     0.00233) **
   3            11              0.00096     (     zero,     0.00200) **
  11          B-vinsonii        0.00421     (  0.00217,     0.00626) **
  11          B-arupensi        0.00341     (  0.00156,     0.00527) **
   3          B-berhoffi        0.00520     (  0.00291,     0.00750) **
   1             2              0.00089     (     zero,     0.00185) **
   2          B--doshiae        0.00310     (  0.00128,     0.00481) **
   2             4              0.00103     (     zero,     0.00217) **
   4          B-grahamii        0.00653     (  0.00395,     0.00908) **
   4            12              0.00201     (  0.00061,     0.00349) **
  12          B-elizabet        0.01072     (  0.00747,     0.01397) **
  12             8              0.00289     (  0.00113,     0.00468) **
   8          B-quintana        0.01109     (  0.00780,     0.01442) **
   8          B-henselae        0.00605     (  0.00360,     0.00851) **
   7          B-clarridg        0.01203     (  0.00841,     0.01573) **
   7          A-tumefaci        0.08295     (  0.07389,     0.09288) **

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


Data set # 8:


Empirical Base Frequencies:

   A       0.25994
   C       0.21710
   G       0.31389
  T(U)     0.20907

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.456071)


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


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

Ln Likelihood = -10722.33133

Examined  570 trees

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

   7             3              0.00644     (  0.00367,     0.00916) **
   3             2              0.00421     (  0.00199,     0.00643) **
   2            11              0.00912     (  0.00598,     0.01219) **
  11          B--weissii        0.00376     (  0.00178,     0.00577) **
  11          B-spp-Deer        0.00597     (  0.00353,     0.00844) **
   2          B-bacillif        0.01103     (  0.00766,     0.01449) **
   3          B-clarridg        0.01713     (  0.01286,     0.02131) **
   7             9              0.00359     (  0.00132,     0.00584) **
   9             6              0.00274     (  0.00088,     0.00449) **
   6             5              0.00161     (  0.00019,     0.00302) **
   5             1              0.00182     (  0.00030,     0.00324) **
   1          B-birtlesi        0.00577     (  0.00331,     0.00813) **
   1             4              0.00213     (  0.00060,     0.00364) **
   4          B-elizabet        0.01017     (  0.00707,     0.01335) **
   4          B-grahamii        0.00523     (  0.00290,     0.00747) **
   5            12              0.00069     (     zero,     0.00171) **
  12          B--doshiae        0.00270     (  0.00107,     0.00439) **
  12          B-henselae        0.00934     (  0.00634,     0.01235) **
   6             8              0.00217     (  0.00070,     0.00366) **
   8          B-vinsonii        0.00336     (  0.00153,     0.00524) **
   8            10              0.00253     (  0.00083,     0.00423) **
  10          B-arupensi        0.00156     (  0.00021,     0.00283) **
  10          B-berhoffi        0.00246     (  0.00095,     0.00400) **
   9          B-quintana        0.01304     (  0.00939,     0.01659) **
   7          A-tumefaci        0.09746     (  0.08753,     0.10818) **

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


Data set # 9:


Empirical Base Frequencies:

   A       0.26280
   C       0.22385
   G       0.30558
  T(U)     0.20778

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.460915)


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


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

Ln Likelihood = -10978.52856

Examined  574 trees

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

  11          B-clarridg        0.00966     (  0.00636,     0.01292) **
  11             6              0.00475     (  0.00217,     0.00734) **
   6            12              0.00638     (  0.00362,     0.00916) **
  12             1              0.00492     (  0.00255,     0.00727) **
   1             5              0.00152     (  0.00022,     0.00281) **
   5             2              0.00158     (  0.00026,     0.00288) **
   2          B-arupensi        0.00341     (  0.00149,     0.00523) **
   2          B-berhoffi        0.00813     (  0.00531,     0.01096) **
   5          B-vinsonii        0.00627     (  0.00375,     0.00879) **
   1             4              0.00138     (     zero,     0.00277) **
   4             8              0.00072     (     zero,     0.00172) **
   8             7              0.00368     (  0.00175,     0.00561) **
   7          B-grahamii        0.00886     (  0.00591,     0.01186) **
   7          B-elizabet        0.00973     (  0.00660,     0.01281) **
   8          B--doshiae        0.00316     (  0.00135,     0.00497) **
   4             9              0.00098     (  0.00001,     0.00200) **
   9          B-henselae        0.00876     (  0.00577,     0.01164) **
   9          B-birtlesi        0.00780     (  0.00506,     0.01062) **
  12          B-quintana        0.01137     (  0.00799,     0.01478) **
   6             3              0.00368     (  0.00165,     0.00574) **
   3          B-bacillif        0.01096     (  0.00751,     0.01435) **
   3            10              0.00998     (  0.00674,     0.01327) **
  10          B--weissii        0.00281     (  0.00109,     0.00454) **
  10          B-spp-Deer        0.00751     (  0.00477,     0.01023) **
  11          A-tumefaci        0.09651     (  0.08652,     0.10711) **

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


Data set # 10:


Empirical Base Frequencies:

   A       0.27055
   C       0.22046
   G       0.30174
  T(U)     0.20726

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.451955)


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


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

Ln Likelihood = -11367.26092

Examined  516 trees

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

   1          B-clarridg        0.01083     (  0.00733,     0.01433) **
   1            12              0.00632     (  0.00348,     0.00924) **
  12          B-bacillif        0.01489     (  0.01094,     0.01894) **
  12             4              0.00428     (  0.00213,     0.00645) **
   4             8              0.00791     (  0.00490,     0.01090) **
   8          B--weissii        0.00662     (  0.00406,     0.00923) **
   8          B-spp-Deer        0.00818     (  0.00528,     0.01103) **
   4            11              0.01146     (  0.00791,     0.01503) **
  11          B-berhoffi        0.00259     (  0.00092,     0.00425) **
  11             3              0.00263     (  0.00096,     0.00432) **
   3          B-arupensi        0.00346     (  0.00159,     0.00532) **
   3             9              0.00220     (  0.00071,     0.00370) **
   9          B-vinsonii        0.00389     (  0.00192,     0.00582) **
   9             6              0.00093     (     zero,     0.00195) **
   6            10              0.00093     (     zero,     0.00193) **
  10          B--doshiae        0.00481     (  0.00266,     0.00701) **
  10             5              0.00144     (  0.00004,     0.00290) **
   5             7              0.00554     (  0.00313,     0.00799) **
   7          B-quintana        0.01548     (  0.01162,     0.01945) **
   7          B-henselae        0.00571     (  0.00325,     0.00816) **
   5             2              0.00492     (  0.00269,     0.00715) **
   2          B-elizabet        0.01169     (  0.00827,     0.01512) **
   2          B-grahamii        0.00695     (  0.00426,     0.00964) **
   6          B-birtlesi        0.00874     (  0.00582,     0.01165) **
   1          A-tumefaci        0.10102     (  0.09094,     0.11205) **

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


Data set # 11:


Empirical Base Frequencies:

   A       0.26020
   C       0.23254
   G       0.30629
  T(U)     0.20097

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.467788)


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


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

Ln Likelihood = -11071.64882

Examined  670 trees

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

  11             7              0.00317     (  0.00090,     0.00532) **
   7             1              0.00549     (  0.00308,     0.00794) **
   1            10              0.00280     (  0.00115,     0.00455) **
  10          B-arupensi        0.00327     (  0.00144,     0.00507) **
  10          B-berhoffi        0.00334     (  0.00152,     0.00516) **
   1             4              0.00297     (  0.00112,     0.00480) **
   4             6              0.00080     (     zero,     0.00169) **
   6          B-vinsonii        0.00498     (  0.00277,     0.00720) **
   6          B-birtlesi        0.00744     (  0.00476,     0.01017) **
   4             2              0.00112     (     zero,     0.00236) **
   2             5              0.00136     (  0.00015,     0.00258) **
   5          B-henselae        0.00816     (  0.00528,     0.01100) **
   5            12              0.00310     (  0.00133,     0.00487) **
  12          B-grahamii        0.00585     (  0.00341,     0.00828) **
  12          B-elizabet        0.01014     (  0.00698,     0.01331) **
   2          B--doshiae        0.00532     (  0.00305,     0.00767) **
   7          B-quintana        0.01444     (  0.01064,     0.01826) **
  11             8              0.00412     (  0.00188,     0.00630) **
   8             9              0.00586     (  0.00329,     0.00841) **
   9             3              0.01042     (  0.00714,     0.01374) **
   3          B--weissii        0.00349     (  0.00150,     0.00550) **
   3          B-spp-Deer        0.00745     (  0.00467,     0.01022) **
   9          B-bacillif        0.01211     (  0.00854,     0.01575) **
   8          B-clarridg        0.01243     (  0.00888,     0.01606) **
  11          A-tumefaci        0.09883     (  0.08897,     0.10980) **

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


Data set # 12:


Empirical Base Frequencies:

   A       0.26670
   C       0.22589
   G       0.29454
  T(U)     0.21287

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.466031)


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


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

Ln Likelihood = -10839.57331

Examined  618 trees

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

   3             9              0.00701     (  0.00392,     0.00998) **
   9            12              0.00392     (  0.00173,     0.00607) **
  12          B-bacillif        0.00816     (  0.00520,     0.01115) **
  12             5              0.00916     (  0.00604,     0.01228) **
   5          B--weissii        0.00318     (  0.00137,     0.00500) **
   5          B-spp-Deer        0.00856     (  0.00565,     0.01146) **
   9             8              0.00670     (  0.00386,     0.00949) **
   8             6              0.00384     (  0.00167,     0.00590) **
   6             4              0.00270     (  0.00097,     0.00441) **
   4          B-vinsonii        0.00450     (  0.00232,     0.00669) **
   4            11              0.00185     (  0.00038,     0.00337) **
  11          B-berhoffi        0.00249     (  0.00089,     0.00409) **
  11          B-arupensi        0.00352     (  0.00164,     0.00544) **
   6             2              0.00153     (  0.00008,     0.00294) **
   2             1              0.00025     (     zero,     0.00079)
   1          B-henselae        0.00638     (  0.00384,     0.00887) **
   1             7              0.00279     (  0.00117,     0.00449) **
   7          B-elizabet        0.00978     (  0.00667,     0.01285) **
   7          B-grahamii        0.00671     (  0.00417,     0.00929) **
   2            10              0.00173     (  0.00038,     0.00307) **
  10          B-birtlesi        0.00914     (  0.00618,     0.01217) **
  10          B--doshiae        0.00638     (  0.00383,     0.00884) **
   8          B-quintana        0.00984     (  0.00663,     0.01298) **
   3          B-clarridg        0.01029     (  0.00681,     0.01377) **
   3          A-tumefaci        0.09747     (  0.08760,     0.10831) **

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


Data set # 13:


Empirical Base Frequencies:

   A       0.26978
   C       0.22065
   G       0.29950
  T(U)     0.21006

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.455630)


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


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

Ln Likelihood = -10957.09916

Examined  500 trees

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

   5          B-clarridg        0.01261     (  0.00886,     0.01640) **
   5             2              0.00761     (  0.00460,     0.01074) **
   2             4              0.00665     (  0.00387,     0.00946) **
   4          B-quintana        0.00981     (  0.00665,     0.01300) **
   4            11              0.00484     (  0.00262,     0.00706) **
  11          B-henselae        0.00787     (  0.00504,     0.01070) **
  11             3              0.00217     (  0.00057,     0.00381) **
   3            12              0.00226     (  0.00062,     0.00392) **
  12          B-birtlesi        0.00868     (  0.00575,     0.01161) **
  12            10              0.00223     (  0.00056,     0.00382) **
  10          B-elizabet        0.01175     (  0.00839,     0.01516) **
  10          B-grahamii        0.00715     (  0.00445,     0.00979) **
   3             7              0.00013     (     zero,     0.00083)
   7          B--doshiae        0.00492     (  0.00280,     0.00712) **
   7             9              0.00252     (  0.00100,     0.00411) **
   9          B-vinsonii        0.00393     (  0.00195,     0.00586) **
   9             8              0.00175     (  0.00048,     0.00308) **
   8          B-arupensi        0.00482     (  0.00266,     0.00698) **
   8          B-berhoffi        0.00331     (  0.00151,     0.00509) **
   2             1              0.00337     (  0.00141,     0.00541) **
   1          B-bacillif        0.00946     (  0.00632,     0.01266) **
   1             6              0.01043     (  0.00714,     0.01373) **
   6          B-spp-Deer        0.00847     (  0.00556,     0.01139) **
   6          B--weissii        0.00228     (  0.00064,     0.00392) **
   5          A-tumefaci        0.08978     (  0.08039,     0.10013) **

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


Data set # 14:


Empirical Base Frequencies:

   A       0.27011
   C       0.21943
   G       0.31018
  T(U)     0.20027

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.442752)


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


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

Ln Likelihood = -10623.50232

Examined  576 trees

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

   3             1              0.00457     (  0.00217,     0.00699) **
   1            10              0.00140     (  0.00017,     0.00261) **
  10          B-vinsonii        0.00338     (  0.00147,     0.00518) **
  10             4              0.00135     (  0.00006,     0.00273) **
   4             8              0.00166     (  0.00031,     0.00309) **
   8          B-birtlesi        0.00908     (  0.00608,     0.01212) **
   8          B--doshiae        0.00455     (  0.00243,     0.00668) **
   4             5              0.00085     (     zero,     0.00199) **
   5             9              0.00477     (  0.00256,     0.00698) **
   9          B-quintana        0.01218     (  0.00867,     0.01563) **
   9          B-henselae        0.00439     (  0.00229,     0.00654) **
   5             2              0.00385     (  0.00182,     0.00580) **
   2          B-elizabet        0.01166     (  0.00826,     0.01506) **
   2          B-grahamii        0.00589     (  0.00337,     0.00835) **
   1             7              0.00308     (  0.00127,     0.00489) **
   7          B-berhoffi        0.00283     (  0.00116,     0.00449) **
   7          B-arupensi        0.00135     (  0.00015,     0.00248) **
   3             6              0.00368     (  0.00151,     0.00584) **
   6            11              0.00486     (  0.00256,     0.00717) **
  11          B-bacillif        0.00988     (  0.00654,     0.01315) **
  11            12              0.00795     (  0.00498,     0.01094) **
  12          B--weissii        0.00534     (  0.00302,     0.00767) **
  12          B-spp-Deer        0.00772     (  0.00497,     0.01050) **
   6          B-clarridg        0.01308     (  0.00931,     0.01677) **
   3          A-tumefaci        0.08242     (  0.07342,     0.09228) **

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


Data set # 15:


Empirical Base Frequencies:

   A       0.25629
   C       0.21991
   G       0.30763
  T(U)     0.21617

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.468703)


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


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

Ln Likelihood = -10794.18227

Examined  860 trees

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

   4             2              0.00638     (  0.00357,     0.00917) **
   2             1              0.00209     (  0.00034,     0.00377) **
   1             9              0.00294     (  0.00111,     0.00474) **
   9             6              0.00112     (     zero,     0.00228) **
   6            11              0.00059     (     zero,     0.00146) **
  11          B--doshiae        0.00319     (  0.00143,     0.00498) **
  11          B-henselae        0.00957     (  0.00657,     0.01265) **
   6            10              0.00199     (  0.00046,     0.00354) **
  10             7              0.00085     (     zero,     0.00193) **
   7          B-grahamii        0.00643     (  0.00393,     0.00894) **
   7          B-elizabet        0.00945     (  0.00648,     0.01253) **
  10          B-birtlesi        0.00797     (  0.00511,     0.01075) **
   9          B-vinsonii        0.00379     (  0.00180,     0.00571) **
   1             3              0.00104     (     zero,     0.00218) **
   3          B-arupensi        0.00482     (  0.00259,     0.00695) **
   3          B-berhoffi        0.00265     (  0.00109,     0.00431) **
   2          B-quintana        0.01461     (  0.01080,     0.01844) **
   4             8              0.00408     (  0.00182,     0.00641) **
   8          B-bacillif        0.01086     (  0.00747,     0.01436) **
   8             5              0.00405     (  0.00181,     0.00620) **
   5          B-clarridg        0.01236     (  0.00874,     0.01596) **
   5            12              0.00955     (  0.00638,     0.01272) **
  12          B-spp-Deer        0.00617     (  0.00365,     0.00867) **
  12          B--weissii        0.00481     (  0.00258,     0.00704) **
   4          A-tumefaci        0.09492     (  0.08494,     0.10538) **

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


Data set # 16:


Empirical Base Frequencies:

   A       0.27121
   C       0.22512
   G       0.30684
  T(U)     0.19683

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.447073)


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


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

Ln Likelihood = -11066.35886

Examined  562 trees

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

  10             4              0.00708     (  0.00413,     0.01006) **
   4             3              0.00419     (  0.00192,     0.00647) **
   3          B-bacillif        0.01216     (  0.00847,     0.01585) **
   3            12              0.00883     (  0.00578,     0.01200) **
  12             5              0.00437     (  0.00203,     0.00664) **
   5             1              0.00166     (  0.00037,     0.00299) **
   1          B-vinsonii        0.00528     (  0.00286,     0.00771) **
   1             2              0.00304     (  0.00110,     0.00493) **
   2          B-arupensi        0.00356     (  0.00160,     0.00551) **
   2          B-berhoffi        0.00540     (  0.00307,     0.00774) **
   5             6              0.00189     (  0.00032,     0.00341) **
   6             8              0.00104     (     zero,     0.00222) **
   8          B-henselae        0.01040     (  0.00716,     0.01359) **
   8             9              0.00298     (  0.00124,     0.00466) **
   9          B-grahamii        0.00634     (  0.00387,     0.00891) **
   9          B-elizabet        0.01062     (  0.00734,     0.01384) **
   6             7              0.00174     (  0.00049,     0.00331) **
   7          B-birtlesi        0.00778     (  0.00503,     0.01053) **
   7          B--doshiae        0.00366     (  0.00173,     0.00555) **
  12          B-quintana        0.01235     (  0.00873,     0.01587) **
   4            11              0.00754     (  0.00463,     0.01047) **
  11          B-spp-Deer        0.00710     (  0.00437,     0.00974) **
  11          B--weissii        0.00414     (  0.00210,     0.00626) **
  10          B-clarridg        0.01061     (  0.00712,     0.01403) **
  10          A-tumefaci        0.08941     (  0.07990,     0.09963) **

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


Data set # 17:


Empirical Base Frequencies:

   A       0.26770
   C       0.21472
   G       0.30513
  T(U)     0.21245

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.451932)


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


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

Ln Likelihood = -11130.60276

Examined  866 trees

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

   1             8              0.00481     (  0.00231,     0.00731) **
   8            11              0.00102     (     zero,     0.00215) **
  11             4              0.00091     (     zero,     0.00192) **
   4             3              0.00220     (  0.00070,     0.00371) **
   3             5              0.00231     (  0.00081,     0.00386) **
   5          B-berhoffi        0.00589     (  0.00346,     0.00831) **
   5          B-arupensi        0.00337     (  0.00156,     0.00518) **
   3          B-vinsonii        0.00462     (  0.00250,     0.00674) **
   4             9              0.00085     (     zero,     0.00202) **
   9            12              0.00414     (  0.00211,     0.00626) **
  12          B-elizabet        0.01104     (  0.00772,     0.01434) **
  12          B-grahamii        0.00567     (  0.00322,     0.00811) **
   9            10              0.00652     (  0.00386,     0.00913) **
  10          B-quintana        0.01173     (  0.00834,     0.01520) **
  10          B-henselae        0.00443     (  0.00225,     0.00664) **
  11          B--doshiae        0.00568     (  0.00330,     0.00802) **
   8          B-birtlesi        0.00861     (  0.00567,     0.01160) **
   1             6              0.00471     (  0.00221,     0.00726) **
   6             2              0.00569     (  0.00321,     0.00819) **
   2             7              0.00776     (  0.00477,     0.01072) **
   7          B-spp-Deer        0.00778     (  0.00492,     0.01056) **
   7          B--weissii        0.00451     (  0.00236,     0.00671) **
   2          B-clarridg        0.01362     (  0.00978,     0.01745) **
   6          B-bacillif        0.01400     (  0.01009,     0.01789) **
   1          A-tumefaci        0.10257     (  0.09192,     0.11323) **

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


Data set # 18:


Empirical Base Frequencies:

   A       0.25299
   C       0.22888
   G       0.31690
  T(U)     0.20123

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.469139)


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


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

Ln Likelihood = -10880.73984

Examined  530 trees

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

   3            10              0.00761     (  0.00451,     0.01074) **
  10          B-bacillif        0.01249     (  0.00876,     0.01624) **
  10             7              0.00458     (  0.00235,     0.00688) **
   7          B-clarridg        0.01393     (  0.01002,     0.01786) **
   7             6              0.00895     (  0.00575,     0.01214) **
   6          B--weissii        0.00470     (  0.00247,     0.00692) **
   6          B-spp-Deer        0.00676     (  0.00414,     0.00940) **
   3             1              0.00659     (  0.00362,     0.00964) **
   1             2              0.00250     (  0.00076,     0.00420) **
   2          B-arupensi        0.00402     (  0.00204,     0.00602) **
   2          B-berhoffi        0.00428     (  0.00219,     0.00627) **
   1             4              0.00181     (  0.00044,     0.00313) **
   4             5              0.00120     (     zero,     0.00242) **
   5             8              0.00233     (  0.00074,     0.00391) **
   8          B-elizabet        0.00761     (  0.00489,     0.01036) **
   8            12              0.00286     (  0.00116,     0.00456) **
  12          B-quintana        0.01269     (  0.00915,     0.01623) **
  12          B-henselae        0.00494     (  0.00270,     0.00720) **
   5            11              0.00034     (     zero,     0.00111)
  11          B-birtlesi        0.00616     (  0.00369,     0.00861) **
  11             9              0.00102     (     zero,     0.00200) **
   9          B-grahamii        0.00550     (  0.00317,     0.00780) **
   9          B--doshiae        0.00371     (  0.00179,     0.00561) **
   4          B-vinsonii        0.00731     (  0.00463,     0.01004) **
   3          A-tumefaci        0.09909     (  0.08900,     0.10990) **

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


Data set # 19:


Empirical Base Frequencies:

   A       0.26047
   C       0.23158
   G       0.29859
  T(U)     0.20936

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.472540)


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


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

Ln Likelihood = -10944.78654

Examined 1024 trees

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

  10             4              0.00572     (  0.00309,     0.00830) **
   4             5              0.00426     (  0.00203,     0.00650) **
   5             6              0.00949     (  0.00635,     0.01274) **
   6          B--weissii        0.00367     (  0.00168,     0.00565) **
   6          B-spp-Deer        0.00958     (  0.00648,     0.01267) **
   5          B-bacillif        0.01080     (  0.00738,     0.01425) **
   4          B-clarridg        0.01631     (  0.01216,     0.02046) **
  10             9              0.00516     (  0.00264,     0.00768) **
   9             8              0.00228     (  0.00046,     0.00397) **
   8             1              0.00122     (  0.00004,     0.00248) **
   1            12              0.00398     (  0.00205,     0.00597) **
  12          B-henselae        0.00645     (  0.00394,     0.00900) **
  12          B-quintana        0.01137     (  0.00801,     0.01471) **
   1          B-vinsonii        0.00255     (  0.00091,     0.00416) **
   8             2              0.00094     (     zero,     0.00197) **
   2             7              0.00090     (     zero,     0.00186) **
   7          B--doshiae        0.00355     (  0.00169,     0.00543) **
   7             3              0.00327     (  0.00149,     0.00506) **
   3          B-elizabet        0.01256     (  0.00908,     0.01606) **
   3          B-grahamii        0.00347     (  0.00161,     0.00534) **
   2            11              0.00174     (  0.00038,     0.00310) **
  11          B-berhoffi        0.00281     (  0.00116,     0.00447) **
  11          B-arupensi        0.00382     (  0.00189,     0.00575) **
   9          B-birtlesi        0.00739     (  0.00457,     0.01020) **
  10          A-tumefaci        0.10084     (  0.09072,     0.11185) **

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


Data set # 20:


Empirical Base Frequencies:

   A       0.25917
   C       0.22137
   G       0.31337
  T(U)     0.20610

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.458830)


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


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

Ln Likelihood = -11049.38042

Examined  604 trees

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

  10             2              0.00673     (  0.00355,     0.00994) **
   2             1              0.00960     (  0.00616,     0.01305) **
   1          B-spp-Deer        0.00818     (  0.00528,     0.01107) **
   1          B--weissii        0.00507     (  0.00276,     0.00739) **
   2             3              0.00649     (  0.00376,     0.00920) **
   3             5              0.01115     (  0.00751,     0.01478) **
   5             4              0.00081     (     zero,     0.00191) **
   4             6              0.00219     (  0.00067,     0.00370) **
   6            11              0.00144     (  0.00025,     0.00265) **
  11          B-berhoffi        0.00271     (  0.00106,     0.00438) **
  11          B-arupensi        0.00306     (  0.00130,     0.00480) **
   6          B-vinsonii        0.00316     (  0.00131,     0.00492) **
   4             8              0.00043     (     zero,     0.00127) **
   8            12              0.00232     (  0.00071,     0.00385) **
  12          B-grahamii        0.00854     (  0.00562,     0.01144) **
  12          B--doshiae        0.00562     (  0.00330,     0.00799) **
   8             7              0.00279     (  0.00103,     0.00448) **
   7             9              0.00379     (  0.00175,     0.00584) **
   9          B-henselae        0.00611     (  0.00359,     0.00861) **
   9          B-quintana        0.01292     (  0.00931,     0.01652) **
   7          B-elizabet        0.00919     (  0.00621,     0.01225) **
   5          B-birtlesi        0.00830     (  0.00542,     0.01121) **
   3          B-bacillif        0.01240     (  0.00864,     0.01626) **
  10          B-clarridg        0.00956     (  0.00618,     0.01294) **
  10          A-tumefaci        0.10014     (  0.09018,     0.11119) **

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


Data set # 21:


Empirical Base Frequencies:

   A       0.27150
   C       0.22234
   G       0.30374
  T(U)     0.20242

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.448800)


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


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

Ln Likelihood = -11322.60805

Examined  838 trees

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

   1             4              0.00546     (  0.00280,     0.00804) **
   4            11              0.00463     (  0.00234,     0.00694) **
  11             6              0.00696     (  0.00417,     0.00981) **
   6          B--weissii        0.00482     (  0.00255,     0.00708) **
   6          B-spp-Deer        0.00987     (  0.00677,     0.01307) **
  11          B-clarridg        0.01959     (  0.01513,     0.02420) **
   4          B-bacillif        0.01430     (  0.01039,     0.01824) **
   1             2              0.00573     (  0.00306,     0.00843) **
   2            10              0.00099     (     zero,     0.00208) **
  10          B-vinsonii        0.00448     (  0.00240,     0.00661) **
  10             9              0.00474     (  0.00255,     0.00694) **
   9          B-henselae        0.00411     (  0.00201,     0.00620) **
   9          B-quintana        0.01437     (  0.01062,     0.01816) **
   2             8              0.00131     (  0.00000,     0.00252) **
   8             3              0.00136     (  0.00022,     0.00257) **
   3            12              0.00232     (  0.00072,     0.00387) **
  12          B-arupensi        0.00518     (  0.00300,     0.00744) **
  12          B-berhoffi        0.00335     (  0.00149,     0.00512) **
   3             5              0.00157     (  0.00026,     0.00289) **
   5             7              0.00499     (  0.00270,     0.00724) **
   7          B-elizabet        0.01126     (  0.00797,     0.01460) **
   7          B-grahamii        0.00600     (  0.00354,     0.00848) **
   5          B--doshiae        0.00540     (  0.00309,     0.00773) **
   8          B-birtlesi        0.00981     (  0.00671,     0.01291) **
   1          A-tumefaci        0.09798     (  0.08796,     0.10874) **

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


Data set # 22:


Empirical Base Frequencies:

   A       0.27038
   C       0.21920
   G       0.30431
  T(U)     0.20610

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.449013)


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


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

Ln Likelihood = -10692.24413

Examined  520 trees

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

  12          B-clarridg        0.01197     (  0.00832,     0.01567) **
  12             2              0.00619     (  0.00328,     0.00909) **
   2             7              0.00737     (  0.00426,     0.01048) **
   7             8              0.00526     (  0.00295,     0.00759) **
   8             9              0.00215     (  0.00049,     0.00374) **
   9             6              0.00032     (     zero,     0.00093) *
   6             1              0.00249     (  0.00092,     0.00410) **
   1          B-vinsonii        0.00368     (  0.00179,     0.00561) **
   1             5              0.00337     (  0.00156,     0.00519) **
   5          B-berhoffi        0.00230     (  0.00071,     0.00382) **
   5          B-arupensi        0.00306     (  0.00130,     0.00485) **
   6            10              0.00087     (     zero,     0.00187) **
  10            11              0.00210     (  0.00062,     0.00353) **
  11          B-elizabet        0.00780     (  0.00505,     0.01057) **
  11          B-grahamii        0.00510     (  0.00284,     0.00735) **
  10          B-birtlesi        0.00896     (  0.00601,     0.01194) **
   9          B--doshiae        0.00368     (  0.00180,     0.00557) **
   8          B-henselae        0.00635     (  0.00381,     0.00892) **
   7          B-quintana        0.00955     (  0.00642,     0.01270) **
   2             4              0.00518     (  0.00274,     0.00765) **
   4          B-bacillif        0.01093     (  0.00754,     0.01435) **
   4             3              0.00827     (  0.00530,     0.01126) **
   3          B--weissii        0.00367     (  0.00173,     0.00563) **
   3          B-spp-Deer        0.00561     (  0.00324,     0.00798) **
  12          A-tumefaci        0.09386     (  0.08419,     0.10455) **

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


Data set # 23:


Empirical Base Frequencies:

   A       0.26134
   C       0.22560
   G       0.30045
  T(U)     0.21261

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.468078)


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


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

Ln Likelihood = -10505.45366

Examined  598 trees

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

   2             8              0.00563     (  0.00296,     0.00831) **
   8            11              0.00532     (  0.00295,     0.00770) **
  11          B-clarridg        0.01181     (  0.00834,     0.01540) **
  11            12              0.00781     (  0.00489,     0.01069) **
  12          B--weissii        0.00322     (  0.00140,     0.00505) **
  12          B-spp-Deer        0.00700     (  0.00436,     0.00964) **
   8             5              0.00590     (  0.00324,     0.00855) **
   5             7              0.00127     (  0.00010,     0.00243) **
   7          B-berhoffi        0.00348     (  0.00166,     0.00531) **
   7          B-arupensi        0.00315     (  0.00141,     0.00491) **
   5             1              0.00075     (     zero,     0.00169) **
   1             4              0.00143     (  0.00015,     0.00269) **
   4             3              0.00030     (     zero,     0.00097)
   3          B-henselae        0.00882     (  0.00589,     0.01176) **
   3            10              0.00180     (  0.00042,     0.00313) **
  10          B-grahamii        0.00644     (  0.00392,     0.00898) **
  10          B-elizabet        0.01027     (  0.00710,     0.01343) **
   4             9              0.00163     (  0.00031,     0.00292) **
   9          B--doshiae        0.00394     (  0.00196,     0.00592) **
   9          B-birtlesi        0.00946     (  0.00642,     0.01251) **
   1             6              0.00147     (  0.00025,     0.00268) **
   6          B-vinsonii        0.00204     (  0.00065,     0.00349) **
   6          B-quintana        0.01184     (  0.00839,     0.01520) **
   2          B-bacillif        0.00668     (  0.00387,     0.00956) **
   2          A-tumefaci        0.09203     (  0.08243,     0.10247) **

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


Data set # 24:


Empirical Base Frequencies:

   A       0.26916
   C       0.21896
   G       0.29211
  T(U)     0.21977

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.464361)


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


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

Ln Likelihood = -10961.42268

Examined  838 trees

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

   8            10              0.00615     (  0.00332,     0.00903) **
  10             7              0.00474     (  0.00246,     0.00702) **
   7            12              0.00688     (  0.00413,     0.00970) **
  12          B-quintana        0.01137     (  0.00802,     0.01481) **
  12             2              0.00285     (  0.00094,     0.00470) **
   2             6              0.00255     (  0.00096,     0.00419) **
   6          B-berhoffi        0.00371     (  0.00182,     0.00566) **
   6          B-arupensi        0.00326     (  0.00140,     0.00509) **
   2             5              0.00205     (  0.00059,     0.00353) **
   5            11              0.00169     (  0.00040,     0.00299) **
  11          B-birtlesi        0.00653     (  0.00401,     0.00904) **
  11          B-vinsonii        0.00748     (  0.00480,     0.01015) **
   5             3              0.00003     (     zero,     0.00088)
   3             4              0.00229     (  0.00078,     0.00386) **
   4          B-henselae        0.00538     (  0.00310,     0.00771) **
   4          B-elizabet        0.00774     (  0.00499,     0.01049) **
   3             9              0.00203     (  0.00062,     0.00344) **
   9          B-grahamii        0.00774     (  0.00498,     0.01046) **
   9          B--doshiae        0.00565     (  0.00333,     0.00800) **
   7             1              0.00969     (  0.00640,     0.01300) **
   1          B--weissii        0.00506     (  0.00282,     0.00733) **
   1          B-spp-Deer        0.00672     (  0.00413,     0.00930) **
  10          B-bacillif        0.01177     (  0.00814,     0.01534) **
   8          B-clarridg        0.01165     (  0.00799,     0.01531) **
   8          A-tumefaci        0.09926     (  0.08925,     0.11020) **

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


Data set # 25:


Empirical Base Frequencies:

   A       0.27140
   C       0.21653
   G       0.30216
  T(U)     0.20992

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.449428)


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


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

Ln Likelihood = -10974.36622

Examined  514 trees

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

   7             2              0.00562     (  0.00291,     0.00831) **
   2             6              0.00597     (  0.00339,     0.00852) **
   6          B-bacillif        0.00849     (  0.00546,     0.01156) **
   6            11              0.00981     (  0.00652,     0.01302) **
  11          B--weissii        0.00249     (  0.00083,     0.00414) **
  11          B-spp-Deer        0.00782     (  0.00507,     0.01062) **
   2             3              0.00829     (  0.00513,     0.01139) **
   3             9              0.00071     (     zero,     0.00167) **
   9             5              0.00064     (     zero,     0.00155) **
   5             1              0.00118     (     zero,     0.00232) **
   1             4              0.00526     (  0.00293,     0.00761) **
   4          B-henselae        0.00558     (  0.00325,     0.00801) **
   4          B-quintana        0.01389     (  0.01017,     0.01757) **
   1            10              0.00284     (  0.00109,     0.00453) **
  10          B-grahamii        0.00501     (  0.00267,     0.00724) **
  10          B-elizabet        0.01503     (  0.01124,     0.01892) **
   5          B--doshiae        0.00332     (  0.00154,     0.00516) **
   9          B-birtlesi        0.00976     (  0.00669,     0.01284) **
   3            12              0.00107     (  0.00005,     0.00215) **
  12          B-vinsonii        0.00702     (  0.00443,     0.00969) **
  12             8              0.00182     (  0.00036,     0.00327) **
   8          B-arupensi        0.00467     (  0.00250,     0.00683) **
   8          B-berhoffi        0.00315     (  0.00138,     0.00493) **
   7          B-clarridg        0.01047     (  0.00694,     0.01389) **
   7          A-tumefaci        0.09174     (  0.08214,     0.10218) **

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


Data set # 26:


Empirical Base Frequencies:

   A       0.26364
   C       0.21814
   G       0.31162
  T(U)     0.20661

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.452070)


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


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

Ln Likelihood = -10839.04503

Examined  932 trees

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

   7          B-clarridg        0.01021     (  0.00682,     0.01362) **
   7             3              0.00539     (  0.00265,     0.00814) **
   3            11              0.00651     (  0.00371,     0.00935) **
  11            12              0.00393     (  0.00188,     0.00599) **
  12          B-quintana        0.01076     (  0.00749,     0.01402) **
  12          B-henselae        0.00652     (  0.00396,     0.00911) **
  11             6              0.00186     (  0.00033,     0.00341) **
   6             2              0.00034     (     zero,     0.00100) *
   2            10              0.00227     (  0.00062,     0.00392) **
  10          B-birtlesi        0.00817     (  0.00531,     0.01103) **
  10             1              0.00254     (  0.00087,     0.00425) **
   1          B-elizabet        0.01122     (  0.00794,     0.01454) **
   1          B-grahamii        0.00369     (  0.00182,     0.00563) **
   2             5              0.00270     (  0.00097,     0.00437) **
   5             8              0.00314     (  0.00135,     0.00492) **
   8          B-arupensi        0.00480     (  0.00252,     0.00697) **
   8          B-berhoffi        0.00475     (  0.00259,     0.00693) **
   5          B-vinsonii        0.00475     (  0.00256,     0.00692) **
   6          B--doshiae        0.00427     (  0.00226,     0.00633) **
   3             4              0.00531     (  0.00292,     0.00772) **
   4             9              0.00656     (  0.00390,     0.00930) **
   9          B-spp-Deer        0.00832     (  0.00547,     0.01117) **
   9          B--weissii        0.00124     (     zero,     0.00240) **
   4          B-bacillif        0.01221     (  0.00864,     0.01579) **
   7          A-tumefaci        0.09514     (  0.08525,     0.10567) **

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


Data set # 27:


Empirical Base Frequencies:

   A       0.25774
   C       0.21769
   G       0.31208
  T(U)     0.21249

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.461905)


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


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

Ln Likelihood = -10592.80551

Examined 1660 trees

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

  11             2              0.00411     (  0.00185,     0.00634) **
   2          B-clarridg        0.01289     (  0.00931,     0.01658) **
   2            10              0.00290     (  0.00110,     0.00472) **
  10             6              0.00968     (  0.00654,     0.01290) **
   6          B--weissii        0.00376     (  0.00185,     0.00568) **
   6          B-spp-Deer        0.00666     (  0.00413,     0.00921) **
  10          B-bacillif        0.01048     (  0.00711,     0.01375) **
  11            12              0.00386     (  0.00165,     0.00613) **
  12             1              0.00455     (  0.00239,     0.00670) **
   1          B-henselae        0.00565     (  0.00325,     0.00802) **
   1             5              0.00096     (     zero,     0.00201) **
   5             8              0.00140     (  0.00016,     0.00272) **
   8             9              0.00119     (  0.00007,     0.00226) **
   9          B--doshiae        0.00380     (  0.00191,     0.00573) **
   9             4              0.00130     (  0.00006,     0.00252) **
   4          B-grahamii        0.00479     (  0.00260,     0.00699) **
   4             7              0.00233     (  0.00083,     0.00385) **
   7          B-berhoffi        0.00515     (  0.00292,     0.00745) **
   7          B-arupensi        0.00318     (  0.00130,     0.00499) **
   8             3              0.00057     (     zero,     0.00137) **
   3          B-birtlesi        0.00896     (  0.00603,     0.01192) **
   3          B-vinsonii        0.00282     (  0.00115,     0.00447) **
   5          B-elizabet        0.01283     (  0.00933,     0.01638) **
  12          B-quintana        0.00823     (  0.00533,     0.01108) **
  11          A-tumefaci        0.09339     (  0.08363,     0.10379) **

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


Data set # 28:


Empirical Base Frequencies:

   A       0.26946
   C       0.21289
   G       0.31261
  T(U)     0.20504

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.439383)


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


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

Ln Likelihood = -11104.02021

Examined  864 trees

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

  10          B-birtlesi        0.00728     (  0.00450,     0.01005) **
  10             8              0.00336     (  0.00131,     0.00534) **
   8          B--doshiae        0.00515     (  0.00292,     0.00739) **
   8            12              0.00152     (  0.00027,     0.00287) **
  12             7              0.00068     (     zero,     0.00157) **
   7          B-vinsonii        0.00457     (  0.00242,     0.00668) **
   7             1              0.00194     (  0.00040,     0.00348) **
   1             2              0.00233     (  0.00076,     0.00392) **
   2          B-grahamii        0.00655     (  0.00399,     0.00911) **
   2          B-elizabet        0.01158     (  0.00822,     0.01497) **
   1             5              0.00175     (  0.00033,     0.00321) **
   5          B-arupensi        0.00440     (  0.00230,     0.00653) **
   5          B-berhoffi        0.00388     (  0.00192,     0.00585) **
  12             3              0.00338     (  0.00139,     0.00538) **
   3          B-henselae        0.00637     (  0.00378,     0.00895) **
   3             6              0.00279     (  0.00095,     0.00457) **
   6          B-quintana        0.00869     (  0.00566,     0.01172) **
   6             4              0.00787     (  0.00479,     0.01091) **
   4          B-clarridg        0.01470     (  0.01071,     0.01866) **
   4            11              0.00582     (  0.00325,     0.00840) **
  11          B-bacillif        0.01157     (  0.00796,     0.01512) **
  11             9              0.01213     (  0.00855,     0.01577) **
   9          B-spp-Deer        0.00706     (  0.00435,     0.00975) **
   9          B--weissii        0.00399     (  0.00189,     0.00608) **
  10          A-tumefaci        0.10255     (  0.09236,     0.11351) **

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


Data set # 29:


Empirical Base Frequencies:

   A       0.26053
   C       0.23564
   G       0.29370
  T(U)     0.21013

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.477438)


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


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

Ln Likelihood = -10803.83561

Examined  590 trees

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

   9          B-clarridg        0.01129     (  0.00770,     0.01487) **
   9             8              0.00726     (  0.00422,     0.01029) **
   8            10              0.00729     (  0.00443,     0.01015) **
  10          B-spp-Deer        0.00883     (  0.00587,     0.01181) **
  10          B--weissii        0.00318     (  0.00133,     0.00504) **
   8            11              0.00312     (  0.00115,     0.00511) **
  11             3              0.00919     (  0.00604,     0.01235) **
   3             2              0.00426     (  0.00200,     0.00641) **
   2             1              0.00216     (  0.00062,     0.00363) **
   1             4              0.00018     (     zero,     0.00092)
   4            12              0.00053     (     zero,     0.00128) **
  12          B-vinsonii        0.00518     (  0.00294,     0.00741) **
  12             5              0.00129     (     zero,     0.00249) **
   5          B-henselae        0.00853     (  0.00564,     0.01144) **
   5          B-elizabet        0.01119     (  0.00789,     0.01449) **
   4          B-birtlesi        0.00758     (  0.00487,     0.01030) **
   1             7              0.00116     (  0.00001,     0.00230) **
   7          B-grahamii        0.00636     (  0.00392,     0.00886) **
   7          B--doshiae        0.00403     (  0.00200,     0.00595) **
   2             6              0.00167     (  0.00034,     0.00301) **
   6          B-berhoffi        0.00365     (  0.00169,     0.00551) **
   6          B-arupensi        0.00352     (  0.00167,     0.00541) **
   3          B-quintana        0.01356     (  0.00988,     0.01723) **
  11          B-bacillif        0.00867     (  0.00557,     0.01175) **
   9          A-tumefaci        0.09156     (  0.08206,     0.10210) **

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


Data set # 30:


Empirical Base Frequencies:

   A       0.27013
   C       0.22054
   G       0.30385
  T(U)     0.20548

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.450284)


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


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

Ln Likelihood = -10936.75607

Examined  554 trees

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

  11          B-bacillif        0.00463     (  0.00226,     0.00706) **
  11             9              0.00767     (  0.00461,     0.01074) **
   9             4              0.00892     (  0.00578,     0.01204) **
   4          B-spp-Deer        0.00631     (  0.00377,     0.00879) **
   4          B--weissii        0.00244     (  0.00086,     0.00407) **
   9             6              0.00357     (  0.00148,     0.00565) **
   6             3              0.00710     (  0.00416,     0.00996) **
   3            10              0.00287     (  0.00096,     0.00478) **
  10             1              0.00230     (  0.00066,     0.00386) **
   1          B-vinsonii        0.00304     (  0.00133,     0.00484) **
   1             2              0.00141     (  0.00011,     0.00266) **
   2          B-arupensi        0.00494     (  0.00270,     0.00716) **
   2             5              0.00089     (     zero,     0.00190) **
   5          B-berhoffi        0.00442     (  0.00239,     0.00654) **
   5             7              0.00363     (  0.00166,     0.00552) **
   7          B-elizabet        0.01176     (  0.00836,     0.01511) **
   7          B-grahamii        0.00410     (  0.00212,     0.00612) **
  10            12              0.00198     (  0.00044,     0.00354) **
  12          B--doshiae        0.00536     (  0.00305,     0.00773) **
  12          B-birtlesi        0.00709     (  0.00437,     0.00973) **
   3             8              0.00333     (  0.00142,     0.00524) **
   8          B-quintana        0.01329     (  0.00959,     0.01691) **
   8          B-henselae        0.00676     (  0.00410,     0.00944) **
   6          B-clarridg        0.01984     (  0.01541,     0.02447) **
  11          A-tumefaci        0.09562     (  0.08587,     0.10631) **

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


Data set # 31:


Empirical Base Frequencies:

   A       0.27157
   C       0.21714
   G       0.30072
  T(U)     0.21057

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.450943)


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


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

Ln Likelihood = -11050.35788

Examined  574 trees

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

  11          B-clarridg        0.01074     (  0.00727,     0.01421) **
  11             3              0.00589     (  0.00305,     0.00874) **
   3             4              0.01046     (  0.00691,     0.01390) **
   4          B-spp-Deer        0.00625     (  0.00382,     0.00876) **
   4          B--weissii        0.00317     (  0.00138,     0.00496) **
   3             8              0.00477     (  0.00245,     0.00709) **
   8             2              0.01079     (  0.00727,     0.01433) **
   2             1              0.00201     (  0.00034,     0.00370) **
   1          B-arupensi        0.00373     (  0.00178,     0.00567) **
   1          B-berhoffi        0.00421     (  0.00221,     0.00623) **
   2             7              0.00169     (  0.00027,     0.00305) **
   7            12              0.00240     (  0.00077,     0.00402) **
  12             5              0.00258     (  0.00091,     0.00421) **
   5          B-birtlesi        0.00897     (  0.00601,     0.01192) **
   5             6              0.00195     (  0.00042,     0.00337) **
   6          B-elizabet        0.00898     (  0.00605,     0.01192) **
   6          B-grahamii        0.00522     (  0.00299,     0.00746) **
  12             9              0.00117     (     zero,     0.00228) **
   9            10              0.00415     (  0.00213,     0.00617) **
  10          B-quintana        0.01043     (  0.00725,     0.01365) **
  10          B-henselae        0.00462     (  0.00243,     0.00678) **
   9          B--doshiae        0.00597     (  0.00351,     0.00833) **
   7          B-vinsonii        0.00628     (  0.00383,     0.00883) **
   8          B-bacillif        0.01384     (  0.01006,     0.01779) **
  11          A-tumefaci        0.09556     (  0.08586,     0.10636) **

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


Data set # 32:


Empirical Base Frequencies:

   A       0.27350
   C       0.22477
   G       0.30136
  T(U)     0.20036

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.449318)


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


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

Ln Likelihood = -11202.28109

Examined 1142 trees

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

   5          B-bacillif        0.00907     (  0.00575,     0.01242) **
   5             2              0.00775     (  0.00452,     0.01096) **
   2             4              0.00690     (  0.00415,     0.00966) **
   4          B-spp-Deer        0.01040     (  0.00713,     0.01363) **
   4          B--weissii        0.00384     (  0.00178,     0.00592) **
   2            11              0.00458     (  0.00210,     0.00698) **
  11             8              0.00585     (  0.00326,     0.00851) **
   8             1              0.00538     (  0.00299,     0.00782) **
   1            10              0.00195     (  0.00055,     0.00342) **
  10          B-arupensi        0.00356     (  0.00167,     0.00547) **
  10             3              0.00324     (  0.00137,     0.00512) **
   3          B-vinsonii        0.00431     (  0.00223,     0.00637) **
   3            12              0.00225     (  0.00060,     0.00384) **
  12             6              0.00082     (     zero,     0.00173) **
   6             7              0.00048     (     zero,     0.00118) **
   7          B--doshiae        0.00473     (  0.00254,     0.00692) **
   7          B-grahamii        0.00745     (  0.00471,     0.01017) **
   6             9              0.00331     (  0.00143,     0.00516) **
   9          B-henselae        0.00738     (  0.00465,     0.01016) **
   9          B-elizabet        0.01270     (  0.00917,     0.01628) **
  12          B-birtlesi        0.01011     (  0.00699,     0.01326) **
   1          B-berhoffi        0.00194     (  0.00051,     0.00337) **
   8          B-quintana        0.01305     (  0.00937,     0.01663) **
  11          B-clarridg        0.01660     (  0.01245,     0.02079) **
   5          A-tumefaci        0.09989     (  0.08975,     0.11076) **

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


Data set # 33:


Empirical Base Frequencies:

   A       0.26173
   C       0.22342
   G       0.30566
  T(U)     0.20919

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.462371)


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


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

Ln Likelihood = -11173.50554

Examined 1238 trees

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

  11          B-clarridg        0.01043     (  0.00695,     0.01390) **
  11             9              0.00864     (  0.00520,     0.01199) **
   9             1              0.00520     (  0.00270,     0.00772) **
   1          B-bacillif        0.01099     (  0.00751,     0.01448) **
   1             3              0.00954     (  0.00624,     0.01283) **
   3            12              0.00277     (  0.00104,     0.00446) **
  12             8              0.00172     (  0.00030,     0.00304) **
   8             6              0.00082     (     zero,     0.00179) **
   6          B--doshiae        0.00443     (  0.00228,     0.00647) **
   6            10              0.00131     (  0.00020,     0.00253) **
  10          B-vinsonii        0.00499     (  0.00285,     0.00723) **
  10          B-birtlesi        0.00902     (  0.00598,     0.01200) **
   8             2              0.00429     (  0.00208,     0.00646) **
   2          B-quintana        0.01382     (  0.01013,     0.01753) **
   2          B-henselae        0.00655     (  0.00390,     0.00917) **
  12             5              0.00180     (  0.00045,     0.00316) **
   5          B-grahamii        0.00688     (  0.00434,     0.00952) **
   5          B-elizabet        0.00834     (  0.00546,     0.01115) **
   3             4              0.00146     (  0.00019,     0.00275) **
   4          B-arupensi        0.00418     (  0.00217,     0.00618) **
   4          B-berhoffi        0.00462     (  0.00249,     0.00674) **
   9             7              0.01063     (  0.00713,     0.01414) **
   7          B--weissii        0.00441     (  0.00216,     0.00666) **
   7          B-spp-Deer        0.00821     (  0.00528,     0.01115) **
  11          A-tumefaci        0.09982     (  0.08967,     0.11071) **

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


Data set # 34:


Empirical Base Frequencies:

   A       0.27475
   C       0.21453
   G       0.31270
  T(U)     0.19801

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.429685)


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


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

Ln Likelihood = -11148.48425

Examined 1388 trees

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

  11          B-bacillif        0.00790     (  0.00482,     0.01099) **
  11             8              0.00630     (  0.00334,     0.00927) **
   8             5              0.01115     (  0.00776,     0.01463) **
   5          B-spp-Deer        0.00656     (  0.00397,     0.00912) **
   5          B--weissii        0.00393     (  0.00191,     0.00595) **
   8             3              0.00450     (  0.00218,     0.00683) **
   3          B-clarridg        0.01528     (  0.01137,     0.01932) **
   3             7              0.00635     (  0.00362,     0.00904) **
   7             1              0.00553     (  0.00310,     0.00800) **
   1            12              0.00184     (  0.00036,     0.00334) **
  12             4              0.00116     (     zero,     0.00239) **
   4          B-henselae        0.01056     (  0.00735,     0.01379) **
   4          B--doshiae        0.00560     (  0.00328,     0.00799) **
  12            10              0.00371     (  0.00173,     0.00577) **
  10          B-birtlesi        0.00753     (  0.00481,     0.01032) **
  10             6              0.00220     (  0.00055,     0.00385) **
   6          B-elizabet        0.01002     (  0.00691,     0.01319) **
   6          B-grahamii        0.00753     (  0.00476,     0.01027) **
   1             9              0.00112     (  0.00009,     0.00224) **
   9          B-vinsonii        0.00405     (  0.00200,     0.00607) **
   9             2              0.00218     (  0.00066,     0.00372) **
   2          B-arupensi        0.00422     (  0.00224,     0.00625) **
   2          B-berhoffi        0.00522     (  0.00299,     0.00746) **
   7          B-quintana        0.01123     (  0.00788,     0.01460) **
  11          A-tumefaci        0.09547     (  0.08577,     0.10624) **

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


Data set # 35:


Empirical Base Frequencies:

   A       0.26658
   C       0.22120
   G       0.30514
  T(U)     0.20708

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.454704)


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


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

Ln Likelihood = -11027.16242

Examined 1142 trees

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

   5             8              0.00709     (  0.00410,     0.01009) **
   8             4              0.00545     (  0.00287,     0.00800) **
   4             6              0.01039     (  0.00705,     0.01373) **
   6          B--weissii        0.00320     (  0.00129,     0.00505) **
   6          B-spp-Deer        0.00602     (  0.00355,     0.00852) **
   4          B-bacillif        0.01170     (  0.00810,     0.01528) **
   8            10              0.00854     (  0.00536,     0.01173) **
  10             9              0.00308     (  0.00131,     0.00486) **
   9          B-vinsonii        0.00594     (  0.00350,     0.00840) **
   9            12              0.00351     (  0.00156,     0.00539) **
  12          B-arupensi        0.00288     (  0.00113,     0.00464) **
  12          B-berhoffi        0.00331     (  0.00149,     0.00515) **
  10             3              0.00080     (     zero,     0.00182) **
   3             1              0.00279     (  0.00107,     0.00453) **
   1          B-grahamii        0.00906     (  0.00610,     0.01209) **
   1          B-birtlesi        0.00696     (  0.00429,     0.00957) **
   3             2              0.00117     (     zero,     0.00233) **
   2             7              0.00324     (  0.00140,     0.00499) **
   7          B-elizabet        0.01413     (  0.01047,     0.01788) **
   7            11              0.00179     (  0.00039,     0.00319) **
  11          B-henselae        0.00512     (  0.00290,     0.00736) **
  11          B-quintana        0.01226     (  0.00881,     0.01571) **
   2          B--doshiae        0.00346     (  0.00156,     0.00530) **
   5          B-clarridg        0.01058     (  0.00703,     0.01412) **
   5          A-tumefaci        0.09621     (  0.08639,     0.10700) **

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


Data set # 36:


Empirical Base Frequencies:

   A       0.26472
   C       0.22991
   G       0.30137
  T(U)     0.20400

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.464075)


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


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

Ln Likelihood = -10634.12053

Examined  792 trees

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

   4          B-clarridg        0.01133     (  0.00775,     0.01497) **
   4             5              0.00681     (  0.00386,     0.00983) **
   5             3              0.00508     (  0.00270,     0.00745) **
   3            12              0.00571     (  0.00321,     0.00821) **
  12          B--weissii        0.00472     (  0.00250,     0.00690) **
  12          B-spp-Deer        0.00502     (  0.00277,     0.00729) **
   3          B-bacillif        0.00921     (  0.00610,     0.01233) **
   5             2              0.00797     (  0.00502,     0.01097) **
   2            11              0.00296     (  0.00122,     0.00470) **
  11          B-quintana        0.00992     (  0.00680,     0.01302) **
  11          B-henselae        0.00407     (  0.00208,     0.00609) **
   2            10              0.00138     (  0.00016,     0.00264) **
  10             8              0.00078     (     zero,     0.00167) **
   8             9              0.00182     (  0.00050,     0.00318) **
   9          B-vinsonii        0.00234     (  0.00084,     0.00386) **
   9             7              0.00193     (  0.00053,     0.00334) **
   7          B-arupensi        0.00312     (  0.00139,     0.00492) **
   7          B-berhoffi        0.00360     (  0.00175,     0.00549) **
   8             1              0.00076     (     zero,     0.00164) **
   1          B-birtlesi        0.00601     (  0.00361,     0.00841) **
   1             6              0.00202     (  0.00055,     0.00339) **
   6          B-grahamii        0.00601     (  0.00359,     0.00840) **
   6          B-elizabet        0.01077     (  0.00754,     0.01398) **
  10          B--doshiae        0.00543     (  0.00318,     0.00775) **
   4          A-tumefaci        0.10525     (  0.09477,     0.11643) **

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


Data set # 37:


Empirical Base Frequencies:

   A       0.26370
   C       0.23003
   G       0.29346
  T(U)     0.21281

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.471836)


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


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

Ln Likelihood = -10882.66517

Examined  552 trees

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

   6          B-clarridg        0.01377     (  0.00993,     0.01773) **
   6             4              0.00773     (  0.00457,     0.01086) **
   4             8              0.00514     (  0.00273,     0.00756) **
   8          B-bacillif        0.00928     (  0.00605,     0.01245) **
   8             5              0.00909     (  0.00595,     0.01225) **
   5          B--weissii        0.00495     (  0.00269,     0.00723) **
   5          B-spp-Deer        0.00663     (  0.00407,     0.00923) **
   4             1              0.00888     (  0.00556,     0.01208) **
   1             3              0.00069     (     zero,     0.00167) **
   3          B-birtlesi        0.00598     (  0.00352,     0.00835) **
   3             9              0.00085     (     zero,     0.00182) **
   9            11              0.00191     (  0.00044,     0.00337) **
  11            12              0.00229     (  0.00074,     0.00388) **
  12          B-quintana        0.01285     (  0.00932,     0.01645) **
  12          B-henselae        0.00659     (  0.00398,     0.00918) **
  11          B-elizabet        0.00829     (  0.00542,     0.01119) **
   9            10              0.00125     (  0.00005,     0.00235) **
  10          B--doshiae        0.00301     (  0.00131,     0.00471) **
  10          B-grahamii        0.00814     (  0.00535,     0.01095) **
   1             7              0.00367     (  0.00176,     0.00564) **
   7             2              0.00236     (  0.00075,     0.00394) **
   2          B-berhoffi        0.00338     (  0.00156,     0.00527) **
   2          B-arupensi        0.00369     (  0.00174,     0.00565) **
   7          B-vinsonii        0.00552     (  0.00315,     0.00793) **
   6          A-tumefaci        0.08829     (  0.07899,     0.09863) **

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


Data set # 38:


Empirical Base Frequencies:

   A       0.26407
   C       0.23397
   G       0.29687
  T(U)     0.20508

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.470379)


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


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

Ln Likelihood = -11111.41238

Examined  534 trees

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

   7             8              0.00629     (  0.00354,     0.00906) **
   8            11              0.00161     (  0.00039,     0.00292) **
  11          B-vinsonii        0.00378     (  0.00178,     0.00573) **
  11            12              0.00231     (  0.00069,     0.00385) **
  12          B-arupensi        0.00396     (  0.00192,     0.00595) **
  12          B-berhoffi        0.00437     (  0.00226,     0.00643) **
   8             4              0.00034     (     zero,     0.00099) *
   4             9              0.00310     (  0.00133,     0.00487) **
   9          B-elizabet        0.01028     (  0.00714,     0.01348) **
   9             3              0.00245     (  0.00081,     0.00410) **
   3          B-henselae        0.00786     (  0.00505,     0.01069) **
   3          B-quintana        0.01220     (  0.00881,     0.01574) **
   4             6              0.00042     (     zero,     0.00128)
   6          B--doshiae        0.00393     (  0.00194,     0.00591) **
   6            10              0.00317     (  0.00132,     0.00498) **
  10          B-grahamii        0.00592     (  0.00348,     0.00837) **
  10          B-birtlesi        0.00978     (  0.00669,     0.01290) **
   7             5              0.00498     (  0.00235,     0.00753) **
   5          B-bacillif        0.01153     (  0.00801,     0.01510) **
   5             2              0.00401     (  0.00184,     0.00611) **
   2             1              0.00874     (  0.00562,     0.01186) **
   1          B--weissii        0.00559     (  0.00311,     0.00797) **
   1          B-spp-Deer        0.00769     (  0.00493,     0.01053) **
   2          B-clarridg        0.01451     (  0.01064,     0.01850) **
   7          A-tumefaci        0.10301     (  0.09285,     0.11417) **

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


Data set # 39:


Empirical Base Frequencies:

   A       0.26999
   C       0.22326
   G       0.29332
  T(U)     0.21343

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.462299)


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


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

Ln Likelihood = -10902.68129

Examined  566 trees

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

  12          B-clarridg        0.01207     (  0.00830,     0.01576) **
  12             1              0.00845     (  0.00524,     0.01177) **
   1             3              0.00793     (  0.00479,     0.01106) **
   3             2              0.00175     (  0.00032,     0.00310) **
   2             9              0.00145     (  0.00011,     0.00281) **
   9          B--doshiae        0.00448     (  0.00232,     0.00665) **
   9             7              0.00190     (  0.00053,     0.00336) **
   7          B-grahamii        0.00726     (  0.00457,     0.01000) **
   7          B-birtlesi        0.00807     (  0.00523,     0.01096) **
   2             6              0.00230     (  0.00070,     0.00391) **
   6          B-elizabet        0.01096     (  0.00762,     0.01424) **
   6             4              0.00288     (  0.00114,     0.00465) **
   4          B-henselae        0.00492     (  0.00266,     0.00717) **
   4          B-quintana        0.01212     (  0.00872,     0.01563) **
   3             5              0.00134     (  0.00017,     0.00250) **
   5             8              0.00350     (  0.00162,     0.00538) **
   8          B-berhoffi        0.00458     (  0.00247,     0.00668) **
   8          B-arupensi        0.00222     (  0.00073,     0.00373) **
   5          B-vinsonii        0.00351     (  0.00163,     0.00539) **
   1            10              0.00624     (  0.00356,     0.00892) **
  10            11              0.00671     (  0.00397,     0.00947) **
  11          B--weissii        0.00369     (  0.00169,     0.00571) **
  11          B-spp-Deer        0.00621     (  0.00368,     0.00872) **
  10          B-bacillif        0.01239     (  0.00873,     0.01598) **
  12          A-tumefaci        0.08865     (  0.07916,     0.09885) **

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


Data set # 40:


Empirical Base Frequencies:

   A       0.26622
   C       0.21807
   G       0.31472
  T(U)     0.20100

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.443986)


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


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

Ln Likelihood = -11062.49247

Examined  722 trees

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

   8             4              0.00350     (  0.00120,     0.00584) **
   4             1              0.00200     (  0.00060,     0.00349) **
   1             6              0.00242     (  0.00066,     0.00418) **
   6             2              0.00078     (     zero,     0.00184) **
   2             9              0.00419     (  0.00207,     0.00632) **
   9          B-birtlesi        0.00813     (  0.00530,     0.01098) **
   9             5              0.00234     (  0.00073,     0.00396) **
   5          B-grahamii        0.00527     (  0.00304,     0.00760) **
   5          B-elizabet        0.01564     (  0.01176,     0.01957) **
   2          B--doshiae        0.00410     (  0.00202,     0.00609) **
   6            12              0.00286     (  0.00110,     0.00463) **
  12          B-henselae        0.00397     (  0.00196,     0.00600) **
  12          B-quintana        0.01479     (  0.01104,     0.01863) **
   1          B-vinsonii        0.00543     (  0.00307,     0.00781) **
   4             3              0.00220     (  0.00056,     0.00380) **
   3          B-arupensi        0.00416     (  0.00215,     0.00618) **
   3          B-berhoffi        0.00258     (  0.00092,     0.00416) **
   8             7              0.00432     (  0.00206,     0.00667) **
   7          B-clarridg        0.01605     (  0.01202,     0.02016) **
   7            11              0.00562     (  0.00317,     0.00816) **
  11          B-bacillif        0.01209     (  0.00856,     0.01575) **
  11            10              0.00881     (  0.00571,     0.01189) **
  10          B-spp-Deer        0.00864     (  0.00577,     0.01162) **
  10          B--weissii        0.00409     (  0.00203,     0.00617) **
   8          A-tumefaci        0.09637     (  0.08651,     0.10704) **

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


Data set # 41:


Empirical Base Frequencies:

   A       0.26503
   C       0.22141
   G       0.30334
  T(U)     0.21022

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.459042)


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


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

Ln Likelihood = -10787.73878

Examined  798 trees

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

   4          B-bacillif        0.00713     (  0.00425,     0.01002) **
   4            11              0.00410     (  0.00175,     0.00648) **
  11             6              0.00693     (  0.00423,     0.00963) **
   6          B-spp-Deer        0.00528     (  0.00302,     0.00755) **
   6          B--weissii        0.00441     (  0.00235,     0.00648) **
  11             5              0.00448     (  0.00227,     0.00672) **
   5          B-clarridg        0.01190     (  0.00838,     0.01540) **
   5             8              0.00867     (  0.00561,     0.01176) **
   8          B-quintana        0.01087     (  0.00753,     0.01430) **
   8            12              0.00418     (  0.00199,     0.00637) **
  12          B-henselae        0.00729     (  0.00456,     0.01000) **
  12             3              0.00169     (  0.00027,     0.00316) **
   3             2              0.00037     (     zero,     0.00112)
   2          B--doshiae        0.00437     (  0.00225,     0.00640) **
   2             1              0.00227     (  0.00072,     0.00377) **
   1          B-vinsonii        0.00582     (  0.00347,     0.00825) **
   1             7              0.00143     (  0.00019,     0.00267) **
   7          B-berhoffi        0.00600     (  0.00357,     0.00842) **
   7          B-arupensi        0.00237     (  0.00082,     0.00394) **
   3             9              0.00236     (  0.00064,     0.00404) **
   9          B-birtlesi        0.00586     (  0.00340,     0.00827) **
   9            10              0.00254     (  0.00087,     0.00419) **
  10          B-elizabet        0.01146     (  0.00814,     0.01482) **
  10          B-grahamii        0.00480     (  0.00258,     0.00697) **
   4          A-tumefaci        0.10185     (  0.09171,     0.11289) **

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


Data set # 42:


Empirical Base Frequencies:

   A       0.27341
   C       0.20976
   G       0.30418
  T(U)     0.21265

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.443145)


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


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

Ln Likelihood = -11116.50408

Examined  594 trees

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

   9          B-birtlesi        0.00854     (  0.00552,     0.01151) **
   9             8              0.00264     (  0.00077,     0.00453) **
   8             1              0.00153     (  0.00033,     0.00277) **
   1          B-vinsonii        0.00198     (  0.00060,     0.00335) **
   1             7              0.00174     (  0.00044,     0.00302) **
   7          B-berhoffi        0.00466     (  0.00262,     0.00681) **
   7          B-arupensi        0.00227     (  0.00074,     0.00371) **
   8             4              0.00084     (     zero,     0.00178) **
   4             3              0.00146     (  0.00016,     0.00269) **
   3            11              0.00349     (  0.00163,     0.00538) **
  11          B-elizabet        0.01023     (  0.00708,     0.01338) **
  11          B-grahamii        0.00636     (  0.00386,     0.00886) **
   3             2              0.00177     (  0.00018,     0.00337) **
   2             6              0.00387     (  0.00178,     0.00601) **
   6          B-quintana        0.01310     (  0.00953,     0.01675) **
   6          B-henselae        0.00486     (  0.00256,     0.00716) **
   2             5              0.01156     (  0.00803,     0.01512) **
   5            12              0.00571     (  0.00326,     0.00825) **
  12          B-clarridg        0.01911     (  0.01474,     0.02366) **
  12            10              0.00708     (  0.00422,     0.00993) **
  10          B--weissii        0.00437     (  0.00221,     0.00654) **
  10          B-spp-Deer        0.00865     (  0.00569,     0.01162) **
   5          B-bacillif        0.01014     (  0.00673,     0.01349) **
   4          B--doshiae        0.00454     (  0.00244,     0.00666) **
   9          A-tumefaci        0.10340     (  0.09308,     0.11436) **

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


Data set # 43:


Empirical Base Frequencies:

   A       0.27160
   C       0.23096
   G       0.29815
  T(U)     0.19929

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.458260)


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


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

Ln Likelihood = -11102.01251

Examined 1298 trees

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

  11             1              0.00493     (  0.00236,     0.00752) **
   1             3              0.00519     (  0.00281,     0.00758) **
   3             5              0.01077     (  0.00741,     0.01420) **
   5          B-spp-Deer        0.00882     (  0.00594,     0.01181) **
   5          B--weissii        0.00186     (  0.00042,     0.00329) **
   3          B-clarridg        0.01746     (  0.01318,     0.02172) **
   1             7              0.00727     (  0.00436,     0.01017) **
   7             2              0.00124     (  0.00004,     0.00246) **
   2            10              0.00030     (     zero,     0.00088) *
  10             6              0.00228     (  0.00067,     0.00380) **
   6             8              0.00296     (  0.00119,     0.00476) **
   8          B-quintana        0.01282     (  0.00923,     0.01640) **
   8          B-henselae        0.00801     (  0.00512,     0.01087) **
   6          B-elizabet        0.00777     (  0.00499,     0.01054) **
  10          B-vinsonii        0.00488     (  0.00271,     0.00707) **
   2             4              0.00176     (  0.00048,     0.00308) **
   4             9              0.00079     (     zero,     0.00168) **
   9          B-grahamii        0.00797     (  0.00522,     0.01078) **
   9          B--doshiae        0.00464     (  0.00249,     0.00674) **
   4            12              0.00335     (  0.00155,     0.00516) **
  12          B-arupensi        0.00279     (  0.00112,     0.00441) **
  12          B-berhoffi        0.00492     (  0.00275,     0.00709) **
   7          B-birtlesi        0.00912     (  0.00613,     0.01212) **
  11          B-bacillif        0.00744     (  0.00444,     0.01037) **
  11          A-tumefaci        0.09956     (  0.08933,     0.11024) **

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


Data set # 44:


Empirical Base Frequencies:

   A       0.26417
   C       0.22094
   G       0.30872
  T(U)     0.20617

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.454860)


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


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

Ln Likelihood = -11180.15694

Examined  606 trees

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

   2            10              0.00194     (  0.00029,     0.00359) **
  10            11              0.00392     (  0.00189,     0.00598) **
  11             1              0.00077     (     zero,     0.00169) **
   1          B-vinsonii        0.00622     (  0.00375,     0.00871) **
   1          B-birtlesi        0.00718     (  0.00449,     0.00987) **
  11             7              0.00083     (     zero,     0.00180) **
   7          B--doshiae        0.00626     (  0.00372,     0.00872) **
   7            12              0.00201     (  0.00045,     0.00359) **
  12          B-henselae        0.00759     (  0.00481,     0.01043) **
  12             8              0.00306     (  0.00132,     0.00481) **
   8          B-elizabet        0.01007     (  0.00687,     0.01328) **
   8          B-grahamii        0.00589     (  0.00346,     0.00843) **
  10             3              0.00345     (  0.00159,     0.00539) **
   3          B-berhoffi        0.00415     (  0.00211,     0.00617) **
   3          B-arupensi        0.00435     (  0.00226,     0.00646) **
   2             6              0.00313     (  0.00123,     0.00510) **
   6          B-quintana        0.01422     (  0.01044,     0.01801) **
   6             5              0.00827     (  0.00514,     0.01134) **
   5          B-clarridg        0.01829     (  0.01388,     0.02272) **
   5             4              0.00569     (  0.00312,     0.00818) **
   4             9              0.00878     (  0.00570,     0.01194) **
   9          B-spp-Deer        0.00654     (  0.00396,     0.00914) **
   9          B--weissii        0.00445     (  0.00229,     0.00662) **
   4          B-bacillif        0.01230     (  0.00863,     0.01599) **
   2          A-tumefaci        0.09027     (  0.08077,     0.10046) **

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


Data set # 45:


Empirical Base Frequencies:

   A       0.26276
   C       0.22743
   G       0.30587
  T(U)     0.20394

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.461960)


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


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

Ln Likelihood = -10709.31968

Examined 1300 trees

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

   5             4              0.00373     (  0.00148,     0.00593) **
   4             2              0.00220     (  0.00072,     0.00371) **
   2             7              0.00247     (  0.00090,     0.00407) **
   7          B-arupensi        0.00319     (  0.00137,     0.00496) **
   7          B-berhoffi        0.00388     (  0.00197,     0.00586) **
   2          B-vinsonii        0.00386     (  0.00189,     0.00583) **
   4             1              0.00083     (     zero,     0.00181) **
   1             6              0.00043     (     zero,     0.00117)
   6             3              0.00328     (  0.00142,     0.00512) **
   3          B-henselae        0.00626     (  0.00372,     0.00875) **
   3          B-quintana        0.01114     (  0.00782,     0.01444) **
   6            11              0.00250     (  0.00082,     0.00415) **
  11          B-birtlesi        0.00782     (  0.00502,     0.01057) **
  11             8              0.00075     (     zero,     0.00187) **
   8          B-grahamii        0.00635     (  0.00387,     0.00884) **
   8          B-elizabet        0.01154     (  0.00820,     0.01488) **
   1          B--doshiae        0.00422     (  0.00223,     0.00623) **
   5            12              0.00401     (  0.00169,     0.00642) **
  12          B-bacillif        0.01112     (  0.00765,     0.01457) **
  12             9              0.00457     (  0.00234,     0.00682) **
   9          B-clarridg        0.01232     (  0.00870,     0.01598) **
   9            10              0.00829     (  0.00528,     0.01132) **
  10          B-spp-Deer        0.00746     (  0.00474,     0.01021) **
  10          B--weissii        0.00318     (  0.00134,     0.00504) **
   5          A-tumefaci        0.09582     (  0.08611,     0.10653) **

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


Data set # 46:


Empirical Base Frequencies:

   A       0.26546
   C       0.22961
   G       0.30248
  T(U)     0.20245

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.461973)


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


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

Ln Likelihood = -10964.65772

Examined  588 trees

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

   8          B-clarridg        0.01303     (  0.00923,     0.01691) **
   8             6              0.00883     (  0.00549,     0.01217) **
   6             3              0.00619     (  0.00337,     0.00897) **
   3             4              0.00370     (  0.00183,     0.00565) **
   4             2              0.00197     (  0.00045,     0.00350) **
   2          B--doshiae        0.00670     (  0.00416,     0.00924) **
   2             9              0.00051     (     zero,     0.00125) **
   9             1              0.00210     (  0.00058,     0.00359) **
   1             7              0.00221     (  0.00071,     0.00373) **
   7          B-grahamii        0.00733     (  0.00467,     0.01001) **
   7          B-elizabet        0.00838     (  0.00552,     0.01122) **
   1          B-birtlesi        0.00712     (  0.00450,     0.00976) **
   9            10              0.00330     (  0.00152,     0.00510) **
  10            12              0.00125     (  0.00014,     0.00233) **
  12          B-arupensi        0.00289     (  0.00121,     0.00456) **
  12          B-berhoffi        0.00182     (  0.00049,     0.00316) **
  10          B-vinsonii        0.00517     (  0.00290,     0.00738) **
   4          B-henselae        0.00597     (  0.00351,     0.00844) **
   3          B-quintana        0.01073     (  0.00752,     0.01407) **
   6             5              0.00391     (  0.00165,     0.00616) **
   5            11              0.01010     (  0.00681,     0.01336) **
  11          B-spp-Deer        0.00701     (  0.00432,     0.00974) **
  11          B--weissii        0.00555     (  0.00310,     0.00800) **
   5          B-bacillif        0.01032     (  0.00697,     0.01369) **
   8          A-tumefaci        0.09826     (  0.08809,     0.10891) **

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


Data set # 47:


Empirical Base Frequencies:

   A       0.25827
   C       0.21931
   G       0.29986
  T(U)     0.22256

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.472555)


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


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

Ln Likelihood = -11300.97034

Examined  568 trees

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

  10             3              0.00555     (  0.00297,     0.00815) **
   3          B-bacillif        0.01158     (  0.00802,     0.01514) **
   3             9              0.00437     (  0.00216,     0.00659) **
   9          B-clarridg        0.01746     (  0.01325,     0.02178) **
   9             5              0.00893     (  0.00584,     0.01208) **
   5          B-spp-Deer        0.00907     (  0.00600,     0.01205) **
   5          B--weissii        0.00291     (  0.00117,     0.00476) **
  10             4              0.00477     (  0.00218,     0.00745) **
   4             1              0.00187     (  0.00045,     0.00326) **
   1            11              0.00167     (  0.00027,     0.00307) **
  11            12              0.00359     (  0.00166,     0.00553) **
  12          B-grahamii        0.00645     (  0.00389,     0.00899) **
  12          B-birtlesi        0.00770     (  0.00491,     0.01044) **
  11             7              0.00073     (     zero,     0.00174) **
   7          B--doshiae        0.00484     (  0.00263,     0.00702) **
   7             2              0.00373     (  0.00172,     0.00570) **
   2             6              0.00362     (  0.00161,     0.00567) **
   6          B-quintana        0.01650     (  0.01253,     0.02062) **
   6          B-henselae        0.00504     (  0.00276,     0.00737) **
   2          B-elizabet        0.01316     (  0.00946,     0.01674) **
   1          B-vinsonii        0.00331     (  0.00147,     0.00517) **
   4             8              0.00205     (  0.00054,     0.00364) **
   8          B-arupensi        0.00275     (  0.00111,     0.00437) **
   8          B-berhoffi        0.00597     (  0.00359,     0.00837) **
  10          A-tumefaci        0.10376     (  0.09325,     0.11470) **

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


Data set # 48:


Empirical Base Frequencies:

   A       0.25800
   C       0.22495
   G       0.30185
  T(U)     0.21520

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.471569)


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


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

Ln Likelihood = -10957.29682

Examined  880 trees

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

   9             8              0.00596     (  0.00324,     0.00872) **
   8             2              0.00588     (  0.00326,     0.00851) **
   2             6              0.00336     (  0.00141,     0.00530) **
   6            10              0.00095     (     zero,     0.00201) **
  10            11              0.00177     (  0.00034,     0.00318) **
  11          B-berhoffi        0.00367     (  0.00178,     0.00559) **
  11          B-arupensi        0.00302     (  0.00129,     0.00476) **
  10          B-vinsonii        0.00422     (  0.00212,     0.00634) **
   6             3              0.00183     (  0.00036,     0.00324) **
   3            12              0.00088     (     zero,     0.00194) **
  12          B--doshiae        0.00563     (  0.00325,     0.00794) **
  12             7              0.00220     (  0.00066,     0.00375) **
   7          B-birtlesi        0.00786     (  0.00509,     0.01065) **
   7             1              0.00196     (  0.00046,     0.00347) **
   1          B-elizabet        0.01158     (  0.00824,     0.01493) **
   1          B-grahamii        0.00479     (  0.00263,     0.00696) **
   3          B-henselae        0.00966     (  0.00663,     0.01275) **
   2          B-quintana        0.01302     (  0.00939,     0.01661) **
   8             5              0.00426     (  0.00194,     0.00658) **
   5             4              0.00525     (  0.00282,     0.00766) **
   4          B-spp-Deer        0.00944     (  0.00629,     0.01249) **
   4          B--weissii        0.00507     (  0.00277,     0.00741) **
   5          B-bacillif        0.01561     (  0.01160,     0.01964) **
   9          B-clarridg        0.01133     (  0.00775,     0.01487) **
   9          A-tumefaci        0.09283     (  0.08319,     0.10335) **

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


Data set # 49:


Empirical Base Frequencies:

   A       0.24463
   C       0.22920
   G       0.30901
  T(U)     0.21716

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.487127)


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


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

Ln Likelihood = -10827.90552

Examined  628 trees

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

   7          B-clarridg        0.01237     (  0.00868,     0.01614) **
   7             9              0.00625     (  0.00332,     0.00918) **
   9             4              0.00823     (  0.00515,     0.01134) **
   4             2              0.00060     (     zero,     0.00151) **
   2             3              0.00078     (     zero,     0.00170) **
   3          B--doshiae        0.00376     (  0.00187,     0.00567) **
   3             6              0.00421     (  0.00219,     0.00623) **
   6          B-quintana        0.01329     (  0.00970,     0.01687) **
   6          B-henselae        0.00424     (  0.00216,     0.00623) **
   2             8              0.00244     (  0.00071,     0.00410) **
   8          B-birtlesi        0.00714     (  0.00447,     0.00982) **
   8            12              0.00293     (  0.00117,     0.00470) **
  12          B-grahamii        0.00685     (  0.00427,     0.00946) **
  12          B-elizabet        0.00933     (  0.00632,     0.01236) **
   4             5              0.00108     (  0.00005,     0.00216) **
   5          B-vinsonii        0.00573     (  0.00335,     0.00812) **
   5             1              0.00166     (  0.00036,     0.00303) **
   1          B-arupensi        0.00277     (  0.00111,     0.00444) **
   1          B-berhoffi        0.00459     (  0.00247,     0.00670) **
   9            10              0.00467     (  0.00237,     0.00693) **
  10            11              0.00667     (  0.00395,     0.00941) **
  11          B-spp-Deer        0.00706     (  0.00446,     0.00973) **
  11          B--weissii        0.00459     (  0.00245,     0.00674) **
  10          B-bacillif        0.01036     (  0.00702,     0.01371) **
   7          A-tumefaci        0.09796     (  0.08802,     0.10880) **

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


Data set # 50:


Empirical Base Frequencies:

   A       0.27575
   C       0.21865
   G       0.28901
  T(U)     0.21659

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.458706)


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


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

Ln Likelihood = -10599.87296

Examined  558 trees

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

   4            11              0.00503     (  0.00235,     0.00778) **
  11            12              0.00755     (  0.00456,     0.01053) **
  12          B-spp-Deer        0.00792     (  0.00517,     0.01070) **
  12          B--weissii        0.00136     (  0.00011,     0.00253) **
  11             3              0.00464     (  0.00241,     0.00688) **
   3          B-bacillif        0.00941     (  0.00625,     0.01263) **
   3             2              0.01001     (  0.00672,     0.01331) **
   2             1              0.00074     (     zero,     0.00161) **
   1             6              0.00119     (  0.00001,     0.00232) **
   6             7              0.00408     (  0.00208,     0.00610) **
   7          B-elizabet        0.00755     (  0.00484,     0.01024) **
   7          B-grahamii        0.00569     (  0.00334,     0.00804) **
   6             8              0.00427     (  0.00219,     0.00632) **
   8          B-henselae        0.00385     (  0.00184,     0.00582) **
   8          B-quintana        0.00939     (  0.00640,     0.01245) **
   1             9              0.00079     (     zero,     0.00168) **
   9          B-birtlesi        0.00803     (  0.00524,     0.01081) **
   9          B--doshiae        0.00422     (  0.00220,     0.00624) **
   2            10              0.00198     (  0.00050,     0.00338) **
  10          B-vinsonii        0.00304     (  0.00130,     0.00477) **
  10             5              0.00254     (  0.00101,     0.00414) **
   5          B-arupensi        0.00419     (  0.00215,     0.00624) **
   5          B-berhoffi        0.00367     (  0.00177,     0.00558) **
   4          B-clarridg        0.01020     (  0.00683,     0.01358) **
   4          A-tumefaci        0.09243     (  0.08292,     0.10303) **

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


Data set # 51:


Empirical Base Frequencies:

   A       0.26157
   C       0.21736
   G       0.30628
  T(U)     0.21478

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.461134)


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


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

Ln Likelihood = -10961.12534

Examined 1058 trees

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

   1          B-bacillif        0.00878     (  0.00566,     0.01197) **
   1             8              0.00446     (  0.00191,     0.00698) **
   8             7              0.00499     (  0.00271,     0.00733) **
   7          B-clarridg        0.01658     (  0.01245,     0.02080) **
   7            10              0.00752     (  0.00466,     0.01042) **
  10          B--weissii        0.00336     (  0.00140,     0.00528) **
  10          B-spp-Deer        0.01193     (  0.00848,     0.01540) **
   8             4              0.00644     (  0.00364,     0.00923) **
   4             5              0.00195     (  0.00053,     0.00338) **
   5             9              0.00351     (  0.00155,     0.00541) **
   9          B-berhoffi        0.00426     (  0.00219,     0.00631) **
   9          B-arupensi        0.00360     (  0.00172,     0.00552) **
   5          B-vinsonii        0.00325     (  0.00145,     0.00507) **
   4             3              0.00093     (     zero,     0.00195) **
   3          B-birtlesi        0.00710     (  0.00444,     0.00974) **
   3             2              0.00107     (  0.00006,     0.00215) **
   2             6              0.00071     (     zero,     0.00164) **
   6          B--doshiae        0.00425     (  0.00220,     0.00633) **
   6            12              0.00329     (  0.00149,     0.00508) **
  12          B-elizabet        0.01066     (  0.00742,     0.01389) **
  12          B-grahamii        0.00466     (  0.00247,     0.00682) **
   2            11              0.00772     (  0.00494,     0.01049) **
  11          B-henselae        0.00495     (  0.00271,     0.00719) **
  11          B-quintana        0.01245     (  0.00894,     0.01596) **
   1          A-tumefaci        0.09492     (  0.08491,     0.10530) **

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


Data set # 52:


Empirical Base Frequencies:

   A       0.27394
   C       0.20824
   G       0.30340
  T(U)     0.21442

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.443381)


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


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

Ln Likelihood = -10998.73547

Examined  558 trees

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

  12          B-birtlesi        0.00623     (  0.00359,     0.00887) **
  12             2              0.00411     (  0.00182,     0.00632) **
   2             3              0.00150     (  0.00027,     0.00272) **
   3             5              0.00083     (     zero,     0.00183) **
   5          B-henselae        0.00702     (  0.00444,     0.00967) **
   5             1              0.00226     (  0.00081,     0.00380) **
   1          B-elizabet        0.00993     (  0.00682,     0.01305) **
   1          B-grahamii        0.00672     (  0.00416,     0.00931) **
   3             4              0.00201     (  0.00037,     0.00361) **
   4             6              0.00581     (  0.00328,     0.00836) **
   6             9              0.00653     (  0.00377,     0.00928) **
   9          B-clarridg        0.01438     (  0.01046,     0.01823) **
   9             7              0.00518     (  0.00279,     0.00757) **
   7          B-bacillif        0.01204     (  0.00848,     0.01560) **
   7            11              0.00896     (  0.00587,     0.01207) **
  11          B--weissii        0.00339     (  0.00153,     0.00521) **
  11          B-spp-Deer        0.00705     (  0.00445,     0.00969) **
   6          B-quintana        0.00902     (  0.00593,     0.01211) **
   4             8              0.00158     (  0.00025,     0.00291) **
   8            10              0.00360     (  0.00162,     0.00555) **
  10          B-arupensi        0.00240     (  0.00077,     0.00397) **
  10          B-berhoffi        0.00353     (  0.00166,     0.00540) **
   8          B-vinsonii        0.00440     (  0.00220,     0.00651) **
   2          B--doshiae        0.00369     (  0.00178,     0.00561) **
  12          A-tumefaci        0.10509     (  0.09479,     0.11627) **

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


Data set # 53:


Empirical Base Frequencies:

   A       0.26490
   C       0.22695
   G       0.30047
  T(U)     0.20768

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.463428)


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


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

Ln Likelihood = -10878.20867

Examined  580 trees

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

  11            10              0.00507     (  0.00225,     0.00792) **
  10             8              0.00421     (  0.00193,     0.00643) **
   8          B-clarridg        0.01191     (  0.00833,     0.01554) **
   8             6              0.01353     (  0.00966,     0.01741) **
   6            12              0.00269     (  0.00101,     0.00436) **
  12          B-henselae        0.00556     (  0.00320,     0.00795) **
  12          B-quintana        0.01387     (  0.01014,     0.01754) **
   6             9              0.00110     (  0.00004,     0.00224) **
   9             5              0.00097     (     zero,     0.00212) **
   5             4              0.00098     (  0.00006,     0.00199) **
   4          B--doshiae        0.00526     (  0.00299,     0.00755) **
   4          B-grahamii        0.00774     (  0.00494,     0.01046) **
   5          B-birtlesi        0.00978     (  0.00663,     0.01285) **
   9             1              0.00200     (  0.00054,     0.00346) **
   1          B-elizabet        0.01285     (  0.00932,     0.01643) **
   1             7              0.00365     (  0.00173,     0.00556) **
   7          B-vinsonii        0.00402     (  0.00201,     0.00607) **
   7             3              0.00327     (  0.00140,     0.00512) **
   3          B-arupensi        0.00152     (  0.00018,     0.00279) **
   3          B-berhoffi        0.00490     (  0.00268,     0.00710) **
  10             2              0.00667     (  0.00382,     0.00944) **
   2          B--weissii        0.00405     (  0.00193,     0.00615) **
   2          B-spp-Deer        0.00747     (  0.00469,     0.01025) **
  11          B-bacillif        0.00752     (  0.00447,     0.01049) **
  11          A-tumefaci        0.09219     (  0.08251,     0.10256) **

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


Data set # 54:


Empirical Base Frequencies:

   A       0.27585
   C       0.22109
   G       0.29467
  T(U)     0.20839

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.452227)


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


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

Ln Likelihood = -10548.65561

Examined  508 trees

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

   8             5              0.00464     (  0.00232,     0.00695) **
   5            12              0.00278     (  0.00103,     0.00454) **
  12          B-bacillif        0.01386     (  0.01010,     0.01764) **
  12            11              0.00577     (  0.00331,     0.00830) **
  11          B--weissii        0.00291     (  0.00119,     0.00464) **
  11          B-spp-Deer        0.00655     (  0.00401,     0.00910) **
   5          B-clarridg        0.01440     (  0.01066,     0.01831) **
   8             6              0.00283     (  0.00089,     0.00485) **
   6             3              0.00300     (  0.00113,     0.00488) **
   3             2              0.00118     (     zero,     0.00234) **
   2             1              0.00138     (  0.00013,     0.00256) **
   1          B-birtlesi        0.00749     (  0.00478,     0.01018) **
   1             9              0.00046     (     zero,     0.00116) **
   9          B-henselae        0.00732     (  0.00468,     0.01000) **
   9          B--doshiae        0.00369     (  0.00178,     0.00558) **
   2             4              0.00265     (  0.00106,     0.00428) **
   4          B-grahamii        0.00371     (  0.00186,     0.00562) **
   4          B-elizabet        0.01052     (  0.00734,     0.01370) **
   3             7              0.00200     (  0.00058,     0.00344) **
   7          B-vinsonii        0.00438     (  0.00223,     0.00651) **
   7            10              0.00188     (  0.00046,     0.00331) **
  10          B-arupensi        0.00223     (  0.00077,     0.00377) **
  10          B-berhoffi        0.00498     (  0.00272,     0.00717) **
   6          B-quintana        0.00843     (  0.00554,     0.01133) **
   8          A-tumefaci        0.09840     (  0.08866,     0.10947) **

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


Data set # 55:


Empirical Base Frequencies:

   A       0.25740
   C       0.22193
   G       0.30057
  T(U)     0.22010

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.473188)


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


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

Ln Likelihood = -10759.11419

Examined  614 trees

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

   7            12              0.00376     (  0.00162,     0.00585) **
  12          B-clarridg        0.01228     (  0.00870,     0.01585) **
  12             4              0.00556     (  0.00305,     0.00805) **
   4             8              0.00872     (  0.00569,     0.01176) **
   8          B-spp-Deer        0.00641     (  0.00383,     0.00896) **
   8          B--weissii        0.00367     (  0.00166,     0.00567) **
   4          B-bacillif        0.00870     (  0.00561,     0.01178) **
   7             2              0.00315     (  0.00103,     0.00527) **
   2          B-quintana        0.00991     (  0.00669,     0.01306) **
   2             1              0.00551     (  0.00303,     0.00801) **
   1             6              0.00223     (  0.00064,     0.00378) **
   6          B-vinsonii        0.00317     (  0.00122,     0.00509) **
   6             9              0.00231     (  0.00064,     0.00402) **
   9          B-arupensi        0.00368     (  0.00170,     0.00567) **
   9          B-berhoffi        0.00421     (  0.00213,     0.00626) **
   1            11              0.00294     (  0.00104,     0.00488) **
  11          B--doshiae        0.00469     (  0.00256,     0.00682) **
  11             5              0.00087     (     zero,     0.00186) **
   5             3              0.00149     (  0.00011,     0.00287) **
   3            10              0.00286     (  0.00118,     0.00464) **
  10          B-grahamii        0.00477     (  0.00253,     0.00689) **
  10          B-elizabet        0.01004     (  0.00698,     0.01319) **
   3          B-birtlesi        0.00719     (  0.00451,     0.00986) **
   5          B-henselae        0.00804     (  0.00520,     0.01081) **
   7          A-tumefaci        0.09980     (  0.08933,     0.11023) **

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


Data set # 56:


Empirical Base Frequencies:

   A       0.25541
   C       0.22616
   G       0.31578
  T(U)     0.20265

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.464741)


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


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

Ln Likelihood = -10734.68368

Examined  468 trees

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

   2          B-clarridg        0.01209     (  0.00850,     0.01576) **
   2            12              0.00508     (  0.00255,     0.00762) **
  12             7              0.00311     (  0.00124,     0.00499) **
   7             1              0.00775     (  0.00481,     0.01071) **
   1          B--weissii        0.00348     (  0.00164,     0.00538) **
   1          B-spp-Deer        0.00801     (  0.00518,     0.01079) **
   7             9              0.00915     (  0.00604,     0.01228) **
   9             5              0.00272     (  0.00094,     0.00457) **
   5             4              0.00164     (  0.00028,     0.00303) **
   4             8              0.00083     (     zero,     0.00181) **
   8            10              0.00054     (     zero,     0.00134) **
  10             3              0.00226     (  0.00056,     0.00385) **
   3             6              0.00171     (  0.00045,     0.00308) **
   6          B-grahamii        0.00523     (  0.00291,     0.00752) **
   6          B-elizabet        0.00862     (  0.00573,     0.01155) **
   3          B-birtlesi        0.00598     (  0.00349,     0.00841) **
  10          B-vinsonii        0.00597     (  0.00355,     0.00834) **
   8          B--doshiae        0.00380     (  0.00182,     0.00568) **
   4          B-henselae        0.00594     (  0.00352,     0.00833) **
   5            11              0.00279     (  0.00112,     0.00449) **
  11          B-arupensi        0.00226     (  0.00073,     0.00379) **
  11          B-berhoffi        0.00329     (  0.00151,     0.00511) **
   9          B-quintana        0.01345     (  0.00978,     0.01712) **
  12          B-bacillif        0.01322     (  0.00949,     0.01696) **
   2          A-tumefaci        0.09553     (  0.08593,     0.10635) **

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


Data set # 57:


Empirical Base Frequencies:

   A       0.27185
   C       0.21563
   G       0.29922
  T(U)     0.21330

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.452169)


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


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

Ln Likelihood = -10948.16982

Examined  748 trees

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

  12          B-clarridg        0.01223     (  0.00851,     0.01596) **
  12             7              0.00685     (  0.00372,     0.01002) **
   7             9              0.01011     (  0.00668,     0.01351) **
   9          B--weissii        0.00292     (  0.00111,     0.00467) **
   9          B-spp-Deer        0.01106     (  0.00779,     0.01439) **
   7            10              0.00405     (  0.00192,     0.00619) **
  10          B-bacillif        0.01130     (  0.00778,     0.01486) **
  10             4              0.01326     (  0.00945,     0.01707) **
   4             5              0.00207     (  0.00063,     0.00349) **
   5          B-vinsonii        0.00476     (  0.00260,     0.00692) **
   5            11              0.00163     (  0.00035,     0.00292) **
  11          B-berhoffi        0.00283     (  0.00114,     0.00447) **
  11          B-arupensi        0.00340     (  0.00160,     0.00522) **
   4             1              0.00052     (     zero,     0.00130) **
   1             3              0.00080     (     zero,     0.00175) **
   3             6              0.00320     (  0.00141,     0.00499) **
   6          B-quintana        0.01247     (  0.00904,     0.01597) **
   6          B-henselae        0.00427     (  0.00221,     0.00632) **
   3          B--doshiae        0.00428     (  0.00220,     0.00627) **
   1             2              0.00144     (  0.00021,     0.00271) **
   2             8              0.00167     (  0.00025,     0.00299) **
   8          B-elizabet        0.00790     (  0.00521,     0.01072) **
   8          B-grahamii        0.00875     (  0.00578,     0.01162) **
   2          B-birtlesi        0.00867     (  0.00570,     0.01153) **
  12          A-tumefaci        0.09117     (  0.08151,     0.10146) **

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


Data set # 58:


Empirical Base Frequencies:

   A       0.27738
   C       0.21239
   G       0.30853
  T(U)     0.20170

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.430039)


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


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

Ln Likelihood = -11013.94588

Examined  532 trees

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

   7          B-clarridg        0.01009     (  0.00674,     0.01347) **
   7             5              0.00782     (  0.00481,     0.01090) **
   5             8              0.00320     (  0.00121,     0.00520) **
   8             9              0.01026     (  0.00701,     0.01355) **
   9          B--weissii        0.00555     (  0.00318,     0.00797) **
   9          B-spp-Deer        0.00764     (  0.00483,     0.01041) **
   8          B-bacillif        0.01517     (  0.01120,     0.01915) **
   5             4              0.00584     (  0.00322,     0.00847) **
   4             3              0.00503     (  0.00276,     0.00735) **
   3          B-berhoffi        0.00390     (  0.00189,     0.00592) **
   3             6              0.00260     (  0.00098,     0.00421) **
   6          B-arupensi        0.00476     (  0.00255,     0.00697) **
   6             1              0.00168     (  0.00037,     0.00307) **
   1             2              0.00134     (  0.00011,     0.00259) **
   2            12              0.00076     (     zero,     0.00162) **
  12          B-henselae        0.00924     (  0.00628,     0.01229) **
  12            11              0.00138     (  0.00016,     0.00259) **
  11          B-elizabet        0.01064     (  0.00742,     0.01390) **
  11            10              0.00214     (  0.00067,     0.00362) **
  10          B-grahamii        0.00693     (  0.00433,     0.00955) **
  10          B--doshiae        0.00322     (  0.00141,     0.00503) **
   2          B-birtlesi        0.00957     (  0.00650,     0.01265) **
   1          B-vinsonii        0.00248     (  0.00086,     0.00411) **
   4          B-quintana        0.00877     (  0.00582,     0.01171) **
   7          A-tumefaci        0.09057     (  0.08086,     0.10074) **

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


Data set # 59:


Empirical Base Frequencies:

   A       0.27993
   C       0.22357
   G       0.28128
  T(U)     0.21522

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.462840)


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


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

Ln Likelihood = -10953.28505

Examined  614 trees

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

   9             4              0.00631     (  0.00332,     0.00929) **
   4             5              0.00828     (  0.00527,     0.01133) **
   5          B--weissii        0.00452     (  0.00239,     0.00674) **
   5          B-spp-Deer        0.00769     (  0.00494,     0.01051) **
   4             6              0.00499     (  0.00247,     0.00748) **
   6          B-clarridg        0.01595     (  0.01187,     0.02010) **
   6             3              0.00899     (  0.00582,     0.01220) **
   3          B-quintana        0.01031     (  0.00703,     0.01359) **
   3            11              0.00411     (  0.00196,     0.00627) **
  11             7              0.00202     (  0.00044,     0.00351) **
   7             1              0.00196     (  0.00049,     0.00344) **
   1            12              0.00132     (  0.00010,     0.00244) **
  12          B-grahamii        0.00828     (  0.00540,     0.01115) **
  12          B--doshiae        0.00410     (  0.00211,     0.00620) **
   1          B-birtlesi        0.00651     (  0.00391,     0.00904) **
   7             8              0.00258     (  0.00087,     0.00422) **
   8             2              0.00163     (  0.00037,     0.00294) **
   2          B-vinsonii        0.00428     (  0.00218,     0.00639) **
   2            10              0.00291     (  0.00123,     0.00467) **
  10          B-arupensi        0.00258     (  0.00098,     0.00424) **
  10          B-berhoffi        0.00511     (  0.00288,     0.00740) **
   8          B-elizabet        0.00971     (  0.00659,     0.01282) **
  11          B-henselae        0.00654     (  0.00393,     0.00906) **
   9          B-bacillif        0.00745     (  0.00443,     0.01044) **
   9          A-tumefaci        0.09205     (  0.08219,     0.10228) **

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


Data set # 60:


Empirical Base Frequencies:

   A       0.26193
   C       0.22079
   G       0.29888
  T(U)     0.21840

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.467986)


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


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

Ln Likelihood = -10928.39471

Examined  574 trees

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

   6            10              0.00310     (  0.00105,     0.00516) **
  10             3              0.00419     (  0.00201,     0.00635) **
   3             4              0.00169     (  0.00021,     0.00317) **
   4             1              0.00109     (     zero,     0.00236) **
   1             8              0.00128     (  0.00019,     0.00245) **
   8          B-birtlesi        0.00818     (  0.00539,     0.01106) **
   8          B--doshiae        0.00403     (  0.00196,     0.00601) **
   1          B-grahamii        0.00592     (  0.00349,     0.00834) **
   4             5              0.00186     (  0.00042,     0.00327) **
   5          B-henselae        0.00741     (  0.00471,     0.01007) **
   5          B-elizabet        0.00848     (  0.00566,     0.01136) **
   3             2              0.00156     (  0.00027,     0.00289) **
   2            11              0.00283     (  0.00096,     0.00462) **
  11          B-berhoffi        0.00502     (  0.00277,     0.00722) **
  11          B-arupensi        0.00244     (  0.00075,     0.00408) **
   2          B-vinsonii        0.00367     (  0.00170,     0.00565) **
  10          B-quintana        0.01346     (  0.00978,     0.01715) **
   6             7              0.00479     (  0.00254,     0.00711) **
   7             9              0.00347     (  0.00143,     0.00549) **
   9          B-bacillif        0.01034     (  0.00704,     0.01362) **
   9            12              0.00970     (  0.00657,     0.01287) **
  12          B--weissii        0.00259     (  0.00085,     0.00435) **
  12          B-spp-Deer        0.00844     (  0.00548,     0.01134) **
   7          B-clarridg        0.01505     (  0.01119,     0.01900) **
   6          A-tumefaci        0.10580     (  0.09564,     0.11729) **

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


Data set # 61:


Empirical Base Frequencies:

   A       0.26152
   C       0.22553
   G       0.29604
  T(U)     0.21691

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.471525)


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


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

Ln Likelihood = -11062.34089

Examined 1496 trees

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

   9             5              0.00671     (  0.00376,     0.00966) **
   5             4              0.00339     (  0.00141,     0.00528) **
   4            12              0.00829     (  0.00529,     0.01134) **
  12          B--weissii        0.00422     (  0.00215,     0.00628) **
  12          B-spp-Deer        0.00961     (  0.00660,     0.01271) **
   4             3              0.00720     (  0.00434,     0.01006) **
   3             6              0.00295     (  0.00121,     0.00470) **
   6             7              0.00172     (  0.00028,     0.00304) **
   7          B--doshiae        0.00177     (  0.00035,     0.00319) **
   7             8              0.00111     (     zero,     0.00238) **
   8             1              0.00368     (  0.00173,     0.00571) **
   1          B-quintana        0.01766     (  0.01355,     0.02185) **
   1          B-henselae        0.00404     (  0.00204,     0.00610) **
   8            10              0.00340     (  0.00154,     0.00527) **
  10          B-grahamii        0.00770     (  0.00499,     0.01053) **
  10          B-elizabet        0.00952     (  0.00639,     0.01256) **
   6          B-birtlesi        0.01025     (  0.00705,     0.01341) **
   3             2              0.00232     (  0.00073,     0.00383) **
   2          B-berhoffi        0.00408     (  0.00212,     0.00613) **
   2            11              0.00103     (     zero,     0.00205) **
  11          B-arupensi        0.00181     (  0.00042,     0.00318) **
  11          B-vinsonii        0.00418     (  0.00217,     0.00623) **
   5          B-bacillif        0.01097     (  0.00747,     0.01438) **
   9          B-clarridg        0.01262     (  0.00888,     0.01637) **
   9          A-tumefaci        0.09965     (  0.08951,     0.11047) **

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


Data set # 62:


Empirical Base Frequencies:

   A       0.26147
   C       0.22491
   G       0.30715
  T(U)     0.20647

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.461859)


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


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

Ln Likelihood = -10991.63752

Examined  682 trees

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

   4            10              0.00548     (  0.00275,     0.00814) **
  10          B-clarridg        0.01250     (  0.00883,     0.01617) **
  10             3              0.00505     (  0.00271,     0.00742) **
   3          B-bacillif        0.01019     (  0.00687,     0.01355) **
   3             2              0.01090     (  0.00748,     0.01434) **
   2          B-spp-Deer        0.00729     (  0.00463,     0.01000) **
   2          B--weissii        0.00401     (  0.00197,     0.00605) **
   4             9              0.00764     (  0.00447,     0.01069) **
   9            12              0.00100     (  0.00004,     0.00199) **
  12             1              0.00184     (  0.00039,     0.00332) **
   1             7              0.00043     (     zero,     0.00126) *
   7             5              0.00250     (  0.00083,     0.00405) **
   5          B-elizabet        0.01140     (  0.00801,     0.01471) **
   5             6              0.00290     (  0.00104,     0.00469) **
   6          B-quintana        0.01217     (  0.00872,     0.01564) **
   6          B-henselae        0.00562     (  0.00315,     0.00799) **
   7          B--doshiae        0.00371     (  0.00180,     0.00562) **
   1             8              0.00301     (  0.00124,     0.00479) **
   8          B-birtlesi        0.00743     (  0.00471,     0.01015) **
   8          B-grahamii        0.00902     (  0.00602,     0.01199) **
  12          B-vinsonii        0.00501     (  0.00280,     0.00725) **
   9            11              0.00197     (  0.00056,     0.00342) **
  11          B-arupensi        0.00301     (  0.00131,     0.00472) **
  11          B-berhoffi        0.00520     (  0.00297,     0.00744) **
   4          A-tumefaci        0.09462     (  0.08484,     0.10523) **

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


Data set # 63:


Empirical Base Frequencies:

   A       0.25875
   C       0.22245
   G       0.30270
  T(U)     0.21611

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.469407)


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


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

Ln Likelihood = -11231.39324

Examined  584 trees

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

   2             5              0.00839     (  0.00510,     0.01169) **
   5             7              0.00752     (  0.00450,     0.01048) **
   7             8              0.00418     (  0.00199,     0.00632) **
   8             3              0.00079     (     zero,     0.00168) **
   3             4              0.00158     (  0.00023,     0.00290) **
   4             6              0.00089     (     zero,     0.00214) **
   6             9              0.00172     (  0.00041,     0.00305) **
   9          B--doshiae        0.00368     (  0.00175,     0.00571) **
   9          B-grahamii        0.00871     (  0.00569,     0.01165) **
   6            12              0.00202     (  0.00050,     0.00364) **
  12          B-elizabet        0.01235     (  0.00889,     0.01585) **
  12          B-henselae        0.00952     (  0.00643,     0.01258) **
   4          B-birtlesi        0.00840     (  0.00558,     0.01129) **
   3             1              0.00291     (  0.00108,     0.00467) **
   1          B-berhoffi        0.00383     (  0.00184,     0.00571) **
   1          B-arupensi        0.00170     (  0.00037,     0.00307) **
   8          B-vinsonii        0.00598     (  0.00354,     0.00841) **
   7          B-quintana        0.01061     (  0.00740,     0.01389) **
   5            10              0.00369     (  0.00154,     0.00578) **
  10            11              0.00799     (  0.00493,     0.01099) **
  11          B-spp-Deer        0.00804     (  0.00519,     0.01093) **
  11          B--weissii        0.00527     (  0.00287,     0.00763) **
  10          B-bacillif        0.01344     (  0.00964,     0.01729) **
   2          B-clarridg        0.01454     (  0.01049,     0.01862) **
   2          A-tumefaci        0.10209     (  0.09172,     0.11306) **

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


Data set # 64:


Empirical Base Frequencies:

   A       0.26021
   C       0.22591
   G       0.29804
  T(U)     0.21583

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.471712)


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


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

Ln Likelihood = -10829.32261

Examined  636 trees

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

   3             2              0.00693     (  0.00396,     0.00991) **
   2            11              0.00351     (  0.00149,     0.00551) **
  11          B-bacillif        0.01103     (  0.00759,     0.01437) **
  11             4              0.00858     (  0.00558,     0.01160) **
   4          B--weissii        0.00428     (  0.00219,     0.00636) **
   4          B-spp-Deer        0.00724     (  0.00456,     0.00991) **
   2             8              0.00822     (  0.00512,     0.01128) **
   8             7              0.00438     (  0.00222,     0.00660) **
   7          B-henselae        0.00692     (  0.00425,     0.00961) **
   7             1              0.00198     (  0.00045,     0.00352) **
   1             6              0.00044     (     zero,     0.00142)
   6            10              0.00108     (  0.00005,     0.00216) **
  10          B--doshiae        0.00425     (  0.00219,     0.00627) **
  10          B-birtlesi        0.00673     (  0.00418,     0.00931) **
   6             5              0.00179     (  0.00039,     0.00312) **
   5          B-grahamii        0.00547     (  0.00315,     0.00777) **
   5          B-elizabet        0.00848     (  0.00561,     0.01133) **
   1             9              0.00192     (  0.00047,     0.00335) **
   9            12              0.00352     (  0.00164,     0.00542) **
  12          B-berhoffi        0.00547     (  0.00315,     0.00778) **
  12          B-arupensi        0.00359     (  0.00170,     0.00551) **
   9          B-vinsonii        0.00262     (  0.00101,     0.00422) **
   8          B-quintana        0.01170     (  0.00827,     0.01519) **
   3          B-clarridg        0.01418     (  0.01032,     0.01819) **
   3          A-tumefaci        0.09197     (  0.08233,     0.10237) **

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


Data set # 65:


Empirical Base Frequencies:

   A       0.26062
   C       0.22393
   G       0.30051
  T(U)     0.21494

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.468737)


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


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

Ln Likelihood = -11185.17686

Examined 1024 trees

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

  11          B-birtlesi        0.00489     (  0.00252,     0.00726) **
  11            10              0.00336     (  0.00134,     0.00539) **
  10             4              0.00174     (  0.00042,     0.00311) **
   4          B-grahamii        0.00474     (  0.00261,     0.00688) **
   4          B-elizabet        0.01047     (  0.00733,     0.01366) **
  10             9              0.00106     (     zero,     0.00218) **
   9             5              0.00232     (  0.00082,     0.00384) **
   5            12              0.00263     (  0.00098,     0.00427) **
  12          B-berhoffi        0.00332     (  0.00153,     0.00512) **
  12          B-arupensi        0.00421     (  0.00216,     0.00626) **
   5          B-vinsonii        0.00492     (  0.00279,     0.00715) **
   9             8              0.00063     (     zero,     0.00152) **
   8          B--doshiae        0.00414     (  0.00211,     0.00613) **
   8             6              0.00292     (  0.00104,     0.00477) **
   6             2              0.00538     (  0.00303,     0.00776) **
   2             3              0.00817     (  0.00507,     0.01133) **
   3          B-clarridg        0.02171     (  0.01702,     0.02653) **
   3             1              0.00670     (  0.00397,     0.00949) **
   1          B-bacillif        0.01279     (  0.00912,     0.01658) **
   1             7              0.00936     (  0.00613,     0.01260) **
   7          B-spp-Deer        0.00946     (  0.00633,     0.01252) **
   7          B--weissii        0.00394     (  0.00181,     0.00599) **
   2          B-quintana        0.01134     (  0.00786,     0.01478) **
   6          B-henselae        0.00703     (  0.00437,     0.00976) **
  11          A-tumefaci        0.09815     (  0.08820,     0.10885) **

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


Data set # 66:


Empirical Base Frequencies:

   A       0.25476
   C       0.22015
   G       0.30336
  T(U)     0.22174

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.474845)


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


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

Ln Likelihood = -11136.28651

Examined  640 trees

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

  10          B-clarridg        0.00917     (  0.00588,     0.01243) **
  10             7              0.00748     (  0.00447,     0.01053) **
   7             2              0.00554     (  0.00295,     0.00816) **
   2             8              0.00387     (  0.00179,     0.00594) **
   8          B-henselae        0.00860     (  0.00569,     0.01154) **
   8             4              0.00258     (  0.00090,     0.00425) **
   4             1              0.00041     (     zero,     0.00119) *
   1             3              0.00244     (  0.00084,     0.00402) **
   3            11              0.00171     (  0.00030,     0.00311) **
  11          B-berhoffi        0.00391     (  0.00196,     0.00588) **
  11          B-arupensi        0.00401     (  0.00195,     0.00604) **
   3          B-vinsonii        0.00493     (  0.00266,     0.00710) **
   1             5              0.00280     (  0.00094,     0.00467) **
   5             6              0.00291     (  0.00105,     0.00476) **
   6          B-elizabet        0.01438     (  0.01065,     0.01816) **
   6          B-grahamii        0.00699     (  0.00433,     0.00964) **
   5          B-birtlesi        0.00722     (  0.00454,     0.00992) **
   4          B--doshiae        0.00723     (  0.00457,     0.00987) **
   2          B-quintana        0.00941     (  0.00629,     0.01254) **
   7             9              0.00401     (  0.00178,     0.00615) **
   9            12              0.00986     (  0.00662,     0.01311) **
  12          B-spp-Deer        0.00648     (  0.00395,     0.00908) **
  12          B--weissii        0.00480     (  0.00258,     0.00705) **
   9          B-bacillif        0.01331     (  0.00959,     0.01705) **
  10          A-tumefaci        0.09707     (  0.08690,     0.10759) **

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


Data set # 67:


Empirical Base Frequencies:

   A       0.25564
   C       0.21879
   G       0.30770
  T(U)     0.21787

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.469668)


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


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

Ln Likelihood = -10642.25998

Examined  896 trees

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

   1             5              0.00632     (  0.00356,     0.00909) **
   5          B-clarridg        0.01788     (  0.01354,     0.02221) **
   5             4              0.00469     (  0.00240,     0.00700) **
   4             8              0.00860     (  0.00551,     0.01169) **
   8          B--weissii        0.00346     (  0.00150,     0.00539) **
   8          B-spp-Deer        0.00724     (  0.00457,     0.00999) **
   4          B-bacillif        0.01028     (  0.00687,     0.01367) **
   1             2              0.00489     (  0.00238,     0.00738) **
   2             3              0.00179     (  0.00047,     0.00312) **
   3             7              0.00044     (     zero,     0.00114) **
   7          B-vinsonii        0.00457     (  0.00247,     0.00669) **
   7          B-birtlesi        0.00763     (  0.00490,     0.01035) **
   3             6              0.00092     (     zero,     0.00196) **
   6            10              0.00090     (     zero,     0.00192) **
  10          B-elizabet        0.01212     (  0.00864,     0.01554) **
  10             9              0.00206     (  0.00053,     0.00349) **
   9          B-henselae        0.00538     (  0.00303,     0.00767) **
   9          B-quintana        0.00669     (  0.00417,     0.00930) **
   6            12              0.00101     (     zero,     0.00214) **
  12          B-grahamii        0.00629     (  0.00386,     0.00881) **
  12          B--doshiae        0.00506     (  0.00279,     0.00724) **
   2            11              0.00256     (  0.00090,     0.00414) **
  11          B-arupensi        0.00397     (  0.00203,     0.00595) **
  11          B-berhoffi        0.00398     (  0.00201,     0.00594) **
   1          A-tumefaci        0.09186     (  0.08200,     0.10204) **

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


Data set # 68:


Empirical Base Frequencies:

   A       0.27374
   C       0.20732
   G       0.29469
  T(U)     0.22425

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.455987)


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


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

Ln Likelihood = -11166.53897

Examined  550 trees

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

   9          B-clarridg        0.01220     (  0.00850,     0.01587) **
   9             6              0.00687     (  0.00386,     0.00989) **
   6             3              0.00422     (  0.00201,     0.00643) **
   3             7              0.01167     (  0.00810,     0.01527) **
   7          B-birtlesi        0.00958     (  0.00650,     0.01267) **
   7             4              0.00153     (  0.00021,     0.00281) **
   4             1              0.00107     (     zero,     0.00209) **
   1             8              0.00069     (     zero,     0.00166) **
   8            12              0.00346     (  0.00152,     0.00536) **
  12          B-elizabet        0.01417     (  0.01045,     0.01792) **
  12          B-grahamii        0.00615     (  0.00357,     0.00867) **
   8          B--doshiae        0.00555     (  0.00319,     0.00791) **
   1            10              0.00426     (  0.00217,     0.00634) **
  10          B-quintana        0.00941     (  0.00639,     0.01244) **
  10          B-henselae        0.00548     (  0.00312,     0.00783) **
   4             2              0.00200     (  0.00058,     0.00344) **
   2          B-vinsonii        0.00420     (  0.00217,     0.00624) **
   2             5              0.00223     (  0.00080,     0.00372) **
   5          B-arupensi        0.00198     (  0.00056,     0.00340) **
   5          B-berhoffi        0.00349     (  0.00163,     0.00535) **
   3            11              0.00806     (  0.00505,     0.01111) **
  11          B-spp-Deer        0.00613     (  0.00366,     0.00865) **
  11          B--weissii        0.00517     (  0.00286,     0.00749) **
   6          B-bacillif        0.01260     (  0.00887,     0.01632) **
   9          A-tumefaci        0.10336     (  0.09314,     0.11460) **

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


Data set # 69:


Empirical Base Frequencies:

   A       0.27020
   C       0.21734
   G       0.30612
  T(U)     0.20634

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.446812)


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


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

Ln Likelihood = -10596.45539

Examined  534 trees

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

  12          B-clarridg        0.01033     (  0.00695,     0.01370) **
  12             7              0.00485     (  0.00242,     0.00734) **
   7             5              0.00858     (  0.00555,     0.01171) **
   5          B-birtlesi        0.00382     (  0.00180,     0.00576) **
   5             3              0.00171     (  0.00019,     0.00314) **
   3             4              0.00100     (     zero,     0.00207) **
   4             9              0.00281     (  0.00107,     0.00450) **
   9          B-quintana        0.01095     (  0.00769,     0.01420) **
   9          B-henselae        0.00511     (  0.00286,     0.00736) **
   4            11              0.00158     (  0.00031,     0.00283) **
  11          B-grahamii        0.00501     (  0.00278,     0.00724) **
  11          B--doshiae        0.00414     (  0.00210,     0.00616) **
   3             2              0.00183     (  0.00039,     0.00325) **
   2          B-elizabet        0.01365     (  0.00993,     0.01731) **
   2             6              0.00150     (  0.00018,     0.00279) **
   6            10              0.00230     (  0.00077,     0.00381) **
  10          B-arupensi        0.00298     (  0.00118,     0.00477) **
  10          B-berhoffi        0.00288     (  0.00113,     0.00464) **
   6          B-vinsonii        0.00379     (  0.00185,     0.00573) **
   7             1              0.00488     (  0.00253,     0.00724) **
   1             8              0.00612     (  0.00349,     0.00870) **
   8          B--weissii        0.00249     (  0.00091,     0.00410) **
   8          B-spp-Deer        0.00798     (  0.00518,     0.01076) **
   1          B-bacillif        0.01089     (  0.00753,     0.01430) **
  12          A-tumefaci        0.09460     (  0.08479,     0.10520) **

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


Data set # 70:


Empirical Base Frequencies:

   A       0.25931
   C       0.23052
   G       0.30078
  T(U)     0.20938

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.472070)


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


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

Ln Likelihood = -10948.71580

Examined  532 trees

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

   4             2              0.00743     (  0.00445,     0.01042) **
   2            11              0.00131     (  0.00003,     0.00248) **
  11          B-vinsonii        0.00202     (  0.00054,     0.00348) **
  11             6              0.00470     (  0.00251,     0.00690) **
   6          B-henselae        0.00725     (  0.00451,     0.01000) **
   6          B-quintana        0.01004     (  0.00687,     0.01321) **
   2             5              0.00080     (     zero,     0.00172) **
   5             9              0.00050     (     zero,     0.00119) **
   9          B--doshiae        0.00490     (  0.00276,     0.00710) **
   9            12              0.00178     (  0.00048,     0.00311) **
  12          B-berhoffi        0.00498     (  0.00280,     0.00717) **
  12          B-arupensi        0.00247     (  0.00096,     0.00402) **
   5             7              0.00239     (  0.00079,     0.00407) **
   7            10              0.00289     (  0.00120,     0.00463) **
  10          B-grahamii        0.00683     (  0.00423,     0.00946) **
  10          B-elizabet        0.00982     (  0.00674,     0.01295) **
   7          B-birtlesi        0.00690     (  0.00433,     0.00957) **
   4             3              0.00519     (  0.00256,     0.00781) **
   3             1              0.00514     (  0.00276,     0.00748) **
   1          B-bacillif        0.01048     (  0.00706,     0.01389) **
   1             8              0.00928     (  0.00606,     0.01249) **
   8          B--weissii        0.00408     (  0.00208,     0.00613) **
   8          B-spp-Deer        0.00915     (  0.00614,     0.01214) **
   3          B-clarridg        0.01538     (  0.01135,     0.01944) **
   4          A-tumefaci        0.09985     (  0.08950,     0.11052) **

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


Data set # 71:


Empirical Base Frequencies:

   A       0.25683
   C       0.22067
   G       0.30263
  T(U)     0.21987

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.472261)


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


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

Ln Likelihood = -10997.86683

Examined  796 trees

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

  10             8              0.00514     (  0.00262,     0.00768) **
   8          B-clarridg        0.01179     (  0.00827,     0.01537) **
   8             4              0.00570     (  0.00323,     0.00818) **
   4             6              0.01120     (  0.00778,     0.01468) **
   6          B--weissii        0.00451     (  0.00236,     0.00667) **
   6          B-spp-Deer        0.00569     (  0.00334,     0.00814) **
   4          B-bacillif        0.01155     (  0.00800,     0.01508) **
  10             1              0.00384     (  0.00166,     0.00608) **
   1             7              0.00366     (  0.00165,     0.00567) **
   7             3              0.00098     (     zero,     0.00201) **
   3             5              0.00131     (  0.00006,     0.00258) **
   5             2              0.00003     (     zero,     0.00094)
   2          B-henselae        0.00840     (  0.00556,     0.01125) **
   2            11              0.00111     (     zero,     0.00218) **
  11          B-birtlesi        0.01033     (  0.00716,     0.01350) **
  11          B--doshiae        0.00439     (  0.00228,     0.00646) **
   5            12              0.00359     (  0.00167,     0.00544) **
  12          B-grahamii        0.00690     (  0.00433,     0.00952) **
  12          B-elizabet        0.00898     (  0.00601,     0.01192) **
   3          B-vinsonii        0.00498     (  0.00272,     0.00719) **
   7             9              0.00237     (  0.00075,     0.00399) **
   9          B-berhoffi        0.00318     (  0.00144,     0.00498) **
   9          B-arupensi        0.00486     (  0.00262,     0.00706) **
   1          B-quintana        0.01273     (  0.00917,     0.01629) **
  10          A-tumefaci        0.09979     (  0.08950,     0.11046) **

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


Data set # 72:


Empirical Base Frequencies:

   A       0.26111
   C       0.22886
   G       0.29793
  T(U)     0.21209

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.471278)


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


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

Ln Likelihood = -10608.76857

Examined  556 trees

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

   3             6              0.00370     (  0.00130,     0.00603) **
   6             5              0.00723     (  0.00434,     0.01007) **
   5          B--weissii        0.00173     (  0.00040,     0.00308) **
   5          B-spp-Deer        0.00776     (  0.00495,     0.01047) **
   6             4              0.00485     (  0.00250,     0.00717) **
   4             1              0.00750     (  0.00466,     0.01045) **
   1             8              0.00181     (  0.00025,     0.00337) **
   8             7              0.00150     (  0.00035,     0.00274) **
   7          B-arupensi        0.00298     (  0.00127,     0.00475) **
   7             2              0.00180     (  0.00040,     0.00320) **
   2             9              0.00245     (  0.00090,     0.00405) **
   9            10              0.00148     (  0.00005,     0.00281) **
  10          B-birtlesi        0.00528     (  0.00296,     0.00760) **
  10            11              0.00305     (  0.00126,     0.00484) **
  11          B-grahamii        0.00636     (  0.00381,     0.00883) **
  11          B-elizabet        0.00993     (  0.00681,     0.01304) **
   9            12              0.00193     (  0.00037,     0.00340) **
  12          B-henselae        0.00669     (  0.00408,     0.00929) **
  12          B--doshiae        0.00439     (  0.00223,     0.00649) **
   2          B-vinsonii        0.00347     (  0.00161,     0.00532) **
   8          B-berhoffi        0.00191     (  0.00052,     0.00335) **
   1          B-quintana        0.01357     (  0.00988,     0.01727) **
   4          B-bacillif        0.00828     (  0.00520,     0.01134) **
   3          B-clarridg        0.00989     (  0.00660,     0.01316) **
   3          A-tumefaci        0.10021     (  0.09025,     0.11122) **

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


Data set # 73:


Empirical Base Frequencies:

   A       0.26486
   C       0.23240
   G       0.30643
  T(U)     0.19630

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.461066)


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


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

Ln Likelihood = -10939.81719

Examined  592 trees

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

   8             5              0.00674     (  0.00379,     0.00968) **
   5             9              0.00435     (  0.00188,     0.00673) **
   9             3              0.00564     (  0.00317,     0.00808) **
   3          B-henselae        0.00714     (  0.00442,     0.00981) **
   3             2              0.00245     (  0.00077,     0.00412) **
   2            11              0.00089     (     zero,     0.00190) **
  11          B-birtlesi        0.01033     (  0.00718,     0.01350) **
  11            10              0.00185     (  0.00051,     0.00324) **
  10          B-vinsonii        0.00767     (  0.00492,     0.01037) **
  10             4              0.00097     (  0.00005,     0.00197) **
   4          B-arupensi        0.00290     (  0.00121,     0.00458) **
   4          B-berhoffi        0.00440     (  0.00233,     0.00648) **
   2             1              0.00096     (     zero,     0.00199) **
   1            12              0.00266     (  0.00105,     0.00433) **
  12          B-elizabet        0.01030     (  0.00713,     0.01349) **
  12          B-grahamii        0.00828     (  0.00540,     0.01113) **
   1          B--doshiae        0.00485     (  0.00262,     0.00706) **
   9          B-quintana        0.00891     (  0.00585,     0.01197) **
   5             7              0.00457     (  0.00232,     0.00680) **
   7          B-bacillif        0.01289     (  0.00918,     0.01660) **
   7             6              0.00972     (  0.00643,     0.01290) **
   6          B--weissii        0.00338     (  0.00136,     0.00528) **
   6          B-spp-Deer        0.00643     (  0.00388,     0.00903) **
   8          B-clarridg        0.00950     (  0.00622,     0.01279) **
   8          A-tumefaci        0.09420     (  0.08452,     0.10484) **

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


Data set # 74:


Empirical Base Frequencies:

   A       0.26160
   C       0.22501
   G       0.31301
  T(U)     0.20038

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.456358)


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


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

Ln Likelihood = -10841.65267

Examined  676 trees

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

   3             6              0.00410     (  0.00167,     0.00649) **
   6             1              0.00358     (  0.00159,     0.00552) **
   1          B-henselae        0.00940     (  0.00629,     0.01251) **
   1             2              0.00264     (  0.00086,     0.00443) **
   2             5              0.00068     (     zero,     0.00159) **
   5             9              0.00113     (     zero,     0.00219) **
   9          B--doshiae        0.00522     (  0.00294,     0.00748) **
   9             4              0.00262     (  0.00104,     0.00423) **
   4          B-berhoffi        0.00360     (  0.00171,     0.00547) **
   4          B-arupensi        0.00237     (  0.00084,     0.00390) **
   5            11              0.00216     (  0.00053,     0.00376) **
  11            12              0.00258     (  0.00088,     0.00430) **
  12          B-elizabet        0.01024     (  0.00709,     0.01341) **
  12          B-grahamii        0.00677     (  0.00414,     0.00937) **
  11          B-birtlesi        0.00548     (  0.00311,     0.00783) **
   2          B-vinsonii        0.00381     (  0.00188,     0.00575) **
   6          B-quintana        0.01145     (  0.00804,     0.01491) **
   3             8              0.00598     (  0.00328,     0.00869) **
   8             7              0.00367     (  0.00157,     0.00577) **
   7          B-bacillif        0.01094     (  0.00759,     0.01438) **
   7            10              0.00881     (  0.00573,     0.01184) **
  10          B--weissii        0.00388     (  0.00188,     0.00586) **
  10          B-spp-Deer        0.00679     (  0.00425,     0.00942) **
   8          B-clarridg        0.01220     (  0.00858,     0.01582) **
   3          A-tumefaci        0.10060     (  0.09044,     0.11154) **

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


Data set # 75:


Empirical Base Frequencies:

   A       0.28525
   C       0.22332
   G       0.29164
  T(U)     0.19979

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.443460)


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


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

Ln Likelihood = -11324.16525

Examined  718 trees

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

   7             5              0.00677     (  0.00381,     0.00977) **
   5            12              0.00443     (  0.00209,     0.00676) **
  12          B-bacillif        0.01255     (  0.00888,     0.01623) **
  12             6              0.00977     (  0.00645,     0.01300) **
   6          B--weissii        0.00473     (  0.00254,     0.00699) **
   6          B-spp-Deer        0.00904     (  0.00597,     0.01202) **
   5            11              0.00666     (  0.00375,     0.00957) **
  11          B-quintana        0.01094     (  0.00760,     0.01427) **
  11            10              0.00650     (  0.00383,     0.00918) **
  10             3              0.00187     (  0.00048,     0.00325) **
   3          B-arupensi        0.00369     (  0.00169,     0.00565) **
   3             1              0.00238     (  0.00069,     0.00396) **
   1             8              0.00386     (  0.00189,     0.00586) **
   8             2              0.00029     (     zero,     0.00087) *
   2          B--doshiae        0.00405     (  0.00208,     0.00606) **
   2          B-birtlesi        0.00918     (  0.00617,     0.01217) **
   8             4              0.00108     (     zero,     0.00218) **
   4             9              0.00248     (  0.00091,     0.00405) **
   9          B-grahamii        0.00694     (  0.00430,     0.00956) **
   9          B-elizabet        0.01210     (  0.00867,     0.01557) **
   4          B-henselae        0.01273     (  0.00921,     0.01629) **
   1          B-vinsonii        0.00535     (  0.00298,     0.00759) **
  10          B-berhoffi        0.00426     (  0.00216,     0.00635) **
   7          B-clarridg        0.01208     (  0.00841,     0.01573) **
   7          A-tumefaci        0.09455     (  0.08486,     0.10526) **

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


Data set # 76:


Empirical Base Frequencies:

   A       0.25747
   C       0.22633
   G       0.30454
  T(U)     0.21166

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.470493)


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


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

Ln Likelihood = -11312.03650

Examined  776 trees

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

   7             9              0.00775     (  0.00448,     0.01100) **
   9             8              0.00476     (  0.00246,     0.00706) **
   8             1              0.00954     (  0.00631,     0.01280) **
   1             6              0.00197     (  0.00044,     0.00344) **
   6             4              0.00086     (     zero,     0.00187) **
   4             3              0.00106     (  0.00003,     0.00210) **
   3             5              0.00098     (  0.00004,     0.00199) **
   5          B-grahamii        0.01052     (  0.00728,     0.01369) **
   5          B--doshiae        0.00466     (  0.00253,     0.00681) **
   3             2              0.00313     (  0.00125,     0.00497) **
   2          B-henselae        0.00879     (  0.00579,     0.01174) **
   2          B-quintana        0.01627     (  0.01229,     0.02025) **
   4            12              0.00162     (  0.00037,     0.00293) **
  12          B-vinsonii        0.00488     (  0.00268,     0.00707) **
  12            11              0.00344     (  0.00158,     0.00525) **
  11          B-berhoffi        0.00387     (  0.00192,     0.00583) **
  11          B-arupensi        0.00284     (  0.00113,     0.00451) **
   6          B-birtlesi        0.01192     (  0.00851,     0.01532) **
   1          B-elizabet        0.01232     (  0.00880,     0.01580) **
   8          B-bacillif        0.01105     (  0.00765,     0.01456) **
   9            10              0.00544     (  0.00282,     0.00807) **
  10          B-spp-Deer        0.00632     (  0.00375,     0.00888) **
  10          B--weissii        0.00574     (  0.00329,     0.00819) **
   7          B-clarridg        0.01194     (  0.00819,     0.01562) **
   7          A-tumefaci        0.10073     (  0.09046,     0.11156) **

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


Data set # 77:


Empirical Base Frequencies:

   A       0.25660
   C       0.22715
   G       0.29743
  T(U)     0.21882

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.477217)


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


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

Ln Likelihood = -11056.29856

Examined  520 trees

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

   6             3              0.00413     (  0.00190,     0.00637) **
   3          B-clarridg        0.01425     (  0.01038,     0.01807) **
   3             4              0.00680     (  0.00410,     0.00956) **
   4          B-bacillif        0.01288     (  0.00921,     0.01654) **
   4             9              0.00934     (  0.00623,     0.01247) **
   9          B--weissii        0.00494     (  0.00270,     0.00719) **
   9          B-spp-Deer        0.00858     (  0.00565,     0.01150) **
   6             5              0.00448     (  0.00205,     0.00688) **
   5             8              0.00406     (  0.00199,     0.00613) **
   8             2              0.00114     (     zero,     0.00235) **
   2             1              0.00112     (  0.00001,     0.00218) **
   1          B-elizabet        0.01322     (  0.00965,     0.01682) **
   1            10              0.00193     (  0.00058,     0.00338) **
  10          B-vinsonii        0.00324     (  0.00147,     0.00507) **
  10            11              0.00377     (  0.00183,     0.00571) **
  11          B-berhoffi        0.00333     (  0.00150,     0.00517) **
  11          B-arupensi        0.00235     (  0.00073,     0.00395) **
   2             7              0.00149     (  0.00018,     0.00282) **
   7            12              0.00171     (  0.00046,     0.00302) **
  12          B-grahamii        0.00760     (  0.00485,     0.01033) **
  12          B--doshiae        0.00339     (  0.00153,     0.00527) **
   7          B-birtlesi        0.01079     (  0.00755,     0.01408) **
   8          B-henselae        0.00695     (  0.00425,     0.00955) **
   5          B-quintana        0.00995     (  0.00677,     0.01315) **
   6          A-tumefaci        0.09653     (  0.08669,     0.10726) **

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


Data set # 78:


Empirical Base Frequencies:

   A       0.26813
   C       0.21613
   G       0.30324
  T(U)     0.21250

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.453487)


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


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

Ln Likelihood = -10734.32691

Examined  574 trees

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

   4          B-clarridg        0.00922     (  0.00595,     0.01245) **
   4             6              0.00448     (  0.00200,     0.00698) **
   6             7              0.00465     (  0.00232,     0.00700) **
   7            12              0.01043     (  0.00707,     0.01376) **
  12          B-spp-Deer        0.00766     (  0.00483,     0.01042) **
  12          B--weissii        0.00260     (  0.00087,     0.00434) **
   7          B-bacillif        0.01103     (  0.00756,     0.01451) **
   6             8              0.00732     (  0.00436,     0.01022) **
   8             2              0.00434     (  0.00212,     0.00666) **
   2             3              0.00284     (  0.00104,     0.00465) **
   3          B-vinsonii        0.00451     (  0.00232,     0.00670) **
   3             1              0.00242     (  0.00065,     0.00427) **
   1            11              0.00060     (     zero,     0.00145) **
  11             5              0.00312     (  0.00135,     0.00489) **
   5          B-grahamii        0.00495     (  0.00271,     0.00717) **
   5          B-elizabet        0.00971     (  0.00664,     0.01280) **
  11          B-henselae        0.00707     (  0.00443,     0.00970) **
   1            10              0.00131     (  0.00016,     0.00248) **
  10          B--doshiae        0.00326     (  0.00149,     0.00503) **
  10          B-birtlesi        0.00723     (  0.00456,     0.00989) **
   2             9              0.00211     (  0.00051,     0.00376) **
   9          B-arupensi        0.00420     (  0.00215,     0.00624) **
   9          B-berhoffi        0.00194     (  0.00053,     0.00335) **
   8          B-quintana        0.01115     (  0.00784,     0.01448) **
   4          A-tumefaci        0.09711     (  0.08736,     0.10805) **

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


Data set # 79:


Empirical Base Frequencies:

   A       0.25612
   C       0.21851
   G       0.31045
  T(U)     0.21492

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.466327)


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


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

Ln Likelihood = -11199.69964

Examined  602 trees

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

  12          B-clarridg        0.01487     (  0.01081,     0.01893) **
  12             3              0.00561     (  0.00274,     0.00841) **
   3             4              0.00707     (  0.00405,     0.01010) **
   4             5              0.00302     (  0.00105,     0.00491) **
   5             2              0.00131     (  0.00001,     0.00253) **
   2            10              0.00131     (  0.00009,     0.00256) **
  10          B-arupensi        0.00537     (  0.00302,     0.00763) **
  10          B-berhoffi        0.00231     (  0.00078,     0.00384) **
   2          B-vinsonii        0.00634     (  0.00381,     0.00886) **
   5             7              0.00268     (  0.00082,     0.00455) **
   7             6              0.00232     (  0.00061,     0.00398) **
   6          B-birtlesi        0.00726     (  0.00455,     0.00997) **
   6            11              0.00247     (  0.00072,     0.00422) **
  11          B-elizabet        0.01019     (  0.00708,     0.01336) **
  11          B-grahamii        0.00660     (  0.00408,     0.00917) **
   7             1              0.00147     (  0.00013,     0.00286) **
   1          B-henselae        0.00872     (  0.00582,     0.01165) **
   1          B--doshiae        0.00441     (  0.00229,     0.00653) **
   4          B-quintana        0.01243     (  0.00888,     0.01599) **
   3             8              0.00521     (  0.00273,     0.00769) **
   8             9              0.00896     (  0.00579,     0.01211) **
   9          B-spp-Deer        0.00998     (  0.00681,     0.01316) **
   9          B--weissii        0.00402     (  0.00194,     0.00613) **
   8          B-bacillif        0.01224     (  0.00856,     0.01590) **
  12          A-tumefaci        0.10008     (  0.08999,     0.11104) **

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


Data set # 80:


Empirical Base Frequencies:

   A       0.26695
   C       0.22357
   G       0.30204
  T(U)     0.20744

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.457929)


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


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

Ln Likelihood = -10690.11689

Examined  996 trees

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

   9             3              0.00563     (  0.00292,     0.00832) **
   3             6              0.00642     (  0.00374,     0.00918) **
   6             1              0.00456     (  0.00239,     0.00675) **
   1            10              0.00151     (  0.00022,     0.00280) **
  10             5              0.00028     (     zero,     0.00083) *
   5             7              0.00197     (  0.00052,     0.00343) **
   7          B-birtlesi        0.00804     (  0.00524,     0.01086) **
   7            11              0.00127     (  0.00010,     0.00246) **
  11          B-elizabet        0.00966     (  0.00659,     0.01272) **
  11          B-grahamii        0.00495     (  0.00273,     0.00716) **
   5             2              0.00199     (  0.00056,     0.00342) **
   2          B-vinsonii        0.00420     (  0.00219,     0.00624) **
   2             4              0.00149     (  0.00030,     0.00269) **
   4          B-berhoffi        0.00648     (  0.00398,     0.00901) **
   4          B-arupensi        0.00277     (  0.00104,     0.00440) **
  10          B--doshiae        0.00347     (  0.00166,     0.00529) **
   1          B-henselae        0.00746     (  0.00473,     0.01015) **
   6          B-quintana        0.00868     (  0.00564,     0.01160) **
   3             8              0.00421     (  0.00200,     0.00633) **
   8            12              0.01016     (  0.00693,     0.01344) **
  12          B--weissii        0.00393     (  0.00190,     0.00595) **
  12          B-spp-Deer        0.00786     (  0.00506,     0.01066) **
   8          B-bacillif        0.00630     (  0.00366,     0.00893) **
   9          B-clarridg        0.01097     (  0.00751,     0.01445) **
   9          A-tumefaci        0.09593     (  0.08598,     0.10649) **

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


Data set # 81:


Empirical Base Frequencies:

   A       0.25912
   C       0.22639
   G       0.31062
  T(U)     0.20386

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.463048)


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


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

Ln Likelihood = -10987.86087

Examined  626 trees

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

   1             3              0.00555     (  0.00280,     0.00829) **
   3             8              0.00340     (  0.00147,     0.00534) **
   8          B-henselae        0.00725     (  0.00452,     0.00997) **
   8             2              0.00393     (  0.00179,     0.00606) **
   2            11              0.00147     (  0.00022,     0.00279) **
  11          B-grahamii        0.00812     (  0.00527,     0.01099) **
  11          B--doshiae        0.00506     (  0.00281,     0.00734) **
   2             4              0.00108     (     zero,     0.00231) **
   4          B-birtlesi        0.01117     (  0.00784,     0.01444) **
   4            12              0.00108     (     zero,     0.00220) **
  12          B-elizabet        0.01193     (  0.00855,     0.01533) **
  12             6              0.00098     (     zero,     0.00206) **
   6             5              0.00191     (  0.00055,     0.00329) **
   5          B-arupensi        0.00321     (  0.00134,     0.00499) **
   5          B-vinsonii        0.00331     (  0.00148,     0.00515) **
   6          B-berhoffi        0.00468     (  0.00249,     0.00684) **
   3          B-quintana        0.00946     (  0.00633,     0.01266) **
   1             9              0.00639     (  0.00353,     0.00922) **
   9          B-clarridg        0.01156     (  0.00806,     0.01504) **
   9            10              0.00357     (  0.00149,     0.00566) **
  10          B-bacillif        0.01209     (  0.00855,     0.01562) **
  10             7              0.00775     (  0.00484,     0.01056) **
   7          B-spp-Deer        0.00727     (  0.00457,     0.00997) **
   7          B--weissii        0.00489     (  0.00271,     0.00716) **
   1          A-tumefaci        0.10147     (  0.09155,     0.11272) **

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


Data set # 82:


Empirical Base Frequencies:

   A       0.27745
   C       0.21720
   G       0.29681
  T(U)     0.20854

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.446509)


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


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

Ln Likelihood = -10958.10333

Examined  966 trees

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

   3             6              0.00589     (  0.00315,     0.00855) **
   6             9              0.00071     (     zero,     0.00162) **
   9             4              0.00027     (     zero,     0.00082) *
   4             5              0.00131     (  0.00017,     0.00248) **
   5            10              0.00189     (  0.00050,     0.00327) **
  10          B-berhoffi        0.00415     (  0.00211,     0.00615) **
  10          B-arupensi        0.00472     (  0.00254,     0.00687) **
   5          B-vinsonii        0.00131     (  0.00022,     0.00248) **
   4             8              0.00223     (  0.00073,     0.00375) **
   8             7              0.00109     (  0.00004,     0.00223) **
   7          B-elizabet        0.01390     (  0.01023,     0.01758) **
   7          B-grahamii        0.00687     (  0.00429,     0.00947) **
   8          B-birtlesi        0.00818     (  0.00537,     0.01103) **
   9            11              0.00522     (  0.00280,     0.00755) **
  11          B-quintana        0.01205     (  0.00860,     0.01547) **
  11          B-henselae        0.00556     (  0.00310,     0.00797) **
   6          B--doshiae        0.00404     (  0.00200,     0.00603) **
   3            12              0.00510     (  0.00251,     0.00759) **
  12             2              0.00437     (  0.00213,     0.00668) **
   2             1              0.00983     (  0.00656,     0.01308) **
   1          B--weissii        0.00370     (  0.00171,     0.00570) **
   1          B-spp-Deer        0.00731     (  0.00457,     0.01003) **
   2          B-bacillif        0.01242     (  0.00880,     0.01611) **
  12          B-clarridg        0.01381     (  0.00996,     0.01764) **
   3          A-tumefaci        0.10525     (  0.09466,     0.11632) **

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


Data set # 83:


Empirical Base Frequencies:

   A       0.26973
   C       0.21695
   G       0.29831
  T(U)     0.21501

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.456627)


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


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

Ln Likelihood = -10831.81719

Examined  732 trees

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

   7             6              0.00810     (  0.00509,     0.01121) **
   6          B-bacillif        0.01015     (  0.00682,     0.01346) **
   6             9              0.00401     (  0.00189,     0.00616) **
   9          B-clarridg        0.01749     (  0.01322,     0.02176) **
   9             2              0.00868     (  0.00564,     0.01174) **
   2          B--weissii        0.00370     (  0.00161,     0.00572) **
   2          B-spp-Deer        0.00937     (  0.00628,     0.01247) **
   7             1              0.00588     (  0.00317,     0.00862) **
   1             8              0.00144     (  0.00019,     0.00265) **
   8            10              0.00197     (  0.00054,     0.00340) **
  10          B-arupensi        0.00304     (  0.00128,     0.00477) **
  10          B-berhoffi        0.00434     (  0.00231,     0.00640) **
   8          B-vinsonii        0.00296     (  0.00126,     0.00470) **
   1             3              0.00068     (     zero,     0.00159) *
   3            12              0.00215     (  0.00051,     0.00370) **
  12          B-birtlesi        0.00802     (  0.00520,     0.01085) **
  12            11              0.00180     (  0.00042,     0.00327) **
  11          B-grahamii        0.00490     (  0.00271,     0.00707) **
  11          B-elizabet        0.01034     (  0.00720,     0.01352) **
   3             4              0.00100     (     zero,     0.00206) **
   4          B--doshiae        0.00287     (  0.00120,     0.00455) **
   4             5              0.00259     (  0.00099,     0.00420) **
   5          B-quintana        0.01164     (  0.00829,     0.01502) **
   5          B-henselae        0.00375     (  0.00183,     0.00569) **
   7          A-tumefaci        0.10124     (  0.09115,     0.11228) **

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


Data set # 84:


Empirical Base Frequencies:

   A       0.25561
   C       0.24094
   G       0.29060
  T(U)     0.21285

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.486577)


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


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

Ln Likelihood = -10869.94252

Examined  720 trees

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

   8          B-bacillif        0.00791     (  0.00479,     0.01102) **
   8             3              0.00754     (  0.00439,     0.01073) **
   3            11              0.00900     (  0.00575,     0.01222) **
  11          B-spp-Deer        0.00725     (  0.00451,     0.00995) **
  11          B--weissii        0.00455     (  0.00239,     0.00677) **
   3             6              0.00441     (  0.00208,     0.00675) **
   6             1              0.00798     (  0.00491,     0.01109) **
   1          B-quintana        0.00897     (  0.00589,     0.01205) **
   1             9              0.00380     (  0.00174,     0.00586) **
   9          B-henselae        0.00611     (  0.00360,     0.00859) **
   9             4              0.00252     (  0.00078,     0.00422) **
   4             7              0.00034     (     zero,     0.00099) **
   7             2              0.00116     (  0.00002,     0.00228) **
   2          B--doshiae        0.00348     (  0.00165,     0.00531) **
   2          B-birtlesi        0.00729     (  0.00462,     0.00995) **
   7            12              0.00189     (  0.00049,     0.00328) **
  12          B-vinsonii        0.00482     (  0.00268,     0.00705) **
  12            10              0.00251     (  0.00087,     0.00415) **
  10          B-berhoffi        0.00387     (  0.00196,     0.00585) **
  10          B-arupensi        0.00381     (  0.00178,     0.00578) **
   4             5              0.00316     (  0.00137,     0.00494) **
   5          B-grahamii        0.00599     (  0.00357,     0.00846) **
   5          B-elizabet        0.00856     (  0.00567,     0.01146) **
   6          B-clarridg        0.01455     (  0.01067,     0.01853) **
   8          A-tumefaci        0.10081     (  0.09082,     0.11201) **

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


Data set # 85:


Empirical Base Frequencies:

   A       0.27234
   C       0.21721
   G       0.30090
  T(U)     0.20955

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.449497)


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


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

Ln Likelihood = -10631.95097

Examined  980 trees

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

   8             4              0.00556     (  0.00278,     0.00826) **
   4            10              0.00591     (  0.00339,     0.00847) **
  10            11              0.01151     (  0.00807,     0.01500) **
  11          B-spp-Deer        0.00824     (  0.00545,     0.01113) **
  11          B--weissii        0.00248     (  0.00080,     0.00407) **
  10          B-bacillif        0.00695     (  0.00420,     0.00976) **
   4             5              0.00560     (  0.00290,     0.00822) **
   5            12              0.00164     (  0.00030,     0.00297) **
  12          B-arupensi        0.00221     (  0.00071,     0.00369) **
  12          B-berhoffi        0.00289     (  0.00123,     0.00458) **
   5             1              0.00223     (  0.00065,     0.00371) **
   1             3              0.00112     (     zero,     0.00237) **
   3             2              0.00167     (  0.00039,     0.00305) **
   2          B--doshiae        0.00352     (  0.00164,     0.00540) **
   2          B-birtlesi        0.00467     (  0.00250,     0.00685) **
   3             7              0.00219     (  0.00074,     0.00373) **
   7          B-grahamii        0.00539     (  0.00310,     0.00770) **
   7          B-elizabet        0.00982     (  0.00671,     0.01290) **
   1             6              0.00066     (     zero,     0.00153) **
   6             9              0.00399     (  0.00200,     0.00599) **
   9          B-quintana        0.01106     (  0.00776,     0.01438) **
   9          B-henselae        0.00728     (  0.00459,     0.01000) **
   6          B-vinsonii        0.00349     (  0.00164,     0.00531) **
   8          B-clarridg        0.01308     (  0.00932,     0.01687) **
   8          A-tumefaci        0.09420     (  0.08465,     0.10498) **

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


Data set # 86:


Empirical Base Frequencies:

   A       0.26602
   C       0.21892
   G       0.31213
  T(U)     0.20293

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.447498)


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


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

Ln Likelihood = -10755.42677

Examined  620 trees

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

  10          B-bacillif        0.00805     (  0.00493,     0.01106) **
  10             7              0.00409     (  0.00167,     0.00649) **
   7          B-clarridg        0.01927     (  0.01480,     0.02373) **
   7             5              0.00394     (  0.00190,     0.00607) **
   5             8              0.00748     (  0.00464,     0.01030) **
   8          B--weissii        0.00332     (  0.00150,     0.00514) **
   8          B-spp-Deer        0.00663     (  0.00408,     0.00918) **
   5             4              0.00883     (  0.00577,     0.01192) **
   4          B-birtlesi        0.00882     (  0.00587,     0.01177) **
   4             2              0.00154     (  0.00021,     0.00280) **
   2             1              0.00231     (  0.00077,     0.00381) **
   1             9              0.00260     (  0.00102,     0.00420) **
   9          B-arupensi        0.00245     (  0.00087,     0.00401) **
   9          B-berhoffi        0.00387     (  0.00195,     0.00582) **
   1          B-vinsonii        0.00257     (  0.00098,     0.00415) **
   2             3              0.00063     (     zero,     0.00150) **
   3            11              0.00060     (     zero,     0.00146) **
  11            12              0.00272     (  0.00097,     0.00433) **
  12          B-quintana        0.00880     (  0.00589,     0.01172) **
  12          B-henselae        0.00445     (  0.00239,     0.00653) **
  11             6              0.00439     (  0.00230,     0.00648) **
   6          B-grahamii        0.00635     (  0.00389,     0.00890) **
   6          B-elizabet        0.00963     (  0.00651,     0.01266) **
   3          B--doshiae        0.00467     (  0.00255,     0.00678) **
  10          A-tumefaci        0.09592     (  0.08609,     0.10659) **

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


Data set # 87:


Empirical Base Frequencies:

   A       0.26369
   C       0.22049
   G       0.30591
  T(U)     0.20990

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.458392)


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


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

Ln Likelihood = -10933.77161

Examined  558 trees

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

   9             1              0.00390     (  0.00141,     0.00638) **
   1             2              0.00379     (  0.00163,     0.00587) **
   2          B-bacillif        0.01091     (  0.00749,     0.01436) **
   2             7              0.00981     (  0.00665,     0.01309) **
   7          B-spp-Deer        0.00870     (  0.00576,     0.01163) **
   7          B--weissii        0.00402     (  0.00198,     0.00605) **
   1             4              0.00682     (  0.00399,     0.00968) **
   4             6              0.00126     (  0.00009,     0.00241) **
   6             5              0.00136     (  0.00011,     0.00254) **
   5            11              0.00443     (  0.00238,     0.00652) **
  11          B-elizabet        0.01042     (  0.00731,     0.01365) **
  11          B-grahamii        0.00476     (  0.00261,     0.00693) **
   5            10              0.00406     (  0.00205,     0.00608) **
  10          B-henselae        0.00430     (  0.00222,     0.00638) **
  10          B-quintana        0.01108     (  0.00782,     0.01438) **
   6             8              0.00181     (  0.00069,     0.00326) **
   8          B--doshiae        0.00379     (  0.00187,     0.00571) **
   8          B-birtlesi        0.00949     (  0.00645,     0.01253) **
   4            12              0.00105     (  0.00005,     0.00213) **
  12          B-vinsonii        0.00420     (  0.00216,     0.00624) **
  12             3              0.00181     (  0.00044,     0.00321) **
   3          B-arupensi        0.00347     (  0.00156,     0.00533) **
   3          B-berhoffi        0.00407     (  0.00209,     0.00607) **
   9          B-clarridg        0.01535     (  0.01130,     0.01945) **
   9          A-tumefaci        0.09771     (  0.08775,     0.10849) **

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


Data set # 88:


Empirical Base Frequencies:

   A       0.26409
   C       0.21801
   G       0.29472
  T(U)     0.22317

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.468926)


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


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

Ln Likelihood = -11600.97930

Examined 1130 trees

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

  11          B-bacillif        0.00924     (  0.00594,     0.01257) **
  11            12              0.00748     (  0.00425,     0.01061) **
  12             3              0.00924     (  0.00605,     0.01250) **
   3          B-spp-Deer        0.01153     (  0.00808,     0.01488) **
   3          B--weissii        0.00281     (  0.00096,     0.00457) **
  12             1              0.00604     (  0.00334,     0.00875) **
   1             4              0.00976     (  0.00640,     0.01322) **
   4          B-quintana        0.01495     (  0.01091,     0.01889) **
   4            10              0.00776     (  0.00481,     0.01066) **
  10             7              0.00313     (  0.00112,     0.00517) **
   7             9              0.00422     (  0.00214,     0.00624) **
   9          B-grahamii        0.00769     (  0.00487,     0.01052) **
   9          B-elizabet        0.01262     (  0.00905,     0.01618) **
   7             5              0.00118     (     zero,     0.00243) **
   5             8              0.00198     (  0.00041,     0.00351) **
   8          B-birtlesi        0.00995     (  0.00683,     0.01307) **
   8          B--doshiae        0.00468     (  0.00256,     0.00689) **
   5             2              0.00338     (  0.00157,     0.00526) **
   2          B-vinsonii        0.00540     (  0.00308,     0.00776) **
   2             6              0.00423     (  0.00211,     0.00636) **
   6          B-berhoffi        0.00439     (  0.00231,     0.00646) **
   6          B-arupensi        0.00491     (  0.00268,     0.00710) **
  10          B-henselae        0.00542     (  0.00301,     0.00783) **
   1          B-clarridg        0.01281     (  0.00910,     0.01656) **
  11          A-tumefaci        0.09528     (  0.08543,     0.10586) **

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


Data set # 89:


Empirical Base Frequencies:

   A       0.27591
   C       0.21172
   G       0.31183
  T(U)     0.20054

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.427997)


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


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

Ln Likelihood = -10685.71825

Examined  508 trees

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

   9          B-bacillif        0.00858     (  0.00546,     0.01170) **
   9             8              0.00586     (  0.00308,     0.00870) **
   8             3              0.00498     (  0.00268,     0.00728) **
   3             1              0.00932     (  0.00608,     0.01256) **
   1             2              0.00364     (  0.00168,     0.00559) **
   2          B-henselae        0.00472     (  0.00254,     0.00693) **
   2             6              0.00198     (  0.00047,     0.00350) **
   6          B--doshiae        0.00323     (  0.00148,     0.00498) **
   6             4              0.00024     (     zero,     0.00073) *
   4             5              0.00212     (  0.00058,     0.00358) **
   5          B-vinsonii        0.00291     (  0.00113,     0.00460) **
   5            12              0.00150     (  0.00036,     0.00275) **
  12          B-arupensi        0.00404     (  0.00203,     0.00607) **
  12          B-berhoffi        0.00458     (  0.00246,     0.00673) **
   4            10              0.00158     (  0.00018,     0.00297) **
  10          B-birtlesi        0.00819     (  0.00537,     0.01102) **
  10             7              0.00135     (     zero,     0.00267) **
   7          B-elizabet        0.00818     (  0.00538,     0.01098) **
   7          B-grahamii        0.00489     (  0.00271,     0.00708) **
   1          B-quintana        0.01060     (  0.00735,     0.01393) **
   3            11              0.00975     (  0.00655,     0.01300) **
  11          B-spp-Deer        0.00626     (  0.00376,     0.00874) **
  11          B--weissii        0.00444     (  0.00235,     0.00656) **
   8          B-clarridg        0.01537     (  0.01138,     0.01940) **
   9          A-tumefaci        0.09332     (  0.08380,     0.10396) **

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


Data set # 90:


Empirical Base Frequencies:

   A       0.27288
   C       0.22878
   G       0.29322
  T(U)     0.20513

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.460235)


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


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

Ln Likelihood = -11125.11049

Examined  564 trees

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

  11             5              0.00835     (  0.00509,     0.01155) **
   5             8              0.00470     (  0.00239,     0.00703) **
   8            10              0.00865     (  0.00552,     0.01176) **
  10          B--weissii        0.00593     (  0.00341,     0.00845) **
  10          B-spp-Deer        0.00965     (  0.00651,     0.01281) **
   8            12              0.01003     (  0.00660,     0.01346) **
  12          B-quintana        0.01087     (  0.00743,     0.01432) **
  12             3              0.00459     (  0.00228,     0.00685) **
   3             9              0.00258     (  0.00083,     0.00442) **
   9             4              0.00075     (     zero,     0.00173) **
   4          B--doshiae        0.00388     (  0.00191,     0.00582) **
   4             2              0.00256     (  0.00102,     0.00418) **
   2          B-vinsonii        0.00292     (  0.00126,     0.00468) **
   2             6              0.00365     (  0.00169,     0.00551) **
   6          B-berhoffi        0.00435     (  0.00229,     0.00641) **
   6          B-arupensi        0.00136     (  0.00018,     0.00253) **
   9             1              0.00312     (  0.00130,     0.00499) **
   1          B-birtlesi        0.00863     (  0.00569,     0.01156) **
   1             7              0.00136     (     zero,     0.00276) **
   7          B-grahamii        0.00379     (  0.00178,     0.00571) **
   7          B-elizabet        0.01258     (  0.00908,     0.01606) **
   3          B-henselae        0.00625     (  0.00361,     0.00878) **
   5          B-bacillif        0.01590     (  0.01175,     0.02004) **
  11          B-clarridg        0.00963     (  0.00624,     0.01301) **
  11          A-tumefaci        0.09517     (  0.08555,     0.10597) **

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


Data set # 91:


Empirical Base Frequencies:

   A       0.26883
   C       0.22723
   G       0.29871
  T(U)     0.20523

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.459698)


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


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

Ln Likelihood = -11134.28495

Examined 1494 trees

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

  11             8              0.00855     (  0.00535,     0.01183) **
   8             2              0.00655     (  0.00389,     0.00925) **
   2             6              0.00945     (  0.00620,     0.01267) **
   6          B-spp-Deer        0.00605     (  0.00351,     0.00848) **
   6          B--weissii        0.00352     (  0.00166,     0.00549) **
   2          B-bacillif        0.01627     (  0.01214,     0.02044) **
   8             4              0.00835     (  0.00514,     0.01159) **
   4             9              0.00544     (  0.00307,     0.00787) **
   9          B-henselae        0.00647     (  0.00390,     0.00905) **
   9             3              0.00374     (  0.00169,     0.00578) **
   3             7              0.00058     (     zero,     0.00138) **
   7             5              0.00073     (     zero,     0.00160) **
   5          B-birtlesi        0.00983     (  0.00676,     0.01293) **
   5             1              0.00255     (  0.00097,     0.00412) **
   1            12              0.00238     (  0.00084,     0.00392) **
  12          B-arupensi        0.00364     (  0.00175,     0.00551) **
  12          B-berhoffi        0.00379     (  0.00187,     0.00571) **
   1          B-vinsonii        0.00322     (  0.00149,     0.00499) **
   7          B--doshiae        0.00542     (  0.00315,     0.00771) **
   3            10              0.00323     (  0.00146,     0.00503) **
  10          B-elizabet        0.01164     (  0.00827,     0.01500) **
  10          B-grahamii        0.00510     (  0.00287,     0.00734) **
   4          B-quintana        0.00820     (  0.00522,     0.01118) **
  11          B-clarridg        0.00700     (  0.00411,     0.00989) **
  11          A-tumefaci        0.10211     (  0.09148,     0.11275) **

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


Data set # 92:


Empirical Base Frequencies:

   A       0.26117
   C       0.22423
   G       0.31036
  T(U)     0.20424

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.459186)


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


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

Ln Likelihood = -10837.35248

Examined  574 trees

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

  12          B-bacillif        0.00941     (  0.00613,     0.01280) **
  12             2              0.00673     (  0.00360,     0.00986) **
   2             4              0.00542     (  0.00301,     0.00786) **
   4             3              0.00756     (  0.00458,     0.01055) **
   3             8              0.00216     (  0.00052,     0.00373) **
   8          B-quintana        0.00995     (  0.00681,     0.01309) **
   8          B-henselae        0.00639     (  0.00385,     0.00892) **
   3             5              0.00294     (  0.00118,     0.00474) **
   5             7              0.00147     (  0.00008,     0.00287) **
   7            10              0.00230     (  0.00066,     0.00387) **
  10          B-elizabet        0.00917     (  0.00619,     0.01215) **
  10          B-grahamii        0.00621     (  0.00375,     0.00869) **
   7             1              0.00141     (  0.00017,     0.00265) **
   1          B-birtlesi        0.00756     (  0.00481,     0.01032) **
   1          B--doshiae        0.00489     (  0.00262,     0.00710) **
   5            11              0.00242     (  0.00078,     0.00401) **
  11          B-vinsonii        0.00502     (  0.00279,     0.00731) **
  11             6              0.00214     (  0.00066,     0.00364) **
   6          B-arupensi        0.00421     (  0.00218,     0.00627) **
   6          B-berhoffi        0.00399     (  0.00200,     0.00599) **
   4             9              0.00971     (  0.00647,     0.01296) **
   9          B-spp-Deer        0.00507     (  0.00277,     0.00731) **
   9          B--weissii        0.00316     (  0.00134,     0.00497) **
   2          B-clarridg        0.01295     (  0.00922,     0.01676) **
  12          A-tumefaci        0.09344     (  0.08366,     0.10389) **

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


Data set # 93:


Empirical Base Frequencies:

   A       0.26429
   C       0.22540
   G       0.29574
  T(U)     0.21457

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.468056)


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


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

Ln Likelihood = -11181.19897

Examined  920 trees

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

  12          B-clarridg        0.00989     (  0.00651,     0.01336) **
  12             7              0.00589     (  0.00314,     0.00860) **
   7             2              0.01019     (  0.00674,     0.01366) **
   2          B-quintana        0.00988     (  0.00665,     0.01308) **
   2            11              0.00508     (  0.00271,     0.00737) **
  11          B-henselae        0.00743     (  0.00467,     0.01018) **
  11             6              0.00243     (  0.00071,     0.00411) **
   6             8              0.00160     (  0.00035,     0.00297) **
   8             4              0.00074     (     zero,     0.00161) **
   4          B--doshiae        0.00379     (  0.00183,     0.00576) **
   4          B-grahamii        0.00683     (  0.00424,     0.00944) **
   8          B-birtlesi        0.01135     (  0.00802,     0.01468) **
   6             1              0.00071     (     zero,     0.00162) **
   1          B-elizabet        0.01083     (  0.00762,     0.01408) **
   1             5              0.00158     (  0.00030,     0.00282) **
   5            10              0.00389     (  0.00200,     0.00586) **
  10          B-arupensi        0.00435     (  0.00227,     0.00640) **
  10          B-berhoffi        0.00358     (  0.00173,     0.00547) **
   5          B-vinsonii        0.00265     (  0.00109,     0.00431) **
   7             3              0.00821     (  0.00512,     0.01124) **
   3          B-bacillif        0.01130     (  0.00774,     0.01479) **
   3             9              0.01221     (  0.00863,     0.01579) **
   9          B-spp-Deer        0.00740     (  0.00461,     0.01015) **
   9          B--weissii        0.00357     (  0.00156,     0.00559) **
  12          A-tumefaci        0.09977     (  0.08980,     0.11074) **

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


Data set # 94:


Empirical Base Frequencies:

   A       0.26334
   C       0.22579
   G       0.30063
  T(U)     0.21025

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.465145)


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


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

Ln Likelihood = -11502.92472

Examined  920 trees

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

  10             6              0.00471     (  0.00220,     0.00720) **
   6          B-clarridg        0.01720     (  0.01300,     0.02160) **
   6            11              0.00541     (  0.00292,     0.00791) **
  11             8              0.01244     (  0.00882,     0.01616) **
   8          B-spp-Deer        0.00936     (  0.00631,     0.01243) **
   8          B--weissii        0.00446     (  0.00230,     0.00662) **
  11          B-bacillif        0.01162     (  0.00805,     0.01521) **
  10             5              0.00853     (  0.00532,     0.01177) **
   5          B-berhoffi        0.00457     (  0.00240,     0.00674) **
   5             1              0.00141     (  0.00003,     0.00268) **
   1          B-arupensi        0.00530     (  0.00303,     0.00760) **
   1            12              0.00289     (  0.00115,     0.00463) **
  12             7              0.00285     (  0.00111,     0.00461) **
   7          B-birtlesi        0.00673     (  0.00419,     0.00936) **
   7             2              0.00129     (     zero,     0.00265) **
   2             4              0.00175     (  0.00036,     0.00317) **
   4          B-grahamii        0.00731     (  0.00464,     0.01010) **
   4          B--doshiae        0.00589     (  0.00340,     0.00833) **
   2             3              0.00377     (  0.00170,     0.00584) **
   3          B-elizabet        0.00973     (  0.00656,     0.01293) **
   3             9              0.00478     (  0.00242,     0.00705) **
   9          B-henselae        0.00659     (  0.00395,     0.00921) **
   9          B-quintana        0.01502     (  0.01109,     0.01888) **
  12          B-vinsonii        0.00446     (  0.00241,     0.00659) **
  10          A-tumefaci        0.09905     (  0.08883,     0.10980) **

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


Data set # 95:


Empirical Base Frequencies:

   A       0.26767
   C       0.22727
   G       0.28990
  T(U)     0.21515

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.469283)


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


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

Ln Likelihood = -11432.49341

Examined  610 trees

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

   9             1              0.00646     (  0.00341,     0.00943) **
   1          B-bacillif        0.01359     (  0.00976,     0.01747) **
   1             7              0.00388     (  0.00176,     0.00604) **
   7            11              0.01105     (  0.00757,     0.01451) **
  11          B--weissii        0.00590     (  0.00338,     0.00838) **
  11          B-spp-Deer        0.00839     (  0.00548,     0.01133) **
   7             2              0.01053     (  0.00709,     0.01398) **
   2             8              0.00164     (  0.00034,     0.00294) **
   8          B-vinsonii        0.00363     (  0.00172,     0.00552) **
   8             4              0.00359     (  0.00163,     0.00548) **
   4          B-arupensi        0.00371     (  0.00175,     0.00566) **
   4          B-berhoffi        0.00339     (  0.00153,     0.00520) **
   2            10              0.00054     (     zero,     0.00131) **
  10             3              0.00311     (  0.00133,     0.00496) **
   3          B-elizabet        0.01253     (  0.00896,     0.01602) **
   3             6              0.00341     (  0.00147,     0.00531) **
   6          B-henselae        0.00759     (  0.00478,     0.01039) **
   6          B-quintana        0.01033     (  0.00707,     0.01355) **
  10             5              0.00134     (  0.00001,     0.00261) **
   5          B-birtlesi        0.00838     (  0.00551,     0.01128) **
   5            12              0.00150     (  0.00028,     0.00269) **
  12          B-grahamii        0.00763     (  0.00489,     0.01038) **
  12          B--doshiae        0.00331     (  0.00140,     0.00514) **
   9          B-clarridg        0.01406     (  0.01014,     0.01811) **
   9          A-tumefaci        0.10962     (  0.09893,     0.12107) **

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


Data set # 96:


Empirical Base Frequencies:

   A       0.26148
   C       0.22178
   G       0.29698
  T(U)     0.21975

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.470414)


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


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

Ln Likelihood = -11197.93974

Examined  858 trees

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

  12          B-clarridg        0.01015     (  0.00660,     0.01367) **
  12             9              0.00774     (  0.00454,     0.01084) **
   9             5              0.00694     (  0.00404,     0.00981) **
   5          B-bacillif        0.01213     (  0.00849,     0.01591) **
   5             7              0.00959     (  0.00630,     0.01292) **
   7          B--weissii        0.00497     (  0.00264,     0.00734) **
   7          B-spp-Deer        0.00803     (  0.00517,     0.01092) **
   9             1              0.00957     (  0.00621,     0.01297) **
   1          B-birtlesi        0.00617     (  0.00367,     0.00868) **
   1             2              0.00157     (  0.00025,     0.00301) **
   2            10              0.00106     (     zero,     0.00217) **
  10          B--doshiae        0.00388     (  0.00192,     0.00584) **
  10             6              0.00142     (  0.00012,     0.00274) **
   6          B-grahamii        0.00976     (  0.00666,     0.01289) **
   6             3              0.00361     (  0.00170,     0.00553) **
   3          B-henselae        0.00557     (  0.00319,     0.00796) **
   3          B-quintana        0.01424     (  0.01057,     0.01804) **
   2             4              0.00163     (  0.00029,     0.00302) **
   4          B-elizabet        0.01321     (  0.00965,     0.01687) **
   4            11              0.00183     (  0.00050,     0.00322) **
  11          B-vinsonii        0.00575     (  0.00339,     0.00812) **
  11             8              0.00048     (     zero,     0.00131) **
   8          B-berhoffi        0.00654     (  0.00403,     0.00908) **
   8          B-arupensi        0.00235     (  0.00084,     0.00392) **
  12          A-tumefaci        0.09996     (  0.08999,     0.11105) **

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


Data set # 97:


Empirical Base Frequencies:

   A       0.26904
   C       0.22616
   G       0.28518
  T(U)     0.21962

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.471734)


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


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

Ln Likelihood = -11135.16733

Examined  650 trees

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

  11             5              0.00649     (  0.00357,     0.00940) **
   5             4              0.00776     (  0.00473,     0.01084) **
   4             3              0.01009     (  0.00682,     0.01338) **
   3             1              0.00472     (  0.00238,     0.00704) **
   1             2              0.00213     (  0.00066,     0.00359) **
   2          B-arupensi        0.00349     (  0.00167,     0.00537) **
   2             7              0.00150     (  0.00021,     0.00283) **
   7             6              0.00392     (  0.00192,     0.00593) **
   6             8              0.00032     (     zero,     0.00093) **
   8          B--doshiae        0.00341     (  0.00159,     0.00526) **
   8          B-birtlesi        0.00868     (  0.00579,     0.01160) **
   6            12              0.00089     (     zero,     0.00188) **
  12          B-henselae        0.00749     (  0.00478,     0.01022) **
  12             9              0.00332     (  0.00150,     0.00516) **
   9          B-elizabet        0.01049     (  0.00728,     0.01369) **
   9          B-grahamii        0.00584     (  0.00343,     0.00826) **
   7          B-vinsonii        0.00575     (  0.00339,     0.00810) **
   1          B-berhoffi        0.00278     (  0.00111,     0.00444) **
   3          B-quintana        0.01201     (  0.00853,     0.01552) **
   4          B-clarridg        0.01321     (  0.00938,     0.01696) **
   5            10              0.00625     (  0.00358,     0.00884) **
  10          B--weissii        0.00464     (  0.00235,     0.00691) **
  10          B-spp-Deer        0.00885     (  0.00587,     0.01191) **
  11          B-bacillif        0.00962     (  0.00623,     0.01293) **
  11          A-tumefaci        0.09640     (  0.08667,     0.10724) **

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


Data set # 98:


Empirical Base Frequencies:

   A       0.26741
   C       0.22543
   G       0.30859
  T(U)     0.19858

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.451404)


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


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

Ln Likelihood = -10899.94277

Examined  586 trees

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

   7          B-bacillif        0.00618     (  0.00343,     0.00894) **
   7             5              0.00566     (  0.00301,     0.00839) **
   5            11              0.00621     (  0.00347,     0.00899) **
  11          B-quintana        0.01103     (  0.00767,     0.01440) **
  11             1              0.00484     (  0.00255,     0.00711) **
   1             6              0.00169     (  0.00027,     0.00307) **
   6             3              0.00060     (     zero,     0.00141) **
   3          B-henselae        0.00676     (  0.00420,     0.00932) **
   3             2              0.00077     (     zero,     0.00165) **
   2             8              0.00109     (     zero,     0.00211) **
   8          B--doshiae        0.00428     (  0.00223,     0.00634) **
   8          B-birtlesi        0.00688     (  0.00429,     0.00945) **
   2          B-vinsonii        0.00615     (  0.00372,     0.00860) **
   6             9              0.00274     (  0.00099,     0.00448) **
   9          B-grahamii        0.00916     (  0.00615,     0.01217) **
   9          B-elizabet        0.01100     (  0.00773,     0.01426) **
   1            10              0.00353     (  0.00153,     0.00550) **
  10          B-berhoffi        0.00226     (  0.00083,     0.00381) **
  10          B-arupensi        0.00390     (  0.00188,     0.00592) **
   5             4              0.00503     (  0.00262,     0.00747) **
   4            12              0.01057     (  0.00726,     0.01394) **
  12          B-spp-Deer        0.00781     (  0.00502,     0.01061) **
  12          B--weissii        0.00513     (  0.00283,     0.00741) **
   4          B-clarridg        0.01255     (  0.00887,     0.01618) **
   7          A-tumefaci        0.09267     (  0.08308,     0.10317) **

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


Data set # 99:


Empirical Base Frequencies:

   A       0.25461
   C       0.21642
   G       0.31047
  T(U)     0.21850

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.468902)


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


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

Ln Likelihood = -10692.21178

Examined  544 trees

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

   2             3              0.00365     (  0.00139,     0.00603) **
   3             7              0.00143     (  0.00016,     0.00262) **
   7             9              0.00227     (  0.00060,     0.00393) **
   9             4              0.00109     (     zero,     0.00219) **
   4          B--doshiae        0.00598     (  0.00349,     0.00838) **
   4          B-henselae        0.00886     (  0.00596,     0.01185) **
   9            11              0.00207     (  0.00054,     0.00361) **
  11          B-birtlesi        0.00694     (  0.00430,     0.00958) **
  11            10              0.00181     (  0.00034,     0.00319) **
  10          B-grahamii        0.00372     (  0.00177,     0.00569) **
  10          B-elizabet        0.01191     (  0.00849,     0.01533) **
   7             1              0.00125     (  0.00010,     0.00244) **
   1          B-berhoffi        0.00386     (  0.00190,     0.00583) **
   1            12              0.00081     (     zero,     0.00174) **
  12          B-arupensi        0.00392     (  0.00196,     0.00589) **
  12          B-vinsonii        0.00353     (  0.00166,     0.00539) **
   3          B-quintana        0.00999     (  0.00688,     0.01320) **
   2             5              0.00503     (  0.00255,     0.00753) **
   5             8              0.00453     (  0.00231,     0.00676) **
   8          B-clarridg        0.01678     (  0.01268,     0.02101) **
   8             6              0.00771     (  0.00483,     0.01062) **
   6          B--weissii        0.00400     (  0.00194,     0.00599) **
   6          B-spp-Deer        0.00696     (  0.00436,     0.00961) **
   5          B-bacillif        0.00969     (  0.00644,     0.01292) **
   2          A-tumefaci        0.09416     (  0.08417,     0.10446) **

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


Data set # 100:


Empirical Base Frequencies:

   A       0.26361
   C       0.22130
   G       0.30446
  T(U)     0.21063

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.460124)


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


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

Ln Likelihood = -11154.31913

Examined  562 trees

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

   6          B-clarridg        0.01400     (  0.01005,     0.01796) **
   6             3              0.00623     (  0.00334,     0.00912) **
   3             4              0.00564     (  0.00315,     0.00813) **
   4             9              0.00969     (  0.00646,     0.01296) **
   9          B-spp-Deer        0.00652     (  0.00398,     0.00909) **
   9          B--weissii        0.00343     (  0.00154,     0.00533) **
   4             5              0.01207     (  0.00846,     0.01572) **
   5            10              0.00133     (  0.00003,     0.00253) **
  10             2              0.00022     (     zero,     0.00073)
   2          B--doshiae        0.00626     (  0.00381,     0.00872) **
   2             1              0.00389     (  0.00183,     0.00594) **
   1             8              0.00255     (  0.00086,     0.00426) **
   8          B-elizabet        0.00894     (  0.00601,     0.01188) **
   8          B-grahamii        0.00529     (  0.00303,     0.00755) **
   1          B-birtlesi        0.00986     (  0.00676,     0.01300) **
  10            11              0.00178     (  0.00033,     0.00317) **
  11          B-vinsonii        0.00366     (  0.00178,     0.00561) **
  11            12              0.00270     (  0.00105,     0.00434) **
  12          B-berhoffi        0.00278     (  0.00108,     0.00446) **
  12          B-arupensi        0.00347     (  0.00157,     0.00538) **
   5             7              0.00282     (  0.00112,     0.00459) **
   7          B-quintana        0.01309     (  0.00950,     0.01669) **
   7          B-henselae        0.00719     (  0.00449,     0.00987) **
   3          B-bacillif        0.01091     (  0.00744,     0.01444) **
   6          A-tumefaci        0.09801     (  0.08781,     0.10862) **

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