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 (