Nucleic acid sequence Maximum Likelihood method, version 3.573c Data set # 1: Empirical Base Frequencies: A 0.24654 C 0.24065 G 0.29411 T(U) 0.21869 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.494041) +B-clarridg ! ! +B-spp-Deer ! +-10 ! ! +B--weissii ! ! ! ! +B-arupensi --5--3 ! ! ! ! +B-quintana ! ! ! +--9 ! ! ! ! +B-bacillif ! ! ! ! ! +--8 +-11 +B-elizabet ! ! ! ! +--6 ! ! ! ! ! +B-grahamii ! ! ! +--7 ! ! ! ! +B-birtlesi ! ! ! ! ! ! +--2 +-12 +B-vinsonii ! ! ! +--4 ! ! +--1 +B-henselae ! ! ! ! ! +B--doshiae ! ! ! +B-berhoffi ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2957.34621 Examined 956 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 5 B-clarridg 0.01193 ( 0.00595, 0.01795) ** 5 3 0.00459 ( 0.00076, 0.00846) ** 3 10 0.00680 ( 0.00231, 0.01123) ** 10 B-spp-Deer 0.00003 ( zero, infinity) 10 B--weissii 0.00003 ( zero, infinity) 3 8 0.00276 ( zero, 0.00567) ** 8 B-arupensi 0.00076 ( zero, 0.00223) ** 8 2 0.00150 ( zero, 0.00354) ** 2 11 0.00151 ( zero, 0.00355) ** 11 9 0.00220 ( zero, 0.00471) ** 9 B-quintana 0.01111 ( 0.00548, 0.01673) ** 9 B-bacillif 0.00817 ( 0.00331, 0.01298) ** 11 7 0.00221 ( zero, 0.00470) ** 7 6 0.00219 ( zero, 0.00467) ** 6 B-elizabet 0.00661 ( 0.00227, 0.01091) ** 6 B-grahamii 0.00006 ( zero, infinity) 7 12 0.00141 ( zero, 0.00342) ** 12 B-birtlesi 0.00363 ( 0.00046, 0.00684) ** 12 1 0.00006 ( zero, 0.00218) 1 4 0.00070 ( zero, 0.00211) ** 4 B-vinsonii 0.00006 ( zero, infinity) 4 B-henselae 0.00298 ( 0.00001, 0.00584) ** 1 B--doshiae 0.00003 ( zero, infinity) 2 B-berhoffi 0.00149 ( zero, 0.00352) ** 5 A-tumefaci 0.05453 ( 0.04175, 0.06740) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 2: Empirical Base Frequencies: A 0.24261 C 0.23236 G 0.31201 T(U) 0.21302 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.489540) +B-clarridg ! ! +B-bacillif ! +--2 ! ! ! +B--weissii ! +--6 +-10 ! ! ! +B-spp-Deer ! +--1 ! ! ! ! +B-henselae ! ! ! ! ! +B-quintana ! +--3 ! ! ! +B-grahamii ! ! ! +-12 ! ! ! ! ! +B-birtlesi ! +--9 +--8 +-11 ! ! ! ! +B--doshiae ! ! ! ! ! +--4 ! +B-vinsonii ! ! ! ! ! ! ! +B-arupensi --5--7 ! ! ! +B-berhoffi ! ! ! +B-elizabet ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3091.90401 Examined 868 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 5 B-clarridg 0.00987 ( 0.00439, 0.01537) ** 5 7 0.00522 ( 0.00115, 0.00928) ** 7 4 0.00206 ( zero, 0.00463) ** 4 9 0.00070 ( zero, 0.00211) ** 9 3 0.00003 ( zero, infinity) 3 1 0.00218 ( zero, 0.00468) ** 1 6 0.00248 ( zero, 0.00526) ** 6 2 0.00645 ( 0.00203, 0.01093) ** 2 B-bacillif 0.01468 ( 0.00810, 0.02132) ** 2 10 0.00851 ( 0.00345, 0.01356) ** 10 B--weissii 0.00222 ( zero, 0.00470) ** 10 B-spp-Deer 0.00006 ( zero, 0.00201) 6 B-henselae 0.00569 ( 0.00156, 0.00976) ** 1 B-quintana 0.00888 ( 0.00386, 0.01391) ** 3 8 0.00293 ( 0.00007, 0.00580) ** 8 12 0.00006 ( zero, 0.00151) 12 B-grahamii 0.00143 ( zero, 0.00344) ** 12 11 0.00006 ( zero, infinity) 11 B-birtlesi 0.00146 ( zero, 0.00349) ** 11 B--doshiae 0.00146 ( zero, 0.00349) ** 8 B-vinsonii 0.00146 ( zero, 0.00349) ** 9 B-arupensi 0.00365 ( 0.00049, 0.00688) ** 4 B-berhoffi 0.00003 ( zero, infinity) 7 B-elizabet 0.00597 ( 0.00181, 0.01017) ** 5 A-tumefaci 0.06049 ( 0.04711, 0.07429) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 3: Empirical Base Frequencies: A 0.23843 C 0.24073 G 0.32726 T(U) 0.19357 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.495474) +B-clarridg ! ! +B-arupensi ! ! ! ! +B-elizabet ! ! ! ! +-12 +--9 +B-grahamii ! ! ! ! ! ! ! ! ! ! +--8 +B--doshiae ! ! ! ! ! +-10 ! ! +--4 +-11 +B-birtlesi ! +--1 ! ! ! ! ! ! +B-vinsonii ! ! ! ! ! +--2 ! +B-henselae ! ! ! ! ! ! ! +B-berhoffi --7--5 ! ! ! +B-quintana ! ! ! ! +B-bacillif ! +--3 ! ! +B--weissii ! +--6 ! +B-spp-Deer ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3162.01819 Examined 876 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 B-clarridg 0.00817 ( 0.00310, 0.01326) ** 7 5 0.00636 ( 0.00157, 0.01105) ** 5 2 0.00373 ( 0.00018, 0.00722) ** 2 1 0.00333 ( zero, 0.00660) ** 1 12 0.00003 ( zero, 0.00213) 12 B-arupensi 0.00077 ( zero, 0.00224) ** 12 4 0.00354 ( 0.00011, 0.00697) ** 4 9 0.00003 ( zero, 0.00214) 9 B-elizabet 0.01030 ( 0.00491, 0.01570) ** 9 8 0.00229 ( zero, 0.00517) ** 8 B-grahamii 0.00068 ( zero, 0.00208) * 8 11 0.00006 ( zero, 0.00171) 11 10 0.00003 ( zero, infinity) 10 B--doshiae 0.00003 ( zero, infinity) 10 B-birtlesi 0.00291 ( 0.00007, 0.00577) ** 11 B-vinsonii 0.00220 ( zero, 0.00468) ** 4 B-henselae 0.00657 ( 0.00224, 0.01087) ** 1 B-berhoffi 0.00221 ( zero, 0.00470) ** 2 B-quintana 0.00860 ( 0.00355, 0.01365) ** 5 3 0.00626 ( 0.00176, 0.01074) ** 3 B-bacillif 0.01051 ( 0.00476, 0.01627) ** 3 6 0.00734 ( 0.00258, 0.01211) ** 6 B--weissii 0.00112 ( zero, 0.00320) ** 6 B-spp-Deer 0.00325 ( 0.00008, 0.00642) ** 7 A-tumefaci 0.07362 ( 0.05883, 0.08909) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 4: Empirical Base Frequencies: A 0.22877 C 0.24720 G 0.31061 T(U) 0.21342 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.514892) +B-berhoffi ! ! +B-birtlesi ! +-12 ! ! +B--doshiae ! ! ! ! +B-bacillif ! +--5 +-10 ! ! ! ! ! +B-spp-Deer ! ! ! +--8 +-11 ! ! ! ! ! +B--weissii ! ! +--4 ! ! +--1 ! +B-henselae ! ! ! ! ! ! ! +B-vinsonii ! ! ! ! ! ! +B-grahamii --3--2 +--7 ! ! +B-elizabet ! ! ! ! +B-quintana ! ! +--6 ! +--9 +B-clarridg ! ! ! +B-arupensi ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3132.91573 Examined 544 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 3 B-berhoffi 0.00006 ( zero, 0.00152) 3 2 0.00075 ( zero, 0.00221) ** 2 1 0.00367 ( 0.00046, 0.00689) ** 1 5 0.00150 ( zero, 0.00355) ** 5 12 0.00003 ( zero, infinity) 12 B-birtlesi 0.00436 ( 0.00092, 0.00788) ** 12 B--doshiae 0.00003 ( zero, infinity) 5 4 0.00069 ( zero, 0.00209) ** 4 8 0.00593 ( 0.00180, 0.01001) ** 8 10 0.00591 ( 0.00180, 0.01002) ** 10 B-bacillif 0.01188 ( 0.00605, 0.01771) ** 10 11 0.00370 ( 0.00045, 0.00695) ** 11 B-spp-Deer 0.00074 ( zero, 0.00218) ** 11 B--weissii 0.00072 ( zero, 0.00214) ** 8 B-henselae 0.00218 ( zero, 0.00468) ** 4 B-vinsonii 0.00151 ( zero, 0.00357) ** 1 7 0.00064 ( zero, 0.00209) 7 B-grahamii 0.00011 ( zero, 0.00155) 7 B-elizabet 0.00959 ( 0.00438, 0.01480) ** 2 9 0.00003 ( zero, 0.00217) 9 6 0.00645 ( 0.00202, 0.01089) ** 6 B-quintana 0.01138 ( 0.00559, 0.01721) ** 6 B-clarridg 0.01248 ( 0.00653, 0.01854) ** 9 B-arupensi 0.00364 ( 0.00048, 0.00687) ** 3 A-tumefaci 0.06496 ( 0.05105, 0.07924) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 5: Empirical Base Frequencies: A 0.24379 C 0.24394 G 0.29232 T(U) 0.21996 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.498334) +B-clarridg ! ! +B-arupensi ! +--4 ! ! +B-berhoffi ! ! ! ! +B-elizabet ! ! +--8 ! ! +--2 +B-grahamii --9--5 ! ! ! ! +-10 +B-birtlesi ! ! ! ! ! ! +--6 +B-vinsonii ! ! ! ! ! ! ! +B--doshiae ! +--3 ! ! +B-bacillif ! ! +-12 ! ! ! +B-quintana ! +--7 ! ! +B--weissii ! ! +-11 ! +--1 +B-spp-Deer ! ! ! +B-henselae ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3088.38505 Examined 828 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 9 B-clarridg 0.00808 ( 0.00304, 0.01315) ** 9 5 0.00811 ( 0.00304, 0.01318) ** 5 4 0.00006 ( zero, infinity) 4 B-arupensi 0.00220 ( zero, 0.00468) ** 4 B-berhoffi 0.00220 ( zero, 0.00469) ** 5 3 0.00073 ( zero, 0.00217) ** 3 6 0.00145 ( zero, 0.00349) ** 6 10 0.00006 ( zero, 0.00181) 10 2 0.00003 ( zero, 0.00188) 2 8 0.00146 ( zero, 0.00350) ** 8 B-elizabet 0.01174 ( 0.00601, 0.01752) ** 8 B-grahamii 0.00006 ( zero, 0.00181) 2 B-birtlesi 0.00292 ( 0.00007, 0.00578) ** 10 B-vinsonii 0.00146 ( zero, 0.00347) ** 6 B--doshiae 0.00006 ( zero, infinity) 3 7 0.00293 ( 0.00006, 0.00580) ** 7 12 0.00512 ( 0.00131, 0.00895) ** 12 B-bacillif 0.01256 ( 0.00660, 0.01857) ** 12 B-quintana 0.00516 ( 0.00131, 0.00900) ** 7 1 0.00072 ( zero, 0.00218) * 1 11 0.00807 ( 0.00331, 0.01286) ** 11 B--weissii 0.00149 ( zero, 0.00352) ** 11 B-spp-Deer 0.00076 ( zero, 0.00222) ** 1 B-henselae 0.00372 ( 0.00042, 0.00694) ** 9 A-tumefaci 0.07167 ( 0.05706, 0.08669) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 6: Empirical Base Frequencies: A 0.25343 C 0.22562 G 0.31730 T(U) 0.20364 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.466659) +B-elizabet ! ! +B-berhoffi ! ! ! ! +B-grahamii ! ! ! ! ! ! +B-henselae ! ! +--9 +--5 ! ! ! ! +--3 +B-vinsonii --7--4 ! ! ! ! ! ! +--8 +-12 +B-birtlesi ! ! ! ! ! ! ! ! ! +B--doshiae ! ! ! ! ! ! ! +B-arupensi ! ! ! ! +--6 +B--weissii ! ! +-10 ! ! +--1 +B-spp-Deer ! ! ! ! ! ! +--2 +B-clarridg ! ! ! ! ! +-11 +B-bacillif ! ! ! +B-quintana ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3021.72187 Examined 840 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 B-elizabet 0.00557 ( 0.00140, 0.00980) ** 7 4 0.00573 ( 0.00150, 0.00994) ** 4 B-berhoffi 0.00050 ( zero, 0.00192) 4 6 0.00168 ( zero, 0.00396) ** 6 8 0.00003 ( zero, 0.00168) 8 9 0.00219 ( zero, 0.00467) ** 9 B-grahamii 0.00070 ( zero, 0.00211) ** 9 12 0.00068 ( zero, 0.00205) ** 12 3 0.00003 ( zero, infinity) 3 5 0.00145 ( zero, 0.00348) ** 5 B-henselae 0.00659 ( 0.00230, 0.01091) ** 5 B-vinsonii 0.00147 ( zero, 0.00351) ** 3 B-birtlesi 0.00219 ( zero, 0.00466) ** 12 B--doshiae 0.00071 ( zero, 0.00211) ** 8 B-arupensi 0.00513 ( 0.00134, 0.00895) ** 6 11 0.00374 ( 0.00025, 0.00726) ** 11 2 0.00381 ( 0.00050, 0.00720) ** 2 1 0.00158 ( zero, 0.00431) ** 1 10 0.00788 ( 0.00313, 0.01266) ** 10 B--weissii 0.00165 ( zero, 0.00387) ** 10 B-spp-Deer 0.00130 ( zero, 0.00331) ** 1 B-clarridg 0.00893 ( 0.00380, 0.01404) ** 2 B-bacillif 0.00942 ( 0.00406, 0.01479) ** 11 B-quintana 0.00951 ( 0.00417, 0.01485) ** 7 A-tumefaci 0.04898 ( 0.03715, 0.06135) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 7: Empirical Base Frequencies: A 0.23713 C 0.22719 G 0.32986 T(U) 0.20582 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.488316) +B-spp-Deer +--9 ! +B--weissii ! +--6 +B-berhoffi ! ! ! ! ! ! +B-quintana ! ! ! +--8 ! +--1 ! +B-arupensi ! ! ! ! ! ! +B-vinsonii ! ! ! +-11 ! +--3 ! ! +B-birtlesi ! ! ! +--2 ! ! +--5 +B--doshiae ! ! ! ! ! ! ! ! +B-elizabet ! ! ! ! +-12 ! +-10 +--4 +B-grahamii ! ! ! ! ! +B-henselae ! ! ! +B-bacillif ! --7-B-clarridg ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3034.79178 Examined 1012 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 6 0.00488 ( 0.00089, 0.00886) ** 6 9 0.01043 ( 0.00496, 0.01594) ** 9 B-spp-Deer 0.00121 ( zero, 0.00337) ** 9 B--weissii 0.00243 ( zero, 0.00525) ** 6 1 0.00450 ( 0.00073, 0.00831) ** 1 B-berhoffi 0.00146 ( zero, 0.00348) ** 1 3 0.00006 ( zero, infinity) 3 8 0.00076 ( zero, 0.00221) ** 8 B-quintana 0.01176 ( 0.00601, 0.01754) ** 8 B-arupensi 0.00006 ( zero, infinity) 3 10 0.00221 ( zero, 0.00470) ** 10 5 0.00151 ( zero, 0.00356) ** 5 11 0.00006 ( zero, infinity) 11 B-vinsonii 0.00292 ( 0.00007, 0.00579) ** 11 2 0.00006 ( zero, infinity) 2 B-birtlesi 0.00223 ( zero, 0.00471) ** 2 B--doshiae 0.00003 ( zero, infinity) 5 4 0.00076 ( zero, 0.00222) ** 4 12 0.00075 ( zero, 0.00219) ** 12 B-elizabet 0.00882 ( 0.00382, 0.01380) ** 12 B-grahamii 0.00006 ( zero, infinity) 4 B-henselae 0.00586 ( 0.00181, 0.00992) ** 10 B-bacillif 0.01330 ( 0.00714, 0.01944) ** 7 B-clarridg 0.00465 ( 0.00081, 0.00848) ** 7 A-tumefaci 0.06761 ( 0.05321, 0.08199) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 8: Empirical Base Frequencies: A 0.22968 C 0.24170 G 0.31401 T(U) 0.21461 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.510947) +B-clarridg ! ! +B-arupensi ! +-10 ! ! +B-vinsonii ! +--4 ! ! ! +B-grahamii ! ! ! +--2 ! ! +-12 +B-birtlesi ! +--8 ! ! ! ! +B--doshiae ! ! ! ! ! ! +B-henselae ! ! ! ! ! ! +--5 +B-quintana ! +--1 ! ! ! ! ! +--9 +B--weissii ! ! ! ! +-11 ! ! ! +--3 +B-spp-Deer --7--6 ! ! ! ! ! +B-bacillif ! ! ! ! ! +B-elizabet ! ! ! +B-berhoffi ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3081.90701 Examined 542 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 B-clarridg 0.00954 ( 0.00426, 0.01494) ** 7 6 0.00587 ( 0.00164, 0.01020) ** 6 1 0.00225 ( zero, 0.00477) ** 1 8 0.00223 ( zero, 0.00475) ** 8 4 0.00018 ( zero, 0.00219) 4 10 0.00150 ( zero, 0.00354) ** 10 B-arupensi 0.00294 ( 0.00007, 0.00582) ** 10 B-vinsonii 0.00215 ( zero, 0.00462) ** 4 12 0.00059 ( zero, 0.00260) 12 2 0.00059 ( zero, 0.00260) 2 B-grahamii 0.00144 ( zero, 0.00344) ** 2 B-birtlesi 0.00074 ( zero, 0.00218) ** 12 B--doshiae 0.00006 ( zero, infinity) 8 5 0.00357 ( 0.00034, 0.00679) ** 5 B-henselae 0.00229 ( zero, 0.00491) ** 5 9 0.00260 ( zero, 0.00552) ** 9 B-quintana 0.01582 ( 0.00902, 0.02266) ** 9 3 0.00446 ( 0.00073, 0.00826) ** 3 11 0.00508 ( 0.00112, 0.00908) ** 11 B--weissii 0.00076 ( zero, 0.00222) ** 11 B-spp-Deer 0.00221 ( zero, 0.00470) ** 3 B-bacillif 0.00598 ( 0.00160, 0.01036) ** 1 B-elizabet 0.00807 ( 0.00331, 0.01285) ** 6 B-berhoffi 0.00003 ( zero, infinity) 7 A-tumefaci 0.06420 ( 0.05043, 0.07848) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 9: Empirical Base Frequencies: A 0.25233 C 0.21850 G 0.31746 T(U) 0.21171 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.466666) +B-bacillif ! ! +B--weissii ! +-10 ! ! +B-spp-Deer ! ! ! ! +B-henselae ! ! +--9 ! ! ! +B--doshiae --3--6 +--4 ! ! ! ! +B-vinsonii ! ! ! ! ! ! ! ! +--8 +B-grahamii ! ! ! ! +--7 ! ! ! +--2 +B-elizabet ! +--5 ! ! ! +B-birtlesi ! ! ! ! +B-clarridg ! ! +-11 ! ! +-12 +B-quintana ! ! ! ! ! +--1 +B-berhoffi ! ! ! +B-arupensi ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3120.62511 Examined 1204 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 3 B-bacillif 0.00636 ( 0.00175, 0.01099) ** 3 6 0.00554 ( 0.00109, 0.01001) ** 6 10 0.01041 ( 0.00484, 0.01598) ** 10 B--weissii 0.00003 ( zero, infinity) 10 B-spp-Deer 0.00365 ( 0.00046, 0.00684) ** 6 5 0.00602 ( 0.00157, 0.01054) ** 5 4 0.00337 ( 0.00015, 0.00650) ** 4 9 0.00218 ( zero, 0.00465) ** 9 B-henselae 0.00364 ( 0.00047, 0.00683) ** 9 B--doshiae 0.00006 ( zero, infinity) 4 8 0.00003 ( zero, 0.00168) 8 B-vinsonii 0.00219 ( zero, 0.00466) ** 8 2 0.00006 ( zero, 0.00279) 2 7 0.00213 ( zero, 0.00459) ** 7 B-grahamii 0.00006 ( zero, infinity) 7 B-elizabet 0.01175 ( 0.00599, 0.01751) ** 2 B-birtlesi 0.00359 ( 0.00044, 0.00679) ** 5 1 0.00006 ( zero, 0.00163) 1 12 0.00250 ( zero, 0.00525) ** 12 11 0.00587 ( 0.00177, 0.00997) ** 11 B-clarridg 0.01778 ( 0.01065, 0.02492) ** 11 B-quintana 0.00438 ( 0.00084, 0.00795) ** 12 B-berhoffi 0.00070 ( zero, 0.00211) * 1 B-arupensi 0.00070 ( zero, 0.00210) ** 3 A-tumefaci 0.06094 ( 0.04734, 0.07462) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 10: Empirical Base Frequencies: A 0.24740 C 0.23132 G 0.32259 T(U) 0.19869 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.476025) +B-berhoffi ! ! +B-quintana ! ! ! +--7 +B-bacillif ! ! ! +-12 ! ! ! ! ! +B--weissii ! ! +--4 +--8 ! +--1 ! +B-spp-Deer ! ! ! ! ! ! ! +B-clarridg ! ! ! ! ! +B-arupensi ! ! -11--3 +B-henselae ! ! +--5 ! ! ! ! +B-elizabet ! ! ! +--2 ! ! +-10 +B-grahamii ! ! ! ! ! ! ! ! +B-birtlesi ! +--9 +--6 ! ! +B--doshiae ! ! ! +B-vinsonii ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2981.88858 Examined 690 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 B-berhoffi 0.00006 ( zero, 0.00152) 11 3 0.00149 ( zero, 0.00357) ** 3 1 0.00003 ( zero, infinity) 1 7 0.00296 ( 0.00008, 0.00591) ** 7 B-quintana 0.00662 ( 0.00230, 0.01097) ** 7 4 0.00090 ( zero, 0.00269) * 4 12 0.00589 ( 0.00177, 0.01003) ** 12 B-bacillif 0.00893 ( 0.00379, 0.01407) ** 12 8 0.01114 ( 0.00543, 0.01686) ** 8 B--weissii 0.00223 ( zero, 0.00473) ** 8 B-spp-Deer 0.00003 ( zero, 0.00185) 4 B-clarridg 0.00574 ( 0.00156, 0.00982) ** 1 B-arupensi 0.00291 ( 0.00010, 0.00580) ** 3 9 0.00439 ( 0.00088, 0.00792) ** 9 10 0.00003 ( zero, 0.00174) 10 5 0.00150 ( zero, 0.00355) ** 5 B-henselae 0.00807 ( 0.00333, 0.01287) ** 5 2 0.00077 ( zero, 0.00224) ** 2 B-elizabet 0.00586 ( 0.00183, 0.00994) ** 2 B-grahamii 0.00003 ( zero, infinity) 10 6 0.00003 ( zero, infinity) 6 B-birtlesi 0.00146 ( zero, 0.00349) ** 6 B--doshiae 0.00074 ( zero, 0.00219) ** 9 B-vinsonii 0.00220 ( zero, 0.00468) ** 11 A-tumefaci 0.06421 ( 0.05048, 0.07835) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 11: Empirical Base Frequencies: A 0.25287 C 0.21950 G 0.31945 T(U) 0.20818 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.464027) +B-clarridg ! ! +B-quintana ! ! ! +--7 +B-berhoffi ! ! ! ! ! ! ! ! +B-arupensi ! ! +--1 ! ! ! ! ! +B-vinsonii ! ! ! ! +--6 ! ! ! ! +-12 +B-birtlesi ! ! +-10 ! ! ! ! ! +--4 +B-grahamii -11--8 ! ! ! ! ! ! +--2 +B--doshiae ! ! ! ! ! ! ! +--5 +B-henselae ! ! ! ! ! +B-elizabet ! ! ! ! +B--weissii ! ! +--3 ! +--9 +B-spp-Deer ! ! ! +B-bacillif ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3222.94988 Examined 796 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 B-clarridg 0.00845 ( 0.00325, 0.01369) ** 11 8 0.00636 ( 0.00166, 0.01113) ** 8 7 0.00343 ( zero, 0.00702) ** 7 B-quintana 0.00874 ( 0.00358, 0.01379) ** 7 1 0.00463 ( 0.00078, 0.00842) ** 1 B-berhoffi 0.00143 ( zero, 0.00344) ** 1 10 0.00003 ( zero, 0.00188) 10 B-arupensi 0.00661 ( 0.00230, 0.01093) ** 10 5 0.00390 ( 0.00042, 0.00734) ** 5 2 0.00003 ( zero, 0.00189) 2 4 0.00191 ( zero, 0.00445) ** 4 12 0.00006 ( zero, 0.00182) 12 6 0.00006 ( zero, infinity) 6 B-vinsonii 0.00292 ( 0.00007, 0.00578) ** 6 B-birtlesi 0.00069 ( zero, 0.00208) ** 12 B-grahamii 0.00144 ( zero, 0.00345) ** 4 B--doshiae 0.00003 ( zero, infinity) 2 B-henselae 0.00586 ( 0.00180, 0.00991) ** 5 B-elizabet 0.01031 ( 0.00490, 0.01570) ** 8 9 0.00762 ( 0.00260, 0.01270) ** 9 3 0.00962 ( 0.00413, 0.01508) ** 3 B--weissii 0.00113 ( zero, 0.00318) ** 3 B-spp-Deer 0.00327 ( 0.00010, 0.00645) ** 9 B-bacillif 0.01074 ( 0.00490, 0.01669) ** 11 A-tumefaci 0.06617 ( 0.05232, 0.08082) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 12: Empirical Base Frequencies: A 0.24647 C 0.22937 G 0.32030 T(U) 0.20387 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.477960) +B-quintana ! +--4 +B-arupensi ! ! ! ! ! ! +B-berhoffi ! +-11 ! ! ! ! +B-elizabet ! ! ! +--7 ! +--2 ! +B-grahamii ! ! +--6 +--9 ! ! ! +B-henselae ! ! ! ! +--1 ! ! +-10 +B-vinsonii ! ! ! ! ! ! +B--doshiae +-12 ! +--8 ! ! ! +B-birtlesi ! ! ! ! ! +B-clarridg ! ! ! +B-bacillif ! ! +B--weissii --3--5 ! +B-spp-Deer ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2914.47974 Examined 586 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 3 12 0.00491 ( 0.00101, 0.00876) ** 12 9 0.00231 ( zero, 0.00500) ** 9 4 0.00348 ( 0.00028, 0.00669) ** 4 B-quintana 0.00815 ( 0.00324, 0.01303) ** 4 11 0.00289 ( zero, 0.00590) ** 11 B-arupensi 0.00146 ( zero, 0.00348) ** 11 2 0.00003 ( zero, infinity) 2 B-berhoffi 0.00150 ( zero, 0.00353) ** 2 10 0.00146 ( zero, 0.00348) ** 10 6 0.00003 ( zero, 0.00162) 6 7 0.00219 ( zero, 0.00467) ** 7 B-elizabet 0.01169 ( 0.00603, 0.01749) ** 7 B-grahamii 0.00006 ( zero, 0.00181) 6 1 0.00146 ( zero, 0.00348) ** 1 B-henselae 0.00371 ( 0.00041, 0.00690) ** 1 B-vinsonii 0.00075 ( zero, 0.00220) ** 10 8 0.00006 ( zero, infinity) 8 B--doshiae 0.00071 ( zero, 0.00211) ** 8 B-birtlesi 0.00074 ( zero, 0.00218) ** 9 B-clarridg 0.00684 ( 0.00230, 0.01138) ** 12 B-bacillif 0.00739 ( 0.00267, 0.01207) ** 3 5 0.00247 ( zero, 0.00554) ** 5 B--weissii 0.00076 ( zero, 0.00222) ** 5 B-spp-Deer 0.00072 ( zero, 0.00213) ** 3 A-tumefaci 0.05826 ( 0.04517, 0.07178) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 13: Empirical Base Frequencies: A 0.25067 C 0.23017 G 0.29985 T(U) 0.21931 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.483923) +B-bacillif ! ! +B-spp-Deer ! +--6 ! ! +B--weissii --5--1 ! ! +B-clarridg ! ! ! ! +--2 +B-quintana ! ! ! ! ! ! +B-arupensi ! +--4 ! ! ! ! +B-elizabet ! ! ! ! ! +--3 +-10 +B-grahamii ! ! ! ! ! ! ! ! +--7 +B--doshiae ! ! ! ! +-12 ! ! ! ! ! ! +B-henselae ! +--8 +--9 +-11 ! ! ! +B-vinsonii ! ! ! ! ! +B-birtlesi ! ! ! +B-berhoffi ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3084.53615 Examined 722 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 5 B-bacillif 0.00537 ( 0.00128, 0.00946) ** 5 1 0.00467 ( 0.00073, 0.00862) ** 1 6 0.00486 ( 0.00096, 0.00876) ** 6 B-spp-Deer 0.00146 ( zero, 0.00350) ** 6 B--weissii 0.00003 ( zero, 0.00224) 1 2 0.00521 ( 0.00131, 0.00919) ** 2 B-clarridg 0.00989 ( 0.00441, 0.01530) ** 2 4 0.00459 ( 0.00076, 0.00845) ** 4 B-quintana 0.00906 ( 0.00387, 0.01427) ** 4 3 0.00438 ( 0.00059, 0.00812) ** 3 B-arupensi 0.00515 ( 0.00134, 0.00897) ** 3 8 0.00006 ( zero, 0.00179) 8 10 0.00217 ( zero, 0.00466) ** 10 B-elizabet 0.00592 ( 0.00180, 0.01001) ** 10 7 0.00143 ( zero, 0.00346) ** 7 B-grahamii 0.00003 ( zero, 0.00183) 7 9 0.00220 ( zero, 0.00469) ** 9 12 0.00003 ( zero, 0.00222) 12 B--doshiae 0.00006 ( zero, infinity) 12 11 0.00069 ( zero, 0.00209) ** 11 B-henselae 0.00368 ( 0.00045, 0.00689) ** 11 B-vinsonii 0.00295 ( 0.00005, 0.00583) ** 9 B-birtlesi 0.00365 ( 0.00044, 0.00685) ** 8 B-berhoffi 0.00145 ( zero, 0.00347) ** 5 A-tumefaci 0.06774 ( 0.05361, 0.08240) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 14: Empirical Base Frequencies: A 0.25278 C 0.23624 G 0.31552 T(U) 0.19546 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.474839) +B-birtlesi +--2 ! ! +B-elizabet ! +--4 +--5 +B-grahamii ! ! ! ! +B-vinsonii ! +--8 +-10 ! +B--doshiae ! ! +--6 ! ! +B-henselae ! ! ! ! +B-arupensi +--1 +--7 ! ! ! +B--weissii ! ! +-12 +--9 ! +B-spp-Deer ! ! ! ! ! +B-berhoffi +-11 ! ! ! +B-quintana ! ! ! +B-bacillif ! --3-B-clarridg ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3042.41039 Examined 1092 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 3 11 0.00376 ( 0.00034, 0.00717) ** 11 9 0.00509 ( 0.00125, 0.00896) ** 9 1 0.00077 ( zero, 0.00236) * 1 10 0.00292 ( 0.00007, 0.00578) ** 10 5 0.00365 ( 0.00046, 0.00685) ** 5 2 0.00003 ( zero, 0.00266) 2 B-birtlesi 0.00656 ( 0.00227, 0.01086) ** 2 4 0.00435 ( 0.00086, 0.00786) ** 4 B-elizabet 0.00585 ( 0.00180, 0.00990) ** 4 B-grahamii 0.00006 ( zero, 0.00201) 5 8 0.00003 ( zero, infinity) 8 B-vinsonii 0.00149 ( zero, 0.00352) ** 8 6 0.00151 ( zero, 0.00354) ** 6 B--doshiae 0.00006 ( zero, infinity) 6 B-henselae 0.00364 ( 0.00046, 0.00684) ** 10 7 0.00006 ( zero, infinity) 7 B-arupensi 0.00219 ( zero, 0.00467) ** 7 12 0.01100 ( 0.00542, 0.01656) ** 12 B--weissii 0.00146 ( zero, 0.00348) ** 12 B-spp-Deer 0.00003 ( zero, infinity) 1 B-berhoffi 0.00149 ( zero, 0.00352) ** 9 B-quintana 0.01020 ( 0.00484, 0.01561) ** 11 B-bacillif 0.01176 ( 0.00599, 0.01764) ** 3 B-clarridg 0.00447 ( 0.00080, 0.00819) ** 3 A-tumefaci 0.05842 ( 0.04510, 0.07178) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 15: Empirical Base Frequencies: A 0.22974 C 0.23222 G 0.33428 T(U) 0.20376 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.502655) +B-berhoffi +--5 ! ! +B-arupensi ! +--1 ! +B-quintana +--2 ! ! +B-bacillif ! ! ! ! ! ! +B-birtlesi ! +--8 +--7 ! ! ! ! +B-henselae ! ! ! +--3 ! ! ! ! +B-elizabet +--6 +--9 +-10 ! ! ! +B-grahamii ! ! ! ! ! ! +B-vinsonii ! ! +-11 ! ! +B--doshiae ! ! ! ! +B-spp-Deer ! +-12 ! +B--weissii ! --4-B-clarridg ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2972.16668 Examined 1976 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 4 6 0.00358 ( zero, 0.00713) ** 6 2 0.00353 ( 0.00026, 0.00680) ** 2 5 0.00003 ( zero, 0.00208) 5 B-berhoffi 0.00217 ( zero, 0.00465) ** 5 1 0.00074 ( zero, 0.00218) ** 1 B-arupensi 0.00220 ( zero, 0.00468) ** 1 B-quintana 0.01175 ( 0.00598, 0.01750) ** 2 8 0.00308 ( zero, 0.00618) ** 8 B-bacillif 0.00876 ( 0.00385, 0.01376) ** 8 9 0.00202 ( zero, 0.00464) ** 9 7 0.00006 ( zero, 0.00187) 7 B-birtlesi 0.00145 ( zero, 0.00346) ** 7 3 0.00147 ( zero, 0.00350) ** 3 B-henselae 0.00365 ( 0.00046, 0.00685) ** 3 10 0.00070 ( zero, 0.00209) ** 10 B-elizabet 0.00877 ( 0.00382, 0.01375) ** 10 B-grahamii 0.00006 ( zero, 0.00149) 9 11 0.00004 ( zero, infinity) 11 B-vinsonii 0.00146 ( zero, 0.00347) ** 11 B--doshiae 0.00070 ( zero, 0.00209) ** 6 12 0.00746 ( 0.00278, 0.01212) ** 12 B-spp-Deer 0.00003 ( zero, 0.00181) 12 B--weissii 0.00290 ( 0.00007, 0.00576) ** 4 B-clarridg 0.00782 ( 0.00285, 0.01281) ** 4 A-tumefaci 0.05829 ( 0.04521, 0.07176) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 16: Empirical Base Frequencies: A 0.23552 C 0.23264 G 0.34362 T(U) 0.18822 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.488020) +B-elizabet ! ! +B-berhoffi ! ! ! ! +B-grahamii +--3 ! +--9 ! ! ! ! +B-birtlesi ! ! ! ! ! ! ! ! +B-bacillif ! ! ! +--5 +--4 ! +--6 ! ! ! ! +B-spp-Deer ! ! ! ! +--2 +-11 ! ! ! ! ! ! +B--weissii ! ! +--7 +--8 ! ! ! ! ! ! +B-henselae ! ! ! ! ! ! ! +--1 ! +B--doshiae ! ! ! ! ! ! ! ! ! +B-vinsonii ! +-12 ! ! ! +B-arupensi ! ! ! +B-quintana ! -10-B-clarridg ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2896.02821 Examined 978 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 10 3 0.00780 ( 0.00293, 0.01271) ** 3 B-elizabet 0.00907 ( 0.00391, 0.01419) ** 3 6 0.00125 ( zero, 0.00333) * 6 B-berhoffi 0.00003 ( zero, infinity) 6 12 0.00216 ( zero, 0.00463) ** 12 1 0.00098 ( zero, 0.00284) ** 1 7 0.00294 ( zero, 0.00600) ** 7 5 0.00098 ( zero, 0.00284) ** 5 9 0.00097 ( zero, 0.00287) 9 B-grahamii 0.00219 ( zero, 0.00466) ** 9 B-birtlesi 0.00006 ( zero, 0.00164) 5 8 0.00072 ( zero, 0.00214) ** 8 2 0.00145 ( zero, 0.00348) ** 2 4 0.00556 ( 0.00153, 0.00961) ** 4 B-bacillif 0.00508 ( 0.00119, 0.00906) ** 4 11 0.00546 ( 0.00144, 0.00951) ** 11 B-spp-Deer 0.00142 ( zero, 0.00343) ** 11 B--weissii 0.00076 ( zero, 0.00222) ** 2 B-henselae 0.00293 ( 0.00006, 0.00581) ** 8 B--doshiae 0.00003 ( zero, infinity) 7 B-vinsonii 0.00003 ( zero, infinity) 1 B-arupensi 0.00221 ( zero, 0.00470) ** 12 B-quintana 0.00735 ( 0.00277, 0.01188) ** 10 B-clarridg 0.00651 ( 0.00187, 0.01106) ** 10 A-tumefaci 0.05245 ( 0.04011, 0.06529) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 17: Empirical Base Frequencies: A 0.23934 C 0.24327 G 0.28623 T(U) 0.23116 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.502557) +B-berhoffi ! ! +B-quintana ! +-10 ! ! +B-arupensi ! ! ! ! +B-clarridg --1--5 ! ! ! ! +B-henselae ! ! ! ! ! ! ! ! +B-birtlesi ! ! ! +--4 +-11 ! +--6 ! ! ! ! +B-elizabet ! ! ! ! +--8 +-12 ! ! ! ! ! ! +B-grahamii ! ! +--3 +--9 ! ! ! ! ! ! +B--doshiae ! ! ! ! ! ! ! ! ! +B-vinsonii ! +--2 ! ! ! +B-bacillif ! ! ! ! +B-spp-Deer ! +--7 ! +B--weissii ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2933.46923 Examined 896 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 1 B-berhoffi 0.00003 ( zero, 0.00180) 1 5 0.00311 ( 0.00012, 0.00617) ** 5 10 0.00146 ( zero, 0.00349) ** 10 B-quintana 0.00643 ( 0.00209, 0.01071) ** 10 B-arupensi 0.00095 ( zero, 0.00272) ** 5 6 0.00138 ( zero, 0.00359) ** 6 B-clarridg 0.01259 ( 0.00660, 0.01859) ** 6 2 0.00342 ( zero, 0.00686) ** 2 3 0.00372 ( 0.00028, 0.00717) ** 3 4 0.00505 ( 0.00097, 0.00910) ** 4 B-henselae 0.00410 ( 0.00064, 0.00760) ** 4 9 0.00348 ( 0.00014, 0.00682) ** 9 8 0.00003 ( zero, 0.00242) 8 11 0.00006 ( zero, 0.00158) 11 B-birtlesi 0.00003 ( zero, infinity) 11 12 0.00144 ( zero, 0.00346) ** 12 B-elizabet 0.00807 ( 0.00331, 0.01285) ** 12 B-grahamii 0.00006 ( zero, 0.00181) 8 B--doshiae 0.00003 ( zero, infinity) 9 B-vinsonii 0.00292 ( 0.00002, 0.00579) ** 3 B-bacillif 0.00301 ( zero, 0.00624) ** 2 7 0.00349 ( 0.00017, 0.00680) ** 7 B-spp-Deer 0.00003 ( zero, 0.00187) 7 B--weissii 0.00141 ( zero, 0.00342) ** 1 A-tumefaci 0.06099 ( 0.04763, 0.07473) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 18: Empirical Base Frequencies: A 0.25185 C 0.23545 G 0.30252 T(U) 0.21019 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.482640) +B-quintana +-12 ! ! +B-clarridg ! +--7 ! ! +B--weissii ! +--6 ! +B-spp-Deer ! +--3 +B-elizabet ! ! ! ! ! ! +B--doshiae ! ! +--2 ! ! ! ! ! +--5 +B-grahamii ! ! ! ! ! ! +--9 ! ! ! ! ! +--8 +B-henselae ! ! ! +-11 ! ! +--4 ! +B-birtlesi ! ! ! ! ! +B-vinsonii ! ! ! ! +B-arupensi ! +--1 ! +B-berhoffi ! -10-B-bacillif ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2948.63046 Examined 1250 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 10 3 0.00441 ( 0.00034, 0.00852) ** 3 12 0.00442 ( 0.00086, 0.00794) ** 12 B-quintana 0.00589 ( 0.00166, 0.01011) ** 12 7 0.00233 ( zero, 0.00529) ** 7 B-clarridg 0.00644 ( 0.00211, 0.01075) ** 7 6 0.00805 ( 0.00328, 0.01282) ** 6 B--weissii 0.00166 ( zero, 0.00390) ** 6 B-spp-Deer 0.00202 ( zero, 0.00448) ** 3 4 0.00144 ( zero, 0.00383) * 4 2 0.00219 ( zero, 0.00467) ** 2 B-elizabet 0.00657 ( 0.00229, 0.01087) ** 2 11 0.00069 ( zero, 0.00210) ** 11 5 0.00006 ( zero, infinity) 5 B--doshiae 0.00075 ( zero, 0.00220) ** 5 8 0.00006 ( zero, infinity) 8 9 0.00069 ( zero, 0.00208) ** 9 B-grahamii 0.00006 ( zero, infinity) 9 B-henselae 0.00364 ( 0.00046, 0.00683) ** 8 B-birtlesi 0.00006 ( zero, infinity) 11 B-vinsonii 0.00507 ( 0.00136, 0.00886) ** 4 1 0.00006 ( zero, 0.00156) 1 B-arupensi 0.00292 ( 0.00007, 0.00579) ** 1 B-berhoffi 0.00218 ( zero, 0.00465) ** 10 B-bacillif 0.00733 ( 0.00249, 0.01218) ** 10 A-tumefaci 0.05956 ( 0.04633, 0.07313) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 19: Empirical Base Frequencies: A 0.25599 C 0.23661 G 0.30080 T(U) 0.20659 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.478992) +B-birtlesi +--9 ! ! +B-grahamii ! +--3 +--1 ! +B-vinsonii ! ! +--7 ! ! +B--doshiae +-12 ! ! ! +B-henselae ! ! ! +B-elizabet ! +-11 +B-quintana ! ! ! ! ! +--8 +B--weissii ! ! ! ! +--6 ! ! ! +--5 +B-spp-Deer +--2 +--4 ! ! ! ! +B-bacillif ! ! ! ! ! +B-clarridg ! ! ! +B-arupensi ! -10-B-berhoffi ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3122.56967 Examined 1772 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 10 2 0.00219 ( zero, 0.00467) ** 2 11 0.00003 ( zero, infinity) 11 12 0.00548 ( 0.00147, 0.00953) ** 12 1 0.00003 ( zero, 0.00183) 1 9 0.00181 ( zero, 0.00425) ** 9 B-birtlesi 0.00075 ( zero, 0.00220) ** 9 3 0.00003 ( zero, infinity) 3 B-grahamii 0.00075 ( zero, 0.00220) ** 3 7 0.00003 ( zero, infinity) 7 B-vinsonii 0.00146 ( zero, 0.00348) ** 7 B--doshiae 0.00076 ( zero, 0.00222) ** 1 B-henselae 0.00513 ( 0.00135, 0.00893) ** 12 B-elizabet 0.01032 ( 0.00491, 0.01572) ** 11 4 0.00644 ( 0.00205, 0.01085) ** 4 8 0.00167 ( zero, 0.00402) ** 8 B-quintana 0.00627 ( 0.00186, 0.01070) ** 8 5 0.00731 ( 0.00247, 0.01218) ** 5 6 0.01118 ( 0.00545, 0.01697) ** 6 B--weissii 0.00003 ( zero, 0.00223) 6 B-spp-Deer 0.00440 ( 0.00085, 0.00791) ** 5 B-bacillif 0.01503 ( 0.00833, 0.02176) ** 4 B-clarridg 0.00979 ( 0.00440, 0.01517) ** 2 B-arupensi 0.00149 ( zero, 0.00353) ** 10 B-berhoffi 0.00003 ( zero, 0.00169) 10 A-tumefaci 0.06113 ( 0.04771, 0.07486) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 20: Empirical Base Frequencies: A 0.23495 C 0.22751 G 0.30562 T(U) 0.23192 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.502501) +B-arupensi ! ! +B-clarridg ! +-10 ! ! +B-quintana ! ! --3--7 +B-berhoffi ! ! ! ! ! ! +B-elizabet ! +-11 ! ! ! +--4 +B-spp-Deer ! ! ! ! +--1 ! ! ! +--2 +B--weissii ! +--5 ! ! ! +B-bacillif ! ! ! ! +B-grahamii ! +-12 ! ! +B-birtlesi ! +--8 ! ! +B-vinsonii ! +--6 ! ! +B-henselae ! +--9 ! +B--doshiae ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3158.84951 Examined 1762 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 3 B-arupensi 0.00231 ( zero, 0.00518) ** 3 7 0.00361 ( 0.00020, 0.00705) ** 7 10 0.00480 ( 0.00095, 0.00867) ** 10 B-clarridg 0.01247 ( 0.00655, 0.01852) ** 10 B-quintana 0.01221 ( 0.00622, 0.01819) ** 7 11 0.00003 ( zero, 0.00171) 11 B-berhoffi 0.00141 ( zero, 0.00341) ** 11 5 0.00137 ( zero, 0.00374) ** 5 4 0.00289 ( 0.00004, 0.00577) ** 4 B-elizabet 0.00737 ( 0.00264, 0.01208) ** 4 2 0.00281 ( zero, 0.00601) ** 2 1 0.01103 ( 0.00546, 0.01667) ** 1 B-spp-Deer 0.00114 ( zero, 0.00308) ** 1 B--weissii 0.00105 ( zero, 0.00292) ** 2 B-bacillif 0.00754 ( 0.00277, 0.01227) ** 5 12 0.00235 ( zero, 0.00519) ** 12 B-grahamii 0.00070 ( zero, 0.00210) ** 12 8 0.00070 ( zero, 0.00211) * 8 B-birtlesi 0.00291 ( 0.00005, 0.00577) ** 8 6 0.00006 ( zero, 0.00181) 6 B-vinsonii 0.00219 ( zero, 0.00467) ** 6 9 0.00217 ( zero, 0.00464) ** 9 B-henselae 0.00516 ( 0.00130, 0.00893) ** 9 B--doshiae 0.00006 ( zero, infinity) 3 A-tumefaci 0.06651 ( 0.05249, 0.08090) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 21: Empirical Base Frequencies: A 0.26857 C 0.21955 G 0.30449 T(U) 0.20739 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.451832) +B--weissii +--6 +--4 +B-spp-Deer ! ! ! +B-bacillif ! +--5 +B-quintana ! ! ! ! ! ! +B-arupensi ! ! ! ! ! ! ! ! +B-henselae ! +--8 ! +--9 ! ! +-12 +--3 +B--doshiae ! ! ! ! ! ! ! ! ! ! +-10 +B-vinsonii ! ! ! ! ! ! ! ! ! +--2 +B-birtlesi ! +--1 ! ! ! ! +B-elizabet ! ! +--7 ! ! +B-grahamii ! ! ! +B-berhoffi ! -11-B-clarridg ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3041.59493 Examined 570 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 5 0.00664 ( 0.00207, 0.01129) ** 5 4 0.00627 ( 0.00185, 0.01070) ** 4 6 0.00597 ( 0.00164, 0.01037) ** 6 B--weissii 0.00003 ( zero, infinity) 6 B-spp-Deer 0.00368 ( 0.00046, 0.00690) ** 4 B-bacillif 0.00770 ( 0.00277, 0.01267) ** 5 8 0.00215 ( zero, 0.00490) ** 8 B-quintana 0.00837 ( 0.00328, 0.01343) ** 8 1 0.00350 ( 0.00000, 0.00701) ** 1 12 0.00003 ( zero, 0.00187) 12 B-arupensi 0.00512 ( 0.00138, 0.00897) ** 12 2 0.00294 ( 0.00007, 0.00582) ** 2 10 0.00139 ( zero, 0.00340) ** 10 3 0.00006 ( zero, 0.00219) 3 9 0.00075 ( zero, 0.00219) ** 9 B-henselae 0.00587 ( 0.00183, 0.00995) ** 9 B--doshiae 0.00006 ( zero, infinity) 3 B-vinsonii 0.00294 ( 0.00007, 0.00581) ** 10 B-birtlesi 0.00290 ( 0.00004, 0.00578) ** 2 7 0.00148 ( zero, 0.00352) ** 7 B-elizabet 0.00366 ( 0.00047, 0.00688) ** 7 B-grahamii 0.00003 ( zero, infinity) 1 B-berhoffi 0.00075 ( zero, 0.00220) ** 11 B-clarridg 0.00809 ( 0.00299, 0.01319) ** 11 A-tumefaci 0.05703 ( 0.04410, 0.07054) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 22: Empirical Base Frequencies: A 0.24096 C 0.24001 G 0.30651 T(U) 0.21253 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.496767) +B-clarridg ! ! +B-arupensi ! ! ! ! +B-elizabet ! ! +-11 ! +--5 ! +B-grahamii ! ! ! +-10 ! ! ! ! ! +B-birtlesi ! ! ! ! +--6 ! ! ! ! ! +B--doshiae ! ! +--1 +--9 ! +--7 ! ! +B-henselae ! ! ! ! +--8 ! ! ! ! +B-vinsonii ! ! ! ! ! +--2 ! +B-berhoffi ! ! ! ! ! ! ! +B-quintana ! ! ! -12--4 ! +B--weissii ! ! +--3 ! ! +B-spp-Deer ! ! ! +B-bacillif ! +----A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3107.57576 Examined 582 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 12 B-clarridg 0.00641 ( 0.00190, 0.01095) ** 12 4 0.00636 ( 0.00184, 0.01094) ** 4 2 0.00243 ( zero, 0.00533) ** 2 7 0.00148 ( zero, 0.00401) ** 7 5 0.00210 ( zero, 0.00457) ** 5 B-arupensi 0.00439 ( 0.00086, 0.00791) ** 5 1 0.00006 ( zero, 0.00162) 1 10 0.00291 ( 0.00007, 0.00576) ** 10 11 0.00076 ( zero, 0.00224) ** 11 B-elizabet 0.00730 ( 0.00278, 0.01183) ** 11 B-grahamii 0.00003 ( zero, 0.00157) 10 6 0.00133 ( zero, 0.00335) ** 6 B-birtlesi 0.00088 ( zero, 0.00289) 6 9 0.00067 ( zero, 0.00268) 9 B--doshiae 0.00006 ( zero, infinity) 9 8 0.00291 ( 0.00006, 0.00576) ** 8 B-henselae 0.00657 ( 0.00229, 0.01087) ** 8 B-vinsonii 0.00150 ( zero, 0.00354) ** 1 B-berhoffi 0.00220 ( zero, 0.00470) ** 7 B-quintana 0.00812 ( 0.00332, 0.01292) ** 2 3 0.00932 ( 0.00414, 0.01451) ** 3 B--weissii 0.00074 ( zero, 0.00218) ** 3 B-spp-Deer 0.00003 ( zero, 0.00155) 4 B-bacillif 0.00936 ( 0.00415, 0.01461) ** 12 A-tumefaci 0.07798 ( 0.06288, 0.09393) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 23: Empirical Base Frequencies: A 0.26489 C 0.21167 G 0.31752 T(U) 0.20591 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.441858) +B-clarridg ! +--8 +B--weissii ! ! +-12 ! +-11 +B-spp-Deer ! ! ! +B-quintana ! ! +B-berhoffi +--4 ! ! ! ! +B-grahamii ! ! ! ! ! ! +--6 +-10 +B-vinsonii ! ! ! ! ! ! +--5 ! ! ! ! ! ! ! ! +B--doshiae ! ! ! ! ! +--3 +--9 ! ! ! +--1 ! +B-henselae ! +--7 ! ! ! ! ! +B-birtlesi ! ! ! ! ! +B-elizabet ! ! ! +B-arupensi ! --2-B-bacillif ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3029.34688 Examined 1248 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 2 4 0.00547 ( 0.00127, 0.00963) ** 4 8 0.00294 ( 0.00002, 0.00589) ** 8 B-clarridg 0.01280 ( 0.00667, 0.01895) ** 8 11 0.00218 ( zero, 0.00488) ** 11 12 0.00679 ( 0.00237, 0.01126) ** 12 B--weissii 0.00139 ( zero, 0.00343) ** 12 B-spp-Deer 0.00084 ( zero, 0.00246) ** 11 B-quintana 0.00644 ( 0.00201, 0.01081) ** 4 7 0.00140 ( zero, 0.00383) * 7 6 0.00003 ( zero, 0.00183) 6 B-berhoffi 0.00219 ( zero, 0.00467) ** 6 1 0.00274 ( zero, 0.00559) ** 1 10 0.00088 ( zero, 0.00260) ** 10 B-grahamii 0.00075 ( zero, 0.00220) ** 10 3 0.00069 ( zero, 0.00209) * 3 5 0.00006 ( zero, 0.00176) 5 B-vinsonii 0.00219 ( zero, 0.00466) ** 5 9 0.00141 ( zero, 0.00340) ** 9 B--doshiae 0.00003 ( zero, infinity) 9 B-henselae 0.00731 ( 0.00279, 0.01185) ** 3 B-birtlesi 0.00216 ( zero, 0.00463) ** 1 B-elizabet 0.00659 ( 0.00228, 0.01090) ** 7 B-arupensi 0.00293 ( 0.00007, 0.00580) ** 2 B-bacillif 0.00410 ( 0.00036, 0.00791) ** 2 A-tumefaci 0.06740 ( 0.05341, 0.08211) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 24: Empirical Base Frequencies: A 0.23716 C 0.24456 G 0.30560 T(U) 0.21268 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.503736) +B-elizabet ! ! +B-birtlesi ! +--5 ! ! ! +B-vinsonii ! ! +-11 ! ! +B--doshiae ! ! ! ! +B--weissii ! ! +--1 ! +--2 ! +B-spp-Deer ! ! ! +--8 ! ! ! ! ! +B-quintana ! ! ! ! ! +-12 ! ! ! +--4 +-10 +B-bacillif ! ! ! ! ! ! ! +--6 ! ! ! +B-clarridg ! ! ! +--3 ! ! ! ! ! +B-henselae ! ! ! ! --7--9 ! +B-arupensi ! ! ! ! ! +B-berhoffi ! ! ! +B-grahamii ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2926.07664 Examined 826 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 B-elizabet 0.00336 ( 0.00004, 0.00669) ** 7 9 0.00478 ( 0.00099, 0.00862) ** 9 6 0.00156 ( zero, 0.00372) ** 6 2 0.00076 ( zero, 0.00222) ** 2 5 0.00072 ( zero, 0.00214) * 5 B-birtlesi 0.00146 ( zero, 0.00347) ** 5 11 0.00003 ( zero, infinity) 11 B-vinsonii 0.00074 ( zero, 0.00218) ** 11 B--doshiae 0.00003 ( zero, infinity) 2 3 0.00003 ( zero, 0.00182) 3 4 0.00145 ( zero, 0.00348) ** 4 8 0.00215 ( zero, 0.00464) ** 8 1 0.00519 ( 0.00131, 0.00899) ** 1 B--weissii 0.00145 ( zero, 0.00348) ** 1 B-spp-Deer 0.00146 ( zero, 0.00348) ** 8 10 0.00075 ( zero, 0.00221) ** 10 12 0.00290 ( 0.00000, 0.00580) ** 12 B-quintana 0.01039 ( 0.00490, 0.01581) ** 12 B-bacillif 0.00736 ( 0.00280, 0.01197) ** 10 B-clarridg 0.00959 ( 0.00437, 0.01479) ** 4 B-henselae 0.00294 ( 0.00005, 0.00581) ** 3 B-arupensi 0.00147 ( zero, 0.00351) ** 6 B-berhoffi 0.00222 ( zero, 0.00471) ** 9 B-grahamii 0.00066 ( zero, 0.00215) 7 A-tumefaci 0.06460 ( 0.05069, 0.07877) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 25: Empirical Base Frequencies: A 0.23961 C 0.22926 G 0.31940 T(U) 0.21173 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.489850) +B-berhoffi ! ! +B-arupensi ! +--8 ! ! +B-vinsonii ! +-12 +--1 ! ! +B-birtlesi ! ! ! +--9 ! ! +--5 +B--doshiae ! ! ! ! ! ! ! ! +B-henselae ! ! ! +--4 ! +--2 ! +B--weissii +--3 ! +-11 ! ! ! +B-spp-Deer ! ! ! ! ! ! +B-grahamii +--7 ! +-10 ! ! ! +B-elizabet ! ! ! ! ! +B-quintana ! ! ! +B-clarridg ! --6-B-bacillif ! +----A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3195.32822 Examined 1228 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 6 7 0.00804 ( 0.00289, 0.01320) ** 7 3 0.00368 ( 0.00038, 0.00698) ** 3 1 0.00303 ( 0.00006, 0.00601) ** 1 B-berhoffi 0.00218 ( zero, 0.00465) ** 1 2 0.00076 ( zero, 0.00224) ** 2 5 0.00222 ( zero, 0.00470) ** 5 12 0.00142 ( zero, 0.00344) ** 12 8 0.00145 ( zero, 0.00347) ** 8 B-arupensi 0.00364 ( 0.00045, 0.00684) ** 8 B-vinsonii 0.00144 ( zero, 0.00345) ** 12 9 0.00003 ( zero, 0.00194) 9 B-birtlesi 0.00290 ( 0.00007, 0.00575) ** 9 B--doshiae 0.00075 ( zero, 0.00220) ** 5 4 0.00437 ( 0.00091, 0.00792) ** 4 B-henselae 0.00144 ( zero, 0.00348) ** 4 11 0.01027 ( 0.00491, 0.01567) ** 11 B--weissii 0.00149 ( zero, 0.00352) ** 11 B-spp-Deer 0.00072 ( zero, 0.00215) ** 2 10 0.00148 ( zero, 0.00352) ** 10 B-grahamii 0.00144 ( zero, 0.00346) ** 10 B-elizabet 0.01099 ( 0.00545, 0.01657) ** 3 B-quintana 0.00794 ( 0.00317, 0.01270) ** 7 B-clarridg 0.01235 ( 0.00638, 0.01832) ** 6 B-bacillif 0.00618 ( 0.00151, 0.01075) ** 6 A-tumefaci 0.07620 ( 0.06118, 0.09179) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 26: Empirical Base Frequencies: A 0.25403 C 0.23026 G 0.30384 T(U) 0.21188 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.477031) +B-clarridg ! ! +B-quintana ! +-12 ! +--5 +B-arupensi ! ! ! ! ! +B-berhoffi ! ! ! ! +B--doshiae ! +--8 +-10 ! ! ! ! ! +B-vinsonii ! ! ! +--6 +--1 ! ! ! ! ! +B-henselae ! ! ! ! ! ! ! +-11 +B-birtlesi --4--3 ! ! ! ! +B-grahamii ! ! +--2 ! ! +B-elizabet ! ! ! ! +B-spp-Deer ! ! +--9 ! +--7 +B--weissii ! ! ! +B-bacillif ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3032.25317 Examined 1242 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 4 B-clarridg 0.00357 ( 0.00027, 0.00688) ** 4 3 0.00526 ( 0.00130, 0.00924) ** 3 8 0.00140 ( zero, 0.00344) ** 8 5 0.00006 ( zero, 0.00189) 5 12 0.00146 ( zero, 0.00349) ** 12 B-quintana 0.00955 ( 0.00436, 0.01475) ** 12 B-arupensi 0.00220 ( zero, 0.00470) ** 5 B-berhoffi 0.00151 ( zero, 0.00356) ** 8 11 0.00512 ( 0.00131, 0.00892) ** 11 6 0.00075 ( zero, 0.00221) * 6 10 0.00006 ( zero, 0.00181) 10 B--doshiae 0.00003 ( zero, infinity) 10 1 0.00074 ( zero, 0.00219) ** 1 B-vinsonii 0.00219 ( zero, 0.00468) ** 1 B-henselae 0.00588 ( 0.00182, 0.00995) ** 6 B-birtlesi 0.00291 ( 0.00005, 0.00577) ** 11 2 0.00042 ( zero, 0.00185) 2 B-grahamii 0.00031 ( zero, 0.00174) 2 B-elizabet 0.01031 ( 0.00490, 0.01570) ** 3 7 0.00467 ( 0.00095, 0.00841) ** 7 9 0.00580 ( 0.00170, 0.00990) ** 9 B-spp-Deer 0.00076 ( zero, 0.00222) ** 9 B--weissii 0.00075 ( zero, 0.00219) ** 7 B-bacillif 0.01097 ( 0.00533, 0.01663) ** 4 A-tumefaci 0.06405 ( 0.05026, 0.07822) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 27: Empirical Base Frequencies: A 0.23427 C 0.23570 G 0.30056 T(U) 0.22947 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.504786) +B-clarridg ! ! +B-elizabet ! ! -11-10 +B-grahamii ! ! ! ! ! ! +B-quintana ! +--5 +-12 ! ! ! +B-berhoffi ! ! ! ! +--4 +B-arupensi ! ! ! ! ! ! +B-vinsonii ! ! ! ! ! +--1 +--8 +B--doshiae ! ! ! ! ! ! ! ! +--9 +B-henselae ! ! ! ! ! ! ! ! +--3 +B--weissii ! +--7 ! +--6 ! ! +--2 +B-spp-Deer ! ! ! ! ! +B-bacillif ! ! ! +B-birtlesi ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2942.78728 Examined 674 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 B-clarridg 0.00580 ( 0.00166, 0.00995) ** 11 10 0.00443 ( 0.00084, 0.00812) ** 10 B-elizabet 0.00296 ( 0.00002, 0.00583) ** 10 5 0.00220 ( zero, 0.00470) ** 5 B-grahamii 0.00072 ( zero, 0.00215) * 5 4 0.00072 ( zero, 0.00215) ** 4 12 0.00221 ( zero, 0.00471) ** 12 B-quintana 0.00952 ( 0.00436, 0.01471) ** 12 B-berhoffi 0.00075 ( zero, 0.00221) * 4 1 0.00072 ( zero, 0.00213) ** 1 B-arupensi 0.00220 ( zero, 0.00470) ** 1 7 0.00068 ( zero, 0.00209) * 7 8 0.00003 ( zero, infinity) 8 B-vinsonii 0.00070 ( zero, 0.00210) ** 8 9 0.00218 ( zero, 0.00466) ** 9 B--doshiae 0.00003 ( zero, infinity) 9 3 0.00352 ( 0.00034, 0.00673) ** 3 B-henselae 0.00307 ( 0.00006, 0.00606) ** 3 2 0.00515 ( 0.00132, 0.00898) ** 2 6 0.00237 ( zero, 0.00500) ** 6 B--weissii 0.00003 ( zero, infinity) 6 B-spp-Deer 0.00141 ( zero, 0.00341) ** 2 B-bacillif 0.01237 ( 0.00648, 0.01837) ** 7 B-birtlesi 0.00292 ( 0.00007, 0.00577) ** 11 A-tumefaci 0.06213 ( 0.04872, 0.07616) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 28: Empirical Base Frequencies: A 0.25002 C 0.22249 G 0.32482 T(U) 0.20267 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.465594) +B-berhoffi ! ! +B-birtlesi ! +--2 ! ! ! +B-grahamii ! ! +--8 ! +--7 +B-elizabet ! ! ! ! ! ! +B-vinsonii ! ! +-12 ! ! +B--doshiae -10--1 ! ! +B-arupensi ! ! ! ! ! ! +B-clarridg ! ! ! +--4 ! +--5 ! ! +B-bacillif ! ! ! +-11 ! ! +--6 ! +B-spp-Deer ! ! ! ! +--9 ! ! ! ! +B--weissii ! +--3 ! ! ! +B-quintana ! ! ! +B-henselae ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3115.26022 Examined 1030 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 10 B-berhoffi 0.00003 ( zero, 0.00181) 10 1 0.00220 ( zero, 0.00468) ** 1 7 0.00584 ( 0.00179, 0.00990) ** 7 2 0.00003 ( zero, 0.00188) 2 B-birtlesi 0.00146 ( zero, 0.00348) ** 2 8 0.00142 ( zero, 0.00342) ** 8 B-grahamii 0.00006 ( zero, infinity) 8 B-elizabet 0.01100 ( 0.00548, 0.01661) ** 7 12 0.00003 ( zero, infinity) 12 B-vinsonii 0.00142 ( zero, 0.00342) ** 12 B--doshiae 0.00220 ( zero, 0.00468) ** 1 5 0.00003 ( zero, infinity) 5 B-arupensi 0.00371 ( 0.00045, 0.00693) ** 5 3 0.00438 ( 0.00088, 0.00789) ** 3 6 0.00003 ( zero, 0.00158) 6 4 0.00302 ( 0.00004, 0.00600) ** 4 B-clarridg 0.00952 ( 0.00428, 0.01474) ** 4 11 0.00549 ( 0.00143, 0.00955) ** 11 B-bacillif 0.00853 ( 0.00355, 0.01356) ** 11 9 0.00517 ( 0.00124, 0.00906) ** 9 B-spp-Deer 0.00363 ( 0.00041, 0.00683) ** 9 B--weissii 0.00003 ( zero, 0.00256) 6 B-quintana 0.01251 ( 0.00658, 0.01849) ** 3 B-henselae 0.00293 ( 0.00007, 0.00580) ** 10 A-tumefaci 0.07156 ( 0.05699, 0.08655) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 29: Empirical Base Frequencies: A 0.22737 C 0.23526 G 0.32005 T(U) 0.21732 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.511209) +B-arupensi ! ! +B-clarridg ! +--8 ! ! ! +B-bacillif ! ! +-11 +--6 +--3 +B-quintana ! ! ! ! ! ! ! ! +B-spp-Deer ! ! ! +-10 ! ! ! +B--weissii ! ! ! ! +--2 +B-vinsonii ! ! +-12 ! ! ! ! +B-birtlesi ! ! ! +--5 ! ! +--1 ! +B-grahamii ! ! ! ! +--7 ! ! ! ! +B-elizabet ! +--4 ! ! ! +B--doshiae ! ! ! +B-henselae ! --9-B-berhoffi ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2882.00959 Examined 542 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 9 6 0.00150 ( zero, 0.00358) ** 6 B-arupensi 0.00070 ( zero, 0.00210) ** 6 2 0.00076 ( zero, 0.00225) ** 2 3 0.00169 ( zero, 0.00402) ** 3 8 0.00173 ( zero, 0.00416) ** 8 B-clarridg 0.01179 ( 0.00591, 0.01772) ** 8 11 0.00452 ( 0.00072, 0.00826) ** 11 B-bacillif 0.01066 ( 0.00507, 0.01627) ** 11 B-quintana 0.00522 ( 0.00120, 0.00927) ** 3 10 0.00565 ( 0.00154, 0.00969) ** 10 B-spp-Deer 0.00075 ( zero, 0.00220) ** 10 B--weissii 0.00076 ( zero, 0.00222) ** 2 4 0.00501 ( 0.00113, 0.00879) ** 4 1 0.00087 ( zero, 0.00255) ** 1 12 0.00084 ( zero, 0.00245) ** 12 B-vinsonii 0.00141 ( zero, 0.00342) ** 12 5 0.00003 ( zero, 0.00166) 5 B-birtlesi 0.00147 ( zero, 0.00349) ** 5 7 0.00142 ( zero, 0.00342) ** 7 B-grahamii 0.00003 ( zero, infinity) 7 B-elizabet 0.00808 ( 0.00331, 0.01285) ** 1 B--doshiae 0.00003 ( zero, infinity) 4 B-henselae 0.00222 ( zero, 0.00472) ** 9 B-berhoffi 0.00003 ( zero, 0.00176) 9 A-tumefaci 0.05300 ( 0.04070, 0.06584) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 30: Empirical Base Frequencies: A 0.24205 C 0.24266 G 0.29780 T(U) 0.21748 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.498546) +B-bacillif ! ! +B-spp-Deer ! +--4 ! ! +B--weissii ! ! ! ! +B-arupensi ! ! ! ! ! ! +B-elizabet ! ! +--3 ! ! ! ! ! ! +B--doshiae ! ! ! ! ! +-12 -11--9 ! +--5 +--1 +B-henselae ! ! ! ! ! ! ! ! +--2 ! +--7 +B-vinsonii ! ! ! ! ! ! ! ! ! ! ! +-10 +B-birtlesi ! ! ! ! ! ! ! +--8 ! +B-grahamii ! ! ! ! ! ! ! ! ! +B-berhoffi ! +--6 ! ! ! +B-quintana ! ! ! +B-clarridg ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3102.58353 Examined 2124 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 B-bacillif 0.00694 ( 0.00233, 0.01157) ** 11 9 0.00428 ( 0.00041, 0.00812) ** 9 4 0.00664 ( 0.00215, 0.01108) ** 4 B-spp-Deer 0.00290 ( 0.00006, 0.00576) ** 4 B--weissii 0.00006 ( zero, 0.00211) 9 6 0.00461 ( 0.00064, 0.00859) ** 6 8 0.00511 ( 0.00121, 0.00894) ** 8 2 0.00260 ( zero, 0.00557) ** 2 3 0.00006 ( zero, infinity) 3 B-arupensi 0.00292 ( 0.00009, 0.00579) ** 3 5 0.00161 ( zero, 0.00382) ** 5 B-elizabet 0.01315 ( 0.00698, 0.01926) ** 5 10 0.00147 ( zero, 0.00350) ** 10 7 0.00083 ( zero, 0.00248) ** 7 1 0.00006 ( zero, 0.00180) 1 12 0.00147 ( zero, 0.00349) ** 12 B--doshiae 0.00006 ( zero, infinity) 12 B-henselae 0.00511 ( 0.00134, 0.00890) ** 1 B-vinsonii 0.00219 ( zero, 0.00466) ** 7 B-birtlesi 0.00219 ( zero, 0.00466) ** 10 B-grahamii 0.00059 ( zero, 0.00202) 2 B-berhoffi 0.00144 ( zero, 0.00345) ** 8 B-quintana 0.00550 ( 0.00140, 0.00959) ** 6 B-clarridg 0.01092 ( 0.00529, 0.01657) ** 11 A-tumefaci 0.06610 ( 0.05222, 0.08067) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 31: Empirical Base Frequencies: A 0.25167 C 0.22161 G 0.31744 T(U) 0.20928 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.468390) +B-clarridg ! ! +B-bacillif ! +--8 ! ! ! +B-spp-Deer ! ! +--4 ! ! +B--weissii ! ! ! ! +B-elizabet -11--3 +--6 ! ! ! +B-grahamii ! ! ! ! ! +--5 +B-vinsonii ! ! ! ! +--9 ! ! ! ! ! ! +B--doshiae ! ! ! +--7 +-12 ! +--1 ! +B-henselae ! ! ! ! ! +B-birtlesi ! ! ! ! +B-arupensi ! +--2 ! ! +B-quintana ! +-10 ! +B-berhoffi ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3025.94482 Examined 1866 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 B-clarridg 0.00649 ( 0.00210, 0.01097) ** 11 3 0.00381 ( 0.00021, 0.00743) ** 3 8 0.00478 ( 0.00096, 0.00859) ** 8 B-bacillif 0.00884 ( 0.00361, 0.01402) ** 8 4 0.00722 ( 0.00257, 0.01191) ** 4 B-spp-Deer 0.00138 ( zero, 0.00340) ** 4 B--weissii 0.00082 ( zero, 0.00242) ** 3 1 0.00274 ( zero, 0.00575) ** 1 5 0.00518 ( 0.00118, 0.00908) ** 5 6 0.00223 ( zero, 0.00473) ** 6 B-elizabet 0.00955 ( 0.00437, 0.01476) ** 6 B-grahamii 0.00006 ( zero, 0.00181) 5 7 0.00067 ( zero, 0.00206) * 7 9 0.00003 ( zero, 0.00188) 9 B-vinsonii 0.00003 ( zero, infinity) 9 12 0.00075 ( zero, 0.00220) ** 12 B--doshiae 0.00003 ( zero, infinity) 12 B-henselae 0.00512 ( 0.00134, 0.00892) ** 7 B-birtlesi 0.00365 ( 0.00045, 0.00685) ** 1 2 0.00072 ( zero, 0.00256) 2 B-arupensi 0.00291 ( 0.00007, 0.00578) ** 2 10 0.00003 ( zero, 0.00232) 10 B-quintana 0.00953 ( 0.00436, 0.01473) ** 10 B-berhoffi 0.00003 ( zero, infinity) 11 A-tumefaci 0.06580 ( 0.05192, 0.08031) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 32: Empirical Base Frequencies: A 0.24941 C 0.23018 G 0.31742 T(U) 0.20299 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.475259) +B-clarridg +-11 +--8 +B-quintana ! ! +--2 +B-bacillif ! ! ! ! +B-spp-Deer ! +--4 +--3 +B--weissii ! ! ! ! +B-arupensi ! ! ! ! +--5 +B--doshiae ! ! ! ! ! ! +B-elizabet ! +--6 +--9 ! ! ! +B-grahamii ! ! +-12 ! ! ! ! +B-vinsonii ! +--7 +--1 ! ! +B-henselae ! ! ! +B-birtlesi ! -10-B-berhoffi ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3043.83026 Examined 810 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 10 3 0.00151 ( zero, 0.00359) ** 3 2 0.00327 ( zero, 0.00659) ** 2 8 0.00270 ( zero, 0.00571) ** 8 11 0.00311 ( zero, 0.00648) ** 11 B-clarridg 0.01416 ( 0.00777, 0.02068) ** 11 B-quintana 0.00841 ( 0.00336, 0.01349) ** 8 B-bacillif 0.01133 ( 0.00537, 0.01723) ** 2 4 0.00699 ( 0.00238, 0.01162) ** 4 B-spp-Deer 0.00222 ( zero, 0.00469) ** 4 B--weissii 0.00072 ( zero, 0.00215) ** 3 5 0.00003 ( zero, 0.00181) 5 B-arupensi 0.00293 ( 0.00007, 0.00581) ** 5 6 0.00287 ( 0.00007, 0.00572) ** 6 B--doshiae 0.00075 ( zero, 0.00219) ** 6 7 0.00003 ( zero, 0.00180) 7 12 0.00003 ( zero, 0.00187) 12 9 0.00138 ( zero, 0.00337) ** 9 B-elizabet 0.00582 ( 0.00181, 0.00987) ** 9 B-grahamii 0.00003 ( zero, 0.00186) 12 1 0.00138 ( zero, 0.00337) ** 1 B-vinsonii 0.00144 ( zero, 0.00346) ** 1 B-henselae 0.00221 ( zero, 0.00469) ** 7 B-birtlesi 0.00146 ( zero, 0.00348) ** 10 B-berhoffi 0.00006 ( zero, 0.00166) 10 A-tumefaci 0.07201 ( 0.05757, 0.08718) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 33: Empirical Base Frequencies: A 0.25062 C 0.21818 G 0.30556 T(U) 0.22564 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.479731) +B-clarridg ! ! +B-berhoffi ! ! ! ! +B-grahamii ! ! ! ! ! +--8 +B--weissii ! ! ! ! +--7 ! ! ! +--1 +B-spp-Deer ! +--6 ! ! ! ! ! +--2 +B-bacillif ! ! ! ! ! ! ! ! ! ! +B-vinsonii ! ! ! ! ! +--5 ! ! ! ! ! ! +B-birtlesi ! ! ! ! +-12 -11--3 +--4 ! +B-quintana ! ! ! ! +--9 ! ! ! +-10 +B-henselae ! ! ! ! ! ! ! +B--doshiae ! ! ! ! ! +B-elizabet ! ! ! +B-arupensi ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3104.97804 Examined 2026 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 B-clarridg 0.00924 ( 0.00388, 0.01461) ** 11 3 0.01000 ( 0.00441, 0.01559) ** 3 6 0.00003 ( zero, 0.00182) 6 B-berhoffi 0.00003 ( zero, 0.00163) 6 4 0.00366 ( 0.00045, 0.00687) ** 4 2 0.00364 ( 0.00045, 0.00683) ** 2 8 0.00006 ( zero, infinity) 8 B-grahamii 0.00003 ( zero, infinity) 8 1 0.00691 ( 0.00249, 0.01143) ** 1 7 0.00952 ( 0.00430, 0.01473) ** 7 B--weissii 0.00003 ( zero, infinity) 7 B-spp-Deer 0.00438 ( 0.00088, 0.00787) ** 1 B-bacillif 0.00774 ( 0.00300, 0.01249) ** 2 12 0.00006 ( zero, infinity) 12 5 0.00006 ( zero, infinity) 5 B-vinsonii 0.00141 ( zero, 0.00341) ** 5 B-birtlesi 0.00006 ( zero, infinity) 12 10 0.00218 ( zero, 0.00464) ** 10 9 0.00295 ( zero, 0.00582) ** 9 B-quintana 0.01032 ( 0.00491, 0.01572) ** 9 B-henselae 0.00361 ( 0.00048, 0.00683) ** 10 B--doshiae 0.00006 ( zero, infinity) 4 B-elizabet 0.00511 ( 0.00133, 0.00890) ** 3 B-arupensi 0.00512 ( 0.00133, 0.00893) ** 11 A-tumefaci 0.06430 ( 0.05070, 0.07869) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 34: Empirical Base Frequencies: A 0.25472 C 0.21724 G 0.31314 T(U) 0.21490 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.466190) +B-arupensi ! ! +B-henselae ! +--3 ! ! ! +B-spp-Deer ! ! +--5 ! +--1 +B--weissii ! ! ! ! ! ! +B-quintana ! +-11 +--7 ! ! ! +B-bacillif ! ! ! ! ! +B-clarridg --8--4 ! ! +B-berhoffi ! ! ! ! ! ! +B-birtlesi ! +--2 +-10 ! ! ! ! +B--doshiae ! ! ! +-12 ! +--9 +B-vinsonii ! ! ! ! +B-elizabet ! +--6 ! +B-grahamii ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2964.70792 Examined 558 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 8 B-arupensi 0.00264 ( zero, 0.00551) ** 8 4 0.00332 ( 0.00009, 0.00653) ** 4 11 0.00324 ( zero, 0.00661) ** 11 1 0.00227 ( zero, 0.00481) ** 1 3 0.00214 ( zero, 0.00463) ** 3 B-henselae 0.00599 ( 0.00175, 0.01033) ** 3 5 0.00352 ( 0.00008, 0.00694) ** 5 B-spp-Deer 0.00223 ( zero, 0.00472) ** 5 B--weissii 0.00142 ( zero, 0.00343) ** 1 7 0.00316 ( 0.00006, 0.00626) ** 7 B-quintana 0.00905 ( 0.00377, 0.01440) ** 7 B-bacillif 0.00692 ( 0.00221, 0.01163) ** 11 B-clarridg 0.00823 ( 0.00315, 0.01324) ** 4 2 0.00031 ( zero, 0.00176) 2 B-berhoffi 0.00079 ( zero, 0.00229) ** 2 9 0.00218 ( zero, 0.00466) ** 9 10 0.00070 ( zero, 0.00212) * 10 B-birtlesi 0.00147 ( zero, 0.00349) ** 10 12 0.00003 ( zero, 0.00178) 12 B--doshiae 0.00073 ( zero, 0.00215) ** 12 B-vinsonii 0.00365 ( 0.00046, 0.00685) ** 9 6 0.00149 ( zero, 0.00355) ** 6 B-elizabet 0.00952 ( 0.00437, 0.01472) ** 6 B-grahamii 0.00003 ( zero, 0.00191) 8 A-tumefaci 0.04967 ( 0.03749, 0.06188) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 35: Empirical Base Frequencies: A 0.24897 C 0.25383 G 0.29660 T(U) 0.20060 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.499922) +B-clarridg ! ! +B-quintana ! +-10 ! ! ! +B--weissii ! ! +--6 ! ! +B-spp-Deer ! ! ! ! +B-birtlesi ! ! ! ! ! +--9 +B-vinsonii --8--4 ! ! ! ! ! ! +--1 +B-elizabet ! ! ! ! +--7 ! ! ! ! ! +B-grahamii ! ! +--5 +--3 ! ! ! ! ! +B-henselae ! ! ! ! +-11 ! ! ! ! +B--doshiae ! +--2 ! ! ! +B-bacillif ! ! ! ! +B-arupensi ! +-12 ! +B-berhoffi ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3006.01687 Examined 590 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 8 B-clarridg 0.00827 ( 0.00320, 0.01341) ** 8 4 0.00647 ( 0.00192, 0.01103) ** 4 10 0.00231 ( zero, 0.00497) ** 10 B-quintana 0.00725 ( 0.00267, 0.01184) ** 10 6 0.00610 ( 0.00182, 0.01027) ** 6 B--weissii 0.00003 ( zero, 0.00185) 6 B-spp-Deer 0.00362 ( 0.00046, 0.00683) ** 4 2 0.00141 ( zero, 0.00363) ** 2 5 0.00224 ( zero, 0.00473) ** 5 9 0.00293 ( 0.00006, 0.00581) ** 9 B-birtlesi 0.00075 ( zero, 0.00219) ** 9 1 0.00006 ( zero, infinity) 1 B-vinsonii 0.00220 ( zero, 0.00468) ** 1 3 0.00006 ( zero, infinity) 3 7 0.00218 ( zero, 0.00466) ** 7 B-elizabet 0.00807 ( 0.00332, 0.01285) ** 7 B-grahamii 0.00006 ( zero, 0.00182) 3 11 0.00069 ( zero, 0.00209) ** 11 B-henselae 0.00443 ( 0.00085, 0.00793) ** 11 B--doshiae 0.00006 ( zero, infinity) 5 B-bacillif 0.01177 ( 0.00602, 0.01757) ** 2 12 0.00003 ( zero, 0.00156) 12 B-arupensi 0.00298 ( 0.00003, 0.00586) ** 12 B-berhoffi 0.00146 ( zero, 0.00349) ** 8 A-tumefaci 0.05946 ( 0.04631, 0.07313) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 36: Empirical Base Frequencies: A 0.23852 C 0.22069 G 0.32701 T(U) 0.21378 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.485665) +B-quintana ! +--4 +B-berhoffi ! ! ! ! ! ! +B-arupensi ! +--7 ! ! ! ! +B--weissii ! ! ! +-12 ! +--2 +--3 +B-spp-Deer ! ! ! ! ! ! ! +B-bacillif ! ! ! ! +-11 +B--doshiae ! ! +-10 ! ! ! ! +B-birtlesi ! ! ! +--8 ! ! ! ! +B-vinsonii ! +--1 +--9 ! ! +B-henselae ! ! ! ! +B-grahamii ! +--6 ! +B-elizabet ! --5-B-clarridg ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2938.25701 Examined 1042 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 5 4 0.00848 ( 0.00338, 0.01359) ** 4 B-quintana 0.00763 ( 0.00283, 0.01252) ** 4 7 0.00191 ( zero, 0.00483) 7 B-berhoffi 0.00006 ( zero, infinity) 7 2 0.00146 ( zero, 0.00349) ** 2 B-arupensi 0.00515 ( 0.00134, 0.00896) ** 2 11 0.00095 ( zero, 0.00274) ** 11 3 0.00360 ( 0.00022, 0.00695) ** 3 12 0.00599 ( 0.00180, 0.01020) ** 12 B--weissii 0.00006 ( zero, infinity) 12 B-spp-Deer 0.00217 ( zero, 0.00464) ** 3 B-bacillif 0.00508 ( 0.00111, 0.00909) ** 11 1 0.00270 ( zero, 0.00553) ** 1 10 0.00003 ( zero, infinity) 10 B--doshiae 0.00006 ( zero, infinity) 10 8 0.00006 ( zero, infinity) 8 B-birtlesi 0.00292 ( 0.00007, 0.00578) ** 8 9 0.00073 ( zero, 0.00217) ** 9 B-vinsonii 0.00072 ( zero, 0.00213) ** 9 B-henselae 0.00365 ( 0.00046, 0.00685) ** 1 6 0.00292 ( 0.00007, 0.00578) ** 6 B-grahamii 0.00003 ( zero, infinity) 6 B-elizabet 0.00506 ( 0.00137, 0.00887) ** 5 B-clarridg 0.00549 ( 0.00110, 0.00981) ** 5 A-tumefaci 0.05841 ( 0.04508, 0.07183) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 37: Empirical Base Frequencies: A 0.24860 C 0.23722 G 0.30489 T(U) 0.20930 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.486448) +B-grahamii ! +--6 +B--doshiae ! ! ! ! ! ! +B-bacillif ! +--1 +--8 ! ! ! ! +B-quintana ! ! ! +-12 ! ! ! +B-birtlesi ! +-10 ! ! +B-arupensi ! ! +--7 ! ! ! +B-vinsonii ! +--2 ! ! +B-berhoffi ! +--3 ! ! +B-elizabet ! +--9 ! ! +B-clarridg ! +--4 ! ! +B--weissii ! +--5 ! +B-spp-Deer ! -11-B-henselae ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3062.04693 Examined 624 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 6 0.00051 ( zero, 0.00202) 6 B-grahamii 0.00006 ( zero, infinity) 6 1 0.00292 ( 0.00007, 0.00578) ** 1 B--doshiae 0.00076 ( zero, 0.00222) ** 1 10 0.00006 ( zero, infinity) 10 8 0.00294 ( 0.00006, 0.00582) ** 8 B-bacillif 0.00966 ( 0.00437, 0.01487) ** 8 12 0.00075 ( zero, 0.00221) * 12 B-quintana 0.01399 ( 0.00773, 0.02032) ** 12 B-birtlesi 0.00003 ( zero, 0.00156) 10 2 0.00006 ( zero, 0.00179) 2 7 0.00151 ( zero, 0.00356) ** 7 B-arupensi 0.00365 ( 0.00045, 0.00686) ** 7 B-vinsonii 0.00149 ( zero, 0.00354) ** 2 3 0.00218 ( zero, 0.00466) ** 3 B-berhoffi 0.00006 ( zero, 0.00152) 3 9 0.00081 ( zero, 0.00240) ** 9 B-elizabet 0.00651 ( 0.00225, 0.01084) ** 9 4 0.00309 ( 0.00007, 0.00617) ** 4 B-clarridg 0.01021 ( 0.00481, 0.01568) ** 4 5 0.00950 ( 0.00427, 0.01473) ** 5 B--weissii 0.00440 ( 0.00089, 0.00792) ** 5 B-spp-Deer 0.00070 ( zero, 0.00212) ** 11 B-henselae 0.00536 ( 0.00142, 0.00932) ** 11 A-tumefaci 0.06677 ( 0.05281, 0.08128) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 38: Empirical Base Frequencies: A 0.24798 C 0.22838 G 0.32320 T(U) 0.20044 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.473042) +B-bacillif ! +--5 +B--weissii ! ! +--1 ! ! ! +B-spp-Deer ! +--2 ! ! +B-henselae ! ! ! ! +--6 +B--doshiae ! ! ! ! +--4 +B-arupensi ! ! +-12 ! ! ! +B-vinsonii ! +-11 ! ! +B-birtlesi ! ! ! ! +--3 +B-grahamii ! ! +-10 ! ! ! +B-elizabet ! +--8 ! ! +B-berhoffi ! +--9 ! +B-quintana ! --7-B-clarridg ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2920.76444 Examined 562 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 5 0.00541 ( 0.00120, 0.00970) ** 5 B-bacillif 0.00763 ( 0.00276, 0.01255) ** 5 2 0.00329 ( 0.00009, 0.00650) ** 2 1 0.00299 ( zero, 0.00630) ** 1 B--weissii 0.00076 ( zero, 0.00223) ** 1 B-spp-Deer 0.00218 ( zero, 0.00466) ** 2 6 0.00340 ( zero, 0.00677) ** 6 B-henselae 0.00342 ( 0.00022, 0.00660) ** 6 4 0.00171 ( zero, 0.00403) ** 4 B--doshiae 0.00006 ( zero, infinity) 4 11 0.00074 ( zero, 0.00218) ** 11 12 0.00073 ( zero, 0.00216) ** 12 B-arupensi 0.00596 ( 0.00177, 0.01003) ** 12 B-vinsonii 0.00073 ( zero, 0.00216) ** 11 3 0.00006 ( zero, 0.00218) 3 B-birtlesi 0.00289 ( 0.00004, 0.00575) ** 3 8 0.00145 ( zero, 0.00347) ** 8 10 0.00145 ( zero, 0.00347) ** 10 B-grahamii 0.00003 ( zero, 0.00194) 10 B-elizabet 0.00880 ( 0.00384, 0.01379) ** 8 9 0.00223 ( zero, 0.00472) ** 9 B-berhoffi 0.00151 ( zero, 0.00356) ** 9 B-quintana 0.00732 ( 0.00280, 0.01188) ** 7 B-clarridg 0.00759 ( 0.00285, 0.01242) ** 7 A-tumefaci 0.04764 ( 0.03591, 0.05980) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 39: Empirical Base Frequencies: A 0.24649 C 0.23051 G 0.31957 T(U) 0.20342 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.478880) +B-arupensi ! ! +B-clarridg ! +--2 ! ! ! +B--weissii ! +--1 +-11 ! ! ! +B-spp-Deer ! +-10 ! ! ! ! +B-quintana ! ! ! -12--8 +B-bacillif ! ! ! ! +B-berhoffi ! ! ! ! +--6 +B-elizabet ! ! ! ! ! ! +B-grahamii ! +--3 +--9 ! ! ! +B-birtlesi ! ! +--5 ! ! ! ! +B-henselae ! +--7 +--4 ! ! +B--doshiae ! ! ! +B-vinsonii ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3002.79954 Examined 1966 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 12 B-arupensi 0.00369 ( 0.00044, 0.00693) ** 12 8 0.00146 ( zero, 0.00353) ** 8 10 0.00356 ( 0.00025, 0.00677) ** 10 1 0.00423 ( 0.00069, 0.00774) ** 1 2 0.00033 ( zero, 0.00229) 2 B-clarridg 0.00734 ( 0.00278, 0.01191) ** 2 11 0.00809 ( 0.00330, 0.01288) ** 11 B--weissii 0.00146 ( zero, 0.00347) ** 11 B-spp-Deer 0.00006 ( zero, infinity) 1 B-quintana 0.01093 ( 0.00527, 0.01650) ** 10 B-bacillif 0.01046 ( 0.00499, 0.01595) ** 8 6 0.00003 ( zero, 0.00186) 6 B-berhoffi 0.00070 ( zero, 0.00210) ** 6 3 0.00307 ( zero, 0.00619) ** 3 B-elizabet 0.00658 ( 0.00227, 0.01089) ** 3 7 0.00200 ( zero, 0.00463) ** 7 5 0.00003 ( zero, 0.00193) 5 9 0.00006 ( zero, 0.00187) 9 B-grahamii 0.00003 ( zero, infinity) 9 B-birtlesi 0.00074 ( zero, 0.00218) ** 5 4 0.00291 ( 0.00007, 0.00577) ** 4 B-henselae 0.00958 ( 0.00437, 0.01478) ** 4 B--doshiae 0.00003 ( zero, infinity) 7 B-vinsonii 0.00220 ( zero, 0.00468) ** 12 A-tumefaci 0.05561 ( 0.04289, 0.06872) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 40: Empirical Base Frequencies: A 0.26686 C 0.23557 G 0.30164 T(U) 0.19593 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.464304) +B-berhoffi ! ! +B-grahamii ! +--5 ! ! ! +B-bacillif ! ! +-11 ! +--2 +B-elizabet ! ! ! ! ! ! +B-birtlesi ! ! ! ! ! ! +--4 +B--doshiae ! +--3 ! +--1 ! ! ! +--9 +B-henselae ! ! ! ! ! ! ! +B-vinsonii ! ! ! --6--7 +B-arupensi ! ! ! ! +B-quintana ! ! +-12 ! ! ! +B-clarridg ! +--8 ! ! +B-spp-Deer ! +-10 ! +B--weissii ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3120.60226 Examined 1706 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 6 B-berhoffi 0.00003 ( zero, 0.00157) 6 7 0.00073 ( zero, 0.00216) ** 7 3 0.00003 ( zero, 0.00178) 3 2 0.00360 ( 0.00048, 0.00680) ** 2 5 0.00003 ( zero, 0.00186) 5 B-grahamii 0.00287 ( 0.00006, 0.00573) ** 5 11 0.00288 ( 0.00002, 0.00576) ** 11 B-bacillif 0.01111 ( 0.00548, 0.01673) ** 11 B-elizabet 0.00584 ( 0.00183, 0.00995) ** 2 4 0.00073 ( zero, 0.00217) * 4 B-birtlesi 0.00212 ( zero, 0.00458) ** 4 9 0.00006 ( zero, 0.00177) 9 1 0.00218 ( zero, 0.00465) ** 1 B--doshiae 0.00003 ( zero, infinity) 1 B-henselae 0.00511 ( 0.00133, 0.00890) ** 9 B-vinsonii 0.00142 ( zero, 0.00342) ** 3 B-arupensi 0.00513 ( 0.00135, 0.00894) ** 7 8 0.00401 ( 0.00055, 0.00754) ** 8 12 0.00214 ( zero, 0.00467) ** 12 B-quintana 0.01192 ( 0.00595, 0.01780) ** 12 B-clarridg 0.01334 ( 0.00710, 0.01959) ** 8 10 0.01069 ( 0.00508, 0.01627) ** 10 B-spp-Deer 0.00218 ( zero, 0.00466) ** 10 B--weissii 0.00220 ( zero, 0.00470) ** 6 A-tumefaci 0.05860 ( 0.04550, 0.07201) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 41: Empirical Base Frequencies: A 0.23963 C 0.22602 G 0.32051 T(U) 0.21385 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.488408) +B-clarridg ! ! +B-arupensi ! +--2 ! ! ! +B-quintana ! ! +-12 ! +--1 +B-berhoffi ! ! ! ! ! ! +B-bacillif ! ! +-11 ! ! ! +B-birtlesi ! ! +--9 ! ! ! +B-vinsonii ! ! +--7 --5--4 ! +B--doshiae ! ! +--3 ! ! ! +B-henselae ! ! +--8 ! ! ! +B-elizabet ! ! +-10 ! ! +B-grahamii ! ! ! ! +B-spp-Deer ! +--6 ! +B--weissii ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3155.29908 Examined 694 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 5 B-clarridg 0.01019 ( 0.00460, 0.01584) ** 5 4 0.00416 ( 0.00035, 0.00798) ** 4 1 0.00269 ( zero, 0.00554) ** 1 2 0.00003 ( zero, 0.00194) 2 B-arupensi 0.00366 ( 0.00046, 0.00687) ** 2 12 0.00080 ( zero, 0.00237) ** 12 B-quintana 0.01248 ( 0.00654, 0.01841) ** 12 B-berhoffi 0.00071 ( zero, 0.00213) ** 1 11 0.00323 ( 0.00013, 0.00633) ** 11 B-bacillif 0.01326 ( 0.00713, 0.01940) ** 11 9 0.00326 ( 0.00013, 0.00637) ** 9 B-birtlesi 0.00222 ( zero, 0.00469) ** 9 7 0.00003 ( zero, infinity) 7 B-vinsonii 0.00145 ( zero, 0.00346) ** 7 3 0.00006 ( zero, 0.00179) 3 B--doshiae 0.00074 ( zero, 0.00218) * 3 8 0.00218 ( zero, 0.00465) ** 8 B-henselae 0.00656 ( 0.00226, 0.01085) ** 8 10 0.00294 ( 0.00006, 0.00582) ** 10 B-elizabet 0.01248 ( 0.00654, 0.01841) ** 10 B-grahamii 0.00003 ( zero, 0.00156) 4 6 0.00761 ( 0.00288, 0.01229) ** 6 B-spp-Deer 0.00146 ( zero, 0.00349) ** 6 B--weissii 0.00365 ( 0.00045, 0.00685) ** 5 A-tumefaci 0.05510 ( 0.04244, 0.06821) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 42: Empirical Base Frequencies: A 0.26927 C 0.21826 G 0.31179 T(U) 0.20069 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.441966) +B-elizabet ! ! +B--weissii ! +-10 ! +--5 +B-spp-Deer ! ! ! ! ! +B-bacillif ! ! ! ! +B-berhoffi ! ! ! ! ! ! +B-vinsonii --7-11 ! ! ! ! ! +--2 +B-henselae ! ! +--9 ! ! +--8 ! ! ! ! ! ! ! ! +B-grahamii ! ! ! ! ! +--6 +--4 ! ! ! ! +--1 ! +B-birtlesi ! ! ! ! ! ! ! ! +-12 ! ! ! +B--doshiae ! ! +--3 ! ! ! ! +B-arupensi ! ! ! ! ! +B-quintana ! ! ! +B-clarridg ! +--A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2875.73795 Examined 596 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 B-elizabet 0.00672 ( 0.00226, 0.01115) ** 7 11 0.00225 ( zero, 0.00495) ** 11 5 0.00423 ( 0.00066, 0.00780) ** 5 10 0.00887 ( 0.00385, 0.01389) ** 10 B--weissii 0.00006 ( zero, 0.00173) 10 B-spp-Deer 0.00145 ( zero, 0.00347) ** 5 B-bacillif 0.00220 ( zero, 0.00475) ** 11 12 0.00229 ( zero, 0.00485) ** 12 9 0.00304 ( zero, 0.00606) ** 9 B-berhoffi 0.00367 ( 0.00048, 0.00691) ** 9 3 0.00151 ( zero, 0.00356) ** 3 1 0.00084 ( zero, 0.00248) ** 1 2 0.00333 ( 0.00014, 0.00646) ** 2 B-vinsonii 0.00073 ( zero, 0.00216) ** 2 6 0.00169 ( zero, 0.00394) ** 6 8 0.00003 ( zero, 0.00167) 8 B-henselae 0.00512 ( 0.00134, 0.00892) ** 8 4 0.00070 ( zero, 0.00229) 4 B-grahamii 0.00144 ( zero, 0.00347) ** 4 B-birtlesi 0.00013 ( zero, 0.00158) 6 B--doshiae 0.00003 ( zero, infinity) 1 B-arupensi 0.00146 ( zero, 0.00348) ** 3 B-quintana 0.00661 ( 0.00224, 0.01091) ** 12 B-clarridg 0.00798 ( 0.00317, 0.01279) ** 7 A-tumefaci 0.05061 ( 0.03852, 0.06304) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 43: Empirical Base Frequencies: A 0.23837 C 0.24661 G 0.32550 T(U) 0.18952 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.501489) +B-arupensi +-12 +--8 +B-quintana ! ! ! +B-berhoffi ! +--2 +B-grahamii ! ! +--9 ! ! ! +B-elizabet ! ! ! ! +--4 +B-birtlesi ! ! +--6 +--1 ! ! +B--doshiae ! ! +-10 ! ! ! +B-vinsonii ! ! +--7 ! ! +B-henselae ! ! ! ! +B-bacillif ! +-11 ! ! +B-spp-Deer ! +--5 ! +B--weissii ! --3-B-clarridg ! +----A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2973.68719 Examined 706 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 3 1 0.00671 ( 0.00211, 0.01134) ** 1 2 0.00447 ( 0.00080, 0.00815) ** 2 8 0.00006 ( zero, 0.00181) 8 12 0.00151 ( zero, 0.00356) ** 12 B-arupensi 0.00227 ( zero, 0.00477) ** 12 B-quintana 0.00659 ( 0.00229, 0.01090) ** 8 B-berhoffi 0.00071 ( zero, 0.00213) ** 2 4 0.00217 ( zero, 0.00464) ** 4 9 0.00074 ( zero, 0.00219) ** 9 B-grahamii 0.00006 ( zero, infinity) 9 B-elizabet 0.00733 ( 0.00279, 0.01187) ** 4 10 0.00074 ( zero, 0.00218) ** 10 6 0.00003 ( zero, infinity) 6 B-birtlesi 0.00149 ( zero, 0.00352) ** 6 B--doshiae 0.00003 ( zero, infinity) 10 7 0.00075 ( zero, 0.00220) ** 7 B-vinsonii 0.00222 ( zero, 0.00471) ** 7 B-henselae 0.00219 ( zero, 0.00467) ** 1 11 0.00373 ( 0.00047, 0.00708) ** 11 B-bacillif 0.00655 ( 0.00216, 0.01090) ** 11 5 0.00374 ( 0.00045, 0.00709) ** 5 B-spp-Deer 0.00363 ( 0.00048, 0.00684) ** 5 B--weissii 0.00003 ( zero, infinity) 3 B-clarridg 0.00726 ( 0.00248, 0.01204) ** 3 A-tumefaci 0.07568 ( 0.06084, 0.09143) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 44: Empirical Base Frequencies: A 0.25702 C 0.22212 G 0.31295 T(U) 0.20790 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.463081) +B-henselae +-12 ! ! +B-spp-Deer ! +--9 +--4 +B--weissii ! ! ! ! +B-quintana +--3 +--6 ! ! +B-bacillif ! ! ! ! +B-grahamii ! +--8 ! ! +B--doshiae +--2 +-11 ! ! ! +B-birtlesi ! ! +--7 ! ! ! +B-arupensi +-10 ! +--1 ! ! ! +B-vinsonii ! ! ! ! ! +B-elizabet ! ! ! +B-berhoffi ! --5-B-clarridg ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -3261.81975 Examined 768 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 5 10 0.00726 ( 0.00244, 0.01215) ** 10 2 0.00072 ( zero, 0.00214) ** 2 3 0.00077 ( zero, 0.00225) ** 3 4 0.00369 ( 0.00042, 0.00690) ** 4 12 0.00224 ( zero, 0.00476) ** 12 B-henselae 0.00440 ( 0.00087, 0.00794) ** 12 9 0.01032 ( 0.00491, 0.01574) ** 9 B-spp-Deer 0.00293 ( 0.00006, 0.00581) ** 9 B--weissii 0.00214 ( zero, 0.00462) ** 4 6 0.00505 ( 0.00122, 0.00890) ** 6 B-quintana 0.01186 ( 0.00610, 0.01776) ** 6 B-bacillif 0.01638 ( 0.00951, 0.02326) ** 3 8 0.00217 ( zero, 0.00464) ** 8 B-grahamii 0.00219 ( zero, 0.00467) ** 8 11 0.00075 ( zero, 0.00220) ** 11 B--doshiae 0.00003 ( zero, infinity) 11 7 0.00006 ( zero, infinity) 7 B-birtlesi 0.00364 ( 0.00047, 0.00683) ** 7 1 0.00219 ( zero, 0.00468) ** 1 B-arupensi 0.00364 ( 0.00048, 0.00686) ** 1 B-vinsonii 0.00293 ( 0.00005, 0.00579) ** 2 B-elizabet 0.00954 ( 0.00436, 0.01473) ** 10 B-berhoffi 0.00006 ( zero, 0.00150) 5 B-clarridg 0.01043 ( 0.00477, 0.01615) ** 5 A-tumefaci 0.06079 ( 0.04734, 0.07456) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 45: Empirical Base Frequencies: A 0.22719 C 0.22712 G 0.32330 T(U) 0.22239 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.509164) +B-berhoffi ! ! +B-vinsonii ! +--2 ! ! ! +B--doshiae ! +-11 +--1 ! ! ! +B-henselae ! +--8 ! ! ! ! +B-birtlesi ! +--4 ! ! ! ! +B-grahamii ! +--3 ! ! ! ! +B-elizabet ! ! ! ! ! +B-arupensi ! ! --6--7 +B-bacillif ! ! +-12 ! ! ! ! +B-spp-Deer ! ! +--9 +-10 ! ! ! ! +B--weissii ! +--5 ! ! ! +B-quintana ! ! ! +B-clarridg ! +---A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -2969.00114 Examined 876 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 6 B-berhoffi 0.00003 ( zero, 0.00158) 6 7 0.00221 ( zero, 0.00471) ** 7 3 0.00006 ( zero, infinity) 3 4 0.00294 ( 0.00007, 0.00582) ** 4