Nucleic acid sequence Maximum Likelihood method, version 3.573c Data set # 1: Empirical Base Frequencies: A 0.26696 C 0.21719 G 0.29948 T(U) 0.21637 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.459645) +---B-clarridg ! +--3 +-B-spp-Deer ! ! +-10 ! +--8 +--B-bacillif ! ! ! +B--weissii ! +--7 +B-henselae ! ! ! ! ! +--1 +B-elizabet ! ! ! ! +--6 ! ! ! ! ! ! +--B-birtlesi ! ! ! +--9 +-12 ! +--5 ! +B-grahamii ! ! ! ! ! +B-quintana ! ! ! ! +B-vinsonii ! +--4 ! ! +B-arupensi ! +-11 ! +-B-berhoffi ! --2-B--doshiae ! +-------------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1295.90638 Examined 596 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 2 7 0.01788 ( 0.00138, 0.03450) ** 7 3 0.01820 ( 0.00156, 0.03483) ** 3 B-clarridg 0.06234 ( 0.03222, 0.09266) ** 3 8 0.01537 ( zero, 0.03109) ** 8 10 0.00641 ( zero, 0.01638) * 10 B-spp-Deer 0.02098 ( 0.00373, 0.03825) ** 10 B-bacillif 0.04971 ( 0.02341, 0.07630) ** 8 B--weissii 0.01008 ( zero, 0.02202) ** 7 5 0.01354 ( zero, 0.02804) ** 5 1 0.00003 ( zero, 0.00982) 1 B-henselae 0.01043 ( zero, 0.02233) ** 1 9 0.00691 ( zero, 0.01662) ** 9 6 0.03520 ( 0.01318, 0.05744) ** 6 B-elizabet 0.00340 ( zero, 0.01041) * 6 12 0.00688 ( zero, 0.01671) ** 12 B-birtlesi 0.05902 ( 0.03008, 0.08857) ** 12 B-grahamii 0.00003 ( zero, infinity) 9 B-quintana 0.00369 ( zero, 0.01102) ** 5 4 0.00982 ( zero, 0.02151) ** 4 B-vinsonii 0.00362 ( zero, 0.01071) ** 4 11 0.00328 ( zero, 0.01011) * 11 B-arupensi 0.00708 ( zero, 0.01703) ** 11 B-berhoffi 0.03804 ( 0.01545, 0.06101) ** 2 B--doshiae 0.00003 ( zero, 0.01474) 2 A-tumefaci 0.32762 ( 0.24560, 0.41259) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 2: Empirical Base Frequencies: A 0.29758 C 0.22920 G 0.29116 T(U) 0.18206 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.431346) +B-grahamii +-12 +--9 +-B-birtlesi ! ! +--4 +B-elizabet ! ! ! ! +B-arupensi ! +--7 ! +-B-bacillif ! ! +B--weissii +--5 +-10 ! ! ! ! +--B-clarridg ! ! ! +--3 ! ! +--2 +B-spp-Deer ! ! ! ! ! ! ! ! +B-henselae ! ! ! +--1 ! +--8 ! +-B-berhoffi ! ! +--6 ! ! +B-quintana ! ! ! +B-vinsonii ! -11-B--doshiae ! +------------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1107.50213 Examined 1894 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 5 0.02550 ( 0.00656, 0.04445) ** 5 4 0.00358 ( zero, 0.01059) ** 4 9 0.01091 ( zero, 0.02330) ** 9 12 0.00719 ( zero, 0.01724) ** 12 B-grahamii 0.00003 ( zero, 0.00848) 12 B-birtlesi 0.02945 ( 0.00899, 0.04994) ** 9 B-elizabet 0.01033 ( zero, 0.02209) ** 4 7 0.00003 ( zero, infinity) 7 B-arupensi 0.00003 ( zero, infinity) 7 B-bacillif 0.04184 ( 0.01809, 0.06582) ** 5 8 0.00003 ( zero, infinity) 8 2 0.01028 ( zero, 0.02194) ** 2 10 0.02061 ( 0.00420, 0.03727) ** 10 B--weissii 0.00006 ( zero, 0.00735) 10 3 0.01439 ( 0.00016, 0.02866) ** 3 B-clarridg 0.05040 ( 0.02379, 0.07724) ** 3 B-spp-Deer 0.01015 ( zero, 0.02218) ** 2 1 0.00003 ( zero, 0.00729) 1 B-henselae 0.00688 ( zero, 0.01643) ** 1 6 0.00346 ( zero, 0.01027) ** 6 B-berhoffi 0.02446 ( 0.00631, 0.04271) ** 6 B-quintana 0.00349 ( zero, 0.01034) ** 8 B-vinsonii 0.00342 ( zero, 0.01010) ** 11 B--doshiae 0.00003 ( zero, 0.00947) 11 A-tumefaci 0.31032 ( 0.23027, 0.39259) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 3: Empirical Base Frequencies: A 0.32251 C 0.23271 G 0.26523 T(U) 0.17955 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.447117) +B-vinsonii ! ! +-B--doshiae ! +-10 ! ! ! +B--weissii ! ! +--6 +--7 ! ! +---B-bacillif ! ! ! +--3 ! ! +--9 ! +B-spp-Deer ! ! ! ! +--5 ! ! ! ! +---B-clarridg ! ! ! ! +--1 +--4 ! +-B-berhoffi ! ! ! +-12 ! ! ! +B-henselae ! ! ! +--2 ! +B-quintana ! ! ! ! ! +B-arupensi ! ! ! ! +B-grahamii ! +-11 ! +-B-elizabet ! --8--B-birtlesi ! +--------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1371.78717 Examined 1380 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 8 2 0.04282 ( 0.01449, 0.07130) ** 2 1 0.03213 ( 0.00915, 0.05534) ** 1 7 0.01352 ( zero, 0.02712) ** 7 B-vinsonii 0.00348 ( zero, 0.01061) * 7 4 0.01478 ( 0.00037, 0.02920) ** 4 9 0.00006 ( zero, 0.00747) 9 10 0.02039 ( 0.00387, 0.03692) ** 10 B--doshiae 0.03225 ( 0.01128, 0.05337) ** 10 6 0.01012 ( zero, 0.02212) ** 6 B--weissii 0.00485 ( zero, 0.01359) ** 6 3 0.01026 ( zero, 0.02234) ** 3 B-bacillif 0.07380 ( 0.04218, 0.10611) ** 3 5 0.01007 ( zero, 0.02194) ** 5 B-spp-Deer 0.00003 ( zero, infinity) 5 B-clarridg 0.05818 ( 0.03046, 0.08647) ** 9 12 0.00915 ( zero, 0.02092) ** 12 B-berhoffi 0.02949 ( 0.00978, 0.04946) ** 12 B-henselae 0.00003 ( zero, 0.00817) 4 B-quintana 0.01003 ( zero, 0.02140) ** 1 B-arupensi 0.00695 ( zero, 0.01706) ** 2 11 0.02565 ( 0.00587, 0.04574) ** 11 B-grahamii 0.00763 ( zero, 0.02029) 11 B-elizabet 0.02957 ( 0.00914, 0.05032) ** 8 B-birtlesi 0.04336 ( 0.01313, 0.07361) ** 8 A-tumefaci 0.25307 ( 0.18413, 0.32410) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 4: Empirical Base Frequencies: A 0.28039 C 0.19671 G 0.34382 T(U) 0.17908 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.359943) +B-arupensi +--9 +--2 +-B-berhoffi ! ! ! +B-vinsonii ! +--4 +B-grahamii ! ! +--7 ! ! ! ! +---B-birtlesi ! ! +--1 +-12 ! ! ! ! +B-elizabet ! +--3 ! +--6 ! +B-quintana ! ! ! ! ! +B-henselae ! ! ! ! +B--weissii ! ! ! ! +--8 +B-spp-Deer ! ! +-11 ! +-10 +-B-bacillif ! ! ! +-B-clarridg ! --5-B--doshiae ! +-----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1283.32901 Examined 642 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 5 6 0.03518 ( 0.01312, 0.05758) ** 6 4 0.00998 ( zero, 0.02208) ** 4 2 0.01323 ( zero, 0.02653) ** 2 9 0.01010 ( zero, 0.02157) ** 9 B-arupensi 0.00006 ( zero, infinity) 9 B-berhoffi 0.03719 ( 0.01525, 0.05952) ** 2 B-vinsonii 0.00329 ( zero, 0.00990) * 4 3 0.00003 ( zero, 0.00956) 3 1 0.00679 ( zero, 0.01651) ** 1 7 0.05250 ( 0.02575, 0.07963) ** 7 B-grahamii 0.00003 ( zero, infinity) 7 12 0.01007 ( zero, 0.02203) ** 12 B-birtlesi 0.06148 ( 0.03209, 0.09131) ** 12 B-elizabet 0.01363 ( 0.00011, 0.02732) ** 1 B-quintana 0.00698 ( zero, 0.01682) ** 3 B-henselae 0.01044 ( zero, 0.02224) ** 6 8 0.02803 ( 0.00829, 0.04782) ** 8 B--weissii 0.00665 ( zero, 0.01625) ** 8 10 0.01383 ( 0.00002, 0.02759) ** 10 11 0.00310 ( zero, 0.01016) 11 B-spp-Deer 0.00681 ( zero, 0.01640) ** 11 B-bacillif 0.04459 ( 0.02008, 0.06904) ** 10 B-clarridg 0.03406 ( 0.01294, 0.05554) ** 5 B--doshiae 0.00003 ( zero, 0.01383) 5 A-tumefaci 0.30153 ( 0.22538, 0.38046) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 5: Empirical Base Frequencies: A 0.27842 C 0.21538 G 0.30400 T(U) 0.20220 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.435101) +B-grahamii +--6 ! ! +B-elizabet ! +--8 ! +--B-birtlesi +--1 ! ! +B-henselae ! ! ! ! ! ! +B-arupensi ! ! ! +--4 ! +--7 +--2 +B-vinsonii ! ! ! ! ! ! +--3 +-B-berhoffi ! ! ! ! ! +--9 +B-quintana ! ! ! ! +B--weissii ! +--5 ! ! +-B-bacillif ! +-12 ! ! +B-spp-Deer ! +-11 ! +-B-clarridg ! -10-B--doshiae ! +----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1235.11084 Examined 1752 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 10 1 0.02364 ( 0.00496, 0.04234) ** 1 6 0.04283 ( 0.01857, 0.06747) ** 6 B-grahamii 0.00003 ( zero, 0.01038) 6 8 0.01396 ( zero, 0.02812) ** 8 B-elizabet 0.01340 ( zero, 0.02710) ** 8 B-birtlesi 0.05869 ( 0.02979, 0.08801) ** 1 7 0.00617 ( zero, 0.01580) * 7 B-henselae 0.00337 ( zero, 0.00996) ** 7 9 0.00003 ( zero, 0.00700) 9 3 0.00329 ( zero, 0.00978) ** 3 2 0.00769 ( zero, 0.01833) ** 2 4 0.01015 ( zero, 0.02184) ** 4 B-arupensi 0.01272 ( zero, 0.02603) ** 4 B-vinsonii 0.00752 ( zero, 0.01801) ** 2 B-berhoffi 0.03350 ( 0.01206, 0.05494) ** 3 B-quintana 0.00003 ( zero, 0.00695) 9 5 0.02739 ( 0.00831, 0.04656) ** 5 B--weissii 0.00653 ( zero, 0.01608) ** 5 12 0.01890 ( 0.00241, 0.03533) ** 12 B-bacillif 0.03321 ( 0.01191, 0.05452) ** 12 11 0.00955 ( zero, 0.02129) ** 11 B-spp-Deer 0.00006 ( zero, 0.00744) 11 B-clarridg 0.03800 ( 0.01539, 0.06063) ** 10 B--doshiae 0.00143 ( zero, 0.01216) 10 A-tumefaci 0.27726 ( 0.20413, 0.35217) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 6: Empirical Base Frequencies: A 0.27932 C 0.21224 G 0.33404 T(U) 0.17441 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.387844) +B--doshiae ! ! +B-arupensi ! +--8 ! +--4 +-B-berhoffi ! ! ! ! ! +B-vinsonii ! ! --7--5 +B-henselae ! ! ! ! ! ! +--B-bacillif ! ! ! +--6 ! +--2 ! ! +B-spp-Deer ! ! +-10 +--1 ! ! ! ! +--B-clarridg ! ! ! ! ! +--3 +B--weissii ! ! ! ! +B-quintana ! ! ! ! +-11 +---B-birtlesi ! ! +-12 ! +--9 +B-grahamii ! ! ! +B-elizabet ! +------------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1303.67347 Examined 838 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 B--doshiae 0.00003 ( zero, 0.01521) 7 5 0.04613 ( 0.02093, 0.07153) ** 5 4 0.00348 ( zero, 0.01031) ** 4 8 0.00333 ( zero, 0.01005) * 8 B-arupensi 0.00678 ( zero, 0.01628) ** 8 B-berhoffi 0.02731 ( 0.00846, 0.04649) ** 4 B-vinsonii 0.00003 ( zero, infinity) 5 2 0.00288 ( zero, 0.00970) 2 B-henselae 0.02112 ( 0.00424, 0.03808) ** 2 3 0.00003 ( zero, 0.00764) 3 10 0.01433 ( 0.00009, 0.02857) ** 10 6 0.01026 ( zero, 0.02298) ** 6 B-bacillif 0.04182 ( 0.01756, 0.06629) ** 6 1 0.00668 ( zero, 0.01703) ** 1 B-spp-Deer 0.00652 ( zero, 0.01712) * 1 B-clarridg 0.05578 ( 0.02806, 0.08412) ** 10 B--weissii 0.00650 ( zero, 0.01691) ** 3 11 0.00677 ( zero, 0.01662) ** 11 B-quintana 0.01386 ( 0.00016, 0.02755) ** 11 9 0.03856 ( 0.01485, 0.06232) ** 9 12 0.00852 ( zero, 0.02112) * 12 B-birtlesi 0.06848 ( 0.03754, 0.09995) ** 12 B-grahamii 0.00006 ( zero, 0.00819) 9 B-elizabet 0.03040 ( 0.00984, 0.05101) ** 7 A-tumefaci 0.31896 ( 0.23786, 0.40236) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 7: Empirical Base Frequencies: A 0.25875 C 0.24324 G 0.32340 T(U) 0.17461 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.468493) +B-birtlesi ! ! +B-elizabet ! +-12 ! ! +B-grahamii ! ! ! ! +---B-clarridg ! ! +--9 ! ! +-10 +B-spp-Deer ! ! ! ! ! ! +--6 +-B-bacillif --7--5 ! ! ! ! +--2 +B--weissii ! ! ! ! ! ! ! +-B--doshiae ! ! ! ! ! +--1 +B-vinsonii ! ! ! ! +-11 ! ! ! ! +--3 +B-arupensi ! ! ! ! ! ! ! +--8 +--4 +B-berhoffi ! ! ! ! ! +B-henselae ! ! ! +B-quintana ! +---------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1197.47176 Examined 1010 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 B-birtlesi 0.01449 ( zero, 0.03613) 7 5 0.05414 ( 0.02456, 0.08410) ** 5 12 0.00777 ( zero, 0.01888) ** 12 B-elizabet 0.01194 ( zero, 0.02481) ** 12 B-grahamii 0.00130 ( zero, 0.00817) 5 8 0.01785 ( 0.00171, 0.03418) ** 8 1 0.00666 ( zero, 0.01590) ** 1 2 0.00993 ( zero, 0.02164) ** 2 6 0.02395 ( 0.00601, 0.04187) ** 6 10 0.00611 ( zero, 0.01551) ** 10 9 0.00347 ( zero, 0.01044) * 9 B-clarridg 0.06886 ( 0.03809, 0.10002) ** 9 B-spp-Deer 0.00392 ( zero, 0.01182) * 10 B-bacillif 0.03427 ( 0.01299, 0.05580) ** 6 B--weissii 0.00003 ( zero, infinity) 2 B--doshiae 0.02421 ( 0.00606, 0.04229) ** 1 4 0.00005 ( zero, infinity) 4 3 0.00678 ( zero, 0.01619) ** 3 11 0.00669 ( zero, 0.01612) ** 11 B-vinsonii 0.00673 ( zero, 0.01611) ** 11 B-arupensi 0.01014 ( zero, 0.02165) ** 3 B-berhoffi 0.01686 ( 0.00204, 0.03171) ** 4 B-henselae 0.01348 ( 0.00027, 0.02672) ** 8 B-quintana 0.00003 ( zero, 0.00735) 7 A-tumefaci 0.27125 ( 0.19950, 0.34500) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 8: Empirical Base Frequencies: A 0.25683 C 0.23677 G 0.31572 T(U) 0.19068 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.469155) +B-grahamii +--1 ! +B-elizabet +--4 ! ! +B-arupensi ! ! ! ! +-10 +B-vinsonii ! ! ! ! ! ! +-B-berhoffi ! +--9 +--6 ! ! +--5 +B-henselae ! ! ! ! ! ! ! +B-quintana ! +--8 ! ! +-B--doshiae ! ! ! ! +-12 +B--weissii ! ! +-11 ! ! ! ! +B-spp-Deer ! +--2 +--3 ! ! +-B-clarridg ! ! ! +--B-bacillif ! --7-B-birtlesi ! +----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1142.38045 Examined 570 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 4 0.02657 ( 0.00552, 0.04772) ** 4 1 0.00730 ( zero, 0.01737) ** 1 B-grahamii 0.00996 ( zero, 0.02138) ** 1 B-elizabet 0.00337 ( zero, 0.01010) ** 4 10 0.00293 ( zero, 0.00972) 10 B-arupensi 0.00006 ( zero, infinity) 10 9 0.01342 ( 0.00026, 0.02658) ** 9 B-vinsonii 0.01003 ( zero, 0.02142) ** 9 8 0.00003 ( zero, infinity) 8 5 0.00006 ( zero, 0.00819) 5 6 0.01202 ( zero, 0.02529) ** 6 B-berhoffi 0.02866 ( 0.00877, 0.04872) ** 6 B-henselae 0.00006 ( zero, 0.00829) 5 B-quintana 0.01015 ( zero, 0.02166) ** 8 12 0.00987 ( zero, 0.02164) ** 12 B--doshiae 0.02428 ( 0.00608, 0.04242) ** 12 2 0.02770 ( 0.00844, 0.04725) ** 2 11 0.00006 ( zero, 0.01236) 11 B--weissii 0.00980 ( zero, 0.02125) ** 11 3 0.01033 ( zero, 0.02209) ** 3 B-spp-Deer 0.00661 ( zero, 0.01602) ** 3 B-clarridg 0.02055 ( 0.00415, 0.03719) ** 2 B-bacillif 0.04820 ( 0.02266, 0.07378) ** 7 B-birtlesi 0.02050 ( 0.00088, 0.04007) ** 7 A-tumefaci 0.28437 ( 0.21185, 0.36056) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 9: Empirical Base Frequencies: A 0.28211 C 0.19138 G 0.33296 T(U) 0.19355 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.375984) +-B-birtlesi ! ! +B-grahamii ! +--7 ! +--8 +B-elizabet ! ! ! ! ! +B--doshiae ! ! ! ! +B-berhoffi -11--1 +--5 ! ! ! ! +B-vinsonii ! ! ! +--2 ! ! ! +B-arupensi ! ! ! ! +--4 +B-henselae ! ! +--9 ! ! ! ! +-B-bacillif ! ! ! +--6 ! ! ! ! +B--weissii ! +-12 +-10 ! ! ! +B-spp-Deer ! ! +--3 ! ! +-B-clarridg ! ! ! +B-quintana ! +---------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1096.38595 Examined 750 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 B-birtlesi 0.03091 ( 0.00608, 0.05591) ** 11 1 0.03136 ( 0.00675, 0.05625) ** 1 8 0.00336 ( zero, 0.01031) * 8 7 0.02418 ( 0.00586, 0.04251) ** 7 B-grahamii 0.00417 ( zero, 0.01233) * 7 B-elizabet 0.00656 ( zero, 0.01617) ** 8 B--doshiae 0.01046 ( zero, 0.02239) ** 1 4 0.00003 ( zero, 0.00979) 4 5 0.01050 ( zero, 0.02241) ** 5 B-berhoffi 0.02075 ( 0.00400, 0.03751) ** 5 2 0.00695 ( zero, 0.01677) ** 2 B-vinsonii 0.01030 ( zero, 0.02201) ** 2 B-arupensi 0.00338 ( zero, 0.01012) ** 4 12 0.00331 ( zero, 0.00998) * 12 9 0.00004 ( zero, infinity) 9 B-henselae 0.00684 ( zero, 0.01631) ** 9 6 0.01362 ( 0.00034, 0.02706) ** 6 B-bacillif 0.02747 ( 0.00849, 0.04674) ** 6 10 0.00006 ( zero, infinity) 10 B--weissii 0.00006 ( zero, infinity) 10 3 0.00704 ( zero, 0.01684) ** 3 B-spp-Deer 0.00668 ( zero, 0.01621) ** 3 B-clarridg 0.03534 ( 0.01340, 0.05752) ** 12 B-quintana 0.01031 ( zero, 0.02198) ** 11 A-tumefaci 0.26621 ( 0.19458, 0.34028) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 10: Empirical Base Frequencies: A 0.25245 C 0.23261 G 0.30318 T(U) 0.21175 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.480362) +B--doshiae ! ! +B-vinsonii ! +--9 ! ! +B-arupensi ! ! ! ! +B-henselae ! ! ! -10--3 +--5 +B-quintana ! ! ! ! ! ! ! ! +--7 +-B-berhoffi ! ! ! ! ! ! ! ! +-11 +-B-bacillif ! ! ! ! ! ! +--1 +-12 +B--weissii ! ! ! +--8 ! ! +--4 +B-spp-Deer ! ! ! ! ! +-B-clarridg ! ! ! ! +--B-birtlesi ! +--6 ! ! +B-elizabet ! +--2 ! +B-grahamii ! +---------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1165.41483 Examined 514 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 10 B--doshiae 0.00003 ( zero, 0.01188) 10 3 0.03643 ( 0.01361, 0.05930) ** 3 9 0.00707 ( zero, 0.01695) ** 9 B-vinsonii 0.00364 ( zero, 0.01083) ** 9 B-arupensi 0.01017 ( zero, 0.02194) ** 3 1 0.00352 ( zero, 0.01123) 1 5 0.00698 ( zero, 0.01674) ** 5 B-henselae 0.01059 ( zero, 0.02257) ** 5 7 0.00342 ( zero, 0.01023) * 7 B-quintana 0.00691 ( zero, 0.01649) ** 7 11 0.00308 ( zero, 0.01025) 11 B-berhoffi 0.02467 ( 0.00639, 0.04324) ** 11 12 0.03172 ( 0.01063, 0.05313) ** 12 B-bacillif 0.03228 ( 0.01110, 0.05377) ** 12 4 0.00655 ( zero, 0.01686) * 4 8 0.00752 ( zero, 0.01813) ** 8 B--weissii 0.00343 ( zero, 0.01014) ** 8 B-spp-Deer 0.00003 ( zero, infinity) 4 B-clarridg 0.04203 ( 0.01796, 0.06658) ** 1 6 0.01729 ( 0.00106, 0.03354) ** 6 B-birtlesi 0.04485 ( 0.01920, 0.07049) ** 6 2 0.00805 ( zero, 0.01929) ** 2 B-elizabet 0.01033 ( zero, 0.02203) ** 2 B-grahamii 0.00006 ( zero, 0.00704) 10 A-tumefaci 0.27421 ( 0.20162, 0.34867) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 11: Empirical Base Frequencies: A 0.33390 C 0.22109 G 0.27203 T(U) 0.17298 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.411128) +B-birtlesi ! ! +B-grahamii ! +-12 ! ! +B-elizabet ! ! ! ! +B-quintana ! ! +--7 ! ! ! ! +B-vinsonii ! ! ! +--6 ! ! ! ! +B--doshiae -11--4 ! +--2 ! ! ! ! +B--weissii ! ! +--1 +--3 ! ! ! ! ! +-B-bacillif ! ! ! ! +--9 ! ! ! ! ! +--B-clarridg ! ! +--5 ! +--8 ! ! ! ! ! +B-spp-Deer ! ! ! ! ! ! +-10 ! +B-henselae ! ! ! ! ! +B-berhoffi ! ! ! +B-arupensi ! +----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1153.48674 Examined 550 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 B-birtlesi 0.02336 ( zero, 0.04714) ** 11 4 0.02527 ( 0.00233, 0.04842) ** 4 12 0.01803 ( 0.00201, 0.03407) ** 12 B-grahamii 0.00294 ( zero, 0.01017) 12 B-elizabet 0.01094 ( zero, 0.02343) ** 4 10 0.01071 ( zero, 0.02359) ** 10 5 0.00699 ( zero, 0.01675) ** 5 1 0.00340 ( zero, 0.01031) * 1 7 0.00003 ( zero, 0.00718) 7 B-quintana 0.01045 ( zero, 0.02228) ** 7 6 0.00006 ( zero, infinity) 6 B-vinsonii 0.01037 ( zero, 0.02212) ** 6 2 0.00308 ( zero, 0.01010) 2 B--doshiae 0.02514 ( 0.00641, 0.04388) ** 2 3 0.03583 ( 0.01344, 0.05819) ** 3 B--weissii 0.00348 ( zero, 0.01044) * 3 9 0.00350 ( zero, 0.01056) * 9 B-bacillif 0.02444 ( 0.00630, 0.04267) ** 9 8 0.00362 ( zero, 0.01079) ** 8 B-clarridg 0.05772 ( 0.02930, 0.08659) ** 8 B-spp-Deer 0.00336 ( zero, 0.01021) * 1 B-henselae 0.01046 ( zero, 0.02230) ** 5 B-berhoffi 0.03161 ( 0.01101, 0.05256) ** 10 B-arupensi 0.00006 ( zero, infinity) 11 A-tumefaci 0.28650 ( 0.21078, 0.36414) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 12: Empirical Base Frequencies: A 0.29363 C 0.21905 G 0.28628 T(U) 0.20104 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.437766) +B-henselae ! ! +B-berhoffi ! ! ! ! +B-vinsonii ! +-11 +--1 ! ! ! ! ! +----B-birtlesi ! ! ! ! +-10 ! ! ! ! ! +-B--doshiae ! ! +--4 +--6 ! ! ! ! +B-elizabet ! +--8 ! +--7 ! ! ! ! +B-grahamii ! ! ! ! ! ! ! +B-arupensi ! ! ! ! ! ! +B--weissii --2--3 +--5 ! ! ! +----B-bacillif ! ! +-12 ! ! ! +---B-clarridg ! ! +--9 ! ! +B-spp-Deer ! ! ! +B-quintana ! +-------------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1275.40023 Examined 1280 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 2 B-henselae 0.00003 ( zero, infinity) 2 3 0.01056 ( zero, 0.02252) ** 3 8 0.00003 ( zero, infinity) 8 11 0.00003 ( zero, infinity) 11 B-berhoffi 0.02403 ( 0.00631, 0.04205) ** 11 4 0.00697 ( zero, 0.01663) ** 4 1 0.00003 ( zero, infinity) 1 B-vinsonii 0.00682 ( zero, 0.01628) ** 1 10 0.00003 ( zero, 0.01134) 10 B-birtlesi 0.08045 ( 0.04678, 0.11514) ** 10 6 0.01020 ( zero, 0.02217) ** 6 B--doshiae 0.03903 ( 0.01590, 0.06249) ** 6 7 0.01396 ( 0.00003, 0.02789) ** 7 B-elizabet 0.02055 ( 0.00414, 0.03712) ** 7 B-grahamii 0.00003 ( zero, infinity) 4 B-arupensi 0.00003 ( zero, infinity) 8 5 0.04216 ( 0.01803, 0.06633) ** 5 B--weissii 0.01040 ( zero, 0.02254) ** 5 12 0.01037 ( zero, 0.02264) ** 12 B-bacillif 0.08589 ( 0.05099, 0.12120) ** 12 9 0.00354 ( zero, 0.01084) * 9 B-clarridg 0.06433 ( 0.03440, 0.09471) ** 9 B-spp-Deer 0.00003 ( zero, 0.00845) 3 B-quintana 0.00341 ( zero, 0.01008) ** 2 A-tumefaci 0.32548 ( 0.24377, 0.40958) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 13: Empirical Base Frequencies: A 0.27323 C 0.25288 G 0.30176 T(U) 0.17213 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.475842) +B-birtlesi ! ! +B-arupensi ! ! ! ! +B-elizabet ! ! +-10 ! ! +--7 +B-grahamii ! ! ! ! ! ! ! +B--doshiae --5-12 ! ! ! ! +B-quintana ! ! +--8 ! ! ! ! ! +--1 +-B-bacillif ! ! ! ! ! ! +--3 ! ! ! ! ! ! ! ! +B-spp-Deer ! ! ! ! ! +--2 +--6 ! ! ! +--4 ! +B--weissii ! +--9 ! ! ! ! ! +-B-clarridg ! ! ! ! ! ! +B-henselae ! ! +-11 ! ! +B-berhoffi ! ! ! +B-vinsonii ! +-----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1105.28295 Examined 616 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 5 B-birtlesi 0.02068 ( 0.00128, 0.04008) ** 5 12 0.01522 ( zero, 0.03257) ** 12 B-arupensi 0.01027 ( zero, 0.02193) ** 12 9 0.00006 ( zero, 0.01012) 9 8 0.00686 ( zero, 0.01641) ** 8 7 0.01030 ( zero, 0.02228) ** 7 10 0.01978 ( 0.00280, 0.03676) ** 10 B-elizabet 0.01347 ( zero, 0.02711) ** 10 B-grahamii 0.00501 ( zero, 0.01463) * 7 B--doshiae 0.01752 ( 0.00203, 0.03303) ** 8 4 0.00687 ( zero, 0.01644) ** 4 1 0.00003 ( zero, infinity) 1 B-quintana 0.00685 ( zero, 0.01633) ** 1 2 0.00683 ( zero, 0.01628) ** 2 3 0.00003 ( zero, infinity) 3 B-bacillif 0.03459 ( 0.01312, 0.05626) ** 3 6 0.00341 ( zero, 0.01015) ** 6 B-spp-Deer 0.00342 ( zero, 0.01015) ** 6 B--weissii 0.01031 ( zero, 0.02201) ** 2 B-clarridg 0.03497 ( 0.01319, 0.05682) ** 4 11 0.00467 ( zero, 0.01372) * 11 B-henselae 0.01048 ( zero, 0.02238) ** 11 B-berhoffi 0.01939 ( 0.00284, 0.03599) ** 9 B-vinsonii 0.00006 ( zero, infinity) 5 A-tumefaci 0.29472 ( 0.21718, 0.37434) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 14: Empirical Base Frequencies: A 0.32908 C 0.18789 G 0.28843 T(U) 0.19460 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.367436) +B--doshiae ! ! +B--weissii ! +-12 ! ! ! +--B-bacillif ! ! +-11 ! ! ! +B-spp-Deer ! ! +--6 ! ! +--B-clarridg ! ! --4--5 +B-quintana ! ! ! ! ! ! +B-vinsonii ! ! +--1 +-10 ! ! ! ! ! ! +B-arupensi ! ! ! ! ! +--7 ! ! ! ! ! ! +-B-birtlesi ! ! ! +--9 +--8 ! +--3 ! ! +B-elizabet ! ! ! +--2 ! ! ! +B-grahamii ! ! ! ! ! +-B-berhoffi ! ! ! +B-henselae ! +-----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1230.10342 Examined 582 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 4 B--doshiae 0.00006 ( zero, 0.01249) 4 5 0.02499 ( 0.00587, 0.04412) ** 5 12 0.02486 ( 0.00623, 0.04368) ** 12 B--weissii 0.00006 ( zero, 0.00838) 12 11 0.00350 ( zero, 0.01113) 11 B-bacillif 0.04553 ( 0.02060, 0.07086) ** 11 6 0.01455 ( 0.00011, 0.02901) ** 6 B-spp-Deer 0.00308 ( zero, 0.00991) 6 B-clarridg 0.04257 ( 0.01839, 0.06698) ** 5 3 0.02161 ( 0.00397, 0.03932) ** 3 1 0.00251 ( zero, 0.00951) 1 B-quintana 0.01489 ( 0.00043, 0.02937) ** 1 9 0.00405 ( zero, 0.01218) * 9 10 0.01743 ( 0.00164, 0.03337) ** 10 B-vinsonii 0.00679 ( zero, 0.01646) ** 10 7 0.01430 ( 0.00024, 0.02844) ** 7 B-arupensi 0.00006 ( zero, 0.00770) 7 8 0.01790 ( 0.00193, 0.03390) ** 8 B-birtlesi 0.03346 ( 0.01147, 0.05554) ** 8 2 0.01379 ( 0.00002, 0.02768) ** 2 B-elizabet 0.01379 ( 0.00024, 0.02734) ** 2 B-grahamii 0.00006 ( zero, 0.00932) 9 B-berhoffi 0.03234 ( 0.01088, 0.05377) ** 3 B-henselae 0.01073 ( zero, 0.02291) ** 4 A-tumefaci 0.29285 ( 0.21721, 0.37133) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 15: Empirical Base Frequencies: A 0.30061 C 0.19152 G 0.31373 T(U) 0.19414 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.369850) +B-bacillif +--5 ! ! +B-spp-Deer +--8 +-12 ! ! +-B-clarridg ! ! ! +B--weissii ! +--1 +B-quintana ! ! +--3 ! ! ! +B-vinsonii ! ! ! ! ! ! +-B-berhoffi ! +--2 +--6 ! ! ! +B-arupensi ! ! +--4 ! ! ! ! +--B-birtlesi ! ! ! +--7 ! +--9 ! +B-elizabet ! ! +-10 ! ! +B-grahamii ! ! ! +B-henselae ! -11-B--doshiae ! +------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1139.22205 Examined 1524 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 1 0.02157 ( 0.00426, 0.03899) ** 1 8 0.01740 ( 0.00197, 0.03282) ** 8 5 0.00659 ( zero, 0.01624) ** 5 B-bacillif 0.02396 ( 0.00609, 0.04200) ** 5 12 0.01398 ( 0.00022, 0.02773) ** 12 B-spp-Deer 0.00003 ( zero, 0.00954) 12 B-clarridg 0.04105 ( 0.01780, 0.06464) ** 8 B--weissii 0.01371 ( 0.00010, 0.02731) ** 1 2 0.00680 ( zero, 0.01677) ** 2 3 0.00003 ( zero, infinity) 3 B-quintana 0.01017 ( zero, 0.02167) ** 3 B-vinsonii 0.00674 ( zero, 0.01608) ** 2 9 0.00003 ( zero, infinity) 9 4 0.00349 ( zero, 0.01034) ** 4 6 0.00003 ( zero, infinity) 6 B-berhoffi 0.03062 ( 0.01067, 0.05088) ** 6 B-arupensi 0.00337 ( zero, 0.00998) ** 4 7 0.02151 ( 0.00400, 0.03895) ** 7 B-birtlesi 0.04044 ( 0.01645, 0.06462) ** 7 10 0.01003 ( zero, 0.02190) ** 10 B-elizabet 0.02046 ( 0.00405, 0.03690) ** 10 B-grahamii 0.00006 ( zero, 0.01093) 9 B-henselae 0.02063 ( 0.00418, 0.03729) ** 11 B--doshiae 0.00003 ( zero, 0.01479) 11 A-tumefaci 0.21545 ( 0.15469, 0.27791) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 16: Empirical Base Frequencies: A 0.28923 C 0.17618 G 0.36793 T(U) 0.16666 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.271639) +B-henselae ! ! +-B-berhoffi ! ! ! ! +B-quintana ! ! ! ! ! +-12 +B-grahamii ! ! ! ! +--9 --3--8 ! +--7 +-B-birtlesi ! ! +--2 ! ! ! ! ! +B-elizabet ! ! ! ! ! ! ! ! +B-vinsonii ! ! ! +--6 ! ! ! +B-arupensi ! +--1 ! ! +B-spp-Deer ! ! +-11 ! ! ! +B--weissii ! ! +--4 ! ! ! ! +-B-clarridg ! +--5 +-10 ! ! +B--doshiae ! ! ! +-B-bacillif ! +-----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1119.20528 Examined 1422 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 3 B-henselae 0.00006 ( zero, 0.00769) 3 8 0.01070 ( zero, 0.02284) ** 8 B-berhoffi 0.03118 ( 0.01082, 0.05182) ** 8 1 0.00329 ( zero, 0.01015) 1 2 0.00003 ( zero, infinity) 2 12 0.00339 ( zero, 0.01028) * 12 B-quintana 0.01040 ( zero, 0.02217) ** 12 7 0.01979 ( 0.00286, 0.03670) ** 7 9 0.00570 ( zero, 0.01597) ** 9 B-grahamii 0.00006 ( zero, infinity) 9 B-birtlesi 0.03935 ( 0.01611, 0.06292) ** 7 B-elizabet 0.00592 ( zero, 0.01543) * 2 6 0.00339 ( zero, 0.01007) ** 6 B-vinsonii 0.00342 ( zero, 0.01013) ** 6 B-arupensi 0.01026 ( zero, 0.02187) ** 1 5 0.02066 ( 0.00409, 0.03750) ** 5 4 0.01015 ( zero, 0.02203) ** 4 11 0.00006 ( zero, 0.00940) 11 B-spp-Deer 0.01367 ( 0.00027, 0.02709) ** 11 B--weissii 0.00003 ( zero, infinity) 4 10 0.01714 ( 0.00173, 0.03267) ** 10 B-clarridg 0.03900 ( 0.01581, 0.06250) ** 10 B--doshiae 0.01741 ( 0.00174, 0.03309) ** 5 B-bacillif 0.02424 ( 0.00613, 0.04240) ** 3 A-tumefaci 0.29706 ( 0.22093, 0.37679) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 17: Empirical Base Frequencies: A 0.31271 C 0.20186 G 0.32940 T(U) 0.15602 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.308660) +B-arupensi ! ! +B-vinsonii ! ! +--1 ! +B-berhoffi ! ! ! +--4 ! ! ! ! +B-henselae ! ! ! ! ! ! ! +-10 +B-spp-Deer ! +--5 ! ! +--7 ! ! ! ! +--6 +B--weissii ! ! ! ! ! ! ! ! +--3 +--2 +--B-bacillif ! ! ! ! ! ! ! ! ! +--B-clarridg ! ! ! ! ! +--9 +B-quintana ! ! ! ! +B-elizabet ! ! +-12 ! +-11 +B-grahamii ! ! ! +-B-birtlesi ! --8-B--doshiae ! +-------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1116.72190 Examined 1308 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 8 1 0.01652 ( 0.00091, 0.03211) ** 1 B-arupensi 0.00976 ( zero, 0.02134) ** 1 5 0.01182 ( zero, 0.02498) ** 5 B-vinsonii 0.02338 ( 0.00574, 0.04102) ** 5 9 0.00003 ( zero, 0.00910) 9 3 0.00710 ( zero, 0.01688) ** 3 10 0.00003 ( zero, infinity) 10 4 0.00660 ( zero, 0.01590) ** 4 B-berhoffi 0.01701 ( 0.00206, 0.03198) ** 4 B-henselae 0.00679 ( zero, 0.01622) ** 10 2 0.02022 ( 0.00401, 0.03647) ** 2 6 0.00003 ( zero, infinity) 6 7 0.01003 ( zero, 0.02143) ** 7 B-spp-Deer 0.01012 ( zero, 0.02157) ** 7 B--weissii 0.00006 ( zero, infinity) 6 B-bacillif 0.04430 ( 0.02007, 0.06867) ** 2 B-clarridg 0.04917 ( 0.02331, 0.07536) ** 3 B-quintana 0.01358 ( 0.00021, 0.02684) ** 9 11 0.00863 ( zero, 0.02011) ** 11 12 0.00871 ( zero, 0.02025) ** 12 B-elizabet 0.00668 ( zero, 0.01593) ** 12 B-grahamii 0.00006 ( zero, infinity) 11 B-birtlesi 0.02435 ( 0.00609, 0.04283) ** 8 B--doshiae 0.00003 ( zero, 0.01380) 8 A-tumefaci 0.23984 ( 0.17441, 0.30797) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 18: Empirical Base Frequencies: A 0.24489 C 0.21223 G 0.35337 T(U) 0.18952 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.446038) +B-vinsonii ! ! +B-henselae ! ! ! +--8 +B-quintana +--3 ! ! ! ! ! ! +-12 +B-berhoffi ! ! ! ! ! ! ! ! +--1 +B-bacillif ! ! ! ! +-10 ! ! ! ! ! +B--weissii ! +--2 +--7 ! ! ! +B-spp-Deer +--4 ! +--6 ! ! ! +--B-clarridg ! ! ! ! ! ! +B-elizabet ! ! ! +--9 ! ! +--5 +B-grahamii ! ! ! ! ! +B--doshiae ! ! ! +B-arupensi ! -11-B-birtlesi ! +----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1065.29089 Examined 1120 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 4 0.01498 ( zero, 0.03290) ** 4 3 0.00145 ( zero, 0.00800) 3 B-vinsonii 0.00339 ( zero, 0.01001) ** 3 2 0.01012 ( zero, 0.02157) ** 2 8 0.00006 ( zero, 0.00978) 8 B-henselae 0.00998 ( zero, 0.02138) ** 8 12 0.00674 ( zero, 0.01610) ** 12 B-quintana 0.00677 ( zero, 0.01612) ** 12 1 0.00313 ( zero, 0.00993) 1 B-berhoffi 0.01365 ( 0.00017, 0.02711) ** 1 7 0.03757 ( 0.01536, 0.06010) ** 7 10 0.00581 ( zero, 0.01522) * 10 B-bacillif 0.02610 ( 0.00733, 0.04497) ** 10 B--weissii 0.00523 ( zero, 0.01484) ** 7 6 0.00003 ( zero, infinity) 6 B-spp-Deer 0.00333 ( zero, 0.00985) ** 6 B-clarridg 0.03429 ( 0.01292, 0.05569) ** 2 5 0.00670 ( zero, 0.01615) ** 5 9 0.01013 ( zero, 0.02168) ** 9 B-elizabet 0.00003 ( zero, infinity) 9 B-grahamii 0.00668 ( zero, 0.01593) ** 5 B--doshiae 0.01363 ( 0.00023, 0.02704) ** 4 B-arupensi 0.00182 ( zero, 0.00834) 11 B-birtlesi 0.02721 ( 0.00552, 0.04897) ** 11 A-tumefaci 0.28029 ( 0.20582, 0.35674) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 19: Empirical Base Frequencies: A 0.31855 C 0.17815 G 0.28506 T(U) 0.21825 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.403686) +B--doshiae ! ! +B-arupensi ! +-11 ! ! +B-vinsonii ! ! ! ! +B-quintana ! ! +--1 -10--9 ! +-B-berhoffi ! ! ! ! ! +--8 +--B-bacillif ! ! ! ! +--4 ! ! ! ! ! ! +B--weissii ! ! ! +--5 +--6 ! +--2 ! +B-spp-Deer ! ! ! ! ! +--B-clarridg ! ! ! ! +B-henselae ! +-12 ! ! +--B-birtlesi ! +--7 ! ! +B-elizabet ! +--3 ! +B-grahamii ! +-------------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1248.76929 Examined 564 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 10 B--doshiae 0.00003 ( zero, 0.01317) 10 9 0.03938 ( 0.01595, 0.06298) ** 9 11 0.01062 ( zero, 0.02279) ** 11 B-arupensi 0.02080 ( 0.00408, 0.03769) ** 11 B-vinsonii 0.00350 ( zero, 0.01060) * 9 2 0.00235 ( zero, 0.00974) 2 8 0.00326 ( zero, 0.01000) * 8 1 0.00003 ( zero, 0.00717) 1 B-quintana 0.00348 ( zero, 0.01027) ** 1 B-berhoffi 0.04254 ( 0.01833, 0.06687) ** 8 5 0.01765 ( 0.00199, 0.03337) ** 5 4 0.00663 ( zero, 0.01697) * 4 B-bacillif 0.04257 ( 0.01851, 0.06715) ** 4 6 0.01046 ( zero, 0.02262) ** 6 B--weissii 0.01041 ( zero, 0.02226) ** 6 B-spp-Deer 0.00700 ( zero, 0.01679) ** 5 B-clarridg 0.05104 ( 0.02413, 0.07828) ** 2 12 0.00124 ( zero, 0.00814) 12 B-henselae 0.00347 ( zero, 0.01031) ** 12 7 0.02476 ( 0.00499, 0.04464) ** 7 B-birtlesi 0.04385 ( 0.01863, 0.06925) ** 7 3 0.01471 ( zero, 0.03064) ** 3 B-elizabet 0.01388 ( 0.00028, 0.02752) ** 3 B-grahamii 0.00006 ( zero, infinity) 10 A-tumefaci 0.33408 ( 0.25178, 0.42026) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 20: Empirical Base Frequencies: A 0.32619 C 0.20353 G 0.29598 T(U) 0.17430 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.357573) +B--doshiae ! ! +B-quintana ! +--7 ! ! ! +B-vinsonii ! ! +--5 ! ! ! +B-arupensi ! ! +--6 ! ! ! +-B-birtlesi ! ! +--4 ! ! ! +B-grahamii --2-11 +-12 ! ! +B-elizabet ! ! ! ! +--B-berhoffi ! ! ! ! ! +--9 +B-bacillif ! ! ! ! ! ! ! ! +--1 +---B-clarridg ! ! ! ! +-10 ! +--8 +--3 +B-spp-Deer ! ! ! ! ! +B--weissii ! ! ! +B-henselae ! +-----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1174.71531 Examined 1330 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 2 B--doshiae 0.00003 ( zero, 0.01018) 2 11 0.03528 ( 0.01339, 0.05738) ** 11 7 0.00003 ( zero, infinity) 7 B-quintana 0.00673 ( zero, 0.01608) ** 7 5 0.00346 ( zero, 0.01026) ** 5 B-vinsonii 0.01022 ( zero, 0.02177) ** 5 6 0.00346 ( zero, 0.01026) ** 6 B-arupensi 0.00003 ( zero, infinity) 6 4 0.02084 ( 0.00295, 0.03869) ** 4 B-birtlesi 0.03965 ( 0.01563, 0.06391) ** 4 12 0.01366 ( zero, 0.02753) ** 12 B-grahamii 0.00370 ( zero, 0.01311) 12 B-elizabet 0.00644 ( zero, 0.01708) ** 11 8 0.00003 ( zero, infinity) 8 9 0.00003 ( zero, infinity) 9 B-berhoffi 0.04148 ( 0.01797, 0.06529) ** 9 1 0.03461 ( 0.01308, 0.05631) ** 1 B-bacillif 0.00674 ( zero, 0.01642) ** 1 3 0.01032 ( zero, 0.02221) ** 3 10 0.00711 ( zero, 0.01711) ** 10 B-clarridg 0.06719 ( 0.03683, 0.09821) ** 10 B-spp-Deer 0.00997 ( zero, 0.02163) ** 3 B--weissii 0.00333 ( zero, 0.00996) ** 8 B-henselae 0.00680 ( zero, 0.01622) ** 2 A-tumefaci 0.29929 ( 0.22232, 0.37841) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 21: Empirical Base Frequencies: A 0.25482 C 0.21414 G 0.35976 T(U) 0.17129 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.413636) +B--weissii +--6 ! ! +-B-clarridg ! +-11 ! +B-spp-Deer +--1 ! ! +B-arupensi ! ! ! ! ! ! +B-quintana ! +-12 +--8 ! ! ! ! +B-henselae ! ! ! +--9 ! +--5 +B-berhoffi ! ! ! ! +B-vinsonii ! ! ! ! +-10 +--B-bacillif ! ! ! ! +--4 +B-elizabet ! ! +--7 ! +--3 +B-grahamii ! ! ! +--B-birtlesi ! --2-B--doshiae ! +------------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1218.60801 Examined 572 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 2 1 0.02213 ( 0.00434, 0.04012) ** 1 6 0.02422 ( 0.00614, 0.04245) ** 6 B--weissii 0.00003 ( zero, infinity) 6 11 0.02114 ( 0.00415, 0.03816) ** 11 B-clarridg 0.03864 ( 0.01561, 0.06168) ** 11 B-spp-Deer 0.00630 ( zero, 0.01583) ** 1 12 0.01088 ( zero, 0.02370) ** 12 B-arupensi 0.01025 ( zero, 0.02199) ** 12 5 0.01085 ( zero, 0.02325) ** 5 8 0.00339 ( zero, 0.01006) ** 8 B-quintana 0.01018 ( zero, 0.02173) ** 8 9 0.00336 ( zero, 0.01007) ** 9 B-henselae 0.00342 ( zero, 0.01013) ** 9 B-berhoffi 0.01699 ( 0.00207, 0.03192) ** 5 10 0.00003 ( zero, infinity) 10 B-vinsonii 0.00679 ( zero, 0.01618) ** 10 4 0.01457 ( zero, 0.03025) ** 4 B-bacillif 0.05633 ( 0.02800, 0.08474) ** 4 3 0.01546 ( zero, 0.03313) ** 3 7 0.01179 ( zero, 0.02676) ** 7 B-elizabet 0.01629 ( 0.00088, 0.03181) ** 7 B-grahamii 0.00750 ( zero, 0.01886) * 3 B-birtlesi 0.03934 ( 0.01472, 0.06425) ** 2 B--doshiae 0.00006 ( zero, 0.01098) 2 A-tumefaci 0.32341 ( 0.24163, 0.40879) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 22: Empirical Base Frequencies: A 0.30823 C 0.21058 G 0.32782 T(U) 0.15337 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.331345) +B--doshiae ! ! +B-henselae ! +--8 ! ! ! +B-quintana ! ! +--7 ! ! ! +-B-berhoffi ! ! +--1 ! ! ! +-B-bacillif ! ! +--4 ! +--9 ! +B--weissii ! ! ! +--3 ! ! ! ! +B-spp-Deer ! ! ! +--2 ! ! ! +--B-clarridg ! ! ! -12-10 ! +-B-birtlesi ! ! +--5 ! ! ! +B-vinsonii ! ! +--6 ! ! +B-arupensi ! ! ! ! +B-elizabet ! +-11 ! +B-grahamii ! +-------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1147.65283 Examined 494 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 12 B--doshiae 0.00006 ( zero, 0.00972) 12 10 0.03662 ( 0.01378, 0.05964) ** 10 9 0.01032 ( zero, 0.02277) ** 9 8 0.01411 ( 0.00021, 0.02793) ** 8 B-henselae 0.00340 ( zero, 0.01011) ** 8 7 0.00003 ( zero, infinity) 7 B-quintana 0.00349 ( zero, 0.01027) ** 7 1 0.00672 ( zero, 0.01663) ** 1 B-berhoffi 0.02839 ( 0.00862, 0.04834) ** 1 4 0.02869 ( 0.00871, 0.04903) ** 4 B-bacillif 0.03909 ( 0.01597, 0.06263) ** 4 3 0.00638 ( zero, 0.01633) * 3 B--weissii 0.00333 ( zero, 0.01003) * 3 2 0.00702 ( zero, 0.01672) ** 2 B-spp-Deer 0.00006 ( zero, infinity) 2 B-clarridg 0.04956 ( 0.02353, 0.07599) ** 9 5 0.00339 ( zero, 0.01040) * 5 B-birtlesi 0.03605 ( 0.01367, 0.05864) ** 5 6 0.00361 ( zero, 0.01067) ** 6 B-vinsonii 0.01058 ( zero, 0.02255) ** 6 B-arupensi 0.00325 ( zero, 0.01003) 10 11 0.02430 ( 0.00573, 0.04313) ** 11 B-elizabet 0.00657 ( zero, 0.01623) ** 11 B-grahamii 0.00419 ( zero, 0.01238) * 12 A-tumefaci 0.23960 ( 0.17363, 0.30807) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 23: Empirical Base Frequencies: A 0.31722 C 0.19065 G 0.28073 T(U) 0.21140 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.410473) +-B-birtlesi ! ! +B-berhoffi ! ! ! +--1 +B-bacillif ! ! ! ! ! ! +--8 +--B--doshiae ! ! ! +--9 ! ! ! ! ! +B--weissii ! +--7 +-11 +-12 ! ! ! ! +B-spp-Deer ! ! ! ! ! ! ! +--B-clarridg ! ! ! ! +--3 ! +B-grahamii ! ! ! +-10 ! ! ! +B-elizabet ! ! ! --2--5 ! +B-henselae ! ! +--4 ! ! +B-quintana ! ! ! ! +-B-arupensi ! +--6 ! +B-vinsonii ! +-----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1319.70465 Examined 1348 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 2 B-birtlesi 0.03914 ( 0.01168, 0.06664) ** 2 5 0.03351 ( 0.00798, 0.05910) ** 5 3 0.00508 ( zero, 0.01417) * 3 7 0.00958 ( zero, 0.02113) ** 7 1 0.00003 ( zero, 0.00722) 1 B-berhoffi 0.02576 ( 0.00686, 0.04468) ** 1 8 0.02805 ( 0.00825, 0.04813) ** 8 B-bacillif 0.02954 ( 0.00892, 0.05054) ** 8 11 0.02319 ( 0.00372, 0.04268) ** 11 9 0.01700 ( 0.00116, 0.03294) ** 9 B--doshiae 0.04453 ( 0.01955, 0.06986) ** 9 12 0.00718 ( zero, 0.01899) * 12 B--weissii 0.00006 ( zero, 0.00802) 12 B-spp-Deer 0.01016 ( zero, 0.02166) ** 11 B-clarridg 0.05027 ( 0.02331, 0.07756) ** 7 10 0.02250 ( 0.00488, 0.04013) ** 10 B-grahamii 0.00334 ( zero, 0.00992) ** 10 B-elizabet 0.00006 ( zero, 0.00807) 3 4 0.00248 ( zero, 0.01277) 4 B-henselae 0.01301 ( zero, 0.02638) ** 4 B-quintana 0.01001 ( zero, 0.02157) ** 5 6 0.00719 ( zero, 0.01737) ** 6 B-arupensi 0.02723 ( 0.00831, 0.04640) ** 6 B-vinsonii 0.01702 ( 0.00193, 0.03208) ** 2 A-tumefaci 0.30476 ( 0.22649, 0.38536) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 24: Empirical Base Frequencies: A 0.28090 C 0.19893 G 0.33959 T(U) 0.18058 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.367410) +B--doshiae ! ! +B--weissii ! +--1 ! ! ! +-B-clarridg ! +-12 +--8 ! ! ! +B-spp-Deer ! ! ! ! +--4 +B-quintana ! ! ! ! ! ! +-B-berhoffi ! ! +--6 ! ! +B-henselae ! ! --7--3 +---B-birtlesi ! ! +-11 ! ! ! +B-grahamii ! ! +--9 ! ! ! ! +--B-bacillif ! ! ! +-10 ! +--2 +B-elizabet ! ! ! ! +B-vinsonii ! +--5 ! +B-arupensi ! +------------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1242.70857 Examined 590 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 B--doshiae 0.00312 ( zero, 0.01590) 7 3 0.02145 ( 0.00334, 0.03960) ** 3 4 0.01716 ( 0.00217, 0.03231) ** 4 12 0.00005 ( zero, infinity) 12 1 0.01665 ( 0.00177, 0.03170) ** 1 B--weissii 0.01410 ( 0.00028, 0.02797) ** 1 8 0.00323 ( zero, 0.01022) 8 B-clarridg 0.04506 ( 0.02012, 0.06997) ** 8 B-spp-Deer 0.00726 ( zero, 0.01741) ** 12 B-quintana 0.00336 ( zero, 0.00998) ** 4 6 0.00782 ( zero, 0.01898) ** 6 B-berhoffi 0.03343 ( 0.01194, 0.05524) ** 6 B-henselae 0.01757 ( 0.00210, 0.03307) ** 3 2 0.00003 ( zero, 0.00816) 2 9 0.01743 ( 0.00187, 0.03306) ** 9 11 0.01749 ( 0.00200, 0.03302) ** 11 B-birtlesi 0.05690 ( 0.02905, 0.08542) ** 11 B-grahamii 0.00006 ( zero, 0.00774) 9 10 0.01362 ( 0.00002, 0.02719) ** 10 B-bacillif 0.05217 ( 0.02548, 0.07887) ** 10 B-elizabet 0.00003 ( zero, 0.00819) 2 5 0.00687 ( zero, 0.01637) ** 5 B-vinsonii 0.01046 ( zero, 0.02227) ** 5 B-arupensi 0.00313 ( zero, 0.00976) 7 A-tumefaci 0.30962 ( 0.23024, 0.39077) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 25: Empirical Base Frequencies: A 0.27868 C 0.20693 G 0.32867 T(U) 0.18572 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.395038) +B--doshiae ! ! +B-quintana ! ! ! +--5 +B-henselae ! ! ! ! +--4 ! +--2 +B-berhoffi ! ! ! ! ! ! ! ! +--1 +B--weissii ! ! ! ! ! ! ! ! +-11 +B-spp-Deer ! ! ! ! +--7 ! +--8 +--6 +B-bacillif ! ! ! ! ! +--B-clarridg ! ! ! ! +B-grahamii ! ! +-10 ! ! +--3 +B-elizabet ! ! ! ! ! +-12 +B-arupensi ! ! ! +B-vinsonii ! --9-B-birtlesi ! +-----------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1089.22552 Examined 618 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 9 4 0.02242 ( 0.00242, 0.04236) ** 4 B--doshiae 0.01366 ( 0.00005, 0.02721) ** 4 8 0.00309 ( zero, 0.01011) 8 5 0.00336 ( zero, 0.00991) ** 5 B-quintana 0.00667 ( zero, 0.01590) ** 5 2 0.00003 ( zero, 0.00789) 2 B-henselae 0.00333 ( zero, 0.00986) ** 2 1 0.01337 ( 0.00004, 0.02672) ** 1 B-berhoffi 0.01356 ( 0.00018, 0.02704) ** 1 11 0.02361 ( 0.00605, 0.04133) ** 11 B--weissii 0.00003 ( zero, 0.00825) 11 6 0.01026 ( zero, 0.02194) ** 6 7 0.00308 ( zero, 0.00980) 7 B-spp-Deer 0.00003 ( zero, infinity) 7 B-bacillif 0.02002 ( 0.00399, 0.03611) ** 6 B-clarridg 0.05190 ( 0.02546, 0.07857) ** 8 12 0.00335 ( zero, 0.00996) ** 12 3 0.01338 ( 0.00025, 0.02651) ** 3 10 0.03379 ( 0.01261, 0.05515) ** 10 B-grahamii 0.00356 ( zero, 0.01112) 10 B-elizabet 0.01340 ( 0.00007, 0.02679) ** 3 B-arupensi 0.00006 ( zero, 0.00765) 12 B-vinsonii 0.00332 ( zero, 0.00988) ** 9 B-birtlesi 0.03822 ( 0.01334, 0.06327) ** 9 A-tumefaci 0.19278 ( 0.13557, 0.25162) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 26: Empirical Base Frequencies: A 0.30039 C 0.19237 G 0.34745 T(U) 0.15979 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.293048) +B-spp-Deer +--3 +--9 +--B-clarridg ! ! ! +B--weissii +--2 ! ! +B-henselae ! ! ! ! ! ! +B-quintana ! +--4 +-12 ! ! ! ! +--B-birtlesi ! ! ! +-10 ! ! ! ! +B-elizabet +--7 +-11 +--1 ! ! ! +B-grahamii ! ! ! ! ! ! +B-vinsonii ! ! ! +--5 ! ! +--8 +B-arupensi ! ! ! ! ! +B-berhoffi ! ! ! +-B-bacillif ! --6-B--doshiae ! +------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1082.11718 Examined 840 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 6 7 0.01426 ( 0.00001, 0.02851) ** 7 2 0.01045 ( zero, 0.02264) ** 2 9 0.00003 ( zero, 0.00903) 9 3 0.00703 ( zero, 0.01684) ** 3 B-spp-Deer 0.00675 ( zero, 0.01640) ** 3 B-clarridg 0.04561 ( 0.02054, 0.07073) ** 9 B--weissii 0.00349 ( zero, 0.01033) ** 2 4 0.01030 ( zero, 0.02212) ** 4 B-henselae 0.01025 ( zero, 0.02185) ** 4 11 0.00003 ( zero, infinity) 11 12 0.00536 ( zero, 0.01506) 12 B-quintana 0.00839 ( zero, 0.01972) ** 12 10 0.01633 ( 0.00083, 0.03189) ** 10 B-birtlesi 0.04601 ( 0.02021, 0.07227) ** 10 1 0.00954 ( zero, 0.02244) ** 1 B-elizabet 0.02042 ( 0.00410, 0.03692) ** 1 B-grahamii 0.00003 ( zero, 0.00851) 11 8 0.00675 ( zero, 0.01615) ** 8 5 0.00006 ( zero, 0.00821) 5 B-vinsonii 0.00338 ( zero, 0.01000) ** 5 B-arupensi 0.00679 ( zero, 0.01621) ** 8 B-berhoffi 0.02407 ( 0.00617, 0.04197) ** 7 B-bacillif 0.03108 ( 0.01056, 0.05168) ** 6 B--doshiae 0.00003 ( zero, 0.01091) 6 A-tumefaci 0.21825 ( 0.15616, 0.28191) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 27: Empirical Base Frequencies: A 0.28197 C 0.19440 G 0.32775 T(U) 0.19589 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.386504) +B--doshiae ! ! +B-quintana ! +-12 ! ! +B-henselae ! +--9 ! ! ! +--B-berhoffi ! ! +--7 ! ! ! +B-vinsonii ! ! +--8 ! ! +B-arupensi ! ! -11--3 +--B-clarridg ! ! +-10 ! ! +--6 +B--weissii ! ! ! ! ! ! +--2 +B-spp-Deer ! ! ! ! ! ! ! +-B-bacillif ! +--1 ! ! +--B-birtlesi ! ! +--4 ! +--5 +B-grahamii ! ! ! +B-elizabet ! +--------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1283.03839 Examined 840 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 B--doshiae 0.00006 ( zero, 0.01248) 11 3 0.03894 ( 0.01593, 0.06227) ** 3 9 0.00003 ( zero, 0.00721) 9 12 0.00491 ( zero, 0.01455) 12 B-quintana 0.02752 ( 0.00821, 0.04684) ** 12 B-henselae 0.01578 ( 0.00058, 0.03092) ** 9 7 0.00696 ( zero, 0.01664) ** 7 B-berhoffi 0.04873 ( 0.02305, 0.07470) ** 7 8 0.00326 ( zero, 0.01007) 8 B-vinsonii 0.00006 ( zero, infinity) 8 B-arupensi 0.01017 ( zero, 0.02169) ** 3 1 0.01768 ( 0.00191, 0.03344) ** 1 2 0.01722 ( 0.00148, 0.03296) ** 2 6 0.02784 ( 0.00839, 0.04749) ** 6 10 0.00978 ( zero, 0.02163) ** 10 B-clarridg 0.05704 ( 0.02899, 0.08569) ** 10 B--weissii 0.02101 ( 0.00407, 0.03815) ** 6 B-spp-Deer 0.00003 ( zero, 0.00950) 2 B-bacillif 0.02404 ( 0.00601, 0.04225) ** 1 5 0.02062 ( 0.00337, 0.03786) ** 5 4 0.01324 ( zero, 0.02720) ** 4 B-birtlesi 0.04765 ( 0.02165, 0.07388) ** 4 B-grahamii 0.00303 ( zero, 0.00984) 5 B-elizabet 0.00176 ( zero, 0.00872) 11 A-tumefaci 0.25222 ( 0.18451, 0.32334) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 28: Empirical Base Frequencies: A 0.28474 C 0.19232 G 0.31079 T(U) 0.21214 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.412789) +B-vinsonii ! +-10 +-B--doshiae ! ! ! ! ! ! +B-henselae ! +--1 ! ! ! ! +-B-clarridg ! ! ! +--4 ! +--3 ! ! +-B-bacillif ! ! +--9 +-11 ! ! ! ! +B-spp-Deer ! ! +--6 ! ! ! ! ! +B--weissii ! +--5 ! ! ! +-B-berhoffi ! ! ! +B-quintana ! ! +B-grahamii ! +--8 ! +--2 +B-elizabet ! ! ! -12--7 +-B-birtlesi ! ! ! +B-arupensi ! +-----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1260.12576 Examined 892 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 12 10 0.00006 ( zero, 0.01165) 10 B-vinsonii 0.00006 ( zero, infinity) 10 1 0.00661 ( zero, 0.01614) ** 1 B--doshiae 0.02396 ( 0.00619, 0.04191) ** 1 3 0.01710 ( 0.00198, 0.03223) ** 3 B-henselae 0.00006 ( zero, 0.00991) 3 5 0.00674 ( zero, 0.01623) ** 5 6 0.00307 ( zero, 0.01075) 6 9 0.03165 ( 0.01054, 0.05281) ** 9 4 0.00702 ( zero, 0.01746) ** 4 B-clarridg 0.03467 ( 0.01285, 0.05674) ** 4 11 0.00736 ( zero, 0.01795) ** 11 B-bacillif 0.03852 ( 0.01573, 0.06156) ** 11 B-spp-Deer 0.00618 ( zero, 0.01580) ** 9 B--weissii 0.02019 ( 0.00319, 0.03733) ** 6 B-berhoffi 0.03105 ( 0.01054, 0.05183) ** 5 B-quintana 0.02400 ( 0.00626, 0.04196) ** 12 7 0.01051 ( zero, 0.02255) ** 7 2 0.01603 ( zero, 0.03352) ** 2 8 0.02408 ( 0.00584, 0.04241) ** 8 B-grahamii 0.00709 ( zero, 0.02041) 8 B-elizabet 0.01315 ( zero, 0.02838) ** 2 B-birtlesi 0.04277 ( 0.01666, 0.06892) ** 7 B-arupensi 0.00340 ( zero, 0.01023) * 12 A-tumefaci 0.30155 ( 0.22455, 0.38088) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 29: Empirical Base Frequencies: A 0.28344 C 0.24633 G 0.29157 T(U) 0.17866 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.464325) +-B-birtlesi ! ! +B--doshiae ! ! ! +--1 +-B-berhoffi ! ! ! +--3 ! ! ! ! +B-quintana ! ! +--5 ! ! ! +B-henselae ! ! ! ! ! +-12 +--2 +B-spp-Deer ! ! ! ! +-10 ! ! ! +--8 +---B-clarridg ! ! ! ! ! +--6 ! +B--weissii ! ! ! ! ! ! ! +B-vinsonii ! ! ! --9--7 +B-arupensi ! ! ! ! +---B-bacillif ! ! +-11 ! +--4 +B-elizabet ! ! ! +B-grahamii ! +---------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1314.31073 Examined 564 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 9 B-birtlesi 0.03210 ( 0.00510, 0.05934) ** 9 7 0.04288 ( 0.01421, 0.07153) ** 7 6 0.01160 ( zero, 0.02525) ** 6 12 0.01420 ( 0.00025, 0.02821) ** 12 1 0.00331 ( zero, 0.01048) 1 B--doshiae 0.01062 ( zero, 0.02270) ** 1 5 0.02132 ( 0.00411, 0.03851) ** 5 3 0.00710 ( zero, 0.01710) ** 3 B-berhoffi 0.03932 ( 0.01573, 0.06281) ** 3 B-quintana 0.01434 ( 0.00018, 0.02852) ** 5 2 0.00006 ( zero, 0.01036) 2 B-henselae 0.01048 ( zero, 0.02247) ** 2 8 0.03195 ( 0.01099, 0.05300) ** 8 10 0.02616 ( 0.00673, 0.04584) ** 10 B-spp-Deer 0.00953 ( zero, 0.02183) ** 10 B-clarridg 0.07113 ( 0.03888, 0.10396) ** 8 B--weissii 0.00006 ( zero, infinity) 12 B-vinsonii 0.02138 ( 0.00422, 0.03858) ** 6 B-arupensi 0.00006 ( zero, 0.00751) 7 4 0.01084 ( zero, 0.02351) ** 4 11 0.01497 ( 0.00007, 0.02977) ** 11 B-bacillif 0.06105 ( 0.03186, 0.09068) ** 11 B-elizabet 0.00003 ( zero, infinity) 4 B-grahamii 0.00605 ( zero, 0.01613) 9 A-tumefaci 0.25979 ( 0.18763, 0.33382) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 30: Empirical Base Frequencies: A 0.29555 C 0.21466 G 0.30958 T(U) 0.18022 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.395521) +B-henselae ! ! +B-elizabet ! +--7 ! +-10 +B-grahamii ! ! ! ! ! +-B-birtlesi ! +-12 ! ! ! +-B-bacillif ! ! ! +--9 ! ! ! ! ! +--B-clarridg ! ! +--4 +--6 ! ! ! +B-spp-Deer -11--2 ! ! ! +B--weissii ! ! ! ! +B-arupensi ! ! +--5 ! ! +--1 +B-vinsonii ! ! ! ! ! +--3 +B--doshiae ! ! ! ! +B-quintana ! +--8 ! +B-berhoffi ! +--------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1121.63896 Examined 1146 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 B-henselae 0.00003 ( zero, infinity) 11 2 0.00670 ( zero, 0.01600) ** 2 12 0.00004 ( zero, infinity) 12 10 0.02858 ( 0.00844, 0.04863) ** 10 7 0.01238 ( zero, 0.02615) ** 7 B-elizabet 0.01670 ( 0.00203, 0.03136) ** 7 B-grahamii 0.00003 ( zero, infinity) 10 B-birtlesi 0.03812 ( 0.01539, 0.06115) ** 12 4 0.01993 ( 0.00403, 0.03600) ** 4 9 0.00006 ( zero, 0.00755) 9 B-bacillif 0.04382 ( 0.01996, 0.06802) ** 9 6 0.00686 ( zero, 0.01639) ** 6 B-clarridg 0.04480 ( 0.02036, 0.06951) ** 6 B-spp-Deer 0.00313 ( zero, 0.00969) 4 B--weissii 0.00006 ( zero, infinity) 2 3 0.00006 ( zero, 0.00750) 3 1 0.00657 ( zero, 0.01588) ** 1 5 0.00678 ( zero, 0.01627) ** 5 B-arupensi 0.00668 ( zero, 0.01597) ** 5 B-vinsonii 0.00671 ( zero, 0.01600) ** 1 B--doshiae 0.02698 ( 0.00829, 0.04590) ** 3 8 0.00330 ( zero, 0.00980) ** 8 B-quintana 0.00006 ( zero, infinity) 8 B-berhoffi 0.02011 ( 0.00400, 0.03627) ** 11 A-tumefaci 0.24347 ( 0.17810, 0.31047) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 31: Empirical Base Frequencies: A 0.25504 C 0.24347 G 0.30887 T(U) 0.19263 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.481029) +B-henselae ! ! +B-vinsonii ! ! ! +--7 +B-berhoffi ! ! ! ! ! ! ! ! +---B-birtlesi ! ! +--2 +--6 ! ! ! +--5 +B-elizabet ! +--9 ! ! ! ! ! ! +--1 +B-grahamii ! ! ! ! ! ! ! +B-arupensi ! ! ! -11-10 +B-quintana ! ! ! ! +-B--doshiae ! ! ! ! ! ! +--B-bacillif ! +-12 +--8 ! ! +--4 +B-spp-Deer ! ! ! ! ! +--3 +-B-clarridg ! ! ! +B--weissii ! +--------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1118.31785 Examined 524 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 11 B-henselae 0.00003 ( zero, 0.00691) 11 10 0.00349 ( zero, 0.01033) ** 10 9 0.00003 ( zero, infinity) 9 7 0.00003 ( zero, infinity) 7 B-vinsonii 0.00676 ( zero, 0.01614) ** 7 2 0.01062 ( zero, 0.02271) ** 2 B-berhoffi 0.01358 ( 0.00029, 0.02704) ** 2 1 0.00698 ( zero, 0.01680) ** 1 5 0.02471 ( 0.00634, 0.04306) ** 5 6 0.01045 ( zero, 0.02227) ** 6 B-birtlesi 0.06321 ( 0.03299, 0.09375) ** 6 B-elizabet 0.00006 ( zero, infinity) 5 B-grahamii 0.00006 ( zero, infinity) 1 B-arupensi 0.00006 ( zero, 0.00754) 9 B-quintana 0.00006 ( zero, infinity) 10 12 0.02071 ( 0.00394, 0.03753) ** 12 B--doshiae 0.02075 ( 0.00393, 0.03757) ** 12 3 0.01711 ( 0.00182, 0.03240) ** 3 4 0.01305 ( zero, 0.02669) ** 4 8 0.00664 ( zero, 0.01663) ** 8 B-bacillif 0.05517 ( 0.02743, 0.08289) ** 8 B-spp-Deer 0.00746 ( zero, 0.01810) ** 4 B-clarridg 0.03569 ( 0.01349, 0.05801) ** 3 B--weissii 0.00003 ( zero, infinity) 11 A-tumefaci 0.24678 ( 0.17956, 0.31608) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 32: Empirical Base Frequencies: A 0.25600 C 0.19630 G 0.33126 T(U) 0.21643 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.445282) +B-quintana +--3 ! +B-vinsonii +--8 ! ! +B-elizabet ! ! +--9 ! +--7 +B-grahamii ! ! +--1 +B-arupensi ! ! ! ! +-B-berhoffi ! ! ! ! ! ! +B-clarridg ! +-10 +-11 +--5 ! +--4 +B-spp-Deer ! ! ! ! ! ! ! +--2 +-B-bacillif ! ! ! +-12 ! +B--weissii ! ! ! ! ! +B-henselae ! ! ! +B--doshiae ! --6-B-birtlesi ! +--------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1115.32003 Examined 876 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 6 12 0.02685 ( 0.00487, 0.04891) ** 12 5 0.00637 ( zero, 0.01852) 5 1 0.00401 ( zero, 0.01549) 1 8 0.00006 ( zero, infinity) 8 3 0.00004 ( zero, infinity) 3 B-quintana 0.01015 ( zero, 0.02163) ** 3 B-vinsonii 0.01015 ( zero, 0.02165) ** 8 7 0.00336 ( zero, 0.00995) ** 7 9 0.02736 ( 0.00803, 0.04667) ** 9 B-elizabet 0.01361 ( 0.00008, 0.02721) ** 9 B-grahamii 0.00374 ( zero, 0.01155) 7 B-arupensi 0.00003 ( zero, infinity) 1 10 0.00418 ( zero, 0.01288) 10 B-berhoffi 0.02658 ( 0.00754, 0.04588) ** 10 2 0.02073 ( 0.00409, 0.03751) ** 2 4 0.00773 ( zero, 0.01856) ** 4 11 0.00687 ( zero, 0.01643) ** 11 B-clarridg 0.03128 ( 0.01073, 0.05183) ** 11 B-spp-Deer 0.00003 ( zero, infinity) 4 B-bacillif 0.02398 ( 0.00615, 0.04186) ** 2 B--weissii 0.00576 ( zero, 0.01523) * 5 B-henselae 0.01325 ( zero, 0.02674) ** 12 B--doshiae 0.01394 ( zero, 0.02794) ** 6 B-birtlesi 0.02781 ( 0.00519, 0.05049) ** 6 A-tumefaci 0.25364 ( 0.18485, 0.32540) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 33: Empirical Base Frequencies: A 0.29655 C 0.25514 G 0.24219 T(U) 0.20613 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.506466) +B-arupensi ! ! +B-vinsonii ! ! +--4 ! +B-quintana ! ! ! +--6 ! ! ! ! ! +B-grahamii ! ! ! ! +--5 ! +-11 +--2 +B-elizabet ! ! ! ! ! ! ! ! +B-henselae ! ! ! +-10 ! ! ! +-B-berhoffi ! ! ! ! +--3 +--B-clarridg ! ! +--9 ! ! +--1 +B-spp-Deer ! ! ! ! ! ! +--7 +-B-bacillif ! ! ! ! ! +--8 +B--weissii ! ! ! +--B--doshiae ! -12-B-birtlesi ! +---------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1176.57316 Examined 638 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 12 4 0.02180 ( 0.00092, 0.04265) ** 4 B-arupensi 0.01023 ( zero, 0.02185) ** 4 11 0.00006 ( zero, 0.01018) 11 B-vinsonii 0.00006 ( zero, infinity) 11 3 0.01691 ( 0.00200, 0.03186) ** 3 2 0.00006 ( zero, 0.00722) 2 6 0.00670 ( zero, 0.01621) ** 6 B-quintana 0.00703 ( zero, 0.01685) ** 6 5 0.02746 ( 0.00826, 0.04667) ** 5 B-grahamii 0.00003 ( zero, infinity) 5 B-elizabet 0.01019 ( zero, 0.02169) ** 2 10 0.00340 ( zero, 0.01023) * 10 B-henselae 0.00346 ( zero, 0.01027) ** 10 B-berhoffi 0.03461 ( 0.01313, 0.05632) ** 3 8 0.01370 ( zero, 0.02750) ** 8 7 0.01374 ( zero, 0.02759) ** 7 1 0.01008 ( zero, 0.02167) ** 1 9 0.00694 ( zero, 0.01664) ** 9 B-clarridg 0.05572 ( 0.02809, 0.08336) ** 9 B-spp-Deer 0.00003 ( zero, 0.00787) 1 B-bacillif 0.03445 ( 0.01294, 0.05597) ** 7 B--weissii 0.00006 ( zero, infinity) 8 B--doshiae 0.04198 ( 0.01805, 0.06620) ** 12 B-birtlesi 0.03352 ( 0.00901, 0.05803) ** 12 A-tumefaci 0.26367 ( 0.19243, 0.33676) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 34: Empirical Base Frequencies: A 0.28259 C 0.19613 G 0.32705 T(U) 0.19423 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.386276) +-B-birtlesi +-10 ! ! +B-elizabet ! +--6 ! +B-grahamii ! ! +B-quintana +--4 ! ! ! ! +B--weissii ! ! +--7 ! ! ! ! ! +--3 +--B-clarridg ! ! ! ! ! ! +--5 ! ! ! ! ! +-11 +B-spp-Deer ! +--1 +--2 ! +--8 ! ! +--B-bacillif ! ! ! ! ! ! ! +B-berhoffi ! ! ! ! ! +B-henselae ! ! ! ! +B-vinsonii ! +--9 ! +B-arupensi ! -12-B--doshiae ! +----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1236.45427 Examined 876 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 12 8 0.02077 ( 0.00405, 0.03749) ** 8 4 0.00313 ( zero, 0.01003) 4 10 0.02267 ( 0.00414, 0.04117) ** 10 B-birtlesi 0.03923 ( 0.01572, 0.06287) ** 10 6 0.02950 ( 0.00907, 0.05007) ** 6 B-elizabet 0.02360 ( 0.00607, 0.04117) ** 6 B-grahamii 0.00006 ( zero, 0.01065) 4 1 0.01025 ( zero, 0.02196) ** 1 7 0.00328 ( zero, 0.00992) * 7 B-quintana 0.00672 ( zero, 0.01604) ** 7 2 0.00691 ( zero, 0.01720) ** 2 3 0.02759 ( 0.00829, 0.04692) ** 3 B--weissii 0.00966 ( zero, 0.02121) ** 3 11 0.00374 ( zero, 0.01135) * 11 5 0.00003 ( zero, 0.00716) 5 B-clarridg 0.05217 ( 0.02578, 0.07917) ** 5 B-spp-Deer 0.00003 ( zero, infinity) 11 B-bacillif 0.05480 ( 0.02788, 0.08221) ** 2 B-berhoffi 0.03051 ( 0.01009, 0.05096) ** 1 B-henselae 0.00687 ( zero, 0.01644) ** 8 9 0.00687 ( zero, 0.01641) ** 9 B-vinsonii 0.01012 ( zero, 0.02158) ** 9 B-arupensi 0.00327 ( zero, 0.00983) * 12 B--doshiae 0.00006 ( zero, 0.01166) 12 A-tumefaci 0.27523 ( 0.20359, 0.34873) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 35: Empirical Base Frequencies: A 0.30891 C 0.23216 G 0.29735 T(U) 0.16159 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.410371) +B--doshiae ! ! +B-elizabet ! +--1 ! +--7 +B-grahamii ! ! ! ! +-12 +--B-birtlesi ! ! ! ! ! +B-arupensi --8--4 ! ! +B-vinsonii ! ! ! ! +--5 +B-henselae ! ! ! ! +-11 +B-quintana ! ! ! ! +-10 +-B-berhoffi ! ! ! ! +--9 +--B-bacillif ! ! +--2 ! ! ! ! +B-spp-Deer ! +--3 +--6 ! ! +-B-clarridg ! ! ! +B--weissii ! +---------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1257.08713 Examined 2038 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 8 B--doshiae 0.00006 ( zero, 0.01430) 8 4 0.05018 ( 0.02363, 0.07679) ** 4 12 0.01759 ( 0.00215, 0.03314) ** 12 7 0.01560 ( zero, 0.03181) ** 7 1 0.01355 ( zero, 0.02746) ** 1 B-elizabet 0.01064 ( zero, 0.02373) ** 1 B-grahamii 0.00305 ( zero, 0.01370) 7 B-birtlesi 0.05054 ( 0.02298, 0.07839) ** 12 B-arupensi 0.00331 ( zero, 0.01024) 4 5 0.00003 ( zero, 0.00878) 5 B-vinsonii 0.01033 ( zero, 0.02201) ** 5 11 0.00595 ( zero, 0.01638) ** 11 B-henselae 0.01577 ( 0.00051, 0.03093) ** 11 10 0.00595 ( zero, 0.01557) * 10 B-quintana 0.00351 ( zero, 0.01035) ** 10 9 0.00716 ( zero, 0.01756) ** 9 B-berhoffi 0.03470 ( 0.01290, 0.05678) ** 9 3 0.01785 ( 0.00183, 0.03389) ** 3 2 0.00458 ( zero, 0.01384) 2 B-bacillif 0.05932 ( 0.03038, 0.08853) ** 2 6 0.00376 ( zero, 0.01138) * 6 B-spp-Deer 0.01235 ( zero, 0.02580) ** 6 B-clarridg 0.03994 ( 0.01640, 0.06382) ** 3 B--weissii 0.01662 ( 0.00130, 0.03215) ** 8 A-tumefaci 0.27442 ( 0.20128, 0.35088) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 36: Empirical Base Frequencies: A 0.27177 C 0.24093 G 0.26857 T(U) 0.21873 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.485852) +B--doshiae ! ! +--B-clarridg ! +--3 ! ! ! +B--weissii ! ! +-12 ! ! ! +B-spp-Deer ! ! +--5 ! ! +--B-bacillif ! ! ! ! +-B-berhoffi --8-10 ! ! ! ! +--B-birtlesi ! ! +--2 +--4 ! ! ! ! ! ! +B-grahamii ! ! ! ! +--6 +--1 ! ! ! ! ! ! +B-elizabet ! ! +-11 +--9 ! ! ! ! ! ! +B-arupensi ! ! ! ! ! ! +--7 ! +B-vinsonii ! ! ! ! ! +B-quintana ! ! ! +B-henselae ! +-------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1222.07712 Examined 614 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 8 B--doshiae 0.00006 ( zero, 0.01747) 8 10 0.03889 ( 0.01528, 0.06248) ** 10 3 0.01365 ( zero, 0.02775) ** 3 B-clarridg 0.04477 ( 0.02002, 0.06999) ** 3 12 0.01416 ( zero, 0.02851) ** 12 B--weissii 0.00006 ( zero, 0.00773) 12 5 0.01350 ( zero, 0.02706) ** 5 B-spp-Deer 0.01010 ( zero, 0.02192) ** 5 B-bacillif 0.04848 ( 0.02303, 0.07441) ** 10 7 0.01120 ( zero, 0.02426) ** 7 11 0.00003 ( zero, 0.00736) 11 2 0.00356 ( zero, 0.01057) ** 2 B-berhoffi 0.02706 ( 0.00836, 0.04606) ** 2 9 0.00703 ( zero, 0.01683) ** 9 6 0.00704 ( zero, 0.01677) ** 6 4 0.02907 ( 0.00880, 0.04958) ** 4 B-birtlesi 0.05249 ( 0.02499, 0.08057) ** 4 1 0.00946 ( zero, 0.02135) ** 1 B-grahamii 0.00003 ( zero, 0.01035) 1 B-elizabet 0.01681 ( 0.00205, 0.03160) ** 6 B-arupensi 0.00006 ( zero, infinity) 9 B-vinsonii 0.00332 ( zero, 0.00991) ** 11 B-quintana 0.01007 ( zero, 0.02149) ** 7 B-henselae 0.01696 ( 0.00207, 0.03186) ** 8 A-tumefaci 0.23034 ( 0.16664, 0.29668) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 37: Empirical Base Frequencies: A 0.29297 C 0.22408 G 0.31435 T(U) 0.16860 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.400396) +B-henselae ! ! +-B--doshiae ! +-10 ! ! ! +B-arupensi ! ! +--6 ! +--2 +B-vinsonii ! ! ! ! ! ! +---B-birtlesi ! ! +--1 ! +--3 ! +-B-elizabet ! ! ! +--9 ! ! ! +B-grahamii ! ! ! ! ! ! +B--weissii ! ! +--5 --7-11 ! +--B-bacillif ! ! +--8 ! ! ! +--B-clarridg ! ! +--4 ! ! +B-spp-Deer ! ! ! ! +-B-berhoffi ! +-12 ! +B-quintana ! +-------------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1335.45810 Examined 1038 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 B-henselae 0.00631 ( zero, 0.01674) * 7 11 0.01475 ( zero, 0.02970) ** 11 3 0.00006 ( zero, 0.00756) 3 2 0.01429 ( 0.00017, 0.02846) ** 2 10 0.00854 ( zero, 0.02025) ** 10 B--doshiae 0.03359 ( 0.01182, 0.05548) ** 10 6 0.00695 ( zero, 0.01696) ** 6 B-arupensi 0.00512 ( zero, 0.01443) * 6 B-vinsonii 0.01916 ( 0.00275, 0.03570) ** 2 1 0.01993 ( 0.00240, 0.03747) ** 1 B-birtlesi 0.06283 ( 0.03271, 0.09345) ** 1 9 0.01522 ( zero, 0.03055) ** 9 B-elizabet 0.02759 ( 0.00851, 0.04693) ** 9 B-grahamii 0.00006 ( zero, 0.00960) 3 5 0.01914 ( 0.00272, 0.03559) ** 5 B--weissii 0.00506 ( zero, 0.01427) * 5 8 0.01376 ( zero, 0.02954) ** 8 B-bacillif 0.05931 ( 0.02983, 0.08924) ** 8 4 0.01735 ( 0.00125, 0.03363) ** 4 B-clarridg 0.05336 ( 0.02559, 0.08159) ** 4 B-spp-Deer 0.00671 ( zero, 0.01878) 11 12 0.00695 ( zero, 0.01663) ** 12 B-berhoffi 0.02078 ( 0.00413, 0.03754) ** 12 B-quintana 0.00689 ( zero, 0.01651) ** 7 A-tumefaci 0.33134 ( 0.24811, 0.41725) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 38: Empirical Base Frequencies: A 0.31355 C 0.21918 G 0.26673 T(U) 0.20055 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.444754) +B--doshiae ! ! +B-arupensi ! +-12 ! ! +B-vinsonii ! +-11 ! ! ! +B-grahamii ! ! ! +-10 ! ! +--9 +B-elizabet ! +--6 ! ! ! ! +--B-birtlesi ! ! ! ! ! ! +--B-berhoffi ! ! ! +--8 --5--4 +--3 +B-henselae ! ! ! ! ! +B-quintana ! ! ! ! +B--weissii ! ! ! ! +--1 +B-spp-Deer ! ! +--2 ! +--7 +--B-bacillif ! ! ! +--B-clarridg ! +------------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1278.84199 Examined 578 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 5 B--doshiae 0.00003 ( zero, 0.01399) 5 4 0.04256 ( 0.01717, 0.06835) ** 4 6 0.02684 ( 0.00636, 0.04731) ** 6 11 0.01110 ( zero, 0.02550) ** 11 12 0.00782 ( zero, 0.01963) ** 12 B-arupensi 0.00981 ( zero, 0.02175) ** 12 B-vinsonii 0.01122 ( zero, 0.02389) ** 11 9 0.02039 ( 0.00219, 0.03862) ** 9 10 0.02198 ( 0.00316, 0.04094) ** 10 B-grahamii 0.00006 ( zero, 0.00826) 10 B-elizabet 0.00693 ( zero, 0.01655) ** 9 B-birtlesi 0.04410 ( 0.01744, 0.07078) ** 6 3 0.00006 ( zero, 0.00996) 3 8 0.00380 ( zero, 0.01122) ** 8 B-berhoffi 0.03882 ( 0.01575, 0.06234) ** 8 B-henselae 0.00003 ( zero, infinity) 3 B-quintana 0.02111 ( 0.00426, 0.03813) ** 4 1 0.02481 ( 0.00586, 0.04403) ** 1 B--weissii 0.00351 ( zero, 0.01063) * 1 7 0.00588 ( zero, 0.01598) * 7 2 0.00699 ( zero, 0.01719) ** 2 B-spp-Deer 0.00491 ( zero, 0.01429) * 2 B-bacillif 0.05250 ( 0.02499, 0.08005) ** 7 B-clarridg 0.04781 ( 0.02160, 0.07408) ** 5 A-tumefaci 0.31470 ( 0.23516, 0.39740) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 39: Empirical Base Frequencies: A 0.27861 C 0.24050 G 0.32960 T(U) 0.15128 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.428581) +B--doshiae ! ! +B-vinsonii ! ! ! ! +----B-bacillif ! ! ! ! ! +-10 +---B-birtlesi ! ! ! ! +--3 -12--9 ! +--7 +B-grahamii ! ! +--6 ! ! ! ! ! +B-elizabet ! ! ! ! ! ! ! +B-arupensi ! ! ! ! +--5 +B-henselae ! ! +--4 ! ! ! ! +B--weissii ! ! ! +--1 ! ! ! ! +B-spp-Deer ! +--2 +-11 ! ! +--B-clarridg ! ! ! ! +-B-berhoffi ! +--8 ! +B-quintana ! +----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1308.36666 Examined 928 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 12 B--doshiae 0.01051 ( zero, 0.03033) 12 9 0.03480 ( 0.01046, 0.05915) ** 9 B-vinsonii 0.00003 ( zero, infinity) 9 5 0.00006 ( zero, infinity) 5 6 0.01029 ( zero, 0.02192) ** 6 10 0.01125 ( zero, 0.02501) ** 10 B-bacillif 0.07195 ( 0.04048, 0.10427) ** 10 7 0.02340 ( 0.00488, 0.04206) ** 7 3 0.02153 ( 0.00368, 0.03940) ** 3 B-birtlesi 0.05791 ( 0.02939, 0.08679) ** 3 B-grahamii 0.00249 ( zero, 0.00957) 7 B-elizabet 0.00451 ( zero, 0.01513) 6 B-arupensi 0.00003 ( zero, infinity) 5 2 0.01332 ( 0.00019, 0.02652) ** 2 4 0.00006 ( zero, 0.01002) 4 B-henselae 0.02042 ( 0.00408, 0.03689) ** 4 1 0.01689 ( 0.00206, 0.03172) ** 1 B--weissii 0.00003 ( zero, 0.00809) 1 11 0.01394 ( 0.00006, 0.02789) ** 11 B-spp-Deer 0.01645 ( 0.00155, 0.03151) ** 11 B-clarridg 0.05555 ( 0.02799, 0.08326) ** 2 8 0.00675 ( zero, 0.01629) ** 8 B-berhoffi 0.02700 ( 0.00828, 0.04602) ** 8 B-quintana 0.01697 ( 0.00200, 0.03197) ** 12 A-tumefaci 0.28110 ( 0.20694, 0.35748) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 40: Empirical Base Frequencies: A 0.30165 C 0.23248 G 0.28474 T(U) 0.18113 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.438153) +B-birtlesi ! ! +B-grahamii ! +--5 ! ! +B-elizabet ! ! ! ! +B-henselae ! ! +--1 ! ! +-12 +-B-berhoffi ! ! ! ! ! ! ! +B-quintana --7--9 +--6 ! ! ! ! +B--doshiae ! ! ! ! ! ! ! ! +--2 +-B-bacillif ! ! ! ! +-11 ! ! +--4 ! ! ! +B-spp-Deer ! ! ! ! +--8 +-10 ! ! ! ! ! +--B-clarridg ! ! ! ! ! ! +--3 ! +B--weissii ! ! ! ! ! +B-vinsonii ! ! ! +B-arupensi ! +---------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1131.28933 Examined 558 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 7 B-birtlesi 0.02223 ( 0.00252, 0.04205) ** 7 9 0.01661 ( zero, 0.03417) ** 9 5 0.02040 ( 0.00401, 0.03686) ** 5 B-grahamii 0.00332 ( zero, 0.01031) 5 B-elizabet 0.00332 ( zero, 0.01031) 9 3 0.00694 ( zero, 0.01688) ** 3 4 0.01000 ( zero, 0.02132) ** 4 6 0.00475 ( zero, 0.01335) ** 6 12 0.00463 ( zero, 0.01391) 12 1 0.00764 ( zero, 0.01834) ** 1 B-henselae 0.00624 ( zero, 0.01570) ** 1 B-berhoffi 0.03108 ( 0.01026, 0.05183) ** 12 B-quintana 0.01785 ( 0.00228, 0.03348) ** 6 2 0.00661 ( zero, 0.01604) ** 2 B--doshiae 0.01501 ( 0.00056, 0.02953) ** 2 8 0.01909 ( 0.00287, 0.03553) ** 8 11 0.00327 ( zero, 0.01000) * 11 B-bacillif 0.03388 ( 0.01286, 0.05520) ** 11 10 0.00339 ( zero, 0.01022) * 10 B-spp-Deer 0.00003 ( zero, infinity) 10 B-clarridg 0.04115 ( 0.01785, 0.06478) ** 8 B--weissii 0.00649 ( zero, 0.01593) ** 4 B-vinsonii 0.00006 ( zero, infinity) 3 B-arupensi 0.00006 ( zero, infinity) 7 A-tumefaci 0.26580 ( 0.19612, 0.33883) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 41: Empirical Base Frequencies: A 0.25200 C 0.23382 G 0.34971 T(U) 0.16447 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.451462) +B--doshiae ! ! +B-spp-Deer ! +--6 ! +--4 +B--weissii ! ! ! ! ! +-B-clarridg ! ! ! ! +B-henselae ! ! ! ! ! +--2 +B-berhoffi --5--3 ! ! ! ! ! ! +--8 +--B-bacillif ! ! ! ! +-11 ! ! ! ! ! +B-elizabet ! ! +-12 +-10 ! ! ! ! ! +---B-birtlesi ! ! ! ! +--9 ! ! ! ! +B-grahamii ! +--7 ! ! ! ! +B-arupensi ! ! +--1 ! ! +B-vinsonii ! ! ! +B-quintana ! +------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1126.05622 Examined 780 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 5 B--doshiae 0.00006 ( zero, 0.01031) 5 3 0.00544 ( zero, 0.01657) 3 4 0.01012 ( zero, 0.02213) ** 4 6 0.01366 ( zero, 0.02840) ** 6 B-spp-Deer 0.01356 ( 0.00026, 0.02688) ** 6 B--weissii 0.00006 ( zero, 0.00781) 4 B-clarridg 0.04213 ( 0.01751, 0.06675) ** 3 7 0.02063 ( 0.00247, 0.03868) ** 7 12 0.00006 ( zero, infinity) 12 2 0.00003 ( zero, 0.00788) 2 B-henselae 0.01708 ( 0.00204, 0.03205) ** 2 8 0.00743 ( zero, 0.01776) ** 8 B-berhoffi 0.02056 ( 0.00407, 0.03709) ** 8 10 0.00297 ( zero, 0.01055) 10 11 0.01015 ( zero, 0.02180) ** 11 B-bacillif 0.04733 ( 0.02215, 0.07288) ** 11 B-elizabet 0.00403 ( zero, 0.01198) * 10 9 0.01168 ( zero, 0.02489) ** 9 B-birtlesi 0.07284 ( 0.04012, 0.10610) ** 9 B-grahamii 0.00003 ( zero, infinity) 12 1 0.00679 ( zero, 0.01622) ** 1 B-arupensi 0.01018 ( zero, 0.02173) ** 1 B-vinsonii 0.00336 ( zero, 0.01002) ** 7 B-quintana 0.00677 ( zero, 0.01616) ** 5 A-tumefaci 0.21308 ( 0.15128, 0.27629) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 42: Empirical Base Frequencies: A 0.27477 C 0.25144 G 0.30257 T(U) 0.17121 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.471769) +B--doshiae ! ! +B-vinsonii ! +--2 ! ! +B-arupensi ! +--8 ! ! ! +B-quintana ! ! ! ! ! ! +--6 +B-berhoffi ! ! ! +--7 ! ! ! ! +B-henselae ! ! +--3 ! ! ! +-B-clarridg --9--1 ! ! ! ! +-12 +B--weissii ! ! ! +-10 ! ! +--5 +B-spp-Deer ! ! ! ! ! +-B-bacillif ! ! ! ! +B-elizabet ! ! +-11 ! +--4 +B-grahamii ! ! ! +-B-birtlesi ! +--------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1190.38145 Examined 650 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 9 B--doshiae 0.00382 ( zero, 0.01869) 9 1 0.02760 ( 0.00714, 0.04818) ** 1 8 0.00003 ( zero, 0.01080) 8 2 0.01023 ( zero, 0.02178) ** 2 B-vinsonii 0.00006 ( zero, infinity) 2 B-arupensi 0.00336 ( zero, 0.00996) ** 8 6 0.00678 ( zero, 0.01615) ** 6 B-quintana 0.00341 ( zero, 0.01008) ** 6 3 0.00003 ( zero, infinity) 3 7 0.00739 ( zero, 0.01768) ** 7 B-berhoffi 0.02700 ( 0.00783, 0.04640) ** 7 B-henselae 0.00688 ( zero, 0.01644) ** 3 12 0.02751 ( 0.00806, 0.04726) ** 12 B-clarridg 0.04329 ( 0.01854, 0.06822) ** 12 5 0.01713 ( 0.00126, 0.03302) ** 5 10 0.00292 ( zero, 0.00976) 10 B--weissii 0.00663 ( zero, 0.01602) ** 10 B-spp-Deer 0.01384 ( 0.00025, 0.02744) ** 5 B-bacillif 0.04157 ( 0.01785, 0.06529) ** 1 4 0.01768 ( 0.00191, 0.03348) ** 4 11 0.01334 ( zero, 0.02696) ** 11 B-elizabet 0.02374 ( 0.00613, 0.04146) ** 11 B-grahamii 0.00003 ( zero, 0.00908) 4 B-birtlesi 0.03946 ( 0.01598, 0.06310) ** 9 A-tumefaci 0.25420 ( 0.18621, 0.32466) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 43: Empirical Base Frequencies: A 0.27031 C 0.19794 G 0.37006 T(U) 0.16169 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.339935) +B-vinsonii ! +--7 +-B-birtlesi ! ! +-10 ! ! ! +B--doshiae ! +--6 ! ! +B-arupensi +--8 +-12 ! ! ! +B-grahamii ! ! +--9 ! ! +B-elizabet +--4 ! ! ! ! +B-henselae ! ! +--3 ! ! +--B-berhoffi ! ! ! +B-quintana ! ! +B--weissii ! ! --2--1 +--B-clarridg ! ! +--5 ! +-11 +B-spp-Deer ! ! ! +-B-bacillif ! +-----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1167.33347 Examined 532 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 2 4 0.00003 ( zero, 0.01109) 4 8 0.00003 ( zero, infinity) 8 7 0.01068 ( zero, 0.02278) ** 7 B-vinsonii 0.01403 ( 0.00024, 0.02777) ** 7 6 0.00004 ( zero, infinity) 6 10 0.00713 ( zero, 0.01728) ** 10 B-birtlesi 0.03686 ( 0.01407, 0.06007) ** 10 B--doshiae 0.01051 ( zero, 0.02258) ** 6 12 0.01390 ( 0.00026, 0.02764) ** 12 B-arupensi 0.00706 ( zero, 0.01688) ** 12 9 0.01388 ( 0.00019, 0.02758) ** 9 B-grahamii 0.00003 ( zero, infinity) 9 B-elizabet 0.00689 ( zero, 0.01645) ** 8 3 0.00655 ( zero, 0.01630) ** 3 B-henselae 0.01808 ( 0.00215, 0.03399) ** 3 B-berhoffi 0.04341 ( 0.01883, 0.06845) ** 4 B-quintana 0.01411 ( 0.00023, 0.02792) ** 2 1 0.02792 ( 0.00850, 0.04741) ** 1 B--weissii 0.00003 ( zero, infinity) 1 11 0.00341 ( zero, 0.01024) * 11 5 0.00355 ( zero, 0.01057) ** 5 B-clarridg 0.05390 ( 0.02655, 0.08174) ** 5 B-spp-Deer 0.00006 ( zero, infinity) 11 B-bacillif 0.04231 ( 0.01829, 0.06659) ** 2 A-tumefaci 0.30759 ( 0.22934, 0.38949) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 44: Empirical Base Frequencies: A 0.27013 C 0.22091 G 0.34990 T(U) 0.15906 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.394470) +B--doshiae ! ! +B-clarridg ! ! ! ! +B-spp-Deer ! ! ! ! ! +--5 +-B-bacillif ! ! ! ! ! -12--7 ! +--4 +-B-birtlesi ! ! ! ! ! ! ! ! ! ! +B-quintana ! ! ! +--3 +--6 ! ! ! ! ! ! +B-elizabet ! ! ! ! ! +--8 ! ! ! +--2 +B-grahamii ! +--9 ! ! ! ! +B-henselae ! ! ! ! ! ! +-11 +B-arupensi ! ! ! +-10 ! ! +--1 +B-berhoffi ! ! ! ! ! +B-vinsonii ! ! ! +B--weissii ! +---------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1054.80898 Examined 1002 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 12 B--doshiae 0.00006 ( zero, 0.01193) 12 7 0.02219 ( 0.00441, 0.04017) ** 7 B-clarridg 0.01066 ( zero, 0.02304) ** 7 9 0.01711 ( 0.00159, 0.03264) ** 9 5 0.00342 ( zero, 0.01012) ** 5 B-spp-Deer 0.00003 ( zero, 0.00721) 5 4 0.01031 ( zero, 0.02229) ** 4 B-bacillif 0.02391 ( 0.00612, 0.04185) ** 4 3 0.01783 ( 0.00193, 0.03361) ** 3 B-birtlesi 0.03531 ( 0.01346, 0.05750) ** 3 2 0.00302 ( zero, 0.00982) 2 6 0.00670 ( zero, 0.01606) ** 6 B-quintana 0.00699 ( zero, 0.01663) ** 6 8 0.01344 ( 0.00020, 0.02682) ** 8 B-elizabet 0.00674 ( zero, 0.01614) ** 8 B-grahamii 0.00336 ( zero, 0.01003) * 2 11 0.00006 ( zero, 0.00766) 11 B-henselae 0.01693 ( 0.00212, 0.03186) ** 11 1 0.00683 ( zero, 0.01627) ** 1 10 0.00003 ( zero, infinity) 10 B-arupensi 0.00333 ( zero, 0.00987) ** 10 B-berhoffi 0.01708 ( 0.00209, 0.03209) ** 1 B-vinsonii 0.01010 ( zero, 0.02155) ** 9 B--weissii 0.00006 ( zero, infinity) 12 A-tumefaci 0.27369 ( 0.20188, 0.34742) ** * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Data set # 45: Empirical Base Frequencies: A 0.30464 C 0.22318 G 0.29439 T(U) 0.17779 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.411600) +-B-birtlesi +-11 ! +B-grahamii +--8 ! ! +-B-bacillif ! +-12 ! +B-elizabet +--1 ! ! +B-berhoffi ! ! +--2 ! ! +--3 +B-henselae ! ! ! ! ! +--5 +B-quintana ! ! +--4 ! +-B-clarridg ! ! +--9 ! ! ! +B-spp-Deer ! ! +-10 ! ! +B--weissii ! ! ! ! +B-arupensi ! +--7 ! +B-vinsonii ! --6-B--doshiae ! +-----------------A-tumefaci remember: (although rooted by outgroup) this is an unrooted tree! Ln Likelihood = -1155.66658 Examined 608 trees Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 6 4 0.03683 ( 0.01411, 0.05997) ** 4 1 0.00003 ( zero, infinity) 1 8 0.00365 ( zero, 0.01107) * 8 11 0.01828 ( 0.00216, 0.03445) ** 11 B-birtlesi 0.03367 ( 0.01176, 0.05590) ** 11 B-grahamii 0.00006 ( zero, infinity)