Data

Ensembl 84, NCBI 07-2016


Alignment

MAFFT7: mafft --globalpair --jtt 100 --maxiterate 1000 --retree 1


Phylogenetic analysis

MEGA 6.06: ML-GTR+G+I, codon positions 1+2, gaps/missing data: 80% coverage, bootstrap (100) support for ML tree

log likelihood: -2693.8319


Model test (original data)

MEGA 6.06: NJ tree, Method ML, gaps/missing data: 80% coverage

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Table. Maximum Likelihood fits of 24 different nucleotide substitution models
Model	Parameters	BIC	AICc	lnL	(+I)	(+G)	R	f(A)	f(T)	f(C)	f(G)	r(AT)	r(AC)	r(AG)	r(TA)	r(TC)	r(TG)	r(CA)	r(CT)	r(CG)	r(GA)	r(GT)	r(GC)
GTR+G	22	14236.995	14077.999	-7016.950	n/a	0.24	 2.50	0.245	0.227	0.261	0.267	0.020	0.075	0.084	0.022	0.298	0.019	0.070	0.260	0.030	0.077	0.016	0.030
GTR+G+I	23	14243.912	14077.693	-7015.793	0.19	0.36	 2.34	0.245	0.227	0.261	0.267	0.023	0.075	0.090	0.025	0.285	0.021	0.070	0.248	0.032	0.082	0.018	0.031
TN93+G	19	14244.405	14107.079	-7034.502	n/a	0.26	 2.40	0.245	0.227	0.261	0.267	0.033	0.038	0.087	0.036	0.290	0.039	0.036	0.252	0.039	0.080	0.033	0.038
TN93+G+I	20	14246.467	14101.917	-7030.917	0.32	0.56	 2.15	0.245	0.227	0.261	0.267	0.036	0.041	0.095	0.038	0.269	0.042	0.038	0.235	0.042	0.087	0.036	0.041
T92+G+I	17	14262.931	14140.054	-7052.997	0.42	0.95	 1.82	0.236	0.236	0.264	0.264	0.042	0.047	0.170	0.042	0.170	0.047	0.042	0.153	0.047	0.153	0.042	0.047
K2+G+I	16	14265.089	14149.437	-7058.692	0.41	0.95	 1.75	0.250	0.250	0.250	0.250	0.045	0.045	0.159	0.045	0.159	0.045	0.045	0.159	0.045	0.159	0.045	0.045
T92+G	16	14267.083	14151.430	-7059.689	n/a	0.28	 1.89	0.236	0.236	0.264	0.264	0.041	0.046	0.173	0.041	0.173	0.046	0.041	0.155	0.046	0.155	0.041	0.046
K2+G	15	14268.753	14160.326	-7065.140	n/a	0.29	 1.81	0.250	0.250	0.250	0.250	0.045	0.045	0.161	0.045	0.161	0.045	0.045	0.161	0.045	0.161	0.045	0.045
HKY+G+I	19	14285.596	14148.270	-7055.098	0.42	0.97	 1.84	0.245	0.227	0.261	0.267	0.040	0.046	0.173	0.043	0.169	0.047	0.043	0.147	0.047	0.159	0.040	0.046
HKY+G	18	14290.253	14160.151	-7062.042	n/a	0.28	 1.91	0.245	0.227	0.261	0.267	0.039	0.045	0.175	0.042	0.171	0.046	0.042	0.149	0.046	0.161	0.039	0.045
T92+I	16	14303.074	14187.421	-7077.684	0.53	n/a	 1.50	0.236	0.236	0.264	0.264	0.047	0.053	0.159	0.047	0.159	0.053	0.047	0.142	0.053	0.142	0.047	0.053
TN93+I	19	14303.730	14166.403	-7064.164	0.53	n/a	 1.50	0.245	0.227	0.261	0.267	0.045	0.052	0.116	0.049	0.203	0.053	0.049	0.177	0.053	0.107	0.045	0.052
GTR+I	22	14318.729	14159.733	-7057.817	0.53	n/a	 1.49	0.245	0.227	0.261	0.267	0.052	0.065	0.116	0.056	0.201	0.045	0.061	0.176	0.042	0.107	0.038	0.041
HKY+I	18	14324.765	14194.663	-7079.298	0.53	n/a	 1.52	0.245	0.227	0.261	0.267	0.045	0.052	0.161	0.049	0.158	0.053	0.049	0.137	0.053	0.148	0.045	0.052
JC+G+I	15	14511.716	14403.289	-7186.621	0.46	1.80	 0.50	0.250	0.250	0.250	0.250	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083
JC+G	14	14519.401	14418.199	-7195.079	n/a	0.33	 0.50	0.250	0.250	0.250	0.250	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083
JC+I	14	14531.271	14430.070	-7201.014	0.53	n/a	 0.50	0.250	0.250	0.250	0.250	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083
GTR	21	15089.331	14937.558	-7447.734	n/a	n/a	 1.23	0.245	0.227	0.261	0.267	0.040	0.082	0.100	0.043	0.195	0.042	0.077	0.170	0.063	0.092	0.036	0.061
TN93	18	15091.941	14961.839	-7462.886	n/a	n/a	 1.23	0.245	0.227	0.261	0.267	0.051	0.058	0.100	0.055	0.194	0.059	0.055	0.169	0.059	0.092	0.051	0.058
K2	14	15110.999	15009.798	-7490.878	n/a	n/a	 1.22	0.250	0.250	0.250	0.250	0.056	0.056	0.137	0.056	0.137	0.056	0.056	0.137	0.056	0.137	0.056	0.056
K2+I	15	15120.214	15011.787	-7490.870	0.00	n/a	 1.22	0.250	0.250	0.250	0.250	0.056	0.056	0.137	0.056	0.137	0.056	0.056	0.137	0.056	0.137	0.056	0.056
T92	15	15127.026	15018.599	-7494.276	n/a	n/a	 1.22	0.236	0.236	0.264	0.264	0.053	0.059	0.145	0.053	0.145	0.059	0.053	0.130	0.059	0.130	0.053	0.059
HKY	17	15151.721	15028.843	-7497.392	n/a	n/a	 1.22	0.245	0.227	0.261	0.267	0.051	0.059	0.147	0.055	0.144	0.060	0.055	0.125	0.060	0.135	0.051	0.059
JC	13	15311.960	15217.985	-7595.975	n/a	n/a	 0.50	0.250	0.250	0.250	0.250	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083	0.083
NOTE.-- Models with the lowest BIC scores (Bayesian Information Criterion) are considered to describe the substitution pattern the best. For each model, AICc value (Akaike Information Criterion, corrected), Maximum Likelihood value (lnL), and the number of parameters (including branch lengths) are also presented [1]. Non-uniformity of evolutionary rates among sites may be modeled by using a discrete Gamma distribution (+G) with 5 rate categories and by assuming that a certain fraction of sites are evolutionarily invariable (+I). Whenever applicable, estimates of gamma shape parameter and/or the estimated fraction of invariant sites are shown. Assumed or estimated values of transition/transversion bias (R) are shown for each model, as well. They are followed by nucleotide frequencies (f) and rates of base substitutions (r) for each nucleotide pair. Relative values of instantaneous r should be considered when evaluating them. For simplicity, sum of r values is made equal to 1 for each model. For estimating ML values, a tree topology was automatically computed. The analysis involved 8 nucleotide sequences. Codon positions included were 1st+2nd+3rd. All positions with less than 80% site coverage were eliminated. That is, fewer than 20% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 1383 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [2].

Abbreviations: GTR: General Time Reversible; HKY: Hasegawa-Kishino-Yano; TN93: Tamura-Nei; T92: Tamura 3-parameter; K2: Kimura 2-parameter; JC: Jukes-Cantor.

1. Nei M. and Kumar S. (2000). Molecular Evolution and Phylogenetics. Oxford University Press, New York.
2. Tamura K., Stecher G., Peterson D., Filipski A., and Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution30: 2725-2729.