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+3, bootstrap (100) support for ML tree

log likelihood: -6018.2278


Model test (original data)

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

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)
TN93+G	31	12373.248	12130.158	-6034.026	n/a	0.23	 2.63	0.228	0.201	0.287	0.285	0.027	0.038	0.136	0.031	0.287	0.038	0.031	0.201	0.038	0.108	0.027	0.038
TN93+G+I	32	12373.670	12122.742	-6029.315	0.53	1.17	 2.67	0.228	0.201	0.287	0.285	0.027	0.038	0.135	0.030	0.289	0.038	0.030	0.202	0.038	0.107	0.027	0.038
T92+G	28	12379.462	12159.888	-6051.901	n/a	0.22	 2.61	0.214	0.214	0.286	0.286	0.029	0.039	0.208	0.029	0.208	0.039	0.029	0.156	0.039	0.156	0.029	0.039
T92+G+I	29	12380.833	12153.420	-6047.664	0.54	1.17	 2.64	0.214	0.214	0.286	0.286	0.029	0.039	0.209	0.029	0.209	0.039	0.029	0.156	0.039	0.156	0.029	0.039
GTR+G	34	12387.233	12120.629	-6026.251	n/a	0.23	 2.62	0.228	0.201	0.287	0.285	0.020	0.060	0.134	0.022	0.288	0.036	0.048	0.202	0.029	0.107	0.025	0.029
GTR+G+I	35	12388.432	12113.990	-6021.928	0.52	1.08	 2.65	0.228	0.201	0.287	0.285	0.021	0.059	0.133	0.023	0.290	0.037	0.047	0.203	0.028	0.107	0.026	0.028
K2+G	27	12395.674	12183.939	-6064.929	n/a	0.23	 2.52	0.250	0.250	0.250	0.250	0.036	0.036	0.179	0.036	0.179	0.036	0.036	0.179	0.036	0.179	0.036	0.036
K2+G+I	28	12398.834	12179.260	-6061.587	0.48	0.82	 2.55	0.250	0.250	0.250	0.250	0.035	0.035	0.180	0.035	0.180	0.035	0.035	0.180	0.035	0.180	0.035	0.035
TN93+I	31	12399.313	12156.223	-6047.059	0.64	n/a	 2.51	0.228	0.201	0.287	0.285	0.028	0.040	0.143	0.032	0.273	0.040	0.032	0.191	0.040	0.114	0.028	0.040
HKY+G	30	12400.354	12165.102	-6052.502	n/a	0.22	 2.64	0.228	0.201	0.287	0.285	0.027	0.039	0.208	0.031	0.209	0.039	0.031	0.146	0.039	0.166	0.027	0.039
HKY+G+I	31	12401.435	12158.345	-6048.120	0.55	1.22	 2.67	0.228	0.201	0.287	0.285	0.027	0.038	0.209	0.031	0.210	0.038	0.031	0.147	0.038	0.167	0.027	0.038
T92+I	28	12406.477	12186.903	-6065.408	0.65	n/a	 2.52	0.214	0.214	0.286	0.286	0.030	0.040	0.206	0.030	0.206	0.040	0.030	0.154	0.040	0.154	0.030	0.040
GTR+I	34	12414.699	12148.095	-6039.984	0.64	n/a	 2.47	0.228	0.201	0.287	0.285	0.028	0.055	0.141	0.032	0.271	0.042	0.044	0.190	0.027	0.113	0.030	0.027
K2+I	27	12436.664	12224.929	-6085.424	0.65	n/a	 2.40	0.250	0.250	0.250	0.250	0.037	0.037	0.177	0.037	0.177	0.037	0.037	0.177	0.037	0.177	0.037	0.037
JC+G	26	12825.615	12621.720	-6284.823	n/a	0.24	 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+I	27	12830.676	12618.941	-6282.430	0.49	0.97	 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
TN93	30	13053.417	12818.165	-6379.033	n/a	n/a	 2.09	0.228	0.201	0.287	0.285	0.032	0.045	0.130	0.036	0.265	0.045	0.036	0.185	0.045	0.104	0.032	0.045
GTR	33	13069.250	12810.484	-6372.182	n/a	n/a	 2.09	0.228	0.201	0.287	0.285	0.025	0.064	0.130	0.028	0.265	0.041	0.051	0.186	0.039	0.104	0.029	0.039
K2	26	13082.828	12878.933	-6413.429	n/a	n/a	 2.07	0.250	0.250	0.250	0.250	0.041	0.041	0.169	0.041	0.169	0.041	0.041	0.169	0.041	0.169	0.041	0.041
T92	27	13086.630	12874.895	-6410.408	n/a	n/a	 2.08	0.214	0.214	0.286	0.286	0.034	0.046	0.194	0.034	0.194	0.046	0.034	0.146	0.046	0.146	0.034	0.046
HKY	29	13111.079	12883.666	-6412.787	n/a	n/a	 2.08	0.228	0.201	0.287	0.285	0.032	0.046	0.194	0.036	0.195	0.046	0.036	0.136	0.046	0.155	0.032	0.046
HKY+I	30	13120.914	12885.662	-6412.782	0.00	n/a	 2.08	0.228	0.201	0.287	0.285	0.032	0.046	0.194	0.036	0.195	0.046	0.036	0.136	0.046	0.155	0.032	0.046
JC	25	13476.811	13280.754	-6615.343	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
JC+I	26	13486.646	13282.751	-6615.338	0.00	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 14 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 1416 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.
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