Data

Ensembl 84, NCBI 04-2016


Alignment

T-coffee (tcoffee.crg.cat, 29.4.2016), mode expresso


Phylogenetic analysis

MEGA 6.06: ML-GTR+G, codon positions 1+2+3, gaps/missing data: all sites used, bootstrap (100) support for ML tree

log likelihood: -12222.3586


Model test (original dataset)

MEGA 6.06: NJ tree, Method ML, codon positions 1+2+3, gaps/missing data: all sites used

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+I	38	24840.213	24518.787	-12221.351	0.40	1.21	 2.90	0.278	0.210	0.228	0.284	0.027	0.029	0.154	0.035	0.229	0.036	0.035	0.212	0.036	0.150	0.027	0.029
K2+G+I	34	24846.981	24559.381	-12245.656	0.38	1.03	 2.89	0.250	0.250	0.250	0.250	0.032	0.032	0.186	0.032	0.186	0.032	0.032	0.186	0.032	0.186	0.032	0.032
TN93+G	37	24847.729	24534.760	-12230.340	n/a	0.35	 2.91	0.278	0.210	0.228	0.284	0.027	0.029	0.156	0.035	0.227	0.036	0.035	0.210	0.036	0.153	0.027	0.029
K2+G	33	24849.986	24570.843	-12252.390	n/a	0.34	 2.90	0.250	0.250	0.250	0.250	0.032	0.032	0.186	0.032	0.186	0.032	0.032	0.186	0.032	0.186	0.032	0.032
T92+G+I	35	24855.946	24559.889	-12244.909	0.39	1.06	 2.89	0.244	0.244	0.256	0.256	0.031	0.033	0.190	0.031	0.190	0.033	0.031	0.181	0.033	0.181	0.031	0.033
GTR+G+I	41	24858.230	24511.435	-12214.668	0.40	1.17	 2.89	0.278	0.210	0.228	0.284	0.026	0.039	0.153	0.034	0.230	0.030	0.047	0.213	0.031	0.149	0.022	0.025
T92+G	34	24858.969	24571.369	-12251.650	n/a	0.34	 2.90	0.244	0.244	0.256	0.256	0.031	0.033	0.190	0.031	0.190	0.033	0.031	0.182	0.033	0.182	0.031	0.033
GTR+G	40	24864.301	24525.962	-12222.934	n/a	0.35	 2.91	0.278	0.210	0.228	0.284	0.026	0.039	0.154	0.034	0.229	0.030	0.048	0.211	0.031	0.151	0.022	0.025
HKY+G+I	37	24891.492	24578.522	-12252.221	0.39	1.04	 2.99	0.278	0.210	0.228	0.284	0.027	0.029	0.211	0.036	0.170	0.036	0.036	0.157	0.036	0.207	0.027	0.029
HKY+G	36	24893.590	24589.077	-12258.500	n/a	0.34	 3.00	0.278	0.210	0.228	0.284	0.027	0.029	0.211	0.035	0.170	0.036	0.035	0.157	0.036	0.207	0.027	0.029
TN93+I	37	24942.603	24629.633	-12277.776	0.53	n/a	 2.67	0.278	0.210	0.228	0.284	0.029	0.031	0.155	0.038	0.220	0.038	0.038	0.203	0.038	0.152	0.029	0.031
GTR+I	40	24962.229	24623.891	-12271.898	0.53	n/a	 2.67	0.278	0.210	0.228	0.284	0.031	0.038	0.155	0.041	0.220	0.035	0.046	0.203	0.031	0.151	0.026	0.025
K2+I	33	24964.313	24685.171	-12309.553	0.53	n/a	 2.66	0.250	0.250	0.250	0.250	0.034	0.034	0.182	0.034	0.182	0.034	0.034	0.182	0.034	0.182	0.034	0.034
T92+I	34	24970.245	24682.645	-12307.289	0.53	n/a	 2.66	0.244	0.244	0.256	0.256	0.033	0.035	0.186	0.033	0.186	0.035	0.033	0.178	0.035	0.178	0.033	0.035
JC+G+I	33	26028.858	25749.715	-12841.825	0.41	1.49	 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	32	26034.121	25763.436	-12849.688	n/a	0.39	 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	36	26144.893	25840.380	-12884.152	n/a	n/a	 2.28	0.278	0.210	0.228	0.284	0.032	0.035	0.145	0.042	0.213	0.043	0.042	0.197	0.043	0.142	0.032	0.035
GTR	39	26163.571	25833.689	-12877.800	n/a	n/a	 2.28	0.278	0.210	0.228	0.284	0.034	0.042	0.145	0.045	0.213	0.038	0.052	0.197	0.036	0.142	0.028	0.029
K2	32	26192.293	25921.608	-12928.774	n/a	n/a	 2.28	0.250	0.250	0.250	0.250	0.038	0.038	0.174	0.038	0.174	0.038	0.038	0.174	0.038	0.174	0.038	0.038
T92	33	26200.528	25921.385	-12927.660	n/a	n/a	 2.28	0.244	0.244	0.256	0.256	0.037	0.039	0.178	0.037	0.178	0.039	0.037	0.170	0.039	0.170	0.037	0.039
HKY	35	26253.293	25957.237	-12943.582	n/a	n/a	 2.27	0.278	0.210	0.228	0.284	0.033	0.036	0.195	0.043	0.157	0.044	0.043	0.145	0.044	0.191	0.033	0.036
HKY+I	36	26263.726	25959.213	-12943.568	0.00	n/a	 2.27	0.278	0.210	0.228	0.284	0.033	0.036	0.195	0.043	0.157	0.044	0.043	0.145	0.044	0.191	0.033	0.036
JC	31	27236.772	26974.544	-13456.244	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	32	27247.207	26976.521	-13456.230	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 17 nucleotide sequences. Codon positions included were 1st+2nd+3rd. There were a total of 2079 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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