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, gaps/missing data: 80% coverage, bootstrap (100) support for ML tree

log likelihood: -8469.2890


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)
K2+G+I	28	17268.855	17050.341	-8497.126	0.58	2.85	 2.46	0.250	0.250	0.250	0.250	0.036	0.036	0.178	0.036	0.178	0.036	0.036	0.178	0.036	0.178	0.036	0.036
T92+G+I	29	17272.719	17046.405	-8494.155	0.58	2.72	 2.44	0.261	0.261	0.239	0.239	0.038	0.035	0.170	0.038	0.170	0.035	0.038	0.185	0.035	0.185	0.038	0.035
GTR+G+I	35	17281.832	17008.717	-8469.289	0.58	2.37	 2.38	0.263	0.259	0.227	0.251	0.059	0.039	0.135	0.060	0.201	0.027	0.046	0.230	0.017	0.142	0.028	0.016
TN93+G+I	32	17293.563	17043.847	-8489.865	0.57	2.25	 2.44	0.263	0.259	0.227	0.251	0.037	0.033	0.134	0.038	0.204	0.036	0.038	0.233	0.036	0.141	0.037	0.033
HKY+G+I	31	17306.477	17064.562	-8501.226	0.58	2.72	 2.48	0.263	0.259	0.227	0.251	0.037	0.033	0.179	0.038	0.162	0.036	0.038	0.185	0.036	0.188	0.037	0.033
K2+I	27	17320.285	17109.573	-8527.745	0.60	n/a	 1.71	0.250	0.250	0.250	0.250	0.046	0.046	0.158	0.046	0.158	0.046	0.046	0.158	0.046	0.158	0.046	0.046
GTR+I	34	17324.868	17059.552	-8495.711	0.60	n/a	 2.06	0.263	0.259	0.227	0.251	0.065	0.039	0.144	0.066	0.178	0.032	0.045	0.203	0.022	0.152	0.033	0.020
HKY+I	30	17361.838	17127.723	-8533.810	0.60	n/a	 1.71	0.263	0.259	0.227	0.251	0.048	0.042	0.158	0.049	0.143	0.046	0.049	0.163	0.046	0.166	0.048	0.042
GTR+G	34	17368.615	17103.299	-8517.584	n/a	0.22	 2.83	0.263	0.259	0.227	0.251	0.045	0.041	0.107	0.046	0.244	0.022	0.048	0.279	0.018	0.113	0.022	0.016
K2+G	27	17369.243	17158.530	-8552.224	n/a	0.21	 2.51	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
TN93+I	31	17372.984	17131.069	-8534.480	0.60	n/a	 1.62	0.263	0.259	0.227	0.251	0.049	0.043	0.108	0.050	0.186	0.048	0.050	0.213	0.048	0.114	0.049	0.043
TN93+G	31	17376.022	17134.107	-8535.999	n/a	0.22	 2.75	0.263	0.259	0.227	0.251	0.034	0.030	0.112	0.035	0.237	0.033	0.035	0.270	0.033	0.117	0.034	0.030
HKY+G	30	17403.755	17169.640	-8554.769	n/a	0.21	 2.53	0.263	0.259	0.227	0.251	0.037	0.032	0.180	0.037	0.163	0.035	0.037	0.186	0.035	0.189	0.037	0.032
T92+G	28	17553.960	17335.446	-8639.678	n/a	0.52	 2.14	0.261	0.261	0.239	0.239	0.041	0.038	0.163	0.041	0.163	0.038	0.041	0.178	0.038	0.178	0.041	0.038
JC+G+I	27	17914.745	17704.033	-8824.975	0.59	6.80	 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+I	26	17918.787	17715.876	-8831.899	0.60	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+G	26	18022.920	17820.009	-8883.966	n/a	0.22	 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	19027.591	18793.476	-9366.687	n/a	n/a	 1.72	0.263	0.259	0.227	0.251	0.047	0.041	0.104	0.048	0.197	0.046	0.048	0.225	0.046	0.109	0.047	0.041
GTR	33	19033.360	18775.845	-9354.860	n/a	n/a	 1.72	0.263	0.259	0.227	0.251	0.058	0.049	0.104	0.059	0.197	0.037	0.057	0.224	0.035	0.110	0.038	0.032
T92	27	19103.110	18892.397	-9419.157	n/a	n/a	 1.71	0.261	0.261	0.239	0.239	0.048	0.044	0.151	0.048	0.151	0.044	0.048	0.165	0.044	0.165	0.048	0.044
K2	26	19107.096	18904.185	-9426.054	n/a	n/a	 1.71	0.250	0.250	0.250	0.250	0.046	0.046	0.158	0.046	0.158	0.046	0.046	0.158	0.046	0.158	0.046	0.046
T92+I	28	19112.883	18894.369	-9419.140	0.00	n/a	 1.71	0.261	0.261	0.239	0.239	0.048	0.044	0.151	0.048	0.151	0.044	0.048	0.165	0.044	0.165	0.048	0.044
HKY	29	19139.699	18913.384	-9427.644	n/a	n/a	 1.71	0.263	0.259	0.227	0.251	0.048	0.042	0.158	0.049	0.143	0.046	0.049	0.163	0.046	0.166	0.048	0.042
JC	25	19641.244	19446.134	-9698.031	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 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 1392 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.