Data

Ensembl 84, NCBI 04-2016


Alignment

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


Phylogenetic analysis

MEGA 6.06: ML-T93+G(5)+I, codon positions 1+2+3, gaps/missing data: 80%, bootstrap (100) support for ML tree

log likelihood: -17584.3090


Model test (original dataset)

MEGA 6.06: NJ tree, Method ML, codon positions 1+2+3, gaps/missing data: 80%

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	64	35881.373	35305.897	-17588.878	0.27	0.54	 2.94	0.272	0.205	0.244	0.279	0.026	0.030	0.142	0.034	0.255	0.035	0.034	0.215	0.035	0.138	0.026	0.030
GTR+G+I	67	35890.225	35287.780	-17576.814	0.26	0.52	 2.93	0.272	0.205	0.244	0.279	0.024	0.042	0.142	0.032	0.256	0.027	0.047	0.215	0.031	0.138	0.020	0.027
TN93+G	63	35892.999	35326.513	-17600.188	n/a	0.30	 2.93	0.272	0.205	0.244	0.279	0.026	0.031	0.147	0.034	0.249	0.035	0.034	0.209	0.035	0.143	0.026	0.031
T92+G+I	61	35897.011	35348.504	-17613.188	0.22	0.45	 2.94	0.238	0.238	0.262	0.262	0.030	0.033	0.195	0.030	0.195	0.033	0.030	0.178	0.033	0.178	0.030	0.033
T92+G	60	35897.174	35357.657	-17618.767	n/a	0.28	 2.94	0.238	0.238	0.262	0.262	0.030	0.033	0.195	0.030	0.195	0.033	0.030	0.178	0.033	0.178	0.030	0.033
GTR+G	66	35898.054	35304.598	-17586.225	n/a	0.29	 2.91	0.272	0.205	0.244	0.279	0.024	0.043	0.146	0.032	0.250	0.026	0.048	0.210	0.032	0.142	0.019	0.028
K2+G	59	35920.672	35390.145	-17636.013	n/a	0.28	 2.94	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
K2+G+I	60	35921.028	35381.511	-17630.694	0.21	0.43	 2.94	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
HKY+G	62	35972.124	35414.627	-17645.248	n/a	0.28	 3.04	0.272	0.205	0.244	0.279	0.026	0.031	0.209	0.034	0.183	0.035	0.034	0.154	0.035	0.203	0.026	0.031
HKY+G+I	63	35972.277	35405.791	-17639.828	0.23	0.45	 3.04	0.272	0.205	0.244	0.279	0.026	0.031	0.209	0.034	0.183	0.035	0.034	0.154	0.035	0.204	0.026	0.031
GTR+I	66	36713.796	36120.340	-17994.096	0.47	n/a	 2.35	0.272	0.205	0.244	0.279	0.036	0.039	0.138	0.047	0.234	0.041	0.043	0.197	0.032	0.134	0.030	0.028
TN93+I	63	36718.484	36151.998	-18012.931	0.47	n/a	 2.05	0.272	0.205	0.244	0.279	0.033	0.039	0.122	0.044	0.237	0.045	0.044	0.199	0.045	0.119	0.033	0.039
T92+I	60	36816.773	36277.256	-18078.566	0.47	n/a	 1.96	0.238	0.238	0.262	0.262	0.040	0.044	0.173	0.040	0.173	0.044	0.040	0.158	0.044	0.158	0.040	0.044
K2+I	59	36858.442	36327.916	-18104.898	0.47	n/a	 1.96	0.250	0.250	0.250	0.250	0.042	0.042	0.165	0.042	0.165	0.042	0.042	0.165	0.042	0.165	0.042	0.042
HKY+I	62	36893.013	36335.516	-18105.692	0.47	n/a	 1.95	0.272	0.205	0.244	0.279	0.035	0.042	0.183	0.046	0.161	0.048	0.046	0.135	0.048	0.179	0.035	0.042
JC+G	58	37651.915	37130.379	-18507.132	n/a	0.32	 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	59	37653.468	37122.941	-18502.411	0.21	0.50	 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	58	38410.412	37888.875	-18886.380	0.47	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
TN93	62	39283.856	38726.359	-19301.114	n/a	n/a	 1.97	0.272	0.205	0.244	0.279	0.034	0.041	0.126	0.045	0.227	0.046	0.045	0.191	0.046	0.123	0.034	0.041
GTR	65	39310.782	38726.317	-19298.086	n/a	n/a	 1.97	0.272	0.205	0.244	0.279	0.035	0.045	0.126	0.046	0.227	0.045	0.050	0.191	0.042	0.123	0.033	0.036
T92	59	39447.525	38916.998	-19399.439	n/a	n/a	 1.96	0.238	0.238	0.262	0.262	0.040	0.044	0.173	0.040	0.173	0.044	0.040	0.158	0.044	0.158	0.040	0.044
K2	58	39465.336	38943.799	-19413.842	n/a	n/a	 1.96	0.250	0.250	0.250	0.250	0.042	0.042	0.165	0.042	0.165	0.042	0.042	0.165	0.042	0.165	0.042	0.042
HKY	61	39541.672	38993.165	-19435.519	n/a	n/a	 1.95	0.272	0.205	0.244	0.279	0.035	0.042	0.183	0.047	0.160	0.048	0.047	0.135	0.048	0.178	0.035	0.042
JC	57	40885.857	40373.311	-20129.600	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 30 nucleotide sequences. Codon positions included were 1st+2nd+3rd. There were a total of 2008 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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