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

log likelihood: -20154.9738


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)
GTR+G	58	40958.864	40453.689	-20168.768	n/a	0.63	 1.60	0.225	0.179	0.292	0.304	0.041	0.074	0.159	0.051	0.214	0.050	0.057	0.131	0.039	0.117	0.029	0.037
GTR+G+I	59	40960.824	40446.942	-20164.392	0.10	0.87	 1.60	0.225	0.179	0.292	0.304	0.041	0.073	0.156	0.052	0.216	0.051	0.056	0.132	0.038	0.116	0.030	0.037
TN93+G	55	40993.203	40514.150	-20202.006	n/a	0.64	 1.61	0.225	0.179	0.292	0.304	0.033	0.054	0.160	0.042	0.217	0.057	0.042	0.133	0.057	0.118	0.033	0.054
TN93+G+I	56	40995.836	40508.076	-20197.967	0.10	0.87	 1.61	0.225	0.179	0.292	0.304	0.033	0.054	0.158	0.042	0.219	0.057	0.042	0.134	0.057	0.117	0.033	0.054
T92+G	52	41009.775	40556.845	-20226.361	n/a	0.63	 1.60	0.202	0.202	0.298	0.298	0.038	0.056	0.186	0.038	0.186	0.056	0.038	0.126	0.056	0.126	0.038	0.056
HKY+G	54	41013.869	40543.524	-20217.696	n/a	0.63	 1.61	0.225	0.179	0.292	0.304	0.033	0.055	0.190	0.042	0.183	0.057	0.042	0.112	0.057	0.140	0.033	0.055
T92+G+I	53	41016.854	40555.217	-20224.545	0.07	0.77	 1.60	0.202	0.202	0.298	0.298	0.038	0.056	0.186	0.038	0.186	0.056	0.038	0.126	0.056	0.126	0.038	0.056
HKY+G+I	55	41020.124	40541.071	-20215.467	0.08	0.79	 1.61	0.225	0.179	0.292	0.304	0.034	0.055	0.190	0.042	0.183	0.057	0.042	0.112	0.057	0.140	0.034	0.055
K2+G	51	41140.853	40696.631	-20297.256	n/a	0.66	 1.51	0.250	0.250	0.250	0.250	0.050	0.050	0.150	0.050	0.150	0.050	0.050	0.150	0.050	0.150	0.050	0.050
K2+G+I	52	41150.318	40697.388	-20296.633	0.04	0.74	 1.50	0.250	0.250	0.250	0.250	0.050	0.050	0.150	0.050	0.150	0.050	0.050	0.150	0.050	0.150	0.050	0.050
GTR+I	58	41655.790	41150.615	-20517.231	0.23	n/a	 1.39	0.225	0.179	0.292	0.304	0.043	0.069	0.139	0.054	0.215	0.065	0.053	0.131	0.046	0.103	0.038	0.044
TN93+I	55	41689.429	41210.377	-20550.120	0.23	n/a	 1.23	0.225	0.179	0.292	0.304	0.039	0.064	0.143	0.049	0.194	0.067	0.049	0.118	0.067	0.106	0.039	0.064
HKY+I	54	41762.085	41291.740	-20591.804	0.24	n/a	 1.21	0.225	0.179	0.292	0.304	0.040	0.065	0.169	0.050	0.163	0.068	0.050	0.099	0.068	0.125	0.040	0.065
T92+I	52	41770.742	41317.812	-20606.845	0.23	n/a	 1.22	0.202	0.202	0.298	0.298	0.045	0.066	0.167	0.045	0.167	0.066	0.045	0.113	0.066	0.113	0.045	0.066
K2+I	51	41875.320	41431.098	-20664.490	0.23	n/a	 1.30	0.250	0.250	0.250	0.250	0.054	0.054	0.142	0.054	0.142	0.054	0.054	0.142	0.054	0.142	0.054	0.054
JC+G	50	41926.480	41490.966	-20695.426	n/a	0.70	 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	51	41935.707	41491.485	-20694.684	0.05	0.80	 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	50	42591.985	42156.471	-21028.179	0.23	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	54	42981.525	42511.180	-21201.524	n/a	n/a	 1.22	0.225	0.179	0.292	0.304	0.039	0.064	0.143	0.049	0.194	0.067	0.049	0.119	0.067	0.105	0.039	0.064
GTR	57	42988.942	42492.475	-21189.164	n/a	n/a	 1.22	0.225	0.179	0.292	0.304	0.038	0.079	0.142	0.047	0.194	0.062	0.060	0.119	0.060	0.105	0.037	0.057
K2	50	43026.861	42591.347	-21245.617	n/a	n/a	 1.36	0.250	0.250	0.250	0.250	0.053	0.053	0.144	0.053	0.144	0.053	0.053	0.144	0.053	0.144	0.053	0.053
T92	51	43027.096	42582.874	-21240.378	n/a	n/a	 1.22	0.202	0.202	0.298	0.298	0.045	0.066	0.166	0.045	0.166	0.066	0.045	0.113	0.066	0.113	0.045	0.066
HKY	53	43029.823	42568.185	-21231.029	n/a	n/a	 1.21	0.225	0.179	0.292	0.304	0.040	0.065	0.169	0.050	0.162	0.068	0.050	0.099	0.068	0.125	0.040	0.065
JC	49	43679.664	43252.858	-21577.375	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 26 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 1752 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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