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, bootstrap (100) consensus gene tree (100)


Model test (original data)

MEGA 6.06: NJ tree, Method ML

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	33	7513.796	7263.757	-3598.801	n/a	0.16	 0.83	0.250	0.250	0.250	0.250	0.068	0.068	0.113	0.068	0.113	0.068	0.068	0.113	0.068	0.113	0.068	0.068
K2+G+I	34	7519.861	7262.250	-3597.043	0.32	0.29	 0.83	0.250	0.250	0.250	0.250	0.068	0.068	0.114	0.068	0.114	0.068	0.068	0.114	0.068	0.114	0.068	0.068
GTR+G	40	7520.359	7217.321	-3568.547	n/a	0.18	 0.87	0.294	0.219	0.232	0.255	0.037	0.108	0.118	0.050	0.109	0.025	0.137	0.103	0.082	0.136	0.021	0.074
HKY+G	36	7521.632	7248.878	-3588.347	n/a	0.16	 0.84	0.294	0.219	0.232	0.255	0.060	0.063	0.116	0.080	0.105	0.070	0.080	0.099	0.070	0.133	0.060	0.063
GTR+G+I	41	7524.308	7213.700	-3565.731	0.38	0.38	 0.87	0.294	0.219	0.232	0.255	0.036	0.110	0.115	0.049	0.113	0.023	0.139	0.106	0.082	0.132	0.020	0.075
JC+G	32	7524.755	7282.289	-3609.072	n/a	0.16	 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
T92+G	34	7524.780	7267.169	-3599.502	n/a	0.16	 0.82	0.256	0.256	0.244	0.244	0.070	0.067	0.110	0.070	0.110	0.067	0.070	0.116	0.067	0.116	0.070	0.067
HKY+G+I	37	7527.318	7246.992	-3586.399	0.33	0.30	 0.85	0.294	0.219	0.232	0.255	0.060	0.063	0.116	0.080	0.106	0.069	0.080	0.100	0.069	0.134	0.060	0.063
T92+G+I	35	7530.798	7265.616	-3597.721	0.32	0.30	 0.83	0.256	0.256	0.244	0.244	0.070	0.066	0.111	0.070	0.111	0.066	0.070	0.116	0.066	0.116	0.070	0.066
JC+G+I	33	7531.062	7281.023	-3607.434	0.31	0.29	 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+G	37	7531.211	7250.885	-3588.345	n/a	0.16	 0.84	0.294	0.219	0.232	0.255	0.060	0.063	0.116	0.080	0.105	0.070	0.080	0.099	0.070	0.134	0.060	0.063
K2+I	33	7535.664	7285.626	-3609.735	0.73	n/a	 0.82	0.250	0.250	0.250	0.250	0.069	0.069	0.113	0.069	0.113	0.069	0.069	0.113	0.069	0.113	0.069	0.069
TN93+G+I	38	7536.836	7248.939	-3586.367	0.33	0.30	 0.85	0.294	0.219	0.232	0.255	0.060	0.063	0.113	0.080	0.108	0.069	0.080	0.102	0.069	0.131	0.060	0.063
JC+I	32	7546.327	7303.861	-3619.858	0.73	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
T92+I	34	7546.789	7289.179	-3610.507	0.73	n/a	 0.82	0.256	0.256	0.244	0.244	0.071	0.067	0.109	0.071	0.109	0.067	0.071	0.115	0.067	0.115	0.071	0.067
GTR	39	7883.609	7588.142	-3754.963	n/a	n/a	 0.64	0.294	0.219	0.232	0.255	0.035	0.118	0.107	0.047	0.080	0.050	0.149	0.076	0.089	0.124	0.043	0.081
GTR+I	40	7893.187	7590.149	-3754.961	0.00	n/a	 0.64	0.294	0.219	0.232	0.255	0.035	0.118	0.107	0.047	0.080	0.050	0.149	0.076	0.089	0.124	0.043	0.081
K2	32	7894.170	7651.704	-3793.779	n/a	n/a	 0.78	0.250	0.250	0.250	0.250	0.070	0.070	0.109	0.070	0.109	0.070	0.070	0.109	0.070	0.109	0.070	0.070
JC	31	7903.169	7668.275	-3803.069	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
T92	33	7903.632	7653.594	-3793.719	n/a	n/a	 0.78	0.256	0.256	0.244	0.244	0.072	0.068	0.107	0.072	0.107	0.068	0.072	0.112	0.068	0.112	0.072	0.068
HKY	35	7905.499	7640.316	-3785.071	n/a	n/a	 0.78	0.294	0.219	0.232	0.255	0.062	0.066	0.110	0.083	0.101	0.072	0.083	0.095	0.072	0.127	0.062	0.066
TN93	36	7914.821	7642.067	-3784.941	n/a	n/a	 0.78	0.294	0.219	0.232	0.255	0.062	0.066	0.107	0.083	0.105	0.072	0.083	0.099	0.072	0.123	0.062	0.066
HKY+I	36	7915.077	7642.322	-3785.069	0.00	n/a	 0.78	0.294	0.219	0.232	0.255	0.062	0.066	0.110	0.083	0.101	0.072	0.083	0.095	0.072	0.127	0.062	0.066
TN93+I	37	7924.399	7644.073	-3784.939	0.00	n/a	 0.78	0.294	0.219	0.232	0.255	0.062	0.066	0.107	0.083	0.105	0.072	0.083	0.099	0.072	0.123	0.062	0.066
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. There were a total of 1004 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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