Data

Ensembl 84, NCBI 07-2016


Alignment

MAFFT7: mafft --jtt 200 --seed PF04831_seed --maxiterate 1000 --retree 1 --localpair


Phylogenetic analysis

MEGA 6.06: ML-GTR+G(5); bootstrap (100) support for ML tree

log likelihood: -3560.0583


Model test (original dataset)

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	29	7439.670	7226.732	-3584.290	n/a	0.35	 2.93	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	30	7449.017	7228.742	-3584.290	0.00	0.35	 2.93	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	30	7452.882	7232.606	-3586.222	n/a	0.35	 2.96	0.270	0.270	0.230	0.230	0.034	0.029	0.173	0.034	0.173	0.029	0.034	0.202	0.029	0.202	0.034	0.029
HKY+G	32	7460.385	7225.435	-3580.625	n/a	0.35	 2.96	0.227	0.312	0.228	0.233	0.039	0.029	0.174	0.029	0.171	0.029	0.029	0.234	0.029	0.170	0.039	0.029
T92+G+I	31	7462.230	7234.617	-3586.222	0.00	0.35	 2.96	0.270	0.270	0.230	0.230	0.034	0.029	0.173	0.034	0.173	0.029	0.034	0.202	0.029	0.202	0.034	0.029
TN93+G	33	7465.741	7223.455	-3578.630	n/a	0.35	 3.00	0.227	0.312	0.228	0.233	0.039	0.029	0.147	0.029	0.193	0.029	0.029	0.265	0.029	0.143	0.039	0.029
T92+I	30	7467.660	7247.385	-3593.611	0.56	n/a	 2.85	0.270	0.270	0.230	0.230	0.035	0.030	0.171	0.035	0.171	0.030	0.035	0.200	0.030	0.200	0.035	0.030
HKY+G+I	33	7469.732	7227.447	-3580.625	0.00	0.35	 2.96	0.227	0.312	0.228	0.233	0.039	0.029	0.174	0.029	0.171	0.029	0.029	0.234	0.029	0.170	0.039	0.029
TN93+G+I	34	7475.088	7225.467	-3578.630	0.00	0.35	 3.00	0.227	0.312	0.228	0.233	0.039	0.029	0.147	0.029	0.193	0.029	0.029	0.265	0.029	0.143	0.039	0.029
HKY+I	32	7478.361	7243.412	-3589.614	0.56	n/a	 2.82	0.227	0.312	0.228	0.233	0.041	0.030	0.172	0.030	0.168	0.030	0.030	0.231	0.030	0.167	0.041	0.030
GTR+G	36	7479.959	7215.667	-3571.717	n/a	0.36	 2.58	0.227	0.312	0.228	0.233	0.030	0.053	0.152	0.022	0.176	0.027	0.053	0.241	0.031	0.148	0.037	0.031
GTR+G+I	37	7489.307	7217.680	-3571.717	0.00	0.36	 2.58	0.227	0.312	0.228	0.233	0.030	0.053	0.152	0.022	0.176	0.027	0.053	0.241	0.031	0.148	0.037	0.031
K2	28	7708.566	7502.966	-3723.412	n/a	n/a	 2.50	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
K2+I	29	7717.909	7504.971	-3723.410	0.00	n/a	 2.50	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
T92	29	7725.163	7512.225	-3727.037	n/a	n/a	 2.50	0.270	0.270	0.230	0.230	0.038	0.033	0.165	0.038	0.165	0.033	0.038	0.193	0.033	0.193	0.038	0.033
HKY	31	7731.606	7503.993	-3720.910	n/a	n/a	 2.51	0.227	0.312	0.228	0.233	0.044	0.032	0.166	0.032	0.163	0.033	0.032	0.223	0.033	0.162	0.044	0.032
TN93	32	7735.543	7500.594	-3718.205	n/a	n/a	 2.51	0.227	0.312	0.228	0.233	0.045	0.033	0.144	0.032	0.181	0.033	0.032	0.248	0.033	0.140	0.045	0.033
TN93+I	33	7744.886	7502.601	-3718.202	0.00	n/a	 2.51	0.227	0.312	0.228	0.233	0.045	0.033	0.144	0.032	0.181	0.033	0.032	0.248	0.033	0.140	0.045	0.033
GTR	35	7754.754	7497.797	-3713.788	n/a	n/a	 2.14	0.227	0.312	0.228	0.233	0.039	0.054	0.144	0.028	0.167	0.034	0.053	0.228	0.035	0.140	0.045	0.034
JC+G	28	7761.993	7556.393	-3750.126	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
GTR+I	36	7764.097	7499.804	-3713.786	0.00	n/a	 2.14	0.227	0.312	0.228	0.233	0.039	0.054	0.144	0.028	0.167	0.034	0.053	0.228	0.035	0.140	0.045	0.034
JC+G+I	29	7771.341	7558.404	-3750.126	0.00	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
JC	27	8008.418	7810.156	-3878.012	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	28	8017.761	7812.161	-3878.010	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 15 nucleotide sequences. Codon positions included were 1st+2nd+3rd. There were a total of 765 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.
Disclaimer: Although utmost care has been taken to ensure the correctness of the caption, the caption text is provided "as is" without any warranty of any kind. Authors advise the user to carefully check the caption prior to its use for any purpose and report any errors or problems to the authors immediately (www.megasoftware.net). In no event shall the authors and their employers be liable for any damages, including but not limited to special, consequential, or other damages. Authors specifically disclaim all other warranties expressed or implied, including but not limited to the determination of suitability of this caption text for a specific purpose, use, or application.