Data

Ensembl 84, NCBI 07-2016


Alignment

MAFFT7: mafft --globalpair --jtt 100 --maxiterate 1000 --retree 1


Phylogenetic analysis

MEGA 6.06: ML-T92+G+I, codon positions 1+2+3, bootstrap (100) support for ML tree

log likelihood: -7078.5343


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	33	14512.819	14243.370	-7088.642	n/a	0.24	 3.10	0.250	0.250	0.250	0.250	0.031	0.031	0.189	0.031	0.189	0.031	0.031	0.189	0.031	0.189	0.031	0.031
K2+G+I	34	14517.004	14239.393	-7085.651	0.39	0.61	 3.14	0.250	0.250	0.250	0.250	0.030	0.030	0.190	0.030	0.190	0.030	0.030	0.190	0.030	0.190	0.030	0.030
T92+G	34	14519.714	14242.103	-7087.006	n/a	0.24	 3.11	0.261	0.261	0.239	0.239	0.032	0.029	0.181	0.032	0.181	0.029	0.032	0.197	0.029	0.197	0.032	0.029
T92+G+I	35	14523.683	14237.909	-7083.906	0.39	0.59	 3.16	0.261	0.261	0.239	0.239	0.031	0.029	0.182	0.031	0.182	0.029	0.031	0.198	0.029	0.198	0.031	0.029
HKY+G	36	14545.661	14251.725	-7089.811	n/a	0.24	 3.14	0.265	0.256	0.228	0.251	0.031	0.028	0.190	0.032	0.173	0.030	0.032	0.194	0.030	0.201	0.031	0.028
HKY+G+I	37	14549.729	14247.631	-7086.762	0.39	0.60	 3.19	0.265	0.256	0.228	0.251	0.031	0.027	0.191	0.032	0.174	0.030	0.032	0.195	0.030	0.202	0.031	0.027
TN93+G	37	14549.896	14247.798	-7086.845	n/a	0.25	 3.11	0.265	0.256	0.228	0.251	0.031	0.028	0.166	0.032	0.196	0.030	0.032	0.220	0.030	0.176	0.031	0.028
TN93+G+I	38	14552.772	14242.512	-7083.199	0.37	0.57	 3.15	0.265	0.256	0.228	0.251	0.031	0.027	0.164	0.032	0.199	0.030	0.032	0.224	0.030	0.173	0.031	0.027
GTR+G	40	14570.966	14244.383	-7082.128	n/a	0.25	 3.09	0.265	0.256	0.228	0.251	0.031	0.038	0.165	0.033	0.196	0.022	0.044	0.220	0.028	0.175	0.023	0.025
GTR+G+I	41	14573.924	14239.180	-7078.524	0.38	0.58	 3.14	0.265	0.256	0.228	0.251	0.031	0.038	0.163	0.032	0.200	0.022	0.044	0.224	0.027	0.173	0.022	0.025
K2+I	33	14578.048	14308.599	-7121.256	0.64	n/a	 2.97	0.250	0.250	0.250	0.250	0.031	0.031	0.187	0.031	0.187	0.031	0.031	0.187	0.031	0.187	0.031	0.031
T92+I	34	14587.334	14309.722	-7120.815	0.64	n/a	 2.98	0.261	0.261	0.239	0.239	0.033	0.030	0.179	0.033	0.179	0.030	0.033	0.195	0.030	0.195	0.033	0.030
HKY+I	36	14612.375	14318.439	-7123.168	0.64	n/a	 3.01	0.265	0.256	0.228	0.251	0.032	0.028	0.188	0.033	0.171	0.031	0.033	0.192	0.031	0.199	0.032	0.028
TN93+I	37	14620.677	14318.579	-7122.235	0.64	n/a	 2.98	0.265	0.256	0.228	0.251	0.032	0.029	0.177	0.033	0.182	0.031	0.033	0.204	0.031	0.187	0.032	0.029
GTR+I	40	14640.774	14314.191	-7117.032	0.64	n/a	 2.97	0.265	0.256	0.228	0.251	0.035	0.038	0.176	0.036	0.182	0.023	0.045	0.204	0.027	0.187	0.024	0.024
JC+G	32	15186.429	14925.142	-7430.531	n/a	0.26	 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	33	15194.217	14924.768	-7429.341	0.35	0.59	 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	32	15240.433	14979.146	-7457.533	0.63	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
K2	32	15325.390	15064.104	-7500.011	n/a	n/a	 2.61	0.250	0.250	0.250	0.250	0.035	0.035	0.181	0.035	0.181	0.035	0.035	0.181	0.035	0.181	0.035	0.035
T92	33	15336.422	15066.973	-7500.443	n/a	n/a	 2.61	0.261	0.261	0.239	0.239	0.036	0.033	0.173	0.036	0.173	0.033	0.036	0.189	0.033	0.189	0.036	0.033
TN93	36	15350.856	15056.920	-7492.409	n/a	n/a	 2.61	0.265	0.256	0.228	0.251	0.035	0.031	0.148	0.037	0.198	0.035	0.037	0.222	0.035	0.157	0.035	0.031
HKY	35	15366.250	15080.477	-7505.190	n/a	n/a	 2.61	0.265	0.256	0.228	0.251	0.035	0.032	0.181	0.037	0.165	0.035	0.037	0.185	0.035	0.192	0.035	0.032
GTR	39	15373.106	15054.684	-7488.282	n/a	n/a	 2.61	0.265	0.256	0.228	0.251	0.039	0.039	0.148	0.040	0.198	0.027	0.045	0.222	0.030	0.157	0.028	0.028
JC	31	15942.624	15689.500	-7813.712	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 17 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 1533 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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