Base composition, selection, and phylogenetic significance of indels in the recombination activating gene-1 in vertebrates

Table 5 Selection test

		Log-likelihood	d_N/d_S	P-value Chi-square	PSS
Actinopterygii	Log-likelihood M1a	-21118.741643	0.1331	1	-
	Log-likelihood M2a	-21118.741643	0.1331
Amphibia	Log-likelihood M1a	-22490.686927	0.1049	1	-
	Log-likelihood M2a	-22490.686928	0.1049		33 T
Aves	Log-likelihood M1a	-16728.712033	0.1695	10^-7*	76 W
	Log-likelihood M2a	-16714.234740	0.1807
Chondrichthyes	Log-likelihood M1a	-6993.815583	0.1783	1	-
	Log-likelihood M2a	-6993.815583	0.1783
Crocodylia	Log-likelihood M1a	-3538.892722	0.2144	1	-
	Log-likelihood M2a	-3538.892722	0.2144
Lepidosauria	Log-likelihood M1a	-38632.722264	0.2632	0.032*	159 H
	Log-likelihood M2a	-38629.286234	0.2665
Mammalia	Log-likelihood M1a	-10175.360951	0.0713	1	-
	Log-likelihood M2a	-10175.360951	0.0713
Testudines	Log-likelihood M1a	-10208.575616	0.1653	0.1145	23 V
	Log-likelihood M2a	-10206.408516	0.1730

Test for positive selection using the M1a (neutral) and M2a (positive) models, and a maximum of 60 Rag1 sequences for each vertebrate lineage (see Methods for further explanations). "d_N/d_S" indicates the substitution rate ratio averaged across all sites and lineages. "PSS" indicates the positively selected sites (calculated as in [47]). We indicate the position of the amino acid under positive selection (based on the within group alignment used for this analysis) and the corresponding amino acid. * indicates the statistically significant p-values (<0.05) in the Chi-square test.

ISSN: 1742-9994