Table 1. Unique replacement sites and results of branch-site analyses of positive selection for mitochondrial protein-coding genes early in snake evolution.

Gene	Gene Length (codons)	Sites with Unique Replacements	Positively Selected Sites
			Snake Branch			Alethinophidia Branch
			Sites PP>90	Sites PP>95	Sites PP>99	Sites PP>90	Sites PP>95	Sites PP>99
ATP6	221	3	6	5	3	15	6	4
ATP8	45	2	0	0	0	7	5	0
COI	509	23	7	3	0	27	12	5
COII	226	10	4	3	1	25	15	9
COIII	259	9	7	3	2	12	6	4
CytB	366	19	9	4	1	36	16	10
ND1	313	4	2	1	1	9	2	2
ND2	335	5	5	0	0	23	8	4
ND3	109	2	0	0	0	9	5	3
ND4	443	4	1	0	0	11	5	2
ND4L	93	3	1	0	0	6	2	1
ND5	619	12	9	3	2	14	8	3
ND6	143	1	1	1	1	21	8	2

The number of sites per gene inferred as being under positive selection based on branch-site model analyses in PAML are shown at two posterior probability (PP) significance levels. The branch-site model of positive selection was tested for two main snake lineages: the lineage leading to all snakes (“Snake Branch”) and the lineage leading to the Alethinophidia (“Alethinophidia Branch”); relative support for selection at sites is based on posterior probability (PP) support from Bayes empirical Bayes estimates in PAML. Note: in this table, “sites” refer to amino acid sites.