Table 2.

HyPhy branch- and site-specific tests of positive selection in the codon alignment of exon 2 (PBR) of MHC class Iα in Ch. mydas and Ca. caretta. Evidence of positive selection at each codon position is denoted with an X, with method and statistical criteria specified.

method	statistical cut off	codon position
		2	3	10	18	36	42	51
aBSREL	p ≤ 0.05	no evidence of episodic diversifying selection across phylogeny
FEL	p ≤ 0.05	X					X	X
FUBAR	posterior probability ≥ 0.95			X	X			X
MEME	p ≤ 0.05	X	X	X		X		X
SLAC	p ≤ 0.05							X
BUSTED	p ≤ 0.05	gene-wide episodic diversifying selection on at least one branch