Table 1. Site-specific parameter values estimated in a model of codon evolution fitted to alignments of human gamete-recognition genes.

Site-specific parameter values for mixed-effects models of evolution (MEME; Murrell et al., 2012) are shown for five codons in four analyses. Parameters include α, the synonymous rate of change; β⁻, the nonsynonymous rate at that site for lineages in the constrained class of codons with β ≤ α; and β⁺, the unconstrained nonsynonymous rate (for codons in the positively-selected lineages of the gene tree). The probability of positive selection at each site (P) is calculated from the likelihood ratio test of models with the constrained value of β⁺ = α versus the unconstrained β⁺; q is the estimated false-discovery rate. Site-specific model parameter values are not shown for ZP1 (na) because no candidate sites were assigned to the positively selected class with β⁺ > α at P < 0.10.

Codon	MEME model parameter value
	α	β−	β+	P	q
C4PBA 300, rs4844573	0	0	184	0.0079	1
ZP3 31, rs2286428	0	0	73.1	0.048	1
ZP3 315, rs2906999	5.2 × 10−6	5.2 × 10−6	186	0.012	1
ZP3 371, rs200481427	0	0	197	0.021	1
ZP2 36, rs2075520	4.1 × 10−9	4.1 × 10−9	148	0.027	1
ZP1	na	na	na	all P > 0.10