Table 2.

Tests of positive selection among abalone ZP genes

Gene	One ratio model (M0)	Neutral model (M8a)	Selection model (M8)	2 Δ lnL (M8a-vs-M8)
VERL	ω0 = 0.5	ω0 = 1.00, pO = 0.55	ω0 = 2.34, pO = 0.14	0.70
(C terminus only)
VEZP2	ω0 = 0.20	ω0 = 1.00, pO = 0.10	ω0 = 1.00, pO = 0.10	0
VEZP3	ω0 = 0.60	ω0 = 1.00, pO = 0.48	ω0 = 3.7, pO = 0.08	6.24*
VEZP4	ω0 = 0.40	ω0 = 1.00, pO = 0.40	ω0 = 3.5, pO = 0.11	5.86*
VEZP5	ω0 = 1.06	ω0 = 1.00, pO = 0.56	ω0 = 10.16, pO = 0.07	28.64**
VEZP6	ω0 = 0.17	ω0 = 1.00, pO = 0.51	ω0 = 21.34, pO = 0.01	6.20*
VEZP7	ω0 = 0.57	ω0 = 1.00, pO = 0.46	ω0 = 1.00, pO = 0.46	0
VEZP8	ω0 = 0.45	ω0 = 1.00, pO = 0.00	ω0 = 1.00, pO = 0.00	0
VEZP9	ω0 = 1.11	ω0 = 1.00, pO = 0.80	ω0 = 10.06, pO = 0.04	9.22*
VEZP10	ω0 = 0.11	ω0 = 1.00, pO = 0.10	ω0 = 10.74, pO = 0.01	7.96*
ZPA	ω0 = 0.17	ω0 = 1.00, pO = 0.16	ω0 = 1.74, pO = 0.11	1.12

Codon substitution models (46, 47) were used to analyze sequences from four abalone taxa (H. corrugata, H. rufescens, H. fulgens, and H. discus hannai). Sites models allowing for a single ω across sites (M0), as well as several neutral models (M1a, M7, and M8a) or selection models (M2a and M8) allowing for variation in ω among sites, were fit to the data using PAML (40). Despite low power of M0 to detect positive selection, two VE proteins (VEZP5 and VEZP9) show evidence of ω > 1 consistent with adaptive divergence among species. More powerful tests employing likelihood ratio tests comparing neutral and selection models (e.g., M8a-vs-M8) identify four additional VE proteins under positive selection (VEZP3, VEZP4, VEZP6, and VEZP10). Estimates of ω, the proportion of codons in this positively selected site class (ω ₀ and p₀, respectively), and the likelihood ratio test statistic (LRT, 2 Δ lnL) are given. ∗, significant at P ≤ 0.05; ∗∗, significant at P ≤ 0.005.