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Table 1 Summary of results for branch analysis and branch-site analysis of Prm2 domains of primates and rodents

From: Selective constraints on protamine 2 in primates and rodents

Sequence cleaved Prm2 mature Prm2
Foreground Primates Rodentia Primates Rodentia
LRTs for selection at branches over whole sequence
 2Δ(M0-MC) 0.02 1.94 25.86 1.49
 p ns ns <0.01 ns
 2Δ(MCfix-MC) 8.74 15.42 25.60 0.01
 p 0.01 <0.01 <0.01 ns
 M0 - ω 0.54 1.18
 MC - ω 0.530 0.420 3.120 0.980
LRTs for selection at branches on sites
 2Δ(M1-BS) 1.67 5.27 62.21 26.10
 p ns ns <0.01 <0.01
 2Δ(BSfix-BS) 0.00 5.27 96.75 60.63
 p ns 0.05 <0.01 <0.01
Proportion of sites in ω site classes
 0 0.23 0.23 0.18 0.21
 1 0.64 0.74 0.30 0.75
 2a 0.04 0.01 0.20 0.01
 2b 0.10 0.02 0.32 0.03
Positively selected sites (BEB p <0.05)
 PSS - 26G 1Q, 4C, 5Y, 6G, 7Y, 11 L, 24Q, 25R, 29R, 44R, 45 N, 51R, 55 T, 61 T 64R,72H
Interpretation
 Selection at branches over whole sequence conserved conserved positive relaxed
 Selection at branches on sites no signal positive positive positive
 Sexual selection not detected not detected not detected not detected
  1. LRT: Likelihood ratio test (twice the difference (2Δ) between likelihood values of the tested models). ω: nonsynonymous/synonymous substitution rate ratio, evolutionary rate. When LRT of M0 versus MC is significant MC omega is reported. When LRT is non significant, M0 omega is reported
  2. PSS: positively selected sites. Ω site classes: 0: 0 < ω < 1 for foreground and background branches, 1: ω = 1 for foreground and background branches, 2a: 0 < ω < 1 for background and ω > 1 for foreground, 2b: ω = 1 for background and ω > 1 for foreground