Table 1

Likelihood ratio test of positive selection in female and male reproductive proteins

GenenLcSdN/dS2Δℓ M3 vs. M02Δℓ M8 vs. M7Parameter estimates under M8 (beta & ω)Positively selected sites
Female reproductive proteins
 ZP286762.60.53138.8**14.8**p1 = 0.047, ω = 2.5p0 = 0.953, B(0.66, 0.66)38, 57, 117, 161, 170, 198, 241, 287, 339, 342, 665, 674, 710, 711
 ZP383652.90.27219.6**8.6*p1 = 0.076, ω = 1.7p0 = 0.924, B(0.40, 1.24)25, 28, 31, 32, 33, 34, 47, 50, 84, 185, 194, 331, 333, 340, 341, 345, 347, 348, 372, 373
 OGP84471.70.35108.4**8.1*p1 = 0.017, ω = 4.2p0 = 0.983, B(0.31, 0.56)122, 150, 280, 446, 448, 449
Male reproductive proteins
 Protamine P110483.70.9369.5**27.5**p1 = 0.456, ω = 3.6p0 = 0.544, B(131.7, 686.3)10, 12, 16, 18, 19, 20, 22, 23, 29, 30, 36, 37, 38, 42, 43, 44, 45, 46, 48, 49, 51
 Protamine P29991.30.5812.0*0.2p1 = 0.560, ω = 1.2p0 = 0.440, B(1.43, 17.77)4, 5, 6, 9, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 25, 28, 29, 30, 36, 37, 38, 40, 41, 43, 45, 48, 49, 50, 51, 52, 57, 59, 63, 64, 66, 69, 70, 71, 75, 81, 84, 87, 88, 90, 94, 96, 98, 101, 102
 Transition protein 2101013.50.2939.0**2.0p1 = 0.106, ω = 1.6p0 = 0.893, B(0.91, 2.32)36, 64, 66, 71, 73, 88, 98
Controls
 Class I MHC63620.60.5578.6**14.7**p1 = 0.073, ω = 4.0 p0 = 0.927, B(0.10, 0.27)45, 48, 51, 52, 55, 56, 82, 99, 101, 121, 126
 Carbonic anhydrase I62611.20.3445.8**0.6B(0.14, 0.28)None detected
  • The data have n sequences, each of Lc codons after alignment gaps are removed. S is the tree length, measured as the number of nucleotide substitutions per codon, and dN/dS is the average ratio over sites and branches, both calculated under a codon model with one ω for all sites. The proportion of sites under positive selection (p1), or under selective constraint (p0), and parameters p and q for the beta distribution B(p, q) are given under M8. Parameter estimates for carbonic anhydrase I come from M7, because M8 is not a significantly better fit of the data. Parameters indicating positive selection are in bold.  

  • 178 : significant at 5% level;  

  • 208 : significant at 1% level. Sites potentially under positive selection identified under model M8 are listed according to the mouse sequence numbering except for protamine P1 and P2, which are numbered according to the human sequence, and class I MHC, which is numbered according to the protein data bank file 1QLFA. Positively selected sites with posterior probability >0.9 are underlined, 0.8–0.9 in bold, 0.7–0.8 in italics, and 0.5–0.7 in plain text.