Table 3.
Evolutionary rates and tests for positive selection across mammals at 32 recombination genes.
| Gene | bp | N | ω | M | M1—M2 | P | M7—M8 | P | M8a—M8 | P | BEB |
|---|---|---|---|---|---|---|---|---|---|---|---|
| (A) DSB formation | |||||||||||
| HORMAD1 | 1212 | 16 | 0.3036 | 7 | 0 | 1.000 | 1.795 | 0.4076 | — | — | 0 |
| MEI4 | 1170 | 16 | 0.4332 | 7 | 0 | 1.000 | 0.005 | 0.9976 | — | — | 0 |
| REC114 | 870 | 15 | 0.4003 | 7 | 0 | 1.000 | 5.384 | 0.0677 | — | — | 0 |
| IHO1 | 1824 | 16 | 0.7095 | 8 | 13.061 | 0.0015 | 17.571 | 0.0002 | 14.527 | 0.0001 | 1 |
| SPO11 | 1188 | 15 | 0.1654 | 7 | 0 | 1.000 | 4.648 | 0.0980 | — | — | 0 |
| (B) DSB processing | |||||||||||
| HORMAD2 | 981 | 15 | 0.3153 | 7 | 0 | 1.000 | 3.650 | 0.1612 | — | — | 0 |
| MRE11 | 2136 | 16 | 0.1688 | 8 | 0.363 | 0.8342 | 11.931 | 0.0026 | 4.706 | 0.0301 | 0 |
| NBS1 | 2289 | 15 | 0.4183 | 8 | 0 | 1.000 | 12.763 | 0.0017 | 4.087 | 0.0432 | 0 |
| RAD50 | 3936 | 16 | 0.1006 | 7 | 0 | 1.000 | 0.301 | 0.8605 | — | —- | 0 |
| BRCC3 | 954 | 15 | 0.0602 | 7 | 0 | 1.000 | 0.250 | 0.8826 | — | — | 0 |
| (C) Homology search and strand invasion | |||||||||||
| DMC1 | 1020 | 15 | 0.0351 | 1 | 0.488 | 0.7835 | 5.000 | 0.0821 | — | — | 1 |
| RAD51 | 1017 | 16 | 0.0268 | 7 | 0 | 1.000 | 0 | 1.000 | — | — | 0 |
| SPATA22 | 1101 | 16 | 0.4893 | 7 | 0 | 1.000 | 0.429 | 0.8070 | — | — | 0 |
| MEIOB | 1425 | 16 | 0.2341 | 7 | 0 | 1.000 | 0.665 | 0.7172 | — | — | 0 |
| MCMDC2 | 2052 | 16 | 0.2239 | 7 | 0 | 1.000 | 0.628 | 0.7307 | — | — | 0 |
| (D) Synapsis | |||||||||||
| REC8 | 1833 | 16 | 0.3698 | 8 | 0 | 1.000 | 14.690 | 0.0006 | 5.927 | 0.0149 | 0 |
| RAD21L | 1686 | 15 | 0.503 | 8 | 12.124 | 0.0023 | 32.050 | <0.0001 | 12.049 | 0.0005 | 4 |
| SYCP1 | 3015 | 16 | 0.4337 | 8 | 8.711 | 0.0128 | 26.860 | <0.0001 | 9.243 | 0.0024 | 3 |
| SYCP2 | 4650 | 16 | 0.5572 | 8 | 11.584 | 0.0031 | 37.200 | <0.0001 | 15.838 | 0.0001 | 0 |
| TEX12 | 369 | 14 | 0.2297 | 7 | 0.0565 | 0.9721 | 1.549 | 0.4610 | — | — | 0 |
| (E) CO/NCO decision | |||||||||||
| TEX11 | 2844 | 15 | 0.8483 | 8 | 60.872 | <0.0001 | 82.665 | <0.0001 | 61.141 | <0.0001 | 14 |
| SHOC1 | 4644 | 16 | 0.6113 | 8 | 12.447 | 0.0020 | 30.561 | <0.0001 | 15.645 | 0.0001 | 0 |
| RNF212 | 948 | 16 | 0.5014 | 8 | 0 | 1.000 | 16.366 | 0.0003 | 5.202 | 0.0226 | 1 |
| RNF212B | 906 | 14 | 0.4066 | 7 | 0 | 1.000 | 0.500 | 0.7788 | — | — | 0 |
| MSH4 | 2814 | 16 | 0.2132 | 8 | 16.608 | 0.0002 | 39.447 | <0.0001 | 23.238 | <0.0001 | 6 |
| MSH5 | 2565 | 15 | 0.1642 | 7 | 0 | 1.000 | 4.214 | 0.1216 | — | — | 0 |
| (F) Resolution | |||||||||||
| MER3 | 4458 | 16 | 0.3633 | 8a | 0 | 1.000 | 12.838 | 0.0016 | 3.109 | 0.0779 | 0 |
| CNTD1 | 1026 | 15 | 0.2496 | 7 | 0 | 1.000 | 0.936 | 0.6263 | — | — | 0 |
| HEI10 | 831 | 15 | 0.1226 | 7 | 0 | 1.000 | 0.250 | 0.8826 | — | — | 0 |
| MLH1 | 2313 | 15 | 0.1652 | 8a | 0 | 1.000 | 12.221 | 0.0022 | 0.280 | 0.5970 | 0 |
| MLH3 | 4419 | 16 | 0.4444 | 7 | 0 | 1.000 | 3.757 | 0.1528 | — | — | 0 |
| MUS81 | 1665 | 16 | 0.2124 | 7 | 0 | 1.000 | 0.628 | 0.7304 | — | — | 0 |
Note: bp, length of alignment; N, number of sequences; ω, estimated rate of evolution using the model of best fit; M, model of best fit; M1–M2, log-likelihood of M2 over M1; M7–M8, log-likelihood of M8 over M7; M8a–M8, log-likelihood of M8 over M8a; BEB, number of individual amino acids with BEB; P > 0.95.