Table 4.
Selection patterns in recombination genes in maize detected using the likelihood ratio test
| Gene | Selection modelsa | % of codons | ||||
|---|---|---|---|---|---|---|
| M0 vs. M3 (2Δl) b |
M1 vs. M2 (2Δl) c |
M7 vs. M8 (2Δl) d |
Under purifying selection | Under positive selection | Evolving neutrally | |
| Dmc1 | 15.32** | 4.12 | 6.14 | 100 | - | - |
| Mlh1 | 50.48** | 19.46** | 20.54** | 93.3 | 6.7 | - |
| Mre11A | 1.06 | 0.46 | 0.12 | 100.0 | - | - |
| Mre11B | 24.64** | 26.46** | 14.23** | 96.5 | 3.5 | - |
| Msh4 | 0.00 | 0.00 | 0.00 | 100.0 | - | - |
| Mus81-1 | 22.64** | 15.62** | 15.74** | 97.3 | 2.7 | - |
| Rad51A1 | 0.00 | 0.00 | 0.00 | 100.0 | - | - |
| Rad51A2 | 43.76** | 18.94** | 20.62** | 98.7 | 1.3 | - |
| Recq4 | 0.00 | 0.00 | 0.00 | 100.0 | - | - |
| Spo11-1 | 0.00 | 0.00 | 0.00 | 100.0 | - | - |
| Spo11-2 | 80.52** | 33.78** | 35.18** | 98.2 | 1.8 | - |
a Likelihood ratio tests of selection models. Ratios statistically significant at P = 0.01 are denoted with **
b Model M0 (one ratio) assumes a single dN/dS ratio across all sites in the gene’s coding region. Model M3 (discrete) assumes discrete classes of sites with different ω values. df = 4
c Model M1 (neutral model) assumes all sites are either under purifying selection (ω < 0) or evolving neutrally (ω = 1). Model M2 adds a third category of sites under positive selection (ω > 1). df = 2
d Model M7 (beta model) assumes that ω ranges from 0 (strong negative selection) to 1 (neutral evolution) and varies among sites in the gene’s coding region according to the beta distribution. Model M8 (beta& ω) similarly to M7 assumes that ω varies among sites but allows that, in addition to ranging from 0 to 1, ω may take values > 1 (positive selection). df = 2