Table 1. Phylogenetic tests of positive selection in primates.
| Test of selection | Sites under selection identified by different methodsa | |||||||||||
| IgA dataset | lnL M7(neutral)/lnLM8 (selection) | −2lnΔLc | Significance | ps, ωs b | PAML M8 (p>0.5;Abi-Rachedet al, 2007) | PAML M8 (p>0.9;present study) | SLAC | FEL | REL | MEME | FUBAR | PSCc |
| CH1 | −1212.4/−1200.0 | 24.8 | ** (p<0,01) | 0.03, 3.86 | n.a. | 133, 166, 197 | none | none | 133, 137, 166 | 133, 136,_138, 165 | 133 | 133, 166 |
| CH2 | −1365.3/−1361.3 | 8.0 | * (p<0,05) | 0,02, 2.6 | 245, 296, 317, 319, 326, 331, 333 | 319, 326 | none | 245, 296, 319 | 273, 293, 296, 317 | 296, 324, 326, 330 | 319 | 296, 319, 326 |
| CH3 | −907.08/−907.08 | 0.0 | n.s. | 0.00, 1.0 | none | none | none | none | None | none | none | – |
a
Codons identified by more than one ML method are underlined.
b
ps = proportion of the sites under selection, ωs = estimated dN/dS of the sites under selection in M8.
c
Positively Selected Codons: only the codons identified by at least two of the ML methods were considered to be positively selected codons.