3.3 Analysis of Recombination
The recombination detection program not only analyzes brake points but also identify parent sequences. We ran the test of recombination by pooling all putative functional alleles recovered from four species ofTurdidae family. We only find one potential recombination event in Tuna-MHCI*PFA06 inTurdus naumanni at two recombinant breakpoints at position 148 and 253. Tuna-MHCI*PFA02 as major and Tuna-MHCI*PFA011minor parent. Likewise, a single recombination was significant inTueu-MHCI*PFA07. We detected no recombination among other alleles. However, these recombinations were only significant in two out of seven tests and not consistent with recombination breakpoint identified by GARD, hence the results represent that overall recombination is not likely to have any prominent effects on tests for positively selected sites (Table.2). The recombination breakpoints identified by these two programs are often inconsistent, probably because they use different computational methods.
TABLE 2: Recombinants detected in Turdidae family MHC class I alleles; parent sequences, breakpoints detected by the recombination detection program (RDP) and the genetic algorithm for recombination detection (GARD); and the RDP analyses.