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.