Shared ancestral polymorphisms are polymorphic sites that originated in the ancestral species and have survived genetic drift in both the human and the chimpanzee populations.
Furthermore, current populations of P. falcipes have a large effective population size, maintain ancestral polymorphisms, and have a complex network of gene flow.
The presence of haplotypes shared with chickens can be explained by ancestral polymorphisms and/or introgression.
Cases of deep intraspecific divergence (Table 4) can reflect misidentifications, cryptic taxa, ancestral polymorphisms, or introgression.
Introgression and retention of ancestral polymorphisms are relatively rare at all loci.
The ancestral population size for domestic chickens is large and each breed still maintains a substantial portion of ancestral polymorphisms at the genomic level.
A particular attention is paid to polymorphisms shared among three Gallus species that can result from either inheritance of ancestral polymorphisms or introgression.
Shared haplotypes are more frequently found between red junglefowl and chickens, which are attributed to both introgression and ancestral polymorphisms.
The MCMC and TSL methods attempt to remove the effect of ancestral polymorphisms on estimates of the species divergence time.
Introgression and/or retention of ancestral polymorphisms have resulted in the sharing of variation between the An.
