I have two insular populations, one of them have a low number of private alleles. This could be explained by an ancient bottleneck?

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Mark Andrew Chapman

just looking at private alleles doesn't tell you the whole story. is polymorphism lower? there could just be a bottleneck (independent of adaptation). can you calculate Tajima's D?

Yann Dussert

As already mentionned, it's hard to conclude about differences of private allele number with so little information.

To add to the other answers, this could also be explained by asymmetrical gene flow between your populations, if there is gene flow of course (see attached ref).

Article Testing for Asymmetrical Gene Flow in a Drosophila melanogas...