Ancestral polymorphism or recent gene flow? Insight from comparative genome scans

How informative are genome scans for understanding speciation? Peaks and troughs of differentiation metrics have become a central focus in speciation studies yet relatively few attempts have been made to address the difficulties of interpreting these patterns. For example, does low divergence reflect gene flow or shared ancestral polymorphism?

One way to deal with this is to investigate systems where it is possible to compare populations in sympatry and allopatry. If low divergence is due to shared ancestral polymorphism, we would expect no difference in differentiation between comparisons. We therefore focused on the recent speciation between two highly divergent three-spined stickleback species in the Japan Sea (Gasterosteus nipponicus) and the Pacific Ocean (Gasterosteus aculeatus).

We constructed a large population genomic dataset of 280 individuals from sympatric and allopatric populations across the distributions of both species. Our spatially distributed sampling design allows us to identify introgression (lower differentiation in sympatry relative to allopatry) as well as candidate loci underlying reproductive isolation during divergence (divergence common to allopatry) and on secondary contact (divergence found only in sympatry). We suggest that careful consideration of study design can improve the interpretation of genome scan approaches.