what do you think is the best way of delineating species boundaries when gene flow exists? I was thinking if it is possible to distinguish between the most divergent alleles and those alleles that are admixed between the two taxa? perhaps by referring to their genomic annotation and see if there is a difference between the location (exon vs intron) and gene functionality of these two allele sets we could draw some conclusions? it's just a rough idea, maybe too much idealistic or too much simple, please feed with with your knowledge and ideas.