Genomic signals of admixture and reinforcement between two closely related species of European sepsid flies

Interspecific gene flow by hybridization may weaken species barriers and
adaptive divergence, but can also initiate reinforcement of reproductive
isolation through natural and sexual selection. However, the extent of
interspecific gene flow and its consequences for the initiation and
maintenance of species barriers in natural systems remain poorly
understood. We first applied coalescence simulations and approximate
Bayesian calculations based on microsatellite data to infer the yet
unknown demographic history of the two closely related European dung fly
sister species Sepsis cynipsea and Sepsis neocynipsea (Diptera: Sepsidae).
To assess genome-wide patterns of historical gene flow between both
species, we quantified discordances in derived allele sharing
(D-statistics, ABBA-BABA test) in whole-genome resequencing data from
pooled DNA of male specimens originating from natural and laboratory
populations. We contrasted genome-wide variation in DNA sequence
differences between samples from sympatric populations of the two species
in France and Switzerland with that of interspecific differences between
pairs of samples involving allopatric populations from Estonia and Italy.
At one site in the French Cevennes we detected a relative excess of DNA
sequence identity, suggesting interspecific gene flow in sympatry. In
contrast, at two sites in Switzerland, we observed a relative depletion of
DNA sequence identity compatible with reinforcement of species boundaries
in sympatry. Our results suggest that the species boundaries between S.
cynipsea and S. neocynipsea in Europe depend on the eco-geographic
context.