Can secondary contact following range expansion be distinguished from barriers to gene flow?

Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. Although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they have no power to make the distinction. By contrast, the directionality index ψ that was proposed to study range expansion is informative. Additionally, we find that an excess of Linkage Disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. Our findings indicate that inference on secondary contact can be improved when explicitly accounting for the geographical locations of individuals.