Patterns of genomic heterogeneity in a classic field cricket mosaic hybrid zone

Barriers to gene exchange can be semi-permeable; some genes are expected to freely flow across species boundaries whereas others, under divergent selection or responsible for reproductive isolation, might not. Genome scans in recently diverged species have identified divergent genomic regions, a pattern that has often been interpreted as islands of restricted introgression in a background of relatively free gene exchange (“genomic islands of speciation”).  Areas of high differentiation, most located in the X chromosome (females XX, males X0), have been identified in the hybridizing field crickets Gryllus firmus and Gryllus pennsylvanicus.  These species were assumed to follow an islands of speciation model, with highly differentiated areas interpreted as areas of reduced introgression.  We sequenced the G. firmus genome to localize previously studied SNPs and sample a larger area around them in 8 allopatric populations (4 of each species). We use this data to test expectations for the islands model, in which non-introgressing areas should have both high absolute and relative differentiation.  We find that in the allopatric populations, the areas with high relative differentiation (mostly X-linked), previously interpreted as non-introgressing, do not have high absolute differentiation as would be expected under the “islands model.”. We also show that the estimated divergence time based on nuclear DNA is about 4× older than that estimated based on mtDNA (800K vs 200K years ago).  We discuss the implications of our results for introgression into allopatric populations.