The process of species formation is characterized by the accumulation of multiple reproductive barriers. The evolution of hybrid male sterility, or Haldane’s rule, typically characterizes later stages of species formation, when reproductive isolation is strongest. Yet, understanding how quickly reproductive barriers evolve and their consequences for maintaining genetic boundaries between emerging species remains a challenging task because it requires studying taxa that hybridize in nature. Here, we address these questions using the meadow grasshopper Pseudochorthippus parallelus, where populations that show multiple reproductive barriers, including hybrid male sterility, hybridize in two natural hybrid zones. Using mitochondrial data, we infer that such populations diverged some 100,000 years ago, at the beginning of the last glacial cycle in Europe. Nuclear data show that contractions at multiple glacial refugia, and post‐glacial expansions have facilitated genetic differentiation between lineages that today interact in hybrid zones. We find extensive introgression throughout the sampled species range, irrespective of the current strength of reproductive isolation. Populations exhibiting hybrid male sterility in two hybrid zones show repeatable patterns of genomic differentiation, consistent with shared genomic constraints affecting ancestral divergence or with the role of those regions in reproductive isolation. Together, our results suggest that reproductive barriers that characterize late stages of species formation can evolve relatively quickly, particularly when associated with strong demographic changes. Moreover, we show that such barriers persist in the face of extensive gene flow, allowing future studies to identify associated genomic regions.

Despite the marine environment being typified by a lack of obvious barriers to dispersal, levels of genetic divergence can arise in marine organisms from historical changes in habitat availability, current oceanographic regimes and anthropogenic factors. Here we describe the genetic structure of the Gray Parrotfish, Sparisoma axillare, and identify environmental variables associated with patterns of genetic divergence throughout most of its distribution in Brazil. The heavily exploited Gray Parrotfish is endemic to Brazil, and there is lack of data on population structure that is needed to support sustainable management. To address this shortfall we analyzed 5429 SNPs from individuals sampled in nine locations, ranging from tropical to subtropical reef systems and costal to oceanic environments with varying levels of protection. We found low levels of genetic structure along the coast, including the oceanic island of Fernando de Noronha, and that a combination of water depth, ocean currents and geographic distance were the major drivers explaining genetic divergence. We identified a distinct genetic population around Trindade Island, 1000 km from the coast, highlighting the conservation significance of this population. Colonization of this oceanic site probably occurred during the Pleistocene periods of lower sea levels, allowing this shallow water-dependent species to use the seamount chain as stepping stones to Trindade. Our data further suggest that two protected areas, Costa dos Corais and Fernando de Noronha, likely play an important role as larval sources for much of the species distribution.

Although the process of species formation is notoriously idiosyncratic, the observation of pervasive patterns of reproductive isolation across species pairs suggests that generalities, or “rules”, underlie species formation in all animals. Haldane’s rule states that whenever a sex is absent, rare or sterile in a cross between two taxa, that sex is usually the heterogametic sex. Yet, understanding how Haldane’s rule first evolves and whether it is associated to genome wide barriers to gene flow remains a challenging task because this rule is usually studied in highly divergent taxa that no longer hybridize in nature. Here, we address these questions using the meadow grasshopper Pseudochorthippus parallelus where populations that readily hybridize in two natural hybrid zones show hybrid male sterility in laboratorial crosses. Using mitochondrial data, we infer that such populations have diverged some 100,000 years ago, surviving multiple glacial periods in isolated Pleistocenic refugia. Nuclear data shows that secondary contact has led to extensive introgression throughout the species range, including between populations showing hybrid male sterility. We find repeatable patterns of genomic differentiation across the two hybrid zones, yet such patterns are consistent with shared genomic constraints across taxa rather than their role in reproductive isolation. Together, our results suggest that Haldane’s rule can evolve relatively quickly within species, particularly when associated to strong demographic changes. At such early stages of species formation, hybrid male sterility still permits extensive gene flow, allowing future studies to identify genomic regions associated with reproductive barriers.