Geographic breaks and seascape features shape diversification in cryptobenthic reef fishes

Because ocean environments often lack clear barriers to dispersal, the limited mobility and strong habitat fidelity of cryptobenthic reef fishes make them ideal for uncovering spatial patterns of evolutionary divergence in the marine realm. We conducted a comparative phylogeographic study of 23 of the 25 known species in the cryptobenthic fish genus Malacoctenus, integrating genome-wide SNPs from over 500 individuals, geometric morphometrics, and seascape data to assess the effectiveness of historical and contemporary marine barriers in the Tropical Eastern Pacific (TEP) and Greater Caribbean (GC). Population-level analyses across 14 species revealed generally well-structured populations with limited admixture, reinforcing the value of our study system for evaluating the efficacy and permeability of marine barriers. In the TEP, linear coastlines and broad sandy gaps, including the Sinaloan and Central American breaks and the open-ocean Galápagos break, consistently constrained connectivity. In contrast, the GC exhibited more variable structure shaped by dynamic currents and a semi-enclosed geography with a mosaic of islands, with the strongest breaks across the Eastern Caribbean, Bahamas, and Gulf of Mexico. Seascape genomic analyses identified depth, temperature, and chlorophyll-α as key environmental drivers. Depth played a major role in TEP speciation, separating tide pool– and reef-associated clades. Phylogenomic analyses uncovered an early divergence (~23 Ma) linked to Isthmus uplift, followed by asynchronous transisthmian speciation in two clades (~5.2–7.6 Ma). Our results highlight the spatially variable roles of marine barriers and environmental features in the diversification of cryptobenthic reef fishes and marine organisms more broadly.