Marine barriers and seascape features shape divergence in Neotropical cryptobenthic reef fishes

Abstract Because ocean environments often lack clear barriers to dispersal, cryptobenthic reef fishes, with their limited mobility, are ideal for uncovering spatial patterns of evolutionary divergence. We conducted a comparative phylogeographic study of 23 of the 25 known species in the cryptobenthic genus Malacoctenus, integrating genome-wide single nucleotide polymorphisms (500 individuals), geometric morphometrics and seascape data to evaluate historical and contemporary barriers in the Tropical Eastern Pacific (TEP) and Greater Caribbean (GC). Population analyses across 14 species revealed well-structured populations with limited admixture, emphasizing the system’s value for assessing marine barrier permeability. In the TEP, linear coastlines and broad sandy gaps, such as the Sinaloan, Central American, and Galápagos breaks, consistently restricted gene flow. By contrast, the GC showed more variable structure shaped by currents and its semi-enclosed geography, with pronounced breaks across the Eastern Caribbean, Bahamas and Gulf of Mexico. Seascape genomic analyses identified depth, temperature and chlorophyll-α as key environmental drivers, with depth particularly important in separating tide pool- and reef-associated clades. Phylogenomic analyses revealed an early divergence (approx. 23 Ma) between TEP and GC lineages, followed by asynchronous transisthmian speciation in two clades (approx. 5–7 Ma). Overall, our findings demonstrate how historical processes, marine barriers and environmental gradients shape diversification in cryptobenthic fishes.