Data from: 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.