Contrasted patterns of population genetic structure in two related Spondylus species of the Tropical Eastern Pacific

Ongoing global change and anthropogenic pressures are increasingly impacting coastal ecosystems, leading to habitat degradation and disrupted connectivity. Along the Tropical Eastern Pacific, multiple habitat discontinuities and oceanographic barriers, such as biogeographic transition zones, sedimentary coastal gaps, and major current systems, limit dispersal in rocky-shore taxa. Despite their cultural and economic importance, research on Tropical Eastern Pacific Spondylus remains geographically limited, underscoring a critical lack of knowledge on their population dynamics, dispersal, genetic diversity, and evolutionary history. Using high-resolution genome-wide SNPs, we revealed pronounced population structure in Eastern Pacific S. limbatus and S. crassisquama, with strong genetic differentiation of Central American populations from Mexican ones, and the Cortesian population from the others in S. limbatus, whereas S. crassisquama exhibited a similar but weaker pattern, primarily structured by the Southern California Bight. This study provides the first comparative genomic analysis of population structure in both species, with important implications for conservation, as genetically distinct management units must be recognized to ensure the sustainable management of these ecologically and economically important bivalves.