Population genomics reveals population structure, glacial divergence, and intertidal adaptation in the Chinese chiton (Liolophura sinensis).

Chitons (Mollusca: Polyplacophora) are a relatively primitive group within Aculifera that have retained their past life history and ecological traits. While chitons are recognized for their evolutionary significance and societal value (e.g., food, medicine, biomimetics), key aspects of their phylogeographic patterns and microevolutionary processes remain poorly understood, particularly regarding spatial dispersal and adaptation to the challenging intertidal zone environment. Here we show a population genomic analysis of the Chinese chiton (Liolophura sinensis), a species recently delineated from the Liolophura japonica species complex. Using high-depth resequencing of 68 individuals across nine populations, we identify distinct genetic substructure between the Taizhou and southern groups, with divergence dating back to approximately 19.0 thousand years ago, a timing that overlaps with late Pleistocene sea-level minima. A unidirectional gene flow pattern indicates ocean current-mediated larval dispersal, which is consistent with species-specific life history traits. Moreover, selection scans reveal significant enrichment of genes associated with immune responses, cellular homeostasis, and cytoskeleton dynamics, all traits that are potentially relevant for survival in wave-exposed rocky habitats. Our analyses identify strong population structure, recent divergence, and genomic regions potentially associated with local environmental variation, providing a foundational framework for future research on adaptation in marine intertidal species.