Genetic population structure of Geothelphusa dehaani species complex using genome-wide SNP

The Japanese freshwater crab Geothelphusa dehaani species complex is widely distributed throughout the Japanese Archipelago, known for its substantial genetic and morphological diversity. However, understanding of its nuclear DNA (nuDNA) population structure and the correlation between body-color patterns and genetic populations remains incomplete. This study employed genome-wide single nucleotide polymorphisms (SNPs) in nuDNA alongside mitochondrial DNA (mtDNA) COI marker, sampling extensively from Hokkaido to the Tokara Islands. Admixture analysis identified five distinct populations with clear geographic boundaries, reflecting unique patterns across islands and enclaves shaped by historical sea-level changes and volcanic activity. While regional body-color variations partly corresponded with SNP clades, further molecular and morphological investigations are needed for precise identification of the populations. Discordance between mtDNA and nuDNA patterns suggest past gene-flow and adaptive introgression, cautioning against interpretations based solely on combined mtDNA and nuDNA sequences in earlier phylogenetic studies. These findings establish a foundational understanding for future research on the taxonomy, phylogeny, and population dynamics of G. dehaani species complex, enhancing insights into its evolutionary history.