biostudies-literatureUnknown15(1)Kunishima TResearch Laboratory on Environmentally-Conscious Developments and Technologies [E-Code], National Institute of Advanced Industrial Science and TechnologyWakayama Prefecturethe Fujiwara Natural History FoundationSetsunan UniversityThe Japanese freshwater crab Geothelphusa dehaani species complex is distributed widely across the Japanese Archipelago. Despite its suggested high genetic and morphological diversity, key aspects such as nuclear DNA (nuDNA) population structure and relationship between body color patterns and genetic populations remain unclear. To address these gaps, this study analyzed genome-wide single nucleotide polymorphisms (SNPs) in nuDNA and mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) markers in samples from Hokkaido to the Tokara Islands, Japan. ADMIXTURE analysis identified five distinct populations with significant geographic boundaries. These populations exhibited unique geographical patterns, spanning across islands and enclave distribution, indicating that G. dehaani populatScientific reports23781https://www.ebi.ac.uk/biostudies/studies/S-EPMC12264161biostudies-literatureGenetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex using genome wide SNPs.PMC12264161Kunishima TTakata KNishijima MIguchi ANishikawa KGibu KfalseGenetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex using genome wide SNPs.The Japanese freshwater crab Geothelphusa dehaani species complex is distributed widely across the Japanese Archipelago. Despite its suggested high genetic and morphological diversity, key aspects such as nuclear DNA (nuDNA) population structure and relationship between body color patterns and genetic populations remain unclear. To address these gaps, this study analyzed genome-wide single nucleotide polymorphisms (SNPs) in nuDNA and mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) markers in samples from Hokkaido to the Tokara Islands, Japan. ADMIXTURE analysis identified five distinct populations with significant geographic boundaries. These populations exhibited unique geographical patterns, spanning across islands and enclave distribution, indicating that G. dehaani populat2025-01-01T00:00:00Z2025 Jul2026-07-15T10:53:03.973Z2026-07-03T03:15:07.637ZS-EPMC122641614066497410.1038/s41598-025-08085-0