Genetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex using genome wide SNPs
Abstract 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...
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Nature Portfolio
2025-07-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-08085-0 |
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| author | Taiga Kunishima Kento Takata Kanto Nishikawa Kodai Gibu Miyuki Nishijima Akira Iguchi |
| author_facet | Taiga Kunishima Kento Takata Kanto Nishikawa Kodai Gibu Miyuki Nishijima Akira Iguchi |
| author_sort | Taiga Kunishima |
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| description | Abstract 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 populations have been shaped by complex factors, including sea level changes and volcanic activity. Regional body color variations partially aligned with SNP clades. Further, combining body color with collection locality data could help identify the specimen populations. Contrasting patterns between mtDNA and nuDNA suggest historical gene flow and introgression, emphasizing the need for caution when interpreting earlier phylogenetic studies based on combined mtDNA and nuDNA sequences. Our findings provide a foundational baseline for future research into the taxonomy, phylogeny, and population dynamics of the G. dehaani species complex, advancing our understanding of its evolutionary history. |
| format | Article |
| id | doaj-art-b11c0c18439449f58fbf9dccd6946526 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-b11c0c18439449f58fbf9dccd69465262025-08-20T03:42:29ZengNature PortfolioScientific Reports2045-23222025-07-0115111310.1038/s41598-025-08085-0Genetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex using genome wide SNPsTaiga Kunishima0Kento Takata1Kanto Nishikawa2Kodai Gibu3Miyuki Nishijima4Akira Iguchi5Wakayama Prefectural Museum of Natural HistoryWakayama Prefectural Museum of Natural HistoryGraduate School of Human and Environmental Studies, Kyoto UniversityDepartment of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, The University of TokyoGeological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)Abstract 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 populations have been shaped by complex factors, including sea level changes and volcanic activity. Regional body color variations partially aligned with SNP clades. Further, combining body color with collection locality data could help identify the specimen populations. Contrasting patterns between mtDNA and nuDNA suggest historical gene flow and introgression, emphasizing the need for caution when interpreting earlier phylogenetic studies based on combined mtDNA and nuDNA sequences. Our findings provide a foundational baseline for future research into the taxonomy, phylogeny, and population dynamics of the G. dehaani species complex, advancing our understanding of its evolutionary history.https://doi.org/10.1038/s41598-025-08085-0PhylogeographyMIG-seqColor polymorphismCrustaceanJapanese IslandsDemographic history |
| spellingShingle | Taiga Kunishima Kento Takata Kanto Nishikawa Kodai Gibu Miyuki Nishijima Akira Iguchi Genetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex using genome wide SNPs Scientific Reports Phylogeography MIG-seq Color polymorphism Crustacean Japanese Islands Demographic history |
| title | Genetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex using genome wide SNPs |
| title_full | Genetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex using genome wide SNPs |
| title_fullStr | Genetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex using genome wide SNPs |
| title_full_unstemmed | Genetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex using genome wide SNPs |
| title_short | Genetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex using genome wide SNPs |
| title_sort | genetic population structure of japanese freshwater crab geothelphusa dehaani species complex using genome wide snps |
| topic | Phylogeography MIG-seq Color polymorphism Crustacean Japanese Islands Demographic history |
| url | https://doi.org/10.1038/s41598-025-08085-0 |
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