{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T21:55:01Z","timestamp":1791237301766,"version":"4.1.0"},"reference-count":37,"publisher":"Zoological Society of Japan","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Zoological Science"],"published-print":{"date-parts":[[2026,3,31]]},"abstract":"<jats:p>The red fox (Vulpes vulpes), which is widely distributed across the Northern Hemisphere, including Japan, has been studied for its distribution patterns and migration timing, but its population demography remains poorly understood. To solve it, this study conducted double-digest restriction-site-associated DNA sequencing (ddRAD-seq) on 118 samples from Japan, continental Eurasia, and Sakhalin. Based on single nucleotide polymorphisms (SNPs) detected by ddRAD-seq, this study revealed large genetic differentiation among populations of western Eurasia and four Japanese islands (Hokkaido, Honshu, Shikoku, and Kyushu). The eastern Eurasian population, including Sakhalin, was admixed with the western Eurasian and Hokkaido populations. Our results are consistent with previous reports based on mitochondrial DNA analyses that the Hokkaido and Honshu\/Shikoku\/Kyushu populations migrated from the continent independently. Demographic simulations showed that the Honshu\/Shikoku\/Kyushu population could have diverged first from the eastern continental Eurasian population, and that subsequently the Hokkaido population diverged. The simulation results are consistent with the geological record in that Honshu\/Shikoku\/Kyushu islands were the first to separate from continental Eurasia, followed by the isolation of Hokkaido. We propose a scenario in which the two fox populations in the Japanese archipelago became differentiated genetically as the result of geographical isolation from continental Eurasia by straits. In addition, a clustering analysis showed that foxes on Hokkaido could have become genetically divided into two subpopulations, northeastern and southwestern, suggesting that the Ishikari Lowland located between the two subpopulations served as a barrier to fox dispersal.<\/jats:p>","DOI":"10.2108\/zs250063","type":"journal-article","created":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T03:52:56Z","timestamp":1774842776000},"page":"271-279","source":"Crossref","is-referenced-by-count":0,"title":["History of Population Formation for the Red Fox Around the Japanese Archipelago, Revealed by Ddrad-Seq Analysis"],"prefix":"10.2108","volume":"43","author":[{"given":"Ryutaro","family":"Tomita","sequence":"first","affiliation":[{"name":"Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Endo","sequence":"additional","affiliation":[{"name":"Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yosuke","family":"Amaike","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kohji","family":"Uraguchi","sequence":"additional","affiliation":[{"name":"Hokkaido Institute of Public Health, Sapporo 060-0819, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yayoi","family":"Kaneko","sequence":"additional","affiliation":[{"name":"Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-0057, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexei V.","family":"Abramov","sequence":"additional","affiliation":[{"name":"Zoological Institute, Russian Academy of Sciences, Saint Petersburg 199034, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander P.","family":"Saveljev","sequence":"additional","affiliation":[{"name":"Russian Research Institute of Game Management and Fur Farming, Kirov 610000, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavel A.","family":"Kosintsev","sequence":"additional","affiliation":[{"name":"Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Ekaterinburg 620144, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexey P.","family":"Kryukov","sequence":"additional","affiliation":[{"name":"Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stanislava","family":"Peeva","sequence":"additional","affiliation":[{"name":"Faculty of Agriculture, Trakia university, 6000, Stara Zagora, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evgeniy","family":"Raichev","sequence":"additional","affiliation":[{"name":"Faculty of Agriculture, Trakia university, 6000, Stara Zagora, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atsushi J.","family":"Nagano","sequence":"additional","affiliation":[{"name":"Faculty of Agriculture, Ryukoku University, Kyoto 612-8577, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryuichi","family":"Masuda","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"848","reference":[{"key":"24","unstructured":"K Ohshima,  \"Quat Res.\"  19, \"Recording the late-Quaternary sea-level change on the topographic feature of the straits of the Japanese Islands.\" 23 (1980)"},{"key":"8","doi-asserted-by":"publisher","unstructured":"NS Goddard, MJ Statham, BN Sacks,  \"PLoS One.\"  10, \"Mitochondrial analysis of the most basal canid reveals deep divergence between eastern and western North American gray foxes (Urocyon spp.) and ancient roots in Pleistocene California.\" e0136329 (2015)","DOI":"10.1371\/journal.pone.0136329"},{"key":"9","doi-asserted-by":"crossref","unstructured":"J Goudet,  \"Mol Ecol Notes.\"  5, \"hierfstat, a package for r to compute and test hierarchical F-statistics.\" 184 (2005)","DOI":"10.1111\/j.1471-8286.2004.00828.x"},{"key":"3","doi-asserted-by":"crossref","unstructured":"J Catchen, P Hohenlohe, S Bassham, et al.  \"Mol Ecol.\"  22, \"Stacks: an analysis tool set for population genomics.\" 3124 (2013)","DOI":"10.1111\/mec.12354"},{"key":"32","doi-asserted-by":"crossref","unstructured":"S Sakaguchi, T Sugino, Y Tsumura, et al.  \"Tree Genet Genomes.\"  11, \"High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species.\" 1 (2015)","DOI":"10.1007\/s11295-015-0944-0"},{"key":"15","doi-asserted-by":"crossref","unstructured":"G Kinoshita, M Nunome, SH Han, et al.  \"Zool Sci.\"  29, \"Ancient colonization and within-island vicariance revealed by mitochondrial DNA phylogeography of the mountain hare (Lepus timidus) in Hokkaido, Japan.\" 776 (2012)","DOI":"10.2108\/zsj.29.776"},{"key":"7","doi-asserted-by":"crossref","unstructured":"Y Endo, N Osada, T Mano, et al.  \"Genome Biol Evol.\"  13, \"Demographic history of the brown bear (Ursus arctos) on Hokkaido Island, Japan, based on whole-genomic sequence analysis.\" evab195 (2021)","DOI":"10.1093\/gbe\/evab195"},{"key":"2","doi-asserted-by":"crossref","unstructured":"Y Amaike, Y Nishita, K Uraguchi, et al.  \"Zool Sci.\"  35, \"Genetic diversity of MHC class II DRB1 exon 2 in the red fox (Vulpes vulpes) on Hokkaido, Japan.\" 402 (2018)","DOI":"10.2108\/zs170211"},{"key":"4","doi-asserted-by":"crossref","unstructured":"FD Collin, G Durif, L Raynal, et al.  \"Mol Ecol Resour.\"  21, \"Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest.\" 2598 (2021)","DOI":"10.1111\/1755-0998.13413"},{"key":"5","doi-asserted-by":"crossref","unstructured":"P Danecek, A Auton, G Abecasis, et al.  \"Bioinformatics.\"  2, \"The variant call format and VCFtools.\" 2156 (2011)","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"6","doi-asserted-by":"crossref","unstructured":"M Dobson,  \"Mamm Rev.\"  24, \"Patterns of distribution in Japanese land mammals.\" 91 (1994)","DOI":"10.1111\/j.1365-2907.1994.tb00137.x"},{"key":"10","doi-asserted-by":"crossref","unstructured":"B Horecka, A Jakubczak, B \u015alaska, et al.  \"Eur Zool J.\"  89, \"Raccoon dog (Nyctereutes procyonoides) phylogeography including the Polish population: local and global aspects.\" 641 (2022)","DOI":"10.1080\/24750263.2022.2070289"},{"key":"12","doi-asserted-by":"crossref","unstructured":"YS Jo  and JT Baccus  \"Restor Ecol.\"  23, \"Case studies of the history and politics of wild canid restoration in Korea.\" 513 (2015)","DOI":"10.1111\/rec.12256"},{"key":"17","doi-asserted-by":"crossref","unstructured":"VE Kutschera, N Lecomte, A Janke, et al.  \"BMC Evol Biol.\"  13, \"A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes).\" 114 (2013)","DOI":"10.1186\/1471-2148-13-114"},{"key":"19","doi-asserted-by":"crossref","unstructured":"S Larivi\u00e8re  and M Pasitschniak  \"Mammalian Species.\"  537, \"Vulpes vulpes.\" 1 (1996)","DOI":"10.2307\/3504236"},{"key":"20","doi-asserted-by":"crossref","unstructured":"H Machida  and Y Matsushima  \"Quat Res.\"  15, \"Some data concerning the paleoenvironment in the early stage of the last interglacial age.\" 136 (1976)","DOI":"10.4116\/jaqua.15.136"},{"key":"21","doi-asserted-by":"crossref","unstructured":"T Matsuhashi, R Masuda, T Mano, et al.  \"Mol Biol Evol.\"  16, \"Microevolution of the mitochondrial DNA control region in the Japanese brown bear (Ursus arctos) population.\" 676 (1999)","DOI":"10.1093\/oxfordjournals.molbev.a026150"},{"key":"22","doi-asserted-by":"crossref","unstructured":"AD McDevitt, I Coscia, SS Browett, et al.  \"Mol Ecol.\"  31, \"Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe.\" 993 (2022)","DOI":"10.1111\/mec.16276"},{"key":"23","doi-asserted-by":"crossref","unstructured":"BD McKay,  \"J Biogeography.\"  39, \"A new timeframe for the diversification of Japan's mammals.\" 1134 (2012)","DOI":"10.1111\/j.1365-2699.2011.02666.x"},{"key":"25","doi-asserted-by":"crossref","unstructured":"K Ohshima,  \"J Geography.\"  100, \"The late-Quaternary sea-level change of the Japanese Islands.\" 967 (1991)","DOI":"10.5026\/jgeography.100.6_967"},{"key":"26","doi-asserted-by":"crossref","unstructured":"T Oishi, K Uraguchi, K Takahashi, et al.  \"J Hered.\"  102, \"Population structures of the red fox (Vulpes vulpes) on the Hokkaido Island, Japan, revealed by microsatellite analysis.\" 38 (2011)","DOI":"10.1093\/jhered\/esq091"},{"key":"29","doi-asserted-by":"crossref","unstructured":"S Purcell, B Neale, KT Brown, et al.  \"Am J Hum Genet.\"  81, \"PLINK: A tool set for whole-genome association and population-based linkage analyses.\" 559 (2007)","DOI":"10.1086\/519795"},{"key":"31","doi-asserted-by":"crossref","unstructured":"T Sagayama, T Tonosaki, T Kondo, et al.  \"J Geol Soc Japan.\"  116, \"Stratigraphy and paleoenvironment of Upper Pleistocene to Holocene sediments in the Ishikari Plain, Hokkaido, Japan.\" 13 (2010)","DOI":"10.5575\/geosoc.116.13"},{"key":"33","doi-asserted-by":"crossref","unstructured":"JJ Sato, T Hosoda, AP Kryukov, et al.  \"Mamm Study.\"  36, \"Genetic diversity of the sable (Martes zibellina, Mustelidae) in Russian Far East and Hokkaido inferred from mitochondrial NADH dehydrogenase subunit 2 gene sequences.\" 209 (2011)","DOI":"10.3106\/041.036.0404"},{"key":"34","doi-asserted-by":"crossref","unstructured":"MJ Statham, J Murdoch, J Janecka, et al.  \"Mol Ecol.\"  23, \"Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories.\" 4813 (2014)","DOI":"10.1111\/mec.12898"},{"key":"35","doi-asserted-by":"crossref","unstructured":"MJ Statham, CJ Edwards, K Nor\u00e9n, et al.  \"Quat Sci Rev.\"  197, \"Genetic analysis of European red foxes reveals multiple distinct peripheral populations and central continental admixture.\" 257 (2018)","DOI":"10.1016\/j.quascirev.2018.08.019"},{"key":"36","doi-asserted-by":"crossref","unstructured":"T Watanabe  and Y Yamazaki  \"Zool J Linn Soc.\"  202, \"Complex geohistory of continental islands advanced allopatric evolution even for the highly dispersive generalist red fox (Vulpes vulpes): multiple phylogenetic groups in the Japanese Archipelago.\" zlae007 (2024)","DOI":"10.1093\/zoolinnean\/zlae007"},{"key":"37","doi-asserted-by":"crossref","unstructured":"T Watanabe  and Y Yamazaki  \"J Zool.\"  326, \"Sex-specific behavioral patterns significantly affect the phylogeographic process of secondary contact in the red fox: male dispersibility and female philopatry.\" 185 (2025)","DOI":"10.1111\/jzo.70003"},{"key":"11","doi-asserted-by":"crossref","unstructured":"T Inoue, N Nonaka, A Mizuno, et al.  \"Zool Sci.\"  24, \"Mitochondrial DNA phylogeography of the red fox (Vulpes vulpes) in Northern Japan.\" 1178 (2007)","DOI":"10.2108\/zsj.24.1178"},{"key":"16","doi-asserted-by":"crossref","unstructured":"N Kurose, R Masuda, MC Yoshida,  \"Zool Sci.\"  16, \"Phylogeographic variation in two Mustelines, the least weasel Mustela nivalis and the Ermine M. erminea of Japan, based on mitochondrial DNA control region sequences.\" 971 (1999)","DOI":"10.2108\/zsj.16.971"},{"key":"27","doi-asserted-by":"crossref","unstructured":"R Peakall  and PE Smouse  \"Mol Ecol Notes.\"  6, \"GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research.\" 288 (2006)","DOI":"10.1111\/j.1471-8286.2005.01155.x"},{"key":"14","doi-asserted-by":"crossref","unstructured":"T Jombart  and I Ahmed  \"Bioinformatics.\"  27, \"adegenet 1.3-1: new tools for the analysis of genome-wide SNP data.\" 3070 (2011)","DOI":"10.1093\/bioinformatics\/btr521"},{"key":"13","doi-asserted-by":"crossref","unstructured":"T Jombart,  \"Bioinformatics.\"  24, \"adegenet: a R package for the multivariate analysis of genetic markers.\" 1403 (2008)","DOI":"10.1093\/bioinformatics\/btn129"},{"key":"28","doi-asserted-by":"crossref","unstructured":"R Peakall  and PE Smouse  \"Bioinformatics.\"  28, \"GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research\u2014an update.\" 2537 (2012)","DOI":"10.1093\/bioinformatics\/bts460"},{"key":"18","doi-asserted-by":"publisher","unstructured":"B Langmead  and SL Salzberg  \"Nat Methods.\"  9, \"Fast gapped-read alignment with Bowtie 2.\" 357 (2012)","DOI":"10.1038\/nmeth.1923"},{"key":"1","doi-asserted-by":"crossref","unstructured":"DH Alexander, J Novembre, K Lange,  \"Genome Res.\"  19, \"Fast model-based estimation of ancestry in unrelated individuals.\" 1655 (2009)","DOI":"10.1101\/gr.094052.109"},{"key":"30","unstructured":"\"R: A Language and Environment for Statistical Computing.\"  (2023)"}],"container-title":["Zoological Science"],"original-title":[],"deposited":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T21:06:33Z","timestamp":1791234393000},"score":1,"resource":{"primary":{"URL":"https:\/\/bioone.org\/journals\/zoological-science\/volume-43\/issue-3\/zs250063\/History-of-Population-Formation-for-the-Red-Fox-Around-the\/10.2108\/zs250063.full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,31]]},"references-count":37,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,6,1]]}},"URL":"https:\/\/doi.org\/10.2108\/zs250063","relation":{},"ISSN":["0289-0003","2212-3830"],"issn-type":[{"value":"0289-0003","type":"print"},{"value":"2212-3830","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,31]]}}}