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This phylogenomic research reconstructs the evolutionary history of the strictly arboreal and forest\u2010dependent Oriental Giant Squirrels (\n                    <jats:italic>Ratufa<\/jats:italic>\n                    ) to gain insights into the interplay between paleo\u2010forest distribution and regional diversification. By analysing genomic data (complete mitochondrial genomes and approximately 4000 nuclear ultraconserved elements) from historic museum specimens and conducting divergence time estimation and niche modelling, we uncover how global paleoclimate cooling, the uplift of the Himalayas and Tibetan Plateau, and habitat fragmentation led to allopatric speciation in refugia during the mid\u2010Miocene, Miocene\u2013Pliocene boundary, and late Pliocene, in synchrony with other evergreen forest\u2010dependent species. Our findings underscore the potential role of grassland expansion during climatic oscillations and the North Sunda and Mekong paleorivers in isolating populations and promoting vicariance and speciation in this region. This research suggests a species\u2010level diversity underestimation within\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>R. bicolor<\/jats:italic>\n                    <\/jats:styled-content>\n                    and\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>R. affinis<\/jats:italic>\n                    <\/jats:styled-content>\n                    , supporting the recognition of\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>R. gigantea<\/jats:italic>\n                    <\/jats:styled-content>\n                    as a distinct species, along with several candidate species that warrant integrative taxonomic revision. Additionally, this study highlights the rapid and independent evolution of dwarfism in three\n                    <jats:italic>Ratufa<\/jats:italic>\n                    lineages and discusses challenges in museum genomics. Ultimately, this study serves as a valuable reference on the historical biogeography of tropical Asia, providing important insights for the conservation of these threatened taxa and the evolutionary processes that generate and maintain biodiversity in this hyperdiverse region.\n                  <\/jats:p>","DOI":"10.1111\/mec.70179","type":"journal-article","created":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T10:01:23Z","timestamp":1764064883000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Pliocene Forest Fragmentation Shaped Speciation in Tropical Asia's Giant Squirrels (\n                    <i>Ratufa<\/i>\n                    )"],"prefix":"10.1111","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2412-4003","authenticated-orcid":false,"given":"Arlo","family":"Hinckley","sequence":"first","affiliation":[{"name":"Division of Mammals, Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution  Washington DC USA"},{"name":"Departamento de Zoolog\u00eda Universidad de Sevilla  Seville Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gonzalo E.","family":"Pinilla\u2010Buitrago","sequence":"additional","affiliation":[{"name":"Instituto de Ecolog\u00eda (Unidad M\u00e9rida) Universidad Nacional Aut\u00f3noma de M\u00e9xico  Mexico City M\u00e9xico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jes\u00fas E.","family":"Maldonado","sequence":"additional","affiliation":[{"name":"Center for Conservation Genomics Smithsonian National Zoo and Conservation Biology Institute  Washington DC USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary Faith C.","family":"Flores","sequence":"additional","affiliation":[{"name":"Division of Mammals, Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution  Washington DC USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob A.","family":"Esselstyn","sequence":"additional","affiliation":[{"name":"Museum of Natural Science and Department of Biological Sciences Louisiana State University  Baton Rouge Louisiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nurul","family":"Inayah","sequence":"additional","affiliation":[{"name":"Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution National Research and Innovation Agency  Cibinong Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa T. 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