Pliocene Forest Fragmentation Shaped Speciation in Tropical Asia's Giant Squirrels ( <i>Ratufa</i> )

Abstract

Tropical Asia's complex, dynamic geological and climatic history, coupled with its diverse topography, provides a fascinating setting to study evolutionary processes driving high biodiversity. This phylogenomic research reconstructs the evolutionary history of the strictly arboreal and forest‐dependent Oriental Giant Squirrels ( Ratufa ) to gain insights into the interplay between paleo‐forest 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‐Miocene, Miocene–Pliocene boundary, and late Pliocene, in synchrony with other evergreen forest‐dependent 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‐level diversity underestimation within R. bicolor and R. affinis , supporting the recognition of R. gigantea 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 Ratufa 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.