Human activities have driven biodiversity loss for millennia, and conservation of ‘refugee species’ that survive as remnant populations requires insights from historical baselines. However, reconstructing the past distribution and ecology of such species is challenging due to data limitations with specimen-based archives. Here, we assess the taxonomic identity of two gibbon mandibles from the Wumingshan Neolithic site in Guangxi, China. Although ancient DNA extraction was unsuccessful, a suite of linear and geometric morphometric analyses using dental and mandibular characters reveals that these mandibles fall within or close to variation shown by extant Chinese Nomascus gibbons and can be assigned to the cao vit gibbon N. nasutus. This is now one of the world’s rarest mammals, with a surviving population of 74 individuals in one site. Comparative assessment of bioclimatic, abiotic and anthropogenic parameters for Wumingshan and other sites where N. nasutus historically occurred reveals the species was formerly a landscape generalist but is now restricted to a high-elevation refugium with reduced human pressures. Our multidisciplinary analyses provide a new baseline on niche requirements and vulnerability for N. nasutus with implications for population management, demonstrating the importance of integrating environmental archives into conservation planning.
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