Population genomic landscapes and insights for conservation of the critically endangered island-endemic Chinese pangolin in Taiwan.

Island species/populations are characterized by evolutionary uniqueness and a high degree of endemism and extinction. The conservation and restoration of island species/populations have become the most challenging and urgent issues in biodiversity conservation. Chinese pangolin in Taiwan island (Manis pentadactyla pentadactyla) is a well-known, critically endangered, and island-endemic Chinese pangolin subspecies, which has been the focus of conservation concern. Here, we first generated large-scale population genomics data for the Chinese pangolin in Taiwan to address its population structure, demographic history, the genomic consequences of population declines, and survival potential. We revealed that the Chinese pangolin in Taiwan originated in southeast China and was differentiated into Northern and non-Northern populations due to the isolation of the Xueshan and Central Mountain Ranges, proposing to treat them as separate conservation units. The southeast of Taiwan island acted as a refuge for this Chinese pangolin subspecies during the Last Glacial Maximum. The Northern population had experienced a more severe bottleneck and isolation than the non-Northern population, which corresponded to the estimated current lower genetic diversity, higher inbreeding, and genetic load of the Northern population. The modeling results revealed that the Northern population is more seriously affected by climate change than the non-Northern population, which highlights that climate change poses a substantial threat to island biodiversity. The simulation results indicate that the Northern population needs a higher population growth rate to achieve evolutionary potential equal to the non-Northern population over the next 100 years, deserving conservation prioritization. This study enhances the understanding of genetic background, conservation status, and future prospects for Chinese pangolin in Taiwan, as well as the genetic consequences of a small and isolated island population.