Global spatiotemporal patterns of demographic fluctuations in terrestrial vertebrates during the Late Pleistocene

Demographic fluctuations are crucial for assessing species’ threat levels, yet their global spatiotemporal patterns and historical drivers remain unknown. Here, we used single whole-genome sequence data for 527 extant and widespread terrestrial vertebrates to investigate their demographic fluctuations during the Late Pleistocene. Effective population size (Ne) simulations indicated that all taxa experienced a population decline from the Last Interglacial to the Last Glacial Maximum (LGM). After the LGM, birds, and amphibians underwent population expansion, whereas mammals and reptiles’ populations declined. Regions with high Ne shifted from Neotropical to Afrotropical and to Palearctic, some overlapping with recognized glacial refugia and biodiversity hotspots. In addition, climate-related factors exerted long-term effects on Ne, while human disturbances might confine to specific regions around the Pleistocene-Holocene boundary. This study underscores the significance of quantifying vertebrate genetic vulnerability to guide biodiversity conservation in response to environmental changes.