Abstract
Population declines may have long‐term genetic consequences, including genetic erosion and inbreeding depression, which could affect species' evolutionary potential and increase their risk of extinction. Small populations are more vulnerable to genetic threats than common species, but even species with large populations can also be at risk of extinction. The yellow‐breasted bunting ( Emberiza aureola ) is a common and widespread songbird in the northern Palearctic regions, but its global population size has drastically declined by around 90% throughout the past 30 years, leading to an upgrade of its conservation status to critically endangered in the IUCN Red List. In this study, we identified three populations within this species using whole‐genome resequencing data, but the genetic differentiation between populations was shallow. These populations underwent similar population fluctuations but differed in the extent of population decline, resulting in lower genetic diversity and more homozygous deleterious mutations in a population comprising individuals on islands. The ancient demographic history was mainly associated with the climate, while population declines over the past 100 generations are likely due to human activities. Our results suggest that the yellow‐breasted bunting population before the recent collapse faced relatively low genetic threats and had high evolutionary potential. However, we should be vigilant about the genetic threats faced by this species, as our sampling time occurred at the onset of its recent global population collapse. This study provides valuable genetic information for the conservation of yellow‐breasted bunting and also highlights the similar genetic threats faced by other large populations.