Genomic signatures and demographic history of the widespread and critically endangered yellow-breasted bunting

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 population has drastically declined by around 90% throughout the past 30 years, leading to an upgrade of its conservation status to critically endangered. 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 recent population declines are likely due to human activities. Our results suggest that the yellow-breasted bunting population before the recent population 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 appropriate conservation management of the yellow-breasted bunting and sheds light on the extinction risks and genetic consequences common species face.