The genetic consequences of historic climate change on the contemporary population structure of a widespread temperate North American songbird

Studies of widely distributed species can offer insight regarding how past demographic events tied to historic glaciation and ongoing population genetic processes interact to shape contemporaneous patterns of biodiversity at a continental scale. In this study, we used whole-genome resequencing to investigate the current population structure and genetic signatures of past demographic events in the widespread migratory American goldfinch ( Spinus tristis ). In contrast to the low variation in mitochondrial genomes, a genome-wide panel of >4.5 million single nucleotide polymorphisms (SNPs) strongly supported the existence of eastern and western populations separated by western mountain ranges and additional population structuring within the western clade. Demographic modeling indicated that the eastern and western populations diverged approximately one million years ago, and both populations experienced subsequent population bottlenecks during the last glacial period. Species distribution models showed a severe contraction of suitable habitat for the American goldfinch during this period, with predicted discontinuities that are indicative of multiple, isolated glacial refugia that coincide with present-day population structure. This study highlights the power of genome-level sequencing approaches to deepen our understanding of evolutionary processes in nonmodel wild species and to contribute to efforts assessing how historic demographic events and contemporary factors might influence biodiversity.