Genomic and Mitonuclear Patterns of Divergence Among Recently Diverged White‐Crowned Sparrow Subspecies

ABSTRACT Genetic divergence and subsequent speciation are possible within the range and habitat of a population. White‐crowned sparrows are comprised of five subspecies that thrive in a wide range of habitats, latitudes, and elevations across North America, suggesting the ability for local adaptation and rapid divergence. We assessed genome‐wide genetic differentiation in four populations of white‐crowned sparrow ( Zonotrichia leucophrys gambelii , Z. l. oriantha (northern and southern), and Z. l. pugetensis ) and compared patterns of genetic structure using outlier single nucleotide polymorphisms (SNPs), including mitochondrial (255 SNPs) and Z chromosome (580 SNPs) loci. When these four populations are assessed using the full SNP dataset, three genetic clusters are identified: pugetensis , southern oriantha , and northern oriantha grouped with gambelii . However, four genetic clusters are supported by the Z chromosome outlier SNPs corresponding to three subspecies and a north–south split in Z. l. oriantha . Our analyses pointed to consistent divergence of Zonotrichia leucophrys pugetensis from other populations and mitochondrial SNPs showed overlap of southern Z. l. oriantha and Z. l. gambelii . Interestingly, northern Z. l. oriantha populations are more genetically similar to Z. l. gambelii as opposed to its sister population, the southern Z. l. oriantha . We found a region on the Z chromosome with highly elevated F ST among all the populations. The genetic clusters identified in our study may be suggestive of evolutionary events such as selection on the Z chromosome, and this may be driving divergence in white‐crowned sparrows.