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Bird migration has fascinated natural historians and scientists for centuries. While the timing of migration is known to vary by species, population, sex, and individual, identifying the cause of this variation can be challenging. Here we investigate factors underlying migratory timing in a long- distance migratory bird, the Common Yellowthroat (Geothlypas trichas), using a population genomic approach. We begin by creating a map of genetic variation across geographic space (a “genoscape”) using lcWGS from across the breeding range. We then utilize genetic assays to assign 249 wintering and 1050 northward migrating birds to genetically distinct breeding populations. Additionally, we estimate the expected spring onset date in each predicted breeding region and calculate the remaining migratory distance for northward migrating birds. Our findings indicate that when population genetic structure is not a factor in the analysis, it appears that birds captured early in the season are migrating to breeding grounds where spring arrives later, which contrasts with prior research. However, when we incorporate population structure into our analysis, our results align with predictions, indicating that birds captured earlier in the season are indeed heading to breeding grounds where spring arrives earlier. Further analysis revealed that the disparity between results obtained with and without population genetic structure can be attributed to the fact that individuals from the western genetic group migrate three times the distance to the west, despite breeding at the same latitude. Our findings suggest that categorizing large numbers of migrating birds into genetically distinct groups can reveal population-specific patterns in migratory timing and shed light on the relative contributions of different selective forces responsible for the observed patterns. 

Abstract Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low‐coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine‐scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population‐specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate‐Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.