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Abstract Seasonal migration has fascinated scientists and natural historians for centuries. While the genetic basis of migration has been widely studied across different taxa, there is little consensus regarding which genomic regions play a role in the ability to migrate and whether they are similar across species. Here, we examine the genetic basis of intraspecific variation within and between distinct migratory phenotypes in a songbird. We focus on the Common Yellowthroat (Geothlypis trichas) as a model system because the polyphyletic origin of eastern and western clades across North America provides a strong framework for understanding the extent to which there has been parallel or convergent evolution in the genes associated with migratory behavior. First, we investigate genome-wide population genetic structure in the Common Yellowthroat in 196 individuals collected from 22 locations across breeding range. Then, to identify candidate genes involved in seasonal migration, we identify signals of putative selection in replicate comparisons between resident and migratory phenotypes within and between eastern and western clades. Overall, we find wide-spread support for parallel evolution at the genic level, particularly in genes that mediate biological timekeeping. However, we find little evidence of parallelism at the individual SNP level, supporting the idea that there are multiple genetic pathways involved in the modulation of migration. 

Seasonal migration is highly labile from an evolutionary perspective and known to rapidly evolve in response to selective pressures. However, long‐distance migratory birds rely partially on innate genetic programs and may be constrained in their ability to alter their migratory behavior. We take advantage of recent advances in our ability to genotype historical DNA samples to examine the temporal stability of migratory connections between breeding and nonbreeding populations (i.e. migratory connectivity) and population‐level nonbreeding distributions in the Wilson's warblerCardellina pusilla, a long‐distance migratory songbird. By assigning historical and contemporary samples collected across the nonbreeding range to genetically distinct breeding clusters, we suggest that broad‐scale population‐level nonbreeding distributions within this species have remained largely consistent within Mexico from the mid‐1900s to the present day. These findings support the idea that the nonbreeding distributions of long‐distance migrants may remain stable over long time scales, even in the face of rapid environmental change. 

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.