Conclusion
Low-coverage WGS is a powerful and potentially cost-effective approach for population assignment studies. We demonstrate that high assignment accuracy can be obtained for weakly differentiated populations, even for individuals with very low sequencing coverage (< 0.1X). We further demonstrate the importance of balancing the effective sample sizes of source populations to avoid assignment bias due to variation in the precision of allele frequency estimation. By applying these methods to the American Redstart, we reveal broad-scale parallel migration and highlight unique population-specific patterns of connectivity. In combination with our demographic analysis, we demonstrate the importance of the Northern Temperate-Greater Antilles migratory population to the total abundance of the species. Furthermore, our identification of nonbreeding regions for the genetically distinct breeding populations provides a foundation for a full annual cycle approach towards preserving genetic diversity. Together, our results provide a valuable framework for studies that aim to use lcWGS to understand the ecology and evolution of migratory species.