Assignment of wintering Barnacle Geese (Branta leucopsis) to breeding populations using genome-wide single-nucleotide polymorphisms

Abstract Migratory birds often traverse thousands of kilometers, yet some individuals may abandon migration and form sedentary populations—a process termed ‘migratory drop-off’. A key limitation in studying this phenomenon is the inability to distinguish between individuals from different populations, particularly when they share part of their range. We aimed to solve this problem for the Barnacle Goose ( Branta leucopsis ), a species with both migratory and sedentary breeding populations along its flyway. We developed a genetic tool aimed at distinguishing individuals from migratory and sedentary populations. Using genome-wide single-nucleotide polymorphisms (SNPs), we assigned geese wintering in the Netherlands to their breeding populations (i.e., the Netherlands and Russia). While complete assignment accuracy is likely unachievable—with potentially up to 20% of individuals misassigned due to ongoing gene flow and limited genetic differentiation—our results suggest that this error can be managed by focusing on high-confidence assignments or by studying traits with pronounced ecological or physiological differences. In the end, we refined a dataset of over 400,000 SNPs to approximately 1000 candidate markers for potential use in a diagnostic tool. Integrating these genetic markers with other methods, such as stable isotopes or morphological traits, may enhance assignment accuracy and offer novel insights into the ecological and evolutionary consequences of migratory drop-off.