Genetically distinct breeding populations
Given that signatures of population structure can be skewed by closely related individuals, we used NGSrelate version 2 to identify and remove individuals with with up to second-degree relationships (kinship > 0.0884). We implemented principal components analysis (PCA) and estimated individual admixture proportions using Pcangsd , which estimates individual allele frequencies to minimize bias from low and variable sequencing depth. We determined the number of genetically distinct breeding populations of American Redstarts by identifying congruent geographic signatures of clustering in the PCA with groupings of individuals based on admixture proportions. Posterior probabilities of group membership from the admixture proportions were visualized on a base map from Natural Earth (naturalearthdata.com) with each group specified by a different colour, and clipped to the breeding range of the American Redstart (Strimas-Mackey et al., 2021). Colour transparency was scaled such that the highest posterior probability of group membership is opaque while the smallest posterior probability is transparent. Visualization was performed in R (R Core Team, 2021). Genetic differentiation among the breeding populations was calculated by creating site allele frequency files for each breeding population and calculating FST in ANGSD ().