Determining breeding origin of individuals on the nonbreeding range
We assigned individuals sampled from the nonbreeding range to the ESSBPs using WGSassign. Since these individuals are of unknown origin, we assumed the accuracy of their assignment would be comparable to the accuracy achieved with known breeding samples. Individuals at the periphery or boundaries of genetically distinct populations may have admixed genomes that are not truly representative of either population. While posterior probabilities of assignment are typically used to detect admixture and determine confidence of assignment, our preliminary results showed that posterior probabilities of assignment were unreliable with lcWGS data (see Results and Discussion ). Therefore, we split up the genotype likelihood data into 10 subsets of 400,000 SNPs, in order of genomic region, for each individual and used a consistency of assignment threshold of 0.8 (i.e. , at least 8 of the 10 datasets being assigned to the same population) to determine confidence in assignment. We validated this approach on the 47 breeding individuals used as the testing set for the ESSBPs and then used it for the 148 individuals from the nonbreeding range.