Low-coverage and population assignment
Since the majority of our nonbreeding and breeding samples were feathers and blood, respectively, we expected the nonbreeding samples to have lower sequencing depth than breeding samples. Therefore, to ensure that we could still achieve high assignment accuracy at lower depths for the nonbreeding samples, which have unknown breeding origin, we first tested assignment accuracy with low coverage breeding samples of known origin. We used the set of individuals from our ESSBPs to estimate population allele frequencies (our training set) and used the remaining breeding samples as a test set. We created two data sets from the test set individuals by down sampling to 0.1X and 0.01X. These two thresholds were based on the majority of the nonbreeding samples being greater than 0.1X and the lowest coverage sample being 0.02X. To determine the accuracy of assignment of individuals with low sequencing depths, we assigned the test sets back to the standardized breeding populations and compared the population assigned with the known population of origin.