A 50K SNP array reveals genetic structure for bald eagles (Haliaeetus leucocephalus)

Bald eagles (Haliaeetus leucocephalus) underwent a severe population bottleneck in the mid-1900s due to Dichlorodiphenyltrichloroethane (DDT) use as an insecticide. After its ban in 1972, the population began to recover with the increase being attributed to banning DDT and reintroduction/translocation programs. Although bald eagles have increased and may be in a phase of exponential growth, many populations continue to experience anthropogenic stressors. Assessing levels of standing genetic variation and the partitioning of genetic variation within and among populations is critical for the development of informed conservation management plans. To begin addressing these concerns, we developed a custom 50K Affymetrix Axiom myDesign single nucleotide polymorphism (SNP) array and performed preliminary population genomic analyses on geographically disparate populations of bald eagles to test the utility of this SNP array for assessing levels of standing genetic variation in the gene pool and determining the partitioning of genetic variation within and among populations. To develop the array, a combination of RAD-tag sequencing and genome sequencing was used with the final chip consisting of 50,789 SNPs in both genic and intergenic regions of the genome. After genotyping 169 hatchlings, 45,952 SNPs from the array were found to be of quality and were used in Structure, Admixture, and a discriminant analysis of principal components (DAPC) analyses. Results from all of these analyses indicate that despite the significant population bottleneck, sufficient genetic variation is detectable within the bald eagle gene pool. Moreover, based on our disparate geographic sampling of bald eagles, our preliminary analyses indicate statistically significant partitioning of the genetic variation among broad sampling areas.