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

  • Megan E. JudkinsEmail author
  • Brian M. Couger
  • Wesley C. Warren
  • Ronald A. Van Den Bussche
Research Article


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.


SNPs Bald eagles Population genomics Conservation 



We would like to thank Bryan Bedrosian, Brian Millsap, Erica Miller, Kenneth (“Tuk”) Jacobson, Russ Horton, Todd Katzner, Victor Roubidoux, and Victoria Vosberg for contributing the bald eagle blood samples used in this study. Without their generosity this study could not have been completed. We would also like to thank the Iowa Tribe of Oklahoma, Shakopee Mdewakanton Sioux, and the Eppley Foundation for providing the funding necessary for this project. Thanks are also extended to the Ford Foundation for funding Megan Judkins research fellowship while the project was being conducted. This manuscript represents one of four chapters that were part of Megan’s dissertation and therefore a special thanks to the other members of her dissertation committee, Drs. Meredith Hamilton, Andrew Doust, and Jim Lish. Their efforts on previous versions of this manuscript were invaluable.

Supplementary material

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Supplementary material 1 (PDF 2248 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of Integrative BiologyOklahoma State UniversityStillwaterUSA
  2. 2.Grey Snow Eagle House, Iowa Tribe of OklahomaPerkinsUSA
  3. 3.High Performance Computing Center, Oklahoma State UniversityStillwaterUSA
  4. 4.McDonnell Genome Institute, Washington UniversitySt. LouisUSA
  5. 5.Bond Life Sciences Center, University of MissouriColumbiaUSA

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