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Genetic structure and viability selection in the golden eagle (Aquila chrysaetos), a vagile raptor with a Holarctic distribution

Abstract

Molecular markers can reveal interesting aspects of organismal ecology and evolution, especially when surveyed in rare or elusive species. Herein, we provide a preliminary assessment of golden eagle (Aquila chrysaetos) population structure in North America using novel single nucleotide polymorphisms (SNPs). These SNPs included one molecular sexing marker, two mitochondrial markers, 85 putatively neutral markers that were derived from noncoding regions within large intergenic intervals, and 74 putatively nonneutral markers found in or very near protein-coding genes. We genotyped 523 eagle samples at these 162 SNPs and quantified genotyping error rates and variability at each marker. Our samples corresponded to 344 individual golden eagles as assessed by unique multilocus genotypes. Observed heterozygosity of known adults was significantly higher than of chicks, as was the number of heterozygous loci, indicating that mean zygosity measured across all 159 autosomal markers was an indicator of fitness as it is associated with eagle survival to adulthood. Finally, we used chick samples of known provenance to test for population differentiation across portions of North America and found pronounced structure among geographic sampling sites. These data indicate that cryptic genetic population structure is likely widespread in the golden eagle gene pool, and that extensive field sampling and genotyping will be required to more clearly delineate management units within North America and elsewhere.

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Acknowledgments

The authors thank A. Capparella, J. Cooper, D. Driscoll, J. Fallon, D. Kramar, M. Kuishn, M. Lanzone, T. Miller, R. Murphy, K. O’Malley, J. Papp, K. Rogers, S. Slater, D. Stafford, D. Stahlecker, S. Thomas, L. Tran, S. Van Arsdae, and D. Wilst for their assistance collecting golden eagle samples. Special thanks to J. Willoughby for assistance generating Fig. 1, M. Sundaram for assistance with statistics, and to DeWoody lab members for comments on earlier drafts of the manuscript. The Nature Conservancy provided permission to use their lands. This work was supported by the U.S. Fish and Wildlife Service, the U.S. Bureau of Land Management (award numbers L12AC20102, L11PX02237, and L12AC2010), the California Department of Fish and Wildlife (Agreement #P1182024), and the Provost’s Office at Purdue University (University Faculty Scholar program). Eagle tissue and feather samples were collected under appropriate scientific collecting permits. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. The findings and conclusions in this article are those of the authors and do not necessarily represent the views of the U.S. Fish and Wildlife Service.

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Correspondence to Jacqueline M. Doyle.

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Doyle, J.M., Katzner, T.E., Roemer, G.W. et al. Genetic structure and viability selection in the golden eagle (Aquila chrysaetos), a vagile raptor with a Holarctic distribution. Conserv Genet 17, 1307–1322 (2016). https://doi.org/10.1007/s10592-016-0863-0

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Keywords

  • Allelic diversity
  • Effective population size
  • Repeatability
  • Fluidigm
  • Heterozygosity fitness correlation
  • Genetic mating system
  • Genetic monogamy