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A 37 K SNP array for the management and conservation of Golden Eagles (Aquila chrysaetos)

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Abstract

We describe the development of a custom 37 K Affymetrix Axiom myDesign single nucleotide polymorphism (SNP) array for a culturally and ecologically important apex predator, the golden eagle (Aquila chrysaetos). Using this SNP array, we performed population genomic analysis on 154 individuals of known natal localities and detected three genetic clusters that we designated as Taiga/High Arctic, Great Basin, and Rocky Mountains/Great Plains. Each of these clusters appears to display clinal variation within these geographic regions. After determining genetic structure, we performed an assignment test of 32 individuals, five of which were siblings of individuals used in the assessment of genetic structure, three had associated telemetry data, and the remaining individuals were of unknown natal locations. Using this array, four siblings were correctly assigned to the same geographic region as their sibling and the genetic assignment of the radio telemetered birds agreed with the expected movement patterns displayed by these individuals. For the remaining individuals, we were able to assign all but five individuals to one of the three genetic clusters. Our genetic assignments illustrates the utility of this SNP array to accurately assign most individuals to predesignated geographical regions. While further compiling genetic and other data types, we can increase the power of this tool for identifying those breeding populations that may need assistance due to anthropogenic stressors that negatively impact their population viability. The use of this genetic resource will help substantiate decisions by multiple conservation groups that seek to preserve the natural population structure of the golden eagle.

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All SNP data will be available from the EVA database once the manuscript has been accepted.

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Acknowledgements

This research was funded by the Iowa Tribe of Oklahoma, Shakopee Mdewakanton Sioux, Eppley Foundation, Ford Foundation, the New Mexico State University Agricultural Experiment Station, U.S. Fish and Wildlife Service, and U.S. Geological Survey (Environmental Health Missions Area-Contaminant Biology Program and Ecosystems Mission Area). We thank J. Anderson, S. Anderson, J. Buck, R. Claremont, B. Couger, R. Crandall, K. Gura, E. Forsman, J. Harper, N. Horton, F. Isaacs, B. Johnson, D. Leal, R. (“Murph”) Murphy, S. Norton, B. Price, D. Shepherdson, V. Slabe, A. Smith, R. Vetter, S. Wilson, B. Woodbridge, and S. Wray for field and laboratory work. A. Doust, M. Hamilton, J. Lish, M. Tobler and several anonymous reviewers provided valuable comments on earlier drafts of this manuscript. Finally, we thank the Oklahoma State University High Performance Computing Center for use of their computing platforms.

Funding

The following entities contributed to funding this project: U.S. Fish and Wildlife Services -Division of Migratory Bird Management and Western Golden Eagle Team (4500063135), U.S. Geological Survey-Environmental Health Missions Area-Contaminant Biology Program and Ecosystems Mission Area, Bureau of Land Management Grant, USFWS Region 2 - SW (F15AC00666-0000-0000), USFWS Region 6 -Rocky Mtns/Plains (F15AC00025-0001-0130), National Fish and Wildlife Foundation, Navajo Nation (CO11020), Jicarilla Nation (PO244242), Iowa Tribe of Oklahoma, Eppley Foundation, Ford Foundation, Shakopee Mdewakanton Sioux.

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RAVDB, MEJ, WCW, and SLC designed the golden eagle SNP array. RAVDB, MEJ, GWR and BAM were responsible for study design. GWR, BAM, JGB, BEB, RD, GH, ML, BWS, DWS, and MJS collected golden eagle blood for other ongoing studies and provided these samples to this study. MEJ and RAVDB performed all aspects of data analysis. MEJ and RAVDB took the initial lead for the interpretation of results from the genetic analyses and wrote the initial draft of the manuscript. All authors provided insight into the biological and management implications of the data and all authors made significant contributions to the manuscript.

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Correspondence to Megan E. Judkins.

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Judkins, M.E., Roemer, G.W., Millsap, B.A. et al. A 37 K SNP array for the management and conservation of Golden Eagles (Aquila chrysaetos). Conserv Genet 24, 391–404 (2023). https://doi.org/10.1007/s10592-023-01508-3

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