We developed single nucleotide polymorphism (SNP) markers to support a genetics-based capture-mark-recapture (CMR) project implemented for the management of Pacific walrus (Odobenus rosmarus divergens). Using a combination of Restriction-site Associated DNA sequencing (RADSeq) and genome resequencing, 57,504 single nucleotide variants were identified from Pacific walrus DNA. RADSeq was performed on genomic DNA from 192 walruses (63 males; 94 females; 35 unknown sex) whereas genome resequencing was performed on 41 individual walruses (21 males, 20 females). All read mappings were subjected to quality-based variant detection and screened for SNPs. These efforts generated a pool of 909 putative SNPs from which 217 unique TaqMan® assays were developed for validation. Ultimately, 116 validated, biallelic SNPs were combined to create a genetic tag for identifying individual walrus during the multi-year CMR project. Conversion to a 116-SNP TaqMan® OpenArray® enabled use of a high-throughput genotyping qPCR platform, which expedited accurate discrimination of individual walrus and reduced the probability of genotyping errors, thereby providing improved resolution for assessing the size and demographic rates of this population.
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Ali OA, O'Rourke SM, Amish SJ, Meek MH, Luikart G, Jeffres C, Miller MR (2016) RAD capture (rapture): flexible and efficient sequence-based genotyping. Genetics. https://doi.org/10.1534/genetics.115.183665
Beatty WS, Lemons PR, Sethi SA, Everett JP, Lewis CJ, Lynn RJ, Cook GM, Garlich-Miller JL, Wenburg JK (2020) Panmixia in a sea ice-associated marine mammal: evaluating genetic structure of the Pacific walrus (Odobenus rosmarus divergens) at multiple spatial scales. J Mammal. https://doi.org/10.1093/jmammal/gyaa050(in press)
Douglas D (2010) Arctic sea ice decline: projected changes in timing and extent of sea ice in the Bering and Chukchi Seas. U.S. Geological Survey Open-File Report:32
Foote AD, Liu Y, Thomas GWC, Vinař T, Alföldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu J, Raney BJ, Vijay N, Wolf JBW, Hahn MW, Muzny DM, Worley KC, Gilbert MT, Gibbs RA (2015) Convergent evolution of the genomes of marine mammals. Nat Genet. https://doi.org/10.1038/ng.3198
Garlich-Miller J (2003) Proceedings of a workshop on the potential application of mark-recapture methods to estimate the size and trend of the Pacific walrus population USFWS Technical Report MMM 03–1:13
Garlich-Miller J, Jay C (2000) Proceedings of a workshop concerning walrus survey methods. U.S. Department of the Interior, U.S. Fish and Wildlife Service, Marine Mammals Management, Technical Report MMM 00–2:97
Garlich-Miller J, MacCracken JG, Snyder J, Meehan R, Myers M, Wilder JM, Lance E, Matz A (2011) Status review of the Pacific walrus (Odobenus rosmarus divergens). U.S. Department of the Interior, U.S. Fish and Wildlife Service, Marine Mammals Management:163
Jay CV, Marcot BG, Douglas DC (2011) Projected status of the Pacific walrus (Odobenus rosmarus divergens) in the twenty-first century. Polar Biol. https://doi.org/10.1007/s00300-011-0967-4
Johannessen OM, Bengtsson L, Miles MW, Kuzmina SI, Semenov VA, Alekseev GV, Nagurnyi AP, Zakharov VF, Bobylev LP, Pettersson LH, Hasselmann K, Cattle AP (2004) Arctic climate change: observed and modelled temperature and sea-ice variability. Tellus A. https://doi.org/10.1111/j.1600-0870.2004.00060.x
Perovich DK, Richter-Menge JA (2009) Loss of Sea Ice in the Arctic. Ann Rev Mar Sci. https://doi.org/10.1146/annurev.marine.010908.163805
Serreze MC, Holland MM, Stroeve J (2007) Perspectives on the Arctic's shrinking sea-ice cover. Science. https://doi.org/10.1126/science.1139426
Sethi SA, Cook GM, Lemons P, Wenburg J (2014) Guidelines for MSAT and SNP panels that lead to high-quality data for genetic mark–recapture studies. Can J Zool. https://doi.org/10.1139/cjz-2013-0302
Sethi SA, Linden D, Wenburg J, Lewis C, Lemons P, Fuller A, Hare MP (2016) Accurate recapture identification for genetic mark-recapture studies with error-tolerant likelihood-based match calling and sample clustering. R Soc Open Sci. https://doi.org/10.1098/rsos.160457
Sikes RS, Animal Care and Use Committee of the American Society of Mammalogists (2016) Guidelines of the American Society of Mammalogists for the use of wild mammals in research and education [published correction appears in J Mammal. 2016 Jun 9;97(3):1013]. J Mammal 97(3):663–688. https://doi.org/10.1093/jmammal/gyw078
Speckman SG, Chernook VI, Burn DM, Udevitz MS, Kochnev AA, Vasilev A, Jay CV, Lisovsky A, Fischbach AS, Benter RB (2011) Results and evaluation of a survey to estimate Pacific walrus population size, 2006. Mar Mamm Sci. https://doi.org/10.1111/j.1748-7692.2010.00419.x
USFWS (2011) Endangered and threatened wildlife and plants; 12-month finding on a petition to list the Pacific walrus as endangered or threatened. Federal Register
Waits LP, Luikart G, Taberlet P (2001) Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol 10:249–256
Wolf S, Siegel K, Cummings B (2008) Petition to list the Pacific Walrus (Odeobenus rosmarus divergens) as a threatened or endangered species under the Endangered Species Act. Center for Biological Diversity, San Francisco, CA. https://www.biologicaldiversity.org/species/mammals/Pacific_walrus/pdfs/CBD-Pacific-walrus-petition.pdf. Accessed 2 Jan 2020
This study was funded by the U.S. Fish and Wildlife Service, the USGS Ecosystems Mission Area, and the Department of Animal Science and College of Agricultural and Environmental Sciences at the University of California, Davis. Any use of trade, product, or firm 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.
Conflict of interest
The authors declare they have no conflicts of interest.
All procedures followed the guidelines of the American Society of Mammalogists (Sikes et al. 2016) and were approved by the U.S. Fish and Wildlife Service Region 7 Animal Care and Use Committee (2011-02, 2017-01) and conducted under a Marine Mammal Protection Act permit (MA039386-2).
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Cook, G.M., Prince, D.J., O’Rourke, S.M. et al. A little SNP of this, a little SNP of that: The discovery of 116 single nucleotide polymorphism markers to enable the rapid identification of individual Pacific walrus (Odobenus rosmarus divergens). Conservation Genet Resour 12, 555–565 (2020). https://doi.org/10.1007/s12686-020-01156-6