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Diversity 2017, 9(3), 33; doi:10.3390/d9030033

An eDNA-Based SNP Assay for Ungulate Species and Sex Identification

1
Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
2
Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Skogsmarksgränd, SE 90183 Umeå, Sweden
3
Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, NC 27695, USA
*
Author to whom correspondence should be addressed.
Received: 30 June 2017 / Revised: 11 August 2017 / Accepted: 18 August 2017 / Published: 22 August 2017
(This article belongs to the Special Issue Application of Environmental DNA for Biological Conservation)
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Abstract

Many processes in wild populations are difficult to study. Genetic data, often non-invasively collected, may provide a solution to these difficulties and are increasingly used to study behavioral, demographic, ecological, and evolutionary processes. Moreover, the improved sensitivity of genetic methods now allows analyses of trace amounts of DNA left by animals in their environment (e.g., saliva, urine, epithelial cells). Environmental DNA (eDNA) thus offers new opportunities to study a range of historic and contemporary questions. Here, we present a species and sex diagnostic kit for studying browsing in a multispecies temperate ungulate assemblage. Using mitochondrial sequences deposited in Genbank, we developed four single nucleotide polymorphisms (SNPs) for identifying four temperate ungulate species. We also sequenced portions of the Amelogenin gene on the X- and Y-chromosomes and developed six SNPs (three on the X-chromosome and three on the Y-chromosome) for sex determination. We tested the SNP assays on high and low quality/quantity DNA samples. View Full-Text
Keywords: ecological genetics; community ecology; diet analysis; species interactions; wildlife management ecological genetics; community ecology; diet analysis; species interactions; wildlife management
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Nichols, R.V.; Spong, G. An eDNA-Based SNP Assay for Ungulate Species and Sex Identification. Diversity 2017, 9, 33.

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