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Improving our conservation genetic toolkit: ddRAD-seq for SNPs in snow leopards

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Abstract

Snow leopards (Panthera uncia) are an enigmatic, high-altitude species whose challenging habitat, low population densities and patchy distribution have presented challenges for scientists studying its biology, population structure, and genetics. Molecular scatology brings a new hope for conservation efforts by providing valuable insights about snow leopards, including their distribution, population densities, connectivity, habitat use, and population structure for assigning conservation units. However, traditional amplification of microsatellites from non-invasive sources of DNA are accompanied by significant genotyping errors due to low DNA yield and poor quality. These errors can lead to incorrect inferences in the number of individuals and estimates of genetic diversity. Next generation technologies have revolutionized the depth of information we can get from a species’ genome. Here we used double digest restriction-site associated DNA sequencing (ddRAD-seq), a well-established technique for studying non-model organisms, to develop a reference sequence library for snow leopards using blood samples from five Mongolian individuals. Our final data set reveals 4504 loci with a median size range of 221 bp. We identified 697 SNPs and low nucleotide diversity (0.00032) within these loci. However, the probability that two random individuals will share identical genotypes is about 10−168. We developed probes for DNA capture using this sequence library which can now be used for genotyping individuals from scat samples. Genetic data from ddRAD-seq will be invaluable for conducting population and landscape scale studies that can inform snow leopard conservation strategies.

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Funding

The funding was provided by Panthera.

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Authors and Affiliations

  1. Department of Biological Sciences, Wright State University, Dayton, USA

    Safia Janjua, Jeffrey L. Peters, Volker Bahn & Thomas P. Rooney

  2. Bioresource Research Centre, Islamabad, Pakistan

    Safia Janjua & Fakhar I. Abbas

  3. PANTHERA, New York, USA

    Byron Weckworth

  4. Grimso Wildlife Research Station, Swedish University of Agricultural Sciences, Uppsala, Sweden

    Orjan Johansson

  5. Snow Leopard Trust, Seattle, USA

    Orjan Johansson

Authors
  1. Safia Janjua
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  2. Jeffrey L. Peters
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  3. Byron Weckworth
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  4. Fakhar I. Abbas
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  5. Volker Bahn
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  6. Orjan Johansson
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  7. Thomas P. Rooney
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Correspondence to Safia Janjua.

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Janjua, S., Peters, J.L., Weckworth, B. et al. Improving our conservation genetic toolkit: ddRAD-seq for SNPs in snow leopards. Conservation Genet Resour 12, 257–261 (2020). https://doi.org/10.1007/s12686-019-01082-2

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  • DOI: https://doi.org/10.1007/s12686-019-01082-2

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