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

  • Safia JanjuaEmail author
  • Jeffrey L. Peters
  • Byron Weckworth
  • Fakhar I. Abbas
  • Volker Bahn
  • Orjan Johansson
  • Thomas P. Rooney
Methods and Resources Article

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.

Keywords

Snow leopard ddRAD-seq Next generation sequencing SNP discovery 

Notes

Funding

The funding was provided by Panthera.

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Safia Janjua
    • 1
    • 2
    Email author
  • Jeffrey L. Peters
    • 1
  • Byron Weckworth
    • 3
  • Fakhar I. Abbas
    • 2
  • Volker Bahn
    • 1
  • Orjan Johansson
    • 4
    • 5
  • Thomas P. Rooney
    • 1
  1. 1.Department of Biological SciencesWright State UniversityDaytonUSA
  2. 2.Bioresource Research CentreIslamabadPakistan
  3. 3.PANTHERANew YorkUSA
  4. 4.Grimso Wildlife Research StationSwedish University of Agricultural SciencesUppsalaSweden
  5. 5.Snow Leopard TrustSeattleUSA

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