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Genotyping-in-thousands by sequencing (GT-seq) of non-invasive fecal and degraded samples: a new panel to enable ongoing monitoring of Canadian polar bear populations
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  • Kristen Hayward,
  • Rute Clemente-Carvalho,
  • Evelyn Jensen,
  • Peter Van Coeverden de Groot,
  • Marsha Branigan,
  • Markus Dyck,
  • Christina Tschritter,
  • Zhengxin Sun,
  • Stephen Lougheed
Kristen Hayward
Queen's University
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Rute Clemente-Carvalho
Queen's University
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Evelyn Jensen
Yale University
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Peter Van Coeverden de Groot
Queen's University
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Marsha Branigan
Government of the Northwest Territories
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Markus Dyck
Government of Nunavut
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Christina Tschritter
Queen's University
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Zhengxin Sun
Queen's University
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Stephen Lougheed
Queen's University
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Abstract

Genetic monitoring using non-invasive samples provides a complement or alternative to traditional population monitoring methods. However, Next Generation Sequencing approaches to monitoring typically require high quality DNA and the use of non-invasive samples (e.g. scat) is often challenged by poor DNA quality and contamination by non-target species. One promising solution is a highly multiplexed sequencing approach called Genotyping-in-thousands by sequencing (GT-seq), which can enable cost-efficient genomics-based monitoring for populations based on non-invasively collected samples. Here, we develop and validate a GT-seq panel of 324 single nucleotide polymorphisms (SNPs) optimized for genotyping of polar bears based on DNA from non-invasively collected fecal samples. We demonstrate 1) successful GT-seq genotyping of DNA from a range of sample sources, including successful genotyping of 85.7% of non-invasively collected fecal samples determined to contain polar bear DNA, and 2) that we can reliably differentiate individuals, ascertain sex, assess relatedness, and resolve population structure of Canadian polar bear subpopulations based on a GT-seq panel of 324 SNPs. Our GT-seq data reveal similar spatial-genetic patterns as previous polar bear studies but at lesser cost per sample and using non-invasively collected samples, indicating the potential of this approach for population monitoring. This GT-seq panel provides the foundation for a non-invasive toolkit for polar bear monitoring and contribute to community-based programs – a framework which may serve as a model for wildlife management and contribute to conservation and policy for species worldwide.

Peer review status:IN REVISION

16 Jun 2021Submitted to Molecular Ecology Resources
28 Jun 2021Assigned to Editor
28 Jun 2021Submission Checks Completed
04 Jul 2021Reviewer(s) Assigned
03 Aug 2021Review(s) Completed, Editorial Evaluation Pending
12 Aug 2021Editorial Decision: Revise Minor