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Empowering conservation practice with efficient and economical genotyping from poor quality samples using MPCRseq

Meghana Natesh, Ryan W. Taylor, Nathan Truelove, Elizabeth A. Hadly, Stephen Palumbi, Dmitri Petrov, Uma Ramakrishnan
doi: https://doi.org/10.1101/349472
Meghana Natesh
1National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore - 560065, India
2Sastra University, Tirumalaisamudram, Thanjavur – 613401, India
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Ryan W. Taylor
3Department of Biology, Stanford University, Stanford, CA - 94305, USA
4End2End Genomics LLC, Davis, CA
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Nathan Truelove
5Hopkins Marine Station, Stanford University, Pacific Grove, CA – 93950, USA
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Elizabeth A. Hadly
3Department of Biology, Stanford University, Stanford, CA - 94305, USA
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Stephen Palumbi
3Department of Biology, Stanford University, Stanford, CA - 94305, USA
5Hopkins Marine Station, Stanford University, Pacific Grove, CA – 93950, USA
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Dmitri Petrov
3Department of Biology, Stanford University, Stanford, CA - 94305, USA
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  • For correspondence: dpetrov@stanford.edu uramakri@ncbs.res.in
Uma Ramakrishnan
1National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore - 560065, India
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  • For correspondence: dpetrov@stanford.edu uramakri@ncbs.res.in
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Abstract

  1. Moderate to high density genotyping (100+ SNPs) is widely used to determine and measure individual identity, relatedness, fitness, population structure and migration in wild populations.

  2. However, these important tools are difficult to apply when high-quality genetic material is unavailable. Most genomic tools are developed for high quality DNA sources from lab or medical settings. As a result, most genetic data from market or field settings is limited to easily amplified mitochondrial DNA or a few microsatellites.

  3. To enable genotyping in conservation contexts, we sequenced multiplex PCR products (we call this MPCRseq) from very low-quality DNA extracted from feces, hair, and cooked samples. We demonstrated utility and wide-ranging potential application in endangered wild tigers and tracking commercial trade in Caribbean queen conch.

  4. We genotyped 100 SNPs from degraded tiger samples to identify individuals, discern close relatives, and detect population differentiation. Co-occurring carnivores do not amplify (e.g. Indian wild dog or Dhole) or are monomorphic (e.g. leopard). 62 SNPs from conch fritters and field-collected samples were used to test relatedness and detect population structure.

  5. We provide proof-of-concept for a rapid, simple, cost-effective, and scalable method (for both samples and number of loci), a framework that can be applied to other conservation scenarios previously limited by low quality DNA samples. These approaches provide a critical advance for wildlife monitoring and forensics, open the door to field-ready testing, and will strengthen the use of science in policy decisions and wildlife trade.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 17, 2019.
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Empowering conservation practice with efficient and economical genotyping from poor quality samples using MPCRseq
Meghana Natesh, Ryan W. Taylor, Nathan Truelove, Elizabeth A. Hadly, Stephen Palumbi, Dmitri Petrov, Uma Ramakrishnan
bioRxiv 349472; doi: https://doi.org/10.1101/349472
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Empowering conservation practice with efficient and economical genotyping from poor quality samples using MPCRseq
Meghana Natesh, Ryan W. Taylor, Nathan Truelove, Elizabeth A. Hadly, Stephen Palumbi, Dmitri Petrov, Uma Ramakrishnan
bioRxiv 349472; doi: https://doi.org/10.1101/349472

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