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Urine as a high-quality source of host genomic DNA from wild populations

View ORCID ProfileAndrew T. Ozga, View ORCID ProfileTimothy H. Webster, Ian C. Gilby, View ORCID ProfileMelissa A. Wilson, Rebecca S. Nockerts, View ORCID ProfileMichael L. Wilson, Anne E. Pusey, Yingying Li, View ORCID ProfileBeatrice H. Hahn, View ORCID ProfileAnne C. Stone
doi: https://doi.org/10.1101/2020.02.18.955377
Andrew T. Ozga
1Halmos College of Natural Science and Oceanography, Nova Southeastern University
2Center for Evolution and Medicine, Arizona State University
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  • For correspondence: aozga@nova.edu timothy.h.webster@utah.edu
Timothy H. Webster
3School of Life Sciences, Arizona State University
4Department of Anthropology, University of Utah
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  • For correspondence: aozga@nova.edu timothy.h.webster@utah.edu
Ian C. Gilby
5School of Human Evolution and Social Change, Arizona State University
6Institute of Human Origins, Arizona State University
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Melissa A. Wilson
2Center for Evolution and Medicine, Arizona State University
3School of Life Sciences, Arizona State University
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Rebecca S. Nockerts
7Department of Anthropology, University of Minnesota
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Michael L. Wilson
7Department of Anthropology, University of Minnesota
8Department of Ecology, Evolution and Behavior, University of Minnesota
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Anne E. Pusey
9Evolutionary Anthropology, Duke University
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Yingying Li
10Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
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Beatrice H. Hahn
10Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
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Anne C. Stone
2Center for Evolution and Medicine, Arizona State University
5School of Human Evolution and Social Change, Arizona State University
6Institute of Human Origins, Arizona State University
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  • ORCID record for Anne C. Stone
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Abstract

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbors significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as feces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.

Footnotes

  • Data citation: Ozga AT, Webster TH, Gilby IC, Wilson MA, Nockerts RS, Wilson ML, Pusey AE, Li Y, Hahn BH, Stone AC. Pan troglodytes schweinfurthii raw sequence reads, NCBI SRA, PRJNA508503.

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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 February 20, 2020.
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Urine as a high-quality source of host genomic DNA from wild populations
Andrew T. Ozga, Timothy H. Webster, Ian C. Gilby, Melissa A. Wilson, Rebecca S. Nockerts, Michael L. Wilson, Anne E. Pusey, Yingying Li, Beatrice H. Hahn, Anne C. Stone
bioRxiv 2020.02.18.955377; doi: https://doi.org/10.1101/2020.02.18.955377
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Urine as a high-quality source of host genomic DNA from wild populations
Andrew T. Ozga, Timothy H. Webster, Ian C. Gilby, Melissa A. Wilson, Rebecca S. Nockerts, Michael L. Wilson, Anne E. Pusey, Yingying Li, Beatrice H. Hahn, Anne C. Stone
bioRxiv 2020.02.18.955377; doi: https://doi.org/10.1101/2020.02.18.955377

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