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

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

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, for many species, it is impossible legally, ethically or logistically to obtain tissue samples of quality sufficient for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (faeces, 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 harbours 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 faeces 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.

Original languageEnglish (US)
Pages (from-to)170-182
Number of pages13
JournalMolecular Ecology Resources
Volume21
Issue number1
DOIs
StatePublished - Jan 2021

Bibliographical note

Funding Information:
We gratefully acknowledge Nasibu Zuberi and Dismas Mwacha for their assistance in sample collection; the Gombe Stream Research Center and the Jane Goodall Institute; TAWIRI, COSTECH and Tanzania National Parks for permission to conduct research; the Leakey Foundation, Arizona State University Institute for Human Origins, and the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH; grant R35 GM124827 to MAW and R01 Al120810 to BHH) for generously providing funding; and Research Computing at Arizona State University for providing computing resources.

Publisher Copyright:
© 2020 John Wiley & Sons Ltd

Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.

Keywords

  • endangered populations
  • genomic methods
  • population genetics—empirical
  • primates

PubMed: MeSH publication types

  • Journal Article

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