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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Ozga, AT; Webster, TH; Gilby, IC; Wilson, MA; Nockerts, RS; Wilson, ML; Pusey, AE; Li, Y; Hahn, BH; Stone, AC

Published Date

  • January 2021

Published In

Volume / Issue

  • 21 / 1

Start / End Page

  • 170 - 182

PubMed ID

  • 32985084

Pubmed Central ID

  • PMC7746602

Electronic International Standard Serial Number (EISSN)

  • 1755-0998

International Standard Serial Number (ISSN)

  • 1755-098X

Digital Object Identifier (DOI)

  • 10.1111/1755-0998.13260

Language

  • eng