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.

中文翻译：

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尿液作为来自野生种群的宿主基因组 DNA 的高质量来源

从野生动物种群中生成基因组数据的能力有可能对自然栖息地中物种的种群历史和动态提供前所未有的洞察力。然而，对于许多物种来说，在法律、伦理或后勤方面不可能获得质量足以进行基因组分析的组织样本。在这项研究中，我们评估了多种遗传物质来源（粪便、尿液、牙本质和牙结石）和几种捕获方法（鸟枪法、全基因组、外显子组）在生成野生东部黑猩猩（Pan troglodytes schweinfurthii ）基因组规模数据方面的成功。) 来自坦桑尼亚贡贝国家公园。我们发现尿液比其他来源含有更多的宿主 DNA，从而导致整个基因组的覆盖范围更广、更深。尿液也表现出较低的等位基因丢失率。我们发现，在从粪便和牙结石等低质量样本中生成可用数据方面，外显子组测序比鸟枪法测序和全基因组捕获要成功得多。这些结果突出表明尿液是一种有前途且尚未开发的 DNA 来源，可以从许多物种的野生种群中非侵入性地收集。