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

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.

Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates

“…As an epidermal tissue, buccal swabs are a relatively less invasive source of low-chimerism epidermal DNA. Recently, urine has also been shown to be a non-invasive source of high-quality DNA 27 , but the amount of chimerism is currently not known for marmoset urine. Urine represents a potentially non-invasive genetic tissue which could be combined with genomic skimming of highly endangered non-model organisms, particularly within captive settings.…”

The Gombe Ecosystem Health Project: 16 years of program evolution and lessons learned

“…In addition, we have integrated physiological monitoring (e.g., Murray et al, 2018) and validated a noninvasive test for IgA (Lantz et al, 2018). Our large biobank of samples has proven useful for a variety of other projects as novel laboratory approaches are validated (e.g., Bibollet-Ruche et al, 2019;Moeller et al, 2015;Ozga et al, 2020;Wroblewski et al, 2009).…”

“…In addition, we have integrated physiological monitoring (e.g., Murray et al, 2018) and validated a noninvasive test for IgA (Lantz et al, 2018). Our large biobank of samples has proven useful for a variety of other projects as novel laboratory approaches are validated (e.g., Bibollet‐Ruche et al, 2019; Moeller et al, 2015; Ozga et al, 2020; Wroblewski et al, 2009). Finally, we have begun to broaden our approach outside of our original target species and area, to incorporate other NHPs, domestic animals, and humans both inside and outside the park (Deere et al, 2019; Parsons et al, 2014, 2015).…”

Genomic Skimming and Nanopore Sequencing Uncover Cryptic Hybridization in One of World’s Most Threatened Primates

“…As an epidermal tissue, buccal swabs are a relatively less invasive source of low-chimerism epidermal DNA. Recently, urine has also been shown to be a non-invasive source of high-quality DNA 26 , but the amount of chimerism is currently not known for marmoset urine. Urine represents a potentially non-invasive genetic tissue which could be combined with genomic skimming of highly endangered non-model organisms, particularly within captive settings.…”