Abstract
Modern human contamination is a common problem in ancient DNA studies. We provide evidence that this issue is also present in studies in great apes, which are our closest living relatives, for example in noninvasive samples. Here, we present a simple method to detect human contamination in short-read sequencing data from different species: HuConTest. We demonstrate its feasibility using blood and tissue samples from these species. This test is particularly useful for more complex samples (such as museum and noninvasive samples) which have smaller amounts of endogenous DNA, as we show here.
Highlights
Contaminationfrom exogenous sources is a problem common in ancient DNA, where multiple tools exist (reviewed by Peyregne and Prufer (2020)), as well as in studies of nonhuman primates (Prado-Martinez et al 2013)
Human contamination may occur in great ape samples of various origin and quality
We first applied the test to blood samples from all great ape species, which are generally expected to contain at most small amounts of human contamination
Summary
Contaminationfrom exogenous sources is a problem common in ancient DNA, where multiple tools exist (reviewed by Peyregne and Prufer (2020)), as well as in studies of nonhuman primates (Prado-Martinez et al 2013). Human contamination can be a confounding factor in genomic studies, especially in the case of fecal, museum, or ancient DNA from great apes.
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