title: Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans.
abstract: When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters-including drift times and admixture rates-for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called 'Demographic Inference with Contamination and Error' (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%.
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America.
authors.forename: Fernando
authors.initials: F
authors.lastname: Racimo
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Renaud
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America.
authors.forename: Montgomery
authors.initials: M
authors.lastname: Slatkin
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000235:genetics*; D059018:DNA Contamination; D004272:DNA, Mitochondrial / Q000235:genetics; D005580:Fossils; D040961:Genetic Drift; D005828:Genetics, Population; D006801:Humans; D008390:Markov Chains; D009010:Monte Carlo Method; D059125:Neanderthals / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004272:DNA, Mitochondrial; D004247:DNA