Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

Erik Ersmark,Maja Krzewińska,Ricardo Rodríguez-Varela,Tatiana R. Feuerborn,Tom van der Valk,Arielle R. Munters,Irene Ureña,Anders Götherström,Love Dalén,Vendela Kempe Lagerholm,Eleftheria Palkopoulou,Patrícia Pečnerová,Johanna von Seth,David Díez-del-Molino,Marianne Dehasque

doi:10.1186/s12864-020-07229-y

Abstract

BackgroundAfter over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.ResultsHere we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.ConclusionsWe propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.

Highlights

After over a decade of developments in field collection, laboratory methods and advances in highthroughput sequencing, contamination remains a key issue in ancient DNA research
When characterizing median read length (mRL) and post-mortem damage scores (PMDR) in the sequences mapping to the different reference genomes we found some differences between the sequences mapping to target compared to non-target and human (Fig. S1), in line with the latter being mostly composed by shorter sequences mapping to conserved regions and the former mostly true endogenous reads
We estimated mRL and PMDR for the true ancient sequences and the contaminant sequences. For both mammoth and dog samples we found a clear distinction in PMDR of the sequences mapping to the target species and the ones mapped to human, with higher PMDR for the target species, representing true ancient sequences, and lower for the human sequences (Fig. 3c, f)

Summary

Introduction

After over a decade of developments in field collection, laboratory methods and advances in highthroughput sequencing, contamination remains a key issue in ancient DNA research. Human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data. A second major challenge of ancient DNA research is contamination from exogenous sources [6, 7]. Environmental DNA molecules in the soil matrix the ancient sample was recovered from can overwhelm the small amounts of endogenous DNA. This is true for DNA from people who collected and handled the samples in the field and/or museum collections [8, 9]. While the use of Polymerase Chain Reaction (PCR) technology allowed ancient DNA research to overcome low concentration problems, the sensitivity of the PCR has made it Feuerborn et al BMC Genomics (2020) 21:844 very difficult to avoid introducing modern contaminant sequences among the authentic ancient DNA [10]

Methods

Results

Discussion

Conclusion