Abstract
In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of estimating contamination measured heterozygosity. These measurements, however, could only be performed on haploid genomic regions, i.e. the mitochondrial genome or male X chromosomes, but provided no measures of contamination in the nuclear genome of females with their two X chromosomes. Instead, female nuclear contamination is routinely extrapolated from mitochondrial contamination estimates, but it remains unclear if this extrapolation is reliable and to what degree variation in mitochondrial to nuclear DNA ratios affects this extrapolation. We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.
Highlights
The emergence of Next-Generation-Sequencing (NGS) technologies has substantially advanced the field of ancient DNA research[1]
Female mitochondrial DNA (mtDNA) contamination estimates are extrapolated to the nuclear level and only female samples with low mtDNA contamination estimates are used for population genetic analysis on the nuclear genome
For each of the three tested skeletal elements we investigated samples from different sites (Table 1), labelled P1 through P7 for petrous bones, T1 through T4 for teeth, and B1 through B4 for other bones
Summary
The emergence of Next-Generation-Sequencing (NGS) technologies has substantially advanced the field of ancient DNA (aDNA) research[1]. As a second step required for authenticating ancient human DNA, NGS data allow estimating contamination levels of human DNA directly[1]. Earlier estimates of contamination levels in NGS data from early modern humans were based on so-called diagnostic positions on the mitochondrial DNA (mtDNA), i.e. nucleotide positions that differ between the sample and a comparative dataset of complete modern human mtDNA sequences from world-wide populations[5]. Female mtDNA contamination estimates are extrapolated to the nuclear level and only female samples with low mtDNA contamination estimates are used for population genetic analysis on the nuclear genome Whether this extrapolation is reliable, remains untested, in particular given that mitochondrial to nuclear DNA ratios can substantially vary between and even within bone samples[9], potentially affecting the extrapolation of mtDNA to nuclear contamination levels
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