Abstract
ObjectivesDental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques.Materials and methodsTotal DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in‐solution hybridization capture and high‐throughput sequencing.ResultsTotal DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four‐fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on‐target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum‐level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off‐target sequences in human genome‐enriched calculus libraries may still be useful for oral microbiome reconstruction.DiscussionWhile ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.
Highlights
The development and application of sequence capture technology has greatly increased the number of archaeological samples that are accessible for genomic studies (e.g., Carpenter et al, 2013; Fu, Mittnik, et al, 2013; Haak et al, 2015; Schroeder et al, 2015)
Total DNA from calculus exceeded that of dentin in all cases, and the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different
While we found no correlation between average DNA fragment length and initial endogenous human DNA content or capture performance, we agree with previous studies that fragment length might be a limiting factor when applying whole genome enrichment (WGE) on extremely degraded ancient DNA samples (Cruz-Dávalos et al, 2016; Enk et al, 2014)
Summary
The development and application of sequence capture technology has greatly increased the number of archaeological samples that are accessible for genomic studies (e.g., Carpenter et al, 2013; Fu, Mittnik, et al, 2013; Haak et al, 2015; Schroeder et al, 2015). To date, targeted enrichment of archaeological specimens has resulted in the successful retrieval of ancient mitochondrial genomes (e.g., Briggs et al, 2009; Llamas et al, 2016; Ozga et al, 2016; Slon et al, 2016), ancient pathogen genomes (Bos et al, 2014; Spyrou et al, 2016; Vågene et al, 2018), human genome-wide SNPs (Haak et al, 2015), partial or whole exomes (Burbano et al, 2010; Da Fonseca et al, 2015), entire chromosomes (Cruz-Dávalos et al, 2017; Fu, Meyer, et al, 2013), and partial nuclear genomes (Carpenter et al, 2013; Schroeder et al, 2015) The majority of these aDNA capture studies have focused on either archaeological bone or dentin as sample material. As dental calculus is a calcified bacterial biofilm, not a human tissue, it might be subject to fewer restrictions with respect to destructive sampling (Ozga et al, 2016)
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