The efficacy of whole human genome capture on ancient dental calculus and dentin

Abstract

Objectives Dental 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 methods Total 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. Results Total 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. Discussion While 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.

Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome

“…Both host whole nuclear genome and whole mitochondrial genome reconstruction from dental calculus samples have generally required target enrichment techniques ( Ozga et al. 2016 ; Ziesemer et al. 2019 ; Modi et al.…”

Urine as a high‐quality source of host genomic DNA from wild populations

“…Individual ID is represented by colour and DNA source is represented by line type. Vertical black lines indicate depth filters of 4× and 8× [Colour figure can be viewed at wileyonlinelibrary.com] been used to recover full mitochondrial and nuclear genomes from human calculus samples (Ozga et al, 2016;Ziesemer et al, 2018).…”

Archaeological mitogenomes illuminate the historical ecology of sea otters ( Enhydra lutris ) and the viability of reintroduction

“…Dental calculus was sampled on location in museum research collections following a calculus-specific sampling protocol designed to reduce contamination (description in the electronic supplementary material with photos/specimen metadata). Dental calculus contains both endogenous (host) and microbial DNA [61][62][63] and can be removed without destruction to the specimen, preserving the integrity of rare museum collections while also addressing research questions regarding biodiversity/conservation biology. Owing to differential preservation of endogenous DNA in dental calculus [63] and documented degradation of DNA in calculus museum specimens [64], the historical DNA was extracted and sequenced following ancient DNA protocols and workflows.…”

“…Nuclear genome data (including from dental calculus) may be used to identify specific adaptations [15,78], and other applied methods such as isotopic analyses should be performed to establish past ecological contexts [79,80]. While human dental calculus has been used in genomic analyses as a source of endogenous DNA [61,62], non-human dental calculus has not been used for this purpose and our study is unique in employing this method. Given the degraded nature of sea otter DNA recovered from dental calculus from recent specimens (ca 1983) in this study (electronic supplementary material, figures S4 and S5) and others [64], we recommend using protocols designed specifically for ancient DNA when collecting calculus from skeletonized museum specimens.…”