Abstract
The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.
Highlights
The invention and development of generation sequencing methods has resulted in a transformation, and a rapid expansion of ancient DNA research
Our results confirm that dense bone parts of the petrous bone can provide high endogenous ancient DNA (aDNA) yields and indicate that endogenous DNA fractions for part within the otic capsule (part C) can exceed those obtained for part B by up to 65-fold and those from part of trabecular bone (part A)
We further investigate the following questions, which are essential for the optimized analysis of ancient DNA from petrous bones: 1. Can optimal high yields be obtained from any dense part of the petrous bone? In particular can we detect a difference between the dense part of the inner ear and other dense parts of the petrous?
Summary
The invention and development of generation sequencing methods has resulted in a transformation, and a rapid expansion of ancient DNA (aDNA) research. [1,2,3]), which represent the vast majority of samples from which ancient DNA is extracted, less work has been done on the identification of the best skeletal elements with regard to aDNA preservation. Bearing in mind that DNA analyses are inherently destructive, it is necessary to identify, if possible, the skeletal elements most likely to yield utilizable and informative aDNA. The general notion in both forensic genetics and aDNA is that the density of a bone is positively correlated with DNA preservation and that sampling should be carried out whenever possible on dense, weight bearing bones, with a preference for the femur and tibia [7]. The analysis of ancient hair samples, when available, has yielded excellent endogenous DNA preservation High amounts of endogenous DNA have been extracted from the crushed cementum of the roots [13,14,15] and dental calculus is beginning to gain popularity as a substrate for the exploration of the oral microbiome and the impact on biocultural transitions in human history [16,17,18]
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