A systematic investigation of human DNA preservation in medieval skeletons

Abstract

Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material.Currently the dense inner portion of the petrous pyramid, the location of the skull that houses the inner ear, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. Destructive sampling of the petrous pyramid, assuming its recovery, is often not recommended for highly valued specimens. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies. 2 26 27 28 29 30 31 32 33 34 35 36 37 38Recent advances in minimally invasive sampling techniques 26 have led to a better balance between preservation of the anthropological record and the need for the production of reliable genetic data 27,28 ; however, the threat of damage to internal microstructures that form an important basis of morphological assessments 29-31 can still introduce hesitancy on the part of curators and physical anthropologists in making the petrous pyramid available for aDNA applications. These factors, in conjunction with the chance of incomplete recovery of crania at excavation 32 or restricted sampling of highly valued specimens, make the identification of alternative sampling locations based on quantitative evaluations of DNA preservation across the skeleton of clear benefit. Teeth have been widely used for the study of aDNA 33,34 , though the 30-fold covered genome of an archaic hominin from Denisova Cave from a distal phalanx demonstrates molecular preservation in elements that are not typically considered for paleogenetics work 4 . Despite these successes, a systematic and extensive study of differential DNA preservation across multiple human skeletal elements, such as those done in the context of modern forensics 35,36 , has yet to be attempted on archaeological remains. Our limited understanding of DNA preservation across the human skeleton is a significant hurdle for the efficient, practical, and ethical study of aDNA, which has particular relevance to the field of ancient population genetics where large sample sizes are needed for robust analytical resolution.DNA preservation can be influenced by many factors including burial practises and treatment of the deceased, geology, as well as environmental and climatic conditions 37 , where the chronological age of a sample is thought to play only a secondary role 38,39 . To serve as a baseline for future investigations seeking to incorporate and extrapolate the effects of these sources of v...

Human mobility at Tell Atchana (Alalakh) during the 2nd millennium BC: integration of isotopic and genomic evidence

“…Every strontium isotope study is faced with the challenge of how best to establish the local bioavailable 87 Sr/ 86 Sr range at the site under study. While two standard deviations from the mean have become common practice to set an objective cut-off to distinguish locals from non-locals [98], the material on which to base this mean is debated and varies between different studies.…”

“…To estimate the typical local 87 Sr/ 86 Sr signature for humans at Alalakh, we measured, in addition to the existing samples from sheep/goat and deer teeth [128], 87 Sr/ 86 Sr ratios of five land snail shells and tooth enamel from two rodents from well-stratified archaeological contexts (see Table 3). As opposed to domesticates, rodents and snails are not managed by humans, and they obtain their food from within a small radius that should be representative for the strontium ratios available directly at the tell [195].…”

“…The key principle in applying δ 18 Strontium in the human body, on the other hand, is incorporated via both food and water, with the biologically available 87 Sr/ 86 Sr composition at a location depending mainly on the underlying geological formations. 87 Sr forms during the radioactive decay of 87 Rb; therefore, while the amount of 86 Sr in each rock is stable, the amount of 87 Sr varies depending on the type of rock (which determines the initial quantity of 87 Rb and total Sr) and the rock's age.…”

“…The surface of the Amuq Plain itself is made up mainly of alluvial sediments from the three major rivers (the Orontes, the Kara Su, and Afrin) and eroded material from the highlands surrounding it [112] (Fig 8). The highlands to the south of the valley, which are part of the Arabian Platform [113], are made up of mostly limestone and other carbonate rocks of relatively young age (mainly Miocene and Eocene formations; 87 Sr/ 86 Sr values typically of 0.707-0.709 [114]). There are areas of basalt bedrock in some parts of the Kurt Mountains to the south, which are mostly from the Miocene and Eocene [112,115], and these can be expected to have somewhat lower 87 Sr/ 86 Sr values (in the range of 0.703-0.705 [116,117]).…”

“…The highlands to the south of the valley, which are part of the Arabian Platform [113], are made up of mostly limestone and other carbonate rocks of relatively young age (mainly Miocene and Eocene formations; 87 Sr/ 86 Sr values typically of 0.707-0.709 [114]). There are areas of basalt bedrock in some parts of the Kurt Mountains to the south, which are mostly from the Miocene and Eocene [112,115], and these can be expected to have somewhat lower 87 Sr/ 86 Sr values (in the range of 0.703-0.705 [116,117]). Basalt of a somewhat later age, from the Pliocene, can also be found in the northeast of the plain [113,118,119], and these areas may be expected to have roughly similar 87 These considerations show that it is crucial to evaluate where the majority of the food consumed by the individuals under study came from: only if the bulk of the diet was produced locally -i.e., at or in the vicinity of the site where an individual lived -will the strontium isotopic signature allow conclusions about the place of residency, and therefore questions of dietary make-up and catchment must be taken into account [35,129,130].…”