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Pinhasi R.,University College Dublin | Fernandes D.,University College Dublin | Sirak K.,Emory University | Novak M.,University College Dublin | And 16 more authors.
PLoS ONE | Year: 2015

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. © 2015 Pinhasi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Gerritsen F.A.,Netherlands Institute in Turkey | Ozbal R.,Koc University
Anatolica | Year: 2013

Excavations at the seventh millennium settlement of Barcin Höyük in NW Anatolia have yielded burials of adults, juveniles and infants. This article reports on 34 burials excavated in the years between 2007 and 2012. Most are single and primary burials, with the body in flexed position on its side. The preferred location to bury adults was in open areas between houses, used also for outdoor activities. Babies in contrast were frequently buried in the rubble of abandoned houses. Grave goods are not numerous and include animal bones and bone implements. Osteological examinations revealed high infant mortality, especially in the 0-3 months range. Coarse food consumption led to bad dental health among adults and juveniles. Among the observed pathological conditions degenerative arthritis was common.


Groenhuijzen M.R.,VU University Amsterdam | Kluiving S.J.,VU University Amsterdam | Gerritsen F.A.,VU University Amsterdam | Gerritsen F.A.,Netherlands Institute in Turkey | Kunzel M.,VU University Amsterdam
Quaternary International | Year: 2015

Landscape archaeological research has been undertaken on the mound of Barcin Höyük in northwest Anatolia, Turkey. It is the oldest Neolithic site in the region, making it of particular interest in regard to the spread of farming from the regions of origin (southeast and central Anatolia) to northwest Anatolia. This study shows that the site was founded approximately 8550 a cal. BP on a natural elevation in a generally wet environment, at the edge of a retreating lake. The site was subject to environmental shifts in younger periods, with a phase of arid conditions and erosion at least prior to the Bronze Age, succeeded by a phase of more humid conditions and rising lake levels mostly in the last two millennia, and finally a return to arid conditions and declining lake levels. Considering the Neolithic environmental conditions, the local environment of Barcin Höyük resembled the local environment of Çatalhöyük, a central Anatolian site. This suggests that despite the general differences between the regions, the earliest sedentary population of northwest Anatolia favoured local conditions similar to those of central Anatolia, while younger sites in the aforementioned region diverge to slightly different localities. © 2014 Elsevier Ltd and INQUA.

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