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Mathieson I.,Harvard University | Lazaridis I.,Harvard University | Lazaridis I.,The Broad Institute of MIT and Harvard | Rohland N.,Harvard University | And 55 more authors.
Nature | Year: 2015

Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height. © 2015 Macmillan Publishers Limited. All rights reserved.


PubMed | Complutense University of Madrid, Independent researcher, Netherlands Institute in Turkey, University Pompeu Fabra and 14 more.
Type: Historical Article | Journal: Nature | Year: 2015

Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europes first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.


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.


Lazaridis I.,Harvard University | Lazaridis I.,The Broad Institute of MIT and Harvard | Nadel D.,Haifa University | Rollefson G.,Whitman College | And 62 more authors.
Nature | Year: 2016

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ∼12,000 and 1,400BC, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia. © 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.


PubMed | Australian National University, independent researcher, Eötvös Loránd University, Museum of Vojvodina and 10 more.
Type: Journal Article | Journal: 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.


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.


Gerritsen F.A.,Netherlands Institute in Turkey | Ozbal R.,Koç 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.

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