TY - GEN A1 - Siska, Veronika A1 - Jones, Eppie Ruth A1 - Jeon, Sungwon A1 - Bhak, Youngjune A1 - Kim, Hak-Min A1 - Cho, Yun Sung A1 - Kim, Hyunho A1 - Lee, Kyusang A1 - Veselovskaya, Elizaveta A1 - Balueva, Tatiana A1 - Gallego-Llorente, Marcos A1 - Hofreiter, Michael A1 - Bradley, Daniel G. A1 - Eriksson, Anders A1 - Pinhasi, Ron A1 - Bhak, Jong A1 - Manica, Andrea T1 - Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently similar to 3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to similar to 7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 791 KW - Mitochondrial-DNA analysis KW - positive selection KW - jomon skeletons KW - ancient DNA KW - pigmentation KW - population KW - admixture KW - edar KW - gene KW - polymorohism Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439977 SN - 1866-8372 IS - 791 ER - TY - GEN A1 - Gallego-Llorente, Marcos A1 - Sarah, Connell A1 - Jones, Eppie R. A1 - Merrett, Deborah C. A1 - Jeon, Y. A1 - Eriksson, Anders A1 - Siska, Veronika A1 - Gamba, Cristina A1 - Meiklejohn, Christopher A1 - Beyer, Robert A1 - Jeon, Sungwon A1 - Cho, Yun Sung A1 - Hofreiter, Michael A1 - Bhak, Jong A1 - Manica, Andrea A1 - Pinhasi, Ron T1 - The genetics of an early Neolithic pastoralist from the Zagros, Iran T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an economy based on goat herding, ca. 10,000 BP. We show that Western Iran was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus, but distinct from the Neolithic Anatolian people who later brought food production into Europe. The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting those of the Central Zagros were somewhat isolated from other populations of the Fertile Crescent. Runs of homozygosity are of a similar length to those from Neolithic farmers, and shorter than those of Caucasus and Western Hunter-Gatherers, suggesting that the inhabitants of Ganj Dareh did not undergo the large population bottleneck suffered by their northern neighbours. While some degree of cultural diffusion between Anatolia, Western Iran and other neighbouring regions is possible, the genetic dissimilarity between early Anatolian farmers and the inhabitants of Ganj Dareh supports a model in which Neolithic societies in these areas were distinct. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 952 KW - whole-genome association KW - ancient KW - domestication KW - agriculture KW - mountains KW - diffusion KW - migration KW - admixture KW - patterns KW - sequence KW - archaeology KW - biological anthropology Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439355 SN - 1866-8372 IS - 952 ER - TY - GEN A1 - González-Fortes, Gloria M. A1 - Jones, Eppie R. A1 - Lightfoot, Emma A1 - Bonsall, Clive A1 - Lazar, Catalin A1 - Grandal-d’Anglade, Aurora A1 - Garralda, María Dolores A1 - Drak, Labib A1 - Siska, Veronika A1 - Simalcsik, Angela A1 - Boroneant, Adina A1 - Romaní, Juan Ramón Vidal A1 - Vaqueiro Rodríguez, Marcos A1 - Arias, Pablo A1 - Pinhasi, Ron A1 - Manica, Andrea A1 - Hofreiter, Michael T1 - Paleogenomic evidence for multi-generational mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the lower Danube Basin T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - The transition from hunting and gathering to farming involved profound cultural and technological changes. In Western and Central Europe, these changes occurred rapidly and synchronously after the arrival of early farmers of Anatolian origin [1-3], who largely replaced the local Mesolithic hunter-gatherers [1, 4-6]. Further east, in the Baltic region, the transition was gradual, with little or no genetic input from incoming farmers [7]. Here we use ancient DNA to investigate the relationship between hunter-gatherers and farmers in the Lower Danube basin, a geographically intermediate area that is characterized by a rapid Neolithic transition but also by the presence of archaeological evidence that points to cultural exchange, and thus possible admixture, between hunter-gatherers and farmers. We recovered four human paleogenomes (1.13 to 4.13 coverage) from Romania spanning a time transect between 8.8 thousand years ago (kya) and 5.4 kya and supplemented them with two Mesolithic genomes (1.73- and 5.33) from Spain to provide further context on the genetic background of Mesolithic Europe. Our results show major Western hunter-gatherer (WHG) ancestry in a Romanian Eneolithic sample with a minor, but sizeable, contribution from Anatolian farmers, suggesting multiple admixture events between hunter-gatherers and farmers. Dietary stableisotope analysis of this sample suggests a mixed terrestrial/ aquatic diet. Our results provide support for complex interactions among hunter-gatherers and farmers in the Danube basin, demonstrating that in some regions, demic and cultural diffusion were not mutually exclusive, but merely the ends of a continuum for the process of Neolithization. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 794 KW - ancient DNA KW - eneolithic KW - neolithic transition KW - Romania KW - Iron Gates KW - mesolithic Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-440115 SN - 1866-8372 IS - 794 SP - 1801 EP - 1820 ER - TY - JOUR A1 - Pinhasi, Ron A1 - Fernandes, Daniel A1 - Sirak, Kendra A1 - Novak, Mario A1 - Connell, Sarah A1 - Alpaslan-Roodenberg, Songul A1 - Gerritsen, Fokke A1 - Moiseyev, Vyacheslav A1 - Gromov, Andrey A1 - Raczky, Pal A1 - Anders, Alexandra A1 - Pietrusewsky, Michael A1 - Rollefson, Gary A1 - Jovanovic, Marija A1 - Trinhhoang, Hiep A1 - Bar-Oz, Guy A1 - Oxenham, Marc A1 - Matsumura, Hirofumi A1 - Hofreiter, Michael T1 - Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone JF - PLoS one N2 - 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 (similar to 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 10,0001,800 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. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0129102 SN - 1932-6203 VL - 10 IS - 6 PB - PLoS CY - San Fransisco ER - TY - GEN A1 - Pinhasi, Ron A1 - Fernandes, Daniel A1 - Sirak, Kendra A1 - Novak, Mario A1 - Connell, Sarah A1 - Alpaslan-Roodenberg, Songül A1 - Gerritsen, Fokke A1 - Moiseyev, Vyacheslav A1 - Gromov, Andrey A1 - Raczky, Pál A1 - Anders, Alexandra A1 - Pietrusewsky, Michael A1 - Rollefson, Gary A1 - Jovanovic, Marija A1 - Trinhhoang, Hiep A1 - Bar-Oz, Guy A1 - Oxenham, Marc A1 - Matsumura, Hirofumi A1 - Hofreiter, Michael T1 - Optimal ancient DNA yields from the inner ear part of the human petrous bone T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschafliche Reihe N2 - 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 (similar to 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 10,0001,800 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 515 KW - genome sequence KW - extraction KW - patterns KW - survival KW - damage Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-409557 SN - 1866-8372 IS - 515 ER -