TY - GEN A1 - Jones, Eppie R. A1 - González-Fortes, Gloria M. A1 - Connell, Sarah A1 - Siska, Veronika A1 - Eriksson, Anders A1 - Martiniano, Rui A1 - McLaughlin, Russell L. A1 - Llorente, Marcos Gallego A1 - Cassidy, Lara M. A1 - Gamba, Cristina A1 - Meshveliani, Tengiz A1 - Bar-Yosef, Ofer A1 - Müller, Werner A1 - Belfer-Cohen, Anna A1 - Matskevich, Zinovi A1 - Jakeli, Nino A1 - Higham, Thomas F. G. A1 - Currat, Mathias A1 - Lordkipanidze, David A1 - Hofreiter, Michael A1 - Manica, Andrea A1 - Pinhasi, Ron A1 - Bradley, Daniel G. T1 - Upper Palaeolithic genomes reveal deep roots of modern Eurasians T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1334 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439317 SN - 1866-8372 IS - 1334 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 - 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 - JOUR A1 - Jones, Eppie R. A1 - González-Fortes, Gloria M. A1 - Connell, Sarah A1 - Siska, Veronika A1 - Eriksson, Anders A1 - Martiniano, Rui A1 - McLaughlin, Russell L. A1 - Llorente, Marcos Gallego A1 - Cassidy, Lara M. A1 - Gamba, Cristina A1 - Meshveliani, Tengiz A1 - Bar-Yosef, Ofer A1 - Mueller, Werner A1 - Belfer-Cohen, Anna A1 - Matskevich, Zinovi A1 - Jakeli, Nino A1 - Higham, Thomas F. G. A1 - Currat, Mathias A1 - Lordkipanidze, David A1 - Hofreiter, Michael A1 - Manica, Andrea A1 - Pinhasi, Ron A1 - Bradley, Daniel G. T1 - Upper Palaeolithic genomes reveal deep roots of modern Eurasians JF - Nature Communications N2 - We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers similar to 45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers similar to 25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe similar to 3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages. Y1 - 2015 U6 - https://doi.org/10.1038/ncomms9912 SN - 2041-1723 VL - 6 PB - Nature Publishing Group CY - London ER -