15 Public Studies

16S Amplicon Analysis of Neandertal Dental Calculus Weyrich, Laura S., Cooper, Alan

Study has been superseded by newer study

Whole genome sequencing of a 7,000 year old Mesolithic European from La Braña, Spain Olalde, Iñigo, Allentoft, Morten E., Marquès-Bonet, Tomàs, Navarro, Arcadi, Willerslev, Eske, Lalueza-Fox, Carles Download data as .tar

Whole genome sequencing of a 7,000 year old Mesolithic European from La Braña, Spain for the analysis of derived immune and ancestral pigmentation alleles in Ancient European Populations (

Genome flux and stasis in a five millennium transect of European prehistory Gamba, Cristina, Jones, Eppie R, Teasdale, Matthew D, McLaughlin, Russell L, Gonzalez-Fortes, Gloria, Mattiangeli, Valeria, Domboróczki, László, Kővári, Ivett, Pap, Ildikó, Anders,Alexandra, Whittle, Alasdair, Dani, János, Raczky, Pál, Higham, Thomas FG, Hofreiter, Michael, Bradley, Daniel G, Pinhasi, Ron Download data as .tar

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.

Reconstructing Neandertal behavior, diet, and disease using ancient DNA from dental calculus Weyrich, Laura, Duchene, Sebastian, Soubrier, Julien, Arriola, Luis, Llamas, Bastien, Breen, James, Morris, Alan G, Alt, Kurt W, Caramelli, David, Dresely, Veit, Farrell, Milly, Farrer, Andrew G, Francken, Michael, Gully, Neville, Haak, Wolfgang, Hardy, Karen, Harvati, Katerina, Held, Petra, Holmes, Edward C, Kaidonis, John, Krause, Johannes, Lalueza Fox, Carles, de la Rasilla, Marco, Rosas, Antonio, Semal, Patrick, Soltysiak, Arkadiusz, Townsend, Grant, Usai, Donatella, Wahl, Joachim, Huson, Daniel, Dobney, Keith, Cooper, Alan Download data as .tar

Recent genomic data has revealed multiple interactions between Neandertals and modern humans1, but there is currently little genetic evidence about Neandertal behavior, diet, or disease. We shotgun sequenced ancient DNA from five Neandertal dental calculus specimens to characterize regional differences in Neandertal ecology. In Spy, Belgium, Neandertal diet was heavily meat based, and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In El Sidrón, Spain, no meat was detected, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering2,3. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota), and suggested that meat consumption contributed to significant variation between Neandertal microbiota. Evidence for self-medication was detected in an El Sidrón Neandertal with a dental abscess4, who also suffered from a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2x depth of coverage) – the oldest draft microbial genome generated to date at ~48,000 years old. DNA preserved within dental calculus represents an important new resource of behavioral and health information for ancient homininspecimens, as well as a unique long-term study system for microbial evolution.

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans Raghavan, Maanasa, Skoglund, Pontus, Graf, Kelly E, Metspalu, Mait, Albrechtsen, Anders, Moltke, Ida, Rasmussen, Simon, Stafford Jr, Thomas W, Orlando, Ludovic, Metspalu, Ene, Karmin, Monika, Tambets, Kristiina, Rootsi, Siiri, Mägi, Reedik, Campos, Paula F, Balanovska, Elena, Balanovsky, Oleg, Khusnutdinova, Elza, Litvinov, Sergey, Osipova, Ludmila P, Fedorova, Sardana A, Voevoda, Mikhail I, DeGiorgio, Michael, Sicheritz-Ponten, Thomas, Brunak, Søren, Demeshchenko, Svetlana, Kivisild, Toomas, Villems, Richard, Nielsen, Rasmus, Jakobsson, Mattias, Willerslev, Eske Download data as .tar

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

A High-Coverage Genome Sequence from an Archaic Denisovan Individual Meyer, Matthias, Kircher, Martin, Gansauge, Marie-Theres, Li, Heng, Racimo, Fernando, Mallick, Swapan, Schraiber, Joshua G, Jay, Flora, Prüfer, Kay, de Filippo, Cesare, Sudmant, Peter H, Alkan, Can, Fu, Qiaomei, Do, Ron, Rohland, Nadin, Tandon, Arti, Siebauer, Michael, Green, Richard E, Bryc, Katarzyna, Briggs, Adrian W, Stenzel, Udo, Dabney, Jesse, Shendure, Jay, Kitzman, Jacob, Hammer, Michael F, Shunkov, Michael V, Derevianko, Anatoli P, Patterson, Nick, Andrés, Aida M, Eichler, Evan E, Slatkin, Montgomery, Reich, David, Kelso, Janet, Pääbo, Svante Download data as .tar

We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.

Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia Tobler, Ray, Rohrlach, Adam, Soubrier, Julien, Bover, Pere, Llamas, Bastien, Tuke, Jonathan, Bean, Nigel, Abdullah-Highfold, Ali, Agius, Shane, O’Donoghue, Amy, O’Loughlin, Isabel, Sutton, Peter, Zilio, Fran, Walshe, Keryn, Williams, Alan, Turney, Chris, Williams, Matthew, Richards, Stephen, Mitchell, Robert, Kowal, Emma, Stephen, John, Williams, Lesley, Haak, Wolfgang, Cooper, Alan Download data as .tar

Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka); however, little is known about the processes underlying the enormous linguistic and phenotypic diversity within Australia. Here we report 111 mitochondrial genomes (mitogenomes) from historical Aboriginal Australian hair samples, whose origins enable us to reconstruct Australian phylogeographic history before European settlement. Marked geographic patterns and deep splits across the major mitochondrial haplogroups imply that the settlement of Australia comprised a single, rapid migration along the east and west coasts that reached southern Australia by 49-45 ka. After continent-wide colonization, strong regional patterns developed and these have survived despite substantial climatic and cultural change during the late Pleistocene and Holocene epochs. Remarkably, we find evidence for the continuous presence of populations in discrete geographic areas dating back to around 50 ka, in agreement with the notable Aboriginal Australian cultural attachment to their country.

A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures Olalde, Iñigo, Schroeder, Hannes, Sandoval-Velasco, Marcela, Vinner, Lasse, Lobón, Irene, Ramirez, Oscar, Civit, Sergi, García Borja, Pablo, Salazar-García, Domingo C, Talamo, Sahra, Fullola, Josep María, Oms, Francesc Xavier, Pedro, Mireia, Martínez, Pablo, Sanz, Montserrat, Daura, Joan, Zilhão, João, Marquès-Bonet, Tomàs, Gilbert, M. Thomas P, Lalueza-Fox, Carles Download data as .tar

In this study, we generated the complete genome of a 7,400 year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. The data in this study contributed to a publication in Molecular Biology and Evolution doi:10.1093/molbev/msv181 (First published online: September 2, 2015)

Ancient human genomes suggest three ancestral populations for present-day Europeans Lazaridis, Iosif, Patterson, Nick, Mittnik, Alissa, Renaud, Gabriel, Mallick, Swapan, Kirsanow, Karola, Sudmant, Peter H, Schraiber, Joshua G, Castellano, Sergi, Lipson, Mark, Berger, Bonnie, Economou, Christos, Bollongino, Ruth, Fu, Qiaomei, Bos, Kirsten I, Nordenfelt, Susanne, Li, Heng, de Filippo, Cesare, Prüfer, Kay, Sawyer, Susanna, Posth, Cosimo, Haak, Wolfgang, Hallgren, Fredrik, Fornander, Elin, Rohland, Nadin, Delsate, Dominique, Francken, Michael, Guinet, Jean-Michel, Wahl, Joachim, Ayodo, George, Babiker, Hamza A, Bailliet, Graciela, Balanovska, Elena, Balanovsky, Oleg, Barrantes, Ramiro, Bedoya, Gabriel, Ben-Ami, Haim, Bene, Judit, Berrada, Fouad, Bravi, Claudio M, Brisighelli, Francesca, Busby, George BJ, Cali, Francesco, Churnosov, Mikhail, Cole, David EC, Corach, Daniel, Damba, Larissa, van Driem, George, Dryomov, Stanislav, Dugoujon, Jean-Michel, Fedorova, Sardana A, Gallego Romero, Irene, Gubina, Marina, Hammer, Michael, Henn, Brenna M, Hervig, Tor, Hodoglugil, Ugur, Jha, Aashish R, Karachanak-Yankova, Sena, Khusainova, Rita, Khusnutdinova, Elza, Kittles, Rick, Kivisild, Toomas, Klitz, William, Kučinskas, Vaidutis, Kushniarevich, Alena, Laredj, Leila, Litvinov, Sergey, Loukidis, Theologos, Mahley, Robert W, Melegh, Béla, Metspalu, Ene, Molina, Julio, Mountain, Joanna, Näkkäläjärvi, Klemetti, Nesheva, Desislava, Nyambo, Thomas, Osipova, Ludmila, Parik, Jüri, Platonov, Fedor, Posukh, Olga, Romano, Valentino, Rothhammer, Francisco, Rudan, Igor, Ruizbakiev, Ruslan, Sahakyan, Hovhannes, Sajantila, Antti, Salas, Antonio, Starikovskaya, Elena B, Tarekegn, Ayele, Toncheva, Draga, Turdikulova, Shahlo, Uktveryte, Ingrida, Utevska, Olga, Vasquez, René, Villena, Mercedes, Voevoda, Mikhail, Winkler, Cheryl A, Yepiskoposyan, Levon, Zalloua, Pierre, Zemunik, Tatijana, Cooper, Alan, Capelli, Cristian, Thomas, Mark G, Ruiz-Linares, Andres, Tishkoff, Sarah A, Singh, Lalji, Thangaraj, Kumarasamy, Villems, Richard, Comas, David, Sukernik, Rem, Metspalu, Mait, Meyer, Matthias, Eichler, Evan E, Burger, Joachim, Slatkin, Montgomery, Pääbo, Svante, Kelso, Janet, Reich, David, Krause, Johannes Download data as .tar

We sequenced the genomes of a ~7,000-year-old farmer from Germany and eight ~8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations’ deep relationships and show that early European farmers had ~44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages.

Ancient human genome sequence of an extinct Palaeo-Eskimo Rasmussen, Morten, Li, Yingrui, Lindgreen, Stinus, Pedersen, Jakob Skou, Albrechtsen, Anders, Moltke, Ida, Metspalu, Mait, Metspalu, Ene, Kivisild, Toomas, Gupta, Ramneek, Bertalan, Marcelo, Nielsen, Kasper, Gilbert, M Thomas P, Wang, Yong, Raghavan, Maanasa, Campos, Paula F, Munkholm Kamp, Hanne, Wilson, Andrew S, Gledhill, Andrew, Tridico, Silvana, Bunce, Michael, Lorenzen, Eline D, Binladen, Jonas, Guo, Xiaosen, Zhao, Jing, Zhang, Xiuqing, Zhang, Hao, Li, Zhuo, Chen, Minfeng, Orlando, Ludovic, Kristiansen, Karsten, Bak, Mads, Tommerup, Niels, Bendixen, Christian, Pierre, Tracey L, Grønnow, Bjarne, Meldgaard, Morten, Andreasen, Claus, Fedorova, Sardana A, Osipova, Ludmila P, Higham, Thomas FG, Bronk Ramsey, Christopher, v. O. Hansen, Thomas, Nielsen, Finn C, Crawford, Michael H, Brunak, Søren, Sicheritz-Pontén, Thomas, Villems, Richard, Nielsen, Rasmus, Krogh, Anders, Wang, Jun, Willerslev, Eske Download data as .tar

We report here the genome sequence of an ancient human. Obtained from ~4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.

Iron Age and Anglo-Saxon genomes from East England reveal British migration history Schiffels, Stephan, Haak, Wolfgang, Llamas, Bastien, Tyler-Smith, Chris, Cooper, Alan, Durbin, Richard Download data as .tar

British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

Genomic structure in Europeans dating back at least 36,200 years Seguin-Orlando, Andaine, Korneliussen, Thorfinn S, Sikora, Martin, Malaspinas, Anna-Sapfo, Manica, Andrea, Moltke, Ida, Albrechtsen, Anders, Ko, Amy, Margaryan, Ashot, Moiseyev, Vyacheslav, Goebel, Ted, Westaway, Michael, Lambert, David, Khartanovich, Valeri, Wall, Jeffrey D, Nigst, Philip R, Foley, Robert A, Mirazon Lahr, Marta, Nielsen, Rasmus, Orlando, Ludovic, Willerslev, Eske Download data as .tar

The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.

390K SNP capture data from 69 prehistoric Europeans Haak, Wolfgang, Lazaridis, Iosif, Patterson, Nick, Rohland, Nadin, Mallick, Swapan, Llamas, Bastien, Mittnik, Alissa, Fu, Qiaomei, Meyer, Matthias, Krause, Johannes, Anthony, David, Alt, Kurt W., Cooper, Alan, Reich, David Download data as .tar

This data set contains genome wide SNP data (390K SNP array) from 69 prehistoric Europeans across a transect through time from Mesolithic times to the early Bronze Age.

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia Rasmussen, Morten, Guo, Xiaosen, Wang, Yong, Lohmueller, Kirk E, Rasmussen, Simon, Albrechtsen, Anders, Skotte, Line, Lindgreen, Stinus, Metspalu, Mait, Jombart, Thibaut, Kivisild, Toomas, Zhai, Weiwei, Eriksson, Anders, Manica, Andrea, Orlando, Ludovic, De La Vega, Francisco M, Tridico, Silvana, Metspalu, Ene, Nielsen, Kasper, Ávila-Arcos, María C, Moreno-Mayar, J Víctor, Muller, Craig, Dortch, Joe, Gilbert, M Thomas P, Lund, Ole, Wesolowska, Agata, Karmin, Monika, Weinert, Lucy A, Wang, Bo, Li, Jun, Tai, Shuaishuai, Xiao, Fei, Hanihara, Tsunehiko, van Driem, George, Jha, Aashish R, Ricaut, François-Xavier, de Knijff, Peter, Migliano, Andrea B, Romero, Irene Gallego, Kristiansen, Karsten, Lambert, David M, Brunak, Søren, Forster, Peter, Brinkmann, Bernd, Nehlich, Olaf, Bunce, Michael, Richards, Michael, Gupta, Ramneek, Bustamante, Carlos D, Krogh, Anders, Foley, Robert A, Lahr, Marta M, Balloux, Francois, Sicheritz-Pontén, Thomas, Villems, Richard, Nielsen, Rasmus, Wang, Jun, Willerslev, Eske Download data as .tar

We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers. Skoglund, Pontus, Malmström, Helena, Omrak, Ayça, Raghavan, Maanasa, Valdiosera, Cristina, Günther, Torsten, Hall, Per, Tambets, Kristiina, Parik, Jüri, Sjögren, Karl-Göran, Apel, Jan, Willerslev, Eske, Storå, Jan, Götherström, Anders, Jakobsson, Mattias Download data as .tar

Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains a contentious idea. Population-genomic data from 11 Scandinavian Stone Age human remains suggest that hunter-gatherers had lower genetic diversity than that of farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer–related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone Age foraging groups were historically in low numbers, likely owing to oscillating living conditions or restricted carrying capacity, and that they were partially incorporated into expanding farming groups.

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