27 Public Studies

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 (

Parallel palaeogenomic transects reveal complex genetic history of early European farmers Lipson, Mark, Szecsenyi-Nagy, Anna, Mallick, Swapan, Posa, Annamaria, Stegmar, Balazs, Keerl, Victoria, Rohland, Nadin, Stewardson, Kristin, Ferry, Matthew, Michel, Megan, Oppenheimer, Jonas, Broomandkhoshbacht, Nasreen, Harney, Eadaoin, Nordenfelt, Susanne, Llamas, Bastien, Gusztav Mende, Balázs, Kohler, Kitti, Oross, Krisztian, Bondar, Maria, Marton, Tibor, Osztas, Anett, Jakucs, Janos, Paluch, Tibor, Horvath, Ferenc, Csengeri, Piroska, Koos, Judit, Sebok, Katalin, Anders, Alexandra, Raczky, Pal, Regenye, Judit, P. Barna, Judit, Fabian, Szilvia, Serlegi, Gabor, Toldi, Zoltan, Gyongyver Nagy, Emese, Dani, Janos, Molnar, Erika, Palfi, Gyorgy, Mark, Laszlo, Melegh, Bela, Banfai, Zsolt, Domboroczki, Laszlo, Fernandez-Eraso, Javier, Antonio Mujika-Alustiza, Jose, Alonso Fernandez, Carmen, Jimenez Echevarria, Javier, Bollongino, Ruth, Orschiedt, Jorg, Schierhold, Kerstin, Meller, Harald, Cooper, Alan, Burger, Joachim, Bánffy, Eszter, W. Alt, Kurt, Lalueza-Fox, Carles, Haak, Wolfgang, Reich, David Download data as .tar

Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000–2900 BC, n = 100), Germany (5500–3000 BC, n = 42) and Spain (5500–2200 BC, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.

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.

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome M. Cassidy, Lara, Martiniano, Rui, M. Murphy, Eileen, D. Teasdale, Matthew, Mallory, James, Hartwell, Barrie, G. Bradley, Daniel Download data as .tar

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individ- uals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a sub- stantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompa- nying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic vari- ants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persis- tence, blue eye color, Y chromosome R1b haplotypes, and the hemo- chromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings to- gether suggest the establishment of central attributes of the Irish genome 4,000 y ago.

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.

The genetic history of Ice Age Europe Fu, Qiaomei, Posth, Cosimo, Hajdinjak, Mateja, Petr, Martin, Mallick, Swapan, Fernandes, Daniel, Furtwängler, Anja, Haak, Wolfgang, Meyer, Matthias, Mittnik, Alissa, Nickel, Birgit, Peltzer, Alexander, Rohland, Nadin, Slon, Viviane, Talamo, Sahra, Lazaridis, Iosif, Lipson, Mark, Mathieson, Iain, Schiffels, Stephan, Skoglund, Pontus, P. Derevianko, Anatoly, Drozdov, Nikolai, Slavinsky, Vyacheslav, Tsybankov, Alexander, Grifoni Cremonesi , Renata, Mallegni, Francesco, Gely, Bernard, Vacca, Eligio, R. Gonzalez Morales, Manuel, G. Straus, Lawrence, Neugebauer-Maresch, Christine, Teschler-Nicola, Maria, Constantin, Silviu, Teodora Moldovan, Oana, Benazzi, Stefano, Peresani, Marco, Coppola, Donato, Lari, Martina, Ricci, Stefano, Ronchitelli, Annamaria, Valentin, Frederique, Thevenet, Corinne, Wehrberger, Kurt, Grigorescu, Dan, Rougier, Helene, Crevecoeur, Isabelle, Flas, Damien, Semal, Patrick, A. Mannino, Marcello, Cupillard, Christophe, Bocherens, Herve, J. Conard, Nicholas, Harvati, Katerina, Moiseyev, Vyacheslav, G. Drucker, Dorothee, Svoboda, Jiri, P. Richards, Michael, Caramelli, David, Pinhasi, Ron, Kelso, Janet, Patterson, Nick, Krause, Johannes, Paabo, Svante, Reich, David Download data as .tar

Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000–7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.

Upper Palaeolithic genomes reveal deep roots of modern Eurasians R. Jones, Eppie, Gonzalez-Fortes, Gloria, Connell, Sarah, Siska, Veronika, Eriksson, Anders, Martiniano, Rui, L. McLaughlin, Russell, Gallego Llorente, Marcos, M. Cassidy, Lara, Gamba, Cristina, Meshveliani, Tengiz, Bar-Yosef, Ofer, Müller, Werner, Belfer-Cohen, Anna, Matskevich, Zinovi, Jakeli, Nino, F. G., Thomas, Currat, Mathias, Lordkipanidze, David, Hofreiter, Michael, Manica, Andrea, Pinhasi, Ron, G. Bradley, Daniel Download data as .tar

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 B45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers B25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe B3,000 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.

The Demographic Development of the First Farmers in Anatolia Merve Kilinc, Gulsah, Omrak, Ayca, Ozer, Fusun, Gunther, Torsten, Metin Buyukkarakaya, Ali, Bicakci, Erhan, Baird, Douglas, Melike Donertas, Handan, Ghalichi, Ayshin, Yaka, Reyhan, Koptekin, Dilek, Can Acan, Sinan, Parvizi, Poorya, Krzewinska, Maja, A. Daskalaki, Evangelia, Yuncu, Eren, Dilsad Dagtas, Nihan, Fairbairn, Andrew, Pearson, Jessica, Mustafaoglu, Gokhan, Selim Erdal, Yilmaz, Gokhan Cakan, Yasin, Togan, Inci, Somel, Mehmet, Stora, Jan, Jakobsson, Mattias, Gotherstrom, Anders Download data as .tar

The archaeological documentation of the develop- ment of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the spread of farming in Europe [1–3]. Sedentary farming communities emerged in parts of the Fertile Crescent during the tenth millennium and early ninth millen- nium calibrated (cal) BC and had appeared in central Anatolia by 8300 cal BC [4]. Farming spread into west Anatolia by the early seventh millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain un- clear. Using genome sequence data that we gener- ated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our re- sults confirm that the earliest Neolithic central Anato- lians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations. We propose that the earliest farming societies demographically resembled foragers and that only after regional gene flow and rising heterogeneity did the farming population expansions into Europe occur.

Population genomics of Bronze Age Eurasia Allentoft E., Morten, Sikora, Martin, Sjögren, Karl-Göran, Rasmussen, Simon, Rasmussen, Morten, Stenderup, Jesper, Damgaard B., Peter, Schroeder, Hannes, Ahlström, Torbjörn, Vinner, Lasse, Malaspinas, Anna-Sapfo, Margaryan, Ashot, Higham, Tom, Chivall, David, Lynnerup, Niels, Harvig, Lise, Baron, Justyna, Casa Della, Philippe, Dąbrowski, Pawel, Duffy R., Paul, Ebel V., Alexander, Epimakhov, Andrey, Frei, Karin, Furmanek, Mirosław, Gralak, Tomasz, Gromov, Andrey, Gronkiewicz, Stanisław, Grupe, Gisela, Hajdu, Tamas, Jarysz, Radoslaw, Khartanovich, Valeri, Khokhlov, Alexandr, Kiss, Viktoria, Kolar, Jan, Kriiska, Aivar, Lasak, Irena, Longhi, Cristina, McGlynn, George, Merkevicius, Algimantas, Merkyte, Inga, Metspalu, Mait, Mkrtchyan, Ruzan, Moiseyev, Vyacheslav, Paja, Laszlo, Palfi, Gyorgy, Pokutta, Dalia, Pospieszny, Lukasz, Price Douglas, T., Saag, Lehti, Sablin, Mikhail, Shishlina, Natalia, Smrcka, Vaclav, Soenov I., Vasilii, Szeverényi, Vajk, Toth, Gusztáv, Trifanova V., Synaru, Varul, Liivi, Vicze, Magdolna, Yepiskoposyan, Levon, Zhitenev, Vladislav, Orlando, Ludovic, Sicheritz-Ponten, Thomas, Brunak, Søren, Nielsen, Rasmus, Kristiansen, Kristian, Willerslev, Eske Download data as .tar

The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

Early farmers from across Europe directly descended from Neolithic Aegeans Hofmanova, Zuzana, Kreutzer, Susanne, Hellenthal, Garrett, Sell, Christian, Diekmann, Yoan, Díez-del-Molino, David, van Dorp, Lucy, López, Saioa, Kousathanas, Athanasios, Link, Vivian, Kirsanow, Karola, M. Cassidy, Lara, Martiniano, Rui, Strobel, Melanie, Scheu, Amelie, Kotsakis, Kostas, Halstead, Paul, Triantaphyllou, Sevi, Kyparissi-Apostolika, Nina, Urem-Kotsou, Dushka, Ziota, Christina, Adaktylou, Fotini, Gopalan, Shyamalika, M. Bobo, Dean, Winkelbach, Laura, Blöcher, Jens, Unterlander, Martina, Leuenberger, Christoph, Cilingiroglu, Ciler, Horejs, Barbara, Gerritsen, Fokke, J. Shennan, Stephen, G. Bradley, Daniel, Currat, Mathias, R. Veeramah, Krishna, Wegmann, Daniel, G. Thomas, Mark, Papageorgopoulou, Christina, Burger, Joachim Download data as .tar

Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

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.

Genomic insights into the origin of farming in the ancient Near East Lazaridis, Iosif, Nadel, Dani, Rollefson, Gary, C. Merrett, Deborah, Rohland, Nadin, Mallick, Swapan, Fernandes, Daniel, Novak, Mario, Gamarra, Beatriz, Sirak, Kendra, Connell, Sarah, Stewardson, Kristin, Harney, Eadaoin, Fu, Qiaomei, Gonzalez-Fortes, Gloria, R. Jones , Eppie, Alpaslan Roodenberg , Songul, Lengyel, Gyorgy, Bocquentin, Fanny, Gasparian, Boris, M. Monge , Janet, Gregg, Michael, Eshed, Vered, Mizrahi, Ahuva-Sivan, Meiklejohn, Christopher, Gerritsen, Fokke, Bejenaru, Luminita, Blüher, Matthias, Campbell, Archie, Cavalleri, Gianpiero, Comas, David, Froguel, Philippe, Gilbert, Edmund, M. Kerr , Shona, Kovacs, Peter, Krause, Johannes, McGettigan, Darren, Merrigan, Michael, Andrew D., Merriwether, OReilly, Seamus, B. Richards, Martin, Semino, Ornella, Shamoon-Pour, Michel, Stefanescu, Gheorghe, Stumvoll, Michael, Tonjes, Anke, Torroni, Antonio, F. Wilson, James, Yengo, Loic, A. Hovhannisyan, Nelli, Patterson, Nick, Pinhasi, Ron, Reich, David Download data as .tar

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, 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.

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.

Early Neolithic genomes from the eastern Fertile Crescent Broushaki, Farnaz, G Thomas, Mark, Link, Vivian, Lopez, Saioa, van Dorp, Lucy, Kirsanow, Karola, Hofmanova, Zuzana, Diekmann, Yoan, M. Cassidy, Lara, Diez-del-Molino, David, Kousathanas, Athanasios, Sell, Christian, K. Robson, Harry, Martiniano, Rui, Blocher, Jens, Scheu, Amelie, Kreutzer, Susanne, Bollongino, Ruth, Bobo, Dean, Davudi, Hossein, Munoz, Olivia, Currat, Mathias, Abdi, Kamyar, Biglari, Fereidoun, E. Craig , Oliver, G Bradley , Daniel, Shennan, Stephen, R Veeramah , Krishna, Mashkour, Marjan, Wegmann, Daniel, Hellenthal, Garrett, Burger, Joachim Download data as .tar

We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed significantly to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46-77,000 years ago and show affinities to modern day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in SW-Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.

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.

16S Amplicon Analysis of Neandertal Dental Calculus Weyrich, Laura S., Cooper, Alan Download data as .tar

Study has been superseded by newer study

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.

The complete genome sequence of a Neanderthal from the Altai Mountains Prufer, Kay, Racimo, Fernando, Patterson, Nick, Jay, Flora, Sankararaman, Sriram, Sawyer, Susanna, Heinze, Anja, Renaud, Gabriel, H. Sudmant, Peter, de Filippo, Cesare, Li, Heng, Mallick, Swapan, Dannemann, Michael, Fu, Qiaomei, Kircher, Martin, Kuhlwilm, Martin, Lachmann, Michael, Meyer, Matthias, Ongyerth, Matthias, Siebauer, Michael, Theunert, Christoph, Tandon, Arti, Moorjani, Priya, Pickrell, Joseph, C. Mullikin, James, H. Vohr, Samuel, E. Green, Richard, Hellmann, Ines, L. F. Johnson, Philip, Blanche, Helene, Cann, Howard, O. Kitzman, Jacob, Shendure, Jay, E. Eichler, Evan, S. Lein, Ed, E. Bakken, Trygve, V. Golovanova, Liubov, B. Doronichev, Vladimir, V. Shunkov, Michael, P. Derevianko, Anatoli, Viola, Bence, Slatkin, Montgomery, Reich, David, Kelso, Janet, Paabo, Svante Download data as .tar

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques Gunther, Torsten, Valdiosera, Cristina, Malmstrom, Helena, Urena, Irene, Rodriguez-Varela, Ricardo, Osk Sverrisdottir , Oddny, A. Daskalaki, Evangelia, Skoglund, Pontus, Naidoo, Thijessen, M. Svensson, Emma, Maria Bermudez de, Jose, Carbonell, Eudald, Dunn, Michael, Stora, Jan, Iriarte, Eneko, Luis Arsuaga , Juan, Carretero, Jose-Miguel, Gotherstrom, Anders, Jakobsson, Mattias

The consequences of the Neolithic transition in Europe—one of the most important cultural changes in human prehistory—is a subject of great interest. However, its effect on prehistoric and modern-day people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, the first genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter–gatherers. The proportion of hunter–gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.

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.

Genome-wide patterns of selection in 230 ancient Eurasians Mathieson, Iain, Lazaridis, Iosif, Rohland, Nadin, Mallick, Swapan, Patterson, Nick, Alpaslan Roodenberg, Songül, Harney, Eadaoin, Stewardson, Kristin, Fernandes, Daniel, Novak, Mario, Sirak, Kendra, Gamba, Cristina, R. Jones, Eppie, Llamas, Bastien, Dryomov, Stanislav, Pickrell, Joseph, Luís Arsuaga, Juan, María Bermúdez de Castro, José, Carbonell, Eudald, Gerritsen, Fokke, Khokhlov, Aleksandr, Kuznetsov, Pavel, Lozano, Marina, Meller, Harald, Mochalov, Oleg, Moiseyev, Vyacheslav, A. Rojo Guerra, Manuel, Roodenberg, Jacob, Maria Vergès, Josep, Krause, Johannes, Cooper, Alan, W. Alt, Kurt, Brown, Dorcas, Anthony, David, Lalueza-Fox, Carles, Haak, Wolfgang, Pinhasi, Ron, Reich, David Download data as .tar

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.

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