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141 results on '"Sawyer, Susanna"'

1. Social and genetic diversity in first farmers of central Europe

Author

Gelabert, Pere, Bickle, Penny, Hofmann, Daniela, Teschler-Nicola, Maria, Anders, Alexandra, Huang, Xin, Hämmerle, Michelle, Olalde, Iñigo, Fournier, Romain, Ringbauer, Harald, Akbari, Ali, Cheronet, Olivia, Lazaridis, Iosif, Broomandkhoshbacht, Nasreen, Fernandes, Daniel M., Buttinger, Katharina, Callan, Kim, Candilio, Francesca, Bravo Morante, Guillermo, Curtis, Elizabeth, Ferry, Matthew, Keating, Denise, Freilich, Suzanne, Kearns, Aisling, Harney, Éadaoin, Lawson, Ann Marie, Mandl, Kirsten, Michel, Megan, Oberreiter, Victoria, Zagorc, Brina, Oppenheimer, Jonas, Sawyer, Susanna, Schattke, Constanze, Özdoğan, Kadir Toykan, Qiu, Lijun, Workman, J. Noah, Zalzala, Fatma, Mallick, Swapan, Mah, Matthew, Micco, Adam, Pieler, Franz, Pavuk, Juraj, Šefčáková, Alena, Lazar, Catalin, Starović, Andrej, Djuric, Marija, Krznarić Škrivanko, Maja, Šlaus, Mario, Bedić, Željka, Novotny, Friederike, D. Szabó, László, Cserpák-Laczi, Orsolya, Hága, Tamara, Szolnoki, László, Hajdú, Zsigmond, Mirea, Pavel, Nagy, Emese Gyöngyvér, Virág, Zsuzsanna M., Horváth M., Attila, Horváth, László András, T. Biró, Katalin, Domboróczki, László, Szeniczey, Tamás, Jakucs, János, Szelekovszky, Márta, Zoltán, Farkas, Sztáncsuj, Sándor József, Tóth, Krisztián, Csengeri, Piroska, Pap, Ildikó, Patay, Róbert, Putica, Anđelka, Vasov, Branislav, Havasi, Bálint, Sebők, Katalin, Raczky, Pál, Lovász, Gabriella, Tvrdý, Zdeněk, Rohland, Nadin, Novak, Mario, Ruttkay, Matej, Krošláková, Maria, Bátora, Jozef, Paluch, Tibor, Borić, Dušan, Dani, János, Kuhlwilm, Martin, Palamara, Pier Francesco, Hajdu, Tamás, Pinhasi, Ron, and Reich, David

Published
2024
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2. Screening great ape museum specimens for DNA viruses

Author

Hämmerle, Michelle, Guellil, Meriam, Trgovec-Greif, Lovro, Cheronet, Olivia, Sawyer, Susanna, Ruiz-Gartzia, Irune, Lizano, Esther, Rymbekova, Aigerim, Gelabert, Pere, Bernardi, Paolo, Han, Sojung, Rattei, Thomas, Schuenemann, Verena J., Marques-Bonet, Tomas, Guschanski, Katerina, Calvignac-Spencer, Sebastien, Pinhasi, Ron, and Kuhlwilm, Martin

Published
2024
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3. Improved detection of methylation in ancient DNA

Author

Sawyer, Susanna, Gelabert, Pere, Yakir, Benjamin, Llanos-Lizcano, Alejandro, Sperduti, Alessandra, Bondioli, Luca, Cheronet, Olivia, Neugebauer-Maresch, Christine, Teschler-Nicola, Maria, Novak, Mario, Pap, Ildikó, Szikossy, Ildikó, Hajdu, Tamás, Moiseyev, Vyacheslav, Gromov, Andrey, Zariņa, Gunita, Meshorer, Eran, Carmel, Liran, and Pinhasi, Ron

Published
2024
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4. Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach

Author

Oberreiter, Victoria, Gelabert, Pere, Brück, Florian, Franz, Stefan, Zelger, Evelyn, Szedlacsek, Sophie, Cheronet, Olivia, Cano, Fernanda Tenorio, Exler, Florian, Zagorc, Brina, Karavanić, Ivor, Banda, Marko, Gasparyan, Boris, Straus, Lawrence Guy, Gonzalez Morales, Manuel R., Kappelman, John, Stahlschmidt, Mareike, Rattei, Thomas, Kraemer, Stephan M., Sawyer, Susanna, and Pinhasi, Ron

Published
2024
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6. Link between Monkeypox Virus Genomes from Museum Specimens and 1965 Zoo Outbreak

Author

Hammerle, Michelle, Rymbekova, Aigerim, Gelabert, Pere, Sawyer, Susanna, Cheronet, Olivia, Bernardi, Paolo, Calvignac-Spencer, Sebastien, Kuhlwilm, Martin, Guellil, Meriam, and Pinhasi, Ron

Subjects
Human monkeypox -- Genetic aspects, Genomics -- Genetic aspects, Orangutan -- Genetic aspects, Museums, Zoos -- Genetic aspects, Health
Abstract

Monkeypox virus (MPXV) (Orthopoxvirus genus, Poxviridae family), which causes mpox, is a large double-stranded DNA zoonotic virus first identified in 1958 in macaque primates (1). The first human case was [...]

Published
2024
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7. A genetic history of continuity and mobility in the Iron Age central Mediterranean

Author

Moots, Hannah M., Antonio, Margaret, Sawyer, Susanna, Spence, Jeffrey P., Oberreiter, Victoria, Weiß, Clemens L., Lucci, Michaela, Cherifi, Yahia Mehdi Seddik, La Pastina, Francesco, Genchi, Francesco, Praxmeier, Elisa, Zagorc, Brina, Cheronet, Olivia, Özdoğan, Kadir T., Demetz, Lea, Amrani, Selma, Candilio, Francesca, De Angelis, Daniela, Gasperetti, Gabriella, Fernandes, Daniel, Gao, Ziyue, Fantar, Mounir, Coppa, Alfredo, Pritchard, Jonathan K., and Pinhasi, Ron

Published
2023
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8. Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea

Author

Gelabert, Pere, Blazyte, Asta, Chang, Yongjoon, Fernandes, Daniel M., Jeon, Sungwon, Hong, Jin Geun, Yoon, Jiyeon, Ko, Youngmin, Oberreiter, Victoria, Cheronet, Olivia, Özdoğan, Kadir T., Sawyer, Susanna, Yang, Songhyok, Greytak, Ellen McRae, Choi, Hansol, Kim, Jungeun, Kim, Jong-Il, Jeong, Choongwon, Bae, Kidong, Bhak, Jong, and Pinhasi, Ron

Published
2022
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9. Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Author

Gelabert, Pere, Sawyer, Susanna, Bergström, Anders, Margaryan, Ashot, Collin, Thomas C., Meshveliani, Tengiz, Belfer-Cohen, Anna, Lordkipanidze, David, Jakeli, Nino, Matskevich, Zinovi, Bar-Oz, Guy, Fernandes, Daniel M., Cheronet, Olivia, Özdoğan, Kadir T., Oberreiter, Victoria, Feeney, Robin N.M., Stahlschmidt, Mareike C., Skoglund, Pontus, and Pinhasi, Ron

Published
2021
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10. Stable population structure in Europe since the Iron Age, despite high mobility

Author

Antonio, Margaret L, Weiß, Clemens L, Gao, Ziyue, Sawyer, Susanna, Oberreiter, Victoria, Moots, Hannah M, Spence, Jeffrey P, Cheronet, Olivia, Zagorc, Brina, Praxmarer, Elisa, Özdoğan, Kadir Toykan, Demetz, Lea, Gelabert, Pere, Fernandes, Daniel, Lucci, Michaela, Alihodžić, Timka, Amrani, Selma, Avetisyan, Pavel, Baillif-Ducros, Christèle, Bedić, Željka, Bertrand, Audrey, Bilić, Maja, Bondioli, Luca, Borówka, Paulina, Botte, Emmanuel, Burmaz, Josip, Bužanić, Domagoj, Candilio, Francesca, Cvetko, Mirna, De Angelis, Daniela, Drnić, Ivan, Elschek, Kristián, Fantar, Mounir, Gaspari, Andrej, Gasperetti, Gabriella, Genchi, Francesco, Golubović, Snežana, Hukeľová, Zuzana, Jankauskas, Rimantas, Vučković, Kristina Jelinčić, Jeremić, Gordana, Kaić, Iva, Kazek, Kevin, Khachatryan, Hamazasp, Khudaverdyan, Anahit, Kirchengast, Sylvia, Korać, Miomir, Kozlowski, Valérie, Krošláková, Mária, Kušan Špalj, Dora, La Pastina, Francesco, Laguardia, Marie, Legrand, Sandra, Leleković, Tino, Leskovar, Tamara, Lorkiewicz, Wiesław, Los, Dženi, Silva, Ana Maria, Masaryk, Rene, Matijević, Vinka, Cherifi, Yahia Mehdi Seddik, Meyer, Nicolas, Mikić, Ilija, Miladinović-Radmilović, Nataša, Milošević Zakić, Branka, Nacouzi, Lina, Natuniewicz-Sekuła, Magdalena, Nava, Alessia, Neugebauer-Maresch, Christine, Nováček, Jan, Osterholtz, Anna, Paige, Julianne, Paraman, Lujana, Pieri, Dominique, Pieta, Karol, Pop-Lazić, Stefan, Ruttkay, Matej, Sanader, Mirjana, Sołtysiak, Arkadiusz, Sperduti, Alessandra, Stankovic Pesterac, Tijana, Teschler-Nicola, Maria, Teul, Iwona, Tončinić, Domagoj, Trapp, Julien, Vulović, Dragana, Waliszewski, Tomasz, Walter, Diethard, Živanović, Miloš, Filah, Mohamed el Mostefa, Čaušević-Bully, Morana, Šlaus, Mario, Borić, Dušan, Novak, Mario, Coppa, Alfredo, Pinhasi, Ron, Pritchard, Jonathan K, Antonio, Margaret L, Weiß, Clemens L, Gao, Ziyue, Sawyer, Susanna, Oberreiter, Victoria, Moots, Hannah M, Spence, Jeffrey P, Cheronet, Olivia, Zagorc, Brina, Praxmarer, Elisa, Özdoğan, Kadir Toykan, Demetz, Lea, Gelabert, Pere, Fernandes, Daniel, Lucci, Michaela, Alihodžić, Timka, Amrani, Selma, Avetisyan, Pavel, Baillif-Ducros, Christèle, Bedić, Željka, Bertrand, Audrey, Bilić, Maja, Bondioli, Luca, Borówka, Paulina, Botte, Emmanuel, Burmaz, Josip, Bužanić, Domagoj, Candilio, Francesca, Cvetko, Mirna, De Angelis, Daniela, Drnić, Ivan, Elschek, Kristián, Fantar, Mounir, Gaspari, Andrej, Gasperetti, Gabriella, Genchi, Francesco, Golubović, Snežana, Hukeľová, Zuzana, Jankauskas, Rimantas, Vučković, Kristina Jelinčić, Jeremić, Gordana, Kaić, Iva, Kazek, Kevin, Khachatryan, Hamazasp, Khudaverdyan, Anahit, Kirchengast, Sylvia, Korać, Miomir, Kozlowski, Valérie, Krošláková, Mária, Kušan Špalj, Dora, La Pastina, Francesco, Laguardia, Marie, Legrand, Sandra, Leleković, Tino, Leskovar, Tamara, Lorkiewicz, Wiesław, Los, Dženi, Silva, Ana Maria, Masaryk, Rene, Matijević, Vinka, Cherifi, Yahia Mehdi Seddik, Meyer, Nicolas, Mikić, Ilija, Miladinović-Radmilović, Nataša, Milošević Zakić, Branka, Nacouzi, Lina, Natuniewicz-Sekuła, Magdalena, Nava, Alessia, Neugebauer-Maresch, Christine, Nováček, Jan, Osterholtz, Anna, Paige, Julianne, Paraman, Lujana, Pieri, Dominique, Pieta, Karol, Pop-Lazić, Stefan, Ruttkay, Matej, Sanader, Mirjana, Sołtysiak, Arkadiusz, Sperduti, Alessandra, Stankovic Pesterac, Tijana, Teschler-Nicola, Maria, Teul, Iwona, Tončinić, Domagoj, Trapp, Julien, Vulović, Dragana, Waliszewski, Tomasz, Walter, Diethard, Živanović, Miloš, Filah, Mohamed el Mostefa, Čaušević-Bully, Morana, Šlaus, Mario, Borić, Dušan, Novak, Mario, Coppa, Alfredo, Pinhasi, Ron, and Pritchard, Jonathan K

Abstract

Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000–3000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed from the historical period onward (3000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia and France). We found that most regions show remarkable inter-individual heterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring geography. We show that, under standard population genetics models with local panmixia, the observed level of dispersal would lead to a collapse of population structure. Persistent population structure thus suggests a lower effective migration rate than indicated by the observed dispersal. We hypothesize that this phenomenon can be explained by extensive transient dispersal arising from drastically improved transportation networks and the Roman Empire’s mobilization of people for trade, labor, and military. This work highlights the utility of ancient DNA in elucidating finer scale human population dynamics in recent history.

Published
2024

11. A complete mitochondrial genome of a Roman-eraPlasmodium falciparum

Author

Llanos-Lizcano, Alejandro, primary, Hämmerle, Michelle, additional, Sperduti, Alessandra, additional, Sawyer, Susanna, additional, Zagorc, Brina, additional, Özdoğan, Kadir Toykan, additional, Guellil, Meriam, additional, Cheronet, Olivia, additional, Kuhlwilm, Martin, additional, Pinhasi, Ron, additional, and Gelabert, Pere, additional

Published
2024
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12. Ancient human genomes suggest three ancestral populations for present-day Europeans

Author

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, Cali, Francesco, Churnosov, Mikhail, Cole, David E. C., Corach, Daniel, Damba, Larissa, van Driem, George, Dryomov, Stanislav, Dugoujon, Jean-Michel, Fedorova, Sardana A., Romero, Irene Gallego, Gubina, Marina, Hammer, Michael, Henn, Brenna, 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, 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, and Krause, Johannes

Subjects
Quantitative Biology - Populations and Evolution
Abstract

We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.

Published
2013
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13. Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico

Author

Williams, Amy L, Jacobs, Suzanne BR, Moreno-Macías, Hortensia, Huerta-Chagoya, Alicia, Churchhouse, Claire, Márquez-Luna, Carla, García-Ortíz, Humberto, José Gómez-Vázquez, María, Burtt, Noël P, Aguilar-Salinas, Carlos A, González-Villalpando, Clicerio, Florez, Jose C, Orozco, Lorena, Haiman, Christopher A, Tusié-Luna, Teresa, Altshuler, David, Ripke, Stephan, Manning, Alisa K, Neale, Benjamin, Reich, David, Stram, Daniel O, Fernández-López, Juan Carlos, Romero-Hidalgo, Sandra, Patterson, Nick, Aguilar-Delfín, Irma, Martínez-Hernández, Angélica, Centeno-Cruz, Federico, Mendoza-Caamal, Elvia, Revilla-Monsalve, Cristina, Islas-Andrade, Sergio, Córdova, Emilio, Rodríguez-Arellano, Eunice, Soberón, Xavier, González-Villalpando, María Elena, Henderson, Brian E, Monroe, Kristine, Wilkens, Lynne, Kolonel, Laurence N, Le Marchand, Loic, Riba, Laura, Ordóñez-Sánchez, María Luisa, Rodríguez-Guillén, Rosario, Cruz-Bautista, Ivette, Rodríguez-Torres, Maribel, Muñoz-Hernández, Linda Liliana, Sáenz, Tamara, Gómez, Donají, Alvirde, Ulices, Onofrio, Robert C, Brodeur, Wendy M, Gage, Diane, Murphy, Jacquelyn, Franklin, Jennifer, Mahan, Scott, Ardlie, Kristin, Crenshaw, Andrew T, Winckler, Wendy, Prüfer, Kay, Shunkov, Michael V, Sawyer, Susanna, Stenzel, Udo, Kelso, Janet, Lek, Monkol, Sankararaman, Sriram, MacArthur, Daniel G, Derevianko, Anatoli P, Pääbo, Svante, Gopal, Shuba, Grammatikos, James A, Smith, Ian C, Bullock, Kevin H, Deik, Amy A, Souza, Amanda L, Pierce, Kerry A, Clish, Clary B, Fennell, Timothy, and Farjoun, Yossi

Subjects
Nutrition, Diabetes, Prevention, Genetics, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Alleles, Animals, Asian People, Black People, Cohort Studies, Diabetes Mellitus, Type 2, Endoplasmic Reticulum, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Haplotypes, HeLa Cells, Humans, Indians, North American, Lipid Metabolism, Liver, Male, Mexico, Monocarboxylic Acid Transporters, Neanderthals, Polymorphism, Single Nucleotide, RNA, Messenger, Triglycerides, White People, SIGMA Type 2 Diabetes Consortium, Hela Cells, General Science & Technology
Abstract

Performing genetic studies in multiple human populations can identify disease risk alleles that are common in one population but rare in others, with the potential to illuminate pathophysiology, health disparities, and the population genetic origins of disease alleles. Here we analysed 9.2 million single nucleotide polymorphisms (SNPs) in each of 8,214 Mexicans and other Latin Americans: 3,848 with type 2 diabetes and 4,366 non-diabetic controls. In addition to replicating previous findings, we identified a novel locus associated with type 2 diabetes at genome-wide significance spanning the solute carriers SLC16A11 and SLC16A13 (P = 3.9 × 10(-13); odds ratio (OR) = 1.29). The association was stronger in younger, leaner people with type 2 diabetes, and replicated in independent samples (P = 1.1 × 10(-4); OR = 1.20). The risk haplotype carries four amino acid substitutions, all in SLC16A11; it is present at ~50% frequency in Native American samples and ~10% in east Asian, but is rare in European and African samples. Analysis of an archaic genome sequence indicated that the risk haplotype introgressed into modern humans via admixture with Neanderthals. The SLC16A11 messenger RNA is expressed in liver, and V5-tagged SLC16A11 protein localizes to the endoplasmic reticulum. Expression of SLC16A11 in heterologous cells alters lipid metabolism, most notably causing an increase in intracellular triacylglycerol levels. Despite type 2 diabetes having been well studied by genome-wide association studies in other populations, analysis in Mexican and Latin American individuals identified SLC16A11 as a novel candidate gene for type 2 diabetes with a possible role in triacylglycerol metabolism.

Published
2014

14. The complete genome sequence of a Neanderthal from the Altai Mountains

Author

Prüfer, Kay, Racimo, Fernando, Patterson, Nick, Jay, Flora, Sankararaman, Sriram, Sawyer, Susanna, Heinze, Anja, Renaud, Gabriel, Sudmant, Peter H, 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, Mullikin, James C, Vohr, Samuel H, Green, Richard E, Hellmann, Ines, Johnson, Philip LF, Blanche, Hélène, Cann, Howard, Kitzman, Jacob O, Shendure, Jay, Eichler, Evan E, Lein, Ed S, Bakken, Trygve E, Golovanova, Liubov V, Doronichev, Vladimir B, Shunkov, Michael V, Derevianko, Anatoli P, Viola, Bence, Slatkin, Montgomery, Reich, David, Kelso, Janet, and Pääbo, Svante

Subjects
Human Genome, Genetics, Africa, Animals, Caves, DNA Copy Number Variations, Female, Fossils, Gene Flow, Gene Frequency, Genome, Heterozygote, Humans, Inbreeding, Models, Genetic, Neanderthals, Phylogeny, Population Density, Siberia, Toe Phalanges, General Science & Technology
Abstract

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.

Published
2014

15. Author response: Stable population structure in Europe since the Iron Age, despite high mobility

Author

Antonio, Margaret L, primary, Weiß, Clemens L, primary, Gao, Ziyue, primary, Sawyer, Susanna, primary, Oberreiter, Victoria, additional, Moots, Hannah M, additional, Spence, Jeffrey P, additional, Cheronet, Olivia, additional, Zagorc, Brina, additional, Praxmarer, Elisa, additional, Özdoğan, Kadir Toykan, additional, Demetz, Lea, additional, Gelabert, Pere, additional, Fernandes, Daniel, additional, Lucci, Michaela, additional, Alihodžić, Timka, additional, Amrani, Selma, additional, Avetisyan, Pavel, additional, Baillif-Ducros, Christèle, additional, Bedić, Željka, additional, Bertrand, Audrey, additional, Bilić, Maja, additional, Bondioli, Luca, additional, Borówka, Paulina, additional, Botte, Emmanuel, additional, Burmaz, Josip, additional, Bužanić, Domagoj, additional, Candilio, Francesca, additional, Cvetko, Mirna, additional, De Angelis, Daniela, additional, Drnić, Ivan, additional, Elschek, Kristián, additional, Fantar, Mounir, additional, Gaspari, Andrej, additional, Gasperetti, Gabriella, additional, Genchi, Francesco, additional, Golubović, Snežana, additional, Hukeľová, Zuzana, additional, Jankauskas, Rimantas, additional, Vučković, Kristina Jelinčić, additional, Jeremić, Gordana, additional, Kaić, Iva, additional, Kazek, Kevin, additional, Khachatryan, Hamazasp, additional, Khudaverdyan, Anahit, additional, Kirchengast, Sylvia, additional, Korać, Miomir, additional, Kozlowski, Valérie, additional, Krošláková, Mária, additional, Kušan Špalj, Dora, additional, La Pastina, Francesco, additional, Laguardia, Marie, additional, Legrand, Sandra, additional, Leleković, Tino, additional, Leskovar, Tamara, additional, Lorkiewicz, Wiesław, additional, Los, Dženi, additional, Silva, Ana Maria, additional, Masaryk, Rene, additional, Matijević, Vinka, additional, Cherifi, Yahia Mehdi Seddik, additional, Meyer, Nicolas, additional, Mikić, Ilija, additional, Miladinović-Radmilović, Nataša, additional, Milošević Zakić, Branka, additional, Nacouzi, Lina, additional, Natuniewicz-Sekuła, Magdalena, additional, Nava, Alessia, additional, Neugebauer-Maresch, Christine, additional, Nováček, Jan, additional, Osterholtz, Anna, additional, Paige, Julianne, additional, Paraman, Lujana, additional, Pieri, Dominique, additional, Pieta, Karol, additional, Pop-Lazić, Stefan, additional, Ruttkay, Matej, additional, Sanader, Mirjana, additional, Sołtysiak, Arkadiusz, additional, Sperduti, Alessandra, additional, Stankovic Pesterac, Tijana, additional, Teschler-Nicola, Maria, additional, Teul, Iwona, additional, Tončinić, Domagoj, additional, Trapp, Julien, additional, Vulović, Dragana, additional, Waliszewski, Tomasz, additional, Walter, Diethard, additional, Živanović, Miloš, additional, Filah, Mohamed el Mostefa, additional, Čaušević-Bully, Morana, additional, Šlaus, Mario, additional, Borić, Dušan, additional, Novak, Mario, additional, Coppa, Alfredo, additional, Pinhasi, Ron, additional, and Pritchard, Jonathan K, additional

Published
2023
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16. Social and genetic diversity among the first farmers of Central Europe

Author

Gelabert, Pere, primary, Bickle, Penny, additional, Hofmann, Daniela, additional, Teschler-Nicola, Maria, additional, Anders, Alexandra, additional, Huang, Xin, additional, Olalde, Iñigo, additional, Fournier, Romain, additional, Ringbauer, Harald, additional, Akbari, Ali, additional, Cheronet, Olivia, additional, Lazaridis, Iosif, additional, Broomandkhoshbacht, Nasreen, additional, Fernandes, Daniel M., additional, Buttinger, Katharina, additional, Callan, Kim, additional, Candilio, Francesca, additional, Bravo, Guillermo, additional, Curtis, Elizabeth, additional, Ferry, Matthew, additional, Keating, Denise, additional, Freilich, Suzanne, additional, Kearns, Aisling, additional, Harney, Éadaoin, additional, Lawson, Ann Marie, additional, Mandl, Kirsten, additional, Michel, Megan, additional, Oberreiter, Victoria, additional, Oppenheimer, Jonas, additional, Sawyer, Susanna, additional, Schattke, Constanze, additional, Ozdogan, Kadir Toykan, additional, Hämmerle, Michelle, additional, Qiu, Lijun, additional, Workman, Noah, additional, Zalzala, Fatma, additional, Mallick, Swapan, additional, Mah, Matthew, additional, Micco, Adam, additional, Pieler, Franz, additional, Pavuk, Juraj, additional, Lazar, Catalin, additional, Paluch, Tibor, additional, Škrivanko, Maja Krznarić, additional, Šlaus, Mario, additional, Bedić, Željka, additional, Novotny, Friederike, additional, Szabó, László D., additional, Cserpák-Laczi, Orsolya, additional, Hága, Tamara, additional, Hajdú, Zsigmond, additional, Mirea, Pavel, additional, Nagy, Emese Gyöngyvér, additional, Virág, Zsuzsanna M., additional, Horváth, Attila M., additional, Horváth, László András, additional, Biró, Katalin T., additional, Domboróczki, László, additional, Szeniczey, Tamás, additional, Jakucs, János, additional, Szelekovszky, Márta, additional, Zoltán, Farkas, additional, Sztáncsuj, Sándor, additional, Tóth, Krisztián, additional, Csengeri, Piroska, additional, Pap, Ildikó, additional, Patay, Róbert, additional, Putica, Anđelka, additional, Vasov, Branislav, additional, Havasi, Bálint, additional, Sebők, Katalin, additional, Raczky, Pál, additional, Lovász, Gabriella, additional, Tvrdý, Zdeněk, additional, Rohland, Nadin, additional, Novak, Mario, additional, Ruttkay, Matej, additional, Boric, Dusan, additional, Dani, János, additional, Kuhlwilm, Martin, additional, Palamara, Pier Francesco, additional, Hajdu, Tamás, additional, Pinhasi, Ron, additional, and Reich, David, additional

Published
2023
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17. Stable population structure in Europe since the Iron Age, despite high mobility.

Author

Antonio, Margaret L., Weiß, Clemens L., Ziyue Gao, Sawyer, Susanna, Oberreiter, Victoria, Moots, Hannah M., Spence, Jeffrey P., Cheronet, Olivia, Zagorc, Brina, Praxmarer, Elisa, Özdoğan, Kadir Toykan, Demetz, Lea, Gelabert, Pere, Fernandes, Daniel, Lucci, Michaela, Alihodžić, Timka, Amrani, Selma, Avetisyan, Pavel, Baillif-Ducros, Christèle, and Bedić, Željka

Published
2024
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19. Density separation of petrous bone powders for optimized ancient DNA yields

Author

Fernandes, Daniel Magalhaes, primary, Sirak, Kendra A, additional, Cheronet, Olivia, additional, Novak, Mario, additional, Brück, Florian, additional, Zelger, Evelyn, additional, Llanos-Lizcano, Alejandro, additional, Wagner, Anna, additional, Zettl, Anna, additional, Mandl, Kirsten, additional, Duffett Carlson, Kellie Sara, additional, Oberreiter, Victoria, additional, Özdoğan, Kadir T, additional, Sawyer, Susanna, additional, La Pastina, Francesco, additional, Borgia, Emanuela, additional, Coppa, Alfredo, additional, Dobeš, Miroslav, additional, Velemínský, Petr, additional, Reich, David E, additional, Bell, Lynne S, additional, and Pinhasi, Ron, additional

Published
2023
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22. Patterns of coding variation in the complete exomes of three Neandertals

Author

Castellano, Sergi, Parra, Genís, Sánchez-Quinto, Federico A., Racimo, Fernando, Kuhlwilm, Martin, Kircher, Martin, Sawyer, Susanna, Fu, Qiaomei, Heinze, Anja, Nickel, Birgit, Dabney, Jesse, Siebauer, Michael, White, Louise, Burbano, Hernán A., Renaud, Gabriel, Stenzel, Udo, Lalueza-Fox, Carles, de la Rasilla, Marco, Rosas, Antonio, Rudan, Pavao, Brajković, Dejana, Kucan, Željko, Gušic, Ivan, Shunkov, Michael V., Derevianko, Anatoli P., Viola, Bence, Meyer, Matthias, Kelso, Janet, Andrés, Aida M., and Pääbo, Svante

Published
2014

24. Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea

Author

LS Late Oudheid, OGKG - Antieke Cultuur, Gelabert, Pere, Blazyte, Asta, Chang, Yongjoon, Fernandes, Daniel M, Jeon, Sungwon, Hong, Jin Geun, Yoon, Jiyeon, Ko, Youngmin, Oberreiter, Victoria, Cheronet, Olivia, Özdoğan, Kadir T, Sawyer, Susanna, Yang, Songhyok, Greytak, Ellen McRae, Choi, Hansol, Kim, Jungeun, Kim, Jong-Il, Jeong, Choongwon, Bae, Kidong, Bhak, Jong, Pinhasi, Ron, LS Late Oudheid, OGKG - Antieke Cultuur, Gelabert, Pere, Blazyte, Asta, Chang, Yongjoon, Fernandes, Daniel M, Jeon, Sungwon, Hong, Jin Geun, Yoon, Jiyeon, Ko, Youngmin, Oberreiter, Victoria, Cheronet, Olivia, Özdoğan, Kadir T, Sawyer, Susanna, Yang, Songhyok, Greytak, Ellen McRae, Choi, Hansol, Kim, Jungeun, Kim, Jong-Il, Jeong, Choongwon, Bae, Kidong, Bhak, Jong, and Pinhasi, Ron

Published
2022

26. Stable population structure in Europe since the Iron Age, despite high mobility

Author

Antonio, Margaret L., primary, Weiß, Clemens L., additional, Gao, Ziyue, additional, Sawyer, Susanna, additional, Oberreiter, Victoria, additional, Moots, Hannah M., additional, Spence, Jeffrey P., additional, Cheronet, Olivia, additional, Zagorc, Brina, additional, Praxmarer, Elisa, additional, Özdoğan, Kadir Toykan, additional, Demetz, Lea, additional, Lucci, Michaela, additional, Alihodžić, Timka, additional, Amrani, Selma, additional, Avetisyan, Pavel, additional, Baillif-Ducros, Christèle, additional, Bedić, Željka, additional, Bertrand, Audrey, additional, Bilić, Maja, additional, Bondioli, Luca, additional, Borówka, Paulina, additional, Botte, Emmanuel, additional, Burmaz, Josip, additional, Bužanić, Domagoj, additional, Candilio, Francesca, additional, Cvetko, Mirna, additional, De Angelis, Daniela, additional, Drnić, Ivan, additional, Elschek, Kristián, additional, Fantar, Mounir, additional, Gaspari, Andrej, additional, Gasperetti, Gabriella, additional, Genchi, Francesco, additional, Golubović, Snežana, additional, Hukeľová, Zuzana, additional, Jankauskas, Rimantas, additional, Vučković, Kristina Jelinčić, additional, Jeremić, Gordana, additional, Kaić, Iva, additional, Kazek, Kevin, additional, Khachatryan, Hamazasp, additional, Khudaverdyan, Anahit, additional, Kirchengast, Sylvia, additional, Korać, Miomir, additional, Kozlowski, Valérie, additional, Krošláková, Mária, additional, Špalj, Dora Kušan, additional, La Pastina, Francesco, additional, Laguardia, Marie, additional, Legrand, Sandra, additional, Leleković, Tino, additional, Leskovar, Tamara, additional, Lorkiewicz, Wiesław, additional, Los, Dženi, additional, Silva, Ana Maria, additional, Masaryk, Rene, additional, Matijević, Vinka, additional, Cherifi, Yahia Mehdi Seddik, additional, Meyer, Nicholas, additional, Mikić, Ilija, additional, Miladinović-Radmilović, Nataša, additional, Zakić, Branka Milošević, additional, Nacouzi, Lina, additional, Natuniewicz-Sekuła, Magdalena, additional, Nava, Alessia, additional, Neugebauer-Maresch, Christine, additional, Nováček, Jan, additional, Osterholtz, Anna, additional, Paige, Julianne, additional, Paraman, Lujana, additional, Pieri, Dominique, additional, Pieta, Karol, additional, Pop-Lazić, Stefan, additional, Ruttkay, Matej, additional, Sanader, Mirjana, additional, Sołtysiak, Arkadiusz, additional, Sperduti, Alessandra, additional, Pesterac, Tijana Stankovic, additional, Teschler-Nicola, Maria, additional, Teul, Iwona, additional, Tončinić, Domagoj, additional, Trapp, Julien, additional, Vulović, Dragana, additional, Waliszewski, Tomasz, additional, Walter, Diethard, additional, Zivanovic, Milos, additional, Filah, Mohamed el Mostefa, additional, Čaušević-Bully, Morana, additional, Šlaus, Mario, additional, Boric, Dusan, additional, Novak, Mario, additional, Coppa, Alfredo, additional, Pinhasi, Ron, additional, and Pritchard, Jonathan K., additional

Published
2022
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27. A Genetic History of Continuity and Mobility in the Iron Age Central Mediterranean

Author

Moots, Hannah M., primary, Antonio, Margaret, additional, Sawyer, Susanna, additional, Spence, Jeffrey P., additional, Oberreiter, Victoria, additional, Weiß, Clemens L., additional, Lucci, Michaela, additional, Cherifi, Yahia Mehdi Seddik, additional, La Pastina, Francesco, additional, Genchi, Francesco, additional, Praxmeier, Elisa, additional, Zagorc, Brina, additional, Cheronot, Olivia, additional, Özdoğan, Kadir T., additional, Demetz, Lea, additional, Amrani, Selma, additional, Candilio, Francesca, additional, De Angelis, Daniela, additional, Gasperetti, Gabriella, additional, Fernandes, Daniel, additional, Gao, Ziyue, additional, Fantar, Mounir, additional, Coppa, Alfredo, additional, Pritchard, Jonathan K., additional, and Pinhasi, Ron, additional

Published
2022
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28. Diverse northern Asian and Jomon-related genetic structure discovered among socially complex Three Kingdoms period Gaya region Koreans

Author

Gelabert, Pere, primary, Blazyte, Asta, additional, Chang, Yongjoon, additional, Fernandes, Daniel M., additional, Jeon, Sungwon, additional, Hong, Jin Geun, additional, Yoon, Jiyeon, additional, Ko, Youngmin, additional, Oberreiter, Victoria, additional, Cheronet, Olivia, additional, Özdoğan, Kadir T., additional, Sawyer, Susanna, additional, Yang, Songhyok, additional, Greytak, Ellen McRae, additional, Choi, Hansol, additional, Kim, Jungeun, additional, Kim, Jong-Il, additional, Bae, Kidong, additional, Bhak, Jong, additional, and Pinhasi, Ron, additional

Published
2021
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29. Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Author

LS Late Oudheid, OGKG - Antieke Cultuur, Gelabert, Pere, Sawyer, Susanna, Bergström, Anders, Margaryan, Ashot, Collin, Thomas C, Meshveliani, Tengiz, Belfer-Cohen, Anna, Lordkipanidze, David, Jakeli, Nino, Matskevich, Zinovi, Bar-Oz, Guy, Fernandes, Daniel M, Cheronet, Olivia, Özdoğan, Kadir T, Oberreiter, Victoria, Feeney, Robin N M, Stahlschmidt, Mareike C, Skoglund, Pontus, Pinhasi, Ron, LS Late Oudheid, OGKG - Antieke Cultuur, Gelabert, Pere, Sawyer, Susanna, Bergström, Anders, Margaryan, Ashot, Collin, Thomas C, Meshveliani, Tengiz, Belfer-Cohen, Anna, Lordkipanidze, David, Jakeli, Nino, Matskevich, Zinovi, Bar-Oz, Guy, Fernandes, Daniel M, Cheronet, Olivia, Özdoğan, Kadir T, Oberreiter, Victoria, Feeney, Robin N M, Stahlschmidt, Mareike C, Skoglund, Pontus, and Pinhasi, Ron

Published
2021

30. Ancient human genomes suggest three ancestral populations for present-day Europeans

Author

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 B. J., Cali, Francesco, Churnosov, Mikhail, Cole, David E. C., 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, and Krause, Johannes

Published
2014
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31. Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

Author

Gelabert, Pere, primary, Sawyer, Susanna, additional, Bergström, Anders, additional, Collin, Thomas C., additional, Meshveliani, Tengiz, additional, Belfer-Cohen, Anna, additional, Lordkipanidze, David, additional, Jakeli, Nino, additional, Matskevich, Zinovi, additional, Bar-Oz, Guy, additional, Fernandes, Daniel M., additional, Cheronet, Olivia, additional, Özdoğan, Kadir T., additional, Oberreiter, Victoria, additional, Feeney, Robin N. M., additional, Stahlschmidt, Mareike C., additional, Skoglund, Pontus, additional, and Pinhasi, Ron, additional

Published
2021
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34. Ancient Rome: A genetic crossroads of Europe and the Mediterranean

Author

Antonio, Margaret L., Gao, Ziyue, Moots, Hannah M., Lucci, Michaela, Candilio, Francesca, Sawyer, Susanna, Oberreiter, Victoria, Calderon, Diego, Devitofranceschi, Katharina, Aikens, Rachael C., Aneli, Serena, Bartoli, Fulvio, Bedini, Alessandro, Cheronet, Olivia, Cotter, Daniel J., Fernandes, Daniel M., Gasperetti, Gabriella, Grifoni, Renata, Guidi, Alessandro, La Pastina, Francesco, Loreti, Ersilia, Manacorda, Daniele, Matullo, Giuseppe, Morretta, Simona, Nava, Alessia, Fiocchi Nicolai, Vincenzo, Nomi, Federico, Pavolini, Carlo, Pentiricci, Massimo, Pergola, Philippe, Piranomonte, Marina, Schmidt, Ryan, Spinola, Giandomenico, Sperduti, Alessandra, Rubini, Mauro, Bondioli, Luca, Coppa, Alfredo, Pinhasi, Ron, Pritchard, Jonathan K., Antonio, Margaret L., Gao, Ziyue, Moots, Hannah M., Lucci, Michaela, Candilio, Francesca, Sawyer, Susanna, Oberreiter, Victoria, Calderon, Diego, Devitofranceschi, Katharina, Aikens, Rachael C., Aneli, Serena, Bartoli, Fulvio, Bedini, Alessandro, Cheronet, Olivia, Cotter, Daniel J., Fernandes, Daniel M., Gasperetti, Gabriella, Grifoni, Renata, Guidi, Alessandro, La Pastina, Francesco, Loreti, Ersilia, Manacorda, Daniele, Matullo, Giuseppe, Morretta, Simona, Nava, Alessia, Fiocchi Nicolai, Vincenzo, Nomi, Federico, Pavolini, Carlo, Pentiricci, Massimo, Pergola, Philippe, Piranomonte, Marina, Schmidt, Ryan, Spinola, Giandomenico, Sperduti, Alessandra, Rubini, Mauro, Bondioli, Luca, Coppa, Alfredo, Pinhasi, Ron, and Pritchard, Jonathan K.

Abstract

Ancient Rome was the capital of an empire of ~70 million inhabitants, but little is known about the genetics of ancient Romans. Here we present 127 genomes from 29 archaeological sites in and around Rome, spanning the past 12,000 years. We observe two major prehistoric ancestry transitions: one with the introduction of farming and another prior to the Iron Age. By the founding of Rome, the genetic composition of the region approximated that of modern Mediterranean populations. During the Imperial period, Rome’s population received net immigration from the Near East, followed by an increase in genetic contributions from Europe. These ancestry shifts mirrored the geopolitical affiliations of Rome and were accompanied by marked interindividual diversity, reflecting gene flow from across the Mediterranean, Europe, and North Africa.

Published
2019

35. Authentication and assessment of contamination in ancient DNA

Author

Shapiro, Beth, Barlow, Axel, Heintzman, Peter D., Hofreiter, Michael, Paijmans, Johanna L. A., Soares, André E. R., Renaud, Gabriel, Schubert, Mikkel, Sawyer, Susanna, Orlando, Ludovic, Shapiro, Beth, Barlow, Axel, Heintzman, Peter D., Hofreiter, Michael, Paijmans, Johanna L. A., Soares, André E. R., Renaud, Gabriel, Schubert, Mikkel, Sawyer, Susanna, and Orlando, Ludovic

Abstract

Contamination from both present-day humans and postmortem microbial sources is a common challenge in ancient DNA studies. Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ancient DNA data including detecting the presence of postmortem damage signatures in sequence alignments and quantifying the amount of present-day human contamination.

Published
2019

36. Sawyer, Susanna

Author

Sawyer, Susanna and Sawyer, Susanna

Published
2019

37. Ancient Rome: A genetic crossroads of Europe and the Mediterranean

Author

Antonio, Margaret L., primary, Gao, Ziyue, additional, Moots, Hannah M., additional, Lucci, Michaela, additional, Candilio, Francesca, additional, Sawyer, Susanna, additional, Oberreiter, Victoria, additional, Calderon, Diego, additional, Devitofranceschi, Katharina, additional, Aikens, Rachael C., additional, Aneli, Serena, additional, Bartoli, Fulvio, additional, Bedini, Alessandro, additional, Cheronet, Olivia, additional, Cotter, Daniel J., additional, Fernandes, Daniel M., additional, Gasperetti, Gabriella, additional, Grifoni, Renata, additional, Guidi, Alessandro, additional, La Pastina, Francesco, additional, Loreti, Ersilia, additional, Manacorda, Daniele, additional, Matullo, Giuseppe, additional, Morretta, Simona, additional, Nava, Alessia, additional, Fiocchi Nicolai, Vincenzo, additional, Nomi, Federico, additional, Pavolini, Carlo, additional, Pentiricci, Massimo, additional, Pergola, Philippe, additional, Piranomonte, Marina, additional, Schmidt, Ryan, additional, Spinola, Giandomenico, additional, Sperduti, Alessandra, additional, Rubini, Mauro, additional, Bondioli, Luca, additional, Coppa, Alfredo, additional, Pinhasi, Ron, additional, and Pritchard, Jonathan K., additional

Published
2019
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38. A fourth Denisovan individual

Author

Slon, Viviane, primary, Viola, Bence, additional, Renaud, Gabriel, additional, Gansauge, Marie-Theres, additional, Benazzi, Stefano, additional, Sawyer, Susanna, additional, Hublin, Jean-Jacques, additional, Shunkov, Michael V., additional, Derevianko, Anatoly P., additional, Kelso, Janet, additional, Prüfer, Kay, additional, Meyer, Matthias, additional, and Pääbo, Svante, additional

Published
2017
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39. Insights into Neandertals and Denisovans from Denisova Cave

Author

Pääbo, Svante, Universität Leipzig, Sawyer, Susanna, Pääbo, Svante, Universität Leipzig, and Sawyer, Susanna

Abstract

Denisova Cave is located in the Altai mountains of Russia. Excavations from this cave have yielded two large hominin molars and three hominin phalanxes from the Pleistocene. One of the phalanxes (Denisova 3) had extraordinary DNA preservation allowing the sequencing of high quality nuclear and mitochondrial DNA (mtDNA) genomes and has been shown to belong to a young girl from hereto unknown sister group of Neandertals, called Denisovans. The mtDNA of Denisova 3 surprisingly split from the mtDNA ancestor of modern humans and Neandertals twice as long ago as the split of modern humans and Neandertals. The mtDNA of one of the molars (Denisova 4) was also sequenced and differs at only two positions from the mtDNA of Denisova 3. A second phalanx (Altai 1) also yielded a high quality genome, and was a Neandertal. While Neandertals show an admixture signal of 1-4% into present-day non-Africans, Denisovans show an admixture of up to 5% in present-day Oceanians, and to a much lesser extent East Asians. This thesis encompasses two studies. In the first study, we sequenced the complete mtDNA genome of the additional molar (Denisova 8), as well as a few megabases of nuclear DNA from Denisova 4 and Denisova 8. While the mtDNA of Denisova 8 is clearly of the Denisova type, its branch to the most recent common ancestor of Denisovans is half as long as the branch leading to Denisova 3 or Denisova 4, indicating that Denisova 8 lived many millenia before the other two. Both Denisova 4 and 8 fall together with Denisova 3 based on nuclear DNA, bringing the number of known Denisovans from one to three. In the second study, we sequenced an almost complete mtDNA and a few megabases of nuclear DNA from the third hominin phalanx from Denisova Cave, Altai 2. Both the mtDNA and the nuclear DNA show Altai 2 to be a Neandertal. The mtDNA also showed the presence of substantial Pleistocene spotted hyena contamination. Low levels of spotted hyena contamination were also found in Altai 1, Denisova

Published
2016

40. Insights into Neandertals and Denisovans from Denisova Cave

Author

Universität Leipzig, Sawyer, Susanna, Universität Leipzig, and Sawyer, Susanna

Abstract

Denisova Cave is located in the Altai mountains of Russia. Excavations from this cave have yielded two large hominin molars and three hominin phalanxes from the Pleistocene. One of the phalanxes (Denisova 3) had extraordinary DNA preservation allowing the sequencing of high quality nuclear and mitochondrial DNA (mtDNA) genomes and has been shown to belong to a young girl from hereto unknown sister group of Neandertals, called Denisovans. The mtDNA of Denisova 3 surprisingly split from the mtDNA ancestor of modern humans and Neandertals twice as long ago as the split of modern humans and Neandertals. The mtDNA of one of the molars (Denisova 4) was also sequenced and differs at only two positions from the mtDNA of Denisova 3. A second phalanx (Altai 1) also yielded a high quality genome, and was a Neandertal. While Neandertals show an admixture signal of 1-4% into present-day non-Africans, Denisovans show an admixture of up to 5% in present-day Oceanians, and to a much lesser extent East Asians. This thesis encompasses two studies. In the first study, we sequenced the complete mtDNA genome of the additional molar (Denisova 8), as well as a few megabases of nuclear DNA from Denisova 4 and Denisova 8. While the mtDNA of Denisova 8 is clearly of the Denisova type, its branch to the most recent common ancestor of Denisovans is half as long as the branch leading to Denisova 3 or Denisova 4, indicating that Denisova 8 lived many millenia before the other two. Both Denisova 4 and 8 fall together with Denisova 3 based on nuclear DNA, bringing the number of known Denisovans from one to three. In the second study, we sequenced an almost complete mtDNA and a few megabases of nuclear DNA from the third hominin phalanx from Denisova Cave, Altai 2. Both the mtDNA and the nuclear DNA show Altai 2 to be a Neandertal. The mtDNA also showed the presence of substantial Pleistocene spotted hyena contamination. Low levels of spotted hyena contamination were also found in Altai 1, Denisova

Published
2016

41. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA

Author

Sawyer, Susanna, Krause, Johannes, Guschanski, K, Savolainen, Vincent, and Pääbo, Svante

Subjects
Time Factors, Biophysics, lcsh:Medicine, DNA Fragmentation, Animals, Base Composition, DNA/genetics, DNA Damage, DNA, Mitochondrial/genetics, Gene Library, Gorilla gorilla, Humans, Paleontology/methods, Polymerase Chain Reaction/methods, Sequence Analysis, DNA, DNA, Mitochondrial, Polymerase Chain Reaction, Biochemistry, Nucleic Acids, Genetics, Genetik, lcsh:Science, Biology, Evolutionary Biology, lcsh:R, Paleontology, DNA, Genomics, Earth Sciences, lcsh:Q, Research Article
Abstract

DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 59-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments.

Published
2011
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42. Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

Author

Sawyer, Susanna, Krause, Johannes, Guschanski, Katerina, Savolainen, Vincent, Paeaebo, Svante, Sawyer, Susanna, Krause, Johannes, Guschanski, Katerina, Savolainen, Vincent, and Paeaebo, Svante

Abstract

DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5'-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments.

Published
2012
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43. Ancient human genomes suggest three ancestral populations for present-day Europeans

Author

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

Published
2013
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44. The complete genome sequence of a Neanderthal from the Altai Mountains

Author

Prüfer, Kay, primary, Racimo, Fernando, additional, Patterson, Nick, additional, Jay, Flora, additional, Sankararaman, Sriram, additional, Sawyer, Susanna, additional, Heinze, Anja, additional, Renaud, Gabriel, additional, Sudmant, Peter H., additional, de Filippo, Cesare, additional, Li, Heng, additional, Mallick, Swapan, additional, Dannemann, Michael, additional, Fu, Qiaomei, additional, Kircher, Martin, additional, Kuhlwilm, Martin, additional, Lachmann, Michael, additional, Meyer, Matthias, additional, Ongyerth, Matthias, additional, Siebauer, Michael, additional, Theunert, Christoph, additional, Tandon, Arti, additional, Moorjani, Priya, additional, Pickrell, Joseph, additional, Mullikin, James C., additional, Vohr, Samuel H., additional, Green, Richard E., additional, Hellmann, Ines, additional, Johnson, Philip L. F., additional, Blanche, Hélène, additional, Cann, Howard, additional, Kitzman, Jacob O., additional, Shendure, Jay, additional, Eichler, Evan E., additional, Lein, Ed S., additional, Bakken, Trygve E., additional, Golovanova, Liubov V., additional, Doronichev, Vladimir B., additional, Shunkov, Michael V., additional, Derevianko, Anatoli P., additional, Viola, Bence, additional, Slatkin, Montgomery, additional, Reich, David, additional, Kelso, Janet, additional, and Pääbo, Svante, additional

Published
2013
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48. Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Author

Gelabert, Pere, Sawyer, Susanna, Bergström, Anders, Margaryan, Ashot, Collin, Thomas C, Meshveliani, Tengiz, Belfer-Cohen, Anna, Lordkipanidze, David, Jakeli, Nino, Matskevich, Zinovi, Bar-Oz, Guy, Fernandes, Daniel M, Cheronet, Olivia, Özdoğan, Kadir T, Oberreiter, Victoria, Feeney, Robin NM, Stahlschmidt, Mareike C, Skoglund, Pontus, and Pinhasi, Ron

Subjects
Ecology,Evolution & Ethology, Infectious Disease, 15. Life on land, Genetics & Genomics
Abstract

Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.

49. Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Author

Gelabert, Pere, Sawyer, Susanna, Bergström, Anders, Margaryan, Ashot, Collin, Thomas C, Meshveliani, Tengiz, Belfer-Cohen, Anna, Lordkipanidze, David, Jakeli, Nino, Matskevich, Zinovi, Bar-Oz, Guy, Fernandes, Daniel M, Cheronet, Olivia, Özdoğan, Kadir T, Oberreiter, Victoria, Feeney, Robin NM, Stahlschmidt, Mareike C, Skoglund, Pontus, and Pinhasi, Ron

Subjects
Ecology,Evolution & Ethology, Infectious Disease, 15. Life on land, Genetics & Genomics
Abstract

Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.

50. A fourth Denisovan individual

Author

Matthias Meyer, Kay Prüfer, Susanna Sawyer, Anatoly P. Derevianko, Stefano Benazzi, Bence Viola, Gabriel Renaud, Svante Pääbo, Janet Kelso, Viviane Slon, Jean-Jacques Hublin, Marie-Theres Gansauge, Michael V. Shunkov, Slon, Viviane, Viola, Bence, Renaud, Gabriel, Gansauge, Marie-there, Benazzi, Stefano, Sawyer, Susanna, Hublin, Jean-jacque, Shunkov, Michael V, Derevianko, Anatoly P, Kelso, Janet, Prüfer, Kay, Meyer, Matthia, and Pääbo, Svante

Subjects
0301 basic medicine, Mitochondrial DNA, Range (biology), Deciduous Tooth, Human Evolution, DNA sequencing, 03 medical and health sciences, Paleontology, 0302 clinical medicine, Cave, Denisovan, Research Articles, geography, Multidisciplinary, geography.geographical_feature_category, Ancient DNA, biology, Denisova, SciAdv r-articles, biology.organism_classification, humanities, Nuclear DNA, 030104 developmental biology, Sister group, Extended time, 030217 neurology & neurosurgery, Research Article
Abstract

DNA retrieved from a tooth discovered deep in Denisova Cave allows us to assign it to the Denisovans, a group of archaic hominins., The presence of Neandertals in Europe and Western Eurasia before the arrival of anatomically modern humans is well supported by archaeological and paleontological data. In contrast, fossil evidence for Denisovans, a sister group of Neandertals recently identified on the basis of DNA sequences, is limited to three specimens, all of which originate from Denisova Cave in the Altai Mountains (Siberia, Russia). We report the retrieval of DNA from a deciduous lower second molar (Denisova 2), discovered in a deep stratigraphic layer in Denisova Cave, and show that this tooth comes from a female Denisovan individual. On the basis of the number of “missing substitutions” in the mitochondrial DNA determined from the specimen, we find that Denisova 2 is substantially older than two of the other Denisovans, reinforcing the view that Denisovans were likely to have been present in the vicinity of Denisova Cave over an extended time period. We show that the level of nuclear DNA sequence diversity found among Denisovans is within the lower range of that of present-day human populations.

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