Author: "Alissa, Mittnik" - Searchworks@Jio Institute Digital Library Search Results

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1. Finding Mycenaeans in Minoan Crete? Isotope and DNA analysis of human mobility in Bronze Age Crete.

Author: Michael Richards, Colin Smith, Olaf Nehlich, Vaughan Grimes, Darlene Weston, Alissa Mittnik, Johannes Krause, Keith Dobney, Yannis Tzedakis, and Holley Martlew
Subjects: Medicine, Science
Abstract: We undertook a large-scale study of Neolithic and Bronze Age human mobility on Crete using biomolecular methods (isotope analysis, DNA), with a particular focus on sites dating to the Late Bronze Age ('Late Minoan') period. We measured the strontium and sulphur isotope values of animal remains from archaeological sites around the island of Crete to determine the local baseline values. We then measured the strontium and sulphur values of humans from Late Neolithic and Bronze Age sites. Our results indicate that most of the humans have sulphur and strontium isotope values consistent with being local to Crete, showing no evidence for a wide-scale movement of people from the Greek mainland or other areas away from Crete in these time periods. However, we found four individuals from the late Bronze Age (Late Minoan III) cemetery of Armenoi with sulphur isotope values not typically found in Crete and are instead consistent with an origin elsewhere. This cemetery at Armenoi also has one of only a few examples of the newly adopted Mycenaean Linear B script on Crete found outside of the palace sites, pointing to an influence (trade and possible migration) from the mainland, which may then be the place of origin of these four individuals. DNA (mtDNA) studies of eight Late Bronze Age individuals from Armenoi have results consistent with people living in Aegean region at this time and cannot be used to distinguish between individuals from Crete ('Minoans') and the Greek mainland ['Mycenaeans']).
Published: 2022
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2. Pedigree-based Bayesian modelling of radiocarbon dates.

Author: Ken Massy, Ronny Friedrich, Alissa Mittnik, and Philipp W Stockhammer
Subjects: Medicine, Science
Abstract: Within the last decade, archaeogenetic analysis has revolutionized archaeological research and enabled novel insights into mobility, relatedness and health of past societies. Now, it is possible to develop these results further and integrate archaeogenetic insights into biological relatedness with radiocarbon dates as means of chronologically sequenced information. In our article, we demonstrate the potential of combining relative chronological information with absolute radiocarbon dates by Bayesian interpretation in order to improve age determinations. Using artificial pedigrees with four sets of simulated radiocarbon dates we show that the combination of relationship information with radiocarbon dates improves the age determination in many cases at least between 20 to 50%. Calibrated age ranges are more constrained than simply calibrating radiocarbon ages independently from each other. Thereby, the precision of modelled ages depends on the precision of the single radiocarbon dates, the number of modelled generations, the shape of the calibration curve and the availability of samples that can be precisely fixed in time due to specific patterns in the calibration curve ("anchor points"). Ambiguous calibrated radiocarbon dates, which are caused by inversions of the calibration curve, can be partly or almost entirely resolved through Bayesian modelling based upon information from pedigrees. Finally, we discuss selected case studies of biological pedigrees achieved for Early Bronze Age Southern Germany by recent archaeogenetic analysis, whereby the sites and pedigrees differ with regard to the quality of information, which can be used for a Bayesian model of the radiocarbon dates. In accordance with the abstract models, radiocarbon dates can again be better constrained and are therefore more applicable for archaeological interpretation and chronological placement of the dated individuals.
Published: 2022
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3. The genetic prehistory of the Baltic Sea region

Author: Alissa Mittnik, Chuan-Chao Wang, Saskia Pfrengle, Mantas Daubaras, Gunita Zariņa, Fredrik Hallgren, Raili Allmäe, Valery Khartanovich, Vyacheslav Moiseyev, Mari Tõrv, Anja Furtwängler, Aida Andrades Valtueña, Michal Feldman, Christos Economou, Markku Oinonen, Andrejs Vasks, Elena Balanovska, David Reich, Rimantas Jankauskas, Wolfgang Haak, Stephan Schiffels, and Johannes Krause
Subjects: Science
Abstract: The population history of Europe is complex and its very north has not yet been comprehensively studied at a genetic level. Here, Mittnik et al. report genome-wide data from 38 ancient individuals from the Eastern Baltic, Russia and Scandinavia to analyse gene flow throughout the Mesolithic and Bronze Age.
Published: 2018
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4. The diverse genetic origins of a Classical period Greek army

Author: Laurie J. Reitsema, Alissa Mittnik, Britney Kyle, Giulio Catalano, Pier Francesco Fabbri, Adam C. S. Kazmi, Katherine L. Reinberger, Luca Sineo, Stefano Vassallo, Rebecca Bernardos, Nasreen Broomandkhoshbacht, Kim Callan, Francesca Candilio, Olivia Cheronet, Elizabeth Curtis, Daniel Fernandes, Martina Lari, Ann Marie Lawson, Matthew Mah, Swapan Mallick, Kirsten Mandl, Adam Micco, Alessandra Modi, Jonas Oppenheimer, Kadir Toykan Özdogan, Nadin Rohland, Kristin Stewardson, Stefania Vai, Chiara Vergata, J. Noah Workman, Fatma Zalzala, Valentina Zaro, Alessandro Achilli, Achilles Anagnostopoulos, Cristian Capelli, Varnavas Constantinou, Hovirag Lancioni, Anna Olivieri, Anastasia Papadopoulou, Nikoleta Psatha, Ornella Semino, John Stamatoyannopoulos, Ioanna Valliannou, Evangelia Yannaki, Iosif Lazaridis, Nick Patterson, Harald Ringbauer, David Caramelli, Ron Pinhasi, David Reich, Reitsema, Laurie J, Mittnik, Alissa, Kyle, Britney, Catalano, Giulio, Fabbri, Pier Francesco, Kazmi, Adam C S, Reinberger, Katherine L, Sineo, Luca, Vassallo, Stefano, Bernardos, Rebecca, Broomandkhoshbacht, Nasreen, Callan, Kim, Candilio, Francesca, Cheronet, Olivia, Curtis, Elizabeth, Fernandes, Daniel, Lari, Martina, Lawson, Ann Marie, Mah, Matthew, Mallick, Swapan, Mandl, Kirsten, Micco, Adam, Modi, Alessandra, Oppenheimer, Jona, Özdogan, Kadir Toykan, Rohland, Nadin, Stewardson, Kristin, Vai, Stefania, Vergata, Chiara, Workman, J Noah, Zalzala, Fatma, Zaro, Valentina, Achilli, Alessandro, Anagnostopoulos, Achille, Capelli, Cristian, Constantinou, Varnava, Lancioni, Hovirag, Olivieri, Anna, Papadopoulou, Anastasia, Psatha, Nikoleta, Semino, Ornella, Stamatoyannopoulos, John, Valliannou, Ioanna, Yannaki, Evangelia, Lazaridis, Iosif, Patterson, Nick, Ringbauer, Harald, Caramelli, David, Pinhasi, Ron, and Reich, David
Subjects: Europe, Warfare, Multidisciplinary, Military Personnel, Archaeology, Greece, Classical world, Humans, history, Settore BIO/08 - Antropologia, ancient DNA, ancient warfare, History, Ancient
Abstract: Trade and colonization caused an unprecedented increase in Mediterranean human mobility in the first millennium BCE. Often seen as a dividing force, warfare is in fact another catalyst of culture contact. We provide insight into the demographic dynamics of ancient warfare by reporting genome-wide data from fifth-century soldiers who fought for the army of the Greek Sicilian colony of Himera, along with representatives of the civilian population, nearby indigenous settlements, and 96 present-day individuals from Italy and Greece. Unlike the rest of the sample, many soldiers had ancestral origins in northern Europe, the Steppe, and the Caucasus. Integrating genetic, archaeological, isotopic, and historical data, these results illustrate the significant role mercenaries played in ancient Greek armies and highlight how participation in war contributed to continental-scale human mobility in the Classical world.
Published: 2022

5. Author Correction: The genetic prehistory of the Baltic Sea region

Author: Alissa Mittnik, Chuan-Chao Wang, Saskia Pfrengle, Mantas Daubaras, Gunita Zariņa, Fredrik Hallgren, Raili Allmäe, Valery Khartanovich, Vyacheslav Moiseyev, Mari Tõrv, Anja Furtwängler, Aida Andrades Valtueña, Michal Feldman, Christos Economou, Markku Oinonen, Andrejs Vasks, Elena Balanovska, David Reich, Rimantas Jankauskas, Wolfgang Haak, Stephan Schiffels, and Johannes Krause
Subjects: Science
Abstract: The original version of this Article omitted references to previous work, which are detailed in the associated Author Correction. These omissions have been corrected in both the PDF and HTML versions of the Article.
Published: 2018
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6. Stone Age

Author: Aida, Andrades Valtueña, Gunnar U, Neumann, Maria A, Spyrou, Lyazzat, Musralina, Franziska, Aron, Arman, Beisenov, Andrey B, Belinskiy, Kirsten I, Bos, Alexandra, Buzhilova, Matthias, Conrad, Leyla B, Djansugurova, Miroslav, Dobeš, Michal, Ernée, Javier, Fernández-Eraso, Bruno, Frohlich, Mirosław, Furmanek, Agata, Hałuszko, Svend, Hansen, Éadaoin, Harney, Alina N, Hiss, Alexander, Hübner, Felix M, Key, Elmira, Khussainova, Egor, Kitov, Alexandra O, Kitova, Corina, Knipper, Denise, Kühnert, Carles, Lalueza-Fox, Judith, Littleton, Ken, Massy, Alissa, Mittnik, José Antonio, Mujika-Alustiza, Iñigo, Olalde, Luka, Papac, Sandra, Penske, Jaroslav, Peška, Ron, Pinhasi, David, Reich, Sabine, Reinhold, Raphaela, Stahl, Harald, Stäuble, Rezeda I, Tukhbatova, Sergey, Vasilyev, Elizaveta, Veselovskaya, Christina, Warinner, Philipp W, Stockhammer, Wolfgang, Haak, Johannes, Krause, and Alexander, Herbig
Subjects: Plague, Yersinia pestis, Human Migration, Animals, Genetic Variation, Humans, Animal Husbandry, DNA, Ancient, Genome, Bacterial, History, Ancient, Phylogeny
Abstract: The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology.
Published: 2022

7. Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia

Author: Iosif Lazaridis, Songül Alpaslan-Roodenberg, Ayşe Acar, Ayşen Açıkkol, Anagnostis Agelarakis, Levon Aghikyan, Uğur Akyüz, Desislava Andreeva, Gojko Andrijašević, Dragana Antonović, Ian Armit, Alper Atmaca, Pavel Avetisyan, Ahmet İhsan Aytek, Krum Bacvarov, Ruben Badalyan, Stefan Bakardzhiev, Jacqueline Balen, Lorenc Bejko, Rebecca Bernardos, Andreas Bertsatos, Hanifi Biber, Ahmet Bilir, Mario Bodružić, Michelle Bonogofsky, Clive Bonsall, Dušan Borić, Nikola Borovinić, Guillermo Bravo Morante, Katharina Buttinger, Kim Callan, Francesca Candilio, Mario Carić, Olivia Cheronet, Stefan Chohadzhiev, Maria-Eleni Chovalopoulou, Stella Chryssoulaki, Ion Ciobanu, Natalija Čondić, Mihai Constantinescu, Emanuela Cristiani, Brendan J. Culleton, Elizabeth Curtis, Jack Davis, Tatiana I. Demcenco, Valentin Dergachev, Zafer Derin, Sylvia Deskaj, Seda Devejyan, Vojislav Djordjević, Kellie Sara Duffett Carlson, Laurie R. Eccles, Nedko Elenski, Atilla Engin, Nihat Erdoğan, Sabiha Erir-Pazarcı, Daniel M. Fernandes, Matthew Ferry, Suzanne Freilich, Alin Frînculeasa, Michael L. Galaty, Beatriz Gamarra, Boris Gasparyan, Bisserka Gaydarska, Elif Genç, Timur Gültekin, Serkan Gündüz, Tamás Hajdu, Volker Heyd, Suren Hobosyan, Nelli Hovhannisyan, Iliya Iliev, Lora Iliev, Stanislav Iliev, İlkay İvgin, Ivor Janković, Lence Jovanova, Panagiotis Karkanas, Berna Kavaz-Kındığılı, Esra Hilal Kaya, Denise Keating, Douglas J. Kennett, Seda Deniz Kesici, Anahit Khudaverdyan, Krisztián Kiss, Sinan Kılıç, Paul Klostermann, Sinem Kostak Boca Negra Valdes, Saša Kovačević, Marta Krenz-Niedbała, Maja Krznarić Škrivanko, Rovena Kurti, Pasko Kuzman, Ann Marie Lawson, Catalin Lazar, Krassimir Leshtakov, Thomas E. Levy, Ioannis Liritzis, Kirsi O. Lorentz, Sylwia Łukasik, Matthew Mah, Swapan Mallick, Kirsten Mandl, Kristine Martirosyan-Olshansky, Roger Matthews, Wendy Matthews, Kathleen McSweeney, Varduhi Melikyan, Adam Micco, Megan Michel, Lidija Milašinović, Alissa Mittnik, Janet M. Monge, Georgi Nekhrizov, Rebecca Nicholls, Alexey G. Nikitin, Vassil Nikolov, Mario Novak, Iñigo Olalde, Jonas Oppenheimer, Anna Osterholtz, Celal Özdemir, Kadir Toykan Özdoğan, Nurettin Öztürk, Nikos Papadimitriou, Niki Papakonstantinou, Anastasia Papathanasiou, Lujana Paraman, Evgeny G. Paskary, Nick Patterson, Ilian Petrakiev, Levon Petrosyan, Vanya Petrova, Anna Philippa-Touchais, Ashot Piliposyan, Nada Pocuca Kuzman, Hrvoje Potrebica, Bianca Preda-Bălănică, Zrinka Premužić, T. Douglas Price, Lijun Qiu, Siniša Radović, Kamal Raeuf Aziz, Petra Rajić Šikanjić, Kamal Rasheed Raheem, Sergei Razumov, Amy Richardson, Jacob Roodenberg, Rudenc Ruka, Victoria Russeva, Mustafa Şahin, Ayşegül Şarbak, Emre Savaş, Constanze Schattke, Lynne Schepartz, Tayfun Selçuk, Ayla Sevim-Erol, Michel Shamoon-Pour, Henry M. Shephard, Athanasios Sideris, Angela Simalcsik, Hakob Simonyan, Vitalij Sinika, Kendra Sirak, Ghenadie Sirbu, Mario Šlaus, Andrei Soficaru, Bilal Söğüt, Arkadiusz Sołtysiak, Çilem Sönmez-Sözer, Maria Stathi, Martin Steskal, Kristin Stewardson, Sharon Stocker, Fadime Suata-Alpaslan, Alexander Suvorov, Anna Szécsényi-Nagy, Tamás Szeniczey, Nikolai Telnov, Strahil Temov, Nadezhda Todorova, Ulsi Tota, Gilles Touchais, Sevi Triantaphyllou, Atila Türker, Marina Ugarković, Todor Valchev, Fanica Veljanovska, Zlatko Videvski, Cristian Virag, Anna Wagner, Sam Walsh, Piotr Włodarczak, J. Noah Workman, Aram Yardumian, Evgenii Yarovoy, Alper Yener Yavuz, Hakan Yılmaz, Fatma Zalzala, Anna Zettl, Zhao Zhang, Rafet Çavuşoğlu, Nadin Rohland, Ron Pinhasi, David Reich, and Edebiyat Fakültesi
Subjects: Europe, History, Multidisciplinary, Origin, Genomes, Article, ancient DNA, Neolithic migrations, Anatolia, Fertile Crescent, hunter-gatherers, early farmers, 1st Farmers
Abstract: We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia., National Institutes of Health [GM100233, HG012287]; John Templeton Foundation [61220]; Allen Discovery Center program; Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation; Howard Hughes Medical Institute, The newly reported dataset is described in detail in an accompanying Research Article, where we also acknowledge the funders who supported dataset generation (12). Analysis of data was supported by the National Institutes of Health (GM100233 and HG012287), the John Templeton Foundation (grant 61220), a private gift from Jean-Francois Clin, the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation, and the Howard Hughes Medical Institute (D.R.).
Published: 2022
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8. A genetic probe into the ancient and medieval history of Southern Europe and West Asia

Author: Iosif, Lazaridis, Songül, Alpaslan-Roodenberg, Ayşe, Acar, Ayşen, Açıkkol, Anagnostis, Agelarakis, Levon, Aghikyan, Uğur, Akyüz, Desislava, Andreeva, Gojko, Andrijašević, Dragana, Antonović, Ian, Armit, Alper, Atmaca, Pavel, Avetisyan, Ahmet İhsan, Aytek, Krum, Bacvarov, Ruben, Badalyan, Stefan, Bakardzhiev, Jacqueline, Balen, Lorenc, Bejko, Rebecca, Bernardos, Andreas, Bertsatos, Hanifi, Biber, Ahmet, Bilir, Mario, Bodružić, Michelle, Bonogofsky, Clive, Bonsall, Dušan, Borić, Nikola, Borovinić, Guillermo, Bravo Morante, Katharina, Buttinger, Kim, Callan, Francesca, Candilio, Mario, Carić, Olivia, Cheronet, Stefan, Chohadzhiev, Maria-Eleni, Chovalopoulou, Stella, Chryssoulaki, Ion, Ciobanu, Natalija, Čondić, Mihai, Constantinescu, Emanuela, Cristiani, Brendan J, Culleton, Elizabeth, Curtis, Jack, Davis, Tatiana I, Demcenco, Valentin, Dergachev, Zafer, Derin, Sylvia, Deskaj, Seda, Devejyan, Vojislav, Djordjević, Kellie Sara, Duffett Carlson, Laurie R, Eccles, Nedko, Elenski, Atilla, Engin, Nihat, Erdoğan, Sabiha, Erir-Pazarcı, Daniel M, Fernandes, Matthew, Ferry, Suzanne, Freilich, Alin, Frînculeasa, Michael L, Galaty, Beatriz, Gamarra, Boris, Gasparyan, Bisserka, Gaydarska, Elif, Genç, Timur, Gültekin, Serkan, Gündüz, Tamás, Hajdu, Volker, Heyd, Suren, Hobosyan, Nelli, Hovhannisyan, Iliya, Iliev, Lora, Iliev, Stanislav, Iliev, İlkay, İvgin, Ivor, Janković, Lence, Jovanova, Panagiotis, Karkanas, Berna, Kavaz-Kındığılı, Esra Hilal, Kaya, Denise, Keating, Douglas J, Kennett, Seda, Deniz Kesici, Anahit, Khudaverdyan, Krisztián, Kiss, Sinan, Kılıç, Paul, Klostermann, Sinem, Kostak Boca Negra Valdes, Saša, Kovačević, Marta, Krenz-Niedbała, Maja, Krznarić Škrivanko, Rovena, Kurti, Pasko, Kuzman, Ann Marie, Lawson, Catalin, Lazar, Krassimir, Leshtakov, Thomas E, Levy, Ioannis, Liritzis, Kirsi O, Lorentz, Sylwia, Łukasik, Matthew, Mah, Swapan, Mallick, Kirsten, Mandl, Kristine, Martirosyan-Olshansky, Roger, Matthews, Wendy, Matthews, Kathleen, McSweeney, Varduhi, Melikyan, Adam, Micco, Megan, Michel, Lidija, Milašinović, Alissa, Mittnik, Janet M, Monge, Georgi, Nekhrizov, Rebecca, Nicholls, Alexey G, Nikitin, Vassil, Nikolov, Mario, Novak, Iñigo, Olalde, Jonas, Oppenheimer, Anna, Osterholtz, Celal, Özdemir, Kadir Toykan, Özdoğan, Nurettin, Öztürk, Nikos, Papadimitriou, Niki, Papakonstantinou, Anastasia, Papathanasiou, Lujana, Paraman, Evgeny G, Paskary, Nick, Patterson, Ilian, Petrakiev, Levon, Petrosyan, Vanya, Petrova, Anna, Philippa-Touchais, Ashot, Piliposyan, Nada, Pocuca Kuzman, Hrvoje, Potrebica, Bianca, Preda-Bălănică, Zrinka, Premužić, T Douglas, Price, Lijun, Qiu, Siniša, Radović, Kamal, Raeuf Aziz, Petra, Rajić Šikanjić, Kamal, Rasheed Raheem, Sergei, Razumov, Amy, Richardson, Jacob, Roodenberg, Rudenc, Ruka, Victoria, Russeva, Mustafa, Şahin, Ayşegül, Şarbak, Emre, Savaş, Constanze, Schattke, Lynne, Schepartz, Tayfun, Selçuk, Ayla, Sevim-Erol, Michel, Shamoon-Pour, Henry M, Shephard, Athanasios, Sideris, Angela, Simalcsik, Hakob, Simonyan, Vitalij, Sinika, Kendra, Sirak, Ghenadie, Sirbu, Mario, Šlaus, Andrei, Soficaru, Bilal, Söğüt, Arkadiusz, Sołtysiak, Çilem, Sönmez-Sözer, Maria, Stathi, Martin, Steskal, Kristin, Stewardson, Sharon, Stocker, Fadime, Suata-Alpaslan, Alexander, Suvorov, Anna, Szécsényi-Nagy, Tamás, Szeniczey, Nikolai, Telnov, Strahil, Temov, Nadezhda, Todorova, Ulsi, Tota, Gilles, Touchais, Sevi, Triantaphyllou, Atila, Türker, Marina, Ugarković, Todor, Valchev, Fanica, Veljanovska, Zlatko, Videvski, Cristian, Virag, Anna, Wagner, Sam, Walsh, Piotr, Włodarczak, J Noah, Workman, Aram, Yardumian, Evgenii, Yarovoy, Alper Yener, Yavuz, Hakan, Yılmaz, Fatma, Zalzala, Anna, Zettl, Zhao, Zhang, Rafet, Çavuşoğlu, Nadin, Rohland, Ron, Pinhasi, David, Reich, Ruben, Davtyan, and Edebiyat Fakültesi
Subjects: Genomic History, Asia, Multidisciplinary, Greece, Ancient DNA, Europe, Turkey, Migration, Urartian Kingdom, Roman and Byzantine Empires, Human Migration, Population, Genetic Variation, Admixture, Dna, human genetics, archaeogentic analysis, literary and archaeological sources, Southern Europe, Western Asia, Eye, History, Medieval, Article, Europe, Archaeology, Languages, Humans, Selection, History, Ancient, Hair, Skin
Abstract: Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom's northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region., National Institutes of Health [GM100233, HG012287]; John Templeton Foundation [61220]; Allen Discovery Center program; Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation; Howard Hughes Medical Institute, The newly reported dataset is described in detail in an accompanying manuscript, where we also acknowledge the funders who supported dataset generation (1). Analysis of data was supported by the National Institutes of Health (GM100233 and HG012287), the John Templeton Foundation (grant 61220), a private gift from Jean-Francois Clin, the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation, and the Howard Hughes Medical Institute (to D.R.).
Published: 2022

9. Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague

Author: Aida Andrades Valtueña, Gunnar U. Neumann, Maria A. Spyrou, Lyazzat Musralina, Franziska Aron, Arman Beisenov, Andrey B. Belinskiy, Kirsten I. Bos, Alexandra Buzhilova, Matthias Conrad, Leyla B. Djansugurova, Miroslav Dobeš, Michal Ernée, Javier Fernández-Eraso, Bruno Frohlich, Mirosław Furmanek, Agata Hałuszko, Svend Hansen, Éadaoin Harney, Alina N. Hiss, Alexander Hübner, Felix M. Key, Elmira Khussainova, Egor Kitov, Alexandra O. Kitova, Corina Knipper, Denise Kühnert, Carles Lalueza-Fox, Judith Littleton, Ken Massy, Alissa Mittnik, José Antonio Mujika-Alustiza, Iñigo Olalde, Luka Papac, Sandra Penske, Jaroslav Peška, Ron Pinhasi, David Reich, Sabine Reinhold, Raphaela Stahl, Harald Stäuble, Rezeda I. Tukhbatova, Sergey Vasilyev, Elizaveta Veselovskaya, Christina Warinner, Philipp W. Stockhammer, Wolfgang Haak, Johannes Krause, Alexander Herbig, Max Planck Society, Max Planck - Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, European Research Council, Heidelberg Academy of Sciences and Humanities, Academy of Sciences of the Czech Republic, Ministerio de Ciencia e Innovación (España), German Research Foundation, Diputación Foral de Álava, Eusko Jaurlaritza, and Ministry of Education and Science (Kazakhstan)
Subjects: Plague, Multidisciplinary, Ancient DNA, Yersinia pestis
Abstract: [Significance] The bacterium Yersinia pestis has caused numerous historically documented outbreaks of plague and research using ancient DNA could demonstrate that it already affected human populations during the Neolithic. However, the pathogen’s genetic diversity, geographic spread, and transmission dynamics during this early period of Y. pestis evolution are largely unexplored. Here, we describe a set of ancient plague genomes up to 5,000 y old from across Eurasia. Our data demonstrate that two genetically distinct forms of Y. pestis evolved in parallel and were both distributed across vast geographic distances, potentially occupying different ecological niches. Interpreted within the archeological context, our results suggest that the spread of plague during this period was linked to increased human mobility and intensification of animal husbandry., The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology., This study was funded by the Max Planck Society, Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean and the European Research Council under the European Union’s Horizon 2020 research and innovation program under Grant Agreement 771234 – PALEoRIDER (to W.H.), 856453 – HistoGenes (to J.K.), and 834616 – ARCHCAUCASUS (to S.H.). The Heidelberg Academy of Science financed the genetic and archeological research on human individuals from the Augsburg region within the project WIN Kolleg: “Times of Upheaval: Changes of Society and Landscape at the Beginning of the Bronze Age. M.E. was supported by the award “Praemium Academiae” of the Czech Academy of Sciences. M.D. was supported by the project RVO 67985912 of the Institute of Archaeology of the Czech Academy of Sciences, Prague. I.O. was supported by the Ramón y Cajal grant from Ministerio de Ciencia e Innovación, Spanish Government (RYC2019-027909-I). A. H€ubner was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy (EXC 2051 – Project-ID 390713860). J.F.-E. and J.A.M.-A. were supported by the Diputación Foral de Alava, IT 1223-19, Gobierno Vasco. A. Buzhilova was supported by the Center of Information Technologies and Systems (CITIS), Moscow, Russia 121041500329-0. L. M., L.B.D., and E. Khussainova were supported by the Grant AP08856654, Ministry of Education and Science of the Republic of Kazakhstan. A. Beisenov was supported by the Grant AP08857177, Ministry of Education and Science of the Republic of Kazakhstan.
Published: 2022

10. A Molecular Approach to the Sexing of the Triple Burial at the Upper Paleolithic Site of Dolní Věstonice.

Author: Alissa Mittnik, Chuan-Chao Wang, Jiří Svoboda, and Johannes Krause
Subjects: Medicine, Science
Abstract: In the past decades ancient DNA research has brought numerous insights to archaeological research where traditional approaches were limited. The determination of sex in human skeletal remains is often challenging for physical anthropologists when dealing with incomplete, juvenile or pathological specimens. Molecular approaches allow sexing on the basis of sex-specific markers or by calculating the ratio of DNA derived from different chromosomes. Here we propose a novel approach that relies on the ratio of X chromosome-derived shotgun sequencing data to the autosomal coverage, thus establishing the probability of an XX or XY karyotype. Applying this approach to the individuals of the Upper Paleolithic triple burial of Dolní Věstonice reveals that all three skeletons, including the individual DV 15, whose sex has long been debated due to a pathological condition, were male.
Published: 2016
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11. Pedigree-based Bayesian modelling of radiocarbon dates

Author: Ken Massy, Ronny Friedrich, Alissa Mittnik, and Philipp W. Stockhammer
Subjects: Multidisciplinary, Archaeology, Germany, Calibration, Radiometric Dating, Humans, Bayes Theorem
Abstract: Within the last decade, archaeogenetic analysis has revolutionized archaeological research and enabled novel insights into mobility, relatedness and health of past societies. Now, it is possible to develop these results further and integrate archaeogenetic insights into biological relatedness with radiocarbon dates as means of chronologically sequenced information. In our article, we demonstrate the potential of combining relative chronological information with absolute radiocarbon dates by Bayesian interpretation in order to improve age determinations. Using artificial pedigrees with four sets of simulated radiocarbon dates we show that the combination of relationship information with radiocarbon dates improves the age determination in many cases at least between 20 to 50%. Calibrated age ranges are more constrained than simply calibrating radiocarbon ages independently from each other. Thereby, the precision of modelled ages depends on the precision of the single radiocarbon dates, the number of modelled generations, the shape of the calibration curve and the availability of samples that can be precisely fixed in time due to specific patterns in the calibration curve (“anchor points”). Ambiguous calibrated radiocarbon dates, which are caused by inversions of the calibration curve, can be partly or almost entirely resolved through Bayesian modelling based upon information from pedigrees. Finally, we discuss selected case studies of biological pedigrees achieved for Early Bronze Age Southern Germany by recent archaeogenetic analysis, whereby the sites and pedigrees differ with regard to the quality of information, which can be used for a Bayesian model of the radiocarbon dates. In accordance with the abstract models, radiocarbon dates can again be better constrained and are therefore more applicable for archaeological interpretation and chronological placement of the dated individuals.
Published: 2021

12. The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean

Author: Francesca Candilio, Beatriz Gamarra, David Caramelli, Alissa Mittnik, Matthew Ferry, Maria Teschler-Nicola, Kirsten Mandl, Alfredo Coppa, Roberto Miccichè, Mario Novak, Swapan Mallick, Gianfranca Salis, Martina Lari, Giulio Catalano, Stefania Vai, Vittoria Schimmenti, Nick Patterson, Nadin Rohland, Nasreen Broomandkhoshbacht, Jonas Oppenheimer, Ron Pinhasi, Marián Cueto, Iñigo Olalde, Olivia Cheronet, Maria Rita Palombo, Margherita Micheletti, Constanze Schattke, Edgard Camarós, Carla Maria Calò, Douglas J. Kennett, Brendan J. Culleton, Kadir T. Özdoğan, Pau Sureda, Elisabetta Marini, Marina Lozano, Luis Teira, Jens Carlsson, Vincenza Forgia, Michaela Lucci, David Reich, Carles Lalueza-Fox, Gabriella Gasperetti, Luca Sineo, Alessandra Modi, Daniel Fernandes, Rebecca Bernardos, Iosif Lazaridis, Kendra Sirak, Megan Michel, Kristin Stewardson, Damià Ramis, Matthew Mah, Irish Research Council, National Science Foundation (US), Fundación 'la Caixa', Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Ministero dell'Istruzione, dell'Università e della Ricerca, Howard Hughes Medical Institute, National Institutes of Health (US), John Templeton Foundation, and Daniel M. Fernandes, Alissa Mittnik, Iñigo Olalde, Iosif Lazaridis, Olivia Cheronet, Nadin Rohland, Swapan Mallick, Rebecca Bernardos, Nasreen Broomandkhoshbacht, Jens Carlsson, Brendan J. Culleton, Matthew Ferry, Beatriz Gamarra, Martina Lari, Matthew Mah, Megan Michel, Alessandra Modi, Mario Novak, Jonas Oppenheimer, Kendra A. Sirak, Kristin Stewardson, Kirsten Mandl, Constanze Schattke, Kadir T. Özdoğan, Michaela Lucci, Gabriella Gasperetti, Francesca Candilio, Gianfranca Salis, Stefania Vai, Edgard Camarós, Carla Calò, Giulio Catalano, Marián Cueto, Vincenza Forgia, Marina Lozano, Elisabetta Marini, Margherita Micheletti, Roberto M. Miccichè, Maria R. Palombo, Damià Ramis, Vittoria Schimmenti, Pau Sureda, Luís Teira, Maria Teschler-Nicola, Douglas J. Kennett, Carles Lalueza-Fox , Nick Patterson, Luca Sineo, Alfredo Coppa, David Caramelli, Ron Pinhasi, David Reich
Subjects: 0301 basic medicine, Mediterranean climate, Steppe, Pastoralism, Population genetics, government.political_district, Settore BIO/08 - Antropologia, Iran, ancient-DNA, western mediterranean islands population, aDNA, Human Ancient migrations, Western Mediterranean Basin, Steppe pastoralists, Anthropology, 03 medical and health sciences, 0302 clinical medicine, Bronze Age, Humans, DNA, Ancient, Sicily, Ecology, Evolution, Behavior and Systematics, Islands, Balearic islands, geography.geographical_feature_category, Ecology, Africa, anthropology, emigration and immigration, Europe, humans, islands, Spain, agriculture, DNA, ancient, genome-wide association study, ancient, Agriculture, DNA, Chalcolithic, Emigration and Immigration, western mediterranean islands population, humanities, Ancient DNA, steppe ancestry, western Mediterranean, 030104 developmental biology, Geography, Anthropology, government, ancient-DNA, Ethnology, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 bc, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 bc. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 bc) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 bc, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium bc, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island’s early farmers until the first millennium bc, with the exception of an outlier from the third millennium bc, who had primarily North African ancestry and who—along with an approximately contemporary Iberian—documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium bc and, at present, no more than 56–62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people., D.M.F. was supported by an Irish Research Council grant GOIPG/2013/36. Radiocarbon work was supported in part by the NSF Archaeometry program BCS-1460369 (to D.J.K. and B.J.C). C.L.-F. was supported by Obra Social La Caixa and by FEDER-MINECO (BFU2015-64699-P and PGC2018-095931-B-100). D.C. was supported by grant 20177PJ9XF MIUR PRIN 2017. D.Reich is an Investigator of the Howard Hughes Medical Institute, and his ancient-DNA laboratory work was supported by National Science Foundation HOMINID grant BCS-1032255, a National Institutes of Health grant GM100233, an Allen Discovery Center grant, and grant no. 61220 from the John Templeton Foundation.
Published: 2020

13. Ten millennia of hepatitis B virus evolution

Author: Oleg Balanovsky, Lourdes Marquez-Morfin, Magdalena Zoledziewska, Susannah J. Salter, Cody E. Parker, Kirsten I. Bos, Kathrin Nägele, Domingo C. Salazar-García, Kerttu Majander, Vittorio Mazzarello, Cosimo Posth, Kurt W. Alt, Elmira Khussainova, Silvia Teresita Hernández Godoy, Richard Mortimer, Ayshin Ghalichi, Alexander Herbig, Lars Fehren-Schmitz, Leyla B. Djansugurova, Dmitry A. Stashenkov, Raiko Krauß, Mikhail S. Chaplygin, Tiago Ferraz, Patrick Semal, Eva Rosenstock, Michal Kostka, Yavor Boyadzhiev, Harald Meller, Petr Limburský, Mario Küßner, Tara Ingman, Maïté Rivollat, Eva Fernández-Domínguez, Rodrigo Barquera, Robin Skeates, Kamen Boyadzhiev, Denise Kühnert, Mirjana Roksandic, Adam Ben Rohrlach, Alexandra P. Buzhilova, Alissa Mittnik, Yadira Chinique de Armas, Johannes Krause, Marie-France Deguilloux, Aleksandr Khokhlov, Rezeda I. Tukhbatova, Elizabeth Popescu, Lucy C. Salazar, Andrey A. Chizhevsky, Christopher Read, Hubert Steiner, Melanie Van Twest, Eveline Altena, Diana Iraíz Hernández-Zaragoza, Lyazzat Musralina, Megan Michel, Íñigo García-Martínez de Lagrán, Anatoly R. Kantorovich, Katrien Van de Vijver, Alžbeta Danielisová, Rachel Clarke, Duncan Sayer, Bastien Llamas, Nikolaj Makarov, Alejandro Romero, Luka Papac, Alessandra Sperduti, Vladimir E. Maslov, Rafael Garrido-Pena, Gunnar U. Neumann, Arman Z. Beisenov, Zainolla Samashev, Guido Alberto Gnecchi-Ruscone, Päivi Onkamo, Eduardo Carmona Ballestero, Javier Jimenez-Echevarria, Valery Khartanovich, Manuel Rojo-Guerra, Fredrik Hallgren, Eirini Skourtanioti, Natalia Shishlina, Luca Lai, Petr Velemínský, Antti Sajantila, Peter C. Ramsl, Claudia Sagona, Susanne Friederich, Miroslav Dobeš, Marcel Keller, Francesco Cucca, Sabine Reinhold, Florian van Bömmel, Luc Amkreutz, Vittoria Schimmenti, Raphaela Stahl, Douglas Baird, Marina K. Karapetian, Kurt Rademaker, Stephan Schiffels, Sacha Kacki, Evelyn K. Guevara, Michael Francken, Christina Warinner, Kay Prüfer, Karen Giffin, Felix M. Key, Joscha Gretzinger, Alexey Kalmykov, Svetlana Shnaider, Sandra Penske, Antje Wissgott, Tiffiny A. Tung, Biaslan Ch. Atabiev, Philippe Lefranc, Elizabeth A. Nelson, Peter de Knijff, Vladimir Slavchev, Jessica Pearson, Yılmaz Selim Erdal, Louise Loe, Jan Nováček, Micaela Alvarez Calmet, José I. Royo-Guillén, Richard L. Burger, Kristiina Mannermaa, K. Aslıhan Yener, Maria Pfefferkorn, Vyacheslav Moiseyev, Svend Hansen, Didier Binder, Michal Ernée, Maria A. Spyrou, Michal Feldman, Vladimir V. Kufterin, Murat Akar, Héctor Arcusa-Magallón, Andrej B. Belinskiy, Egor Kitov, Franziska Aron, Ron Hübler, Vanessa Villalba-Mouco, Sophie Beckett, Jessica Beckett, Arthur Kocher, Michael Schultz, Elena Batieva, Pilar Utrilla, Cristina Tejedor-Rodríguez, Kristin von Heyking, Masnav Navruzbekov, Michaela Langová, Maria Paz Miguel de Ibáñez, Stéphane Rottier, Maria V. Dobrovolskaya, Sandra Lösch, Emma D. Zilivinskaya, Dmitry V. Vasilev, Gabriel García Atiénzar, Marcello A. Mannino, Wolfgang Haak, Philipp W. Stockhammer, Sylvie Saintot, Alice Lyons, Ken Massy, Elena Kaverzneva, Susanna Sabin, Carmen Alonso-Fernández, Anna F. Kochkina, Marieke Sophia van de Loosdrecht, Stefanie Eisenmann, Max Planck Society, European Commission, Slovak Academy of Sciences, Academy of Sciences of the Czech Republic, Russian Foundation for Basic Research, German Research Foundation, Agence Nationale de la Recherche (France), Wenner-Gren Foundation, Ministry of Education and Science (Kazakhstan), Universidad de Alicante. Departamento de Prehistoria, Arqueología, Historia Antigua, Filología Griega y Filología Latina, Universidad de Alicante. Departamento de Biotecnología, Universidad de Alicante. Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Prehistoria y Protohistoria, Grupo de Inmunología, Biología Celular y del Desarrollo, Ingman, Tara, Kocher, A., Papac, L., Barquera, R., Key, FM., Spyrou, MA., Hubler, R., Rohrlach, AB., Aron, F., Stahl, R., Wissgott, A., van Bommel, F., Pfefferkorn, M., Mittnik, A., Villalba-Mouco, V., Neumann, GU., Rivollat, M., van de Loosdrecht, MS., Majander, K., Tukhbatova, RI., Musralina, L., Ghalichi, A., Penske, S., Sabin, S., Michel, M., Gretzinger, J., Nelson, EA., Ferraz, T., Nagele, K., Parker, C., Keller, M., Guevara, EK., Feldman, M., Eisenmann, S., Skourtanioti, E., Giffin, K., Gnecchi-Ruscone, GA., Friederich, S., Schimmenti, V., Khartanovich, V., Karapetian, MK., Chaplygin, MS., Kufterin, VV., Khokhlov, AA., Chizhevsky, AA., Stashenkov, DA., Kochkina, AF., Tejedor-Rodriguez, C., de Lagran, IGM., Arcusa-Magallon, H., Garrido-Pena, R., Royo-Guillen, JI., Novacek, J., Rottier, S., Kacki, S., Saintot, S., Kaverzneva, E., Belinskiy, AB., Veleminsky, P., Limbursky, P., Kostka, M., Loe, L., Popescu, E., Clarke, R., Lyons, A., Mortimer, R., Sajantila, A., de Armas, YC., Godoy, STH., Hernandez-Zaragoza, DI., Pearson, J., Binder, D., Lefranc, P., Kantorovich, AR., Maslov, VE., Lai, L., Zoledziewska, M., Beckett, JF., Langova, M., Atienzar, GG., Ibanez, MPD, Romero, A., Sperduti, A., Beckett, S., Salter, SJ., Zilivinskaya, ED., Vasil, DV., von Heyking, K., Burger, RL., Salazar, LC., Amkreutz, L., Navruzbekov, M., Rosenstock, E., Alonso-Fernandez, C., Slavchev, V., Kalmykov, AA., Atabiev, BC., Batieva, E, Calmet, MA., Llamas, B., Schultz, M., Krauss, R., Jimenez-Echevarria, J., Francken, M., Shnaider, S., de Knijff, P., Altena, E., Van de Vijver, K., Fehren-Schmitz, L., Tung, TA., Losch, S., Dobrovolskaya, M., Makarov, N., Read, C., Van Twest, M., Sagona, C., Ramsl, PC., Akar, M., Yener, KA., Ballestero, EC., Cucca, F., Mazzarello, V., Utrilla, P., Rademaker, K., Fernandez-Dominguez, E., Baird, D., Semal, P., Marquez-Morfin, L, Roksandic, M., Steiner, H., Salazar-Garcia, DC., Shishlina, N. Erdal, YS., Hallgren, F., Boyadzhiev, Y., Boyadzhiev, K., Kussner, M., Sayer, D., Onkamo, P., Skeates, R., Rojo-Guerra, M., Buzhilova, A., Khussainova, E., Djansugurova, LB., Beisenov, AZ., Samashev, Z., Massy, K., Mannino, M., Moiseyev, V., Mannermaa, K., Balanovsky, O., Deguilloux, MF., Reinhold, S., Hansen, S., Kitov, EP., Dobes, M., Ernee, M., Meller, H., Prufer, Kay., Warinner, C., Schiffels, S., Stockhammer, PW., Bos, K., Posth, C., Herbig, A., Haak, W., Krause, J., Kuhnert, D., and Koç University Research Center for Anatolian Civilizations (ANAMED) / Koç Üniversitesi Anadolu Medeniyetleri Araştırma Merkezi (ANAMED)
Subjects: Phylogeographic history, Hepatitis B/history, 01 natural sciences, The Republic, Communicable Diseases, Emerging, German, Communicable Diseases, Emerging/history, Agency (sociology), Science and technology, ComputingMilieux_MISCELLANEOUS, History, Ancient, Phylogeny, media_common, 0303 health sciences, Multidisciplinary, Ancient DNA, European research, virus diseases, Genomics, Hepatitis B, 3. Good health, Europe, language, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Christian ministry, Paleogenomic analyses, Asian Continental Ancestry Group, 010506 paleontology, Hepatitis B virus, Asia, Hepatitis B virus/classification, European Continental Ancestry Group, Library science, Biología Celular, White People, Marie curie, Evolution, Molecular, 03 medical and health sciences, American Natives, Asian People, Political science, Genomic data, media_common.cataloged_instance, Humans, Slovak, European union, American Indian or Alaska Native, 030304 developmental biology, 0105 earth and related environmental sciences, Genetic Variation, Paleontology, Prehistoria, A300, language.human_language, digestive system diseases, American natives, Americas, Asian continental ancestry group, Communicable diseases, Emerging, European continental ancestry group, Evolution, molecular, Genetic variation
Abstract: Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic., The research was funded by the Max Planck Society, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (771234–PALEoRIDER, to W.H.; 805268–CoDisEASe to K. Bos; 834616–ARCHCAUCASUS to S.H.), the Slovak Academy of Sciences and the European Union’s Seventh Framework Programme and Marie Curie Actions under the Programme SASPRO (1340/03/03 to P.C.R.), the ERA.NET RUS Plus–S&T programm of the European Union’s Seventh Framework Programme (277–BIOARCCAUCASUS to S.Re. and S.H.), the Werner Siemens Stiftung (“Paleobiochemistry”, to CW), the Award Praemium Academiae of the Czech Academy of Sciences (to M.E.), the Institute of Archaeology of the Czech Academy of Sciences (RVO 67985912, to M.Dobe.), the Russian Foundation for Basic Research (19-09-00354a, to M.K.K. and V.V.K.; 19-78-10053 to SSh), the German Research Foundation (DFG-HA-5407/4-1–INTERACT to W.H. and RE2688/2 to S.Re.), the French National Research Agency (ANR-17-FRAL-0010–INTERACT, to M.F.D., M.Ri., S.Ro., S.Sai., D.Bi., and P.Le.), the Wenner-Gren Dissertation Fieldwork Grant (9558 to S.Sab.), and the Ministry of Education and Science of the Republic of Kazakhstan (AP08856654 to L.B.D., L.M., and E.Kh. and AP08857177 to A.Z.B.).
Published: 2021
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14. Author Correction: The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean

Author: Ron Pinhasi, Damià Ramis, Marina Lozano, Maria Teschler-Nicola, Michaela Lucci, Maria Rita Palombo, Giulio Catalano, Matthew Ferry, Jonas Oppenheimer, Constanze Schattke, Vincenza Forgia, Iñigo Olalde, Alissa Mittnik, Kristin Stewardson, David Reich, Marián Cueto, Luca Sineo, Nasreen Broomandkhoshbacht, Mario Novak, Luis Teira, Stefania Vai, Megan Michel, Nadin Rohland, Beatriz Gamarra, Martina Lari, Edgard Camarós, Carles Lalueza-Fox, Matthew Mah, Olivia Cheronet, Kirsten Mandl, Rebecca Bernardos, Kadir T. Özdoğan, Pau Sureda, Swapan Mallick, Alfredo Coppa, Francesca Candilio, David Caramelli, Margherita Micheletti, Gabriella Gasperetti, Alessandra Modi, Jens Carlsson, Gianfranca Salis, Daniel Fernandes, Carla Maria Calò, Douglas J. Kennett, Brendan J. Culleton, Elisabetta Marini, Kendra Sirak, Iosif Lazaridis, Roberto Miccichè, Nick Patterson, Vittoria Schimmenti, Irish Research Council, National Science Foundation (US), Fundación 'la Caixa', Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Ministero dell'Istruzione, dell'Università e della Ricerca, Howard Hughes Medical Institute, National Institutes of Health (US), and John Templeton Foundation
Subjects: geography, geography.geographical_feature_category, History, Ecology, Irish, Steppe, Research council, language, Archaeology, Article, Ecology, Evolution, Behavior and Systematics, language.human_language, Archaeological science
Abstract: Correction to: Nature Ecology & Evolution https://doi.org/10.1038/s41559-020-1102-0, published online 24 February 2020., D.M.F. was supported by an Irish Research Council grant GOIPG/2013/36. Radiocarbon work was supported in part by the NSF Archaeometry program BCS-1460369 (to D.J.K. and B.J.C). C.L.-F. was supported by Obra Social La Caixa and by FEDER-MINECO (BFU2015-64699-P and PGC2018-095931-B-100). D.C. was supported by grant 20177PJ9XF MIUR PRIN 2017. D.Reich is an Investigator of the Howard Hughes Medical Institute, and his ancient-DNA laboratory work was supported by National Science Foundation HOMINID grant BCS-1032255, a National Institutes of Health grant GM100233, an Allen Discovery Center grant, and grant no. 61220 from the John Templeton Foundation.
Published: 2020

15. The genetic prehistory of the Baltic Sea region

Author: Valery Khartanovich, David Reich, Michal Feldman, Aida Andrades Valtueña, Fredrik Hallgren, Markku Oinonen, Raili Allmäe, Rimantas Jankauskas, Gunita Zariņa, Christos Economou, Mantas Daubaras, Stephan Schiffels, Chuan-Chao Wang, Wolfgang Haak, Vyacheslav Moiseyev, Elena Balanovska, Alissa Mittnik, Mari Tõrv, Anja Furtwängler, Saskia Pfrengle, Andrejs Vasks, Johannes Krause, Finnish Museum of Natural History, and Natural Sciences Unit
Subjects: 0301 basic medicine, Baltic States, Steppe, Range (biology), Population Dynamics, DIVERSITY, General Physics and Astronomy, 615 History and Archaeology, Stone Age, 0302 clinical medicine, lcsh:Science, History, Ancient, Ancient DNA, Baltic Sea region, Transients and Migrants, GENOMES SUGGEST, Multidisciplinary, geography.geographical_feature_category, Fossils, CHROMOSOME HAPLOGROUP-N, 1184 Genetics, developmental biology, physiology, Agriculture, humanities, ADMIXTURE, population characteristics, geographic locations, Gene Flow, EUROPE, Science, Pastoralism, Scandinavian and Nordic Countries, EURASIA, SEQUENCE, General Biochemistry, Genetics and Molecular Biology, White People, Prehistory, 03 medical and health sciences, ANCIENT DNA, Humans, 14. Life underwater, Author Correction, Mesolithic, geography, Genome, Human, General Chemistry, Before Present, Archaeology, HUNTER-GATHERERS, 030104 developmental biology, lcsh:Q, EARLY FARMERS, 030217 neurology & neurosurgery
Abstract: Correction: Nature communications 9 (2018), art. no. 1494 doi:10.1038/s41467-018-03872-y While the series of events that shaped the transition between foraging societies and food producers are well described for Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here, we report genome-wide DNA data from 38 ancient North Europeans ranging from similar to 9500 to 2200 years before present. Our analysis provides genetic evidence that hunter-gatherers settled Scandinavia via two routes. We reveal that the first Scandinavian farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Mesolithic Western hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers during the Early and Middle Neolithic. The arrival of steppe pastoralists in the Late Neolithic introduced a major shift in economy and mediated the spread of a new ancestry associated with the Corded Ware Complex in Northern Europe.
Published: 2018

16. Ancient DNA sheds light on the genetic origins of early Iron Age Philistines

Author: Philipp W. Stockhammer, Marta Burri, Adam J. Aja, Daniel M. Master, Alissa Mittnik, Choongwon Jeong, Raffaela A. Bianco, Michal Feldman, and Johannes Krause
Subjects: Human Migration, Population, Ancient history, engineering.material, White People, 03 medical and health sciences, Genetic signature, Humans, 0601 history and archaeology, Bronze, DNA, Ancient, education, Research Articles, History, Ancient, 030304 developmental biology, 0303 health sciences, education.field_of_study, Multidisciplinary, 060102 archaeology, SciAdv r-articles, 06 humanities and the arts, Geography, Ancient DNA, Genetics, Population, Iron Age, Anthropology, engineering, Research Article, Genome-Wide Association Study
Abstract: Bronze and Iron Age genomes suggest a European-related gene flow coincided with the Philistines arrival in ancient Ashkelon., The ancient Mediterranean port city of Ashkelon, identified as “Philistine” during the Iron Age, underwent a marked cultural change between the Late Bronze and the early Iron Age. It has been long debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called “Sea Peoples.” Here, we report genome-wide data of 10 Bronze and Iron Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European-related admixture. This genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze to Iron Age transition in Ashkelon but did not leave a long-lasting genetic signature.
Published: 2019

17. Kinship-based social inequality in Bronze Age Europe

Author: Ronny Friedrich, Corina Knipper, Ernst Pernicka, Alissa Mittnik, Kristin von Heyking, Isil Kucukkalipci, Stephan Schiffels, Catharina Kociumaka, Joachim Wahl, Anja Furtwängler, Fabian Wittenborn, Saskia Pfrengle, Philipp W. Stockhammer, Ken Massy, Andreas Thiel, Stephanie E. Metz, Nadine Carlichi-Witjes, Marta Burri, Wolfgang Haak, Anja Staskiewicz, Susanne Lindauer, Johannes Krause, Heidi Deeg, and Michaela Harbeck
Subjects: Male, Archaeogenetics, Family Characteristics, Multidisciplinary, Exogamy, Polymorphism, Single Nucleotide, Pedigree, Prehistory, Geography, Social Class, Bronze Age, Anthropology, Germany, Kinship, Ethnology, Humans, Social inequality, Female, DNA, Ancient, Social organization, History, Ancient, Social status
Abstract: Ancient DNA informs on past culturesArchaeology has used analysis of the artifacts and remains of people to uncover their past behaviors and to infer their cultural practices. However, establishing genetic relationships has only recently become possible. Mittniket al.examined the kinship and inheritance of the remains of people from the German Lech River Valley over a time period spanning the Late Neolithic Corded Ware Culture, the Bell Beaker Complex, the Early Bronze Age, and the Middle Bronze Age (see the Perspective by Feinman and Neitzel). From genetic and archaeological analyses, it was revealed that the Early Bronze Age household's burials over multiple generations consisted of a high-status core family and unrelated low-status individuals. Furthermore, women were not related to the men within the household, suggesting that men stayed within their birth communities in this society, but women did not.Science, this issue p.731; see also p.682
Published: 2019

18. The genomic history of Southern Europe

Author: Richard Cottiaux, Eadaoin Harney, Iain Mathieson, Elizaveta Veselovskaya, Corinne Thevenet, Georgi Ganetsovski, Philipp W. Stockhammer, Petar Stanev, Douglas J. Kennett, Stefan Chohadzhiev, Adina Boroneanţ, Domenico Lo Vetro, Megan Michel, Nicholas J. Conard, Maleen Leppek, Fanica Veljanovska, Harald Meller, Martina Lari, Clive Bonsall, Michael Bolus, Thomas Higham, Andrej Starović, Darko Komšo, Mario Novak, Ivaylo Lozanov, Maja Čuka, Vanya Petrova, Krum Bacvarov, Alicja Budnik, Cosimo Posth, Cristian Virag, Stanislav Iliev, Wolfgang Haak, Francesca Candilio, Iñigo Olalde, Tamás Hajdu, David Caramelli, Raiko Krauß, Ivor Janković, Swapan Mallick, Matthew Ferry, Ben Krause-Kyora, Maria Teschler-Nicola, Kristin Stewardson, Cătălin Lazăr, Anastasia Papathanasiou, Giulio Catalano, Veneta Handzhyiska, Kendra Sirak, Kathrin Nägele, Kurt W. Alt, Bernard Gély, Ivor Karavanić, Svetlana Venelinova, Nedko Elenski, Dragana Antonović, Ron Pinhasi, Maria Malina, Inna Potekhina, Ivan Valchev, Alexey G. Nikitin, Kath McSweeney, Dusan Boric, Alissa Mittnik, Nick Patterson, Saskia Pfrengle, Angela Simalcsik, Anna Szécsényi-Nagy, Abigail Ash, Malcolm Lillie, Mario Šlaus, Fabio Martini, David Reich, Johannes Krause, Tamás Szeniczey, Bence Viola, Dženi Los, Luca Sineo, Hervé Bocherens, Christophe Cupillard, Yavor Boyadzhiev, Pavel Mirea, Sahra Talamo, Alexandra Kozak, Katerina Harvati, Songül Alpaslan-Roodenberg, Nasreen Broomandkhoshbacht, Marko Menđušić, Gunita Zariņa, Olivia Cheronet, Isil Kucukkalipci, Denise Keating, Dorothée G. Drucker, Stefan Alexandrov, Vladimir Slavchev, Radian Andreescu, Eppie R. Jones, Beatriz Gamarra, Michael Francken, Nadin Rohland, Gloria G. Fortes, Jonas Oppenheimer, Stefania Vai, T. Douglas Price, Sergey Vasilyev, Borislava Galabova, Krassimir Leshtakov, Bisserka Gaydarska, Mende Balázs Gusztáv, Joško Zaninović, Nadezhda Atanassova, Vyacheslav Moiseyev, Josip Burmaz, Daniel Fernandes, Steve Zäuner, Damian Labuda, Frédérique Valentin, Iain Mathieson, Songül Alpaslan-Roodenberg, Cosimo Posth, Anna Szécsényi-Nagy, Nadin Rohland1, Swapan Mallick, Iigo Olalde, Nasreen Broomandkhoshbacht, Francesca Candilio, Olivia Cheronet, Daniel Fernandes, Matthew Ferry, Beatriz Gamarra, Gloria González Fortes, Wolfgang Haak, Eadaoin Harney, Eppie Jones, Denise Keating, Ben Krause-Kyora, Isil Kucukkalipci, Megan Michel, Alissa Mittnik, Kathrin N.gele, Mario Novak, Jonas Oppenheimer, Nick Patterson, Saskia Pfrengle, Kendra Sirak, Kristin Stewardson, Stefania Vai, Stefan Alexandrov, Kurt W. Alt, Radian Andreescu, Dragana Antonovic′, Abigail Ash, Nadezhda Atanassova, Krum Bacvarov, Mende Balázs Gusztáv, Hervé Bocherens, Michael Bolus, Adina Boroneant., Yavor Boyadzhiev, Alicja Budnik, Josip Burmaz, Stefan Chohadzhiev, Nicholas J. Conard, Richard Cottiaux, Maja Cuka, Christophe Cupillard, Dorothée G. Drucker, Nedko Elenski, Michael Francken, Borislava Galabova, Georgi Ganetsovski, Bernard Gély, Tamás Hajdu, Veneta Handzhyiska, Katerina Harvati, Thomas Higham, Stanislav Iliev, Ivor Jankovic′, Ivor Karavanic, Douglas J. Kennett, Darko Komšo, Alexandra Kozak, Damian Labuda, Martina Lari, Catalin Lazar, Maleen Leppek, Krassimir Leshtakov, Domenico Lo Vetro, Dženi Los, Ivaylo Lozanov, Maria Malina, Fabio Martini, Kath McSweeney, Harald Meller, Marko Mendˉušic, Pavel Mirea, Vyacheslav Moiseyev, Vanya Petrova, T. Douglas Price, Angela Simalcsik, Luca Sineo, Mario Šlaus, Vladimir Slavchev, Petar Stanev, Andrej Starovic′, Tamás Szeniczey, Sahra Talamo, Maria Teschler-Nicola, Corinne Thevenet, Ivan Valchev, Frédérique Valentin, Sergey Vasilyev, Fanica Veljanovska, Svetlana Venelinova, Elizaveta Veselovskaya, Bence Viola, Cristian Virag, Joško Zaninovic′, Steve Zuner, Philipp W. Stockhammer, Giulio Catalano, Raiko Krau, David Caramelli, Gunita Zarin, Bisserka Gaydarska, Malcolm Lillie, Alexey G. Nikitin, Inna Potekhina, Anastasia Papathanasiou, Dušan Boric, Clive Bonsall, Johannes Krause, Ron Pinhasi, David Reich, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Mathieson I., Alpaslan-Roodenberg S., Posth C., Szecsenyi-Nagy A., Rohland N., Mallick S., Olalde I., Broomandkhoshbacht N., Candilio F., Cheronet O., Fernandes D., Ferry M., Gamarra B., Fortes G.G., Haak W., Harney E., Jones E., Keating D., Krause-Kyora B., Kucukkalipci I., Michel M., Mittnik A., Nagele K., Novak M., Oppenheimer J., Patterson N., Pfrengle S., Sirak K., Stewardson K., Vai S., Alexandrov S., Alt K.W., Andreescu R., Antonovic D., Ash A., Atanassova N., Bacvarov K., Gusztav M.B., Bocherens H., Bolus M., Boroneant A., Boyadzhiev Y., Budnik A., Burmaz J., Chohadzhiev S., Conard N.J., Cottiaux R., Cuka M., Cupillard C., Drucker D.G., Elenski N., Francken M., Galabova B., Ganetsovski G., Gely B., Hajdu T., Handzhyiska V., Harvati K., Higham T., Iliev S., Jankovic I., Karavanic I., Kennett D.J., Komso D., Kozak A., Labuda D., Lari M., Lazar C., Leppek M., Leshtakov K., Vetro D.L., Los D., Lozanov I., Malina M., Martini F., McSweeney K., Meller H., Mentusic M., Mirea P., Moiseyev V., Petrova V., Douglas Price T., Simalcsik A., Sineo L., Slaus M., Slavchev V., Stanev P., Starovic A., Szeniczey T., Talamo S., Teschler-Nicola M., Thevenet C., Valchev I., Valentin F., Vasilyev S., Veljanovska F., Venelinova S., Veselovskaya E., Viola B., Virag C., Zaninovic J., Zauner S., Stockhammer P.W., Catalano G., Krauss R., Caramelli D., Zarina G., Gaydarska B., Lillie M., Nikitin A.G., Potekhina I., Papathanasiou A., Boric D., Bonsall C., Krause J., Pinhasi R., Reich D., Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Male, History, Steppe, 01 natural sciences, genome wide ancient DNA, 0302 clinical medicine, population dynamics, ComputingMilieux_MISCELLANEOUS, History, Ancient, 2. Zero hunger, 0303 health sciences, education.field_of_study, Multidisciplinary, geography.geographical_feature_category, Farmers, Genome, Agriculture, Cline (biology), Genomics, Grassland, Europe, Geography, Western europe, Ethnology, Female, southeastern Europe, Human, Archaeogenetics, 010506 paleontology, Asia, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Human Migration, Population, Settore BIO/08 - Antropologia, Indigenous, Article, Ancient, 03 medical and health sciences, genetic variation, genomics, prehistoric Europe, prehistoric archeology, bioarchaeology, Bioarchaeology, Genetics, Humans, HUMANISTIC SCIENCES. Archeology, Farmer, DNA, Ancient, Sex Distribution, education, Mesolithic, 030304 developmental biology, 0105 earth and related environmental sciences, HUMANISTIČKE ZNANOSTI. Arheologija, Extramural, business.industry, Genome, Human, Ambientale, DNA, Archaeology, PRIRODNE ZNANOSTI. Biologija. Genetika, evolucija i filogenija, 030104 developmental biology, Ancient DNA, Genetics, Population, Ancient DNA, Genomics, Southeastern Europe, Genetic Variation, business, NATURAL SCIENCES. Biology. Genetics, Evolution and Phylogenetics, 030217 neurology & neurosurgery
Abstract: Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. However, the dynamics of the interaction between the first farmers and the indigenous hunter-gatherers remain poorly understood because of the near absence of ancient DNA from the region. We report new genome-wide ancient DNA data from 204 individuals-65 Paleolithic and Mesolithic, 93 Neolithic, and 46 Copper, Bronze and Iron Age-who lived in southeastern Europe and surrounding regions between about 12,000 and 500 BCE. We document that the hunter-gatherer populations of southeastern Europe, the Baltic, and the North Pontic Steppe were distinctive from those of western Europe, with a West-East cline of ancestry. We show that the people who brought farming to Europe were not part of a single population, as early farmers from southern Greece are not descended from the Neolithic population of northwestern Anatolia that was ancestral to all other European farmers. The ancestors of the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but we show that some groups that remained in the region mixed extensively with local hunter-gatherers, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that we show prevailed later in the North and West. After the spread of farming, southeastern Europe continued to be a nexus between East and West, with intermittent steppe ancestry, including in individuals from the Varna I cemetery and associated with the Cucuteni-Trypillian archaeological complex, up to 2,000 years before the Steppe migration that replaced much of northern Europe9s population.
Published: 2018
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19. The Arrival of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean

Author: Beatriz Gamarra, Iñigo Olalde, Maria Teschler-Nicola, Giulio Catalano, Kendra Sirak, Kirstin Stewardson, Marián Cueto, Jonas Oppenheimer, Marina Lozano, Jens Carlsson, Matthew Ferry, Iosif Lazaridis, Alessandra Modi, Carles Lalueza-Fox, David Reich, Stefania Vai, Brendan J. Culleton, Luca Sineo, Pau Sureda, Vincenza Forgia, Luis Teira, Rebecca Bernardos, Megan Michel, Vittoria Schimmenti, Margherita Micheletti, Olivia Cheronet, Alissa Mittnik, Daniel Fernandes, Martina Lari, Roberto Miccichè, David Caramelli, Nick Patterson, Mario Novak, Nadin Rohland, Carla Maria Calò, Douglas J. Kennett, Swapan Mallick, Elisabetta Marini, Nasreen Broomandkhoshbacht, Edgard Camarós, Matthew Mah, Damià Ramis, Ron Pinhasi, and Maria Rita Palombo
Subjects: Mediterranean climate, 0303 health sciences, Balearic islands, geography, geography.geographical_feature_category, Steppe, media_common.quotation_subject, Immigration, Pastoralism, government.political_district, Ancient history, humanities, 03 medical and health sciences, 0302 clinical medicine, Ancient DNA, Bronze Age, Classical period, government, 030217 neurology & neurosurgery, 030304 developmental biology, media_common
Abstract: A series of studies have documented how Steppe pastoralist-related ancestry reached central Europe by at least 2500 BCE, while Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BCE. However, the spread of these ancestries into the western Mediterranean where they have contributed to many populations living today remains poorly understood. We generated genome-wide ancient DNA from the Balearic Islands, Sicily, and Sardinia, increasing the number of individuals with reported data from these islands from 3 to 52. We obtained data from the oldest skeleton excavated from the Balearic islands (dating to ∼2400 BCE), and show that this individual had substantial Steppe pastoralist-derived ancestry; however, later Balearic individuals had less Steppe heritage reflecting geographic heterogeneity or immigration from groups with more European first farmer-related ancestry. In Sicily, Steppe pastoralist ancestry arrived by ∼2200 BCE and likely came at least in part from Spain as it was associated with Iberian-specific Y chromosomes. In Sicily, Iranian-related ancestry also arrived by the Middle Bronze Age, thus revealing that this ancestry type, which was ubiquitous in the Aegean by this time, also spread further west prior to the classical period of Greek expansion. In Sardinia, we find no evidence of either eastern ancestry type in the Nuragic Bronze Age, but show that Iranian-related ancestry arrived by at least ∼300 BCE and Steppe ancestry arrived by ∼300 CE, joined at that time or later by North African ancestry. These results falsify the view that the people of Sardinia are isolated descendants of Europe’s first farmers. Instead, our results show that the island’s admixture history since the Bronze Age is as complex as that in many other parts of Europe.
Published: 2019
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20. Reconciling material cultures in archaeology with genetic data: The nomenclature of clusters emerging from archaeogenomic analysis

Author: Stefanie Eisenmann, Eszter Bánffy, Iosif Lazaridis, Joseph Maran, Alissa Mittnik, Peter van Dommelen, Philipp W. Stockhammer, Johannes Krause, David Reich, Michael McCormick, and Kerstin P. Hofmann
Subjects: 0301 basic medicine, History, lcsh:Medicine, Genomics, Article, Alte Geschichte, Vor- und Frühgeschichte, Archäologie, 03 medical and health sciences, Mixed systems, Archaeological research, Terminology as Topic, Humans, 0601 history and archaeology, DNA, Ancient, lcsh:Science, Nomenclature, Skeleton, Multidisciplinary, 060102 archaeology, Fossils, lcsh:R, History of the ancient world to ca. 499 [T930], Genetic data, Excavation, 06 humanities and the arts, Prehistoric Archaeology [FVFG], Archaeology, 030104 developmental biology, Ancient DNA, lcsh:Q
Abstract: Genome-wide ancient DNA analysis of skeletons retrieved from archaeological excavations has provided a powerful new tool for the investigation of past populations and migrations. An important objective for the coming years is to properly integrate ancient genomics into archaeological research. This article aims to contribute to developing a better understanding and cooperation between the two disciplines and beyond. It focuses on the question of how best to name clusters encountered when analysing the genetic makeup of past human populations. Recent studies have frequently borrowed archaeological cultural designations to name these genetic groups, while neglecting the historically problematic nature of the concept of cultures in archaeology. After reviewing current practices in naming genetic clusters, we introduce three possible nomenclature systems (‘numeric system’, ‘mixed system (a)’, ‘geographic-temporal system’) along with their advantages and challenges.
Published: 2018

21. Author Correction: The genetic prehistory of the Baltic Sea region

Author: Valery Khartanovich, Mantas Daubaras, Chuan-Chao Wang, Vyacheslav Moiseyev, Elena Balanovska, Gunita Zariņa, Johannes Krause, Christos Economou, Mari Tõrv, David Reich, Stephan Schiffels, Anja Furtwängler, Andrejs Vasks, Saskia Pfrengle, Wolfgang Haak, Fredrik Hallgren, Rimantas Jankauskas, Aida Andrades Valtueña, Markku Oinonen, Raili Allmäe, Michal Feldman, and Alissa Mittnik
Subjects: 0301 basic medicine, Multidisciplinary, History, Science, General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology, Genealogy, Article, Prehistory, 03 medical and health sciences, 030104 developmental biology, Work (electrical), Baltic sea, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, lcsh:Q, 14. Life underwater, lcsh:Science
Abstract: While the series of events that shaped the transition between foraging societies and food producers are well described for Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here, we report genome-wide DNA data from 38 ancient North Europeans ranging from ~9500 to 2200 years before present. Our analysis provides genetic evidence that hunter-gatherers settled Scandinavia via two routes. We reveal that the first Scandinavian farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Mesolithic Western hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers during the Early and Middle Neolithic. The arrival of steppe pastoralists in the Late Neolithic introduced a major shift in economy and mediated the spread of a new ancestry associated with the Corded Ware Complex in Northern Europe., The population history of Europe is complex and its very north has not yet been comprehensively studied at a genetic level. Here, Mittnik et al. report genome-wide data from 38 ancient individuals from the Eastern Baltic, Russia and Scandinavia to analyse gene flow throughout the Mesolithic and Bronze Age.
Published: 2018

22. Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe

Author: Wolfgang Haak, Dorothée G. Drucker, Frédérique Valentin, Michael Bolus, Hervé Bocherens, Damien Flas, Elena Gigli, Annamaria Ronchitelli, Michael Francken, Maria Malina, Jiří Svoboda, Isabelle Crevecoeur, Katerina Harvati, David Caramelli, Christoph Wißing, Gabriel Renaud, Cosimo Posth, Corinne Thevenet, Martina Lari, Johannes Krause, Alissa Mittnik, Bernard Gély, Dan Grigorescu, Nicholas J. Conard, Anja Furtwängler, Kurt Wehrberger, Adam Powell, Cédric Beauval, Johannes van der Plicht, Patrick Semal, Christophe Cupillard, Hélène Rougier, Richard Cottiaux, Giulia Capecchi, Mietje Germonpré, Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Max Planck Institute for Evolutionary Anthropology [Leipzig], De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), University College of London [London] (UCL), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente., Università degli Studi di Siena = University of Siena (UNISI), Laboratoire d'Anthropologie et de Préhistoire, Institut Royal des Sciences Naturelles de Belgique (IRSNB), Archéosphère, Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), Ministère de la Culture et de la Communication (MCC)-École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Centre National de la Recherche Scientifique (CNRS), Department of Palaeontology, Royal Belgian Institue of Natural Sciences, Service régional de l'Archéologie Rhône-Alpes, Ministère de la Culture et de la Communication (MCC), U.R. Ecologia Preistorica, Dipartimento di Scienze Ambientali ', Faculty of Science [Brno] (SCI / MUNI), Masaryk University [Brno] (MUNI), Service Anthropologie et Préhistoire [Bruxelles], Laboratorio di Antropologia, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Univ Tubingen, Senckenberg Ctr Human Evolut & Palaeoecol, Palaeoanthropol, Tubingen, Germany, Department of Archaeogenetics [Jena] (DAG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement (UMR 6249) (LCE), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Firenze = University of Florence (UniFI), and Isotope Research
Subjects: 0301 basic medicine, Most recent common ancestor, Genetics and Molecular Biology (all), 010506 paleontology, Pleistocene, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SDV]Life Sciences [q-bio], Population, Black People, Biology, Medicine (all), Biochemistry, Genetics and Molecular Biology (all), Agricultural and Biological Sciences (all), DNA, Mitochondrial, Biochemistry, 01 natural sciences, White People, General Biochemistry, Genetics and Molecular Biology, [SHS]Humanities and Social Sciences, Paleontology, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Glacial period, DNA, Ancient, education, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0105 earth and related environmental sciences, education.field_of_study, 0303 health sciences, Agricultural and Biological Sciences(all), Genome, Human, Biochemistry, Genetics and Molecular Biology(all), Genetic Variation, Emigration and Immigration, Europe, 030104 developmental biology, Population bottleneck, Ancient DNA, Human evolution, Haplotypes, Evolutionary biology, Africa, Genome, Mitochondrial, Biological dispersal, General Agricultural and Biological Sciences
Abstract: How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [1, 2]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [3-5]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [6-9]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [3-5, 8, 9]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.
Published: 2016
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23. Inferring genetic origins and phenotypic traits of George Bähr, the architect of the Dresden Frauenkirche

Author: Cosimo Posth, Alexander Peltzer, Kay Nieselt, Tristan Begg, Alissa Mittnik, Johannes Krause, and Chuan-Chao Wang
Subjects: 0301 basic medicine, Male, Mitochondrial DNA, Light skin, Population, Population genetics, lcsh:Medicine, Skin Pigmentation, Biology, DNA, Mitochondrial, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, 0302 clinical medicine, Humans, DNA, Ancient, education, lcsh:Science, Comparative genomics, education.field_of_study, Multidisciplinary, Eye Color, lcsh:R, Phenotypic trait, Hypervariable region, 030104 developmental biology, Ancient DNA, Genetics, Population, Phenotype, Archaeology, Evolutionary biology, Genome, Mitochondrial, lcsh:Q, 030217 neurology & neurosurgery, DNA Damage
Abstract: For historic individuals, the outward appearance and other phenotypic characteristics remain often non-resolved. Unfortunately, images or detailed written sources are only scarcely available in many cases. Attempts to study historic individuals with genetic data so far focused on hypervariable regions of mitochondrial DNA and to some extent on complete mitochondrial genomes. To elucidate the potential of in-solution based genome-wide SNP capture methods - as now widely applied in population genetics - we extracted DNA from the 17th century remains of George Bähr, the architect of the Dresdner Frauenkirche. We were able to identify the remains to be of male origin, showing sufficient DNA damage, deriving from a single person and being thus likely authentic. Furthermore, we were able to show that George Bähr had light skin pigmentation and most likely brown eyes. His genomic DNA furthermore points to a Central European origin. We see this analysis as an example to demonstrate the prospects that new in-solution SNP capture methods can provide for historic cases of forensic interest, using methods well established in ancient DNA (aDNA) research and population genetics.
Published: 2018

24. Patterns of Transformation from the Final Neolithic to the Early Bronze Age

Author: Ken Massy, Corina Knipper, Alissa Mittnik, Steffen Kraus, Ernst Pernicka, Fabian Wittenborn, Johannes Krause, and Philipp W. Stockhammer
Published: 2017
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25. Reconstructing Prehistoric African Population Structure

Author: Saioa López, Audax Mabulla, Douglas J. Kennett, Elizabeth Gomani-Chindebvu, Svante Pääbo, Kendra Sirak, Iñigo Olalde, Mateja Hajdinjak, Mark Horton, Chrissy Chiumia, Johannes Krause, Mary E. Prendergast, Ceri Shipton, Eadaoin Harney, David Reich, Alison Crowther, Anja Heinze, Pontus Skoglund, Richard F. Helm, Matthew Ferry, Nick Patterson, Jessica I. Cerezo-Román, Kristin Stewardson, Ron Pinhasi, Nicole Boivin, Menno Welling, Mark G. Thomas, Alexander Peltzer, Megan Michel, Agness Gidna, Katherine M. Grillo, Ruth Tibesasa, Vanessa M. Hayes, John Parkington, Nadin Rohland, I. Taneli Helenius, Swapan Mallick, Raj Ramesar, Alissa Mittnik, Garrett Hellenthal, Jessica C. Thompson, Alan G. Morris, Tasneem Salie, and Matthias Meyer
Subjects: 0301 basic medicine, Male, Genetics, Medical, Pastoralism, Population, Population genetics, Black People, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Bone and Bones, Lineage (anthropology), Prehistory, 03 medical and health sciences, 0302 clinical medicine, parasitic diseases, Humans, DNA, Ancient, education, Life Style, education.field_of_study, Fossils, Genome, Human, Population ecology, biology.organism_classification, 030104 developmental biology, Ancient DNA, Tanzania, Genetics, Population, Africa, Ethnology, Female, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP.
Published: 2017

26. Female exogamy and gene pool diversification at the transition from the final neolithic to the early Bronze Age in central Europe

Author: Anja Staskiewicz, Corina Knipper, Philipp W. Stockhammer, Michael Maus, Ken Massy, Johannes Krause, Catharina Kociumaka, Isil Kucukkalipci, Alissa Mittnik, Fabian Wittenborn, and Stephanie E. Metz
Subjects: Male, 0301 basic medicine, engineering.material, Diversification (marketing strategy), 03 medical and health sciences, Bronze Age, Beaker, Kinship, Humans, 0601 history and archaeology, Bronze, Anthropology, Cultural, History, Ancient, Multidisciplinary, 060102 archaeology, Exogamy, Gene Pool, 06 humanities and the arts, Biological Sciences, Archaeology, Europe, 030104 developmental biology, Ancient DNA, Geography, Genome, Mitochondrial, engineering, Female, Gene pool
Abstract: Human mobility has been vigorously debated as a key factor for the spread of bronze technology and profound changes in burial practices as well as material culture in central Europe at the transition from the Neolithic to the Bronze Age. However, the relevance of individual residential changes and their importance among specific age and sex groups are still poorly understood. Here, we present ancient DNA analysis, stable isotope data of oxygen, and radiogenic isotope ratios of strontium for 84 radiocarbon-dated skeletons from seven archaeological sites of the Late Neolithic Bell Beaker Complex and the Early Bronze Age from the Lech River valley in southern Bavaria, Germany. Complete mitochondrial genomes documented a diversification of maternal lineages over time. The isotope ratios disclosed the majority of the females to be nonlocal, while this is the case for only a few males and subadults. Most nonlocal females arrived in the study area as adults, but we do not detect their offspring among the sampled individuals. The striking patterns of patrilocality and female exogamy prevailed over at least 800 y between about 2500 and 1700 BC. The persisting residential rules and even a direct kinship relation across the transition from the Neolithic to the Bronze Age add to the archaeological evidence of continuing traditions from the Bell Beaker Complex to the Early Bronze Age. The results also attest to female mobility as a driving force for regional and supraregional communication and exchange at the dawn of the European metal ages.
Published: 2017

27. A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

Author: David Reich, Martina Lari, Annamaria Ronchitelli, Sergi Castellano, Ralf Schmitz, Ruth Bollongino, Kirsten I. Bos, Liane Giemsch, Alissa Mittnik, Peter Bauer, Renata Grifoni Cremonesi, Svante Pääbo, Fabio Martini, Jiří Svoboda, David Caramelli, Qiaomei Fu, Joachim Burger, Philip L. F. Johnson, Johannes Krause, and Chengkai Sun
Subjects: Mitochondrial DNA, Time Factors, ancient modern humans, Molecular Sequence Data, Population, mitochondrial genome, mitochondrial clock, Biology, Genome, Article, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Humans, education, ancient DNA Human Evolution, Phylogeny, Demography, 030304 developmental biology, Genetics, Human mitochondrial molecular clock, 0303 health sciences, education.field_of_study, Base Sequence, Models, Genetic, Agricultural and Biological Sciences(all), Fossils, Genome, Human, Biochemistry, Genetics and Molecular Biology(all), Haplotype, High-Throughput Nucleotide Sequencing, Bayes Theorem, Haplogroup L3, Haplotypes, Human evolution, Genome, Mitochondrial, Linear Models, Human genome, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery
Abstract: Summary Background Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought. Results Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) that occurred less than 62–95 kya. Conclusions Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population divergence times, they can provide valid upper bounds. Our results exclude most of the older dates for African and non-African population divergences recently suggested by de novo mutation rate estimates in the nuclear genome.
Published: 2013
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28. The Genetic History of Northern Europe

Author: Valery Khartanovich, Alissa Mittnik, Mari Tõrv, Raili Allmäe, Chuan-Chao Wang, Anja Furtwängler, Saskia Pfrengle, Oleg Balanovsky, David Reich, Aida Andrades Valtueña, Michal Feldman, Wolfgang Haak, Fredrik Hallgren, Mantas Daubaras, Vyacheslav Moiseyev, Andrejs Vasks, Markku Oinonen, Johannes Krause, Rimantas Jankauskas, Christos Economou, Stephan Schiffels, and Gunita Zariņa
Subjects: 0303 health sciences, geography, geography.geographical_feature_category, 060102 archaeology, Range (biology), Steppe, Pastoralism, Glacier, 06 humanities and the arts, engineering.material, Archaeology, 03 medical and health sciences, Ancient DNA, Baltic sea, engineering, 0601 history and archaeology, Bronze, Mesolithic, 030304 developmental biology
Abstract: Recent ancient DNA studies have revealed that the genetic history of modern Europeans was shaped by a series of migration and admixture events between deeply diverged groups. While these events are well described in Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here we report genome-wide DNA data from 24 ancient North Europeans ranging from ~7,500 to 200 calBCE spanning the transition from a hunter-gatherer to an agricultural lifestyle, as well as the adoption of bronze metallurgy. We show that Scandinavia was settled after the retreat of the glacial ice sheets from a southern and a northern route, and that the first Scandinavian Neolithic farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Western European Mesolithic hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers until around 2,900 calBCE when the arrival of steppe pastoralists introduced a major shift in economy and established wide-reaching networks of contact within the Corded Ware Complex.
Published: 2017
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29. The Stone Age Plague: 1000 years of Persistence in Eurasia

Author: Alexander Herbig, Maria A. Spyrou, Aida Andrades Valtueña, Anna Szécsényi-Nagy, Ivor Janković, Mario Šlaus, Johannes Krause, Raili Allmäe, Wolfgang Haak, Mari Tõrv, Kirsten I. Bos, Saskia Pfrengle, Alissa Mittnik, Philipp W. Stockhammer, Felix M. Key, Andrej Belinskij, Rimantas Jankauskas, Ken Massy, Michal Feldman, Mario Novak, Mantas Daubaras, Sabine Reinhold, and Svend Hansen
Subjects: education.field_of_study, biology, Population, Context (language use), Plague (disease), biology.organism_classification, Stone Age, Prehistory, Ancient DNA, Geography, Yersinia pestis, Bronze Age, Evolutionary biology, education, pathogen, ancient DNA, prehistory
Abstract: Yersinia pestis, the etiologic agent of plague, is a bacterium associated with wild rodents and their fleas. Historically it was responsible for three pandemics: the Plague of Justinian in the 6th century AD, which persisted until the 8th century [1] ; the renowned Black Death of the 14th century [2, 3], with recurrent outbreaks until the 18th century [4] ; and the most recent 19th century pandemic, in which Y. pestis spread worldwide [5] and became endemic in several regions [6]. The discovery of molecular signatures of Y. pestis in prehistoric Eurasian individuals and two genomes from Southern Siberia suggest that Y. pestis caused some form of disease in humans prior to the first historically documented pandemic [7]. Here, we present six new European Y. pestis genomes spanning the Late Neolithic to the Bronze Age (LNBA ; 4, 800 to 3, 700 calibrated years before present). This time period is characterized by major transformative cultural and social changes that led to cross- European networks of contact and exchange [8, 9]. We show that all known LNBA strains form a single putatively extinct clade in the Y. pestis phylogeny. Interpreting our data within the context of recent ancient human genomic evidence that suggests an increase in human mobility during the LNBA, we propose a possible scenario for the early spread of Y. pestis: the pathogen may have entered Europe from Central Eurasia following an expansion of people from the steppe, persisted within Europe until the mid-Bronze Age, and moved back toward Central Eurasia in parallel with human populations.
Published: 2017

30. The beaker phenomenon and the Genomic transformations of Northwest Europe

Author: Matthew Ferry, Nasreen Broomandkhoshbacht, Anna Endrődi, César Heras Martínez, Balázs Gusztáv Mende, Fraser Brown, András Czene, Morten E. Allentoft, Anna Szécsényi-Nagy, Ian Barnes, Roberto Risch, Milan Kuchařík, Clive Waddington, Benjamin Neil, Róbert Patay, Ignacio Soriano, Jocelyne Desideri, Luc Vergnaud, Gordon Cook, Denise Keating, Francesca Candilio, Karl-Göran Sjögren, Iosif Lazaridis, Kristin Stewardson, Harry Fokkens, Virginia Galera Olmo, Tamás Hajdu, David Caramelli, Aurore Schmitt, Philippe Lefranc, Maya Hoole, Stephany Leach, Megan Michel, Alessandra Modi, Daniel Fernandes, Viktória Kiss, João Luís Cardoso, Václav Smrčka, Swapan Mallick, Zuzana Faltyskova, Wolfgang Haak, Eszter Bánffy, David Billoin, Ron Pinhasi, T. Douglas Price, Ian Armit, Michiel Gazenbeek, Piotr Włodarczak, Eadaoin Harney, Marie Besse, Tim Allen, Douglas J. Kennett, Christopher Evans, Carles Lalueza-Fox, Alessandro Zanini, Selina Brace, Manuel Ángel Rojo Guerra, Philipp W. Stockhammer, Mike Luke, Zsolt Bernert, Peter de Knijff, Richard Mortimer, Michal Ernée, Gill Hey, Emiliano Carnieri, Elżbieta Haduch, Kitti Köhler, Laura Bonsall, João Zilhão, Thomas J. Booth, Mike Parker Pearson, Germán Delibes, Yoan Diekmann, Olivier Lemercier, Iñigo Olalde, János Dani, Eveline Altena, Alistair Barclay, Ken Massy, Sebastiano Tusa, Antonella Valenti, David Reich, Jonas Oppenheimer, Nadin Rohland, Clive Bonsall, Ana Maria Silva, Pierre-Jérôme Rey, Joaquín Lomba Maurandi, Alison Sheridan, Tona Majó, Chris Fowler, Petr Velemínský, Natasha Dodwell, Luigi Lentini, Katina T. Lillios, Miroslav Dobeš, Azucena Avilés Fernández, Olivia Cheronet, Mark G. Thomas, Ana-Mercedes Herrero-Corral, María Haber-Uriarte, Maria Bernabò-Brea, Agata Hałuszko, Ana Bastida Ramírez, Concepción Blasco, Alissa Mittnik, Roberto Menduiña García, Marcus Brittain, Nick Patterson, Tamás Szeniczey, Maksym Mackiewicz, Raúl Flores Fernández, Sophie Carver, Timothy D J Knowles, Volker M Heyd, Rafael Garrido Pena, Arnaud Lefebvre, Kathleen McSweeney, Lindsey Büster, Joël Serralongue, Mirosław Furmanek, Laura Castells Navarro, Kirsten Egging Dinwiddy, Artur Rapiński, Thomas K. Harper, Corina Liesau, Kristian Kristiansen, Barry Cunliffe, Oliver E. Craig, Patricia Ríos, Gabriella Kulcsár, Joan Francès Farré, Pilar Prieto, Jorge Vega de Miguel, Johannes Krause, Saskia Pfrengle, Thomas Higham, Elisa Guerra-Doce, Anthony Denaire, Nick Jowett, Kurt W. Alt, Mark Lipson, Jacqueline I. McKinley, Günter Brücken, Universitat Pompeu Fabra [Barcelona] (UPF), Egham TW20 0EX, Middlesex University, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, Harvard School of Public Health, Max Planck Institute for the Science of Human History (MPI-SHH), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], School of Archaeology [Dublin], University College Dublin [Dublin] (UCD), Center for Human and Clinical Genetics, Leiden University Medical Center (LUMC), Institut national de recherches archéologiques préventives (Inrap), Haematology, St James' Institute of Oncology, Etude des Civilisations de l'Antiquité (UMR 7044), Centre National de la Recherche Scientifique (CNRS)-Université Marc Bloch - Strasbourg II-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), Department of Psychiatry and Biobehavioral Sciences, University of California [Los Angeles] (UCLA), University of California-University of California-Shirley and Stefan Hatos Center for Neuropharmacology, Archéologie, Terre, Histoire, Sociétés [Dijon] (ARTeHiS), Ministère de la Culture et de la Communication (MCC)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Institute of Archaeology [Budapest], Research Centre for The Humanities [Budapest], Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Department of Anthropology [University of Vienna], University of Vienna [Vienna], Department of Anthropology, Národní muzeum, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Laboratoire d'archéologie préhistorique et anthropologie, Université de Genève (UNIGE), Instytut Archeologii Uniwersytetu Wrocławskiego, Institute for Health and Consumer Protection, European Commission - Joint Research Centre, Environnements, Dynamiques et Territoires de la Montagne (EDYTEM), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Universidad de Valladolid [Valladolid] (UVa), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Service archéologique de la Haute-Savoie, Office départemental d'animation culturelle de la Haute-Savoie, University of Minho [Braga], Department of Archaeology and Anthropology, University of Bristol [Bristol], Laboratorio di Antropologia, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Oxford Radiocarbon Accelerator Unit, RLAHA, National Museums of Scotland, Department of Archaeogenetics [Jena] (DAG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, School of Archaeology, Departament de biologia animal, Universitad de barcelona, Universiteit Leiden-Universiteit Leiden, Étude des Civilisations de l'Antiquité : de la Préhistoire à Byzance (ARCHIMEDE), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université Marc Bloch - Strasbourg II-Centre National de la Recherche Scientifique (CNRS), University of California (UC)-University of California (UC)-Shirley and Stefan Hatos Center for Neuropharmacology, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Université de Genève = University of Geneva (UNIGE), Environnements, Dynamiques et Territoires de Montagne (EDYTEM), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Firenze = University of Florence (UniFI), National Museums Scotland (NMS), Repositório da Universidade de Lisboa, Universitat de Barcelona, Desideri, Jocelyne, and Besse, Marie
Subjects: Male, 0301 basic medicine, Steppe, ADN, Néolithique, Bell Beaker, Arqueologia, Bell Beaker culture, genome wide ancient DNA, 0302 clinical medicine, Archéologie, Phenomenon, ddc:550, 0601 history and archaeology, Suisse, History, Ancient, 0303 health sciences, education.field_of_study, geography.geographical_feature_category, Multidisciplinary, 060102 archaeology, [SDE.IE]Environmental Sciences/Environmental Engineering, Human migration, Préhistoire, Neolithic period, Gene Pool, Genomics, [SHS.GEO]Humanities and Social Sciences/Geography, 06 humanities and the arts, bell Beaker, Europe, Geography, Archaeology, Ceràmica, Ethnology, Mégalithisme, Archaeogenetics, Campaniforme, Pottery, Human Migration, [SDE.MCG]Environmental Sciences/Global Changes, Population, Ancient history, Article, 03 medical and health sciences, Spatio-Temporal Analysis, popular genetics, Bronze Age, Beaker, Cultural Evolution, Neolític, genomics, Humans, DNA, Ancient, education, 030304 developmental biology, Chromosomes, Human, Y, Genome, Human, business.industry, Northwest Europe, Chalcolithic, [SDE.ES]Environmental Sciences/Environmental and Society, Ancient DNA, Genetics, Population, 030104 developmental biology, Haplotypes, Period (geology), Genomic, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 030217 neurology & neurosurgery
Abstract: Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200–1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900–1200 BCE. British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion. Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain’s Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.
Published: 2017
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31. Genetic origins of the Minoans and Mycenaeans

Author: P. J. P. McGeorge, Ron Pinhasi, Kristin Stewardson, Yannis Tzedakis, Manolis Michalodimitrakis, Alexander Peltzer, Yannis Maniatis, Songül Alpaslan Roodenberg, Daniel Fernandes, Cosimo Posth, Patrick A. Navas, Eleni Konsolaki-Yannopoulou, David Reich, Anastasia Papathanasiou, Holley Martlew, Philipp W. Stockhammer, Michael P. Richards, John A. Stamatoyannopoulos, Johannes Krause, Dimitra Lotakis, Andonis Vasilakis, George N. Korres, Swapan Mallick, Anja Furtwängler, George Stamatoyannopoulos, Mehmet Özsait, Nadin Rohland, Saskia Pfrengle, Robert Arnott, Iosif Lazaridis, Alissa Mittnik, Nick Patterson, Jeffery R. Hughey, and Nesrin Özsait
Subjects: 0301 basic medicine, Male, Chromosomes, Human, X, Principal Component Analysis, Multidisciplinary, geography.geographical_feature_category, Greece, Steppe, Human Migration, Ancient history, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Geography, Bronze Age, Ethnicity, Humans, Mainland, Female, 030217 neurology & neurosurgery, History, Ancient, Phylogeny
Abstract: The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We assembled genome-wide data from nineteen ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. We show that Minoans and Mycenaeans were genetically similar, having at least three quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean1,2, and most of the remainder from ancient populations like those of the Caucasus3 and Iran4,5. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter-gatherers of eastern Europe and Siberia6–8, introduced via a proximal source related to either the inhabitants of either the Eurasian steppe1,6,9 or Armenia4,9. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.
Published: 2016

32. Pleistocene bears in the Swabian Jura (Germany): Genetic replacement, ecological displacement, extinctions and survival

Author: Michael Hofreiter, Susanne C. Münzel, Nicholas J. Conard, Mathias Stiller, Alissa Mittnik, and Hervé Bocherens
Subjects: Hibernation, geography.geographical_feature_category, Pleistocene, biology, Ecology, Last Glacial Maximum, biology.organism_classification, law.invention, Geography, Cave, Sympatric speciation, law, Cave bear, Radiocarbon dating, Ursus, Earth-Surface Processes
Abstract: Palaeogenetic investigations in three geographically close caves (Hohle Fels, Geisenklosterle, and Sirgenstein) in the Ach Valley near Blaubeuren (Swabian Jura) document the sudden replacement of Ursus spelaeus by Ursus ingressus around 28,000 14 C BP. New radiocarbon dates suggest an earlier immigration of Ursus ingressus and at least a partial coexistence with Ursus spelaeus some 4500 years before the ultimate replacement. These two genetic types of cave bears used the same caves for hibernation and had the same herbivorous diet, as shown by the stable isotope results. In contrast, sympatric brown bears (Ursus arctos) exhibited a clearly different ecology, as shown by the carnivorous pattern of their isotopic signatures, and probably did not use the caves as dens before the Last Glacial Maximum (LGM). Once established, the younger cave bear (Ursus ingressus) remained the only cave bear for only another circa 2000 years after the last appearance of the classical cave bear (Ursus spelaeus) in the Ach Valley and elsewhere. The final appearance of cave bear (sensu lato) is now dated to 25,560 � 130 BP, disproving a refuge area of this species in the Swabian Jura. After the extinction of cave bears (sensu lato), brown bears took over their cave dens and their nutritional niche as they shift to a diet dominated by plant food. 2011 Elsevier Ltd and INQUA.
Published: 2011
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33. The genetic history of Ice Age Europe

Author: Alexander Peltzer, Dorothée G. Drucker, Annamaria Ronchitelli, Stephan Schiffels, Maria Teschler-Nicola, Swapan Mallick, Svante Pääbo, Michael P. Richards, Daniel Fernandes, Martin Petr, Manuel R. González Morales, Marco Peresani, Jiří Svoboda, V. S. Slavinsky, Janet Kelso, David Reich, Isabelle Crevecoeur, Pontus Skoglund, E. Vacca, Francesco Mallegni, Donato Coppola, Oana Teodora Moldovan, Cosimo Posth, Nadin Rohland, Kurt Wehrberger, Anatoly P. Derevianko, Birgit Nickel, A. A. Tsybankov, Viviane Slon, Nicholas J. Conard, Stefano Ricci, Christine Neugebauer-Maresch, Corinne Thevenet, Qiaomei Fu, Lawrence Guy Straus, Vyacheslav Moiseyev, Frédérique Valentin, Johannes Krause, Iain Mathieson, Silviu Constantin, Mateja Hajdinjak, Sahra Talamo, Bernard Gély, Renata Grifoni Cremonesi, Dan Grigorescu, David Caramelli, Mark Lipson, Matthias Meyer, Damien Flas, Stefano Benazzi, Alissa Mittnik, Nick Patterson, Iosif Lazaridis, Martina Lari, Hervé Bocherens, Wolfgang Haak, Katerina Harvati, Patrick Semal, Christophe Cupillard, Hélène Rougier, Ron Pinhasi, Marcello A. Mannino, Anja Furtwängler, Nikolai I. Drozdov, Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Harvard School of Public Health, School of Archaeology [Dublin], University College Dublin [Dublin] (UCD), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Université libre de Bruxelles (ULB), Department of Evolutianory Genetics, Max-Planck-Institut, Sackler Faculty of Medicine, Tel Aviv University (TAU), Department of Human Evolution [Leipzig], Nuffield Department of Medicine, Service régional de l'Archéologie Rhône-Alpes, Ministère de la Culture et de la Communication (MCC), Laboratory of Excellence for Financial Regulation (LABEX ReFi), Université Paris-Sud - Paris 11 (UP11), Institutul de Speologie ‘Emil Racoviţă', Str. Frumoasă 31, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Università degli Studi di Ferrara = University of Ferrara (UniFE), Università degli Studi di Firenze = University of Florence (UniFI), Department of Information Engineering [Firenze], U.R. Ecologia Preistorica, Dipartimento di Scienze Ambientali ', Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Museum Ulm, De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Service Anthropologie et Préhistoire [Bruxelles], Institut Royal des Sciences Naturelles de Belgique (IRSNB), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, University of Tübingen, Faculty of Science [Brno] (SCI / MUNI), Masaryk University [Brno] (MUNI), Department of Physics, University of Sussex, Department of Animal Biology and Genetics, School of Archaeology, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Centre International de Recherche Archéologique sur la Polynésie (CIRAP), Université de la Polynésie Française (UPF), Tel Aviv University [Tel Aviv], Università degli Studi di Ferrara (UniFE), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Max Planck Institute for Evolutionary Anthropology, Eberhard Karls Universität Tübingen, Max-Planck-Institut für evolutionäre Anthropologie (MPI-EVA), University College of London [London] (UCL), Laboratoire Chrono-environnement - CNRS - UFC (UMR 6249) (LCE), Department of Archaeogenetics [Jena] (DAG), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), University of Bologna, Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente., Università degli Studi di Siena = University of Siena (UNISI), Laboratoire d'Anthropologie et de Préhistoire, Institut royal des Sciences naturelles de Belgique (IRSNB), Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), Ministère de la Culture et de la Communication (MCC)-École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Centre National de la Recherche Scientifique (CNRS), Institut Royal des Sciences naturelles de Belgique, Univ Tubingen, Senckenberg Ctr Human Evolut & Palaeoecol, Palaeoanthropol, Tubingen, Germany, Laboratorio di Antropologia, Università degli Studi di Firenze = University of Florence [Firenze], Qiaomei, Fu, Posth, Cosimo, Hajdinjak, Mateja, Petr, Martin, Mallick, Swapan, Fernandes, Daniel, Furtwängler, Anja, Haak, Wolfgang, Meyer, Matthia, Mittnik, Alissa, Nickel, Birgit, Peltzer, Alexander, Rohland, Nadin, Slon, Viviane, Talamo, Sahra, Lazaridis, Iosif, Lipson, Mark, Mathieson, Iain, Schiffels, Stephan, Skoglund, Pontu, Derevianko, Anatoly P., Drozdov, Nikolai, Slavinsky, Vyacheslav, Tsybankov, Alexander, Cremonesi, Renata Grifoni, Mallegni, Francesco, Gély, Bernard, Vacca, Eligio, Morales, Manuel R. González, Straus, Lawrence G., Neugebauer Maresch, Christine, Teschler Nicola, Maria, Constantin, Silviu, Moldovan, Oana Teodora, Benazzi, Stefano, Peresani, Marco, Coppola, Donato, Lari, Martina, Ricci, Stefano, Ronchitelli, Annamaria, Valentin, Frédérique, Thevenet, Corinne, Wehrberger, Kurt, Grigorescu, Dan, Rougier, Hélène, Crevecoeur, Isabelle, Flas, Damien, Semal, Patrick, Mannino, Marcello A., Cupillard, Christophe, Bocherens, Hervé, Conard, Nicholas J., Harvati, Katerina, Moiseyev, Vyacheslav, Drucker, Dorothée G., Svoboda, Jiří, Richards, Michael P., Caramelli, David, Pinhasi, Ron, Kelso, Janet, Patterson, Nick, Krause, Johanne, Pääbo, Svante, and Reich, David
Subjects: 0301 basic medicine, Male, Neanderthal, Time Factors, [SDV]Life Sciences [q-bio], Population Dynamics, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Neanderthal genome project, migration, Ancient Modern Humans, [SHS]Humanities and Social Sciences, 0302 clinical medicine, Ice Cover, History, Ancient, Phylogeny, ComputingMilieux_MISCELLANEOUS, Modern Humans, Neanderthals, Genetics, education.field_of_study, Multidisciplinary, Ancient DNA, Human migration, Biological Evolution, Founder Effect, Pleistocene, Europe, Ethnology, Female, Ancient DNA, Ancient Modern Humans, Neanderthals, Human, Animals, DNA, European Continental Ancestry Group, Genetics, Population, Human Migration, Humans, Middle East, Selection, Genetic, Sequence Analysis, DNA, Medicine (all), Archaeogenetics, Time Factor, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Modern Humans, Genetics, Pleistocene, Europe, migration, culture, Europe glaciaire, Population, Socio-culturale, Biology, Article, White People, Prehistory, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], biology.animal, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, Population Dynamic, Homo sapiens, Animal, business.industry, culture, 030104 developmental biology, [ SHS.ARCHEO ] Humanities and Social Sciences/Archaeology and Prehistory, business, génome humain, 030217 neurology & neurosurgery, Founder effect
Abstract: 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.
Published: 2016
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34. Van der Plicht J., Cottiaux R., Gély B., Ronchitelli A., Wehrberger KPleistocene Mitochondrial genomes suggest a single major dispersal of non-Africans and a Late Glacial population turnover in Europe

Author: Cosimo Posth, Gabriel Renaud, Alissa Mittnik, Drucker, Dorothée G., Hélène Rougier, Christophe Cupillard, Frederique Valentin, Corinne Thevenet, Anja Furtwängler, Christoph Wissing, Michael Francken, Maria Malina, Michael Bolus, Martina Lari, Isabelle Crevecoeur, Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Max Planck Institute for Evolutionary Anthropology [Leipzig], De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Service Régional d'Archéologie de Franche-Comté, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Trajectoires - UMR 8215, Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Laboratoire d'Anthropologie et de Préhistoire, and Institut Royal des Sciences Naturelles de Belgique (IRSNB)
Subjects: préhistoire, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2016

35. A Molecular Approach to the Sexing of the Triple Burial at the Upper Paleolithic Site of Dolní Věstonice

Author: Johannes Krause, Jiří Svoboda, Alissa Mittnik, and Chuan-Chao Wang
Subjects: 0301 basic medicine, Male, Molecular biology, lcsh:Medicine, DNA cloning, Biochemistry, 0302 clinical medicine, lcsh:Science, Multidisciplinary, Sex Chromosomes, Ancient DNA, Shotgun sequencing, Chromosome Biology, XY karyotype, Paleogenetics, High-Throughput Nucleotide Sequencing, Karyotype, X Chromosomes, Y Chromosomes, Nucleic acids, Archaeology, Female, Sex, Sequence Analysis, Research Article, Zoology, Sexing, Biology, Bone and Bones, Chromosomes, 03 medical and health sciences, Genetics, Humans, Sequencing Techniques, Shotgun Sequencing, Chromosomes, Human, X, Biology and life sciences, lcsh:R, Paleontology, DNA, Sequence Analysis, DNA, Cell Biology, Research and analysis methods, Earth sciences, 030104 developmental biology, Molecular biology techniques, Evolutionary biology, Paleoanthropology, Upper Paleolithic, lcsh:Q, Sequence Alignment, 030217 neurology & neurosurgery, Cloning
Abstract: In the past decades ancient DNA research has brought numerous insights to archaeological research where traditional approaches were limited. The determination of sex in human skeletal remains is often challenging for physical anthropologists when dealing with incomplete, juvenile or pathological specimens. Molecular approaches allow sexing on the basis of sex-specific markers or by calculating the ratio of DNA derived from different chromosomes. Here we propose a novel approach that relies on the ratio of X chromosome-derived shotgun sequencing data to the autosomal coverage, thus establishing the probability of an XX or XY karyotype. Applying this approach to the individuals of the Upper Paleolithic triple burial of Dolni Věstonice reveals that all three skeletons, including the individual DV 15, whose sex has long been debated due to a pathological condition, were male.
Published: 2015

36. Massive migration from the steppe was a source for Indo-European languages in Europe

Author: David Reich, Valery Khartanovich, Wolfgang Haak, Anna Szécsényi-Nagy, Roberto Risch, Iosif Lazaridis, Eadaoin Harney, Matthias Meyer, Aleksandr Khokhlov, Harald Meller, Susanne Friederich, Johannes Krause, Guido Brandt, Christina Roth, Rafael Garrido Pena, Qiaomei Fu, Vayacheslav Moiseyev, Eszter Bánffy, Michael Kunst, Pavel Kuznetsov, Michael Francken, Sandra Pichler, Kurt W. Alt, Nadin Rohland, David W. Anthony, Alan Cooper, Alissa Mittnik, Nick Patterson, Joachim Wahl, Oleg Mochalov, Manuel Ángel Rojo Guerra, Christos Economou, Kristin Stewardson, Bastien Llamas, Swapan Mallick, Fredrik Hallgren, Nicole Nicklisch, Dorcas Brown, and Susanne Nordenfelt
Subjects: Male, Archaeogenetics, Steppe, Human Migration, Population Dynamics, Population, Ancient history, Corded Ware culture, Indigenous, Article, Russia, 03 medical and health sciences, Cultural Evolution, Humans, 0601 history and archaeology, Quantitative Biology - Populations and Evolution, education, History, Ancient, Language, 030304 developmental biology, 0303 health sciences, geography, education.field_of_study, Polymorphism, Genetic, Multidisciplinary, geography.geographical_feature_category, 060102 archaeology, Genome, Human, Indo-European languages, Populations and Evolution (q-bio.PE), Languages of Europe, 06 humanities and the arts, Grassland, Europe, Eastern european, Ancient DNA, FOS: Biological sciences, Period (geology), Ethnology
Abstract: We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.
Published: 2015

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

Author: Joanna L. Mountain, Michael F. Hammer, Ruslan Ruizbakiev, Cesare de Filippo, Kumarasamy Thangaraj, David E. C. Cole, Haim Ben-Ami, Leila Laredj, Mark Lipson, Jüri Parik, Valentino Romano, Andres Ruiz-Linares, Fouad Berrada, Dominique Delsate, Ugur Hodoglugil, Antti Sajantila, Olga Utevska, Shahlo Turdikulova, Tor Hervig, Ludmila P. Osipova, Hovhannes Sahakyan, Robert W. Mahley, Ramiro Barrantes, Kirsten I. Bos, Stanislav Dryomov, Peter H. Sudmant, Nadin Rohland, Heng Li, Gabriel Renaud, Mikhail Voevoda, Claudio M. Bravi, Jean-Michel Guinet, Rem I. Sukernik, Joachim Wahl, Matthias Meyer, Christos Economou, Kay Prüfer, Graciela Bailliet, Mait Metspalu, Mikhail Churnosov, Iosif Lazaridis, Johannes Krause, Bonnie Berger, Levon Yepiskoposyan, Francesca Brisighelli, Francesco Calì, Irene Gallego Romero, Oleg Balanovsky, George Ayodo, Alan Cooper, Alissa Mittnik, Julio Molina, George van Driem, Jean-Michel Dugoujon, Larissa Damba, Fedor Platonov, Nick Patterson, David Reich, Thomas B. Nyambo, David Comas, Olga L. Posukh, Béla Melegh, Draga Toncheva, Alena Kushniarevich, Brenna M. Henn, Montgomery Slatkin, René Vasquez, Elena B. Starikovskaya, Joachim Burger, Ayele Tarekegn, Tatijana Zemunik, Ene Metspalu, Sena Karachanak-Yankova, Lalji Singh, Wolfgang Haak, Susanna Sawyer, Rick A. Kittles, Cheryl A. Winkler, Svante Pääbo, Francisco Rothhammer, Marina Gubina, Pierre Zalloua, Aashish R. Jha, Swapan Mallick, Sergi Castellano, Qiaomei Fu, Desislava Nesheva, Sergey Litvinov, Ingrida Uktveryte, Michael Francken, Cosimo Posth, Theologos Loukidis, Cristian Capelli, Janet Kelso, Sarah A. Tishkoff, Toomas Kivisild, Mark G. Thomas, Elin Fornander, Mercedes Villena, Fredrik Hallgren, Vaidutis Kučinskas, Daniel Corach, George B.J. Busby, Judit Bene, William Klitz, Hamza A. Babiker, Karola Kirsanow, Ruth Bollongino, Rita Khusainova, Evan E. Eichler, Sardana A. Fedorova, Klemetti Näkkäläjärvi, Igor Rudan, Susanne Nordenfelt, Joshua G. Schraiber, Elena Balanovska, Antonio Salas, Richard Villems, Gabriel Bedoya, Elza Khusnutdinova, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Mathematics, Lipson, Mark, Berger Leighton, Bonnie, Lazaridis,I, Patterson,P, Mittnik,A, Renaud,G, Mallick,S, Kirsanow,K, Sudmant,PH, Schraiber,JG, Castellano,S, Lipson,M, Berger,B, Economou,C, Bollongino,R, Fu,Q, Bos,KI, Nordenfelt,S, Li,H, De Filippo,C, Pruefer,K, Sawyer, Posth,C, Haak1,H, Hallgren,F, Fornander,E, Rohland,N, Delsate,D, Francken,M, Guinet,JM, Wah,J, Ayodo,G, Babiker,HA, Bailliet,G, Balanovska,E, Balanovsky,O, Barrantes,R, Bedoya,G, Ben-Ami,H, Bene,J, Berrada,F, Bravi,CM, Brisighelli,F, Busby,GBJ, Cali,F, Churnosov,M, Cole,DEC, Corach,D, Damba,L, van Driem,G, Dryomov,S, Dugoujon,JM, Fedorova,SA, Gallego Romero,I, Gubina,M, Hammer,M, Henn,BM, Hervig,T, Hodoglugi,U, Jha,AR, Karachanak-Yankova,S, Khusainova,R, Khusnutdinova,E, Kittles,R:Kivisild,T, Klitz,W, Kucˇinskas,V, Kushniarevich,A, Laredj,L, Litvinov,S, Loukidis,T, Mahley,RW, Melegh,B, Metspalu,E, Molina,J, Mountain,J, Na¨kka¨la¨ja¨rvi,K, Nesheva,D, Nyambo,T, Osipova,L, Parik,J, Platonov,F, Posukh,O, Romano,V, Rothhammer,F, Rudan,I, Ruizbakiev,R, Sahakyan,H, Sajantila,A, Salas,A, Starikovskaya,EB, Tarekegn,A, Toncheva,D, Turdikulova,S, Uktveryte,I, Utevska,O, Vasquez,R, Villena,M, Voevoda,M, Winkler,CA, Yepiskoposyan,L, Zalloua,P, Zemunik,T, Cooper, Capelli,C, Thomas,MG, Ruiz-inares,A, Tishkoff,SA, Singh,L, Thangaraj,K, Villems,R, Comas,D, Sukernik,R, Metspalu,M, Meyer,M, Eichler,EE, Burger,J, Slatkin,M, Pa¨a¨bo,S, Kelso,J, Reich,D, and Krause,J
Subjects: History, Neanderthal, Biología, Population Dynamics, Present day, Genoma humà, Genome, purl.org/becyt/ford/1 [https], Basal (phylogenetics), Settore BIO/13 - Biologia Applicata, History, Ancient, Genetics, Principal Component Analysis, education.field_of_study, 0303 health sciences, Multidisciplinary, Ancient DNA, 030305 genetics & heredity, food and beverages, Agriculture, Genomics, 3. Good health, Europe, Workforce, CIENCIAS NATURALES Y EXACTAS, Human, Archaeogenetics, Asia, Lineage (genetic), EUROPE, Otras Ciencias Biológicas, European Continental Ancestry Group, Population, Settore BIO/08 - ANTROPOLOGIA, evolution, Europeans, Biology, Article, White People, Ancient, Genètica de poblacions humanes, Human origins, Ciencias Biológicas, 03 medical and health sciences, HUMAN ORIGINS, biology.animal, Humans, ANCIENT DNA, purl.org/becyt/ford/1.6 [https], education, Quantitative Biology - Populations and Evolution, Denisovan, 030304 developmental biology, Genetic diversity, ancient DNA, modern DNA, Europeans, prehistory, Genome, Human, Populations and Evolution (q-bio.PE), biology.organism_classification, Evolutionary biology, FOS: Biological sciences, Upper Paleolithic, Human genome, GENOMICS
Abstract: 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 genomes1,2,3,4 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 Siberians3, 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., Instituto Multidisciplinario de Biología Celular
Published: 2014

38. Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death

Author: David J. D. Earn, Brian K. Coombes, Verena J. Schuenemann, James W. Wood, Sarah E. Schmedes, William White, Kirsten I. Bos, Hendrik N. Poinar, Joslyn Jamieson, Alissa Mittnik, Stephen Forrest, Johannes Krause, and Sharon N. DeWitte
Subjects: Genetics, Multidisciplinary, Plasmid, Yersinia pestis, Sequence analysis, Biovar, Virulence, Biology, biology.organism_classification, Genome, Virology, Pathogen, DNA sequencing
Abstract: Although investigations of medieval plague victims have identified Yersinia pestis as the putative etiologic agent of the pandemic, methodological limitations have prevented large-scale genomic investigations to evaluate changes in the pathogen's virulence over time. We screened over 100 skeletal remains from Black Death victims of the East Smithfield mass burial site (1348–1350, London, England). Recent methods of DNA enrichment coupled with high-throughput DNA sequencing subsequently permitted reconstruction of ten full human mitochondrial genomes (16 kb each) and the full pPCP1 (9.6 kb) virulence-associated plasmid at high coverage. Comparisons of molecular damage profiles between endogenous human and Y. pestis DNA confirmed its authenticity as an ancient pathogen, thus representing the longest contiguous genomic sequence for an ancient pathogen to date. Comparison of our reconstructed plasmid against modern Y. pestis shows identity with several isolates matching the Medievalis biovar; however, our chromosomal sequences indicate the victims were infected with a Y. pestis variant that has not been previously reported. Our data reveal that the Black Death in medieval Europe was caused by a variant of Y. pestis that may no longer exist, and genetic data carried on its pPCP1 plasmid were not responsible for the purported epidemiological differences between ancient and modern forms of Y. pestis infections.
Published: 2011
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39. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

Author: Victor Merz, Diimaajav Erdenebaatar, Philipp W. Stockhammer, Eske Willerslev, Aleksei Kasparov, Olivier Bignon-Lau, Marjan Mashkour, Eric Crubézy, Ken Massy, Bazartseren Boldgiv, Lembi Lõugas, Gulmira Mukhtarova, Hossein Davoudi, Vedat Onar, Johannes Krause, Pablo Librado, Dorcas Brown, Sandra Olsen, Gottfried Brem, Norbert Benecke, Ivy J. Owens, Michael Hofreiter, Sainbileg Undrakhbold, David W. Anthony, Nurbol Baimukhanov, Mikkel Schubert, Andaine Seguin-Orlando, Alan K. Outram, Kristian Hanghøj, Vladimir V. Pitulko, Naveed Khan, Ahmed H. Alfarhan, Ludovic Orlando, Alissa Mittnik, Sabine Felkel, Antoine Fages, Azadeh Fatemeh Mohaseb, Viktor Zaibert, Peter de Barros Damgaard, Charleen Gaunitz, Anders Albrechtsen, Arne Ludwig, Barbara Wallner, Ilja Merz, Saleh A. Alquraishi, Sébastien Lepetz, Khaled A. S. Al-Rasheid, Bioinformatics Centre, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), University of Copenhagen = Københavns Universitet (KU), Archéologies et Sciences de l'Antiquité (ArScAn), Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Institut national de recherches archéologiques préventives (Inrap)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Tarbiat Modares University [Tehran], Zoology Department, College of Science, King Saud University, Laboratoire d'Anthropobiologie (LA), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine [Vienna] (Vetmeduni), Department of Evolutianory Genetics, Max-Planck-Institut, Department of Archaeogenetics [Jena] (DAG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Archéozoologie et histoire des sociétés (AHS), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Ruhr University Bochum (RUB), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), King Saud University [Riyadh] (KSU), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Copenhagen = Københavns Universitet (UCPH), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), and University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences
Subjects: 2. Zero hunger, 0301 basic medicine, education.field_of_study, Genome, Multidisciplinary, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Population, Zoology, Chalcolithic, Archaeological evidence, 03 medical and health sciences, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Phenotype, 030104 developmental biology, Geography, Bronze Age, Animals, Horses, DNA, Ancient, Domestication, education, Phylogeny
Abstract: Revisiting the origins of modern horses The domestication of horses was very important in the history of humankind. However, the ancestry of modern horses and the location and timing of their emergence remain unclear. Gaunitz et al. generated 42 ancient-horse genomes. Their source samples included the Botai archaeological site in Central Asia, considered to include the earliest domesticated horses. Unexpectedly, Botai horses were the ancestors not of modern domestic horses, but rather of modern Przewalski's horses. Thus, in contrast to current thinking on horse domestication, modern horses may have been domesticated in other, more Western, centers of origin. Science , this issue p. 111
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