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49 results on '"Kushniarevich, Alena"'

1. Gene pool preservation across time and space In Mongolian-speaking Oirats

Author

Balinova, Natalia, Hudjašov, Georgi, Pankratov, Vasili, Pennarun, Erwan, Reidla, Maere, Metspalu, Ene, Batyrov, Valery, Khomyakova, Irina, Reisberg, Tuuli, Parik, Jüri, Dzhaubermezov, Murat, Aiyzhy, Elena, Balinova, Altana, El’chinova, Galina, Spitsyna, Nailya, Khusnutdinova, Elza, Metspalu, Mait, Tambets, Kristiina, Villems, Richard, and Kushniarevich, Alena

Published
2024
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2. No Evidence from Genome-wide Data of a Khazar Origin for the Ashkenazi Jews

Author

Behar, Doron M., Metspalu, Mait, Baran, Yael, Kopelman, Naama M., Yunusbayen, Bayazit, Gladstein, Ariella, Tzur, Shay, Sahakyan, Hovhannes, Bahmanimehr, Ardeshir, Yepiskoposyan, Levon, Tambets, Kristiina, Khusnutdinova, Elza K., Kushniarevich, Alena, Balanovsky, Oleg, Balanovsky, Elena, Kovacevic, Lejla, Marjanovic, Damir, Mihailov, Evelin, Kouvatsi, Anastasia, Triantaphyllidis, Costas, King, Roy J., Semino, Ornella, Torroni, Antonio, Hammer, Michael F., Metspalu, Ene, Skorecki, Karl, Rosset, Saharon, Halperin, Eran, Villems, Richard, and Rosenberg, Noah A.

Published
2014

3. A common founder effect of the splice site variant c.-23 + 1G > A in GJB2 gene causing autosomal recessive deafness 1A (DFNB1A) in Eurasia

Author

Solovyev, Aisen V., Kushniarevich, Alena, Bliznetz, Elena, Bady-Khoo, Marita, Lalayants, Maria R., Markova, Tatiana G., Minárik, Gabriel, Kádasi, L’udevít, Metspalu, Ene, Pshennikova, Vera G., Teryutin, Fedor M., Khusnutdinova, Elza K., Poliakov, Alexander, Metspalu, Mait, Posukh, Olga L., Barashkov, Nikolay A., and Fedorova, Sardana A.

Published
2022
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4. Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders.

Author

Sasso, Stefania, Saag, Lehti, Spros, Rachèl, Beneker, Owyn, Molinaro, Ludovica, Biagini, Simone A., Lehouck, Alexander, Van De Vijver, Katrien, Ruoyun Hui, D'Atanasio, Eugenia, Kushniarevich, Alena, Kabral, Helja, Metspalu, Ene, Guellil, Meriam, Ali, Muhammad Q. A., Geypen, Jan, Hoebreckx, Maxim, Berk, Birgit, De Winter, Natasja, and Driesen, Petra

Subjects
KINSHIP, WHOLE genome sequencing, SHOTGUN sequencing, GENEALOGY, GENE frequency
Abstract

The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Genomic analyses inform on migration events during the peopling of Eurasia

Author

Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mörseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D, Cardona, Alexia, Mägi, Reedik, Sayres, Melissa A Wilson, Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L, Järve, Mari, Karmin, Monika, Jacobs, Guy S, Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C, Lambert, David M, Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D, Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, François-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P, Barashkov, Nikolay A, Škaro, Vedrana, Mulahasanovic´, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A, Lichman, Daria V, Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph TS, Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanović, Damir, Yepiskoposyan, Levon, Behar, Doron M, Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A, Osipova, Ludmila P, Lahr, Marta Mirazón, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K, Metspalu, Ene, Thomas, Mark G, Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, and Metspalu, Mait

Subjects
Human Genome, Biotechnology, Genetics, Generic health relevance, Africa, Animals, Asia, Datasets as Topic, Estonia, Europe, Fossils, Gene Flow, Genetics, Population, Genome, Human, Genomics, Heterozygote, History, Ancient, Human Migration, Humans, Native Hawaiian or Other Pacific Islander, Neanderthals, New Guinea, Population Dynamics, Racial Groups, General Science & Technology
Abstract

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

Published
2016

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

Author

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

Subjects
Quantitative Biology - Populations and Evolution
Abstract

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

Published
2013
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7. Origin and diffusion of human Y chromosome haplogroup J1-M267

Author

Sahakyan, Hovhannes, Margaryan, Ashot, Saag, Lauri, Karmin, Monika, Flores, Rodrigo, Haber, Marc, Kushniarevich, Alena, Khachatryan, Zaruhi, Bahmanimehr, Ardeshir, Parik, Jüri, Karafet, Tatiana, Yunusbayev, Bayazit, Reisberg, Tuuli, Solnik, Anu, Metspalu, Ene, Hovhannisyan, Anahit, Khusnutdinova, Elza K., Behar, Doron M., Metspalu, Mait, Yepiskoposyan, Levon, Rootsi, Siiri, and Villems, Richard

Published
2021
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9. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin, Monika, Saag, Lauri, Vicente, Mário, Sayres, Melissa A Wilson, Järve, Mari, Talas, Ulvi Gerst, Rootsi, Siiri, Ilumäe, Anne-Mai, Mägi, Reedik, Mitt, Mario, Pagani, Luca, Puurand, Tarmo, Faltyskova, Zuzana, Clemente, Florian, Cardona, Alexia, Metspalu, Ene, Sahakyan, Hovhannes, Yunusbayev, Bayazit, Hudjashov, Georgi, DeGiorgio, Michael, Loogväli, Eva-Liis, Eichstaedt, Christina, Eelmets, Mikk, Chaubey, Gyaneshwer, Tambets, Kristiina, Litvinov, Sergei, Mormina, Maru, Xue, Yali, Ayub, Qasim, Zoraqi, Grigor, Korneliussen, Thorfinn Sand, Akhatova, Farida, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Ricaut, François-Xavier, Kusuma, Pradiptajati, Razafindrazaka, Harilanto, Pierron, Denis, Cox, Murray P, Sultana, Gazi Nurun Nahar, Willerslev, Rane, Muller, Craig, Westaway, Michael, Lambert, David, Skaro, Vedrana, Kovačevic´, Lejla, Turdikulova, Shahlo, Dalimova, Dilbar, Khusainova, Rita, Trofimova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Lichman, Daria V, Isakova, Jainagul, Pocheshkhova, Elvira, Sabitov, Zhaxylyk, Barashkov, Nikolay A, Nymadawa, Pagbajabyn, Mihailov, Evelin, Seng, Joseph Wee Tien, Evseeva, Irina, Migliano, Andrea Bamberg, Abdullah, Syafiq, Andriadze, George, Primorac, Dragan, Atramentova, Lubov, Utevska, Olga, Yepiskoposyan, Levon, Marjanovic´, Damir, Kushniarevich, Alena, Behar, Doron M, Gilissen, Christian, Vissers, Lisenka, Veltman, Joris A, Balanovska, Elena, Derenko, Miroslava, Malyarchuk, Boris, Metspalu, Andres, Fedorova, Sardana, Eriksson, Anders, Manica, Andrea, Mendez, Fernando L, Karafet, Tatiana M, Veeramah, Krishna R, Bradman, Neil, Hammer, Michael F, Osipova, Ludmila P, Balanovsky, Oleg, Khusnutdinova, Elza K, Johnsen, Knut, Remm, Maido, Thomas, Mark G, Tyler-Smith, Chris, Underhill, Peter A, Willerslev, Eske, Nielsen, Rasmus, Metspalu, Mait, Villems, Richard, and Kivisild, Toomas

Subjects
Biological Sciences, Genetics, Human Genome, Base Sequence, Chromosomes, Human, Y, DNA, Mitochondrial, Evolution, Molecular, Genetic Variation, Genetics, Population, Haplotypes, Humans, Male, Models, Genetic, Phylogeny, Racial Groups, Sequence Analysis, DNA, Medical and Health Sciences, Bioinformatics
Abstract

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Published
2015

10. Y-chromosomal analysis of clan structure of Kalmyks, the only European Mongol people, and their relationship to Oirat-Mongols of Inner Asia

Author

Balinova, Natalia, Post, Helen, Kushniarevich, Alena, Flores, Rodrigo, Karmin, Monika, Sahakyan, Hovhannes, Reidla, Maere, Metspalu, Ene, Litvinov, Sergey, Dzhaubermezov, Murat, Akhmetova, Vita, Khusainova, Rita, Endicott, Phillip, Khusnutdinova, Elza, Orlova, Keemya, Bakaeva, Elza, Khomyakova, Irina, Spitsina, Nailya, Zinchenko, Rena, Villems, Richard, and Rootsi, Siiri

Published
2019
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13. Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

Author

Tambets, Kristiina, Yunusbayev, Bayazit, Hudjashov, Georgi, Ilumäe, Anne-Mai, Rootsi, Siiri, Honkola, Terhi, Vesakoski, Outi, Atkinson, Quentin, Skoglund, Pontus, Kushniarevich, Alena, Litvinov, Sergey, Reidla, Maere, Metspalu, Ene, Saag, Lehti, Rantanen, Timo, Karmin, Monika, Parik, Jüri, Zhadanov, Sergey I., Gubina, Marina, Damba, Larisa D., Bermisheva, Marina, Reisberg, Tuuli, Dibirova, Khadizhat, Evseeva, Irina, Nelis, Mari, Klovins, Janis, Metspalu, Andres, Esko, Tõnu, Balanovsky, Oleg, Balanovska, Elena, Khusnutdinova, Elza K., Osipova, Ludmila P., Voevoda, Mikhail, Villems, Richard, Kivisild, Toomas, and Metspalu, Mait

Published
2018
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14. Origin and spread of human mitochondrial DNA haplogroup U7

Author

Sahakyan, Hovhannes, Hooshiar Kashani, Baharak, Tamang, Rakesh, Kushniarevich, Alena, Francis, Amirtharaj, Costa, Marta D, Pathak, Ajai Kumar, Khachatryan, Zaruhi, Sharma, Indu, van Oven, Mannis, Parik, Jüri, Hovhannisyan, Hrant, Metspalu, Ene, Pennarun, Erwan, Karmin, Monika, Tamm, Erika, Tambets, Kristiina, Bahmanimehr, Ardeshir, Reisberg, Tuuli, Reidla, Maere, Achilli, Alessandro, Olivieri, Anna, Gandini, Francesca, Perego, Ugo A., Al-Zahery, Nadia, Houshmand, Massoud, Sanati, Mohammad Hossein, Soares, Pedro, Rai, Ekta, Šarac, Jelena, Šarić, Tena, Sharma, Varun, Pereira, Luisa, Fernandes, Veronica, Černý, Viktor, Farjadian, Shirin, Singh, Deepankar Pratap, Azakli, Hülya, Üstek, Duran, Ekomasova (Trofimova), Natalia, Kutuev, Ildus, Litvinov, Sergei, Bermisheva, Marina, Khusnutdinova, Elza K., Rai, Niraj, Singh, Manvendra, Singh, Vijay Kumar, Reddy, Alla G., Tolk, Helle-Viivi, Cvjetan, Svjetlana, Lauc, Lovorka Barac, Rudan, Pavao, Michalodimitrakis, Emmanuel N., Anagnou, Nicholas P., Pappa, Kalliopi I., Golubenko, Maria V., Orekhov, Vladimir, Borinskaya, Svetlana A, Kaldma, Katrin, Schauer, Monica A., Simionescu, Maya, Gusar, Vladislava, Grechanina, Elena, Govindaraj, Periyasamy, Voevoda, Mikhail, Damba, Larissa, Sharma, Swarkar, Singh, Lalji, Semino, Ornella, Behar, Doron M., Yepiskoposyan, Levon, Richards, Martin B., Metspalu, Mait, Kivisild, Toomas, Thangaraj, Kumarasamy, Endicott, Phillip, Chaubey, Gyaneshwer, Torroni, Antonio, and Villems, Richard

Published
2017
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15. A common founder effect of the splice site variant c.-23 + 1G > A in GJB2 gene causing autosomal recessive deafness 1A (DFNB1A) in Eurasia

Author

Solovyev, Aisen V., primary, Kushniarevich, Alena, additional, Bliznetz, Elena, additional, Bady-Khoo, Marita, additional, Lalayants, Maria R., additional, Markova, Tatiana G., additional, Minárik, Gabriel, additional, Kádasi, L’udevít, additional, Metspalu, Ene, additional, Pshennikova, Vera G., additional, Teryutin, Fedor M., additional, Khusnutdinova, Elza K., additional, Poliakov, Alexander, additional, Metspalu, Mait, additional, Posukh, Olga L., additional, Barashkov, Nikolay A., additional, and Fedorova, Sardana A., additional

Published
2021
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16. Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

Author

Pfrengle, Saskia, primary, Neukamm, Judith, additional, Guellil, Meriam, additional, Keller, Marcel, additional, Molak, Martyna, additional, Avanzi, Charlotte, additional, Kushniarevich, Alena, additional, Montes, Núria, additional, Neumann, Gunnar U., additional, Reiter, Ella, additional, Tukhbatova, Rezeda I., additional, Berezina, Nataliya Y., additional, Buzhilova, Alexandra P., additional, Korobov, Dmitry S., additional, Suppersberger Hamre, Stian, additional, Matos, Vitor M. J., additional, Ferreira, Maria T., additional, González-Garrido, Laura, additional, Wasterlain, Sofia N., additional, Lopes, Célia, additional, Santos, Ana Luisa, additional, Antunes-Ferreira, Nathalie, additional, Duarte, Vitória, additional, Silva, Ana Maria, additional, Melo, Linda, additional, Sarkic, Natasa, additional, Saag, Lehti, additional, Tambets, Kristiina, additional, Busso, Philippe, additional, Cole, Stewart T., additional, Avlasovich, Alexei, additional, Roberts, Charlotte A., additional, Sheridan, Alison, additional, Cessford, Craig, additional, Robb, John, additional, Krause, Johannes, additional, Scheib, Christiana L., additional, Inskip, Sarah A., additional, and Schuenemann, Verena J., additional

Published
2021
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17. A Common Founder Effect of the Splice Site Variant c.-23+1G>A in GJB2 Gene Causing Autosomal Recessive Deafness 1A (DFNB1A) in Eurasia

Author

Solovyev, Aisen V, primary, Kushniarevich, Alena, additional, Bliznetz, Elena, additional, Bady-Khoo, Marita, additional, Lalayants, Maria R, additional, Markova, Tatiana G, additional, Minárik, Gabriel, additional, Kádasi, L'udevít, additional, Metspalu, Ene, additional, Pshennikova, Vera G, additional, Teryutin, Fedor M, additional, Alekseev, Anatoly N, additional, Khusnutdinova, Elza K, additional, Poliakov, Alexander, additional, Мetspalu, Mait, additional, Posukh, Olga L, additional, Barashkov, Nikolay A, additional, and Fedorova, Sardana A, additional

Published
2021
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18. Additional file 1 of Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

Author

Pfrengle, Saskia, Neukamm, Judith, Guellil, Meriam, Keller, Marcel, Molak, Martyna, Avanzi, Charlotte, Kushniarevich, Alena, Montes, Núria, Neumann, Gunnar U., Reiter, Ella, Tukhbatova, Rezeda I., Berezina, Nataliya Y., Buzhilova, Alexandra P., Korobov, Dmitry S., Suppersberger Hamre, Stian, Matos, Vitor M. J., Ferreira, Maria T., González-Garrido, Laura, Wasterlain, Sofia N., Lopes, Célia, Santos, Ana Luisa, Antunes-Ferreira, Nathalie, Duarte, Vitória, Silva, Ana Maria, Melo, Linda, Sarkic, Natasa, Saag, Lehti, Tambets, Kristiina, Busso, Philippe, Cole, Stewart T., Avlasovich, Alexei, Roberts, Charlotte A., Sheridan, Alison, Cessford, Craig, Robb, John, Krause, Johannes, Scheib, Christiana L., Inskip, Sarah A., and Schuenemann, Verena J.

Abstract

Additional file 1: Supplementary Information Supplementary Note 1 Archaeological information for the sites and samples. Radiocarbon dates. Supplementary Note 2 Radiocarbon Dating Supplemetary Note 3 Applied Methods. Fig. S1. Sample Processing and Genome-wide analyses Fig. S2. Combined damage profiles. Fig. S3. Phylogenetic trees of 1-fold covered genomes. Fig. S4. Phylogenetic trees of 3-fold covered genomes. Fig. S5. Bayesian Maximum Clade Credibility time-aware tree for the leprosy genomes. Fig. S6. Date Randomization Test for the M. leprae dataset. Fig. S7. TempEst analysis for the M. leprae dataset. Table S1. Sample information. Table S2. Eager Report. Table S3. SNP subtyping. Table S6. Unique SNPs and virulence factors.

Published
2021
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19. Ancient human genomes suggest three ancestral populations for present-day Europeans

Author

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

Published
2014
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20. The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East

Author

Saag, Lehti, Laneman, Margot, Varul, Liivi, Malve, Martin, Valk, Heiki, Razzak, Maria A., Shirobokov, Ivan G., Khartanovich, Valeri I., Mikhaylova, Elena R., Kushniarevich, Alena, Scheib, Christiana Lyn, Solnik, Anu, Reisberg, Tuuli, Parik, Juri, Saag, Lauri, Metspalu, Ene, Rootsi, Siiri, Montinaro, Francesco, Remm, Maido, Magi, Reedik, D'Atanasio, Eugenia, Crema, Enrico Ryunosuke, Diez-del-Molino, David, Thomas, Mark G., Kriiska, Aivar, Kivisild, Toomas, Villems, Richard, Lang, Valter, Metspalu, Mait, Tambets, Kristiina, Saag, Lehti, Laneman, Margot, Varul, Liivi, Malve, Martin, Valk, Heiki, Razzak, Maria A., Shirobokov, Ivan G., Khartanovich, Valeri I., Mikhaylova, Elena R., Kushniarevich, Alena, Scheib, Christiana Lyn, Solnik, Anu, Reisberg, Tuuli, Parik, Juri, Saag, Lauri, Metspalu, Ene, Rootsi, Siiri, Montinaro, Francesco, Remm, Maido, Magi, Reedik, D'Atanasio, Eugenia, Crema, Enrico Ryunosuke, Diez-del-Molino, David, Thomas, Mark G., Kriiska, Aivar, Kivisild, Toomas, Villems, Richard, Lang, Valter, Metspalu, Mait, and Tambets, Kristiina

Abstract

In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200-400 BC) (EstBA) and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC-50 AD) (EstIA). We also included 5 Pre-Roman to Roman Iron Age Ingrian (500 BC450 AD) (IngIA) and 7 Middle Age Estonian (1200-1600 AD) (EstMA) individuals to build a dataset for studying the demographic history of the northern parts of the Eastern Baltic from the earliest layer of Mesolithic to modern times. Our findings are consistent with EstBA receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities and EstIA from populations related to modern Siberians. The latter inference is in accordance with Y chromosome (chrY) distributions in present day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers [1-5]. This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e., in the same time window as the diversification of west Uralic (Finnic) languages [6]. Furthermore, phenotypic traits often associated with modern Northern Europeans, like light eyes, hair, and skin, as well as lactose tolerance, can be traced back to the Bronze Age in the Eastern Baltic.

Published
2019
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21. Additional file 2: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

Author

Tambets, Kristiina, Bayazit Yunusbayev, Hudjashov, Georgi, Anne-Mai IlumäE, Rootsi, Siiri, Honkola, Terhi, Vesakoski, Outi, Atkinson, Quentin, Skoglund, Pontus, Kushniarevich, Alena, Litvinov, Sergey, Maere Reidla, Metspalu, Ene, Saag, Lehti, Rantanen, Timo, Karmin, Monika, Jßri Parik, Zhadanov, Sergey, Gubina, Marina, Damba, Larisa, Bermisheva, Marina, Reisberg, Tuuli, Khadizhat Dibirova, Evseeva, Irina, Nelis, Mari, Klovins, Janis, Metspalu, Andres, Tþnu Esko, Balanovsky, Oleg, Balanovska, Elena, Khusnutdinova, Elza, Osipova, Ludmila, Voevoda, Mikhail, Villems, Richard, Kivisild, Toomas, and Metspalu, Mait

Abstract

Table S2. Ethnolinguistic characteristics of studied Uralic populations. (PDF 15 kb)

Published
2018
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22. Additional file 3: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

Author

Tambets, Kristiina, Bayazit Yunusbayev, Hudjashov, Georgi, Anne-Mai IlumäE, Rootsi, Siiri, Honkola, Terhi, Vesakoski, Outi, Atkinson, Quentin, Skoglund, Pontus, Kushniarevich, Alena, Litvinov, Sergey, Maere Reidla, Metspalu, Ene, Saag, Lehti, Rantanen, Timo, Karmin, Monika, Jßri Parik, Zhadanov, Sergey, Gubina, Marina, Damba, Larisa, Bermisheva, Marina, Reisberg, Tuuli, Khadizhat Dibirova, Evseeva, Irina, Nelis, Mari, Klovins, Janis, Metspalu, Andres, Tþnu Esko, Balanovsky, Oleg, Balanovska, Elena, Khusnutdinova, Elza, Osipova, Ludmila, Voevoda, Mikhail, Villems, Richard, Kivisild, Toomas, and Metspalu, Mait

Abstract

Figure S1. Principal component analysis of the studied Uralic-speaking populations in Eurasian context. Figure S2. FST distances of the studied Uralic-speaking populations in the global context. Figure S3. ADMIXTURE analysis. Figure S4. D-statistics. Figure S5. fineSTRUCTURE tree. Figure S6. fineSTRUCTURE heatmap. Figure S7. Admixture dates of ALDER. Figure S8. Outgroup f3 test between modern and ancient samples. Figure S9. Outgroup f3 results plotted pairwise against each other. Figure S10. Admixture graphs. Figure S11. Phylogenetic network of Y chromosome hg Q. Figure S12. Trees constructed from linguistic and genetic data of Uralic peoples. Figure S13. Comparison of autosomal and X chromosomal outgroup f3 statistics for Estonians, Udmurts and Khanty. (PDF 11550 kb)

Published
2018
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23. Additional file 12: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

Author

Tambets, Kristiina, Bayazit Yunusbayev, Hudjashov, Georgi, Anne-Mai IlumäE, Rootsi, Siiri, Honkola, Terhi, Vesakoski, Outi, Atkinson, Quentin, Skoglund, Pontus, Kushniarevich, Alena, Litvinov, Sergey, Maere Reidla, Metspalu, Ene, Saag, Lehti, Rantanen, Timo, Karmin, Monika, Jßri Parik, Zhadanov, Sergey, Gubina, Marina, Damba, Larisa, Bermisheva, Marina, Reisberg, Tuuli, Khadizhat Dibirova, Evseeva, Irina, Nelis, Mari, Klovins, Janis, Metspalu, Andres, Tþnu Esko, Balanovsky, Oleg, Balanovska, Elena, Khusnutdinova, Elza, Osipova, Ludmila, Voevoda, Mikhail, Villems, Richard, Kivisild, Toomas, and Metspalu, Mait

Abstract

Table S11. Details of Globetrotter regional analysis. (PDF 50 kb)

Published
2018
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25. Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance

Author

Järve, Mari, primary, Saag, Lehti, additional, Scheib, Christiana Lyn, additional, Pathak, Ajai K., additional, Montinaro, Francesco, additional, Pagani, Luca, additional, Flores, Rodrigo, additional, Guellil, Meriam, additional, Saag, Lauri, additional, Tambets, Kristiina, additional, Kushniarevich, Alena, additional, Solnik, Anu, additional, Varul, Liivi, additional, Zadnikov, Stanislav, additional, Petrauskas, Oleg, additional, Avramenko, Maryana, additional, Magomedov, Boris, additional, Didenko, Serghii, additional, Toshev, Gennadi, additional, Bruyako, Igor, additional, Grechko, Denys, additional, Okatenko, Vitalii, additional, Gorbenko, Kyrylo, additional, Smyrnov, Oleksandr, additional, Heiko, Anatolii, additional, Reida, Roman, additional, Sapiehin, Serheii, additional, Sirotin, Sergey, additional, Tairov, Aleksandr, additional, Beisenov, Arman, additional, Starodubtsev, Maksim, additional, Vasilev, Vitali, additional, Nechvaloda, Alexei, additional, Atabiev, Biyaslan, additional, Litvinov, Sergey, additional, Ekomasova, Natalia, additional, Dzhaubermezov, Murat, additional, Voroniatov, Sergey, additional, Utevska, Olga, additional, Shramko, Irina, additional, Khusnutdinova, Elza, additional, Metspalu, Mait, additional, Savelev, Nikita, additional, Kriiska, Aivar, additional, Kivisild, Toomas, additional, and Villems, Richard, additional

Published
2019
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26. The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East

Author

Saag, Lehti, primary, Laneman, Margot, additional, Varul, Liivi, additional, Malve, Martin, additional, Valk, Heiki, additional, Razzak, Maria A., additional, Shirobokov, Ivan G., additional, Khartanovich, Valeri I., additional, Mikhaylova, Elena R., additional, Kushniarevich, Alena, additional, Scheib, Christiana Lyn, additional, Solnik, Anu, additional, Reisberg, Tuuli, additional, Parik, Jüri, additional, Saag, Lauri, additional, Metspalu, Ene, additional, Rootsi, Siiri, additional, Montinaro, Francesco, additional, Remm, Maido, additional, Mägi, Reedik, additional, D’Atanasio, Eugenia, additional, Crema, Enrico Ryunosuke, additional, Díez-del-Molino, David, additional, Thomas, Mark G., additional, Kriiska, Aivar, additional, Kivisild, Toomas, additional, Villems, Richard, additional, Lang, Valter, additional, Metspalu, Mait, additional, and Tambets, Kristiina, additional

Published
2019
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27. The Genetic Ancestry of Modern Indus Valley Populations from Northwest India

Author

Pathak, Ajai K., primary, Kadian, Anurag, additional, Kushniarevich, Alena, additional, Montinaro, Francesco, additional, Mondal, Mayukh, additional, Ongaro, Linda, additional, Singh, Manvendra, additional, Kumar, Pramod, additional, Rai, Niraj, additional, Parik, Jüri, additional, Metspalu, Ene, additional, Rootsi, Siiri, additional, Pagani, Luca, additional, Kivisild, Toomas, additional, Metspalu, Mait, additional, Chaubey, Gyaneshwer, additional, and Villems, Richard, additional

Published
2018
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28. The genetic variation in the R1a clade among the Ashkenazi Levites’ Y chromosome

Author

Behar, Doron M., primary, Saag, Lauri, additional, Karmin, Monika, additional, Gover, Meir G., additional, Wexler, Jeffrey D., additional, Sanchez, Luisa Fernanda, additional, Greenspan, Elliott, additional, Kushniarevich, Alena, additional, Davydenko, Oleg, additional, Sahakyan, Hovhannes, additional, Yepiskoposyan, Levon, additional, Boattini, Alessio, additional, Sarno, Stefania, additional, Pagani, Luca, additional, Carmi, Shai, additional, Tzur, Shay, additional, Metspalu, Ene, additional, Bormans, Concetta, additional, Skorecki, Karl, additional, Metspalu, Mait, additional, Rootsi, Siiri, additional, and Villems, Richard, additional

Published
2017
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29. East Eurasian ancestry in the middle of Europe: genetic footprints of Steppe nomads in the genomes of Belarusian Lipka Tatars

Author

Pankratov, Vasili, primary, Litvinov, Sergei, additional, Kassian, Alexei, additional, Shulhin, Dzmitry, additional, Tchebotarev, Lieve, additional, Yunusbayev, Bayazit, additional, Möls, Märt, additional, Sahakyan, Hovhannes, additional, Yepiskoposyan, Levon, additional, Rootsi, Siiri, additional, Metspalu, Ene, additional, Golubenko, Maria, additional, Ekomasova, Natalia, additional, Akhatova, Farida, additional, Khusnutdinova, Elza, additional, Heyer, Evelyne, additional, Endicott, Phillip, additional, Derenko, Miroslava, additional, Malyarchuk, Boris, additional, Metspalu, Mait, additional, Davydenko, Oleg, additional, Villems, Richard, additional, and Kushniarevich, Alena, additional

Published
2016
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30. Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families

Author

Ilumäe, Anne-Mai, primary, Reidla, Maere, additional, Chukhryaeva, Marina, additional, Järve, Mari, additional, Post, Helen, additional, Karmin, Monika, additional, Saag, Lauri, additional, Agdzhoyan, Anastasiya, additional, Kushniarevich, Alena, additional, Litvinov, Sergey, additional, Ekomasova, Natalya, additional, Tambets, Kristiina, additional, Metspalu, Ene, additional, Khusainova, Rita, additional, Yunusbayev, Bayazit, additional, Khusnutdinova, Elza K., additional, Osipova, Ludmila P., additional, Fedorova, Sardana, additional, Utevska, Olga, additional, Koshel, Sergey, additional, Balanovska, Elena, additional, Behar, Doron M., additional, Balanovsky, Oleg, additional, Kivisild, Toomas, additional, Underhill, Peter A., additional, Villems, Richard, additional, and Rootsi, Siiri, additional

Published
2016
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31. Ancient DNA Reveals Matrilineal Continuity in Present-Day Poland over the Last Two Millennia

Author

Juras, Anna, Dabert, Miroslawa, Kushniarevich, Alena, Malmström, Helena Jankovic, Raghavan, Maanasa, Kosicki, Jakub Z., Metspalu, Ene, Willerslev, Eske, Piontek, Janusz, Juras, Anna, Dabert, Miroslawa, Kushniarevich, Alena, Malmström, Helena Jankovic, Raghavan, Maanasa, Kosicki, Jakub Z., Metspalu, Ene, Willerslev, Eske, and Piontek, Janusz

Abstract

While numerous ancient human DNA datasets from across Europe have been published till date, modern-day Poland in particular, remains uninvestigated. Besides application in the reconstruction of continent-wide human history, data from this region would also contribute towards our understanding of the history of the Slavs, whose origin is hypothesized to be in East or Central Europe. Here, we present the first population-scale ancient human DNA study from the region of modern-day Poland by establishing mitochondrial DNA profiles for 23 samples dated to 200 BC - 500 AD (Roman Iron Age) and for 20 samples dated to 1000-1400 AD (Medieval Age). Our results show that mitochondrial DNA sequences from both periods belong to haplogroups that are characteristic of contemporary West Eurasia. Haplotype sharing analysis indicates that majority of the ancient haplotypes are widespread in some modern Europeans, including Poles. Notably, the Roman Iron Age samples share more rare haplotypes with Central and Northeast Europeans, whereas the Medieval Age samples share more rare haplotypes with East-Central and South-East Europeans, primarily Slavic populations. Our data demonstrates genetic continuity of certain matrilineages (H5a1 and N1a1a2) in the area of present-day Poland from at least the Roman Iron Age until present. As such, the maternal gene pool of present-day Poles, Czechs and Slovaks, categorized as Western Slavs, is likely to have descended from inhabitants of East-Central Europe during the Roman Iron Age.

Published
2014
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32. Standing at the Gateway to Europe - The Genetic Structure of Western Balkan Populations Based on Autosomal and Haploid Markers

Author

Kovacevic, Lejla, Tambets, Kristiina, Ilumaee, Anne-Mai, Kushniarevich, Alena, Yunusbayev, Bayazit, Solnik, Anu, Bego, Tamer, Primorac, Dragan, Skaro, Vedrana, Leskovac, Andreja, Jakovski, Zlatko, Drobnic, Katja, Tolk, Helle-Viivi, Kovacevic, Sandra, Rudan, Pavao, Metspalu, Ene, Marjanović, Damir, Kovacevic, Lejla, Tambets, Kristiina, Ilumaee, Anne-Mai, Kushniarevich, Alena, Yunusbayev, Bayazit, Solnik, Anu, Bego, Tamer, Primorac, Dragan, Skaro, Vedrana, Leskovac, Andreja, Jakovski, Zlatko, Drobnic, Katja, Tolk, Helle-Viivi, Kovacevic, Sandra, Rudan, Pavao, Metspalu, Ene, and Marjanović, Damir

Abstract

Contemporary inhabitants of the Balkan Peninsula belong to several ethnic groups of diverse cultural background. In this study, three ethnic groups from Bosnia and Herzegovina - Bosniacs, Bosnian Croats and Bosnian Serbs - as well as the populations of Serbians, Croatians, Macedonians from the former Yugoslav Republic of Macedonia, Montenegrins and Kosovars have been characterized for the genetic variation of 660 000 genome-wide autosomal single nucleotide polymorphisms and for haploid markers. New autosomal data of the 70 individuals together with previously published data of 20 individuals from the populations of the Western Balkan region in a context of 695 samples of global range have been analysed. Comparison of the variation data of autosomal and haploid lineages of the studied Western Balkan populations reveals a concordance of the data in both sets and the genetic uniformity of the studied populations, especially of Western South-Slavic speakers. The genetic variation of Western Balkan populations reveals the continuity between the Middle East and Europe via the Balkan region and supports the scenario that one of the major routes of ancient gene flows and admixture went through the Balkan Peninsula.

Published
2014

34. Standing at the Gateway to Europe - The Genetic Structure of Western Balkan Populations Based on Autosomal and Haploid Markers

Author

Kovacevic, Lejla, primary, Tambets, Kristiina, additional, Ilumäe, Anne-Mai, additional, Kushniarevich, Alena, additional, Yunusbayev, Bayazit, additional, Solnik, Anu, additional, Bego, Tamer, additional, Primorac, Dragan, additional, Skaro, Vedrana, additional, Leskovac, Andreja, additional, Jakovski, Zlatko, additional, Drobnic, Katja, additional, Tolk, Helle-Viivi, additional, Kovacevic, Sandra, additional, Rudan, Pavao, additional, Metspalu, Ene, additional, and Marjanovic, Damir, additional

Published
2014
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35. The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Author

Underhill, Peter A, primary, Poznik, G David, additional, Rootsi, Siiri, additional, Järve, Mari, additional, Lin, Alice A, additional, Wang, Jianbin, additional, Passarelli, Ben, additional, Kanbar, Jad, additional, Myres, Natalie M, additional, King, Roy J, additional, Di Cristofaro, Julie, additional, Sahakyan, Hovhannes, additional, Behar, Doron M, additional, Kushniarevich, Alena, additional, Šarac, Jelena, additional, Šaric, Tena, additional, Rudan, Pavao, additional, Pathak, Ajai Kumar, additional, Chaubey, Gyaneshwer, additional, Grugni, Viola, additional, Semino, Ornella, additional, Yepiskoposyan, Levon, additional, Bahmanimehr, Ardeshir, additional, Farjadian, Shirin, additional, Balanovsky, Oleg, additional, Khusnutdinova, Elza K, additional, Herrera, Rene J, additional, Chiaroni, Jacques, additional, Bustamante, Carlos D, additional, Quake, Stephen R, additional, Kivisild, Toomas, additional, and Villems, Richard, additional

Published
2014
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36. Unravelling the distinct strains of Tharu ancestry

Author

Chaubey, Gyaneshwer, primary, Singh, Manvendra, additional, Crivellaro, Federica, additional, Tamang, Rakesh, additional, Nandan, Amrita, additional, Singh, Kamayani, additional, Sharma, Varun Kumar, additional, Pathak, Ajai Kumar, additional, Shah, Anish M, additional, Sharma, Vishwas, additional, Singh, Vipin Kumar, additional, Selvi Rani, Deepa, additional, Rai, Niraj, additional, Kushniarevich, Alena, additional, Ilumäe, Anne-Mai, additional, Karmin, Monika, additional, Phillip, Anand, additional, Verma, Abhilasha, additional, Prank, Erik, additional, Singh, Vijay Kumar, additional, Li, Blaise, additional, Govindaraj, Periyasamy, additional, Chaubey, Akhilesh Kumar, additional, Dubey, Pavan Kumar, additional, Reddy, Alla G, additional, Premkumar, Kumpati, additional, Vishnupriya, Satti, additional, Pande, Veena, additional, Parik, Jüri, additional, Rootsi, Siiri, additional, Endicott, Phillip, additional, Metspalu, Mait, additional, Lahr, Marta Mirazon, additional, van Driem, George, additional, Villems, Richard, additional, Kivisild, Toomas, additional, Singh, Lalji, additional, and Thangaraj, Kumarasamy, additional

Published
2014
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37. Ancient human genomes suggest three ancestral populations for present-day Europeans

Author

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

Published
2013
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38. No Evidence from Genome-Wide Data of a Khazar Origin for the Ashkenazi Jews

Author

Behar, Doron M., primary, Metspalu, Mait, additional, Baran, Yael, additional, Kopelman, Naama M., additional, Yunusbayev, Bayazit, additional, Gladstein, Ariella, additional, Tzur, Shay, additional, Sahakyan, Hovhannes, additional, Bahmanimehr, Ardeshir, additional, Yepiskoposyan, Levon, additional, Tambets, Kristiina, additional, Khusnutdinova, Elza K., additional, Kushniarevich, Alena, additional, Balanovsky, Oleg, additional, Balanovsky, Elena, additional, Kovacevic, Lejla, additional, Marjanovic, Damir, additional, Mihailov, Evelin, additional, Kouvatsi, Anastasia, additional, Triantaphyllidis, Costas, additional, King, Roy J., additional, Semino, Ornella, additional, Torroni, Antonio, additional, Hammer, Michael F., additional, Metspalu, Ene, additional, Skorecki, Karl, additional, Rosset, Saharon, additional, Halperin, Eran, additional, Villems, Richard, additional, and Rosenberg, Noah A., additional

Published
2013
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39. Uniparental Genetic Heritage of Belarusians: Encounter of Rare Middle Eastern Matrilineages with a Central European Mitochondrial DNA Pool

Author

Kushniarevich, Alena, primary, Sivitskaya, Larysa, additional, Danilenko, Nina, additional, Novogrodskii, Tadeush, additional, Tsybovsky, Iosif, additional, Kiseleva, Anna, additional, Kotova, Svetlana, additional, Chaubey, Gyaneshwer, additional, Metspalu, Ene, additional, Sahakyan, Hovhannes, additional, Bahmanimehr, Ardeshir, additional, Reidla, Maere, additional, Rootsi, Siiri, additional, Parik, Jüri, additional, Reisberg, Tuuli, additional, Achilli, Alessandro, additional, Hooshiar Kashani, Baharak, additional, Gandini, Francesca, additional, Olivieri, Anna, additional, Behar, Doron M., additional, Torroni, Antonio, additional, Davydenko, Oleg, additional, and Villems, Richard, additional

Published
2013
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40. Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus

Author

Rootsi, Siiri, primary, Myres, Natalie M, additional, Lin, Alice A, additional, Järve, Mari, additional, King, Roy J, additional, Kutuev, Ildus, additional, Cabrera, Vicente M, additional, Khusnutdinova, Elza K, additional, Varendi, Kärt, additional, Sahakyan, Hovhannes, additional, Behar, Doron M, additional, Khusainova, Rita, additional, Balanovsky, Oleg, additional, Balanovska, Elena, additional, Rudan, Pavao, additional, Yepiskoposyan, Levon, additional, Bahmanimehr, Ardeshir, additional, Farjadian, Shirin, additional, Kushniarevich, Alena, additional, Herrera, Rene J, additional, Grugni, Viola, additional, Battaglia, Vincenza, additional, Nici, Carmela, additional, Crobu, Francesca, additional, Karachanak, Sena, additional, Kashani, Baharak Hooshiar, additional, Houshmand, Massoud, additional, Sanati, Mohammad H, additional, Toncheva, Draga, additional, Lisa, Antonella, additional, Semino, Ornella, additional, Chiaroni, Jacques, additional, Cristofaro, Julie Di, additional, Villems, Richard, additional, Kivisild, Toomas, additional, and Underhill, Peter A, additional

Published
2012
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42. Genetic Heritage of the Balto-Slavic Speaking Populations: A Synthesis of Autosomal, Mitochondrial and Y-Chromosomal Data.

Author

Kushniarevich, Alena, Utevska, Olga, Chuhryaeva, Marina, Agdzhoyan, Anastasia, Dibirova, Khadizhat, Uktveryte, Ingrida, Möls, Märt, Mulahasanovic, Lejla, Pshenichnov, Andrey, Frolova, Svetlana, Shanko, Andrey, Metspalu, Ene, Reidla, Maere, Tambets, Kristiina, Tamm, Erika, Koshel, Sergey, Zaporozhchenko, Valery, Atramentova, Lubov, Kučinskas, Vaidutis, and Davydenko, Oleg

Subjects
*BALTIC languages, *SLAVIC languages, *ELOCUTION, *LOCUS (Genetics), *MITOCHONDRIAL DNA, *AFFILIATION (Psychology)
Abstract

The Slavic branch of the Balto-Slavic sub-family of Indo-European languages underwent rapid divergence as a result of the spatial expansion of its speakers from Central-East Europe, in early medieval times. This expansion–mainly to East Europe and the northern Balkans–resulted in the incorporation of genetic components from numerous autochthonous populations into the Slavic gene pools. Here, we characterize genetic variation in all extant ethnic groups speaking Balto-Slavic languages by analyzing mitochondrial DNA (n = 6,876), Y-chromosomes (n = 6,079) and genome-wide SNP profiles (n = 296), within the context of other European populations. We also reassess the phylogeny of Slavic languages within the Balto-Slavic branch of Indo-European. We find that genetic distances among Balto-Slavic populations, based on autosomal and Y-chromosomal loci, show a high correlation (0.9) both with each other and with geography, but a slightly lower correlation (0.7) with mitochondrial DNA and linguistic affiliation. The data suggest that genetic diversity of the present-day Slavs was predominantly shaped in situ, and we detect two different substrata: ‘central-east European’ for West and East Slavs, and ‘south-east European’ for South Slavs. A pattern of distribution of segments identical by descent between groups of East-West and South Slavs suggests shared ancestry or a modest gene flow between those two groups, which might derive from the historic spread of Slavic people. [ABSTRACT FROM AUTHOR]

Published
2015
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43. The phylogenetic and geographic structure of Y-chromosome haplogroup R1a.

Author

Underhill, Peter A, Poznik, G David, Rootsi, Siiri, Järve, Mari, Lin, Alice A, Wang, Jianbin, Passarelli, Ben, Kanbar, Jad, Myres, Natalie M, King, Roy J, Di Cristofaro, Julie, Sahakyan, Hovhannes, Behar, Doron M, Kushniarevich, Alena, Šarac, Jelena, Šaric, Tena, Rudan, Pavao, Pathak, Ajai Kumar, Chaubey, Gyaneshwer, and Grugni, Viola

Subjects
Y chromosome, SEX chromosomes, GENETICS, PHYLOGENY, CELL nuclei
Abstract

R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ∼25 000 (95% CI: 21 300-29 000) years ago and a coalescence time within R1a-M417 of ∼5800 (95% CI: 4800-6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran. [ABSTRACT FROM AUTHOR]

Published
2015
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44. Genomic analyses inform on migration events during the peopling of Eurasia

Author

Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mörseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D, Cardona, Alexia, Mägi, Reedik, Wilson Sayres, Melissa A, Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L, Järve, Mari, Karmin, Monika, Jacobs, Guy S, Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C, Lambert, David M, Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D, Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, François-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P, Barashkov, Nikolay A, Skaro, Vedrana, Mulahasanovic, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A, Lichman, Daria V, Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph TS, Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanović, Damir, Yepiskoposyan, Levon, Behar, Doron M, Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A, Osipova, Ludmila P, Lahr, Marta Mirazón, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K, Metspalu, Ene, Thomas, Mark G, Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, and Metspalu, Mait

Subjects
Estonia, Gene Flow, Heterozygote, New Guinea, Asia, Continental Population Groups, Fossils, Genome, Human, Human Migration, Population Dynamics, Datasets as Topic, Genomics, 3. Good health, Europe, Oceanic Ancestry Group, Genetics, Population, Africa, Animals, Humans, History, Ancient, Neanderthals
Abstract

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago., Support was provided by: Estonian Research Infrastructure Roadmap grant no 3.2.0304.11-0312; Australian Research Council Discovery grants (DP110102635 and DP140101405) (D.M.L., M.W. and E.W.); Danish National Research Foundation; the Lundbeck Foundation and KU2016 (E.W.); ERC Starting Investigator grant (FP7 - 261213) (T.K.); Estonian Research Council grant PUT766 (G.C. and M.K.); EU European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre (R.V.; M.Me. and A.Me.), and Centre of Excellence for Genomics and Translational Medicine Project No. 2014-2020.4.01.15-0012 to EGC of UT (A.Me.) and EBC (M.Me.); Estonian Institutional Research grant IUT24-1 (L.S., M.J., A.K., B.Y., K.T., C.B.M., Le.S., H.Sa., S.L., D.M.B., E.M., R.V., G.H., M.K., G.C., T.K. and M.Me.) and IUT20-60 (A.Me.); French Ministry of Foreign and European Affairs and French ANR grant number ANR-14-CE31-0013-01 (F.-X.R.); Gates Cambridge Trust Funding (E.J.); ICG SB RAS (No. VI.58.1.1) (D.V.L.); Leverhulme Programme grant no. RP2011-R-045 (A.B.M., P.G. and M.G.T.); Ministry of Education and Science of Russia; Project 6.656.2014/K (S.A.F.); NEFREX grant funded by the European Union (People Marie Curie Actions; International Research Staff Exchange Scheme; call FP7-PEOPLE-2012-IRSES-number 318979) (M.Me., G.H. and M.K.); NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01 (S.Tis.); Russian Foundation for Basic Research (grant N 14-06-00180a) (M.G.); Russian Foundation for Basic Research; grant 16-04-00890 (O.B. and E.B); Russian Science Foundation grant 14-14-00827 (O.B.); The Russian Foundation for Basic Research (14-04-00725-a), The Russian Humanitarian Scientific Foundation (13-11-02014) and the Program of the Basic Research of the RAS Presidium “Biological diversity” (E.K.K.); Wellcome Trust and Royal Society grant WT104125AIA & the Bristol Advanced Computing Research Centre (http://www.bris.ac.uk/acrc/) (D.J.L.); Wellcome Trust grant 098051 (Q.A.; C.T.-S. and Y.X.); Wellcome Trust Senior Research Fellowship grant 100719/Z/12/Z (M.G.T.); Young Explorers Grant from the National Geographic Society (8900-11) (C.A.E.); ERC Consolidator Grant 647787 ‘LocalAdaptatio’ (A.Ma.); Program of the RAS Presidium “Basic research for the development of the Russian Arctic” (B.M.); Russian Foundation for Basic Research grant 16-06-00303 (E.B.); a Rutherford Fellowship (RDF-10-MAU-001) from the Royal Society of New Zealand (M.P.C.).

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

Author

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

Subjects
410 Linguistics, 3. Good health

46. Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

Author

Pfrengle, Saskia, Neukamm, Judith, Guellil, Meriam, Keller, Marcel, Molak, Martyna, Avanzi, Charlotte, Kushniarevich, Alena, Montes, N��ria, Neumann, Gunnar U, Reiter, Ella, Tukhbatova, Rezeda I, Berezina, Nataliya Y, Buzhilova, Alexandra P, Korobov, Dmitry S, Suppersberger Hamre, Stian, Matos, Vitor M J, Ferreira, Maria T, Gonz��lez-Garrido, Laura, Wasterlain, Sofia N, Lopes, C��lia, Santos, Ana Luisa, Antunes-Ferreira, Nathalie, Duarte, Vit��ria, Silva, Ana Maria, Melo, Linda, Sarkic, Natasa, Saag, Lehti, Tambets, Kristiina, Busso, Philippe, Cole, Stewart T, Avlasovich, Alexei, Roberts, Charlotte A, Sheridan, Alison, Cessford, Craig, Robb, John, Krause, Johannes, Scheib, Christiana L, Inskip, Sarah A, and Schuenemann, Verena J

Subjects
Ancient DNA, Paleopathology, Pathogen Population Dynamics, Paleomicrobiology, Pathogen Diversity, Computer Science::Digital Libraries, Mycobacterium Leprae, Computer Science::Computers and Society, Ancient Pathogen Genomics, Leprosaria, 3. Good health
Abstract

Funder: Max-Planck Society, Funder: St John���s College, Cambridge, Funder: Fondation Raoul Follereau, Funder: University of Zurich���s University Research Priority Program ���Evolution in Action: From Genomes to Ecosystems���, Funder: the Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP) at the University of T��bingen, BackgroundHansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period.ResultsHere, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria.ConclusionsOur findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.

47. Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

Author

Pfrengle, Saskia, Neukamm, Judith, Guellil, Meriam, Keller, Marcel, Molak, Martyna, Avanzi, Charlotte, Kushniarevich, Alena, Montes, Núria, Neumann, Gunnar U, Reiter, Ella, Tukhbatova, Rezeda I, Berezina, Nataliya Y, Buzhilova, Alexandra P, Korobov, Dmitry S, Suppersberger Hamre, Stian, Matos, Vitor MJ, Ferreira, Maria T, González-Garrido, Laura, Wasterlain, Sofia N, Lopes, Célia, Santos, Ana Luisa, Antunes-Ferreira, Nathalie, Duarte, Vitória, Silva, Ana Maria, Melo, Linda, Sarkic, Natasa, Saag, Lehti, Tambets, Kristiina, Busso, Philippe, Cole, Stewart T, Avlasovich, Alexei, Roberts, Charlotte A, Sheridan, Alison, Cessford, Craig, Robb, John, Krause, Johannes, Scheib, Christiana L, Inskip, Sarah A, and Schuenemann, Verena J

Subjects
Ancient DNA, Paleopathology, Pathogen population dynamics, Population Dynamics, Paleomicrobiology, Pathogen diversity, Leprosaria, 3. Good health, Ancient pathogen genomics, Mycobacterium leprae, Europe, Leprosy, Humans, Genome, Bacterial
Abstract

BACKGROUND: Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period. RESULTS: Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria. CONCLUSIONS: Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.

48. Vanas DNAs leiduva saastuse tuvastamine vanade ja kaasaegsete mitogenoomide võrdlusanalüüsi abil

Author

Maloverjan, Maria, Tambets, Kristiina, juhendaja, Kushniarevich, Alena, juhendaja, Tartu Ülikool. Loodus- ja täppisteaduste valdkond, and Tartu Ülikool. Molekulaar- ja rakubioloogia instituut

Subjects
bakalaureusetööd, mtDNA, saastus, geneetiline võrdlusanalüüs, vana DNA
Abstract

Vana DNA (ancient DNA, aDNA) on surnud organismide kudedest eraldatud geneetiline materjal. Vana DNA järjestustest saadakse vahetut informatsiooni paljude kunagi elanud liikide geneetilise mitmekesisuse kohta, eriti palju teaduslikke töid on seotud inimese ja tema eellaste uurimisega. Üks DNA omadusi on selle ebastabiilsus: aja jooksul suurenevad selle lagunemisaste ja keemilise modifitseerituse määr. Need protsessid raskendavad vana DNA analüüsi efektiivsust võrreldes kaasaegse DNAga. Arheoloogiliste proovide saastumine kaasaegse geneetilise materjaliga on olnud suureks probleemiks kogu vana DNA uurimisajaloo vältel. Käesoleva töö eesmärgiks on DNA eraldamine Tartu Ülikooli arheoloogide bioloogilisest materjalist, arheoloogide mitokondriaalse DNA (mtDNA) fülogeneetiline analüüs ning kaasaegsete ja vanade mtDNA järjestuste võrdlusanalüüs kompleksse saastuse tuvastamise protseduuri osana.

Published
2018

49. The genetic variation in the R1a clade among the Ashkenazi Levites' y chromosome

Author

Monika Karmin, Lauri Saag, Elliott Greenspan, Meir G. Gover, Luisa Fernanda Sanchez, Jeffrey D. Wexler, Luca Pagani, O. G. Davydenko, Levon Yepiskoposyan, Shay Tzur, Concetta Bormans, Stefania Sarno, Alena Kushniarevich, Richard Villems, Hovhannes Sahakyan, Ene Metspalu, Siiri Rootsi, Shai Carmi, Karl Skorecki, Doron M. Behar, Alessio Boattini, Mait Metspalu, Behar, Doron M., Saag, Lauri, Karmin, Monika, Gover, Meir G., Wexler, Jeffrey D., Sanchez, Luisa Fernanda, Greenspan, Elliott, Kushniarevich, Alena, Davydenko, Oleg, Sahakyan, Hovhanne, Yepiskoposyan, Levon, Boattini, Alessio, Sarno, Stefania, Pagani, Luca, Carmi, Shai, Tzur, Shay, Metspalu, Ene, Bormans, Concetta, Skorecki, Karl, Metspalu, Mait, Rootsi, Siiri, and Villems, Richard

Subjects
0301 basic medicine, Male, congenital, hereditary, and neonatal diseases and abnormalities, endocrine system diseases, lcsh:Medicine, Biology, Y chromosome, Haplogroup, Article, Lineage (anthropology), Evolution, Molecular, 03 medical and health sciences, Gene Frequency, Genetic variation, Humans, Clade, lcsh:Science, skin and connective tissue diseases, Allele frequency, Phylogeny, Ancestor, Genetics, Chromosomes, Human, Y, Multidisciplinary, Haplotype, lcsh:R, Genetic Variation, nutritional and metabolic diseases, 030104 developmental biology, Haplotypes, Evolutionary biology, Jews, lcsh:Q
Abstract

Approximately 300,000 men around the globe self-identify as Ashkenazi Levites, of whom two thirds were previously shown to descend from a single male. The paucity of whole Y-chromosome sequences precluded conclusive identification of this ancestor’s age, geographic origin and migration patterns. Here, we report the variation of 486 Y-chromosomes within the Ashkenazi and non-Ashkenazi Levite R1a clade, other Ashkenazi Jewish paternal lineages, as well as non-Levite Jewish and non-Jewish R1a samples. Cumulatively, the emerging profile is of a Middle Eastern ancestor, self-affiliating as Levite, and carrying the highly resolved R1a-Y2619 lineage, which was likely a minor haplogroup among the Hebrews. A star-like phylogeny, coalescing similarly to other Ashkenazi paternal lineages, ~1,743 ybp, suggests it to be one of the Ashkenazi paternal founders; to have expanded as part of the overall Ashkenazi demographic expansion, without special relation to the Levite affiliation; and to have subsequently spread to non-Ashkenazi Levites.

Published
2017

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