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2. Participant Recruitment, Consent and Post-trial Access to Interventions

Author

Mormina, Maru, Suwalowska, Halina, Schneiders, Mira L., Selgelid, Michael J., Series Editor, Bull, Susan, editor, Parker, Michael, editor, Ali, Joseph, editor, Jonas, Monique, editor, Muthuswamy, Vasantha, editor, Saenz, Carla, editor, Smith, Maxwell J., editor, Voo, Teck Chuan, editor, Wright, Katharine, editor, and de Vries, Jantina, editor

Published
2024
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6. 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

7. 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

13. Resolving the ancestry of Austronesian-speaking populations

Author

Soares, Pedro A., Trejaut, Jean A., Rito, Teresa, Cavadas, Bruno, Hill, Catherine, Eng, Ken Khong, Mormina, Maru, Brandão, Andreia, Fraser, Ross M., Wang, Tse-Yi, Loo, Jun-Hun, Snell, Christopher, Ko, Tsang-Ming, Amorim, António, Pala, Maria, Macaulay, Vincent, Bulbeck, David, Wilson, James F., Gusmão, Leonor, Pereira, Luísa, Oppenheimer, Stephen, Lin, Marie, and Richards, Martin B.

Published
2016
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14. Mosaic maternal ancestry in the Great Lakes region of East Africa

Author

Gomes, Verónica, Pala, Maria, Salas, Antonio, Álvarez-Iglesias, Vanesa, Amorim, António, Gómez-Carballa, Alberto, Carracedo, Ángel, Clarke, Douglas J., Hill, Catherine, Mormina, Maru, Shaw, Marie-Anne, Dunne, David W., Pereira, Rui, Pereira, Vânia, Prata, Maria João, Sánchez-Diz, Paula, Rito, Teresa, Soares, Pedro, Gusmão, Leonor, and Richards, Martin B.

Published
2015
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20. A mitochondrial stratigraphy for Island Southeast Asia

Author

Hill, Catherine, Soares, Pedro, Mormina, Maru, Macaulay, Vincent, Clarke, Dougie, Blumbach, Petya B., Vizuete-Forster, Matthieu, Forster, Peter, Bulbeck, David, Oppenheimer, Stephen, and Richards, Martin

Subjects
Mitochondrial DNA -- Research, Biological diversity -- Research, Human population genetics -- Research, Biological sciences
Abstract

The two-tier population history of Island Southeast Asia (ISEA) is refuted by demonstrating that mitochondrial DNA diversity in the region is extremely high and includes a large number of indigenous clades. The movement and expansion of indigenous mtDNA lineages, studied through coding-region and control-region variants obtained from complete sequence data, suggest that the prehistory of the region has to be rethought.

Published
2007

23. Climate Change and Postglacial Human Dispersals in Southeast Asia

Author

Soares, Pedro, Trejaut, Jean Alain, Loo, Jun-Hun, Hill, Catherine, Mormina, Maru, Lee, Chien-Liang, Chen, Yao-Ming, Hudjashov, Georgi, Forster, Peter, Macaulay, Vincent, Bulbeck, David, Oppenheimer, Stephen, Lin, Marie, and Richards, Martin B.

Published
2008

26. A new deep branch of eurasian mtDNA macrohaplogroup M reveals additional complexity regarding the settlement of Madagascar

Author

Mirazon-Lahr Marta, Mormina Maru, Sambo Clement, Guitard Evelyne, Dugoujon Jean-M, Cox Murray P, Razafindrazaka Harilanto, Ricaut François-X, Ludes Bertrand, and Crubézy Eric

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Current models propose that mitochondrial DNA macrohaplogroups M and N evolved from haplogroup L3 soon after modern humans left Africa. Increasingly, however, analysis of isolated populations is filling in the details of, and in some cases challenging, aspects of this general model. Results Here, we present the first comprehensive study of three such isolated populations from Madagascar: the Mikea hunter-gatherers, the neighbouring Vezo fishermen, and the Merina central highlanders (n = 266). Complete mitochondrial DNA genome sequences reveal several unresolved lineages, and a new, deep branch of the out-of-Africa founder clade M has been identified. This new haplogroup, M23, has a limited global distribution, and is restricted to Madagascar and a limited range of African and Southwest Asian groups. Conclusions The geographic distribution, phylogenetic placement and molecular age of M23 suggest that the colonization of Madagascar was more complex than previously thought.

Published
2009
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27. New evidence of genetic adaptation to high altitude in Andean populations

Author

Eichstaedt, Christina, primary, Pagani, Luca, additional, Antao, Tiago, additional, Inchley, Charlotte, additional, Cardona, Alexia, additional, Mörseburg, Alexander, additional, Clemente, Florian, additional, Sluckin, Timothy, additional, Metspalu, Ene, additional, Mitt, Mario, additional, Mägi, Reedik, additional, Hudjashov, Georgi, additional, Metspalu, Mait, additional, Mormina, Maru, additional, Jacobs, Guy, additional, and Kivisild, Toomas, additional

Published
2018
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30. Evidence of Early-Stage Selection on EPAS1 and GPR126 Genes in Andean High Altitude Populations

Author

Eichstaedt, Christina A., primary, Pagani, Luca, additional, Antao, Tiago, additional, Inchley, Charlotte E., additional, Cardona, Alexia, additional, Mörseburg, Alexander, additional, Clemente, Florian J., additional, Sluckin, Timothy J., additional, Metspalu, Ene, additional, Mitt, Mario, additional, Mägi, Reedik, additional, Hudjashov, Georgi, additional, Metspalu, Mait, additional, Mormina, Maru, additional, Jacobs, Guy S., additional, and Kivisild, Toomas, additional

Published
2017
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31. Selective sweep on human amylase genes postdates the split with Neanderthals

Author

Inchley, Charlotte E., primary, Larbey, Cynthia D. A., additional, Shwan, Nzar A. A., additional, Pagani, Luca, additional, Saag, Lauri, additional, Antão, Tiago, additional, Jacobs, Guy, additional, Hudjashov, Georgi, additional, Metspalu, Ene, additional, Mitt, Mario, additional, Eichstaedt, Christina A., additional, Malyarchuk, Boris, additional, Derenko, Miroslava, additional, Wee, Joseph, additional, Abdullah, Syafiq, additional, Ricaut, François-Xavier, additional, Mormina, Maru, additional, Mägi, Reedik, additional, Villems, Richard, additional, Metspalu, Mait, additional, Jones, Martin K., additional, Armour, John A. L., additional, and Kivisild, Toomas, additional

Published
2016
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33. Ancient Voyaging and Polynesian Origins

Author

Soares, Pedro, Rito, Teresa, Trejaut, Jean, Mormina, Maru, Hill, Catherine, Tinkler-Hundal, Emma, Braid, Michelle, Clarke, Douglas J., Loo, Jun-Hun, Thomson, Noel, Denham, Tim, Donohue, Mark, Macaulay, Vincent, Lin, Marie, Oppenheimer, Stephen, and Richards, Martin B.

Published
2011
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35. Genetic diversity and evidence for population admixture in Batak Negritos from Palawan

Author

Scholes, Clarissa, primary, Siddle, Katherine, additional, Ducourneau, Axel, additional, Crivellaro, Federica, additional, Järve, Mari, additional, Rootsi, Siiri, additional, Bellatti, Maggie, additional, Tabbada, Kristina, additional, Mormina, Maru, additional, Reidla, Maere, additional, Villems, Richard, additional, Kivisild, Toomas, additional, Lahr, Marta Mirazon, additional, and Migliano, Andrea Bamberg, additional

Published
2011
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38. Positive selection of AS3MTto arsenic water in Andean populations

Author

Eichstaedt, Christina A., Antao, Tiago, Cardona, Alexia, Pagani, Luca, Kivisild, Toomas, and Mormina, Maru

Abstract

•Argentine Collas have adapted to minimize consequences of arsenic water.•The selection pressure of arsenic can be identified at genome-wide level.•Beneficial allele frequencies are reduced with distance from arsenic exposure.

Published
2015
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39. Complete mitochondrial DNA sequences provide new insights into the Polynesian motif and the peopling of Madagascar.

Author

Razafindrazaka, Harilanto, Ricaut, François-X, Cox, Murray P., Mormina, Maru, Dugoujon, Jean-Michel, Randriamarolaza, Louis P., Guitard, Evelyne, Tonasso, Laure, Ludes, Bertrand, and Crubézy, Eric

Subjects
MITOCHONDRIAL DNA, NUCLEIC acids, NUCLEOTIDE sequence, ETHNIC groups
Abstract

More than a decade of mitochondrial DNA (mtDNA) studies have given the ‘Polynesian motif’ renowned status as a marker for tracing the late-Holocene expansion of Austronesian speaking populations. Despite considerable research on the Polynesian motif in Oceania, there has been little equivalent work on the western edge of its expansion – leaving major issues unresolved regarding the motif's evolutionary history. This has also led to considerable uncertainty regarding the settlement of Madagascar. In this study, we assess mtDNA variation in 266 individuals from three Malagasy ethnic groups: the Mikea, Vezo, and Merina. Complete mtDNA genome sequencing reveals a new variant of the Polynesian motif in Madagascar; two coding region mutations define a Malagasy-specific sub-branch. This newly defined ‘Malagasy motif’ occurs at high frequency in all three ethnic groups (13–50%), and its phylogenetic position, geographic distribution, and estimated age all support a recent origin, but without conclusively identifying a specific source region. Nevertheless, the haplotype's limited diversity, similar to those of other mtDNA haplogroups found in our Malagasy groups, best supports a small number of initial settlers arriving to Madagascar through the same migratory process. Finally, the discovery of this lineage provides a set of new polymorphic positions to help localize the Austronesian ancestors of the Malagasy, as well as uncover the origin and evolution of the Polynesian motif itself. [ABSTRACT FROM AUTHOR]

Published
2010
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40. A new deep branch of eurasian mtDNA macrohaplogroup Mreveals additional complexity regarding the settlement ofMadagascar.

Author

Ricaut, François-X., Razafindrazaka, Harilanto, Cox, Murray P., Dugoujon, Jean-M., Guitard, Evelyne, Sambo, Clement, Mormina, Maru, Mirazon-Lahr, Marta, Ludes, Bertrand, and Crubézy, Eric

Subjects
MITOCHONDRIAL DNA, POPULATION genetics, PHYLOGENY
Abstract

Background: Current models propose that mitochondrial DNA macrohaplogroups M and N evolved from haplogroup L3 soon after modern humans left Africa. Increasingly, however, analysis of isolated populations is filling in the details of, and in some cases challenging, aspects of this general model. Results: Here, we present the first comprehensive study of three such isolated populations from Madagascar: the Mikea hunter-gatherers, the neighbouring Vezo fishermen, and the Merina central highlanders (n = 266). Complete mitochondrial DNA genome sequences reveal several unresolved lineages, and a new, deep branch of the out-of-Africa founder clade M has been identified. This new haplogroup, M23, has a limited global distribution, and is restricted to Madagascar and a limited range of African and Southwest Asian groups. Conclusions: The geographic distribution, phylogenetic placement and molecular age of M23 suggest that the colonization of Madagascar was more complex than previously thought. [ABSTRACT FROM AUTHOR]

Published
2009
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41. 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.).

42. Selective sweep on human amylase genes postdates the split with Neanderthals

Author

Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Mormina, Maru, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., and Kivisild, Toomas

Abstract

Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.

43. Selective sweep on human amylase genes postdates the split with Neanderthals

Author

Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., Kivisild, Toomas, Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., and Kivisild, Toomas

Abstract

Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.

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44. Selective sweep on human amylase genes postdates the split with Neanderthals

Author

Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., Kivisild, Toomas, Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., and Kivisild, Toomas

Abstract

Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.

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45. Selective sweep on human amylase genes postdates the split with Neanderthals

Author

Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., Kivisild, Toomas, Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., and Kivisild, Toomas

Abstract

Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.

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46. Selective sweep on human amylase genes postdates the split with Neanderthals

Author

Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., Kivisild, Toomas, Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., and Kivisild, Toomas

Abstract

Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.

Full Text
View/download PDF

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