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1. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Author

Mallick, Swapan, Li, Heng, Lipson, Mark, Mathieson, Iain, Gymrek, Melissa, Racimo, Fernando, Zhao, Mengyao, Chennagiri, Niru, Nordenfelt, Susanne, Tandon, Arti, Skoglund, Pontus, Lazaridis, Iosif, Sankararaman, Sriram, Fu, Qiaomei, Rohland, Nadin, Renaud, Gabriel, Erlich, Yaniv, Willems, Thomas, Gallo, Carla, Spence, Jeffrey P, Song, Yun S, Poletti, Giovanni, Balloux, Francois, van Driem, George, de Knijff, Peter, Romero, Irene Gallego, Jha, Aashish R, Behar, Doron M, Bravi, Claudio M, Capelli, Cristian, Hervig, Tor, Moreno-Estrada, Andres, Posukh, Olga L, Balanovska, Elena, Balanovsky, Oleg, Karachanak-Yankova, Sena, Sahakyan, Hovhannes, Toncheva, Draga, Yepiskoposyan, Levon, Tyler-Smith, Chris, Xue, Yali, Abdullah, M Syafiq, Ruiz-Linares, Andres, Beall, Cynthia M, Di Rienzo, Anna, Jeong, Choongwon, Starikovskaya, Elena B, Metspalu, Ene, Parik, Jüri, Villems, Richard, Henn, Brenna M, Hodoglugil, Ugur, Mahley, Robert, Sajantila, Antti, Stamatoyannopoulos, George, Wee, Joseph TS, Khusainova, Rita, Khusnutdinova, Elza, Litvinov, Sergey, Ayodo, George, Comas, David, Hammer, Michael F, Kivisild, Toomas, Klitz, William, Winkler, Cheryl A, Labuda, Damian, Bamshad, Michael, Jorde, Lynn B, Tishkoff, Sarah A, Watkins, W Scott, Metspalu, Mait, Dryomov, Stanislav, Sukernik, Rem, Singh, Lalji, Thangaraj, Kumarasamy, Pääbo, Svante, Kelso, Janet, Patterson, Nick, and Reich, David

Subjects
Human Genome, Genetics, Animals, Australia, Black People, Datasets as Topic, Genetic Variation, Genetics, Population, Genome, Human, Genomics, History, Ancient, Human Migration, Humans, Mutation Rate, Native Hawaiian or Other Pacific Islander, Neanderthals, New Guinea, Phylogeny, Racial Groups, Sequence Analysis, DNA, Species Specificity, Time Factors, General Science & Technology
Abstract

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Published
2016

2. 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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3. Global diversity, population stratification, and selection of human copy-number variation.

Author

Krumm, Niklas, Huddleston, John, Coe, Bradley, Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn, Posukh, Olga, Sahakyan, Hovhannes, Watkins, W, Yepiskoposyan, Levon, Abdullah, M, Bravi, Claudio, Capelli, Cristian, Hervig, Tor, Wee, Joseph, Tyler-Smith, Chris, van Driem, George, Romero, Irene, Jha, Aashish, Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena, Ayodo, George, Beall, Cynthia, Di Rienzo, Anna, Hammer, Michael, Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah, Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, Eichler, Evan, Mallick, Swapan, Nelson, Bradley, Hormozdiari, Fereydoun, Henn, Brenna, and Sudmant, Peter

Subjects
Animals, Black People, DNA Copy Number Variations, Evolution, Molecular, Gene Duplication, Genome, Human, Hominidae, Humans, Native Hawaiian or Other Pacific Islander, Phylogeny, Polymorphism, Single Nucleotide, Population, Selection, Genetic, Sequence Deletion
Abstract

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

Published
2015

4. Global diversity, population stratification, and selection of human copy-number variation

Author

Sudmant, Peter H, Mallick, Swapan, Nelson, Bradley J, Hormozdiari, Fereydoun, Krumm, Niklas, Huddleston, John, Coe, Bradley P, Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn B, Posukh, Olga L, Sahakyan, Hovhannes, Watkins, W Scott, Yepiskoposyan, Levon, Abdullah, M Syafiq, Bravi, Claudio M, Capelli, Cristian, Hervig, Tor, Wee, Joseph TS, Tyler-Smith, Chris, van Driem, George, Romero, Irene Gallego, Jha, Aashish R, Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Henn, Brenna, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena B, Ayodo, George, Beall, Cynthia M, Di Rienzo, Anna, Hammer, Michael F, Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah A, Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, and Eichler, Evan E

Subjects
Genetics, Human Genome, Animals, Black People, DNA Copy Number Variations, Evolution, Molecular, Gene Duplication, Genome, Human, Hominidae, Humans, Native Hawaiian or Other Pacific Islander, Phylogeny, Polymorphism, Single Nucleotide, Population, Selection, Genetic, Sequence Deletion, General Science & Technology
Abstract

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

Published
2015

5. Reconstructing Native American population history

Author

Reich, David, Patterson, Nick, Campbell, Desmond, Tandon, Arti, Mazieres, Stéphane, Ray, Nicolas, Parra, Maria V, Rojas, Winston, Duque, Constanza, Mesa, Natalia, García, Luis F, Triana, Omar, Blair, Silvia, Maestre, Amanda, Dib, Juan C, Bravi, Claudio M, Bailliet, Graciela, Corach, Daniel, Hünemeier, Tábita, Bortolini, Maria Cátira, Salzano, Francisco M, Petzl-Erler, María Luiza, Acuña-Alonzo, Victor, Aguilar-Salinas, Carlos, Canizales-Quinteros, Samuel, Tusié-Luna, Teresa, Riba, Laura, Rodríguez-Cruz, Maricela, Lopez-Alarcón, Mardia, Coral-Vazquez, Ramón, Canto-Cetina, Thelma, Silva-Zolezzi, Irma, Fernandez-Lopez, Juan Carlos, Contreras, Alejandra V, Jimenez-Sanchez, Gerardo, Gómez-Vázquez, Maria José, Molina, Julio, Carracedo, Ángel, Salas, Antonio, Gallo, Carla, Poletti, Giovanni, Witonsky, David B, Alkorta-Aranburu, Gorka, Sukernik, Rem I, Osipova, Ludmila, Fedorova, Sardana A, Vasquez, René, Villena, Mercedes, Moreau, Claudia, Barrantes, Ramiro, Pauls, David, Excoffier, Laurent, Bedoya, Gabriel, Rothhammer, Francisco, Dugoujon, Jean-Michel, Larrouy, Georges, Klitz, William, Labuda, Damian, Kidd, Judith, Kidd, Kenneth, Di Rienzo, Anna, Freimer, Nelson B, Price, Alkes L, and Ruiz-Linares, Andrés

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Historical Studies, Anthropology, American Indian or Alaska Native, Americas, Asia, Cluster Analysis, Emigration and Immigration, Gene Flow, Genetics, Population, History, Ancient, Humans, Indians, North American, Models, Genetic, Phylogeny, Polymorphism, Single Nucleotide, Siberia, General Science & Technology
Abstract

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

Published
2012

6. Natural Selection Shaped Regional mtDNA Variation in Humans

Author

Mishmar, Dan, Ruiz-Pesini, Eduardo, Golik, Pawel, Macaulay, Vincent, Clark, Andrew G., Hosseini, Seyed, Brandon, Martin, Easley, Kirk, Chen, Estella, Brown, Michael D., Sukernik, Rem I., Olckers, Antonel, and Wallace, Douglas C.

Published
2003

9. HUMAN GENOMICS: Global diversity, population stratification, and selection of human copy-number variation

Author

Sudmant, Peter H., Mallick, Swapan, Nelson, Bradley J., Hormozdiari, Fereydoun, Krumm, Niklas, Huddleston, John, Coe, Bradley P., Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn B., Posukh, Olga L., Sahakyan, Hovhannes, Watkins, Scott W., Yepiskoposyan, Levon, Abdullah, Syafiq M., Bravi, Claudio M., Capelli, Cristian, Hervig, Tor, Wee, Joseph T. S., Tyler-Smith, Chris, van Driem, George, Romero, Irene Gallego, Jha, Aashish R., Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Henn, Brenna, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena B., Ayodo, George, Beall, Cynthia M., Di Rienzo, Anna, Hammer, Michael F., Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah A., Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, and Eichler, Evan E.

Published
2015
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11. 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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12. Mitochondrial genome diversity in arctic Siberians, with particular reference to the evolutionary history of Beringia and Pleistocenic peopling of the Americas

Author

Volodko, Natalia V., Starikovskaya, Elena B., Mazunin, Ilya O., Eltsov, Nikolai P., Naidenko, Polina V., Wallace, Douglas C., and Sukernik, Rem I.

Subjects
Mitochondrial DNA -- Research, Human genome -- Research, Human evolution -- Research, Biological sciences
Abstract

The mitochondrial genome diversity with reference to the evolutionary history of Beringia and Pleistocenic peopling of the Americas, as observed in arctic Siberians is studied. The Paleosiberian-speaking Yukaghir is shown to be primarily from the southern belt of Siberia with changing environmental conditions.

Published
2008

19. Mitochondrial genome diversity on the Central Siberian Plateau with particular reference to the prehistory of northernmost Eurasia

Author

Dryomov, Stanislav V., primary, Nazhmidenova, Azhar M., additional, Starikovskaya, Elena B., additional, Shalaurova, Sofia A., additional, Rohland, Nadin, additional, Mallick, Swapan, additional, Bernardos, Rebecca, additional, Derevianko, Anatoly P., additional, Reich, David, additional, and Sukernik, Rem I., additional

Published
2021
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27. mtDNA diversity in Chukchi and Siberian Eskimos: implications for the genetic history of ancient Beringia and the people of the New World

Author

Starikovskaya, Yelena B., Sukernik, Rem I., Schurr, Theodore G., Kogelnik, Andreas M., and Wallace, Douglas C.

Subjects
Siberia -- Emigration and immigration, Kamchatka -- Emigration and immigration, Alaska -- Emigration and immigration, Canada -- Emigration and immigration, Russia -- Emigration and immigration, Amazon River region -- Emigration and immigration, Bering Land Bridge -- Emigration and immigration, Genetic disorders -- Research, Chromosome mapping -- Usage, Inuit -- Genetic aspects, Indigenous peoples -- Russia, Mitochondrial DNA -- Research, Linguistic analysis (Linguistics) -- Usage, Antiquities -- Research, Phylogeny -- Usage, Tlingits, Navajos -- Genetic aspects, Apaches -- Genetic aspects, Paleo-Indians -- Genetic aspects, Glacial epoch -- Emigration and immigration, Hunting and gathering societies -- Emigration and immigration, Native Americans -- Languages, Biological sciences
Abstract

Implications for the genetic history of ancient Beringia and for the people of the New World as found in mtDNA diversity in Chukchi and Siberian Eskimos are discussed. Beringia over millennia was perhaps the location of the respective founding sequences that selectively came into northern North America via western Alaska.

Published
1998

29. Mitochondrial DNA variation in Koryaks and Itel'men: population replacement in the Okhotsk Sea-Bering Sea region during the Neolithic

Author

Schurr, Theodore G., Sukernik, Rem I., Starikovskaya, Yelena B., and Wallace, Douglass C.

Subjects
Kamchatka -- Demographic aspects, Neolithic period, Variation (Biology) -- Research, Mitochondrial DNA -- Research, Soviets (People) -- Genetic aspects, Anthropology/archeology/folklore
Abstract

In this study, we analyzed the mitochondrial DNA (mtDNA) variation in 202 individuals representing one Itel'men and three Koryak populations from different parts of the Kamchatka peninsula. All mtDNAs were subjected to high resolution restriction (RFLP) analysis and control region (CR) sequencing, and the resulting data were combined with those available for other Siberian and east Asian populations and subjected to statistical and phylogenetic analysis. Together, the Koryaks and Itel'men were found to have mtDNAs belonging to three (A, C, and D) of the four major haplotype groups (haplogroups) observed in Siberian and Native American populations (A-D). In addition, they exhibited mtDNAs belonging to haplogroups G, Y, and Z, which were formerly called 'Other' mtDNAs. While Kamchatka harbored the highest frequencies of haplogroup G mtDNAs, which were widely distributed in eastern Siberian and adjacent east Asian populations, the distribution of haplogroup Y was restricted within a relatively small area and pointed to the lower Amur River-Sakhalin Island region as its place of origin. In contrast, the pattern of distribution and the origin of haplogroup Z mtDNAs remained unclear. Furthermore, phylogenetic and statistical analyses showed that Koryaks and Itel'men had stronger genetic affinities with. eastern Siberian/east Asian populations than to those of the north Pacific Rim. These results were consistent with colonization events associated with the relatively recent immigration to Kamchatka of new tribes from the Siberian mainland region, although remnants of ancient Beringian populations were still evident in the Koryak and Itel'men gene pools. KEY WORDS haplotype; haplogroup; control region; sublineage; Kamchatka

Published
1999

31. Reply to Tarazona-Santos and Santos

Author

Lell, Jeffrey T., Sukernik, Rem I., and Wallace, Douglas C.

Subjects
Native Americans -- Genetic aspects, Human population genetics -- Research, Prehistoric peoples -- America, Human beings -- Migrations, Biological sciences
Published
2002

32. 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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33. Erratum: Corrigendum: Reconstructing Native American population history

Author

Reich, David, primary, Patterson, Nick, additional, Campbell, Desmond, additional, Tandon, Arti, additional, Mazieres, Stéphane, additional, Ray, Nicolas, additional, Parra, Maria V., additional, Rojas, Winston, additional, Duque, Constanza, additional, Mesa, Natalia, additional, García, Luis F., additional, Triana, Omar, additional, Blair, Silvia, additional, Maestre, Amanda, additional, Dib, Juan C., additional, Bravi, Claudio M., additional, Bailliet, Graciela, additional, Corach, Daniel, additional, Hünemeier, Tábita, additional, Bortolini, Maria Cátira, additional, Salzano, Francisco M., additional, Petzl-Erler, María Luiza, additional, Acuña-Alonzo, Victor, additional, Aguilar-Salinas, Carlos, additional, Canizales-Quinteros, Samuel, additional, Tusié-Luna, Teresa, additional, Riba, Laura, additional, Rodríguez-Cruz, Maricela, additional, Lopez-Alarcón, Mardia, additional, Coral-Vazquez, Ramón, additional, Canto-Cetina, Thelma, additional, Silva-Zolezzi, Irma, additional, Fernandez-Lopez, Juan Carlos, additional, Contreras, Alejandra V., additional, Jimenez-Sanchez, Gerardo, additional, Gómez-Vázquez, Maria José, additional, Molina, Julio, additional, Carracedo, Ángel, additional, Salas, Antonio, additional, Gallo, Carla, additional, Poletti, Giovanni, additional, B.Witonsky, David, additional, Alkorta-Aranburu, Gorka, additional, Sukernik, Rem I., additional, Osipova, Ludmila, additional, Fedorova, Sardana A., additional, Vasquez, René, additional, Villena, Mercedes, additional, Moreau, Claudia, additional, Barrantes, Ramiro, additional, Pauls, David, additional, Excoffier, Laurent, additional, Bedoya, Gabriel, additional, Rothhammer, Francisco, additional, Dugoujon, Jean-Michel, additional, Larrouy, Georges, additional, Klitz, William, additional, Labuda, Damian, additional, Kidd, Judith, additional, Kidd, Kenneth, additional, Di Rienzo, Anna, additional, Freimer, Nelson B., additional, Price, Alkes L., additional, and Ruiz-Linares, Andrés, additional

Published
2012
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35. Adaptations to Climate-Mediated Selective Pressures in Humans

Author

Hancock, Angela M., primary, Witonsky, David B., additional, Alkorta-Aranburu, Gorka, additional, Beall, Cynthia M., additional, Gebremedhin, Amha, additional, Sukernik, Rem, additional, Utermann, Gerd, additional, Pritchard, Jonathan K., additional, Coop, Graham, additional, and Di Rienzo, Anna, additional

Published
2011
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36. Natural selection shaped regional mtDNA variation in humans

Author

Mishmar, Dan, primary, Ruiz-Pesini, Eduardo, additional, Golik, Pawel, additional, Macaulay, Vincent, additional, Clark, Andrew G., additional, Hosseini, Seyed, additional, Brandon, Martin, additional, Easley, Kirk, additional, Chen, Estella, additional, Brown, Michael D., additional, Sukernik, Rem I., additional, Olckers, Antonel, additional, and Wallace, Douglas C., additional

Published
2002
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42. Reconstructing Native American Population History

Author

Reich, David Emil, Patterson, Nick, Campbell, Desmond, Tandon, Arti, Mazieres, Stéphane, Ray, Nicolas, Parra, Maria V., Rojas, Winston, Duque, Constanza, Mesa, Natalia, García, Luis F., Triana, Omar, Blair, Silvia, Maestre, Amanda, Dib, Juan C., Bravi, Claudio M., Bailliet, Graciela, Corach, Daniel, Hünemeier, Tábita, Bortolini, Maria-Cátira, Salzano, Francisco M., Petzl-Erler, María Luiza, Acuña-Alonzo, Victor, Aguilar-Salinas, Carlos, Canizales-Quinteros, Samuel, Tusié-Luna, Teresa, Riba, Laura, Rodríguez-Cruz, Maricela, Lopez-Alarcón, Mardia, Coral-Vazquez, Ramón, Canto-Cetina, Thelma, Silva-Zolezzi, Irma, Fernandez-Lopez, Juan Carlos, Contreras, Alejandra V., Jimenez-Sanchez, Gerardo, Gómez-Vázquez, María José, Molina, Julio, Carracedo, Ángel, Salas, Antonio, Gallo, Carla, Poletti, Giovanni, Witonsky, David B., Alkorta-Aranburu, Gorka, Sukernik, Rem I., Osipova, Ludmila, Fedorova, Sardana, Vasquez, René, Villena, Mercedes, Moreau, Claudia, Barrantes, Ramiro, Pauls, David L., Excoffier, Laurent, Bedoya, Gabriel, Rothhammer, Francisco, Dugoujon, Jean Michel, Larrouy, Georges, Klitz, William, Labuda, Damian, Kidd, Judith, Kidd, Kenneth, Rienzo, Anna Di, Freimer, Nelson B., Price, Alkes, and Ruiz-Linares, Andrés

Abstract

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1–5. One contentious issue is whether the settlement occurred via a single6–8 or multiple streams of migration from Siberia9–15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. We show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call “First American”. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan-speakers on both sides of the Panama Isthmus, who have ancestry from both North and South America.

Published
2013
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43. 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

44. Global diversity, population stratification and selection of human copy number variation

Author

Ayodo, George, Beall, Cynthia M., Metspalu, Mait, Henn, Brenna, Hammer, Michael, Bamshad, Michael, Yepiskoposyan, Levon, Posukh, Olga L., Sahakyan, Hovhannes, Nelson, Bradley J., Tyler-Smith, Chris, Khusainova, Rita, Parik, Jüri, Hervig, Tor, Sudmant, Peter H., Jorde, Lynn B., Toncheva, Draga, Hormozdiari, Fereydoun, Eichler, Evan E., Coe, Bradley P., Winkler, Cheryl, Sukernik, Rem, Starikovskaya, Elena B., Abdullah, M. Syafiq, Metspalu, Ene, Baker, Carl, Di Rienzo, Anna, Klitz, William, Mallick, Swapan, Wee, Joseph T.S., Watkins, W. Scott, Khusnutdinova, Elza, Bravi, Claudio M., Comas, David, Karachanak-Yankova, Sena, Huddleston, John, Tishkoff, Sarah A., Van Driem, George, Krumm, Niklas, Reich, David, Patterson, Nick, Ruiz-Linares, Andres, Kivisild, Toomas, Villems, Richard, Jha, Aashish R., Gallego Romero, Irene, Labuda, Damian, Nordenfeldt, Susanne, Dryomov, Stanislav, Sajantila, Antti, and Capelli, Christian

Subjects
410 Linguistics, 3. Good health
Abstract

In order to explore the diversity and selective signatures of duplication and deletion human copy number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single nucleotide variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

45. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Author

Capelli, Cristian, Sankararaman, Sriram, Thangaraj, Kumarasamy, Willems, Thomas, De Knijff, Peter, Hervig, Tor, Ayodo, George, Chennagiri, Niru, Lazaridis, Iosif, Karachanak-Yankova, Sena, Gallo, Carla, Wee, Joseph T. S., Mallick, Swapan, Jorde, Lynn B., Behar, Doron M., Hodoglugil, Ugur, Jha, Aashish R., Skoglund, Pontus, Khusainova, Rita, Jeong, Choongwon, Posukh, Olga L., Beall, Cynthia M., Bravi, Claudio M., Hammer, Michael F., Tishkoff, Sarah A., Balloux, Francois, Singh, Lalji, Van Driem, George, Henn, Brenna M., Winkler, Cheryl, Mahley, Robert, Kivisild, Toomas, Klitz, William, Tyler-Smith, Chris, Racimo, Fernando, Poletti, Giovanni, Parik, Jüri, Lipson, Mark, Toncheva, Draga, Fu, Qiaomei, Dryomov, Stanislav, Tandon, Arti, Nordenfelt, Susanne, Bamshad, Michael, Di Rienzo, Anna, Stamatoyannopoulos, George, Reich, David, Abdullah, M. Syafiq, Khusnutdinova, Elza, Sajantila, Antti, Gymrek, Melissa, Litvinov, Sergey, Yepiskoposyan, Levon, Ruiz-Linares, Andres, Metspalu, Ene, Patterson, Nick, Rohland, Nadin, Villems, Richard, Labuda, Damian, Renaud, Gabriel, Comas, David, Li, Heng, Balanovska, Elena, Metspalu, Mait, Mathieson, Iain, Gallego Romero, Irene, Watkins, W. Scott, Yong, Yun S., Zhao, Mengyao, Sukernik, Rem, Xue, Yali, Pääbo, Svante, Starikovskaya, Elena B., Balanovsky, Oleg, Moreno-Estrada, Andres, Kelso, Janet, Spence, Jeffrey P., Erlich, Yaniv, and Sahakyan, Hovhannes

Subjects
570 Life sciences, biology, 410 Linguistics, 3. Good health

48. Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency.

Author

Hancock AM, Witonsky DB, Ehler E, Alkorta-Aranburu G, Beall C, Gebremedhin A, Sukernik R, Utermann G, Pritchard J, Coop G, and Di Rienzo A

Subjects
Animals, Biological Evolution, Ecology, Genetics, Population, Haplotypes, Homozygote, Humans, Models, Biological, Models, Genetic, Selection, Genetic, Adaptation, Physiological, Diet, Gene Frequency
Abstract

Human populations use a variety of subsistence strategies to exploit an exceptionally broad range of ecoregions and dietary components. These aspects of human environments have changed dramatically during human evolution, giving rise to new selective pressures. To understand the genetic basis of human adaptations, we combine population genetics data with ecological information to detect variants that increased in frequency in response to new selective pressures. Our approach detects SNPs that show concordant differences in allele frequencies across populations with respect to specific aspects of the environment. Genic and especially nonsynonymous SNPs are overrepresented among those most strongly correlated with environmental variables. This provides genome-wide evidence for selection due to changes in ecoregion, diet, and subsistence. We find particularly strong signals associated with polar ecoregions, with foraging, and with a diet rich in roots and tubers. Interestingly, several of the strongest signals overlap with those implicated in energy metabolism phenotypes from genome-wide association studies, including SNPs influencing glucose levels and susceptibility to type 2 diabetes. Furthermore, several pathways, including those of starch and sucrose metabolism, are enriched for strong signals of adaptations to a diet rich in roots and tubers, whereas signals associated with polar ecoregions are overrepresented in genes associated with energy metabolism pathways.

Published
2010
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