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1. Distance from sub-Saharan Africa predicts mutational load in diverse human genomes

Author

Henn, Brenna M, Botigué, Laura R, Peischl, Stephan, Dupanloup, Isabelle, Lipatov, Mikhail, Maples, Brian K, Martin, Alicia R, Musharoff, Shaila, Cann, Howard, Snyder, Michael P, Excoffier, Laurent, Kidd, Jeffrey M, and Bustamante, Carlos D

Subjects
Biological Sciences, Genetics, Human Genome, Generic health relevance, Africa South of the Sahara, Alleles, Animals, Asian People, Black People, Computer Simulation, Conserved Sequence, Ethnicity, Evolution, Molecular, Founder Effect, Gene Flow, Genetic Diseases, Inborn, Genetic Drift, Genome, Human, Genotype, Homing Behavior, Human Migration, Humans, Indians, Central American, Models, Genetic, Mutation, Selection, Genetic, mutation, founder effect, range expansion, expansion load, purifying selection
Abstract

The Out-of-Africa (OOA) dispersal ∼ 50,000 y ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from seven geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia, and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.

Published
2016

2. Reconstructing Native American Migrations from Whole-genome and Whole-exome Data

Author

Gravel, Simon, Zakharia, Fouad, Moreno-Estrada, Andres, Byrnes, Jake K, Muzzio, Marina, Rodriguez-Flores, Juan L., Kenny, Eimear E., Gignoux, Christopher R., Maples, Brian K., Guiblet, Wilfried, Dutil, Julie, Via, Marc, Sandoval, Karla, Bedoya, Gabriel, Oleksyk, Taras K, Ruiz-Linares, Andres, Burchard, Esteban G, Martinez-Cruzado, Juan Carlos, Bustamante, Carlos D., and Project, The 1000 Genomes

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics, 92D25
Abstract

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Ta\'ino people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent and ancestry tract length, we show that post-contact populations differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe., Comment: 30 pages, inludes supplement. v2 contains clarifications, extra analyses, and a change in the language classification scheme used

Published
2013

4. A global reference for human genetic variation

Author

Altshuler, David M., (Co-Chair), Durbin, Richard M., (Co-Chair, Principal Investigator), Donnelly, Peter, Green, Eric D., Nickerson, Deborah A., Boerwinkle, Eric, Doddapaneni, Harsha, Han, Yi, Korchina, Viktoriya, Kovar, Christie, Lee, Sandra, Muzny, Donna, Reid, Jeffrey G., Zhu, Yiming, Wang, Jun, (Principal Investigator), Chang, Yuqi, Feng, Qiang, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Lan, Tianming, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Liu, Shengmao, Liu, Xiao, Lu, Yao, Ma, Xuedi, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Xu, Xun, Yin, Ye, Zhang, Dandan, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Lander, Eric S., (Principal Investigator), Gabriel, Stacey B., (Co-Chair), Gupta, Namrata, Gharani, Neda, Toji, Lorraine H., Gerry, Norman P., Resch, Alissa M., Barker, Jonathan, Gil, Laurent, Hunt, Sarah E., Kelman, Gavin, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Smith, Richard E., Streeter, Ian, Thormann, Anja, Toneva, Iliana, Vaughan, Brendan, Zheng-Bradley, Xiangqun, Bentley, David R., (Principal Investigator), Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, (Principal Investigator), Sudbrak, Ralf, (Project Leader), Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Mardis, Elaine R., (Co-Principal Investigator) (Co-Chair), Wilson, Richard K., (Co-Principal Investigator), Fulton, Lucinda, Fulton, Robert, Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Church, Deanna, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, O’Sullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., (Principal Investigator), Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, (Principal Investigator), Campbell, Christopher L., Kong, Yu, Marcketta, Anthony, Yu, Fuli, (Project Leader), Antunes, Lilian, Bainbridge, Matthew, Sabo, Aniko, Huang, Zhuoyi, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Shao, Haojing, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Alkan, Can, Dal, Elif, Kahveci, Fatma, Garrison, Erik P., (Project Lead), Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, Stromberg, Michael, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Daly, Mark J., (Principal Investigator), DePristo, Mark A., (Project Leader), Handsaker, Robert E., (Project Leader), Banks, Eric, Bhatia, Gaurav, del Angel, Guillermo, Genovese, Giulio, Li, Heng, Kashin, Seva, Nemesh, James C., Poplin, Ryan E., Yoon, Seungtai C., (Principal Investigator), Lihm, Jayon, Makarov, Vladimir, Clark, Andrew G., (Principal Investigator), Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Rausch, Tobias, (Project Leader), Fritz, Markus H., Stütz, Adrian M., Beal, Kathryn, Datta, Avik, Herrero, Javier, Ritchie, Graham R. S., Zerbino, Daniel, Sabeti, Pardis C., (Principal Investigator), Shlyakhter, Ilya, Schaffner, Stephen F., Vitti, Joseph, Cooper, David N., (Principal Investigator), Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Cheetham, Keira R., Cox, Anthony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Kenny, Eimear E., (Principal Investigator), Batzer, Mark A., (Principal Investigator), Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., (Principal Investigator), Lek, Monkol, Herwig, Ralf, Koboldt, Daniel C., Larson, David, Ye, Kai, Gravel, Simon, Swaroop, Anand, Chew, Emily, Lappalainen, Tuuli, (Principal Investigator), Erlich, Yaniv, (Principal Investigator), Gymrek, Melissa, Willems, Thomas Frederick, Simpson, Jared T., Shriver, Mark D., (Principal Investigator), Rosenfeld, Jeffrey A., (Principal Investigator), Montgomery, Stephen B., (Principal Investigator), De La Vega, Francisco M., (Principal Investigator), Byrnes, Jake K., Carroll, Andrew W., DeGorter, Marianne K., Lacroute, Phil, Maples, Brian K., Martin, Alicia R., Moreno-Estrada, Andres, Shringarpure, Suyash S., Zakharia, Fouad, Halperin, Eran, (Principal Investigator), Baran, Yael, Cerveira, Eliza, Hwang, Jaeho, Malhotra, Ankit, (Co-Project Lead), Plewczynski, Dariusz, Radew, Kamen, Romanovitch, Mallory, Zhang, Chengsheng, (Co-Project Lead), Hyland, Fiona C. L., Craig, David W., (Principal Investigator), Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, (Principal Investigator), Antaki, Danny, Gujral, Madhusudan, Noor, Amina, Ye, Kenny, Burchard, Esteban G., (Principal Investigator), Hernandez, Ryan D., (Principal Investigator), Gignoux, Christopher R., Haussler, David, (Principal Investigator), Katzman, Sol J., Kent, James W., Howie, Bryan, Ruiz-Linares, Andres, (Principal Investigator), Dermitzakis, Emmanouil T., (Principal Investigator), Devine, Scott E., (Principal Investigator), Abecasis, Gonçalo R., (Principal Investigator) (Co-Chair), Kang, Hyun Min, (Project Leader), Kidd, Jeffrey M., (Principal Investigator), Blackwell, Tom, Caron, Sean, Chen, Wei, Emery, Sarah, Fritsche, Lars, Fuchsberger, Christian, Jun, Goo, Li, Bingshan, Lyons, Robert, Scheller, Chris, Sidore, Carlo, Song, Shiya, Sliwerska, Elzbieta, Taliun, Daniel, Tan, Adrian, Welch, Ryan, Wing, Mary Kate, Zhan, Xiaowei, Awadalla, Philip, (Principal Investigator), Hodgkinson, Alan, Li, Yun, Shi, Xinghua, (Principal Investigator), Quitadamo, Andrew, Lunter, Gerton, (Principal Investigator), McVean, Gil A., (Principal Investigator) (Co-Chair), Marchini, Jonathan L., (Principal Investigator), Myers, Simon, (Principal Investigator), Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Kretzschmar, Warren, Iqbal, Zamin, Mathieson, Iain, Menelaou, Androniki, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., (Principal Investigator), Fu, Yunxin, (Principal Investigator), Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, (Principal Investigator), Witherspoon, David, Xing, Jinchuan, Browning, Brian L., (Principal Investigator), Browning, Sharon R., (Principal Investigator), Hormozdiari, Fereydoun, Sudmant, Peter H., Khurana, Ekta, (Principal Investigator), Hurles, Matthew E., (Principal Investigator), Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Colonna, Vincenza, Jostins, Luke, Walter, Klaudia, Xue, Yali, Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Harmanci, Arif O., Jin, Mike, Lee, Donghoon, Liu, Jeremy, Mu, Xinmeng Jasmine, Zhang, Jing, Zhang, Yan, McCarroll, Steven A., (Principal Investigator), Hartl, Chris, Shakir, Khalid, Degenhardt, Jeremiah, Korbel, Jan O., (Principal Investigator) (Co-Chair), Meiers, Sascha, Raeder, Benjamin, Casale, Francesco Paolo, Stegle, Oliver, Lameijer, Eric-Wubbo, Ding, Li, (Principal Investigator), Hall, Ira, Lee, Charles, (Principal Investigator) (Co-Chair), Bafna, Vineet, Michaelson, Jacob, Gardner, Eugene J., (Project Leader), Mills, Ryan E., (Principal Investigator), Dayama, Gargi, Chen, Ken, (Principle Investigator), Fan, Xian, Chong, Zechen, Chen, Tenghui, Eichler, Evan E., (Principal Investigator) (Co-Chair), Chaisson, Mark J., Huddleston, John, Malig, Maika, Nelson, Bradley J., Parrish, Nicholas F., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, Zhang, Yujun, Lam, Hugo, Sisu, Cristina, Gibbs, Richard A., (Principal Investigator) (Co-Chair), Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Yu, Jin, Li, Wangshen, Marth, Gabor T., (Principal Investigator) (Co-Chair), Habegger, Lukas, Yu, Haiyuan, (Principal Investigator), Cunningham, Fiona, Dunham, Ian, Lage, Kasper, (Principal Investigator), Jespersen, Jakob Berg, Horn, Heiko, Tyler-Smith, Chris, (Principal Investigator) (Co-Chair), Gerstein, Mark B., (Principal Investigator) (Co-Chair), Kim, Donghoon, Desalle, Rob, Narechania, Apurva, Wilson Sayres, Melissa A., Bustamante, Carlos D., (Principal Investigator) (Co-Chair), Mendez, Fernando L., Poznik, David G., Underhill, Peter A., Coin, Lachlan, (Principal Investigator), Mittelman, David, Banerjee, Ruby, Cerezo, Maria, Fitzgerald, Thomas W., Louzada, Sandra, Massaia, Andrea, Ritchie, Graham R., Yang, Fengtang, Kalra, Divya, Hale, Walker, Dan, Xu, Flicek, Paul, (Principal Investigator) (Co-Chair), Clarke, Laura, (Project Lead), Sherry, Stephen T., (Principal Investigator) (Co-Chair), Chakravarti, Aravinda, (Co-Chair), Knoppers, Bartha M., (Co-Chair), Barnes, Kathleen C., Beiswanger, Christine, Cai, Hongyu, Cao, Hongzhi, Henn, Brenna, Jones, Danielle, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Tian, Zhongming, Tishkoff, Sarah, Via, Marc, Wang, Yuhong, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Cai, Zhiming, Gao, Yang, Chu, Jiayou, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Mathias, Rasika A., Hennis, Anselm, Watson, Harold, McKenzie, Colin, Qadri, Firdausi, LaRocque, Regina, Deng, Xiaoyan, Asogun, Danny, Folarin, Onikepe, Happi, Christian, Omoniwa, Omonwunmi, Stremlau, Matt, Tariyal, Ridhi, Jallow, Muminatou, Joof, Fatoumatta Sisay, Corrah, Tumani, Rockett, Kirk, Kwiatkowski, Dominic, Kooner, Jaspal, Hiê`n, Trâ`n Tinh, Dunstan, Sarah J., Hang, Nguyen Thuy, Fonnie, Richard, Garry, Robert, Kanneh, Lansana, Moses, Lina, Schieffelin, John, Grant, Donald S., Gallo, Carla, Poletti, Giovanni, Saleheen, Danish, Rasheed, Asif, Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A., and Yang, Huanming

Published
2015
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5. An integrated map of genetic variation from 1,092 human genomes

Author

McVean, Gil A., Altshuler, David M., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Donnelly, Peter, Eichler, Evan E., Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Green, Eric D., Hurles, Matthew E., Knoppers, Bartha M., Korbel, Jan O., Lander, Eric S., Lee, Charles, Lehrach, Hans, Mardis, Elaine R., Marth, Gabor T., Nickerson, Deborah A., Schmidt, Jeanette P., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Dinh, Huyen, Kovar, Christie, Lee, Sandra, Lewis, Lora, Muzny, Donna, Reid, Jeff, Wang, Min, Wang, Jun, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Li, Zhuo, Liu, Xiao, Lu, Yao, Ma, Xuedi, Su, Zhe, Tai, Shuaishuai, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Yin, Ye, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Zhou, Yan, Lander, Eric S., Gabriel, Stacey B., Gupta, Namrata, Flicek, Paul, Clarke, Laura, Leinonen, Rasko, Smith, Richard E., Zheng-Bradley, Xiangqun, Bentley, David R., Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, Sudbrak, Ralf, Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Sherry, Stephen T., McVean, Gil A., Mardis, Elaine R., Wilson, Richard K., Fulton, Lucinda, Fulton, Robert, Weinstock, George M., Durbin, Richard M., Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, Yu, Fuli, Bainbridge, Matthew, Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Sabo, Aniko, Wang, Yi, Yu, Jin, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Qin, Nan, Shao, Haojing, Wang, Bingqiang, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Garrison, Erik P., Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Lee, Charles, Griffin, Lauren, Hsieh, Chih-Heng, Mills, Ryan E., Shi, Xinghua, von Grotthuss, Marcin, Zhang, Chengsheng, Daly, Mark J., DePristo, Mark A., Banks, Eric, Bhatia, Gaurav, Carneiro, Mauricio O., del Angel, Guillermo, Genovese, Giulio, Handsaker, Robert E., Hartl, Chris, McCarroll, Steven A., Nemesh, James C., Poplin, Ryan E., Schaffner, Stephen F., Shakir, Khalid, Yoon, Seungtai C., Lihm, Jayon, Makarov, Vladimir, Jin, Hanjun, Kim, Wook, Cheol Kim, Ki, Korbel, Jan O., Rausch, Tobias, Beal, Kathryn, Cunningham, Fiona, Herrero, Javier, McLaren, William M., Ritchie, Graham R. S., Clark, Andrew G., Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Sabeti, Pardis C., Grossman, Sharon R., Tabrizi, Shervin, Tariyal, Ridhi, Cooper, David N., Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Keira Cheetham, R., Cox, Tony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Ye, Kai, Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., Lek, Monkol, Sudbrak, Herwig, Ralf, Shriver, Mark D., Bustamante, Carlos D., Byrnes, Jake K., De La Vega, Francisco M., Gravel, Simon, Kenny, Eimear E., Kidd, Jeffrey M., Lacroute, Phil, Maples, Brian K., Moreno-Estrada, Andres, Zakharia, Fouad, Halperin, Eran, Baran, Yael, Craig, David W., Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, Bafna, Vineet, Ye, Kenny, Burchard, Esteban G., Hernandez, Ryan D., Gignoux, Christopher R., Haussler, David, Katzman, Sol J., James Kent, W., Howie, Bryan, Ruiz-Linares, Andres, Dermitzakis, Emmanouil T., Lappalainen, Tuuli, Devine, Scott E., Liu, Xinyue, Maroo, Ankit, Tallon, Luke J., Rosenfeld, Jeffrey A., Min Kang, Hyun, Anderson, Paul, Angius, Andrea, Bigham, Abigail, Blackwell, Tom, Busonero, Fabio, Cucca, Francesco, Fuchsberger, Christian, Jones, Chris, Jun, Goo, Li, Yun, Lyons, Robert, Maschio, Andrea, Porcu, Eleonora, Reinier, Fred, Sanna, Serena, Schlessinger, David, Sidore, Carlo, Tan, Adrian, Kate Trost, Mary, Awadalla, Philip, Hodgkinson, Alan, Lunter, Gerton, McVean, Gil A., Marchini, Jonathan L., Myers, Simon, Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Iqbal, Zamin, Mathieson, Iain, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., Fu, Yunxin, Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, Witherspoon, David, Xing, Jinchuan, Eichler, Evan E., Browning, Brian L., Alkan, Can, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Ko, Arthur, Sudmant, Peter H., Mardis, Elaine R., Chen, Ken, Chinwalla, Asif, Ding, Li, Dooling, David, Koboldt, Daniel C., McLellan, Michael D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Hurles, Matthew E., Tyler-Smith, Chris, Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Coffey, Alison J., Colonna, Vincenza, Huang, Ni, Jostins, Luke, Li, Heng, Scally, Aylwyn, Walter, Klaudia, Xue, Yali, Zhang, Yujun, Gerstein, Mark B., Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Habegger, Lukas, Harmanci, Arif O., Jin, Mike, Khurana, Ekta, Jasmine Mu, Xinmeng, Sisu, Cristina, Lee, Charles, McCarroll, Steven A., Degenhardt, Jeremiah, Korbel, Jan O., Stütz, Adrian M., Church, Deanna, Michaelson, Jacob J., Eichler, Evan E., Hurles, Matthew E., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, DePristo, Mark A., Min Kang, Hyun, Mardis, Elaine R., Yu, Fuli, Michelson, Leslie P., Tyler-Smith, Chris, Frankish, Adam, Harrow, Jennifer, Fowler, Gerald, Hale, Walker, Kalra, Divya, Flicek, Paul, Clarke, Laura, Barker, Jonathan, Kelman, Gavin, Kulesha, Eugene, Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Streeter, Ian, Toneva, Iliana, Vaughan, Brendan, Sherry, Stephen T., Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, OʼSullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Chakravarti, Aravinda, Knoppers, Bartha M., Barnes, Kathleen C., Beiswanger, Christine, Burchard, Esteban G., Bustamante, Carlos D., Cai, Hongyu, Cao, Hongzhi, Durbin, Richard M., Gharani, Neda, Henn, Brenna, Jones, Danielle, Jorde, Lynn, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Reich, David, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Sudbrak, Ralf, Tian, Zhongming, Tishkoff, Sarah, Toji, Lorraine H., Tyler-Smith, Chris, Via, Marc, Wang, Yuhong, Yang, Huanming, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Ruiz-Linares, Andres, Zhi Ming, Cai, Yang, Gao, Jia You, Chu, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Oleksyk, Taras K., Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Clemm, Nicholas C., Duncanson, Audrey, Dunn, Michael, Guyer, Mark S., Peterson, Jane L., Abecasis, Goncalo R., and Auton, Adam

Published
2012
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6. Distance from sub-Saharan Africa predicts mutational load in diverse human genomes

Author

Henn, Brenna M., primary, Botigué, Laura R., additional, Peischl, Stephan, additional, Dupanloup, Isabelle, additional, Lipatov, Mikhail, additional, Maples, Brian K., additional, Martin, Alicia R., additional, Musharoff, Shaila, additional, Cann, Howard, additional, Snyder, Michael P., additional, Excoffier, Laurent, additional, Kidd, Jeffrey M., additional, and Bustamante, Carlos D., additional

Published
2015
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8. Reconstructing Native American migrations from whole-genome and whole-exome data.

Author

Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, and Bustamante CD

Subjects
Black People genetics, Chromosome Mapping, Exome, Genome, Human, Hispanic or Latino genetics, Human Genome Project, Humans, Mexican Americans genetics, Mexico, Puerto Rico, Racial Groups genetics, White People genetics, Gene Frequency genetics, Genetics, Population, Human Migration, Indians, North American genetics
Abstract

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern American ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations., Competing Interests: The authors have declared that no competing interests exist.

Published
2013
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