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2. The language of race, ethnicity, and ancestry in human genetic research

Author

Birney, Ewan, Inouye, Michael, Raff, Jennifer, Rutherford, Adam, and Scally, Aylwyn

Subjects
Quantitative Biology - Populations and Evolution
Abstract

The language commonly used in human genetics can inadvertently pose problems for multiple reasons. Terms like "ancestry", "ethnicity", and other ways of grouping people can have complex, often poorly understood, or multiple meanings within the various fields of genetics, between different domains of biological sciences and medicine, and between scientists and the general public. Furthermore, some categories in frequently used datasets carry scientifically misleading, outmoded or even racist perspectives derived from the history of science. Here, we discuss examples of problematic lexicon in genetics, and how commonly used statistical practices to control for the non-genetic environment may exacerbate difficulties in our terminology, and therefore understanding. Our intention is to stimulate a much-needed discussion about the language of genetics, to begin a process to clarify existing terminology, and in some cases adopt a new lexicon that both serves scientific insight, and cuts us loose from various aspects of a pernicious past.

Published
2021

3. Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?

Author

Scerri, Eleanor ML, Thomas, Mark G, Manica, Andrea, Gunz, Philipp, Stock, Jay T, Stringer, Chris, Grove, Matt, Groucutt, Huw S, Timmermann, Axel, Rightmire, G Philip, d’Errico, Francesco, Tryon, Christian A, Drake, Nick A, Brooks, Alison S, Dennell, Robin W, Durbin, Richard, Henn, Brenna M, Lee-Thorp, Julia, deMenocal, Peter, Petraglia, Michael D, Thompson, Jessica C, Scally, Aylwyn, and Chikhi, Lounès

Subjects
Biological Sciences, Ecology, Africa, Animals, Archaeology, Biological Evolution, Ecosystem, Fossils, Genetics, Population, Geography, Hominidae, Humans, African origins, Middle Stone Age, evolutionary genetics, human evolution, paleoanthropology, paleoecology, Environmental Sciences, Evolutionary Biology, Biological sciences, Environmental sciences
Abstract

We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones. We argue that these fields support an emerging view of a highly structured African prehistory that should be considered in human evolutionary inferences, prompting new interpretations, questions, and interdisciplinary research directions.

Published
2018

6. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

Author

Xue, Yali, Prado-Martinez, Javier, Sudmant, Peter H, Narasimhan, Vagheesh, Ayub, Qasim, Szpak, Michal, Frandsen, Peter, Chen, Yuan, Yngvadottir, Bryndis, Cooper, David N, de Manuel, Marc, Hernandez-Rodriguez, Jessica, Lobon, Irene, Siegismund, Hans R, Pagani, Luca, Quail, Michael A, Hvilsom, Christina, Mudakikwa, Antoine, Eichler, Evan E, Cranfield, Michael R, Marques-Bonet, Tomas, Tyler-Smith, Chris, and Scally, Aylwyn

Subjects
Human Genome, Genetics, Biotechnology, Generic health relevance, Life on Land, Adaptation, Physiological, Animals, Biological Evolution, DNA Copy Number Variations, Democratic Republic of the Congo, Endangered Species, Female, Genetic Variation, Genome, Gorilla gorilla, Homozygote, Inbreeding, Linkage Disequilibrium, Male, Mutation, Population Dynamics, Rwanda, Selection, Genetic, Sequence Analysis, DNA, Species Specificity, Time Factors, General Science & Technology
Abstract

Mountain gorillas are an endangered great ape subspecies and a prominent focus for conservation, yet we know little about their genomic diversity and evolutionary past. We sequenced whole genomes from multiple wild individuals and compared the genomes of all four Gorilla subspecies. We found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation. A further recent decline in the mountain gorilla population has led to extensive inbreeding, such that individuals are typically homozygous at 34% of their sequence, leading to the purging of severely deleterious recessive mutations from the population. We discuss the causes of their decline and the consequences for their future survival.

Published
2015

7. A genome-wide survey of genetic variation in gorillas using reduced representation sequencing

Author

Scally, Aylwyn, Yngvadottir, Bryndis, Xue, Yali, Ayub, Qasim, Durbin, Richard, and Tyler-Smith, Chris

Subjects
Quantitative Biology - Populations and Evolution
Abstract

All non-human great apes are endangered in the wild, and it is therefore important to gain an understanding of their demography and genetic diversity. To date, however, genetic studies within these species have largely been confined to mitochondrial DNA and a small number of other loci. Here, we present a genome-wide survey of genetic variation in gorillas using a reduced representation sequencing approach, focusing on the two lowland subspecies. We identify 3,274,491 polymorphic sites in 14 individuals: 12 western lowland gorillas (Gorilla gorilla gorilla) and 2 eastern lowland gorillas (Gorilla beringei graueri). We find that the two species are genetically distinct, based on levels of heterozygosity and patterns of allele sharing. Focusing on the western lowland population, we observe evidence for population substructure, and a deficit of rare genetic variants suggesting a recent episode of population contraction. In western lowland gorillas, there is an elevation of variation towards telomeres and centromeres on the chromosomal scale. On a finer scale, we find substantial variation in genetic diversity, including a marked reduction close to the major histocompatibility locus, perhaps indicative of recent strong selection there. These findings suggest that despite their maintaining an overall level of genetic diversity equal to or greater than that of humans, population decline, perhaps associated with disease, has been a significant factor in recent and long-term pressures on wild gorilla populations., Comment: 18 pages, 9 figures

Published
2013
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8. Ancient human parallel lineages within North America contributed to a coastal expansion

Author

Scheib, C. L., Li, Hongjie, Desai, Tariq, Link, Vivian, Kendall, Christopher, Dewar, Genevieve, Griffith, Peter William, Mörseburg, Alexander, Johnson, John R., Potter, Amiee, Kerr, Susan L., Endicott, Phillip, Lindo, John, Haber, Marc, Xue, Yali, Tyler-Smith, Chris, Sandhu, Manjinder S., Lorenz, Joseph G., Randall, Tori D., Faltyskova, Zuzana, Pagani, Luca, Danecek, Petr, O’Connell, Tamsin C., Martz, Patricia, Boraas, Alan S., Byrd, Brian F., Leventhal, Alan, Cambra, Rosemary, Williamson, Ronald, Lesage, Louis, Holguin, Brian, Soto, Ernestine Ygnacio-De, Rosas, JohnTommy, Metspalu, Mait, Stock, Jay T., Manica, Andrea, Scally, Aylwyn, Wegmann, Daniel, Malhi, Ripan S., and Kivisild, Toomas

Published
2018

9. Brown dwarf populations in open clusters

Author

Adams, Tim, Davies, Melvyn B., Jameson, Richard F., and Scally, Aylwyn

Subjects
Astrophysics
Abstract

We present the results of multiple simulations of open clusters, modelling the dynamics of a population of brown dwarf members. We consider the effects of a large range of primordial binary populations, including the possibilities of having brown dwarf members contained within a binary system. We also examine the effects of various cluster diameters and masses. Our examination of a population of wide binary systems containing brown dwarfs, reveals evidence for exchange reactions whereby the brown dwarf is ejected from the system and replaced by a heavier main-sequence star. We find that there exists the possibility of hiding a large fraction of the brown dwarfs contained within the primordial binary population. We conclude that it is probable that the majority of brown dwarfs are contained within primordial binary systems which then hides a large proportion of them from detection., Comment: 16 pages, 8 figures; to appear in MNRAS

Published
2002
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10. Destruction of protoplanetary disks in the Orion Nebula Cluster

Author

Scally, Aylwyn and Clarke, Cathie

Subjects
Astrophysics
Abstract

We use numerical N-body simulations of the Orion Nebula Cluster (ONC) to investigate the destruction of protoplanetary disks by close stellar encounters and UV radiation from massive stars. The simulations model a cluster of 4000 stars, and we consider separately cases in which the disks have fixed radii of 100 AU and 10 AU. In the former case, depending on a star's position and orbit in the cluster over 10^7 years, UV photoevaporation removes at least 0.01 Msol from its disk, and can remove up to 1 Msol. We find no dynamical models of the ONC consistent with the suggestion of Storzer and Hollenbach that the observed distribution and abundance of proplyds could be explained by a population of stars on radial orbits which spend relatively little time near Theta 1C Ori (the most massive star in the ONC). Instead the observations require either massive disks (e.g. a typical initial disk mass of 0.4 Msol) or a very recent birth for Theta 1C Ori. When we consider the photoevaporation of the inner 10 AU of disks in the ONC, we find that planet formation would be hardly affected. Outside that region, planets would be prevented from forming in about half the systems, unless either the initial disk masses were very high or they formed in less than ~ 2 Myr and Theta 1C Ori has only very recently appeared. We also present statistics on the distribution of minimum stellar encounter separations. This peaks at 1000 AU, with less than 10% of stars having had an encounter closer than 100 AU after 10^7 years. We conclude that stellar encounters are unlikely to play a significant role in destroying protoplanetary disks. In the absence of any disruption mechanism other than those considered here, we would thus predict planetary systems like our own to be common amongst stars forming in ONC-like environments., Comment: 9 pages, 9 figures, to be published in MNRAS

Published
2000
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11. Mapping copy number variation by population-scale genome sequencing.

Author

Mills, Ryan, Walter, Klaudia, Stewart, Chip, Handsaker, Robert, Chen, Ken, Alkan, Can, Abyzov, Alexej, Yoon, Seungtai, Ye, Kai, Cheetham, R, Chinwalla, Asif, Conrad, Donald, Fu, Yutao, Grubert, Fabian, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Iakoucheva, Lilia, Iqbal, Zamin, Kang, Shuli, Kidd, Jeffrey, Konkel, Miriam, Korn, Joshua, Khurana, Ekta, Kural, Deniz, Lam, Hugo, Leng, Jing, Li, Ruiqiang, Li, Yingrui, Lin, Chang-Yun, Luo, Ruibang, Mu, Xinmeng, Nemesh, James, Peckham, Heather, Rausch, Tobias, Scally, Aylwyn, Shi, Xinghua, Stromberg, Michael, Stütz, Adrian, Urban, Alexander, Walker, Jerilyn, Wu, Jiantao, Zhang, Yujun, Zhang, Zhengdong, Batzer, Mark, Ding, Li, Marth, Gabor, McVean, Gil, Sebat, Jonathan, Snyder, Michael, Wang, Jun, Ye, Kenny, Eichler, Evan, Gerstein, Mark, Hurles, Matthew, Lee, Charles, McCarroll, Steven, and Korbel, Jan

Subjects
DNA Copy Number Variations, Gene Duplication, Genetic Predisposition to Disease, Genetics, Population, Genome, Human, Genomics, Genotype, Humans, Mutagenesis, Insertional, Reproducibility of Results, Sequence Analysis, DNA, Sequence Deletion
Abstract

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.

Published
2011

12. Wide binaries in the Orion Nebula Cluster

Author

Scally, Aylwyn, Clarke, Cathie, and McCaughrean, Mark J.

Subjects
Astrophysics
Abstract

Using proper motion data for 894 stars in the Orion Nebula Cluster (ONC) compiled by Jones & Walker in 1988, we search for binaries with apparent separations in the range 1000-5000 AU, and find an upper limit of three. Using a Monte Carlo method, we test the consistency of this result with two hypotheses: i) that the cluster contains a binary population identical to that found in the solar neighbourhood, and ii) that the cluster contains no binaries at all in this separation range. We obtain results strongly favouring the latter hypothesis. Star formation in the Galaxy is seen to occur in a variety of different environments, but it has been proposed that most stars may be formed in dense regions similar to the ONC, rather than in less dense groupings like that found in Taurus-Auriga. Since roughly 15 per cent of galactic field stars are known to be in binaries with separations greater than 1000 AU, the apparent absence of such binaries in the ONC places an upper limit on the contribution that dense clusters can make to galactic star formation., Comment: 4 pages, 2 Postscript figures, uses mn.sty

Published
1999
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16. Chimpanzee genomic diversity reveals ancient admixture with bonobos

Author

de Manuel, Marc, Kuhlwilm, Martin, Frandsen, Peter, Sousa, Vitor C., Desai, Tariq, Prado-Martinez, Javier, Hernandez-Rodriguez, Jessica, Dupanloup, Isabelle, Lao, Oscar, Hallast, Pille, Schmidt, Joshua M., Heredia-Genestar, José María, Benazzo, Andrea, Barbujani, Guido, Peter, Benjamin M., Kuderna, Lukas F. K., Casals, Ferran, Angedakin, Samuel, Arandjelovic, Mimi, Boesch, Christophe, Kühl, Hjalmar, Vigilant, Linda, Langergraber, Kevin, Novembre, John, Gut, Marta, Gut, Ivo, Navarro, Arcadi, Carlsen, Frauds, Andres, Aida M., Siegismund, Hans. R., Scally, Aylwyn, Excoffier, Laurent, Tyler-Smith, Chris, Castellano, Sergi, Xue, Yali, Hvilsom, Christina, and Marques-Bonet, Tomas

Published
2016

19. NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells

Author

Maskalenka, Katsiaryna, primary, Alagöz, Gökberk, additional, Krueger, Felix, additional, Wright, Joshua, additional, Rostovskaya, Maria, additional, Nakhuda, Asif, additional, Bendall, Adam, additional, Krueger, Christel, additional, Walker, Simon, additional, Scally, Aylwyn, additional, and Rugg-Gunn, Peter J., additional

Published
2023
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21. Complexity in human ancestral demography

Author

Scally, Aylwyn, Scally, Aylwyn [0000-0002-0807-1167], and Apollo - University of Cambridge Repository

Subjects
human demography, Molecular Anthropology, Genetic flow, ancestral demography, genetic admixture
Abstract

Demography – the size and structure of popu- lations, and the movement of individuals within and between them – is central to how we describe and understand the events of human evolution. But while archaeology can reveal the presence of people at a certain time and place, and genetic data may indicate their shared ancestry with oth- ers, we rarely have direct evidence for how many people there were or in what groups they lived. Therefore the inference of these and other aspects of the past using demographic models is a focus for many genetic and archaeological studies.

Published
2021
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22. NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells

Author

Maskalenka, Katsiaryna, primary, Alagöz, Gökberk, additional, Krueger, Felix, additional, Wright, Joshua, additional, Rostovskaya, Maria, additional, Nakhuda, Asif, additional, Bendall, Adam, additional, Krueger, Christel, additional, Walker, Simon, additional, Scally, Aylwyn, additional, and Rugg-Gunn, Peter J., additional

Published
2022
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23. What is ancestry?

Author

Mathieson, Iain, Scally, Aylwyn, Mathieson, Iain [0000-0002-4256-3982], Scally, Aylwyn [0000-0002-0807-1167], and Apollo - University of Cambridge Repository

Subjects
Male, Genome, Human, Humans, Female, DNA, Genomics, Parent-Child Relations, Chromosomes, Pedigree
Abstract

Ancestry connects genetics and society in fundamental ways. For many people it has cultural, religious or even political significance, and can play a key role in shaping personal and public identities. People’s desire to discover their own ancestry drives the multibillion-dollar genealogy industry, which has grown rapidly in the era of consumer genomics. Companies such as 23andMe and Ancestry now claim tens of millions of customers worldwide. In parallel, our scientific understanding of the human past is being transformed by studies of ancient and modern genetic data, which allow us to track changes in ancestry over space and time. Sophisticated methods have been developed to infer and visualise these relationships. Thus, it seems that both scientists and the wider public are learning more and more about ancestry, and there is an optimistic sense that genetic data provide an exhaustive repository of ancestral information.

Published
2020

25. PRIMATE GENOMICS: Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

Author

Xue, Yali, Prado-Martinez, Javier, Sudmant, Peter H., Narasimhan, Vagheesh, Ayub, Qasim, Szpak, Michal, Frandsen, Peter, Chen, Yuan, Yngvadottir, Bryndis, Cooper, David N., de Manuel, Marc, Hernandez-Rodriguez, Jessica, Lobon, Irene, Siegismund, Hans R., Pagani, Luca, Quail, Michael A., Hvilsom, Christina, Mudakikwa, Antoine, Eichler, Evan E., Cranfield, Michael R., Marques-Bonet, Tomas, Tyler-Smith, Chris, and Scally, Aylwyn

Published
2015
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26. Human origins in Southern African palaeo-wetlands? : Strong claims from weak evidence

Author

Schlebusch, Carina, Loog, Liisa, Groucutt, Huw S., King, Turi, Rutherford, Adam, Barbieri, Chiara, Barbujani, Guido, Chikhi, Lounes, Stringer, Chris, Jakobsson, Mattias, Eriksson, Anders, Manica, Andrea, Tishkoff, Sarah A., Scerri, Eleanor ML., Scally, Aylwyn, Brierley, Chris, Thomas, Mark G., Schlebusch, Carina, Loog, Liisa, Groucutt, Huw S., King, Turi, Rutherford, Adam, Barbieri, Chiara, Barbujani, Guido, Chikhi, Lounes, Stringer, Chris, Jakobsson, Mattias, Eriksson, Anders, Manica, Andrea, Tishkoff, Sarah A., Scerri, Eleanor ML., Scally, Aylwyn, Brierley, Chris, and Thomas, Mark G.

Abstract

Attempts to identify a 'homeland' for our species from genetic data are widespread in the academic literature. However, even when putting aside the question of whether a 'homeland' is a useful concept, there are a number of inferential pitfalls in attempting to identify the geographic origin of a species from contemporary patterns of genetic variation. These include making strong claims from weakly informative data, treating genetic lineages as representative of populations, assuming a high degree of regional population continuity over hundreds of thousands of years, and using circumstantial observations as corroborating evidence without considering alternative hypotheses on an equal footing, or formally evaluating any hypothesis. In this commentary we review the recent publication that claims to pinpoint the origins of 'modern humans' to a very specific region in Africa (Chan et al., 2019), demonstrate how it fell into these inferential pitfalls, and discuss how this can be avoided.

Published
2021
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28. 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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29. Insights into hominid evolution from the gorilla genome sequence

Author

Scally, Aylwyn, Dutheil, Julien Y., Hillier, LaDeana W., Jordan, Gregory E., Goodhead, Ian, Herrero, Javier, Hobolth, Asger, Lappalainen, Tuuli, Mailund, Thomas, Marques-Bonet, Tomas, McCarthy, Shane, Montgomery, Stephen H., Schwalie, Petra C., Tang, Amy Y., Ward, Michelle C., Xue, Yali, Yngvadottir, Bryndis, Alkan, Can, Andersen, Lars N., Ayub, Qasim, Ball, Edward V., Beal, Kathryn, Bradley, Brenda J., Chen, Yuan, Clee, Chris M., Fitzgerald, Stephen, Graves, Tina A., Gu, Yong, Heath, Paul, Heger, Andreas, Karakoc, Emre, Kolb-Kokocinski, Anja, Laird, Gavin K., Lunter, Gerton, Meader, Stephen, Mort, Matthew, Mullikin, James C., Munch, Kasper, O’Connor, Timothy D., Phillips, Andrew D., Prado-Martinez, Javier, Rogers, Anthony S., Sajjadian, Saba, Schmidt, Dominic, Shaw, Katy, Simpson, Jared T., Stenson, Peter D., Turner, Daniel J., Vigilant, Linda, Vilella, Albert J., Whitener, Weldon, Zhu, Baoli, Cooper, David N., de Jong, Pieter, Dermitzakis, Emmanouil T., Eichler, Evan E., Flicek, Paul, Goldman, Nick, Mundy, Nicholas I., Ning, Zemin, Odom, Duncan T., Ponting, Chris P., Quail, Michael A., Ryder, Oliver A., Searle, Stephen M., Warren, Wesley C., Wilson, Richard K., Schierup, Mikkel H., Rogers, Jane, Tyler-Smith, Chris, and Durbin, Richard

Published
2012
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31. Insights into human genetic variation and population history from 929 diverse genomes

Author

Bergström, Anders, primary, McCarthy, Shane A., additional, Hui, Ruoyun, additional, Almarri, Mohamed A., additional, Ayub, Qasim, additional, Danecek, Petr, additional, Chen, Yuan, additional, Felkel, Sabine, additional, Hallast, Pille, additional, Kamm, Jack, additional, Blanché, Hélène, additional, Deleuze, Jean-François, additional, Cann, Howard, additional, Mallick, Swapan, additional, Reich, David, additional, Sandhu, Manjinder S., additional, Skoglund, Pontus, additional, Scally, Aylwyn, additional, Xue, Yali, additional, Durbin, Richard, additional, and Tyler-Smith, Chris, additional

Published
2020
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33. Accurate whole human genome sequencing using reversible terminator chemistry

Author

Bentley, David R., Balasubramanian, Shankar, Swerdlow, Harold P., Smith, Geoffrey P., Milton, John, Brown, Clive G., Hall, Kevin P., Evers, Dirk J., Barnes, Colin L., Bignell, Helen R., Boutell, Jonathan M., Bryant, Jason, Carter, Richard J., Cheetham, R. Keira, Cox, Anthony J., Ellis, Darren J., Flatbush, Michael R., Gormley, Niall A., Humphray, Sean J., Irving, Leslie J., Karbelashvili, Mirian S., Kirk, Scott M., Li, Heng, Liu, Xiaohai, Maisinger, Klaus S., Murray, Lisa J., Obradovic, Bojan, Ost, Tobias, Parkinson, Michael L., Pratt, Mark R., Rasolonjatovo, Isabelle M. J., Reed, Mark T., Rigatti, Roberto, Rodighiero, Chiara, Ross, Mark T., Sabot, Andrea, Sankar, Subramanian V., Scally, Aylwyn, Schroth, Gary P., Smith, Mark E., Smith, Vincent P., Spiridou, Anastassia, Torrance, Peta E., Tzonev, Svilen S., Vermaas, Eric H., Walter, Klaudia, Wu, Xiaolin, Zhang, Lu, Alam, Mohammed D., Anastasi, Carole, Aniebo, Ify C., Bailey, David M. D., Bancarz, Iain R., Banerjee, Saibal, Barbour, Selena G., Baybayan, Primo A., Benoit, Vincent A., Benson, Kevin F., Bevis, Claire, Black, Phillip J., Boodhun, Asha, Brennan, Joe S., Bridgham, John A., Brown, Rob C., Brown, Andrew A., Buermann, Dale H., Bundu, Abass A., Burrows, James C., Carter, Nigel P., Castillo, Nestor, Catenazzi, Maria Chiara E., Chang, Simon, Cooley, R. Neil, Crake, Natasha R., Dada, Olubunmi O., Diakoumakos, Konstantinos D., Dominguez-Fernandez, Belen, Earnshaw, David J., Egbujor, Ugonna C., Elmore, David W., Etchin, Sergey S, Ewan, Mark R., Fedurco, Milan, Fraser, Louise J., Fuentes Fajardo, Karin V., Furey, W. Scott, George, David, Gietzen, Kimberley J., Goddard, Colin P., Golda, George S., Granieri, Philip A., Green, David E., Gustafson, David L., Hansen, Nancy F., Harnish, Kevin, Haudenschild, Christian D., Heyer, Narinder I, Hims, Matthew M., Ho, Johnny T., Horgan, Adrian M., Hoschler, Katya, Hurwitz, Steve, Ivanov, Denis V., Johnson, Maria Q., James, Terena, Huw Jones, T. A., Kang, Gyoung-Dong, Kerelska, Tzvetana H., Kersey, Alan D., Khrebtukova, Irina, Kindwall, Alex P., Kingsbury, Zoya, Kokko-Gonzales, Paula I., Kumar, Anil, Laurent, Marc A., Lawley, Cynthia T., Lee, Sarah E., Lee, Xavier, Liao, Arnold K., Loch, Jennifer A., Lok, Mitch, Luo, Shujun, Mammen, Radhika M., Martin, John W., McCauley, Patrick G., McNitt, Paul, Mehta, Parul, Moon, Keith W., Mullens, Joe W., Newington, Taksina, Ning, Zemin, Ling Ng, Bee, Novo, Sonia M., O'Neill, Michael J., Osborne, Mark A., Osnowski, Andrew, Ostadan, Omead, Paraschos, Lambros L., Pickering, Lea, Pike, Andrew C., Pike, Alger C., Pinkard, D. Chris, Pliskin, Daniel P., Podhasky, Joe, Quijano, Victor J., Raczy, Come, Rae, Vicki H., Rawlings, Stephen R., Rodriguez, Ana Chiva, Roe, Phyllida M., Rogers, John, Rogert Bacigalupo, Maria C., Romanov, Nikolai, Romieu, Anthony, Roth, Rithy K., Rourke, Natalie J., Ruediger, Silke T., Rusman, Eli, Sanches-Kuiper, Raquel M., Schenker, Martin R., Seoane, Josefina M., Shaw, Richard J., Shiver, Mitch K., Short, Steven W., Sizto, Ning L., Sluis, Johannes P., Smith, Melanie A., Sohna Sohna, Jean Ernest, Spence, Eric J., Stevens, Kim, Sutton, Neil, Szajkowski, Lukasz, Tregidgo, Carolyn L., Turcatti, Gerardo, vandeVondele, Stephanie, Verhovsky, Yuli, Virk, Selene M., Wakelin, Suzanne, Walcott, Gregory C., Wang, Jingwen, Worsley, Graham J., Yan, Juying, Yau, Ling, Zuerlein, Mike, Rogers, Jane, Mullikin, James C., Hurles, Matthew E., McCooke, Nick J., West, John S., Oaks, Frank L., Lundberg, Peter L., Klenerman, David, Durbin, Richard, and Smith, Anthony J.

Published
2008
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34. Global clues to the nature of genomic mutations in humans

Author

Scally, Aylwyn, Scally, Aylwyn [0000-0002-0807-1167], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, QH301-705.5, Science, DNA Mutational Analysis, genetic processes, information science, Population genetics, Mutagenesis (molecular biology technique), Genomics, mutational signatures, Human genetic variation, Biology, DNA replication and repair, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Genomic mutation, Mutation Rate, Animals, Humans, human, Biology (General), skin and connective tissue diseases, great ape evolution, General Immunology and Microbiology, General Neuroscience, Racial Groups, evolutionary biology, population genetics, Hominidae, General Medicine, Biological Evolution, 030104 developmental biology, human population structure, Genomics and Evolutionary Biology, Evolutionary biology, 030220 oncology & carcinogenesis, Mutation, health occupations, Medicine, sense organs, Insight, mutagenesis, Research Article
Abstract

DNA is a remarkably precise medium for copying and storing biological information. This high fidelity results from the action of hundreds of genes involved in replication, proofreading, and damage repair. Evolutionary theory suggests that in such a system, selection has limited ability to remove genetic variants that change mutation rates by small amounts or in specific sequence contexts. Consistent with this, using SNV variation as a proxy for mutational input, we report here that mutational spectra differ substantially among species, human continental groups and even some closely related populations. Close examination of one signal, an increased TCC→TTC mutation rate in Europeans, indicates a burst of mutations from about 15,000 to 2000 years ago, perhaps due to the appearance, drift, and ultimate elimination of a genetic modifier of mutation rate. Our results suggest that mutation rates can evolve markedly over short evolutionary timescales and suggest the possibility of mapping mutational modifiers. DOI: http://dx.doi.org/10.7554/eLife.24284.001, eLife digest DNA is a molecule that contains the information needed to build an organism. This information is stored as a code made up of four chemicals: adenine (A), guanine (G), cytosine (C), and thymine (T). Every time a cell divides and copies its DNA, it accidentally introduces ‘typos’ into the code, known as mutations. Most mutations are harmless, but some can cause damage. All cells have ways to proofread DNA, and the more resources are devoted to proofreading, the less mutations occur. Simple organisms such as bacteria use less energy to reduce mutations, because their genomes may tolerate more damage. More complex organisms, from yeast to humans, instead need to proofread their genomes more thoroughly. Recent research has shown that humans have a lower mutation rate than chimpanzees and gorillas, their closest living relatives. Humans and other apes copy and proofread their DNA with basically the same biological machinery as yeast, which is about a billion years old. Yet, humans and apes have only existed for a small fraction of this time, a few million years. Why then do humans need to replicate and proofread their DNA differently from apes, and could it be that the way mutations arise is still evolving? Previous research revealed that European people experience more mutations within certain DNA motifs (specifically, the DNA sequences ‘TCC’, ‘TCT’, ‘CCC’ and ‘ACC’) than Africans or East Asians do. Now, Harris (who conducted the previous research) and Pritchard have compared how various human ethnic groups accumulate mutations and how these processes differ in different groups. Statistical analysis of the genomes of thousands of people from all over the world did indeed show that the mutation rates of many different three-letter DNA motifs have changed during the past 20,000 years of human evolution. Harris and Pritchard report that when groups of humans left Africa and settled in isolated populations across different continents, each population quickly became better at avoiding mutations in some genomic contexts, but worse in others. This suggests that the risk of passing on harmful mutations to future generations is changing and evolving at an even faster rate than was originally suspected. The results suggest that every human ethnic group carries specific variants of the genes which ensure that DNA replication and repair are accurate. These differences appear to influence which types of mutations are frequently passed down to future generations. An important next step will be to identify the genetic variants that could be controlling mutational patterns and how they affect human health. DOI: http://dx.doi.org/10.7554/eLife.24284.002

Published
2017

35. Human Origins in Southern African Palaeo-wetlands? Strong Claims from Weak Evidence

Author

Schlebusch, Carina M., primary, Loog, Liisa, additional, Groucutt, Huw S., additional, King, Turi, additional, Rutherford, Adam, additional, Barbieri, Chiara, additional, Barbujani, Guido, additional, Chikhi, Lounès, additional, Jakobsson, Mattias, additional, Eriksson, Anders, additional, Manica, Andrea, additional, Tishkoff, Sarah A., additional, Scerri, Eleanor M.L., additional, Scally, Aylwyn, additional, Brierley, Chris, additional, and Thomas, Mark G., additional

Published
2019
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36. Did our species evolve in subdivided populations across Africa, and Why does it matter?

Author

Scerri, Eleanor M.L., primary, Thomas, Mark G., additional, Manica, Andrea, additional, Gunz, Philipp, additional, Stock, Jay T., additional, Stringer, Chris, additional, Grove, Matt, additional, Groucutt, Huw S., additional, Timmermann, Axel, additional, Rightmire, G. Philip, additional, d'Errico, Francesco, additional, Tryon, Christian A., additional, Drake, Nick A., additional, Brooks, Alison S., additional, Dennell, Robin W., additional, Durbin, Richard, additional, Henn, Brenna M., additional, Lee-Thorp, Julia, additional, deMenocal, Peter, additional, Petraglia, Michael D., additional, Thompson, Jessica C., additional, Scally, Aylwyn, additional, and Chikhi, Lounes, additional

Published
2019
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37. Insights into human genetic variation and population history from 929 diverse genomes

Author

Bergström, Anders, primary, McCarthy, Shane A., additional, Hui, Ruoyun, additional, Almarri, Mohamed A., additional, Ayub, Qasim, additional, Danecek, Petr, additional, Chen, Yuan, additional, Felkel, Sabine, additional, Hallast, Pille, additional, Kamm, Jack, additional, Blanché, Hélène, additional, Deleuze, Jean-François, additional, Cann, Howard, additional, Mallick, Swapan, additional, Reich, David, additional, Sandhu, Manjinder S., additional, Skoglund, Pontus, additional, Scally, Aylwyn, additional, Xue, Yali, additional, Durbin, Richard, additional, and Tyler-Smith, Chris, additional

Published
2019
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38. Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species

Author

Nater, Alexander, Mattle-Greminger, Maja P., Nurcahyo, Anton, Nowak, Matthew G., de Manuel, Marc, Desai, Tariq, Groves, Colin, Pybus, Marc, Sonay, Tugce Bilgin, Roos, Christian, Lameira, Adriano R., Wich, Serge A., Askew, James, Davila-Ross, Marina, Fredriksson, Gabriella, de Valles, Guillem, Casals, Ferran, Prado-Martinez, Javier, Goossens, Benoit, Verschoor, Ernst J., Warren, Kristin S., Singleton, Ian, Marques, David A., Pamungkas, Joko, Perwitasari-Farajallah, Dyah, Rianti, Puji, Tuuga, Augustine, Gut, Ivo G., Gut, Marta, Orozco-terWengel, Pablo, van Schaik, Carel P., Bertranpetit, Jaume, Anisimova, Maria, Scally, Aylwyn, Marques-Bonet, Tomas, Meijaard, Erik, and Krützen, Michael

Published
2017
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39. Genomes reveal marked differences in the adaptive evolution between orangutan species

Author

Mattle-Greminger, Maja P., Bilgin Sonay, Tugce, Nater, Alexander, Pybus, Marc, Desai, Tariq, de Valles, Guillem, Casals, Ferran, Scally, Aylwyn, Bertranpetit, Jaume, Marques-Bonet, Tomas, van Schaik, Carel P., Anisimova, Maria, Krützen, Michael, Mattle-Greminger, Maja P., Bilgin Sonay, Tugce, Nater, Alexander, Pybus, Marc, Desai, Tariq, de Valles, Guillem, Casals, Ferran, Scally, Aylwyn, Bertranpetit, Jaume, Marques-Bonet, Tomas, van Schaik, Carel P., Anisimova, Maria, and Krützen, Michael

Abstract

Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives, in particular if and to what extent adaptions to environmental differences have occurred. Here, we used whole-genome sequencing data from critically endangered orangutans from North Sumatra (Pongo abelii) and Borneo (P. pygmaeus) to investigate adaptive responses of each species to environmental differences during the Pleistocene.

Published
2019

42. Morphometric, behavioral, and genomic evidence for a new orangutan species

Author

Nater, Alexander, Mattle-Greminger, Maja P., Nurcahyo, Anton, Nowak, Matthew G., de Manuel, Marc, Desai, Tariq, Groves, Colin, Pybus, Marc, Sonay, Tugce Bilgin, Roos, Christian, Lameira, Adriano R., Wich, Serge A., Askew, James, Davila-Ross, Marina, Fredriksson, Gabriella, de Valles, Guillem, Casals, Ferran, Prado-Martinez, Javier, Goossens, Benoit, Verschoor, Ernst J., Warren, Kristin S., Singleton, Ian, Marques, David A., Pamungkas, Joko, Perwitasari-Farajallah, Dyah, Rianti, Puji, Tuuga, Augustine, Gut, Ivo G., Gut, Marta, Orozco-terWengel, Pablo, van Schaik, Carel P., Bertranpetit, Jaume, Anisimova, Maria, Scally, Aylwyn, Marques-Bonet, Tomas, Meijaard, Erik, Krützen, Michael, Nater, Alexander, Mattle-Greminger, Maja P., Nurcahyo, Anton, Nowak, Matthew G., de Manuel, Marc, Desai, Tariq, Groves, Colin, Pybus, Marc, Sonay, Tugce Bilgin, Roos, Christian, Lameira, Adriano R., Wich, Serge A., Askew, James, Davila-Ross, Marina, Fredriksson, Gabriella, de Valles, Guillem, Casals, Ferran, Prado-Martinez, Javier, Goossens, Benoit, Verschoor, Ernst J., Warren, Kristin S., Singleton, Ian, Marques, David A., Pamungkas, Joko, Perwitasari-Farajallah, Dyah, Rianti, Puji, Tuuga, Augustine, Gut, Ivo G., Gut, Marta, Orozco-terWengel, Pablo, van Schaik, Carel P., Bertranpetit, Jaume, Anisimova, Maria, Scally, Aylwyn, Marques-Bonet, Tomas, Meijaard, Erik, and Krützen, Michael

Abstract

Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive.

Published
2018

43. Genomes reveal marked differences in the adaptive evolution between orangutan species

Author

Mattle-Greminger, Maja P, Bilgin Sonay, Tugce, Nater, Alexander, Pybus, Marc, Desai, Tariq, de Valles, Guillem, Casals, Ferran, Scally, Aylwyn, Bertranpetit, Jaume, Marques-Bonet, Tomas, van Schaik, Carel P, Anisimova, Maria, Krützen, Michael, Mattle-Greminger, Maja P, Bilgin Sonay, Tugce, Nater, Alexander, Pybus, Marc, Desai, Tariq, de Valles, Guillem, Casals, Ferran, Scally, Aylwyn, Bertranpetit, Jaume, Marques-Bonet, Tomas, van Schaik, Carel P, Anisimova, Maria, and Krützen, Michael

Abstract

BACKGROUND: Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives, in particular if and to what extent adaptions to environmental differences have occurred. Here, we used whole-genome sequencing data from critically endangered orangutans from North Sumatra (Pongo abelii) and Borneo (P. pygmaeus) to investigate adaptive responses of each species to environmental differences during the Pleistocene. RESULTS: Taking into account the markedly disparate demographic histories of each species after their split ~ 1 Ma ago, we show that persistent environmental differences on each island had a strong impact on the adaptive evolution of the genus Pongo. Across a range of tests for positive selection, we find a consistent pattern of between-island and species differences. In the more productive Sumatran environment, the most notable signals of positive selection involve genes linked to brain and neuronal development, learning, and glucose metabolism. On Borneo, however, positive selection comprised genes involved in lipid metabolism, as well as cardiac and muscle activities. CONCLUSIONS: We find strikingly different sets of genes appearing to have evolved under strong positive selection in each species. In Sumatran orangutans, selection patterns were congruent with well-documented cognitive and behavioral differences between the species, such as a larger and more complex cultural repertoire and higher degrees of sociality. However, in Bornean orangutans, selective responses to fluctuating environmental conditions appear to have produced physiological adaptations to generally lower and temporally more unpredictable food supplies.

Published
2018

45. Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes

Author

Narasimhan, Vagheesh M., primary, Rahbari, Raheleh, additional, Scally, Aylwyn, additional, Wuster, Arthur, additional, Mason, Dan, additional, Xue, Yali, additional, Wright, John, additional, Trembath, Richard C., additional, Maher, Eamonn R., additional, van Heel, David A., additional, Auton, Adam, additional, Hurles, Matthew E., additional, Tyler-Smith, Chris, additional, and Durbin, Richard, additional

Published
2017
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49. A direct multi-generational estimate of the human mutation rate from autozygous segments seen in thousands of parentally related individuals

Author

Narasimhan, Vagheesh M, primary, Rahbari, Raheleh, additional, Scally, Aylwyn, additional, Wuster, Arthur, additional, Mason, Dan, additional, Xue, Yali, additional, Wright, John, additional, Trembath, Richard C, additional, Maher, Eamonn R, additional, van Heel, David A, additional, Auton, Adam, additional, Hurles, Matthew E, additional, Tyler-Smith, Chris, additional, and Durbin, Richard, additional

Published
2016
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50. Mapping copy number variation by population-scale genome sequencing

Author

Mills, Ryan E, Walter, Klaudia, Stewart, Chip, Handsaker, Robert E, Chen, Ken, Alkan, Can, Abyzov, Alexej, Yoon, Seungtai Chris, Ye, Kai, Cheetham, R Keira, Chinwalla, Asif, Conrad, Donald F, Fu, Yutao, Grubert, Fabian, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Iakoucheva, Lilia M, Iqbal, Zamin, Kang, Shuli, Kidd, Jeffrey M, Konkel, Miriam K, Korn, Joshua, Khurana, Ekta, Kural, Deniz, Lam, Hugo YK, Leng, Jing, Li, Ruiqiang, Li, Yingrui, Lin, Chang-Yun, Luo, Ruibang, Mu, Xinmeng Jasmine, Nemesh, James, Peckham, Heather E, Rausch, Tobias, Scally, Aylwyn, Shi, Xinghua, Stromberg, Michael P, Stütz, Adrian M, Urban, Alexander Eckehart, Walker, Jerilyn A, Wu, Jiantao, Zhang, Yujun, Zhang, Zhengdong D, Batzer, Mark A, Ding, Li, Marth, Gabor T, McVean, Gil, Sebat, Jonathan, Snyder, Michael, Wang, Jun, Ye, Kenny, Eichler, Evan E, Gerstein, Mark B, Hurles, Matthew E, Lee, Charles, McCarroll, Steven A, Korbel, Jan O, and 1000 Genomes Project

Subjects
Genome, Genotype, DNA Copy Number Variations, General Science & Technology, Population, Human Genome, Genomes Project, Reproducibility of Results, DNA, Genomics, Mutagenesis, Insertional, Gene Duplication, Genetics, Humans, Genetic Predisposition to Disease, Generic health relevance, Sequence Analysis, Sequence Deletion, Human, Biotechnology
Abstract

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.

Published
2011

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