The genetic prehistory of southern Africa
Joseph K. Pickrell,Nick Patterson,Chiara Barbieri,Falko Berthold,Linda Gerlach,Tom Güldemann,Blesswell Kure,Sununguko Wata Mpoloka,Hirosi Nakagawa,Christfried Naumann,Mark Lipson,Po-Ru Loh,Joseph Lachance,Joanna L. Mountain,Carlos Bustamante,Bonnie Berger,Sarah A. Tishkoff,Brenna M. Henn,Mark Stoneking,David Reich,David Reich,Brigitte Pakendorf +21 more
Reads0
Chats0
TLDR
It is found that all individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began ∼1,200 years ago, supporting the hypothesis of an ancient link between southern and eastern Africa.Abstract:
Southern and eastern African populations that speak non-Bantu languages with click consonants are known to harbour some of the most ancient genetic lineages in humans, but their relationships are poorly understood. Here, we report data from 23 populations analysed at over half a million single-nucleotide polymorphisms, using a genome-wide array designed for studying human history. The southern African Khoisan fall into two genetic groups, loosely corresponding to the northwestern and southeastern Kalahari, which we show separated within the last 30,000 years. We find that all individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began ∼1,200 years ago. In addition, the East African Hadza and Sandawe derive a fraction of their ancestry from admixture with a population related to the Khoisan, supporting the hypothesis of an ancient link between southern and eastern Africa.read more
Citations
More filters
Journal ArticleDOI
Robust demographic inference from genomic and SNP data.
Laurent Excoffier,Isabelle Dupanloup,Emilia Huerta-Sanchez,Vitor C. Sousa,Matthieu Foll,Matthieu Foll +5 more
TL;DR: A flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets and shows that it allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods.
Journal ArticleDOI
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Swapan Mallick,Swapan Mallick,Swapan Mallick,Heng Li,Mark Lipson,Iain Mathieson,Melissa Gymrek,Fernando Racimo,Mengyao Zhao,Mengyao Zhao,Mengyao Zhao,Niru Chennagiri,Niru Chennagiri,Niru Chennagiri,Susanne Nordenfelt,Susanne Nordenfelt,Susanne Nordenfelt,Arti Tandon,Arti Tandon,Pontus Skoglund,Pontus Skoglund,Iosif Lazaridis,Iosif Lazaridis,Sriram Sankararaman,Sriram Sankararaman,Sriram Sankararaman,Qiaomei Fu,Qiaomei Fu,Qiaomei Fu,Nadin Rohland,Nadin Rohland,Gabriel Renaud,Yaniv Erlich,Thomas Willems,Carla Gallo,Jeffrey P. Spence,Yun S. Song,Yun S. Song,Giovanni Poletti,Francois Balloux,George van Driem,Peter de Knijff,Irene Gallego Romero,Aashish R. Jha,Doron M. Behar,Claudio M. Bravi,Cristian Capelli,Tor Hervig,Andrés Moreno-Estrada,Olga L. Posukh,Elena Balanovska,Oleg Balanovsky,Sena Karachanak-Yankova,Hovhannes Sahakyan,Hovhannes Sahakyan,Draga Toncheva,Levon Yepiskoposyan,Chris Tyler-Smith,Yali Xue,M. Syafiq Abdullah,Andres Ruiz-Linares,Cynthia M. Beall,Anna Di Rienzo,Choongwon Jeong,Elena B. Starikovskaya,Ene Metspalu,Ene Metspalu,Jüri Parik,Richard Villems,Richard Villems,Richard Villems,Brenna M. Henn,Ugur Hodoglugil,Robert W. Mahley,Antti Sajantila,George Stamatoyannopoulos,Joseph Wee,Rita Khusainova,Elza Khusnutdinova,Sergey Litvinov,Sergey Litvinov,George Ayodo,David Comas,Michael F. Hammer,Toomas Kivisild,Toomas Kivisild,William Klitz,Cheryl A. Winkler,Damian Labuda,Michael J. Bamshad,Lynn B. Jorde,Sarah A. Tishkoff,W. Scott Watkins,Mait Metspalu,Stanislav Dryomov,Rem I. Sukernik,Lalji Singh,Lalji Singh,Kumarasamy Thangaraj,Svante Pääbo,Janet Kelso,Nick Patterson,David Reich,David Reich,David Reich +104 more
TL;DR: It is demonstrated 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.
Journal ArticleDOI
Ancient human genomes suggest three ancestral populations for present-day Europeans
Iosif Lazaridis,Iosif Lazaridis,Nick Patterson,Alissa Mittnik,Gabriel Renaud,Swapan Mallick,Swapan Mallick,Karola Kirsanow,Peter H. Sudmant,Joshua G. Schraiber,Joshua G. Schraiber,Sergi Castellano,Mark Lipson,Bonnie Berger,Bonnie Berger,Christos Economou,Ruth Bollongino,Qiaomei Fu,Kirsten I. Bos,Susanne Nordenfelt,Susanne Nordenfelt,Heng Li,Heng Li,Cesare de Filippo,Kay Prüfer,Susanna Sawyer,Cosimo Posth,Wolfgang Haak,Fredrik Hallgren,Elin Fornander,Nadin Rohland,Nadin Rohland,Dominique Delsate,Michael Francken,Jean-Michel Guinet,Joachim Wahl,George Ayodo,Hamza A. Babiker,Hamza A. Babiker,Graciela Bailliet,Elena Balanovska,Oleg Balanovsky,Ramiro Barrantes,Gabriel Bedoya,Haim Ben-Ami,Judit Bene,Fouad Berrada,Claudio M. Bravi,Francesca Brisighelli,George B.J. Busby,Francesco Calì,Mikhail Churnosov,David E. C. Cole,Daniel Corach,Larissa Damba,George van Driem,Stanislav Dryomov,Jean-Michel Dugoujon,Sardana A. Fedorova,Irene Gallego Romero,Marina Gubina,Michael F. Hammer,Brenna M. Henn,Tor Hervig,Ugur Hodoglugil,Aashish R. Jha,Sena Karachanak-Yankova,Rita Khusainova,Elza Khusnutdinova,Rick A. Kittles,Toomas Kivisild,William Klitz,Vaidutis Kučinskas,Alena Kushniarevich,Leila Laredj,Sergey Litvinov,Theologos Loukidis,Theologos Loukidis,Robert W. Mahley,Béla Melegh,Ene Metspalu,Julio Molina,Joanna L. Mountain,Klemetti Näkkäläjärvi,Desislava Nesheva,Thomas B. Nyambo,Ludmila P. Osipova,Jüri Parik,Fedor Platonov,Olga L. Posukh,Valentino Romano,Francisco Rothhammer,Francisco Rothhammer,Igor Rudan,Ruslan Ruizbakiev,Hovhannes Sahakyan,Hovhannes Sahakyan,Antti Sajantila,Antonio Salas,Elena B. Starikovskaya,Ayele Tarekegn,Draga Toncheva,Shahlo Turdikulova,Ingrida Uktveryte,Olga Utevska,René Vasquez,Mercedes Villena,Mikhail Voevoda,Cheryl A. Winkler,Levon Yepiskoposyan,Pierre Zalloua,Pierre Zalloua,Tatijana Zemunik,Alan Cooper,Cristian Capelli,Mark G. Thomas,Andres Ruiz-Linares,Sarah A. Tishkoff,Lalji Singh,Kumarasamy Thangaraj,Richard Villems,Richard Villems,Richard Villems,David Comas,Rem I. Sukernik,Mait Metspalu,Matthias Meyer,Evan E. Eichler,Joachim Burger,Montgomery Slatkin,Svante Pääbo,Janet Kelso,David Reich,David Reich,David Reich,Johannes Krause,Johannes Krause +136 more
TL;DR: It is shown that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians; and early European farmers, who were mainly of Near Eastern origin but also harboured west Europeanhunter-gatherer related ancestry.
Journal ArticleDOI
Inferring human population size and separation history from multiple genome sequences
Stephan Schiffels,Richard Durbin +1 more
TL;DR: Results from applying multiple sequentially Markovian coalescent (MSMC) to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago and give information about human population history as recent as 2,000 Years ago.
Journal ArticleDOI
A genetic atlas of human admixture history.
Garrett Hellenthal,George B.J. Busby,Gavin Band,James F. Wilson,Cristian Capelli,Daniel Falush,Simon Myers,Simon Myers +7 more
TL;DR: An atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years, is revealed, revealing admixture to be an almost universal force shaping human populations.
References
More filters
Journal Article
R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Journal ArticleDOI
Inference of population structure using multilocus genotype data
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
Journal ArticleDOI
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
Shaun Purcell,Shaun Purcell,Benjamin M. Neale,Benjamin M. Neale,Kathe Todd-Brown,Lori Thomas,Manuel A. R. Ferreira,David Bender,David Bender,Julian Maller,Julian Maller,Pamela Sklar,Pamela Sklar,Paul I.W. de Bakker,Paul I.W. de Bakker,Mark J. Daly,Mark J. Daly,Pak C. Sham +17 more
TL;DR: This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.
Journal ArticleDOI
Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies
TL;DR: Extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data are described and methods that allow for linkage between loci are developed, which allows identification of subtle population subdivisions that were not detectable using the existing method.
Journal ArticleDOI
Fast model-based estimation of ancestry in unrelated individuals
TL;DR: The results show that ADMIXTURE's computational speed opens up the possibility of using a much larger set of markers in model-based ancestry estimation and that its estimates are suitable for use in correcting for population stratification in association studies.
Related Papers (5)
The Genetic Structure and History of Africans and African Americans
Sarah A. Tishkoff,Floyd A. Reed,Françoise R. Friedlaender,Christopher Ehret,Alessia Ranciaro,Alessia Ranciaro,Alessia Ranciaro,Alain Froment,Jibril Hirbo,Jibril Hirbo,Agnes A. Awomoyi,Jean-Marie Bodo,Ogobara K. Doumbo,Muntaser E. Ibrahim,Abdalla T. Juma,Maritha J. Kotze,Godfrey Lema,Jason H. Moore,Holly M. Mortensen,Thomas B. Nyambo,Sabah A. Omar,Kweli Powell,Gideon S. Pretorius,Michael W. Smith,Mahamadou A. Thera,Charles Wambebe,James L. Weber,Scott M. Williams +27 more