Literature DB >> 27810637

Inferences of African evolutionary history from genomic data.

Marcia Holsbach Beltrame1, Meagan A Rubel2, Sarah A Tishkoff3.   

Abstract

Africa is the origin of anatomically modern humans and a continent of linguistic, cultural, environmental, phenotypic, and genetic diversity. However, African populations remain underrepresented in genetic studies, which have largely focused on individuals with European and Asian ancestry. The expansion of high-throughput 'omic' technologies to interrogate multiple tissue types across many biomolecules-DNA, proteins, epigenetic modifications, metabolites, and others-has heralded a new era of investigation into African history. In this review, we summarize how some of these recent advances have been applied to contemporary sub-Saharan African populations to inform studies on human origins and adaptation.
Copyright © 2016 Elsevier Ltd. All rights reserved.

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Year:  2016        PMID: 27810637      PMCID: PMC5161638          DOI: 10.1016/j.gde.2016.10.002

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  71 in total

1.  A human genome diversity cell line panel.

Authors:  Howard M Cann; Claudia de Toma; Lucien Cazes; Marie-Fernande Legrand; Valerie Morel; Laurence Piouffre; Julia Bodmer; Walter F Bodmer; Batsheva Bonne-Tamir; Anne Cambon-Thomsen; Zhu Chen; J Chu; Carlo Carcassi; Licinio Contu; Ruofu Du; Laurent Excoffier; G B Ferrara; Jonathan S Friedlaender; Helena Groot; David Gurwitz; Trefor Jenkins; Rene J Herrera; Xiaoyi Huang; Judith Kidd; Kenneth K Kidd; Andre Langaney; Alice A Lin; S Qasim Mehdi; Peter Parham; Alberto Piazza; Maria Pia Pistillo; Yaping Qian; Qunfang Shu; Jiujin Xu; S Zhu; James L Weber; Henry T Greely; Marcus W Feldman; Gilles Thomas; Jean Dausset; L Luca Cavalli-Sforza
Journal:  Science       Date:  2002-04-12       Impact factor: 47.728

2.  Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.

Authors:  Carlotta De Filippo; Duccio Cavalieri; Monica Di Paola; Matteo Ramazzotti; Jean Baptiste Poullet; Sebastien Massart; Silvia Collini; Giuseppe Pieraccini; Paolo Lionetti
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-02       Impact factor: 11.205

3.  Genome-wide association study indicates two novel resistance loci for severe malaria.

Authors:  Christian Timmann; Thorsten Thye; Maren Vens; Jennifer Evans; Jürgen May; Christa Ehmen; Jürgen Sievertsen; Birgit Muntau; Gerd Ruge; Wibke Loag; Daniel Ansong; Sampson Antwi; Emanuel Asafo-Adjei; Samuel Blay Nguah; Kingsley Osei Kwakye; Alex Osei Yaw Akoto; Justice Sylverken; Michael Brendel; Kathrin Schuldt; Christina Loley; Andre Franke; Christian G Meyer; Tsiri Agbenyega; Andreas Ziegler; Rolf D Horstmann
Journal:  Nature       Date:  2012-08-15       Impact factor: 49.962

4.  Diet and the evolution of human amylase gene copy number variation.

Authors:  George H Perry; Nathaniel J Dominy; Katrina G Claw; Arthur S Lee; Heike Fiegler; Richard Redon; John Werner; Fernando A Villanea; Joanna L Mountain; Rajeev Misra; Nigel P Carter; Charles Lee; Anne C Stone
Journal:  Nat Genet       Date:  2007-09-09       Impact factor: 38.330

5.  The genetic architecture of adaptations to high altitude in Ethiopia.

Authors:  Gorka Alkorta-Aranburu; Cynthia M Beall; David B Witonsky; Amha Gebremedhin; Jonathan K Pritchard; Anna Di Rienzo
Journal:  PLoS Genet       Date:  2012-12-06       Impact factor: 5.917

6.  Genetic adaptation to high altitude in the Ethiopian highlands.

Authors:  Laura B Scheinfeldt; Sameer Soi; Simon Thompson; Alessia Ranciaro; Dawit Woldemeskel; William Beggs; Charla Lambert; Joseph P Jarvis; Dawit Abate; Gurja Belay; Sarah A Tishkoff
Journal:  Genome Biol       Date:  2012-01-20       Impact factor: 13.583

7.  Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging.

Authors:  Viviane Labrie; Orion J Buske; Edward Oh; Richie Jeremian; Carolyn Ptak; Giedrius Gasiūnas; Almantas Maleckas; Rūta Petereit; Aida Žvirbliene; Kęstutis Adamonis; Edita Kriukienė; Karolis Koncevičius; Juozas Gordevičius; Akhil Nair; Aiping Zhang; Sasha Ebrahimi; Gabriel Oh; Virginijus Šikšnys; Limas Kupčinskas; Michael Brudno; Arturas Petronis
Journal:  Nat Struct Mol Biol       Date:  2016-05-09       Impact factor: 15.369

8.  A global reference for human genetic variation.

Authors:  Adam Auton; Lisa D Brooks; Richard M Durbin; Erik P Garrison; Hyun Min Kang; Jan O Korbel; Jonathan L Marchini; Shane McCarthy; Gil A McVean; Gonçalo R Abecasis
Journal:  Nature       Date:  2015-10-01       Impact factor: 49.962

9.  Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection.

Authors:  PingHsun Hsieh; Krishna R Veeramah; Joseph Lachance; Sarah A Tishkoff; Jeffrey D Wall; Michael F Hammer; Ryan N Gutenkunst
Journal:  Genome Res       Date:  2016-02-17       Impact factor: 9.043

10.  Genome-wide and fine-resolution association analysis of malaria in West Africa.

Authors:  Muminatou Jallow; Yik Ying Teo; Kerrin S Small; Kirk A Rockett; Panos Deloukas; Taane G Clark; Katja Kivinen; Kalifa A Bojang; David J Conway; Margaret Pinder; Giorgio Sirugo; Fatou Sisay-Joof; Stanley Usen; Sarah Auburn; Suzannah J Bumpstead; Susana Campino; Alison Coffey; Andrew Dunham; Andrew E Fry; Angela Green; Rhian Gwilliam; Sarah E Hunt; Michael Inouye; Anna E Jeffreys; Alieu Mendy; Aarno Palotie; Simon Potter; Jiannis Ragoussis; Jane Rogers; Kate Rowlands; Elilan Somaskantharajah; Pamela Whittaker; Claire Widden; Peter Donnelly; Bryan Howie; Jonathan Marchini; Andrew Morris; Miguel SanJoaquin; Eric Akum Achidi; Tsiri Agbenyega; Angela Allen; Olukemi Amodu; Patrick Corran; Abdoulaye Djimde; Amagana Dolo; Ogobara K Doumbo; Chris Drakeley; Sarah Dunstan; Jennifer Evans; Jeremy Farrar; Deepika Fernando; Tran Tinh Hien; Rolf D Horstmann; Muntaser Ibrahim; Nadira Karunaweera; Gilbert Kokwaro; Kwadwo A Koram; Martha Lemnge; Julie Makani; Kevin Marsh; Pascal Michon; David Modiano; Malcolm E Molyneux; Ivo Mueller; Michael Parker; Norbert Peshu; Christopher V Plowe; Odile Puijalon; John Reeder; Hugh Reyburn; Eleanor M Riley; Anavaj Sakuntabhai; Pratap Singhasivanon; Sodiomon Sirima; Adama Tall; Terrie E Taylor; Mahamadou Thera; Marita Troye-Blomberg; Thomas N Williams; Michael Wilson; Dominic P Kwiatkowski
Journal:  Nat Genet       Date:  2009-05-24       Impact factor: 38.330

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  10 in total

1.  Global variation in gene expression and the value of diverse sampling.

Authors:  Derek E Kelly; Matthew E B Hansen; Sarah A Tishkoff
Journal:  Curr Opin Syst Biol       Date:  2017-03-03

Review 2.  Tracing the peopling of the world through genomics.

Authors:  Rasmus Nielsen; Joshua M Akey; Mattias Jakobsson; Jonathan K Pritchard; Sarah Tishkoff; Eske Willerslev
Journal:  Nature       Date:  2017-01-18       Impact factor: 49.962

3.  Marked variation in prevalence of malaria-protective human genetic polymorphisms across Uganda.

Authors:  Andrew Walakira; Stephen Tukwasibwe; Moses Kiggundu; Federica Verra; Patrick Kakeeto; Emmanuel Ruhamyankaka; Chris Drakeley; Grant Dorsey; Moses R Kamya; Samuel L Nsobya; Philip J Rosenthal
Journal:  Infect Genet Evol       Date:  2017-09-19       Impact factor: 3.342

4.  Race-Dependent Association of Single-Nucleotide Polymorphisms in TrkB Receptor in People Living with HIV and Depression.

Authors:  Valeria Avdoshina; Futoshi Yumoto; Italo Mocchetti; Scott L Letendre; Rochelle E Tractenberg
Journal:  Neurotox Res       Date:  2021-10-06       Impact factor: 3.911

5.  Loci associated with skin pigmentation identified in African populations.

Authors:  Nicholas G Crawford; Derek E Kelly; Matthew E B Hansen; Marcia H Beltrame; Shaohua Fan; Shanna L Bowman; Ethan Jewett; Alessia Ranciaro; Simon Thompson; Yancy Lo; Susanne P Pfeifer; Jeffrey D Jensen; Michael C Campbell; William Beggs; Farhad Hormozdiari; Sununguko Wata Mpoloka; Gaonyadiwe George Mokone; Thomas Nyambo; Dawit Wolde Meskel; Gurja Belay; Jake Haut; Harriet Rothschild; Leonard Zon; Yi Zhou; Michael A Kovacs; Mai Xu; Tongwu Zhang; Kevin Bishop; Jason Sinclair; Cecilia Rivas; Eugene Elliot; Jiyeon Choi; Shengchao A Li; Belynda Hicks; Shawn Burgess; Christian Abnet; Dawn E Watkins-Chow; Elena Oceana; Yun S Song; Eleazar Eskin; Kevin M Brown; Michael S Marks; Stacie K Loftus; William J Pavan; Meredith Yeager; Stephen Chanock; Sarah A Tishkoff
Journal:  Science       Date:  2017-10-12       Impact factor: 47.728

6.  Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well-documented population from sub-Saharan Africa.

Authors:  T Goeury; L E Creary; L Brunet; M Galan; M Pasquier; B Kervaire; A Langaney; J-M Tiercy; M A Fernández-Viña; J M Nunes; A Sanchez-Mazas
Journal:  HLA       Date:  2018-01       Impact factor: 4.513

7.  Homo naledi and Pleistocene hominin evolution in subequatorial Africa.

Authors:  Lee R Berger; John Hawks; Paul Hgm Dirks; Marina Elliott; Eric M Roberts
Journal:  Elife       Date:  2017-05-09       Impact factor: 8.140

8.  Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations.

Authors:  Belen Lorente-Galdos; Oscar Lao; Gerard Serra-Vidal; Gabriel Santpere; Lukas F K Kuderna; Lara R Arauna; Karima Fadhlaoui-Zid; Ville N Pimenoff; Himla Soodyall; Pierre Zalloua; Tomas Marques-Bonet; David Comas
Journal:  Genome Biol       Date:  2019-04-26       Impact factor: 13.583

9.  African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations.

Authors:  Shaohua Fan; Derek E Kelly; Marcia H Beltrame; Matthew E B Hansen; Swapan Mallick; Alessia Ranciaro; Jibril Hirbo; Simon Thompson; William Beggs; Thomas Nyambo; Sabah A Omar; Dawit Wolde Meskel; Gurja Belay; Alain Froment; Nick Patterson; David Reich; Sarah A Tishkoff
Journal:  Genome Biol       Date:  2019-04-26       Impact factor: 13.583

Review 10.  Prospective avenues for human population genomics and disease mapping in southern Africa.

Authors:  Yolandi Swart; Gerald van Eeden; Anel Sparks; Caitlin Uren; Marlo Möller
Journal:  Mol Genet Genomics       Date:  2020-05-21       Impact factor: 2.980

  10 in total

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