Literature DB >> 25168683

Toward a new history and geography of human genes informed by ancient DNA.

Joseph K Pickrell1, David Reich2.   

Abstract

Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture, and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world's human populations. In light of this we argue that it is time to critically reevaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.
Copyright © 2014 Elsevier Ltd. All rights reserved.

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Year:  2014        PMID: 25168683      PMCID: PMC4163019          DOI: 10.1016/j.tig.2014.07.007

Source DB:  PubMed          Journal:  Trends Genet        ISSN: 0168-9525            Impact factor:   11.639


  131 in total

1.  Using environmental correlations to identify loci underlying local adaptation.

Authors:  Graham Coop; David Witonsky; Anna Di Rienzo; Jonathan K Pritchard
Journal:  Genetics       Date:  2010-06-01       Impact factor: 4.562

2.  Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa.

Authors:  Sohini Ramachandran; Omkar Deshpande; Charles C Roseman; Noah A Rosenberg; Marcus W Feldman; L Luca Cavalli-Sforza
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-21       Impact factor: 11.205

3.  Principal components analysis corrects for stratification in genome-wide association studies.

Authors:  Alkes L Price; Nick J Patterson; Robert M Plenge; Michael E Weinblatt; Nancy A Shadick; David Reich
Journal:  Nat Genet       Date:  2006-07-23       Impact factor: 38.330

4.  The global pattern of gene identity variation reveals a history of long-range migrations, bottlenecks, and local mate exchange: implications for biological race.

Authors:  Keith L Hunley; Meghan E Healy; Jeffrey C Long
Journal:  Am J Phys Anthropol       Date:  2009-05       Impact factor: 2.868

5.  Brief communication: human cranial variation fits iterative founder effect model with African origin.

Authors:  Noreen von Cramon-Taubadel; Stephen J Lycett
Journal:  Am J Phys Anthropol       Date:  2008-05       Impact factor: 2.868

6.  Molecular cloning of Ancient Egyptian mummy DNA.

Authors:  S Pääbo
Journal:  Nature       Date:  1985 Apr 18-24       Impact factor: 49.962

7.  The complete genome sequence of a Neanderthal from the Altai Mountains.

Authors:  Kay Prüfer; Fernando Racimo; Nick Patterson; Flora Jay; Sriram Sankararaman; Susanna Sawyer; Anja Heinze; Gabriel Renaud; Peter H Sudmant; Cesare de Filippo; Heng Li; Swapan Mallick; Michael Dannemann; Qiaomei Fu; Martin Kircher; Martin Kuhlwilm; Michael Lachmann; Matthias Meyer; Matthias Ongyerth; Michael Siebauer; Christoph Theunert; Arti Tandon; Priya Moorjani; Joseph Pickrell; James C Mullikin; Samuel H Vohr; Richard E Green; Ines Hellmann; Philip L F Johnson; Hélène Blanche; Howard Cann; Jacob O Kitzman; Jay Shendure; Evan E Eichler; Ed S Lein; Trygve E Bakken; Liubov V Golovanova; Vladimir B Doronichev; Michael V Shunkov; Anatoli P Derevianko; Bence Viola; Montgomery Slatkin; David Reich; Janet Kelso; Svante Pääbo
Journal:  Nature       Date:  2013-12-18       Impact factor: 49.962

8.  Ancient human genomes suggest three ancestral populations for present-day Europeans.

Authors:  Iosif Lazaridis; Nick Patterson; Alissa Mittnik; Gabriel Renaud; Swapan Mallick; Karola Kirsanow; Peter H Sudmant; Joshua G Schraiber; Sergi Castellano; Mark Lipson; Bonnie Berger; Christos Economou; Ruth Bollongino; Qiaomei Fu; Kirsten I Bos; Susanne Nordenfelt; Heng Li; Cesare de Filippo; Kay Prüfer; Susanna Sawyer; Cosimo Posth; Wolfgang Haak; Fredrik Hallgren; Elin Fornander; Nadin Rohland; Dominique Delsate; Michael Francken; Jean-Michel Guinet; Joachim Wahl; George Ayodo; 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 Cali; 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 Hammer; Brenna M Henn; Tor Hervig; Ugur Hodoglugil; Aashish R Jha; Sena Karachanak-Yankova; Rita Khusainova; Elza Khusnutdinova; Rick Kittles; Toomas Kivisild; William Klitz; Vaidutis Kučinskas; Alena Kushniarevich; Leila Laredj; Sergey Litvinov; Theologos Loukidis; Robert W Mahley; Béla Melegh; Ene Metspalu; Julio Molina; Joanna Mountain; Klemetti Näkkäläjärvi; Desislava Nesheva; Thomas Nyambo; Ludmila Osipova; Jüri Parik; Fedor Platonov; Olga Posukh; Valentino Romano; Francisco Rothhammer; Igor Rudan; Ruslan Ruizbakiev; 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; Tatijana Zemunik; Alan Cooper; Cristian Capelli; Mark G Thomas; Andres Ruiz-Linares; Sarah A Tishkoff; Lalji Singh; Kumarasamy Thangaraj; Richard Villems; David Comas; Rem Sukernik; Mait Metspalu; Matthias Meyer; Evan E Eichler; Joachim Burger; Montgomery Slatkin; Svante Pääbo; Janet Kelso; David Reich; Johannes Krause
Journal:  Nature       Date:  2014-09-18       Impact factor: 49.962

9.  The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation.

Authors:  Jonathan K Pritchard; Joseph K Pickrell; Graham Coop
Journal:  Curr Biol       Date:  2010-02-23       Impact factor: 10.834

10.  Reconstructing the population genetic history of the Caribbean.

Authors:  Andrés Moreno-Estrada; Simon Gravel; Fouad Zakharia; Jacob L McCauley; Jake K Byrnes; Christopher R Gignoux; Patricia A Ortiz-Tello; Ricardo J Martínez; Dale J Hedges; Richard W Morris; Celeste Eng; Karla Sandoval; Suehelay Acevedo-Acevedo; Paul J Norman; Zulay Layrisse; Peter Parham; Juan Carlos Martínez-Cruzado; Esteban González Burchard; Michael L Cuccaro; Eden R Martin; Carlos D Bustamante
Journal:  PLoS Genet       Date:  2013-11-14       Impact factor: 5.917

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  56 in total

1.  Patterns of deleterious variation between human populations reveal an unbalanced load.

Authors:  Rajiv C McCoy; Joshua M Akey
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-19       Impact factor: 11.205

2.  Admixture, Population Structure, and F-Statistics.

Authors:  Benjamin M Peter
Journal:  Genetics       Date:  2016-02-08       Impact factor: 4.562

3.  The Role of Standing Variation in Geographic Convergent Adaptation.

Authors:  Peter L Ralph; Graham Coop
Journal:  Am Nat       Date:  2015-09-08       Impact factor: 3.926

4.  Ancient DNA and human history.

Authors:  Montgomery Slatkin; Fernando Racimo
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-06       Impact factor: 11.205

Review 5.  Reconstructing ancient genomes and epigenomes.

Authors:  Ludovic Orlando; M Thomas P Gilbert; Eske Willerslev
Journal:  Nat Rev Genet       Date:  2015-06-09       Impact factor: 53.242

6.  Inference of Population Structure from Time-Series Genotype Data.

Authors:  Tyler A Joseph; Itsik Pe'er
Journal:  Am J Hum Genet       Date:  2019-06-27       Impact factor: 11.025

7.  [aDNA Research From a Historical Perspective].

Authors:  Elsbeth Bösl
Journal:  NTM       Date:  2017-03

Review 8.  The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research.

Authors:  Francesc Calafell; Maarten H D Larmuseau
Journal:  Hum Genet       Date:  2016-11-05       Impact factor: 4.132

Review 9.  Going global by adapting local: A review of recent human adaptation.

Authors:  Shaohua Fan; Matthew E B Hansen; Yancy Lo; Sarah A Tishkoff
Journal:  Science       Date:  2016-10-07       Impact factor: 47.728

Review 10.  Recent advances in the study of fine-scale population structure in humans.

Authors:  John Novembre; Benjamin M Peter
Journal:  Curr Opin Genet Dev       Date:  2016-09-20       Impact factor: 5.578

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