Literature DB >> 27274045

Ancient DNA and human history.

Montgomery Slatkin1, Fernando Racimo2.   

Abstract

We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history.

Entities:  

Keywords:  Denisovan; Neanderthal; ancient DNA; demography; human history

Mesh:

Substances:

Year:  2016        PMID: 27274045      PMCID: PMC4988579          DOI: 10.1073/pnas.1524306113

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  76 in total

1.  On the probability of Neanderthal ancestry.

Authors:  M Nordborg
Journal:  Am J Hum Genet       Date:  1998-10       Impact factor: 11.025

2.  The genetic prehistory of the New World Arctic.

Authors:  Maanasa Raghavan; Michael DeGiorgio; Anders Albrechtsen; Ida Moltke; Pontus Skoglund; Thorfinn S Korneliussen; Bjarne Grønnow; Martin Appelt; Hans Christian Gulløv; T Max Friesen; William Fitzhugh; Helena Malmström; Simon Rasmussen; Jesper Olsen; Linea Melchior; Benjamin T Fuller; Simon M Fahrni; Thomas Stafford; Vaughan Grimes; M A Priscilla Renouf; Jerome Cybulski; Niels Lynnerup; Marta Mirazon Lahr; Kate Britton; Rick Knecht; Jette Arneborg; Mait Metspalu; Omar E Cornejo; Anna-Sapfo Malaspinas; Yong Wang; Morten Rasmussen; Vibha Raghavan; Thomas V O Hansen; Elza Khusnutdinova; Tracey Pierre; Kirill Dneprovsky; Claus Andreasen; Hans Lange; M Geoffrey Hayes; Joan Coltrain; Victor A Spitsyn; Anders Götherström; Ludovic Orlando; Toomas Kivisild; Richard Villems; Michael H Crawford; Finn C Nielsen; Jørgen Dissing; Jan Heinemeier; Morten Meldgaard; Carlos Bustamante; Dennis H O'Rourke; Mattias Jakobsson; M Thomas P Gilbert; Rasmus Nielsen; Eske Willerslev
Journal:  Science       Date:  2014-08-29       Impact factor: 47.728

3.  Early farmers from across Europe directly descended from Neolithic Aegeans.

Authors:  Zuzana Hofmanová; Susanne Kreutzer; Garrett Hellenthal; Christian Sell; Yoan Diekmann; David Díez-Del-Molino; Lucy van Dorp; Saioa López; Athanasios Kousathanas; Vivian Link; Karola Kirsanow; Lara M Cassidy; Rui Martiniano; Melanie Strobel; Amelie Scheu; Kostas Kotsakis; Paul Halstead; Sevi Triantaphyllou; Nina Kyparissi-Apostolika; Dushka Urem-Kotsou; Christina Ziota; Fotini Adaktylou; Shyamalika Gopalan; Dean M Bobo; Laura Winkelbach; Jens Blöcher; Martina Unterländer; Christoph Leuenberger; Çiler Çilingiroğlu; Barbara Horejs; Fokke Gerritsen; Stephen J Shennan; Daniel G Bradley; Mathias Currat; Krishna R Veeramah; Daniel Wegmann; Mark G Thomas; Christina Papageorgopoulou; Joachim Burger
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-06       Impact factor: 11.205

4.  mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.

Authors:  Hákon Jónsson; Aurélien Ginolhac; Mikkel Schubert; Philip L F Johnson; Ludovic Orlando
Journal:  Bioinformatics       Date:  2013-04-23       Impact factor: 6.937

5.  Inference of human population history from individual whole-genome sequences.

Authors:  Heng Li; Richard Durbin
Journal:  Nature       Date:  2011-07-13       Impact factor: 49.962

6.  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

7.  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

8.  ANGSD: Analysis of Next Generation Sequencing Data.

Authors:  Thorfinn Sand Korneliussen; Anders Albrechtsen; Rasmus Nielsen
Journal:  BMC Bioinformatics       Date:  2014-11-25       Impact factor: 3.169

9.  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

10.  A population genetic signal of polygenic adaptation.

Authors:  Jeremy J Berg; Graham Coop
Journal:  PLoS Genet       Date:  2014-08-07       Impact factor: 5.917

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  31 in total

Review 1.  Methods for detecting introgressed archaic sequences.

Authors:  Sriram Sankararaman
Journal:  Curr Opin Genet Dev       Date:  2020-07-24       Impact factor: 5.578

2.  Issues in human evolution.

Authors:  Richard G Klein
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-07       Impact factor: 11.205

Review 3.  Fostering Responsible Research on Ancient DNA.

Authors:  Jennifer K Wagner; Chip Colwell; Katrina G Claw; Anne C Stone; Deborah A Bolnick; John Hawks; Kyle B Brothers; Nanibaa' A Garrison
Journal:  Am J Hum Genet       Date:  2020-08-06       Impact factor: 11.025

Review 4.  Demographic history, selection and functional diversity of the canine genome.

Authors:  Elaine A Ostrander; Robert K Wayne; Adam H Freedman; Brian W Davis
Journal:  Nat Rev Genet       Date:  2017-09-25       Impact factor: 53.242

5.  Detecting Polygenic Adaptation in Admixture Graphs.

Authors:  Fernando Racimo; Jeremy J Berg; Joseph K Pickrell
Journal:  Genetics       Date:  2018-01-18       Impact factor: 4.562

6.  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 7.  Beyond broad strokes: sociocultural insights from the study of ancient genomes.

Authors:  Fernando Racimo; Martin Sikora; Marc Vander Linden; Hannes Schroeder; Carles Lalueza-Fox
Journal:  Nat Rev Genet       Date:  2020-03-03       Impact factor: 53.242

8.  Neutral evolution of human enamel-dentine junction morphology.

Authors:  Tesla A Monson; Diego Fecker; Marc Scherrer
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-05       Impact factor: 11.205

9.  Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans.

Authors:  Matthias Steinrücken; Jeffrey P Spence; John A Kamm; Emilia Wieczorek; Yun S Song
Journal:  Mol Ecol       Date:  2018-04-17       Impact factor: 6.185

10.  Inference of population genetic parameters from an irregular time series of seasonal influenza virus sequences.

Authors:  Myriam Croze; Yuseob Kim
Journal:  Genetics       Date:  2021-02-09       Impact factor: 4.562

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