Literature DB >> 28890534

Harnessing ancient genomes to study the history of human adaptation.

Stephanie Marciniak1, George H Perry1,2,3.   

Abstract

The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens. Together with evidence of adaptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome data sets for domesticated animals and plants, these studies provide novel insights into human evolution and the evolutionary consequences of human behaviour that go well beyond those that can be obtained from modern genomic data or the fossil and archaeological records alone.

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Year:  2017        PMID: 28890534     DOI: 10.1038/nrg.2017.65

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  184 in total

1.  Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean.

Authors:  Hannes Schroeder; María C Ávila-Arcos; Anna-Sapfo Malaspinas; G David Poznik; Marcela Sandoval-Velasco; Meredith L Carpenter; José Víctor Moreno-Mayar; Martin Sikora; Philip L F Johnson; Morten Erik Allentoft; José Alfredo Samaniego; Jay B Haviser; Michael W Dee; Thomas W Stafford; Antonio Salas; Ludovic Orlando; Eske Willerslev; Carlos D Bustamante; M Thomas P Gilbert
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-09       Impact factor: 11.205

2.  Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849.

Authors:  Alison M Devault; G Brian Golding; Nicholas Waglechner; Jacob M Enk; Melanie Kuch; Joseph H Tien; Mang Shi; David N Fisman; Anna N Dhody; Stephen Forrest; Kirsten I Bos; David J D Earn; Edward C Holmes; Hendrik N Poinar
Journal:  N Engl J Med       Date:  2014-01-08       Impact factor: 91.245

3.  Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins.

Authors:  Matthias Meyer; Juan-Luis Arsuaga; Cesare de Filippo; Sarah Nagel; Ayinuer Aximu-Petri; Birgit Nickel; Ignacio Martínez; Ana Gracia; José María Bermúdez de Castro; Eudald Carbonell; Bence Viola; Janet Kelso; Kay Prüfer; Svante Pääbo
Journal:  Nature       Date:  2016-03-14       Impact factor: 49.962

4.  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

Review 5.  Positive natural selection in the human lineage.

Authors:  P C Sabeti; S F Schaffner; B Fry; J Lohmueller; P Varilly; O Shamovsky; A Palma; T S Mikkelsen; D Altshuler; E S Lander
Journal:  Science       Date:  2006-06-16       Impact factor: 47.728

6.  Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.

Authors:  Pablo Librado; Clio Der Sarkissian; Luca Ermini; Mikkel Schubert; Hákon Jónsson; Anders Albrechtsen; Matteo Fumagalli; Melinda A Yang; Cristina Gamba; Andaine Seguin-Orlando; Cecilie D Mortensen; Bent Petersen; Cindi A Hoover; Belen Lorente-Galdos; Artem Nedoluzhko; Eugenia Boulygina; Svetlana Tsygankova; Markus Neuditschko; Vidhya Jagannathan; Catherine Thèves; Ahmed H Alfarhan; Saleh A Alquraishi; Khaled A S Al-Rasheid; Thomas Sicheritz-Ponten; Ruslan Popov; Semyon Grigoriev; Anatoly N Alekseev; Edward M Rubin; Molly McCue; Stefan Rieder; Tosso Leeb; Alexei Tikhonov; Eric Crubézy; Montgomery Slatkin; Tomas Marques-Bonet; Rasmus Nielsen; Eske Willerslev; Juha Kantanen; Egor Prokhortchouk; Ludovic Orlando
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-23       Impact factor: 11.205

7.  Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone.

Authors:  Ron Pinhasi; Daniel Fernandes; Kendra Sirak; Mario Novak; Sarah Connell; Songül Alpaslan-Roodenberg; Fokke Gerritsen; Vyacheslav Moiseyev; Andrey Gromov; Pál Raczky; Alexandra Anders; Michael Pietrusewsky; Gary Rollefson; Marija Jovanovic; Hiep Trinhhoang; Guy Bar-Oz; Marc Oxenham; Hirofumi Matsumura; Michael Hofreiter
Journal:  PLoS One       Date:  2015-06-18       Impact factor: 3.240

8.  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

9.  Diet adaptation in dog reflects spread of prehistoric agriculture.

Authors:  M Arendt; K M Cairns; J W O Ballard; P Savolainen; E Axelsson
Journal:  Heredity (Edinb)       Date:  2016-07-13       Impact factor: 3.821

10.  Ancient European dog genomes reveal continuity since the Early Neolithic.

Authors:  Laura R Botigué; Shiya Song; Amelie Scheu; Shyamalika Gopalan; Amanda L Pendleton; Matthew Oetjens; Angela M Taravella; Timo Seregély; Andrea Zeeb-Lanz; Rose-Marie Arbogast; Dean Bobo; Kevin Daly; Martina Unterländer; Joachim Burger; Jeffrey M Kidd; Krishna R Veeramah
Journal:  Nat Commun       Date:  2017-07-18       Impact factor: 14.919

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  45 in total

1.  Late Bronze Age cultural origins of dairy pastoralism in Mongolia.

Authors:  Ludovic Orlando
Journal:  Proc Natl Acad Sci U S A       Date:  2018-11-12       Impact factor: 11.205

2.  Identifying and Classifying Shared Selective Sweeps from Multilocus Data.

Authors:  Alexandre M Harris; Michael DeGiorgio
Journal:  Genetics       Date:  2020-03-09       Impact factor: 4.562

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

4.  Beyond drugs: the evolution of genes involved in human response to medications.

Authors:  Silvia Fuselli
Journal:  Proc Biol Sci       Date:  2019-10-23       Impact factor: 5.349

5.  PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations.

Authors:  Chao Zhang; Yang Gao; Zhilin Ning; Yan Lu; Xiaoxi Zhang; Jiaojiao Liu; Bo Xie; Zhe Xue; Xiaoji Wang; Kai Yuan; Xueling Ge; Yuwen Pan; Chang Liu; Lei Tian; Yuchen Wang; Dongsheng Lu; Boon-Peng Hoh; Shuhua Xu
Journal:  Genome Biol       Date:  2019-10-22       Impact factor: 13.583

Review 6.  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

7.  Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.

Authors:  Gabriel Renaud; Kristian Hanghøj; Thorfinn Sand Korneliussen; Eske Willerslev; Ludovic Orlando
Journal:  Genetics       Date:  2019-05-14       Impact factor: 4.562

Review 8.  Human adaptation over the past 40,000 years.

Authors:  Iain Mathieson
Journal:  Curr Opin Genet Dev       Date:  2020-08-01       Impact factor: 5.578

Review 9.  How human behavior can impact the evolution of genetically-mediated behavior in wild non-human species.

Authors:  George H Perry
Journal:  J Comp Physiol A Neuroethol Sens Neural Behav Physiol       Date:  2020-03-23       Impact factor: 1.836

10.  Archaeogenomic evidence from the southwestern US points to a pre-Hispanic scarlet macaw breeding colony.

Authors:  Richard J George; Stephen Plog; Adam S Watson; Kari L Schmidt; Brendan J Culleton; Thomas K Harper; Patricia A Gilman; Steven A LeBlanc; George Amato; Peter Whiteley; Logan Kistler; Douglas J Kennett
Journal:  Proc Natl Acad Sci U S A       Date:  2018-08-13       Impact factor: 11.205

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