Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

Genome Research
PingHsun HsiehMichael F Hammer

Abstract

Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of Afri...Continue Reading

References

May 20, 1999·Molecular Biology and Evolution·H J BandeltA Röhl
Jun 22, 2000·Proceedings of the National Academy of Sciences of the United States of America·R ThomsonM W Feldman
Mar 20, 2003·Molecular Biology and Evolution·Galina V Glazko, Masatoshi Nei
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Jul 27, 2005·Biochemical Society Transactions·J HardyJ Duckworth
Aug 10, 2006·PLoS Genetics·Vincent Plagnol, Jeffrey D Wall
Oct 10, 2006·Current Opinion in Genetics & Development·Jeffrey D Wall, Michael F Hammer
Nov 9, 2006·Proceedings of the National Academy of Sciences of the United States of America·Patrick D EvansBruce T Lahn
Mar 16, 2007·Nature·James Mallet
Jun 5, 2007·PLoS Genetics·Scott H WilliamsonRasmus Nielsen
Oct 19, 2007·Nature·UNKNOWN International HapMap ConsortiumJohn Stewart
Nov 26, 2008·Genome Research·Gary K ChenJeffrey D Wall
May 2, 2009·Science·Sarah A TishkoffScott M Williams
May 8, 2009·Molecular Biology and Evolution·Jeffrey D WallVincent Plagnol
May 13, 2009·Genetics·Alan R Rogers, Chad Huff
Jul 8, 2009·Proceedings of the National Academy of Sciences of the United States of America·G Philip Rightmire
May 8, 2010·Science·Richard E GreenSvante Pääbo
Feb 5, 2011·Science·Peter B deMenocal
May 3, 2011·PLoS Genetics·Priya MoorjaniDavid Reich
Jul 22, 2011·Nature·Anjali G HinchSimon R Myers
Sep 8, 2011·Proceedings of the National Academy of Sciences of the United States of America·Michael F HammerJeffrey D Wall
Sep 8, 2011·Heredity·A D Twyford, R A Ennos
Sep 29, 2011·American Journal of Human Genetics·David ReichMark Stoneking
Sep 29, 2011·PloS One·Katerina HarvatiCaleb Adebayo Folorunso
Oct 29, 2011·Evolutionary Anthropology·Dietmar ZinnerChristian Roos
Apr 12, 2012·Genetics·Simon Gravel
Aug 14, 2012·American Journal of Human Genetics·Fernando L MendezMichael F Hammer
Aug 15, 2012·Proceedings of the National Academy of Sciences of the United States of America·Kevin E LangergraberLinda Vigilant
Oct 12, 2012·PLoS Genetics·Sriram SankararamanDavid Reich
Oct 18, 2012·Nature Communications·Joseph K PickrellBrigitte Pakendorf
Jan 15, 2013·Molecular Biology and Evolution·Fernando L MendezMichael F Hammer
May 1, 2013·Scientific American·Michael F Hammer
Aug 13, 2013·American Journal of Human Genetics·Priya MoorjaniLalji Singh

❮ Previous
Next ❯

Citations

Jun 15, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Chris Stringer
Sep 24, 2016·Current Opinion in Genetics & Development·Jeffrey D Wall, Debora Yoshihara Caldeira Brandt
May 10, 2017·ELife·Jessica C Thompson
May 18, 2017·Annals of Human Biology·Charlotte J HouldcroftSimon J Underdown
Jan 20, 2017·Nature·Rasmus NielsenEske Willerslev
Sep 29, 2017·Molecular Biology and Evolution·Duo XuOmer Gokcumen
Jun 1, 2018·PLoS Genetics·Aaron B Wolf, Joshua M Akey
May 10, 2017·ELife·Lee R BergerEric M Roberts
May 5, 2018·Annual Review of Genomics and Human Genetics·Carina M Schlebusch, Mattias Jakobsson
Sep 19, 2018·PLoS Genetics·Laurits SkovRichard Durbin
May 1, 2019·Nature Ecology & Evolution·Martin KuhlwilmTomas Marques-Bonet
Jun 11, 2019·PLoS Genetics·Aaron P Ragsdale, Simon Gravel
Jun 6, 2019·Annals of Human Biology·Cindy SantanderCristian Capelli
Sep 4, 2019·Nature Genetics·Kelley Harris
Nov 9, 2019·American Journal of Physical Anthropology·Omer Gokcumen
Sep 14, 2017·PloS One·Clément ZanolliCatherine Mollereau
May 10, 2018·Human Molecular Genetics·Ananyo ChoudhuryMichèle Ramsay
Nov 16, 2016·Science·Shaohua FanSarah A Tishkoff
Feb 19, 2019·Frontiers in Plant Science·Concetta BurgarellaCécile Berthouly-Salazar
Oct 19, 2017·Genome Biology and Evolution·Recep Ozgur TaskentOmer Gokcumen
Nov 21, 2017·Evolutionary Applications·Riaan F RifkinDon A Cowan
Feb 7, 2021·Evolutionary Anthropology·Marc Kissel, AgustÍn Fuentes
Feb 12, 2021·Nature·Anders BergströmPontus Skoglund
Jan 8, 2021·Nature Reviews. Genetics·Mary Lauren BentonJohn A Capra
Jan 14, 2021·Human Molecular Genetics·Nina HollfelderMattias Jakobsson
Apr 15, 2021·Journal of Pediatric Endocrinology & Metabolism : JPEM·Aman PulunganJan M Wit
Aug 12, 2020·Journal of Human Evolution·Osbjorn M PearsonChristian A Tryon
May 25, 2021·Genome Biology and Evolution·K D AhlquistKelsey E Witt

❮ Previous
Next ❯

Related Concepts

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.

Ancient DNA

Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, but are notoriously difficult to analyze due to molecular damage and exogenous dna contamination. Discover the latest research on Ancient DNA here.