Literature DB >> 21868630

The shaping of modern human immune systems by multiregional admixture with archaic humans.

Laurent Abi-Rached1, Matthew J Jobin, Subhash Kulkarni, Alasdair McWhinnie, Klara Dalva, Loren Gragert, Farbod Babrzadeh, Baback Gharizadeh, Ma Luo, Francis A Plummer, Joshua Kimani, Mary Carrington, Derek Middleton, Raja Rajalingam, Meral Beksac, Steven G E Marsh, Martin Maiers, Lisbeth A Guethlein, Sofia Tavoularis, Ann-Margaret Little, Richard E Green, Paul J Norman, Peter Parham.   

Abstract

Whole genome comparisons identified introgression from archaic to modern humans. Our analysis of highly polymorphic human leukocyte antigen (HLA) class I, vital immune system components subject to strong balancing selection, shows how modern humans acquired the HLA-B*73 allele in west Asia through admixture with archaic humans called Denisovans, a likely sister group to the Neandertals. Virtual genotyping of Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally distinctive alleles that have introgressed into modern Eurasian and Oceanian populations. These alleles, of which several encode unique or strong ligands for natural killer cell receptors, now represent more than half the HLA alleles of modern Eurasians and also appear to have been later introduced into Africans. Thus, adaptive introgression of archaic alleles has significantly shaped modern human immune systems.

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Year:  2011        PMID: 21868630      PMCID: PMC3677943          DOI: 10.1126/science.1209202

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  30 in total

1.  Synergistic polymorphism at two positions distal to the ligand-binding site makes KIR2DL2 a stronger receptor for HLA-C than KIR2DL3.

Authors:  Achim K Moesta; Paul J Norman; Makoto Yawata; Nobuyo Yawata; Michael Gleimer; Peter Parham
Journal:  J Immunol       Date:  2008-03-15       Impact factor: 5.422

2.  REJECTOR: software for population history inference from genetic data via a rejection algorithm.

Authors:  Matthew J Jobin; Joanna L Mountain
Journal:  Bioinformatics       Date:  2008-10-20       Impact factor: 6.937

3.  A draft sequence of the Neandertal genome.

Authors:  Johannes Krause; Adrian W Briggs; Tomislav Maricic; Udo Stenzel; Martin Kircher; Nick Patterson; Richard E Green; Heng Li; Weiwei Zhai; Markus Hsi-Yang Fritz; Nancy F Hansen; Eric Y Durand; Anna-Sapfo Malaspinas; Jeffrey D Jensen; Tomas Marques-Bonet; Can Alkan; Kay Prüfer; Matthias Meyer; Hernán A Burbano; Jeffrey M Good; Rigo Schultz; Ayinuer Aximu-Petri; Anne Butthof; Barbara Höber; Barbara Höffner; Madlen Siegemund; Antje Weihmann; Chad Nusbaum; Eric S Lander; Carsten Russ; Nathaniel Novod; Jason Affourtit; Michael Egholm; Christine Verna; Pavao Rudan; Dejana Brajkovic; Željko Kucan; Ivan Gušic; Vladimir B Doronichev; Liubov V Golovanova; Carles Lalueza-Fox; Marco de la Rasilla; Javier Fortea; Antonio Rosas; Ralf W Schmitz; Philip L F Johnson; Evan E Eichler; Daniel Falush; Ewan Birney; James C Mullikin; Montgomery Slatkin; Rasmus Nielsen; Janet Kelso; Michael Lachmann; David Reich; Svante Pääbo
Journal:  Science       Date:  2010-05-07       Impact factor: 47.728

4.  Genetic history of an archaic hominin group from Denisova Cave in Siberia.

Authors:  David Reich; Richard E Green; Martin Kircher; Johannes Krause; Nick Patterson; Eric Y Durand; Bence Viola; Adrian W Briggs; Udo Stenzel; Philip L F Johnson; Tomislav Maricic; Jeffrey M Good; Tomas Marques-Bonet; Can Alkan; Qiaomei Fu; Swapan Mallick; Heng Li; Matthias Meyer; Evan E Eichler; Mark Stoneking; Michael Richards; Sahra Talamo; Michael V Shunkov; Anatoli P Derevianko; Jean-Jacques Hublin; Janet Kelso; Montgomery Slatkin; Svante Pääbo
Journal:  Nature       Date:  2010-12-23       Impact factor: 49.962

5.  MHC class I-specific inhibitory receptors and their ligands structure diverse human NK-cell repertoires toward a balance of missing self-response.

Authors:  Makoto Yawata; Nobuyo Yawata; Monia Draghi; Fotini Partheniou; Ann-Margaret Little; Peter Parham
Journal:  Blood       Date:  2008-06-26       Impact factor: 22.113

6.  Out of Africa: modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa.

Authors:  Michael DeGiorgio; Mattias Jakobsson; Noah A Rosenberg
Journal:  Proc Natl Acad Sci U S A       Date:  2009-08-17       Impact factor: 11.205

7.  Balancing selection is the main force shaping the evolution of innate immunity genes.

Authors:  Anna Ferrer-Admetlla; Elena Bosch; Martin Sikora; Tomàs Marquès-Bonet; Anna Ramírez-Soriano; Aura Muntasell; Arcadi Navarro; Ross Lazarus; Francesc Calafell; Jaume Bertranpetit; Ferran Casals
Journal:  J Immunol       Date:  2008-07-15       Impact factor: 5.422

8.  Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations.

Authors:  Faviel F Gonzalez-Galarza; Stephen Christmas; Derek Middleton; Andrew R Jones
Journal:  Nucleic Acids Res       Date:  2010-11-09       Impact factor: 16.971

9.  KIR2DS4 is a product of gene conversion with KIR3DL2 that introduced specificity for HLA-A*11 while diminishing avidity for HLA-C.

Authors:  Thorsten Graef; Achim K Moesta; Paul J Norman; Laurent Abi-Rached; Luca Vago; Anastazia M Older Aguilar; Michael Gleimer; John A Hammond; Lisbeth A Guethlein; David A Bushnell; Philip J Robinson; Peter Parham
Journal:  J Exp Med       Date:  2009-10-26       Impact factor: 14.307

10.  The peopling of the Pacific from a bacterial perspective.

Authors:  Yoshan Moodley; Bodo Linz; Yoshio Yamaoka; Helen M Windsor; Sebastien Breurec; Jeng-Yih Wu; Ayas Maady; Steffie Bernhöft; Jean-Michel Thiberge; Suparat Phuanukoonnon; Gangolf Jobb; Peter Siba; David Y Graham; Barry J Marshall; Mark Achtman
Journal:  Science       Date:  2009-01-23       Impact factor: 63.714

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  159 in total

Review 1.  The impact of recent events on human genetic diversity.

Authors:  Mark A Jobling
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2012-03-19       Impact factor: 6.237

2.  Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes.

Authors:  Matthieu Deschamps; Guillaume Laval; Maud Fagny; Yuval Itan; Laurent Abel; Jean-Laurent Casanova; Etienne Patin; Lluis Quintana-Murci
Journal:  Am J Hum Genet       Date:  2016-01-07       Impact factor: 11.025

3.  Human phylogeography and diversity.

Authors:  Alexander H Harcourt
Journal:  Proc Natl Acad Sci U S A       Date:  2016-07-19       Impact factor: 11.205

Review 4.  Hybridization in human evolution: Insights from other organisms.

Authors:  Rebecca R Ackermann; Michael L Arnold; Marcella D Baiz; James A Cahill; Liliana Cortés-Ortiz; Ben J Evans; B Rosemary Grant; Peter R Grant; Benedikt Hallgrimsson; Robyn A Humphreys; Clifford J Jolly; Joanna Malukiewicz; Christopher J Percival; Terrence B Ritzman; Christian Roos; Charles C Roseman; Lauren Schroeder; Fred H Smith; Kerryn A Warren; Robert K Wayne; Dietmar Zinner
Journal:  Evol Anthropol       Date:  2019-06-20

5.  The Polynesian gene pool: an early contribution by Amerindians to Easter Island.

Authors:  Erik Thorsby
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2012-03-19       Impact factor: 6.237

Review 6.  Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations.

Authors:  Marcelo A Fernandez Vina; Jill A Hollenbach; Kirsten E Lyke; Marcelo B Sztein; Martin Maiers; William Klitz; Pedro Cano; Steven Mack; Richard Single; Chaim Brautbar; Shosahna Israel; Eduardo Raimondi; Evelyne Khoriaty; Adlette Inati; Marco Andreani; Manuela Testi; Maria Elisa Moraes; Glenys Thomson; Peter Stastny; Kai Cao
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2012-03-19       Impact factor: 6.237

7.  Diverse approaches to analysing the history of human and pathogen evolution: how to tell the story of the past 70 000 years.

Authors:  D M Altmann; F Balloux; R J Boyton
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2012-03-19       Impact factor: 6.237

8.  Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.

Authors:  Sharon R Browning; Brian L Browning; Ying Zhou; Serena Tucci; Joshua M Akey
Journal:  Cell       Date:  2018-03-15       Impact factor: 41.582

Review 9.  Evolutionary and population (epi)genetics of immunity to infection.

Authors:  Luis B Barreiro; Lluis Quintana-Murci
Journal:  Hum Genet       Date:  2020-04-13       Impact factor: 4.132

Review 10.  Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction.

Authors:  Federico Sánchez-Quinto; Carles Lalueza-Fox
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2015-01-19       Impact factor: 6.237

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