Literature DB >> 33495542

Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry.

Alexander Immel1, Federica Pierini2, Christoph Rinne3, John Meadows4,5, Rodrigo Barquera6, András Szolek7, Julian Susat1, Lisa Böhme1, Janina Dose1, Joanna Bonczarowska1, Clara Drummer3, Katharina Fuchs1, David Ellinghaus1, Jan Christian Kässens1, Martin Furholt8, Oliver Kohlbacher7,9,10,11, Sabine Schade-Lindig12, Andre Franke1, Stefan Schreiber1,13, Johannes Krause6, Johannes Müller3, Tobias L Lenz2, Almut Nebel1, Ben Krause-Kyora14.   

Abstract

The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We performed genome-wide analyses of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component (34-58%). This component was most likely introduced during the cultural transformation that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct human leukocyte antigen gene pool, possibly reflecting an immune response that was geared towards detecting viral infections.

Entities:  

Year:  2021        PMID: 33495542      PMCID: PMC7835224          DOI: 10.1038/s42003-020-01627-4

Source DB:  PubMed          Journal:  Commun Biol        ISSN: 2399-3642


  55 in total

1.  NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data.

Authors:  Vanessa Jurtz; Sinu Paul; Massimo Andreatta; Paolo Marcatili; Bjoern Peters; Morten Nielsen
Journal:  J Immunol       Date:  2017-10-04       Impact factor: 5.422

2.  MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

Authors:  Sudhir Kumar; Glen Stecher; Michael Li; Christina Knyaz; Koichiro Tamura
Journal:  Mol Biol Evol       Date:  2018-06-01       Impact factor: 16.240

3.  Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load.

Authors:  Paul J McLaren; Cedric Coulonges; István Bartha; Tobias L Lenz; Aaron J Deutsch; Arman Bashirova; Susan Buchbinder; Mary N Carrington; Andrea Cossarizza; Judith Dalmau; Andrea De Luca; James J Goedert; Deepti Gurdasani; David W Haas; Joshua T Herbeck; Eric O Johnson; Gregory D Kirk; Olivier Lambotte; Ma Luo; Simon Mallal; Daniëlle van Manen; Javier Martinez-Picado; Laurence Meyer; José M Miro; James I Mullins; Niels Obel; Guido Poli; Manjinder S Sandhu; Hanneke Schuitemaker; Patrick R Shea; Ioannis Theodorou; Bruce D Walker; Amy C Weintrob; Cheryl A Winkler; Steven M Wolinsky; Soumya Raychaudhuri; David B Goldstein; Amalio Telenti; Paul I W de Bakker; Jean-François Zagury; Jacques Fellay
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-09       Impact factor: 11.205

4.  Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform.

Authors:  Martin Kircher; Susanna Sawyer; Matthias Meyer
Journal:  Nucleic Acids Res       Date:  2011-10-21       Impact factor: 16.971

5.  MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.

Authors:  Daniel H Huson; Sina Beier; Isabell Flade; Anna Górska; Mohamed El-Hadidi; Suparna Mitra; Hans-Joachim Ruscheweyh; Rewati Tappu
Journal:  PLoS Comput Biol       Date:  2016-06-21       Impact factor: 4.475

6.  The Beaker phenomenon and the genomic transformation of northwest Europe.

Authors:  Iñigo Olalde; Selina Brace; Morten E Allentoft; Ian Armit; Kristian Kristiansen; Thomas Booth; Nadin Rohland; Swapan Mallick; Anna Szécsényi-Nagy; Alissa Mittnik; Eveline Altena; Mark Lipson; Iosif Lazaridis; Thomas K Harper; Nick Patterson; Nasreen Broomandkhoshbacht; Yoan Diekmann; Zuzana Faltyskova; Daniel Fernandes; Matthew Ferry; Eadaoin Harney; Peter de Knijff; Megan Michel; Jonas Oppenheimer; Kristin Stewardson; Alistair Barclay; Kurt Werner Alt; Corina Liesau; Patricia Ríos; Concepción Blasco; Jorge Vega Miguel; Roberto Menduiña García; Azucena Avilés Fernández; Eszter Bánffy; Maria Bernabò-Brea; David Billoin; Clive Bonsall; Laura Bonsall; Tim Allen; Lindsey Büster; Sophie Carver; Laura Castells Navarro; Oliver E Craig; Gordon T Cook; Barry Cunliffe; Anthony Denaire; Kirsten Egging Dinwiddy; Natasha Dodwell; Michal Ernée; Christopher Evans; Milan Kuchařík; Joan Francès Farré; Chris Fowler; Michiel Gazenbeek; Rafael Garrido Pena; María Haber-Uriarte; Elżbieta Haduch; Gill Hey; Nick Jowett; Timothy Knowles; Ken Massy; Saskia Pfrengle; Philippe Lefranc; Olivier Lemercier; Arnaud Lefebvre; César Heras Martínez; Virginia Galera Olmo; Ana Bastida Ramírez; Joaquín Lomba Maurandi; Tona Majó; Jacqueline I McKinley; Kathleen McSweeney; Balázs Gusztáv Mende; Alessandra Modi; Gabriella Kulcsár; Viktória Kiss; András Czene; Róbert Patay; Anna Endrődi; Kitti Köhler; Tamás Hajdu; Tamás Szeniczey; János Dani; Zsolt Bernert; Maya Hoole; Olivia Cheronet; Denise Keating; Petr Velemínský; Miroslav Dobeš; Francesca Candilio; Fraser Brown; Raúl Flores Fernández; Ana-Mercedes Herrero-Corral; Sebastiano Tusa; Emiliano Carnieri; Luigi Lentini; Antonella Valenti; Alessandro Zanini; Clive Waddington; Germán Delibes; Elisa Guerra-Doce; Benjamin Neil; Marcus Brittain; Mike Luke; Richard Mortimer; Jocelyne Desideri; Marie Besse; Günter Brücken; Mirosław Furmanek; Agata Hałuszko; Maksym Mackiewicz; Artur Rapiński; Stephany Leach; Ignacio Soriano; Katina T Lillios; João Luís Cardoso; Michael Parker Pearson; Piotr Włodarczak; T Douglas Price; Pilar Prieto; Pierre-Jérôme Rey; Roberto Risch; Manuel A Rojo Guerra; Aurore Schmitt; Joël Serralongue; Ana Maria Silva; Václav Smrčka; Luc Vergnaud; João Zilhão; David Caramelli; Thomas Higham; Mark G Thomas; Douglas J Kennett; Harry Fokkens; Volker Heyd; Alison Sheridan; Karl-Göran Sjögren; Philipp W Stockhammer; Johannes Krause; Ron Pinhasi; Wolfgang Haak; Ian Barnes; Carles Lalueza-Fox; David Reich
Journal:  Nature       Date:  2018-02-21       Impact factor: 49.962

7.  Ancient genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers.

Authors:  Maïté Rivollat; Choongwon Jeong; Stephan Schiffels; İşil Küçükkalıpçı; Marie-Hélène Pemonge; Adam Benjamin Rohrlach; Kurt W Alt; Didier Binder; Susanne Friederich; Emmanuel Ghesquière; Detlef Gronenborn; Luc Laporte; Philippe Lefranc; Harald Meller; Hélène Réveillas; Eva Rosenstock; Stéphane Rottier; Chris Scarre; Ludovic Soler; Joachim Wahl; Johannes Krause; Marie-France Deguilloux; Wolfgang Haak
Journal:  Sci Adv       Date:  2020-05-29       Impact factor: 14.136

8.  Fast and accurate long-read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2010-01-15       Impact factor: 6.937

9.  Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection.

Authors:  Federica Pierini; Tobias L Lenz
Journal:  Mol Biol Evol       Date:  2018-09-01       Impact factor: 16.240

10.  HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation.

Authors:  Jatin Arora; Federica Pierini; Paul J McLaren; Mary Carrington; Jacques Fellay; Tobias L Lenz
Journal:  Mol Biol Evol       Date:  2020-03-01       Impact factor: 16.240

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  2 in total

Review 1.  New insights into human immunity from ancient genomics.

Authors:  Gaspard Kerner; Etienne Patin; Lluis Quintana-Murci
Journal:  Curr Opin Immunol       Date:  2021-05-13       Impact factor: 7.268

2.  Ancient DNA Study in Medieval Europeans Shows an Association Between HLA-DRB1*03 and Paratyphoid Fever.

Authors:  Magdalena Haller; Joanna H Bonczarowska; Dirk Rieger; Tobias L Lenz; Almut Nebel; Ben Krause-Kyora
Journal:  Front Immunol       Date:  2021-07-15       Impact factor: 7.561

  2 in total

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