Literature DB >> 28982794

A high-coverage Neandertal genome from Vindija Cave in Croatia.

Kay Prüfer1, Cesare de Filippo2, Steffi Grote2, Fabrizio Mafessoni2, Petra Korlević2, Mateja Hajdinjak2, Benjamin Vernot2, Laurits Skov3, Pinghsun Hsieh4, Stéphane Peyrégne2, David Reher2, Charlotte Hopfe2, Sarah Nagel2, Tomislav Maricic2, Qiaomei Fu5, Christoph Theunert2,6, Rebekah Rogers6, Pontus Skoglund7, Manjusha Chintalapati2, Michael Dannemann2, Bradley J Nelson4, Felix M Key2, Pavao Rudan8, Željko Kućan8, Ivan Gušić8, Liubov V Golovanova9, Vladimir B Doronichev9, Nick Patterson7, David Reich7,10,11, Evan E Eichler4,12, Montgomery Slatkin6, Mikkel H Schierup3, Aida M Andrés2, Janet Kelso2, Matthias Meyer2, Svante Pääbo1.   

Abstract

To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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Year:  2017        PMID: 28982794      PMCID: PMC6185897          DOI: 10.1126/science.aao1887

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


  107 in total

1.  Patterns of coding variation in the complete exomes of three Neandertals.

Authors:  Sergi Castellano; Genís Parra; Federico A Sánchez-Quinto; Fernando Racimo; Martin Kuhlwilm; Martin Kircher; Susanna Sawyer; Qiaomei Fu; Anja Heinze; Birgit Nickel; Jesse Dabney; Michael Siebauer; Louise White; Hernán A Burbano; Gabriel Renaud; Udo Stenzel; Carles Lalueza-Fox; Marco de la Rasilla; Antonio Rosas; Pavao Rudan; Dejana Brajković; Željko Kucan; Ivan Gušic; Michael V Shunkov; Anatoli P Derevianko; Bence Viola; Matthias Meyer; Janet Kelso; Aida M Andrés; Svante Pääbo
Journal:  Proc Natl Acad Sci U S A       Date:  2014-04-21       Impact factor: 11.205

2.  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

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.  Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico.

Authors:  Amy L Williams; Suzanne B R Jacobs; Hortensia Moreno-Macías; Alicia Huerta-Chagoya; Claire Churchhouse; Carla Márquez-Luna; Humberto García-Ortíz; María José Gómez-Vázquez; Noël P Burtt; Carlos A Aguilar-Salinas; Clicerio González-Villalpando; Jose C Florez; Lorena Orozco; Christopher A Haiman; Teresa Tusié-Luna; David Altshuler
Journal:  Nature       Date:  2013-12-25       Impact factor: 49.962

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.  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

9.  Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations.

Authors:  Hélène Quach; Maxime Rotival; Julien Pothlichet; Yong-Hwee Eddie Loh; Michael Dannemann; Nora Zidane; Guillaume Laval; Etienne Patin; Christine Harmant; Marie Lopez; Matthieu Deschamps; Nadia Naffakh; Darragh Duffy; Anja Coen; Geert Leroux-Roels; Frederic Clément; Anne Boland; Jean-François Deleuze; Janet Kelso; Matthew L Albert; Lluis Quintana-Murci
Journal:  Cell       Date:  2016-10-20       Impact factor: 41.582

10.  Genetic determinants of antithyroid drug-induced agranulocytosis by human leukocyte antigen genotyping and genome-wide association study.

Authors:  Pei-Lung Chen; Shyang-Rong Shih; Pei-Wen Wang; Ying-Chao Lin; Chen-Chung Chu; Jung-Hsin Lin; Szu-Chi Chen; Ching-Chung Chang; Tien-Shang Huang; Keh Sung Tsai; Fen-Yu Tseng; Chih-Yuan Wang; Jin-Ying Lu; Wei-Yih Chiu; Chien-Ching Chang; Yu-Hsuan Chen; Yuan-Tsong Chen; Cathy Shen-Jang Fann; Wei-Shiung Yang; Tien-Chun Chang
Journal:  Nat Commun       Date:  2015-07-07       Impact factor: 14.919

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  138 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

Review 2.  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

3.  Using hominin introgression to trace modern human dispersals.

Authors:  João C Teixeira; Alan Cooper
Journal:  Proc Natl Acad Sci U S A       Date:  2019-07-12       Impact factor: 11.205

4.  DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage.

Authors:  Kristian Hanghøj; Gabriel Renaud; Anders Albrechtsen; Ludovic Orlando
Journal:  Gigascience       Date:  2019-04-01       Impact factor: 6.524

5.  Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment.

Authors:  Cleber A Trujillo; Edward S Rice; Nathan K Schaefer; Isaac A Chaim; Emily C Wheeler; Assael A Madrigal; Justin Buchanan; Sebastian Preissl; Allen Wang; Priscilla D Negraes; Ryan A Szeto; Roberto H Herai; Alik Huseynov; Mariana S A Ferraz; Fernando S Borges; Alexandre H Kihara; Ashley Byrne; Maximillian Marin; Christopher Vollmers; Angela N Brooks; Jonathan D Lautz; Katerina Semendeferi; Beth Shapiro; Gene W Yeo; Stephen E P Smith; Richard E Green; Alysson R Muotri
Journal:  Science       Date:  2021-02-12       Impact factor: 47.728

Review 6.  Origins of modern human ancestry.

Authors:  Anders Bergström; Chris Stringer; Mateja Hajdinjak; Eleanor M L Scerri; Pontus Skoglund
Journal:  Nature       Date:  2021-02-10       Impact factor: 49.962

7.  Impact and Evolutionary Determinants of Neanderthal Introgression on Transcriptional and Post-Transcriptional Regulation.

Authors:  Martin Silvert; Lluis Quintana-Murci; Maxime Rotival
Journal:  Am J Hum Genet       Date:  2019-05-30       Impact factor: 11.025

8.  Genetic susceptibility to severe childhood asthma and rhinovirus-C maintained by balancing selection in humans for 150 000 years.

Authors:  Mary B O'Neill; Guillaume Laval; João C Teixeira; Ann C Palmenberg; Caitlin S Pepperell
Journal:  Hum Mol Genet       Date:  2020-03-27       Impact factor: 6.150

9.  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

10.  No Evidence for Recent Selection at FOXP2 among Diverse Human Populations.

Authors:  Elizabeth Grace Atkinson; Amanda Jane Audesse; Julia Adela Palacios; Dean Michael Bobo; Ashley Elizabeth Webb; Sohini Ramachandran; Brenna Mariah Henn
Journal:  Cell       Date:  2018-08-02       Impact factor: 41.582

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