Targeted investigation of the Neandertal genome by array-based sequence capture
Hernán A. Burbano,Emily Hodges,Emily Hodges,Richard E. Green,Adrian W. Briggs,Johannes Krause,Matthias Meyer,Jeffrey M. Good,Tomislav Maricic,Philipp L.F. Johnson,Zhenyu Xuan,Zhenyu Xuan,Michelle Rooks,Michelle Rooks,Arindam Bhattacharjee,Leonardo Brizuela,Frank W. Albert,Marco de la Rasilla,Javier Fortea,Antonio Rosas,Michael Lachmann,Gregory J. Hannon,Gregory J. Hannon,Svante Pääbo +23 more
TLDR
It is shown that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of ~99.8% microbial DNA.Abstract:
Neandertals, our closest relatives, ranged across Europe and Southwest Asia before their extinction approximately 30,000 years ago. Green et al. (p. [710][1]) report a draft sequence of the Neandertal genome, created from three individuals, and compare it with genomes of five modern humans. The results suggest that ancient genomes of human relatives can be recovered with acceptably low contamination from modern human DNA. Because ancient DNA can be contaminated with microbial DNA, Burbano et al. (p. [723][2]) developed a target sequence capture approach to obtain 14 kilobases of Neandertal DNA from a fairly poorly preserved sample with a high microbial load. A number of genomic regions and genes were revealed as candidates for positive selection early in modern human history. The genomic data suggest that Neandertals mixed with modern human ancestors some 120,000 years ago, leaving traces of Neandertal DNA in contemporary humans.
[1]: /lookup/doi/10.1126/science.1188021
[2]: /lookup/doi/10.1126/science.1188046read more
Citations
More filters
疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI
A Draft Sequence of the Neandertal Genome
Richard E. Green,Johannes Krause,Adrian W. Briggs,Tomislav Maricic,Udo Stenzel,Martin Kircher,Nick Patterson,Heng Li,Weiwei Zhai,Markus Hsi-Yang Fritz,Nancy F. Hansen,Eric Durand,Anna-Sapfo Malaspinas,Jeffrey D. Jensen,Tomas Marques-Bonet,Tomas Marques-Bonet,Can Alkan,Kay Prüfer,Matthias Meyer,Hernán A. Burbano,Jeffrey M. Good,Jeffrey M. Good,Rigo Schultz,Ayinuer Aximu-Petri,Anne Butthof,Barbara Höber,Barbara Höffner,Madien Siegemund,Antje Weihmann,Chad Nusbaum,Eric S. Lander,Carsten Russ,Nathaniel Novod,Jason P. Affourtit,Michael Egholm,Christine Verna,Pavao Rudan,Dejana Brajković,Željko Kućan,Ivan Gušić,Vladimir B. Doronichev,Liubov V. Golovanova,Carles Lalueza-Fox,Marco de la Rasilla,Javier Fortea,Antonio Rosas,Ralf 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,David Reich,Svante Pääbo +58 more
TL;DR: The genomic data suggest that Neandertals mixed with modern human ancestors some 120,000 years ago, leaving traces of Ne andertal DNA in contemporary humans, suggesting that gene flow from Neand Bertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
Journal ArticleDOI
Gut microbiota, metabolites and host immunity
TL;DR: Technological and computational approaches for investigating the microbiome, as well as recent advances in the understanding of host immunity and microbial mutualism are discussed with a focus on specific microbial metabolites, bacterial components and the immune system.
Journal ArticleDOI
A high-coverage genome sequence from an archaic Denisovan individual
Matthias Meyer,Martin Kircher,Marie Theres Gansauge,Heng Li,Fernando Racimo,Swapan Mallick,Swapan Mallick,Joshua G. Schraiber,Flora Jay,Kay Prüfer,Cesare de Filippo,Peter H. Sudmant,Can Alkan,Can Alkan,Qiaomei Fu,Qiaomei Fu,Ron Do,Nadin Rohland,Nadin Rohland,Arti Tandon,Arti Tandon,Michael Siebauer,Richard E. Green,Katarzyna Bryc,Adrian W. Briggs,Udo Stenzel,Jesse Dabney,Jay Shendure,Jacob O. Kitzman,Michael F. Hammer,Michael V. Shunkov,A.P. Derevianko,Nick Patterson,Aida M. Andrés,Evan E. Eichler,Evan E. Eichler,Montgomery Slatkin,David Reich,David Reich,Janet Kelso,Svante Pääbo +40 more
TL;DR: The genomic sequence provides evidence for very low rates of heterozygosity in the Denisova, probably not because of recent inbreeding, but instead because of a small population size, and illuminates the relationships between humans and archaics, including Neandertals, and establishes a catalog of genetic changes within the human lineage.
Journal ArticleDOI
Harnessing the power of RADseq for ecological and evolutionary genomics
TL;DR: This Review provides a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.
References
More filters
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Related Papers (5)
A Draft Sequence of the Neandertal Genome
Richard E. Green,Johannes Krause,Adrian W. Briggs,Tomislav Maricic,Udo Stenzel,Martin Kircher,Nick Patterson,Heng Li,Weiwei Zhai,Markus Hsi-Yang Fritz,Nancy F. Hansen,Eric Durand,Anna-Sapfo Malaspinas,Jeffrey D. Jensen,Tomas Marques-Bonet,Tomas Marques-Bonet,Can Alkan,Kay Prüfer,Matthias Meyer,Hernán A. Burbano,Jeffrey M. Good,Jeffrey M. Good,Rigo Schultz,Ayinuer Aximu-Petri,Anne Butthof,Barbara Höber,Barbara Höffner,Madien Siegemund,Antje Weihmann,Chad Nusbaum,Eric S. Lander,Carsten Russ,Nathaniel Novod,Jason P. Affourtit,Michael Egholm,Christine Verna,Pavao Rudan,Dejana Brajković,Željko Kućan,Ivan Gušić,Vladimir B. Doronichev,Liubov V. Golovanova,Carles Lalueza-Fox,Marco de la Rasilla,Javier Fortea,Antonio Rosas,Ralf 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,David Reich,Svante Pääbo +58 more
Genetic history of an archaic hominin group from Denisova Cave in Siberia
David Reich,Richard E. Green,Martin Kircher,Johannes Krause,Nick Patterson,Eric Durand,Bence Viola,Adrian W. Briggs,Udo Stenzel,Philip L. F. Johnson,Tomislav Maricic,Jeffrey M. Good,Tomas Marques-Bonet,Tomas Marques-Bonet,Can Alkan,Qiaomei Fu,Swapan Mallick,Swapan Mallick,Heng Li,Matthias Meyer,Evan E. Eichler,Mark Stoneking,Michael P. Richards,Sahra Talamo,Michael V. Shunkov,A.P. Derevianko,Jean-Jacques Hublin,Janet Kelso,Montgomery Slatkin,Svante Pääbo +29 more
Ancient human genome sequence of an extinct Palaeo-Eskimo
Morten Rasmussen,Yingrui Li,Stinus Lindgreen,Jakob Skou Pedersen,Anders Albrechtsen,Ida Moltke,Mait Metspalu,Ene Metspalu,Toomas Kivisild,Toomas Kivisild,Ramneek Gupta,Marcelo Bertalan,Kasper Nielsen,M. Thomas P. Gilbert,Yong Wang,Maanasa Raghavan,Maanasa Raghavan,Paula F. Campos,Hanne Munkholm Kamp,Andrew Wilson,Andrew Gledhill,Silvana R. Tridico,Silvana R. Tridico,Michael Bunce,Eline D. Lorenzen,Jonas Binladen,Xiaosen Guo,Jing Zhao,Xiuqing Zhang,Hao Zhang,Zhuo Li,Minfeng Chen,Ludovic Orlando,Karsten Kristiansen,Mads Bak,Niels Tommerup,Christian Bendixen,Tracey Pierre,Bjarne Grønnow,Morten Meldgaard,Claus Andreasen,S. A. Fedorova,S. A. Fedorova,Ludmila P. Osipova,Thomas Higham,Christopher Bronk Ramsey,Thomas Hansen,Finn Cilius Nielsen,Michael H. Crawford,Søren Brunak,Søren Brunak,Thomas Sicheritz-Pontén,Richard Villems,Rasmus Nielsen,Rasmus Nielsen,Anders Krogh,Jun Wang,Eske Willerslev +57 more
A high-coverage genome sequence from an archaic Denisovan individual
Matthias Meyer,Martin Kircher,Marie Theres Gansauge,Heng Li,Fernando Racimo,Swapan Mallick,Swapan Mallick,Joshua G. Schraiber,Flora Jay,Kay Prüfer,Cesare de Filippo,Peter H. Sudmant,Can Alkan,Can Alkan,Qiaomei Fu,Qiaomei Fu,Ron Do,Nadin Rohland,Nadin Rohland,Arti Tandon,Arti Tandon,Michael Siebauer,Richard E. Green,Katarzyna Bryc,Adrian W. Briggs,Udo Stenzel,Jesse Dabney,Jay Shendure,Jacob O. Kitzman,Michael F. Hammer,Michael V. Shunkov,A.P. Derevianko,Nick Patterson,Aida M. Andrés,Evan E. Eichler,Evan E. Eichler,Montgomery Slatkin,David Reich,David Reich,Janet Kelso,Svante Pääbo +40 more