Literature DB >> 26055157

Reconstructing ancient genomes and epigenomes.

Ludovic Orlando1, M Thomas P Gilbert2, Eske Willerslev3.   

Abstract

Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes.

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Year:  2015        PMID： 26055157     DOI： 10.1038/nrg3935

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN： 1471-0056            Impact factor:   53.242


  122 in total

1.  Partial uracil-DNA-glycosylase treatment for screening of ancient DNA.

Authors:  Nadin Rohland; Eadaoin Harney; Swapan Mallick; Susanne Nordenfelt; David Reich
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2015-01-19       Impact factor: 6.237

2.  Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean.

Authors:  Hannes Schroeder; María C Ávila-Arcos; Anna-Sapfo Malaspinas; G David Poznik; Marcela Sandoval-Velasco; Meredith L Carpenter; José Víctor Moreno-Mayar; Martin Sikora; Philip L F Johnson; Morten Erik Allentoft; José Alfredo Samaniego; Jay B Haviser; Michael W Dee; Thomas W Stafford; Antonio Salas; Ludovic Orlando; Eske Willerslev; Carlos D Bustamante; M Thomas P Gilbert
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-09       Impact factor: 11.205

3.  The genetic prehistory of the New World Arctic.

Authors:  Maanasa Raghavan; Michael DeGiorgio; Anders Albrechtsen; Ida Moltke; Pontus Skoglund; Thorfinn S Korneliussen; Bjarne Grønnow; Martin Appelt; Hans Christian Gulløv; T Max Friesen; William Fitzhugh; Helena Malmström; Simon Rasmussen; Jesper Olsen; Linea Melchior; Benjamin T Fuller; Simon M Fahrni; Thomas Stafford; Vaughan Grimes; M A Priscilla Renouf; Jerome Cybulski; Niels Lynnerup; Marta Mirazon Lahr; Kate Britton; Rick Knecht; Jette Arneborg; Mait Metspalu; Omar E Cornejo; Anna-Sapfo Malaspinas; Yong Wang; Morten Rasmussen; Vibha Raghavan; Thomas V O Hansen; Elza Khusnutdinova; Tracey Pierre; Kirill Dneprovsky; Claus Andreasen; Hans Lange; M Geoffrey Hayes; Joan Coltrain; Victor A Spitsyn; Anders Götherström; Ludovic Orlando; Toomas Kivisild; Richard Villems; Michael H Crawford; Finn C Nielsen; Jørgen Dissing; Jan Heinemeier; Morten Meldgaard; Carlos Bustamante; Dennis H O'Rourke; Mattias Jakobsson; M Thomas P Gilbert; Rasmus Nielsen; Eske Willerslev
Journal:  Science       Date:  2014-08-29       Impact factor: 47.728

4.  Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849.

Authors:  Alison M Devault; G Brian Golding; Nicholas Waglechner; Jacob M Enk; Melanie Kuch; Joseph H Tien; Mang Shi; David N Fisman; Anna N Dhody; Stephen Forrest; Kirsten I Bos; David J D Earn; Edward C Holmes; Hendrik N Poinar
Journal:  N Engl J Med       Date:  2014-01-08       Impact factor: 91.245

5.  Reconstructing the DNA methylation maps of the Neandertal and the Denisovan.

Authors:  David Gokhman; Eitan Lavi; Kay Prüfer; Mario F Fraga; José A Riancho; Janet Kelso; Svante Pääbo; Eran Meshorer; Liran Carmel
Journal:  Science       Date:  2014-04-17       Impact factor: 47.728

6.  Multiplexed DNA sequence capture of mitochondrial genomes using PCR products.

Authors:  Tomislav Maricic; Mark Whitten; Svante Pääbo
Journal:  PLoS One       Date:  2010-11-16       Impact factor: 3.240

7.  Sequencing the nuclear genome of the extinct woolly mammoth.

Authors:  Webb Miller; Daniela I Drautz; Aakrosh Ratan; Barbara Pusey; Ji Qi; Arthur M Lesk; Lynn P Tomsho; Michael D Packard; Fangqing Zhao; Andrei Sher; Alexei Tikhonov; Brian Raney; Nick Patterson; Kerstin Lindblad-Toh; Eric S Lander; James R Knight; Gerard P Irzyk; Karin M Fredrikson; Timothy T Harkins; Sharon Sheridan; Tom Pringle; Stephan C Schuster
Journal:  Nature       Date:  2008-11-20       Impact factor: 49.962

8.  DNA damage and DNA sequence retrieval from ancient tissues.

Authors:  M Höss; P Jaruga; T H Zastawny; M Dizdaroglu; S Pääbo
Journal:  Nucleic Acids Res       Date:  1996-04-01       Impact factor: 16.971

9.  mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.

Authors:  Hákon Jónsson; Aurélien Ginolhac; Mikkel Schubert; Philip L F Johnson; Ludovic Orlando
Journal:  Bioinformatics       Date:  2013-04-23       Impact factor: 6.937

10.  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
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  57 in total

1.  Craniodental and Postcranial Characters of Non-Avian Dinosauria Often Imply Different Trees.

Authors:  Yimeng Li; Marcello Ruta; Matthew A Wills
Journal:  Syst Biol       Date:  2020-07-01       Impact factor: 15.683

2.  Genetics: new tales from ancient DNA.

Authors:  Vivien Marx
Journal:  Nat Methods       Date:  2017-07-28       Impact factor: 28.547

3.  Late Bronze Age cultural origins of dairy pastoralism in Mongolia.

Authors:  Ludovic Orlando
Journal:  Proc Natl Acad Sci U S A       Date:  2018-11-12       Impact factor: 11.205

4.  Back to the roots and routes of dromedary domestication.

Authors:  Ludovic Orlando
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-25       Impact factor: 11.205

5.  Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens.

Authors:  Lu Yao; Kelsey Witt; Hongjie Li; Jonathan Rice; Nelson R Salinas; Robert D Martin; Emilia Huerta-Sánchez; Ripan S Malhi
Journal:  Am J Phys Anthropol       Date:  2020-07-08       Impact factor: 2.868

6.  A Simple Test Identifies Selection on Complex Traits.

Authors:  Tim Beissinger; Jochen Kruppa; David Cavero; Ngoc-Thuy Ha; Malena Erbe; Henner Simianer
Journal:  Genetics       Date:  2018-03-15       Impact factor: 4.562

Review 7.  On the origins and domestication of the olive: a review and perspectives.

Authors:  Guillaume Besnard; Jean-Frédéric Terral; Amandine Cornille
Journal:  Ann Bot       Date:  2018-03-05       Impact factor: 4.357

8.  A new model for ancient DNA decay based on paleogenomic meta-analysis.

Authors:  Logan Kistler; Roselyn Ware; Oliver Smith; Matthew Collins; Robin G Allaby
Journal:  Nucleic Acids Res       Date:  2017-06-20       Impact factor: 16.971

9.  A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data.

Authors:  J Víctor Moreno-Mayar; Thorfinn Sand Korneliussen; Jyoti Dalal; Gabriel Renaud; Anders Albrechtsen; Rasmus Nielsen; Anna-Sapfo Malaspinas
Journal:  Bioinformatics       Date:  2020-02-01       Impact factor: 6.937

Review 10.  Harnessing ancient genomes to study the history of human adaptation.

Authors:  Stephanie Marciniak; George H Perry
Journal:  Nat Rev Genet       Date:  2017-09-11       Impact factor: 53.242
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