mapDamage: testing for damage patterns in ancient DNA sequences.
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TLDR
The mapDamage as discussed by the authors is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome, which are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences.Abstract:
Summary: Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequencing reads that could be advantageously used to argue for sequence validity. mapDamage is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. The Perl script outputs are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences. Availability and implementation: The Perl script mapDamage is freely available with documentation and example files at http://geogenetics.ku.dk/all_literature/mapdamage/. The script requires prior installation of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems. Contact: aginolhac@snm.ku.dk Supplementary information: Supplementary data available at Bioinformatics onlineread more
Citations
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mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
TL;DR: This work describes mapDamage 2.0, a user-friendly package that extends the original features of mapDamage by incorporating a statistical model of DNA damage, and provides estimates of four key features of aDNA molecules: the average length of overhangs, nick frequency, cytosine deamination rates in both double-stranded regions and overhangers, and base quality scores according to their probability of being damaged.
Journal ArticleDOI
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
Ludovic Orlando,Aurélien Ginolhac,Guojie Zhang,Duane G. Froese,Anders Albrechtsen,Mathias Stiller,Mikkel Schubert,Enrico Cappellini,Bent O. Petersen,Ida Moltke,Ida Moltke,Philip L. F. Johnson,Matteo Fumagalli,Julia T. Vilstrup,Maanasa Raghavan,Thorfinn Sand Korneliussen,Anna-Sapfo Malaspinas,Josef Korbinian Vogt,Damian Szklarczyk,Damian Szklarczyk,Christian D. Kelstrup,Jakob Vinther,Andrei Dolocan,Jesper Stenderup,Amhed Missael Vargas Velazquez,James A. Cahill,Morten Rasmussen,Xiaoli Wang,Jiumeng Min,Grant D. Zazula,Andaine Seguin-Orlando,Cecilie Mortensen,Kim Magnussen,John F. Thompson,Jacobo Weinstock,Kristian Gregersen,Knut Røed,Véra Eisenmann,Carl-Johan Rubin,Donald Miller,Douglas F. Antczak,Mads F. Bertelsen,Søren Brunak,Khaled A. S. Al-Rasheid,Oliver A. Ryder,Leif Andersson,John Mundy,Anders Krogh,M. Thomas P. Gilbert,Kurt H. Kjær,Thomas Sicheritz-Pontén,Lars Juhl Jensen,Jesper V. Olsen,Michael Hofreiter,Rasmus Nielsen,Beth Shapiro,Jun Wang,Eske Willerslev,Eske Willerslev +58 more
TL;DR: Thealyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0–4.5 million years before present, twice the conventionally accepted time to the most recent common ancestor of the genus Equus, and supports the contention that Przewalski's horses represent the last surviving wild horse population.
Journal ArticleDOI
Genome flux and stasis in a five millennium transect of European prehistory
Cristina Gamba,Cristina Gamba,Eppie R. Jones,Matthew D. Teasdale,Russell L. McLaughlin,Gloria Gonzalez-Fortes,Valeria Mattiangeli,László Domboróczki,Ivett Kővári,Ildikó Pap,Alexandra Anders,Alasdair Whittle,János Dani,Pál Raczky,Thomas Higham,Michael Hofreiter,Daniel G. Bradley,Ron Pinhasi +17 more
TL;DR: A 5,000-year transect of human genomes sampled from petrous bones giving consistently excellent endogenous DNA yields are analysed, suggesting genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability.
Journal ArticleDOI
Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe
Pontus Skoglund,Helena Malmström,Maanasa Raghavan,Jan Storå,Per Hall,Eske Willerslev,M. Thomas P. Gilbert,Anders Götherström,Anders Götherström,Mattias Jakobsson,Mattias Jakobsson +10 more
TL;DR: The results suggest that migration from southern Europe catalyzed the spread of agriculture and that admixture in the wake of this expansion eventually shaped the genomic landscape of modern-day Europe.
Journal ArticleDOI
Pathogens and host immunity in the ancient human oral cavity
Christina Warinner,João Domingos Rodrigues,Rounak Vyas,Christian Trachsel,Natallia Shved,Jonas Grossmann,Anita Radini,Y. Hancock,Raul Y. Tito,Sarah Fiddyment,Camilla Speller,Jessica Hendy,Sophy Charlton,Hans U. Luder,Domingo C. Salazar-García,Elisabeth Eppler,Roger Seiler,Lars Hestbjerg Hansen,José Alfredo Samaniego Castruita,Simon Barkow-Oesterreicher,Kai Yik Teoh,Christian D. Kelstrup,Jesper V. Olsen,Paolo Nanni,Toshihisa Kawai,Eske Willerslev,Christian von Mering,Cecil M. Lewis,Matthew J. Collins,M. Thomas P. Gilbert,Frank J Rühli,Enrico Cappellini +31 more
TL;DR: This work reports the first, to their knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrates that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease.
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