Journal ArticleDOI
A 43 kyr record of protist communities and their response to oxygen minimum zone variability in the Northeastern Arabian Sea
Kuldeep D. More,William D. Orsi,Valier Galy,Liviu Giosan,Lijun He,Kliti Grice,Marco J. L. Coolen +6 more
TLDR
In this paper, the authors provide a comprehensive ancient sedimentary DNA record of both fossilizing and non-fossilizing protists and their response to OMZ variability in the NE Arabian Sea over the last 43 ka.About:
This article is published in Earth and Planetary Science Letters.The article was published on 2018-08-15. It has received 24 citations till now. The article focuses on the topics: Stadial & Interglacial.read more
Citations
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Journal ArticleDOI
Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity : Overview and Recommendations
Eric Capo,Charline Giguet-Covex,Alexandra Rouillard,Kevin Nota,Peter D. Heintzman,Aurèle Vuillemin,Daniel Ariztegui,Fabien Arnaud,Simon Belle,Stefan Bertilsson,Christian Bigler,Richard Bindler,Antony G. Brown,Charlotte Clarke,Sarah E. Crump,Didier Debroas,Göran Englund,Gentile Francesco Ficetola,Rebecca E. Garner,Joanna Gauthier,Irene Gregory-Eaves,Liv Heinecke,Ulrike Herzschuh,Ulrike Herzschuh,Anan Ibrahim,Veljo Kisand,Kurt H. Kjær,Youri Lammers,Joanne E. Littlefair,Erwan Messager,Marie-Eve Monchamp,Fredrik Olajos,William D. Orsi,Mikkel Winther Pedersen,Dilli Prasad Rijal,Johan Rydberg,Trisha L. Spanbauer,Kathleen R. Stoof-Leichsenring,Pierre Taberlet,Liisi Talas,Camille Thomas,David A. Walsh,Y. L. Wang,Y. L. Wang,Eske Willerslev,Anne van Woerkom,Heike Zimmermann,Marco J. L. Coolen,Laura S. Epp,Isabelle Domaizon,Inger Greve Alsos,Laura Parducci,Laura Parducci +52 more
TL;DR: In this article, the authors synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA via high-throughput sequencing technologies.
Journal ArticleDOI
Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation
Linda Armbrecht,Marco J. L. Coolen,Franck Lejzerowicz,Simon C. George,Karita Negandhi,Yohey Suzuki,Jennifer M. Young,Nicole R. Foster,Leanne K. Armand,Alan Cooper,Martin Ostrowski,Martin Ostrowski,Amaranta Focardi,Michael Stat,John W. Moreau,John W. Moreau,Laura S. Weyrich +16 more
TL;DR: In this article, the International Ocean Discovery Program (IODP) has published a review of the use of ancient DNA (aDNA) from seafloor sediments, highlighting common pitfalls and highlighting the urgency behind adopting new standards for marine sedaDNA research, with a focus on sampling optimisation to facilitate the incorporation of routine aDNA research into IODP operations.
Journal ArticleDOI
Preservation of microbial DNA in marine sediments: insights from extracellular DNA pools
TL;DR: The results indicate that in Aarhus Bay the vast majority of prokaryotic exDNA is turned over, thus not contributing to a genetic archive of past environmental change.
Journal ArticleDOI
The potential of sedimentary ancient DNA for reconstructing past sea ice evolution
Stijn De Schepper,Jessica Louise Ray,Katrine Sandnes Skaar,Henrik Sadatzki,Henrik Sadatzki,Umer Zeeshan Ijaz,Ruediger Stein,Ruediger Stein,Aud Larsen +8 more
TL;DR: The results corroborate sea ice reconstructions made by traditional tools, and demonstrate the potential of sedimentary aDNA, focusing primarily on microbial eukaryotes, as a new tool to better understand sea ice evolution in the climate system.
Journal ArticleDOI
Unveiling the Ecological Applications of Ancient DNA from Mollusk Shells
Clio Der Sarkissian,Per Möller,Courtney A. Hofman,Peter Ilsøe,Torben C. Rick,Tom Schiøtte,Martin V. Sørensen,Love Dalén,Ludovic Orlando,Ludovic Orlando +9 more
TL;DR: In this paper, the authors significantly push the temporal limit for shell DNA recovery to 100,000 years with the successful genetic characterization of one Portlandia arctica and one Mytilus mussel sample collected within a dated permafrost layer.
References
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QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
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Non-parametric multivariate analyses of changes in community structure
TL;DR: Which elements of this often-quoted strategy for graphical representation of multivariate (multi-species) abundance data have proved most useful in practical assessment of community change resulting from pollution impact are identified.
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Species assemblages and indicator species:the need for a flexible asymmetrical approach
Marc Dufrêne,Pierre Legendre +1 more
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Extended 14C Data Base and Revised Calib 3.0 14C Age Calibration Program
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TL;DR: The age calibration program, CALIB (Stuiver & Reimer 1986), first made available in 1986 and subsequently modified in 1987 (revision 2.0 and 2.1), has been amended anew as mentioned in this paper.
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Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
J. Gregory Caporaso,Christian L. Lauber,William A. Walters,Donna Berg-Lyons,James Huntley,Noah Fierer,Noah Fierer,Sarah M. Owens,Jason Betley,Louise Fraser,Markus J. Bauer,Niall Anthony Gormley,Jack A. Gilbert,Jack A. Gilbert,Geoff Smith,Rob Knight +15 more
TL;DR: It is shown that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.
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