Literature DB >> 25487334

Ancient and modern environmental DNA.

Mikkel Winther Pedersen1, Søren Overballe-Petersen1, Luca Ermini1, Clio Der Sarkissian1, James Haile2, Micaela Hellstrom1, Johan Spens3, Philip Francis Thomsen1, Kristine Bohmann4, Enrico Cappellini1, Ida Bærholm Schnell5, Nathan A Wales1, Christian Carøe1, Paula F Campos1, Astrid M Z Schmidt1, M Thomas P Gilbert1, Anders J Hansen1, Ludovic Orlando1, Eske Willerslev6.   

Abstract

DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.
© 2014 The Author(s) Published by the Royal Society. All rights reserved.

Entities:  

Keywords:  ancient; ancient DNA; environment; environmental DNA; review

Mesh:

Substances:

Year:  2015        PMID: 25487334      PMCID: PMC4275890          DOI: 10.1098/rstb.2013.0383

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  167 in total

1.  Systematic relationships among Lutzomyia sand flies (Diptera: Psychodidae) of Peru and Colombia based on the analysis of 12S and 28S ribosomal DNA sequences.

Authors:  Lorenza Beati; Abraham G Cáceres; Jamie A Lee; Leonard E Munstermann
Journal:  Int J Parasitol       Date:  2004-02       Impact factor: 3.981

2.  DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments.

Authors:  Gian Marco Luna; A Dell'Anno; R Danovaro
Journal:  Environ Microbiol       Date:  2006-02       Impact factor: 5.491

Review 3.  Release and persistence of extracellular DNA in the environment.

Authors:  Kaare M Nielsen; Pål J Johnsen; Douda Bensasson; Daniele Daffonchio
Journal:  Environ Biosafety Res       Date:  2007-09-12

4.  Accurate determination of microbial diversity from 454 pyrosequencing data.

Authors:  Christopher Quince; Anders Lanzén; Thomas P Curtis; Russell J Davenport; Neil Hall; Ian M Head; L Fiona Read; William T Sloan
Journal:  Nat Methods       Date:  2009-08-09       Impact factor: 28.547

5.  Strain-resolved community genomic analysis of gut microbial colonization in a premature infant.

Authors:  Michael J Morowitz; Vincent J Denef; Elizabeth K Costello; Brian C Thomas; Valeriy Poroyko; David A Relman; Jillian F Banfield
Journal:  Proc Natl Acad Sci U S A       Date:  2010-12-29       Impact factor: 11.205

6.  PhymmBL expanded: confidence scores, custom databases, parallelization and more.

Authors:  Arthur Brady; Steven Salzberg
Journal:  Nat Methods       Date:  2011-05       Impact factor: 28.547

7.  Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores.

Authors:  P B Pope; S E Denman; M Jones; S G Tringe; K Barry; S A Malfatti; A C McHardy; J-F Cheng; P Hugenholtz; C S McSweeney; M Morrison
Journal:  Proc Natl Acad Sci U S A       Date:  2010-07-28       Impact factor: 11.205

8.  Mechanisms of homology-facilitated illegitimate recombination for foreign DNA acquisition in transformable Pseudomonas stutzeri.

Authors:  Petra Meier; Wilfried Wackernagel
Journal:  Mol Microbiol       Date:  2003-05       Impact factor: 3.501

9.  A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy.

Authors:  Kjersti Aagaard; Kevin Riehle; Jun Ma; Nicola Segata; Toni-Ann Mistretta; Cristian Coarfa; Sabeen Raza; Sean Rosenbaum; Ignatia Van den Veyver; Aleksandar Milosavljevic; Dirk Gevers; Curtis Huttenhower; Joseph Petrosino; James Versalovic
Journal:  PLoS One       Date:  2012-06-13       Impact factor: 3.240

10.  External contamination in single cell mtDNA analysis.

Authors:  Yong-Gang Yao; Hans-Jürgen Bandelt; Neal S Young
Journal:  PLoS One       Date:  2007-08-01       Impact factor: 3.240

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  49 in total

1.  Introduction. Ancient DNA: the first three decades.

Authors:  Erika Hagelberg; Michael Hofreiter; Christine Keyser
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2015-01-19       Impact factor: 6.237

2.  Ancient DNA: Muddy messages about American migration.

Authors:  Suzanne McGowan
Journal:  Nature       Date:  2016-08-10       Impact factor: 49.962

3.  Postglacial viability and colonization in North America's ice-free corridor.

Authors:  Mikkel W Pedersen; Anthony Ruter; Charles Schweger; Harvey Friebe; Richard A Staff; Kristian K Kjeldsen; Marie L Z Mendoza; Alwynne B Beaudoin; Cynthia Zutter; Nicolaj K Larsen; Ben A Potter; Rasmus Nielsen; Rebecca A Rainville; Ludovic Orlando; David J Meltzer; Kurt H Kjær; Eske Willerslev
Journal:  Nature       Date:  2016-08-10       Impact factor: 49.962

4.  Sedimentary DNA Reveals Cyanobacterial Community Diversity over 200 Years in Two Perialpine Lakes.

Authors:  Marie-Eve Monchamp; Jean-Claude Walser; Francesco Pomati; Piet Spaak
Journal:  Appl Environ Microbiol       Date:  2016-10-14       Impact factor: 4.792

5.  AntCaller: an accurate variant caller incorporating ancient DNA damage.

Authors:  Boyan Zhou; Shaoqing Wen; Lingxiang Wang; Li Jin; Hui Li; Hong Zhang
Journal:  Mol Genet Genomics       Date:  2017-08-23       Impact factor: 3.291

Review 6.  Human evolution: a tale from ancient genomes.

Authors:  Bastien Llamas; Eske Willerslev; Ludovic Orlando
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-02-05       Impact factor: 6.237

7.  Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA.

Authors:  Masaki Miya; Toshifumi Minamoto; Hiroki Yamanaka; Shin-Ichiro Oka; Keiichi Sato; Satoshi Yamamoto; Tetsuya Sado; Hideyuki Doi
Journal:  J Vis Exp       Date:  2016-11-25       Impact factor: 1.355

8.  Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction.

Authors:  Dominique A Cowart; Katherine R Murphy; C-H Christina Cheng
Journal:  Methods Mol Biol       Date:  2022

9.  Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples.

Authors:  Ming Zhang; Peng Cao; Qingyan Dai; Yongqiang Wang; Xiaotian Feng; Hongru Wang; Hong Wu; Albert Min-Shan Ko; Xiaowei Mao; Yichen Liu; Li Yu; Christian Roos; Tilo Nadler; Wen Xiao; E Andrew Bennett; Qiaomei Fu
Journal:  Zool Res       Date:  2021-05-18

Review 10.  Evolutionary Patterns and Processes: Lessons from Ancient DNA.

Authors:  Michela Leonardi; Pablo Librado; Clio Der Sarkissian; Mikkel Schubert; Ahmed H Alfarhan; Saleh A Alquraishi; Khaled A S Al-Rasheid; Cristina Gamba; Eske Willerslev; Ludovic Orlando
Journal:  Syst Biol       Date:  2017-01-01       Impact factor: 9.160

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