Ancient and modern environmental DNA

Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium

(2014) J. Pawłowska et al.   Geobiology

Shotgun microbial profiling of fossil remains

(2014) C. Der Sarkissian et al.   MOLECULAR ECOLOGY

Fifty thousand years of Arctic vegetation and megafaunal diet

(2014) Eske Willerslev et al.   NATURE

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

(2014) Mikkel Schubert et al.   Nature Protocols

Harnessing DNA to improve environmental management

(2014) R. P. Kelly et al.   SCIENCE

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

(2014) Charline Giguet-Covex et al.   Nature Communications

Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples

(2013) David S. Pilliod et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia

(2013) Laura Parducci et al.   MOLECULAR ECOLOGY

Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility

(2013) Teresita M. Porter et al.   Molecular Ecology Resources

DNA barcoding at riverscape scales: assessing biodiversity among fishes of the genusCottus(Teleostei) in northern Rocky Mountain streams

(2013) Michael K. Young et al.   Molecular Ecology Resources

Eemian interglacial reconstructed from a Greenland folded ice core

(2013) D. Dahl-Jensen et al.   NATURE

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

(2013) Christina J Adler et al.   NATURE GENETICS

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Using Environmental DNA to Estimate the Distribution of an Invasive Fish Species in Ponds

(2013) Teruhiko Takahara et al.   PLoS One

Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

(2013) Jonathan W. Leff et al.   PLoS One

A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

(2013) Weiguo Hou et al.   PLoS One

Evidence for a persistent microbial seed bank throughout the global ocean

(2013) S. M. Gibbons et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial natural transformation by highly fragmented and damaged DNA

(2013) S. Overballe-Petersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

(2013) Mikkel Winther Pedersen et al.   QUATERNARY SCIENCE REVIEWS

Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocene–Holocene cave deposit on Kangaroo Island, South Australia

(2013) Dalal Haouchar et al.   QUATERNARY SCIENCE REVIEWS

An eDNA approach to detect eastern hellbenders (Cryptobranchus a. alleganiensis) using samples of water

(2013) Zachary H. Olson et al.   WILDLIFE RESEARCH

Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum)

(2013) Caren S. Goldberg et al.   Freshwater Science

Real Time Metagenomics: Using k-mers to annotate metagenomes

(2012) Robert A. Edwards et al.   BIOINFORMATICS

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

(2012) David A W Soergel et al.   ISME Journal

Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrogLithobates catesbeianus

(2012) Tony Dejean et al.   JOURNAL OF APPLIED ECOLOGY

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

DNA from soil mirrors plant taxonomic and growth form diversity

(2012) N. G. YOCCOZ et al.   MOLECULAR ECOLOGY

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

(2012) LAURA S. EPP et al.   MOLECULAR ECOLOGY

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Browsed twig environmental DNA: diagnostic PCR to identify ungulate species

(2012) RUTH V. NICHOLS et al.   Molecular Ecology Resources

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Human Occupancy as a Source of Indoor Airborne Bacteria

(2012) Denina Hospodsky et al.   PLoS One

A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy

(2012) Kjersti Aagaard et al.   PLoS One

Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill

(2012) Holly M. Bik et al.   PLoS One

Coral-Bacterial Communities before and after a Coral Mass Spawning Event on Ningaloo Reef

(2012) Janja Ceh et al.   PLoS One

Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale

(2012) Nicholas A. Bokulich et al.   PLoS One

Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine

(2012) Nicholas A. Bokulich et al.   PLoS One

Estimation of Fish Biomass Using Environmental DNA

(2012) Teruhiko Takahara et al.   PLoS One

Microbial Diversity and Potential Pathogens in Ornamental Fish Aquarium Water

(2012) Katherine F. Smith et al.   PLoS One

Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals

(2012) Andrew D. Foote et al.   PLoS One

Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples

(2012) Philip Francis Thomsen et al.   PLoS One

Insights from Characterizing Extinct Human Gut Microbiomes

(2012) Raul Y. Tito et al.   PLoS One

A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable

(2012) Jiri Hulcr et al.   PLoS One

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

(2012) M. E. Allentoft et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancient biomolecules in Quaternary palaeoecology

(2012) Michael Hofreiter et al.   QUATERNARY SCIENCE REVIEWS

Clovis Age Western Stemmed Projectile Points and Human Coprolites at the Paisley Caves

(2012) D. L. Jenkins et al.   SCIENCE

Glacial Survival of Boreal Trees in Northern Scandinavia

(2012) L. Parducci et al.   SCIENCE

Detection of Coxiella burnetii DNA in Wildlife and Ticks in Northern Queensland, Australia

(2012) A. Cooper et al.   VECTOR-BORNE AND ZOONOTIC DISEASES

Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers

(2012) Chiara Boschetti et al.   PLoS Genetics

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

(2011) William A. Walters et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Aligning short reads to reference alignments and trees

(2011) Simon A. Berger et al.   BIOINFORMATICS

Classifying short genomic fragments from novel lineages using composition and homology

(2011) Donovan H Parks et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics

(2011) Lynn L Anderson-Carpenter et al.   BMC EVOLUTIONARY BIOLOGY

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Surveillance of fish species composition using environmental DNA

(2011) Toshifumi Minamoto et al.   LIMNOLOGY

Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

(2011) SANNE BOESSENKOOL et al.   MOLECULAR ECOLOGY

Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

(2011) HOLLY M. BIK et al.   MOLECULAR ECOLOGY

A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability

(2011) TINA JØRGENSEN et al.   MOLECULAR ECOLOGY

Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity

(2011) KENNETH ANDERSEN et al.   MOLECULAR ECOLOGY

Monitoring endangered freshwater biodiversity using environmental DNA

(2011) PHILIP FRANCIS THOMSEN et al.   MOLECULAR ECOLOGY

A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding

(2011) A.-B. ZHANG et al.   MOLECULAR ECOLOGY

Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA Meta-barcoding

(2011) TINA JØRGENSEN et al.   MOLECULAR ECOLOGY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

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

(2011) Arthur Brady et al.   NATURE METHODS

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

(2011) Tiayyba Riaz et al.   NUCLEIC ACIDS RESEARCH

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Molecular Detection of Vertebrates in Stream Water: A Demonstration Using Rocky Mountain Tailed Frogs and Idaho Giant Salamanders

(2011) Caren S. Goldberg et al.   PLoS One

Desert Farming Benefits from Microbial Potential in Arid Soils and Promotes Diversity and Plant Health

(2011) Martina Köberl et al.   PLoS One

Persistence of Environmental DNA in Freshwater Ecosystems

(2011) Tony Dejean et al.   PLoS One

Microbial Biogeography of Public Restroom Surfaces

(2011) Gilberto E. Flores et al.   PLoS One

DNA-Based Faecal Dietary Analysis: A Comparison of qPCR and High Throughput Sequencing Approaches

(2011) Dáithí C. Murray et al.   PLoS One

Composition of Human Skin Microbiota Affects Attractiveness to Malaria Mosquitoes

(2011) Niels O. Verhulst et al.   PLoS One

Soil rotifer communities are extremely diverse globally but spatially autocorrelated locally

(2011) M. S. Robeson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

“Sight-unseen” detection of rare aquatic species using environmental DNA

(2011) Christopher L. Jerde et al.   Conservation Letters

Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

(2011) Sébastien Terrat et al.   Microbial Biotechnology

Evidence of a high-Andean, mid-Holocene plant community: An ancient DNA analysis of glacially preserved remains

(2010) Billie A. Gould et al.   AMERICAN JOURNAL OF BOTANY

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads

(2010) G. L. Rosen et al.   BIOINFORMATICS

An In silico approach for the evaluation of DNA barcodes

(2010) Gentile Ficetola et al.   BMC GENOMICS

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Examining the global distribution of dominant archaeal populations in soil

(2010) Scott T Bates et al.   ISME Journal

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Vertebrate DNA in Fecal Samples from Bonobos and Gorillas: Evidence for Meat Consumption or Artefact?

(2010) Michael Hofreiter et al.   PLoS One

An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications

(2010) Sophie Champlot et al.   PLoS One

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

(2010) M. J. Morowitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) P. B. Pope et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil

(2009) L. M. Feinstein et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts

(2009) Christine E. King et al.   BIOTECHNIQUES

Plant leaf mass loss and DNA release in freshwater sediments

(2009) John Poté et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains

(2009) Carsten Schwarz et al.   NUCLEIC ACIDS RESEARCH

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

(2009) Adrian W. Briggs et al.   NUCLEIC ACIDS RESEARCH

Ancient DNA reveals late survival of mammoth and horse in interior Alaska

(2009) James Haile et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A DNA barcode for land plants

(2009) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

(2009) A. W. Briggs et al.   SCIENCE

Isolation of Microbes from Lake Vostok Accretion Ice

(2008) T. D'Elia et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Species detection using environmental DNA from water samples

(2008) G. F. Ficetola et al.   Biology Letters

Fast phylogenetic DNA barcoding

(2008) K. Munch et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Natural Variability of Greenland Climate, Vegetation, and Ice Volume During the Past Million Years

(2008) A. de Vernal et al.   SCIENCE

Massive Horizontal Gene Transfer in Bdelloid Rotifers

(2008) E. A. Gladyshev et al.   SCIENCE

Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics

(2008) Kasper Munch et al.   SYSTEMATIC BIOLOGY

Optical dating of perennially frozen deposits associated with preserved ancient plant and animal DNA in north-central Siberia

(2007) L.J. Arnold et al.   Quaternary Geochronology

Recovery of DNA and pollen from New Zealand lake sediments

(2007) Elizabeth Matisoo-Smith et al.   QUATERNARY INTERNATIONAL