DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity

Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales

(2016) John B. Kirkpatrick et al.   GEOLOGY

Quantifying relative fish abundance with eDNA: a promising tool for fisheries management

(2016) Anaïs Lacoursière-Roussel et al.   JOURNAL OF APPLIED ECOLOGY

Local human pressures influence gene flow in a hybridizingDaphniaspecies complex

(2016) B. Alric et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Long-term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA

(2016) Eric Capo et al.   MOLECULAR ECOLOGY

Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns

(2016) Sabine Filker et al.   MOLECULAR ECOLOGY

Lake sedimentary DNA accurately records 20thCentury introductions of exotic conifers in Scotland

(2016) Per Sjögren et al.   NEW PHYTOLOGIST

Paleobiogeography and historical biogeography of the non-marine caenogastropod family Melanopsidae

(2016) Thomas A. Neubauer et al.   PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY

Temporal Succession of Ancient Phytoplankton Community in Qinghai Lake and Implication for Paleo-environmental Change

(2016) Gaoyuan Li et al.   Scientific Reports

A case study of the past CH4 cycle in lakes by the combined use of dual isotopes (carbon and hydrogen) and ancient DNA of methane-oxidizing bacteria: rearing experiment and application to Lake Remoray (eastern France)

(2015) Simon Belle et al.   AQUATIC ECOLOGY

Fish environmental DNA is more concentrated in aquatic sediments than surface water

(2015) Cameron R. Turner et al.   BIOLOGICAL CONSERVATION

Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms

(2015) Caren S. Goldberg et al.   BIOLOGICAL CONSERVATION

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

Tainted resurrection: metal pollution is linked with reduced hatching and high juvenile mortality inDaphniaegg banks

(2015) Mary A. Rogalski   ECOLOGY

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

(2015) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

Temporal trends in cyanobacteria revealed through DNA and pigment analyses of temperate lake sediment cores

(2015) S. Pal et al.   JOURNAL OF PALEOLIMNOLOGY

Origin, dynamics, and implications of extracellular DNA pools in marine sediments

(2015) Andrea Torti et al.   Marine Genomics

Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity

(2015) Eric Capo et al.   MICROBIAL ECOLOGY

Evidence for an active rare biosphere within freshwater protists community

(2015) Didier Debroas et al.   MOLECULAR ECOLOGY

Population genetic dynamics of an invasion reconstructed from the sediment egg bank

(2015) Markus Möst et al.   MOLECULAR ECOLOGY

Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA

(2015) Johan Pansu et al.   MOLECULAR ECOLOGY

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

(2015) Johan Decelle et al.   Molecular Ecology Resources

Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish

(2015) Jessica J. Eichmiller et al.   Molecular Ecology Resources

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes

(2015) L.S. Epp et al.   QUATERNARY SCIENCE REVIEWS

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

Genetic data from algae sedimentary DNA reflect the influence of environment over geography

(2015) Kathleen R. Stoof-Leichsenring et al.   Scientific Reports

A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

(2015) Mark A. Lever et al.   Frontiers in Microbiology

Preservation potential of ancient plankton DNA in Pleistocene marine sediments

(2015) A. C. BOERE et al.   Geobiology

The Red Queen Race between Parasitic Chytrids and Their Host, Planktothrix: A Test Using a Time Series Reconstructed from Sediment DNA

(2015) Marcia Kyle et al.   PLoS One

Of Paleo-Genes and Perch: What if an “Alien” Is Actually a Native?

(2015) J. Curt Stager et al.   PLoS One

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities

(2015) Anja Lange et al.   PLoS One

Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood

(2014) Kenneth G Frey et al.   BMC GENOMICS

Lifetime Response of Contemporary Versus Resurrected Daphnia galeata Sars (Crustacea, Cladocera) to Cu(II) Chronic Exposure

(2014) Roberta Piscia et al.   BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY

Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany)

(2014) Andreas Oikonomou et al.   ENVIRONMENTAL MICROBIOLOGY

Effects of nutrients and warming onPlanktothrixdynamics and diversity: a palaeolimnological view based on sedimentary DNA and RNA

(2014) Olga Savichtcheva et al.   FRESHWATER BIOLOGY

Out with the old, in with the new? Younger Daphnia clones are competitively superior over centuries-old ancestors

(2014) Philip K. Morton et al.   HYDROBIOLOGIA

Data analysis for 16S microbial profiling from different benchtop sequencing platforms

(2014) Victor S. Pylro et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Temporal changes in the contribution of methane-oxidizing bacteria to the biomass of chironomid larvae determined using stable carbon isotopes and ancient DNA

(2014) Simon Belle et al.   JOURNAL OF PALEOLIMNOLOGY

A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect

(2014) Kathleen R. Stoof-Leichsenring et al.   JOURNAL OF PALEOLIMNOLOGY

Amplification of DNA in sediment cores to detect historic Planktothrix occurrence in three Norwegian lakes

(2014) Marcia Kyle et al.   JOURNAL OF PALEOLIMNOLOGY

Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects

(2014) NICOLAS J. RAWLENCE et al.   JOURNAL OF QUATERNARY SCIENCE

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

(2014) Gentile F. Ficetola et al.   Molecular Ecology Resources

The Relationship between the Distribution of Common Carp and Their Environmental DNA in a Small Lake

(2014) Jessica J. Eichmiller et al.   PLoS One

Alkenone distribution in Lake Van sediment over the last 270 ka: influence of temperature and haptophyte species composition

(2014) Marie-Ève Randlett et al.   QUATERNARY SCIENCE REVIEWS

The others: our biased perspective of eukaryotic genomes

(2014) Javier del Campo et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

Identification of Photosynthetic Plankton Communities Using Sedimentary Ancient DNA and Their Response to late-Holocene Climate Change on the Tibetan Plateau

(2014) Weiguo Hou et al.   Scientific Reports

Endospore-forming bacteria as new proxies to assess impact of eutrophication in Lake Geneva (Switzerland–France)

(2013) Tina Wunderlin et al.   AQUATIC SCIENCES

Ancient DNA complements microfossil record in deep-sea subsurface sediments

(2013) F. Lejzerowicz et al.   Biology Letters

Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists

(2013) Cheryl-Emiliane T Chow et al.   ISME Journal

Looking forward through the past: identification of 50 priority research questions in palaeoecology

(2013) Alistair W. R. Seddon et al.   JOURNAL OF ECOLOGY

Finding copepod footprints: a protocol for molecular identification of diapausing eggs in lake sediments

(2013) Wataru Makino et al.   LIMNOLOGY

Validation of eDNA Surveillance Sensitivity for Detection of Asian Carps in Controlled and Field Experiments

(2013) Andrew R. Mahon et al.   PLoS One

Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene

(2013) M. J. L. Coolen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes

(2012) Jean-François Mangot et al.   ENVIRONMENTAL MICROBIOLOGY

A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA

(2012) Emily L Kara et al.   ISME Journal

DNA extraction and amplification methods for ephippial cases of Daphnia resting eggs in lake sediments: a novel approach for reconstructing zooplankton population structure from the past

(2012) Seiji Ishida et al.   LIMNOLOGY

Bioinformatic challenges for DNA metabarcoding of plants and animals

(2012) ERIC COISSAC et al.   MOLECULAR ECOLOGY

Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation

(2012) KATHLEEN R. STOOF-LEICHSENRING et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

Estimation of Fish Biomass Using Environmental DNA

(2012) Teruhiko Takahara et al.   PLoS One

Setting the stage – Building and working in an ancient DNA laboratory

(2011) Michael Knapp et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

Quantitative PCR Enumeration of Total/Toxic Planktothrix rubescens and Total Cyanobacteria in Preserved DNA Isolated from Lake Sediments

(2011) Olga Savichtcheva et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

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

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

Palaeolimnological insights for biodiversity science: an emerging field

(2011) IRENE GREGORY-EAVES et al.   FRESHWATER BIOLOGY

Coherent dynamics and association networks among lake bacterioplankton taxa

(2011) Alexander Eiler et al.   ISME Journal

DNA extraction, amplification and analysis of the 28S rRNA portion in sediment-buried copepod DNA in the Great Wall Bay and Xihu Lake, Antarctica

(2011) Z.-H. Xu et al.   JOURNAL OF PLANKTON RESEARCH

An approach to the study of copepod egg banks based on efficient DNA extraction from individual copepod eggs

(2011) Zhi-Huan Xu et al.   Marine Biology Research

Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing High-Performance Liquid Chromatography (PCR-DHPLC)

(2011) LAURA S. EPP et al.   Molecular Ecology Resources

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

(2011) Tiayyba Riaz et al.   NUCLEIC ACIDS RESEARCH

Hundred years of genetic structure in a sediment revived diatom population

(2011) K. Harnstrom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Use of DNA barcoding to detect invertebrate invasive species from diapausing eggs

(2010) Elizabeta Briski et al.   BIOLOGICAL INVASIONS

An In silico approach for the evaluation of DNA barcodes

(2010) Gentile Ficetola et al.   BMC GENOMICS

Multiple stressors in freshwater ecosystems

(2010) S. J. ORMEROD et al.   FRESHWATER BIOLOGY

The power of the past: using sediments to track the effects of multiple stressors on lake ecosystems

(2010) JOHN P. SMOL   FRESHWATER BIOLOGY

Subfossil Chaoborus mandibles confirm historical fish decline in two acidified lakes, SW Sweden

(2010) Fredrik Palm et al.   Fundamental and Applied Limnology

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Identifying century-old long-spined Daphnia: species replacement in a mountain lake characterised by paleogenetic methods

(2010) Eva Hamrová et al.   HYDROBIOLOGIA

Carbon and nitrogen loss rates during aging of lake sediment: Changes over 27 years studied in varved lake sediment

(2010) Veronika Gälman et al.   LIMNOLOGY AND OCEANOGRAPHY

Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments

(2010) C. CORINALDESI et al.   MOLECULAR ECOLOGY

Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

(2010) VIOLA NOLTE et al.   MOLECULAR ECOLOGY

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

Quantitative PCR methods for RNA and DNA in marine sediments: maximizing yield while overcoming inhibition

(2009) Karen G. Lloyd et al.   FEMS MICROBIOLOGY ECOLOGY

Late-Holocene succession of dinoflagellates in an Antarctic fjord using a multi-proxy approach: paleoenvironmental genomics, lipid biomarkers and palynomorphs

(2009) A. C. BOERE et al.   Geobiology

Historical genetics on a sediment core from a Kenyan lake: intraspecific genotype turnover in a tropical rotifer is related to past environmental changes

(2009) Laura S. Epp et al.   JOURNAL OF PALEOLIMNOLOGY

Sources for sedimentary bacteriohopanepolyols as revealed by 16S rDNA stratigraphy

(2008) Marco J. L. Coolen et al.   ENVIRONMENTAL MICROBIOLOGY

Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences

(2008) C. CORINALDESI et al.   MOLECULAR ECOLOGY

DNA barcoding for ecologists

(2008) Alice Valentini et al.   TRENDS IN ECOLOGY & EVOLUTION

Recovery of DNA and pollen from New Zealand lake sediments

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