Population‐level inferences from environmental DNA—Current status and future perspectives

Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?

(2019) Clare I.M. Adams et al.   Genes

Invasion genetics from eDNA and thousands of larvae: A targeted metabarcoding assay that distinguishes species and population variation of zebra and quagga mussels

(2019) Nathaniel T. Marshall et al.   Ecology and Evolution

Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods

(2019) Philip Francis Thomsen et al.   Ecology and Evolution

Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection

(2019) Carol A. Stepien et al.   PLoS One

Environmental DNA for improved detection and environmental surveillance of schistosomiasis

(2019) Mita E. Sengupta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Can Environmental RNA Revolutionize Biodiversity Science?

(2019) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

The hidden half: ecology and evolution of cryptobenthic fishes on coral reefs

(2018) Simon J. Brandl et al.   BIOLOGICAL REVIEWS

Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons

(2018) James Ashley et al.   CELL

Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment

(2018) Nigel Keeley et al.   ECOLOGICAL INDICATORS

Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales

(2018) Halvor Knutsen et al.   Evolutionary Applications

Assessing the abundance of Bristol Bay belugas with genetic mark-recapture methods

(2018) John J. Citta et al.   MARINE MAMMAL SCIENCE

Capture enrichment of aquatic environmental DNA: A first proof of concept

(2018) Taylor M. Wilcox et al.   Molecular Ecology Resources

DNA methylation-based biomarkers and the epigenetic clock theory of ageing

(2018) Steve Horvath et al.   NATURE REVIEWS GENETICS

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species

(2018) Katharina Fietz et al.   Microbiome

Measuring Genetic Differentiation from Pool-seq Data

(2018) Valentin Hivert et al.   GENETICS

Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms

(2018) C. Mariac et al.   PLoS One

Water, water everywhere: environmental DNA can unlock population structure in elusive marine species

(2018) Kim M. Parsons et al.   Royal Society Open Science

Body size determines soil community assembly in a tropical forest

(2018) Lucie Zinger et al.   MOLECULAR ECOLOGY

Putatively adaptive genetic variation in the giant California sea cucumber ( Parastichopus californicus ) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data

(2018) Amanda Xuereb et al.   MOLECULAR ECOLOGY

Age estimation in a long-lived seabird (Ardenna tenuirostris ) using DNA methylation-based biomarkers

(2018) R. De Paoli-Iseppi et al.   Molecular Ecology Resources

MobiSeq: De Novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements

(2018) Alba Rey-Iglesia et al.   Molecular Ecology Resources

Biparental Inheritance of Mitochondrial DNA in Humans

(2018) Shiyu Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environmental DNA Time Series in Ecology

(2018) Miklós Bálint et al.   TRENDS IN ECOLOGY & EVOLUTION

Comparative Cost and Effort of Fish Distribution Detection via Environmental DNA Analysis and Electrofishing

(2017) Nathan T. Evans et al.   FISHERIES

Genetic Kinship Analyses Reveal That Gray’s Beaked Whales Strand in Unrelated Groups

(2017) Selina Patel et al.   JOURNAL OF HEREDITY

Seawater environmental DNA reflects seasonality of a coastal fish community

(2017) Eva Egelyng Sigsgaard et al.   MARINE BIOLOGY

How to optimize the precision of allele and haplotype frequency estimates using pooled-sequencing data

(2017) Nicolas O. Rode et al.   Molecular Ecology Resources

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

A massively parallel strategy for STR marker development, capture, and genotyping

(2017) Logan Kistler et al.   NUCLEIC ACIDS RESEARCH

Neandertal and Denisovan DNA from Pleistocene sediments

(2017) Viviane Slon et al.   SCIENCE

Environmental DNA in subterranean biology: range extension and taxonomic implications for Proteus

(2017) Špela Gorički et al.   Scientific Reports

Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

(2017) Michael Stat et al.   Scientific Reports

RNA in extracellular vesicles

(2017) Kyoung Mi Kim et al.   Wiley Interdisciplinary Reviews-RNA

Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary

(2017) Mark Y. Stoeckle et al.   PLoS One

Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

(2017) Xavier Pochon et al.   PLoS One

Impacts of Early Life Stress on the Methylome and Transcriptome of Atlantic Salmon

(2017) Hooman K. Moghadam et al.   Scientific Reports

Unbiased probabilistic taxonomic classification for DNA barcoding

(2016) Panu Somervuo et al.   BIOINFORMATICS

A framework for inferring biological communities from environmental DNA

(2016) Andrew Olaf Shelton et al.   ECOLOGICAL APPLICATIONS

A decade of seascape genetics: contributions to basic and applied marine connectivity

(2016) KA Selkoe et al.   MARINE ECOLOGY PROGRESS SERIES

First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site

(2016) Olivier Laroche et al.   MARINE ENVIRONMENTAL RESEARCH

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography

(2016) Marguerite Lapierre et al.   MOLECULAR BIOLOGY AND EVOLUTION

Draft genome of the American Eel (Anguilla rostrata )

(2016) Scott A. Pavey et al.   Molecular Ecology Resources

Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carpCyprinus carpio

(2016) Toshifumi Minamoto et al.   Molecular Ecology Resources

Experimental conditions improving in-solution target enrichment for ancient DNA

(2016) Diana I. Cruz-Dávalos et al.   Molecular Ecology Resources

Species phylogeny and diversification process of Northeast Asian Pungitius revealed by AFLP and mtDNA markers

(2016) Hiroshi Takahashi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Evaluation of the global DNA methylation in canine mast cell tumour samples by immunostaining of 5-methyl cytosine

(2016) C. Y. Morimoto et al.   Veterinary and Comparative Oncology

A decade of seascape genetics: contributions to basic and applied marine connectivity

(2016) KA Selkoe et al.   MARINE ECOLOGY PROGRESS SERIES

Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA

(2016) Eva Egelyng Sigsgaard et al.   Nature Ecology & Evolution

Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes

(2016) Philip Francis Thomsen et al.   PLoS One

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix

(2015) Katy E. Klymus et al.   BIOLOGICAL CONSERVATION

Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples

(2015) Eva Egelyng Sigsgaard 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

Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era

(2015) Pierre-Alexandre Gagnaire et al.   Evolutionary Applications

Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %

(2015) Alena K. Oliver et al.   Fungal Ecology

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

(2015) O. A. Ali et al.   GENETICS

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

Resource specialists lead local insect community turnover associated with temperature - analysis of an 18-year full-seasonal record of moths and beetles

(2015) Philip Francis Thomsen et al.   JOURNAL OF ANIMAL ECOLOGY

Population genetic structure and demographic history of Pacific blue sharks (Prionace glauca) inferred from mitochondrial DNA analysis

(2015) Mioko Taguchi et al.   MARINE AND FRESHWATER RESEARCH

A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes

(2015) Kimiko Uchii et al.   Molecular Ecology Resources

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

(2015) Nathan T. Evans et al.   Molecular Ecology Resources

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

(2015) Vasco Elbrecht et al.   PLoS One

High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems

(2015) Franck Lejzerowicz et al.   Scientific Reports

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Population-Genetic Inference from Pooled-Sequencing Data

(2014) Michael Lynch et al.   Genome Biology and Evolution

Ancient Whole Genome Enrichment Using Baits Built from Modern DNA

(2014) Jacob M. Enk et al.   MOLECULAR BIOLOGY AND EVOLUTION

Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing

(2014) Ken Kraaijeveld et al.   Molecular Ecology Resources

Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

(2014) Shadi Shokralla et al.   Molecular Ecology Resources

When can noninvasive samples provide sufficient information in conservation genetics studies?

(2014) O. Smith et al.   Molecular Ecology Resources

ITS1: a DNA barcode better than ITS2 in eukaryotes?

(2014) Xin-Cun Wang et al.   Molecular Ecology Resources

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Ancient genomics

(2014) C. Der Sarkissian et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Release Rate of Environmental DNA from Juvenile and Adult Fish

(2014) Atsushi Maruyama et al.   PLoS One

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

(2014) Mbaye Tine et al.   Nature Communications

Single Cell Genomics: Advances and Future Perspectives

(2014) Iain C. Macaulay et al.   PLoS Genetics

Decrease in cytosine methylation at CpG island shores and increase in DNA fragmentation during zebrafish aging

(2013) Nobuyoshi Shimoda et al.   AGE

STRONG SELECTION BARRIERS EXPLAIN MICROGEOGRAPHIC ADAPTATION IN WILD SALAMANDER POPULATIONS

(2013) Jonathan L. Richardson et al.   EVOLUTION

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

(2013) B. Zhang et al.   GENOME RESEARCH

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples

(2013) Simon Boitard et al.   Molecular Ecology Resources

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

(2013) Yaping Yang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Robust Detection of Rare Species Using Environmental DNA: The Importance of Primer Specificity

(2013) Taylor M. Wilcox et al.   PLoS One

Deep Sequencing of RNA from Ancient Maize Kernels

(2013) Sarah L. Fordyce et al.   PLoS One

Unveiling the Diet of Elusive Rainforest Herbivores in Next Generation Sequencing Era? The Tapir as a Case Study

(2013) Fabrice Hibert et al.   PLoS One

Mitochondrial genome diversity and population structure of the giant squid Architeuthis: genetics sheds new light on one of the most enigmatic marine species

(2013) I. Winkelmann et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Screening mammal biodiversity using DNA from leeches

(2012) Ida Bærholm Schnell et al.   CURRENT BIOLOGY

A review of the biology, fisheries and conservation of the whale shark Rhincodon typus

(2012) D. Rowat et al.   JOURNAL OF FISH BIOLOGY

DNA from soil mirrors plant taxonomic and growth form diversity

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

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Population genetics of the American eel (Anguilla rostrata):FST = 0 and North Atlantic Oscillation effects on demographic fluctuations of a panmictic species

(2012) Caroline L. Côté et al.   MOLECULAR ECOLOGY

Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase

(2012) Elizabeth A Manrao et al.   NATURE BIOTECHNOLOGY

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision

(2012) Gerald M Cherf et al.   NATURE BIOTECHNOLOGY

High-Resolution Analysis of Cytosine Methylation in Ancient DNA

(2012) Bastien Llamas et al.   PLoS One

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson 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

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

Gene-associated markers provide tools for tackling illegal fishing and false eco-certification

(2012) Einar E. Nielsen et al.   Nature Communications

Differences in the climatic debts of birds and butterflies at a continental scale

(2012) Vincent Devictor et al.   Nature Climate Change

Pleistocene isolation, secondary introgression and restricted contemporary gene flow in the pig-eye shark, Carcharhinus amboinensis across northern Australia

(2011) B. J. Tillett et al.   CONSERVATION GENETICS

Ecologically and Evolutionarily Important SNPs Identified in Natural Populations

(2011) L. M. Williams et al.   MOLECULAR BIOLOGY AND EVOLUTION

Monitoring endangered freshwater biodiversity using environmental DNA

(2011) PHILIP FRANCIS THOMSEN et al.   MOLECULAR ECOLOGY

All roads lead to home: panmixia of European eel in the Sargasso Sea

(2011) THOMAS D. ALS et al.   MOLECULAR ECOLOGY

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

Performance comparison of exome DNA sequencing technologies

(2011) Michael J Clark et al.   NATURE BIOTECHNOLOGY

Exome sequencing supports a de novo mutational paradigm for schizophrenia

(2011) Bin Xu et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Nutritional influences on epigenetics and age-related disease

(2011) Lara K. Park et al.   PROCEEDINGS OF THE NUTRITION SOCIETY

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

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

DNA Methylation of the Gonadal Aromatase (cyp19a) Promoter Is Involved in Temperature-Dependent Sex Ratio Shifts in the European Sea Bass

(2011) Laia Navarro-Martín et al.   PLoS Genetics

Comparison of solution-based exome capture methods for next generation sequencing

(2011) Anna-Maija Sulonen et al.   GENOME BIOLOGY

Phylogeography and conservation of the bull shark (Carcharhinus leucas) inferred from mitochondrial and microsatellite DNA

(2010) S. A. Karl et al.   CONSERVATION GENETICS

Exome sequencing: the sweet spot before whole genomes

(2010) J. K. Teer et al.   HUMAN MOLECULAR GENETICS

What can genetics tell us about population connectivity?

(2010) WINSOR H. LOWE et al.   MOLECULAR ECOLOGY

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature

(2010) I. R. Bradbury et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture

(2010) H. A. Burbano et al.   SCIENCE

Long-term datasets in biodiversity research and monitoring: assessing change in ecological communities through time

(2010) Anne E. Magurran et al.   TRENDS IN ECOLOGY & EVOLUTION

Population genomics of marine fishes: identifying adaptive variation in space and time

(2009) EINAR E. NIELSEN et al.   MOLECULAR ECOLOGY

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

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

(2009) Carsten Schwarz et al.   NUCLEIC ACIDS RESEARCH

Low Genetic Differentiation across Three Major Ocean Populations of the Whale Shark, Rhincodon typus

(2009) Jennifer V. Schmidt et al.   PLoS One

Sexual Development in Fish, Practical Applications for Aquaculture

(2009) A. Cnaani et al.   Sexual Development

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Species detection using environmental DNA from water samples

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

Bayesian inference of population size history from multiple loci

(2008) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

(2008) Montgomery Slatkin   NATURE REVIEWS GENETICS

Temperature-Dependent Sex Determination in Fish Revisited: Prevalence, a Single Sex Ratio Response Pattern, and Possible Effects of Climate Change

(2008) Natalia Ospina-Álvarez et al.   PLoS One

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics

(2008) Kasper Munch et al.   SYSTEMATIC BIOLOGY

Genetic evidence for co-occurrence of chromosomal and thermal sex-determining systems in a lizard

(2007) R. S Radder et al.   Biology Letters