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

unmarked: AnRPackage for Fitting Hierarchical Models of Wildlife Occurrence and Abundance

(2015) Ian Fiske et al.   Journal of Statistical Software

Sampling bias inverts ecogeographical relationships in island reptiles

(2014) Gentile Francesco Ficetola et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfishProcambarus clarkiiin freshwater ponds

(2014) Anne Tréguier et al.   JOURNAL OF APPLIED ECOLOGY

Fifty thousand years of Arctic vegetation and megafaunal diet

(2014) Eske Willerslev et al.   NATURE

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

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

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

Meta-genomic surveillance of invasive species in the bait trade

(2014) Andrew R. Mahon et al.   Conservation Genetics Resources

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

Detection of Asian carp DNA as part of a Great Lakes basin-wide surveillance program

(2013) Christopher L. Jerde et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Use of Ancient Sedimentary DNA as a Novel Conservation Tool for High-Altitude Tropical Biodiversity

(2013) SANNE BOESSENKOOL et al.   CONSERVATION BIOLOGY

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Imperfect detection impacts the performance of species distribution models

(2013) José J. Lahoz-Monfort et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

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

(2013) Laura Parducci et al.   MOLECULAR ECOLOGY

DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

(2013) M. De Barba et al.   Molecular Ecology Resources

Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

(2013) Bruce E. Deagle et al.   Molecular Ecology Resources

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen

(2013) Benedikt R. Schmidt et al.   Methods in Ecology and Evolution

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

Tracking earthworm communities from soil DNA

(2012) FRIEDERIKE BIENERT et al.   MOLECULAR ECOLOGY

DNA from soil mirrors plant taxonomic and growth form diversity

(2012) N. G. YOCCOZ 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

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

(2012) C. Q. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol

(2012) Mehrdad Hajibabaei et al.   BMC ECOLOGY

Integrating detection probabilities in species distribution models of amphibians breeding in Mediterranean temporary ponds

(2011) Carola Gómez-Rodríguez et al.   DIVERSITY AND DISTRIBUTIONS

Improving occupancy estimation when two types of observational error occur: non-detection and species misidentification

(2011) David A. Miller et al.   ECOLOGY

From molecules to management: Adopting DNA-based methods for monitoring biological invasions in aquatic environments

(2011) John A. Darling et al.   ENVIRONMENTAL RESEARCH

Monitoring endangered freshwater biodiversity using environmental DNA

(2011) PHILIP FRANCIS THOMSEN et al.   MOLECULAR ECOLOGY

Who is eating what: diet assessment using next generation sequencing

(2011) FRANCOIS POMPANON et al.   MOLECULAR ECOLOGY

Two decades of describing the unseen majority of aquatic microbial diversity

(2011) LUCIE ZINGER 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

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

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

The virtual ecologist approach: simulating data and observers

(2010) Damaris Zurell et al.   OIKOS

Design of occupancy studies with imperfect detection

(2010) Gurutzeta Guillera-Arroita et al.   Methods in Ecology and Evolution

Trend estimation in populations with imperfect detection

(2009) Marc Kéry et al.   JOURNAL OF APPLIED ECOLOGY

Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

(2009) BRUCE E. DEAGLE et al.   MOLECULAR ECOLOGY

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: thetrnL approach

(2009) ALICE VALENTINI et al.   Molecular Ecology Resources

Species detection using environmental DNA from water samples

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

Imperfect detection and its consequences for monitoring for conservation

(2008) M. Kéry et al.   COMMUNITY ECOLOGY

DNA barcoding for ecologists

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