Future-proofing environmental DNA and trait-based predictions of food webs

Climate or diet? The importance of biotic interactions in determining species range size

(2023) Núria Galiana et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Towards exhaustive community ecology via DNA metabarcoding

(2023) Gentile Francesco Ficetola et al.   MOLECULAR ECOLOGY

Machine learning and deep learning—A review for ecologists

(2023) Maximilian Pichler et al.   Methods in Ecology and Evolution

Bringing light onto the Raunkiæran shortfall: A comprehensive review of traits used in functional animal ecology

(2023) Thiago Gonçalves‐Souza et al.   Ecology and Evolution

Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

(2022) François Keck et al.   MOLECULAR ECOLOGY

Disentangling food-web environment relationships: A review with guidelines

(2022) Frederico Mestre et al.   BASIC AND APPLIED ECOLOGY

Biogeography of bird and mammal trophic structures

(2022) Manuel Mendoza et al.   ECOGRAPHY

Trait-based approaches to global change ecology: moving from description to prediction

(2022) Stephanie J. Green et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics uncovered across a river catchment using environmental DNA

(2022) Rosetta C. Blackman et al.   Communications Biology

Environmental nucleic acids: A field‐based comparison for monitoring freshwater habitats using eDNA and eRNA

(2022) Joanne E. Littlefair et al.   Molecular Ecology Resources

Beyond body size—new traits for new heights in trait-based modelling of predator-prey dynamics

(2022) Kate L. Wootton et al.   PLoS One

Human disturbances affect the topology of food webs

(2022) Frederico Mestre et al.   ECOLOGY LETTERS

Towards the fully automated monitoring of ecological communities

(2022) Marc Besson et al.   ECOLOGY LETTERS

Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: Overview and prospects

(2022) Weihan Jia et al.   QUATERNARY SCIENCE REVIEWS

Environmental RNA as a Tool for Marine Community Biodiversity Assessments

(2022) Marissa S. Giroux et al.   Scientific Reports

Ten (mostly) simple rules to future‐proof trait data in ecological and evolutionary sciences

(2022) Alexander Keller et al.   Methods in Ecology and Evolution

Validating eDNA Measurements of the Richness and Abundance of Anurans at a Large Scale

(2021) Wenhao Li et al.   JOURNAL OF ANIMAL ECOLOGY

The evolution of critical thermal limits of life on Earth

(2021) Joanne M. Bennett et al.   Nature Communications

Environmental (e)RNA advances the reliability of eDNA by predicting its age

(2021) Nathaniel T. Marshall et al.   Scientific Reports

Sifting environmental DNA metabarcoding data sets for rapid reconstruction of marine food webs

(2021) Simone D’Alessandro et al.   FISH AND FISHERIES

Global knowledge gaps in species interaction networks data

(2021) Timothée Poisot et al.   JOURNAL OF BIOGEOGRAPHY

Environmental RNA: A Revolution in Ecological Resolution?

(2021) Matthew C. Yates et al.   TRENDS IN ECOLOGY & EVOLUTION

Species richness and food‐web structure jointly drive community biomass and its temporal stability in fish communities

(2021) Alain Danet et al.   ECOLOGY LETTERS

A roadmap towards predicting species interaction networks (across space and time)

(2021) Tanya Strydom et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Environmental DNA and environmental RNA: Current and prospective applications for biological monitoring

(2021) Heather D. Veilleux et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Fine‐tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches

(2021) Cátia Lúcio Pereira et al.   Methods in Ecology and Evolution

A multi‐site method to capture turnover in rare to common interactions in bipartite species networks

(2021) Marie V. Henriksen et al.   JOURNAL OF ANIMAL ECOLOGY

Climate change facilitated the early colonization of the Azores Archipelago during medieval times

(2021) Pedro M. Raposeiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Overcoming the pitfalls of merging dietary metabarcoding into ecological networks

(2021) Jordan P. Cuff et al.   Methods in Ecology and Evolution

Trait-Based Assessments of Climate-Change Impacts on Interacting Species

(2020) Matthias Schleuning et al.   TRENDS IN ECOLOGY & EVOLUTION

Environmental DNA reveals seasonal shifts and potential interactions in a marine community

(2020) Anni Djurhuus et al.   Nature Communications

Open Science principles for accelerating trait-based science across the Tree of Life

(2020) Rachael V. Gallagher et al.   Nature Ecology & Evolution

Co‐occurrence is not evidence of ecological interactions

(2020) F. Guillaume Blanchet et al.   ECOLOGY LETTERS

Novel feeding interactions amplify the impact of species redistribution on an Arctic food web

(2020) Laurene Pecuchet et al.   GLOBAL CHANGE BIOLOGY

Executing multi-taxa eDNA ecological assessment via traditional metrics and interactive networks

(2020) Mathew Seymour et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Trait‐based ecology at large scales: Assessing functional trait correlations, phylogenetic constraints and spatial variability using open data

(2020) Martin A. Wilkes et al.   GLOBAL CHANGE BIOLOGY

Energy Flow Through Marine Ecosystems: Confronting Transfer Efficiency

(2020) Tyler D. Eddy et al.   TRENDS IN ECOLOGY & EVOLUTION

GenBank’s reliability is uncertain for biodiversity researchers seeking species-level assignment for eDNA

(2020) Nicolas S. Locatelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Delineating reef fish trophic guilds with global gut content data synthesis and phylogeny

(2020) Valeriano Parravicini et al.   PLOS BIOLOGY

Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA

(2019) Krista M. Ruppert et al.   Global Ecology and Conservation

Optimizing environmental DNA sampling effort for fish inventories in tropical streams and rivers

(2019) Isabel Cantera et al.   Scientific Reports

Ecogeographical rules and the macroecology of food webs

(2019) Benjamin Baiser et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Predator traits determine food-web architecture across ecosystems

(2019) Ulrich Brose et al.   Nature Ecology & Evolution

Biodiversity–ecosystem functioning relationships in fish communities: biomass is related to evenness and the environment, not to species richness

(2019) Aurore Maureaud et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The marine fish food web is globally connected

(2019) Camille Albouy et al.   Nature Ecology & Evolution

Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

(2019) Laura Parducci et al.   Frontiers in Ecology and Evolution

Environmental DNA provides quantitative estimates of a threatened salmon species

(2019) Andrew Olaf Shelton et al.   BIOLOGICAL CONSERVATION

Exploring the temporal variability of a food web using long‐term biomonitoring data

(2019) Pierre Olivier et al.   ECOGRAPHY

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

(2019) Hannah Weigand et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Can Environmental RNA Revolutionize Biodiversity Science?

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

Towards an ecological trait‐data standard

(2019) Florian D. Schneider et al.   Methods in Ecology and Evolution

Revealing biases in the sampling of ecological interaction networks

(2019) Marcus A.M. de Aguiar et al.   PeerJ

Gaps in DNA-Based Biomonitoring Across the Globe

(2019) Katie M. McGee et al.   Frontiers in Ecology and Evolution

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

(2019) Eva Egelyng Sigsgaard et al.   Evolutionary Applications

GenBank is a reliable resource for 21st century biodiversity research

(2019) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting the fate of eDNA in the environment and implications for studying biodiversity

(2019) Jori B. Harrison et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Climate shapes mammal community trophic structures and humans simplify them

(2019) Manuel Mendoza et al.   Nature Communications

Machine learning algorithms to infer trait‐matching and predict species interactions in ecological networks

(2019) Maximilian Pichler et al.   Methods in Ecology and Evolution

New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality

(2019) C. Giguet-Covex et al.   Scientific Reports

Network-Based Biomonitoring: Exploring Freshwater Food Webs With Stable Isotope Analysis and DNA Metabarcoding

(2019) Zacchaeus G. Compson et al.   Frontiers in Ecology and Evolution

Heat tolerance is more variable than cold tolerance across species of Iberian lizards after controlling for intraspecific variation

(2019) Salvador Herrando‐Pérez et al.   FUNCTIONAL ECOLOGY

Unveiling the food webs of tetrapods across Europe through the prism of the Eltonian niche

(2019) Louise M. J. O’Connor et al.   JOURNAL OF BIOGEOGRAPHY

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Food-web structure varies along environmental gradients in a high-latitude marine ecosystem

(2018) Susanne Kortsch et al.   ECOGRAPHY

Land cover disturbance homogenizes aquatic insect functional structure in neotropical savanna streams

(2018) Diego M. Parreira de Castro et al.   ECOLOGICAL INDICATORS

Predictive power of food web models based on body size decreases with trophic complexity

(2018) Tomas Jonsson et al.   ECOLOGY LETTERS

Water flow and biofilm cover influence environmental DNA (eDNA) detection in recirculating streams

(2018) Arial Shogren et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

On the development of a predictive functional trait approach for studying terrestrial arthropods

(2018) Pierre-Marc Brousseau et al.   JOURNAL OF ANIMAL ECOLOGY

Energy Flux: The Link between Multitrophic Biodiversity and Ecosystem Functioning

(2018) Andrew D. Barnes et al.   TRENDS IN ECOLOGY & EVOLUTION

DNA from lake sediments reveals long-term ecosystem changes after a biological invasion

(2018) Gentile Francesco Ficetola et al.   Science Advances

Cracking the Code of Biodiversity Responses to Past Climate Change

(2018) David Nogués-Bravo et al.   TRENDS IN ECOLOGY & EVOLUTION

Bringing Elton and Grinnell together: a quantitative framework to represent the biogeography of ecological interaction networks

(2018) Dominique Gravel et al.   ECOGRAPHY

DNA metabarcoding unveils multiscale trophic variation in a widespread coastal opportunist

(2018) Andjin Siegenthaler et al.   MOLECULAR ECOLOGY

Diet and trophic interactions of a circumglobally significant gelatinous marine zooplankter, Dolioletta gegenbauri (Uljanin, 1884)

(2018) Tina L. Walters et al.   MOLECULAR ECOLOGY

Approaches to integrating genetic data into ecological networks

(2018) Elizabeth L. Clare et al.   MOLECULAR ECOLOGY

Promises and pitfalls of using high-throughput sequencing for diet analysis

(2018) Antton Alberdi et al.   Molecular Ecology Resources

Estimating species distribution and abundance in river networks using environmental DNA

(2018) Luca Carraro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring predator–prey interactions in food webs

(2018) Justin P. F. Pomeranz et al.   Methods in Ecology and Evolution

Between-lake variation in the trophic ecology of an invasive crayfish

(2017) Michelle C. Jackson et al.   FRESHWATER BIOLOGY

Trait matching and phylogeny as predictors of predator-prey interactions involving ground beetles

(2017) Pierre-Marc Brousseau et al.   FUNCTIONAL ECOLOGY

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

(2017) Isabelle Domaizon et al.   JOURNAL OF PALEOLIMNOLOGY

Assessing the trophic ecology of top predators across a recolonisation frontier using DNA metabarcoding of diets

(2017) N Hardy et al.   MARINE ECOLOGY PROGRESS SERIES

Species traits as drivers of food web structure

(2017) Idaline Laigle et al.   OIKOS

Next-Generation Global Biomonitoring: Large-scale, Automated Reconstruction of Ecological Networks

(2017) David A. Bohan et al.   TRENDS IN ECOLOGY & EVOLUTION

Assessing the trophic ecology of top predators across a recolonisation frontier using DNA metabarcoding of diets

(2017) N Hardy et al.   MARINE ECOLOGY PROGRESS SERIES

Ecological interactions and the Netflix problem

(2017) Philippe Desjardins-Proulx et al.   PeerJ

A common framework for identifying linkage rules across different types of interactions

(2016) Ignasi Bartomeus et al.   FUNCTIONAL ECOLOGY

Handbook of protocols for standardized measurement of terrestrial invertebrate functional traits

(2016) Marco Moretti et al.   FUNCTIONAL ECOLOGY

Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems

(2016) Darren M. Evans et al.   FUNCTIONAL ECOLOGY

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities

(2016) Jessica L. Ray et al.   MOLECULAR ECOLOGY

The meaning of functional trait composition of food webs for ecosystem functioning

(2016) Dominique Gravel et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Labile Limits of Forbidden Interactions

(2016) Juan P. González-Varo et al.   TRENDS IN ECOLOGY & EVOLUTION

Phenotypic Plasticity and Species Coexistence

(2016) Martin M. Turcotte et al.   TRENDS IN ECOLOGY & EVOLUTION

Predicting and mitigating future biodiversity loss using long-term ecological proxies

(2016) Damien A. Fordham et al.   Nature Climate Change

18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species

(2016) Aitor Albaina et al.   Ecology and Evolution

Timescales alter the inferred strength and temporal consistency of intraspecific diet specialization

(2015) Mark Novak et al.   OECOLOGIA

Individual-level niche specialization within populations: emerging areas of study

(2015) Craig A. Layman et al.   OECOLOGIA

A theory for species co-occurrence in interaction networks

(2015) Kévin Cazelles et al.   Theoretical Ecology

Inferring biotic interactions from proxies

(2015) Ignacio Morales-Castilla et al.   TRENDS IN ECOLOGY & EVOLUTION

Empirical Evaluation of Neutral Interactions in Host-Parasite Networks

(2014) E. F. Canard et al.   AMERICAN NATURALIST

The geographic scaling of biotic interactions

(2014) Miguel B. Araújo et al.   ECOGRAPHY

The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change

(2014) Fernando Valladares et al.   ECOLOGY LETTERS

Environmental Conditions Influence eDNA Persistence in Aquatic Systems

(2014) Matthew A. Barnes et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Molecular detection of trophic interactions: emerging trends, distinct advantages, significant considerations and conservation applications

(2014) Elizabeth L. Clare   Evolutionary Applications

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

High intraspecific variability in the functional niche of a predator is associated with ontogenetic shift and individual specialization

(2014) Tian Zhao et al.   Ecology and Evolution

The dimensionality of ecological networks

(2013) Anna Eklöf et al.   ECOLOGY LETTERS

Can We Name Earth's Species Before They Go Extinct?

(2013) M. J. Costello et al.   SCIENCE

Ecosystem ecology: size-based constraints on the pyramids of life

(2013) Rowan Trebilco et al.   TRENDS IN ECOLOGY & EVOLUTION

Inferring food web structure from predator-prey body size relationships

(2013) Dominique Gravel et al.   Methods in Ecology and Evolution

Variability in life-history and ecological traits is a buffer against extinction in mammals

(2012) Manuela González-Suárez et al.   ECOLOGY LETTERS

Life on a tropical planet: niche conservatism and the global diversity gradient

(2012) Tom S. Romdal et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Emergence of Structural Patterns in Neutral Trophic Networks

(2012) Elsa Canard et al.   PLoS One

What we know and don’t know about Earth's missing biodiversity

(2012) Brett R. Scheffers et al.   TRENDS IN ECOLOGY & EVOLUTION

Species interactions: estimating per-individual interaction strength and covariates before simplifying data into per-species ecological networks

(2012) Konstans Wells et al.   Methods in Ecology and Evolution

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

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

Using species co-occurrence networks to assess the impacts of climate change

(2011) Miguel B. Araújo et al.   ECOGRAPHY

Assessment of the impact of anthropogenic activities on the groundwater hydrology and chemistry in Tarsus coastal plain (Mersin, SE Turkey) using fuzzy clustering, multivariate statistics and GIS techniques

(2011) Cüneyt Güler et al.   JOURNAL OF HYDROLOGY

Relevance of evolutionary history for food web structure

(2011) A. Eklof et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

How Many Species Are There on Earth and in the Ocean?

(2011) Camilo Mora et al.   PLOS BIOLOGY

Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate

(2010) J. H. SØNSTEBØ et al.   Molecular Ecology Resources

Evaluating multiple determinants of the structure of plant–animal mutualistic networks

(2009) Diego P. Vázquez et al.   ECOLOGY

Testing the effectiveness of discrete and continuous environmental diversity as a surrogate for species diversity

(2008) Joaquín Hortal et al.   ECOLOGICAL INDICATORS