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Filling reference gaps via assembling DNA barcodes using high-throughput sequencing—moving toward barcoding the world
Shanlin Liu, Chentao Yang, Chengran Zhou, Xin Zhou , Methods in Ecology and Evolution , 2017PythonFree
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Parallel Likelihood Calculation for Phylogenetic Comparative Models: the SPLITT C++ Library
Venelin Mitov, Tanja Stadler , Methods in Ecology and Evolution , 2019ShellFree
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Using taxonomic consistency with semi-automated data pre-processing for high quality DNA barcodes
Björn Rulik, Jonas Eberle, Laura von der Mark, Jana Thormann, Manfred Jung, Frank Köhler, Wolfgang Apfel, Andreas Weigel, Andreas Kopetz, Jonas Köhler, Frank Fritzlar , Methods in Ecology and Evolution , 2017RFree
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Environmental drivers of variability in the movement ecology of turkey vultures (Cathartes aura) in North and South America
Somayeh Dodge , Gil Bohrer , Keith Bildstein , Sarah C. Davidson , Rolf Weinzierl , Marc J. Bechard , David Barber , Roland Kays , David Brandes , Jiawei Han and Martin Wikelski , Methods in Ecology and Evolution , 2014RFree
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momentuHMM: R package for generalized hidden Markov models of animal movement
Brett T. McClintock, Théo Michelot , Methods in Ecology and Evolution , 2018RFree
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Sensitivity of binomial N-mixture models to overdispersion: The importance of assessing model fit
Jonas Knape, Debora Arlt, Frédéric Barraquand, Åke Berg, Mathieu Chevalier, Tomas Pärt, Alejandro Ruete, Michał Żmihorski , Methods in Ecology and Evolution , 2018RFree
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Use of a filter cartridge combined with intra-cartridge bead-beating improves detection of microbial DNA from water samples
Masayuki Ushio , Methods in Ecology and Evolution , 2019RFree
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tRophicPosition, an r package for the Bayesian estimation of trophic position from consumer stable isotope ratios
Claudio Quezada-Romegialli, Andrew L. Jackson, Brian Hayden, Kimmo K. Kahilainen, Christelle Lopes, Chris Harrod , Methods in Ecology and Evolution , 2018RFree
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How should we estimate diversity in the fossil record? Testing richness estimators using sampling-standardised discovery curves
Roger A. Close, Serjoscha W. Evers, John Alroy, Richard J. Butler , Methods in Ecology and Evolution , 2018RFree
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A simulation tool to scrutinise the behaviour of functional diversity metrics
Jana M. McPherson, Lauren A. Yeager, Julia K. Baum , Methods in Ecology and Evolution , 2017RFree
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Differentiating the Lévy walk from a composite correlated random walk
Marie Auger-Méthé, Andrew E. Derocher, Michael J. Plank, Edward A. Codling, Mark A. Lewis , Methods in Ecology and Evolution , 2015RFree
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Continuous traits and speciation rates: Alternatives to state-dependent diversification models
Michael G. Harvey, Daniel L. Rabosky , Methods in Ecology and Evolution , 2017RFree
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ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms
William E. Peterman , Methods in Ecology and Evolution , 2018RFree
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Tipping points in the dynamics of speciation
Patrik Nosil, Jeffrey L. Feder, Samuel M. Flaxman, Zachariah Gompert , Nature Ecology and Evolution , 2017MathematicaFree
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ENMTools 1.0: an R package for comparative ecological biogeography
Dan L. Warren, Nicholas J. Matzke, Marcel Cardillo, John B. Baumartner , Trends in Ecology and Evolution , 2021RFree
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Time to get moving: assisted gene flow of forest trees
Sally N. Aitken, Jordan B. Bemmels , Annual Review of Ecology, Evolution, and Systematics , 2015RebolFree
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Moderm computational approaches for analysing molecular genetic variation data
Paul Marjoram, Simon Tavaré , Annual Review of Ecology, Evolution, and Systematics , 2006PythonFree
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The somatic mutation landscape of the human body
Pablo E. García-Nieto, Ashby J. Morrison, Hunter B. Fraser , Genome Biology , 2019RFree
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Comparative assessment of methods for aligning multiple genome sequences
Xiaoyu Chen, Martin Tompa , Genome Biology , 2010CFree
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Imperfect pathogen detection from non-invasive skin swabs biases disease inference
Graziella V. DiRenzo, Evan H. Campbell Grant, Ana V. Longo, Christian Che-Castaldo, Kelly R. Zamudio, Karen R. Lips , Methods in Ecology and Evolution , 2017RFree
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raptr: Representative and adequate prioritization toolkit in R
Jeffrey O. Hanson, Jonathan R. Rhodes, Hugh P. Possingham, Richard A. Fuller , Methods in Ecology and Evolution , 2017RFree
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Point density and spatial resolution limit estimation of Leaf Area Index using discrete return LiDAR
Milodowski, David ; Swinfield, Thomas ; Coomes, David ; Williams, Mathew , Methods in Ecology and Evolution , 2018PythonFree
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Recombination rate plasticity: revealing mechanisms by design
Laurie S. Stevison , Stephen Sefick , Chase Rushton and Rita M. Graze , Methods in Ecology and Evolution , 2017RFree
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Can time-to-detection models with fewer survey replicates provide a robust alternative to traditional site-occupancy models?
Dominic A. W. Henry, Alan T. K. Lee, Res Altwegg , Methods in Ecology and Evolution , 2020RFree
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Data from: A comparative analysis of common methods to identify waterbird hotspots
Allison L. Sussman, Beth Gardner, Evan M. Adams, Leo Salas, Kevin P. Kenow, David R. Luukkonen , Methods in Ecology and Evolution , 2019RFree
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babette: BEAUti 2, BEAST2 and Tracer for R
Richèl J. C. Bilderbeek, Rampal S. Etienne , Methods in Ecology and Evolution , 2018RFree
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A practical guide to structured expert elicitation using the IDEA protocol
Victoria Hemming, Mark A. Burgman, Anca M. Hanea, Marissa F. McBride, Bonnie C. Wintle , Methods in Ecology and Evolution , 2017RFree
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How should we estimate diversity in the fossil record? Testing richness estimators using sampling-standardised discovery curves
Roger A. Close, Serjoscha W. Evers, John Alroy, Richard J. Butler , Methods in Ecology and Evolution , 2018RFree
-
An r package and online resource for macroevolutionary studies using the ray-finned fish tree of life
Jonathan Chang, Daniel L. Rabosky, Stephen A. Smith, Michael E. Alfaro , Methods in Ecology and Evolution , 2019RFree
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Use of a filter cartridge combined with intra-cartridge bead-beating improves detection of microbial DNA from water samples
Masayuki Ushio , Methods in Ecology and Evolution , 2019RFree
-
Continuous traits and speciation rates: Alternatives to state-dependent diversification models
Michael G. Harvey, Daniel L. Rabosky , Methods in Ecology and Evolution , 2017RFree
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NLMR and landscapetools: An integrated environment for simulating and modifying neutral landscape models in R
Marco Sciaini, Matthias Fritsch, Cédric Scherer, Craig Eric Simpkins , Methods in Ecology and Evolution , 2018NetLogoFree
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A practical method to account for variation in detection range in acoustic telemetry arrays to accurately quantify the spatial ecology of aquatic animals
Jacob W. Brownscombe, Lucas P. Griffin, Jacqueline M. Chapman, Danielle Morley, Alejandro Acosta, Glenn T. Crossin, Sara J. Iverson, Aaron J. Adams, Steven J. Cooke, Andy J. Danylchuk , Methods in Ecology and Evolution , 2019RFree
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Differentiating the Lévy walk from a composite correlated random walk
Marie Auger-Méthé, Andrew E. Derocher, Michael J. Plank, Edward A. Codling, Mark A. Lewis , Methods in Ecology and Evolution , 2015RFree
-
babette: BEAUti 2, BEAST2 and Tracer for R
Richèl J. C. Bilderbeek, Rampal S. Etienne , Methods in Ecology and Evolution , 2018RFree
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Contribution of synchronized GABAergic neurons to dopaminergic neuron firing and bursting
Ekaterina O. Morozova, Maxym Myroshnychenko, Denis Zakharov , PLoS Computational Biology , 2016C++Free
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Dynamic Mechanisms of Neocortical Focal Seizure Onset
Yujiang Wang, Marc Goodfellow, Peter Neal Taylor, Gerold Baier , PLoS Computational Biology , 2014MATLABFree
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Odorant mixtures elicit less variable and faster responses than pure odorants
Ho Ka Chan , Fabian Hersperger, Emiliano Marachlian, Brian H. Smith, Fernando Locatelli, Paul Szyszka, Thomas Nowotny , PLoS Computational Biology , 2018C++Free
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Communication through Resonance in Spiking Neuronal Networks
Gerald Hahn , Alejandro F. Bujan , Yves Frégnac, Ad Aertsen, Arvind Kumar , PLoS Computational Biology , 2014PythonFree
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Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response
Matthew E. MacGilvray , Evgenia Shishkova , Deborah Chasman, Michael Place, Anthony Gitter, Joshua J. Coon, Audrey P. Gasch , PLoS Computational Biology , 2018GAMSFree
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Warming increases the cost of growth in a model vertebrate
Diego R. Barneche, Miki Jahn, Frank Seebacher , Functional Ecology , 2019RFree
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Are variations of direct and indirect plant interactions along a climatic gradient dependent on species’ strategies? An experiment on tree seedlings
Emmanuel Defossez, Benoît Courbaud, Olivier Lasbouygues, Katja Schiffers, Georges Kunstler , Oikos , 2015RFree
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A world of sequences: can we use georeferenced nucleotide databases for a robust automated phylogeography?
Paolo Gratton, Silvio Marta, Gaëlle Bocksberger, Marten Winter, Emiliano Trucchi, Hjalmar Kühl , Journal of Biogeography , 2016RFree
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Testing species assemblage predictions from stacked and joint species distribution models
Damaris Zurell, Niklaus E. Zimmermann, Helge Gross, Andri Baltensweiler, Thomas Sattler, Rafael O. Wüest , Journal of Biogeography , 2019RFree
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Diversity and evolution of the transposable element repertoire in insects
Malte Petersen, David Armisén, Richard A. Gibbs, Lars Hering, Abderrahman Khila, Georg Mayer, Stephen Richards, Oliver Niehuis & Bernhard Misof , BMC Evolutionary Biology , 2019PerlFree
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Reliable species distributions are obtainable with sparse, patchy and biased data by leveraging over species and data types
Samantha L. Peel, Nicole A. Hill, Scott D. Foster, Simon J. Wotherspoon, Claudio Ghiglione, Stefano Schiaparelli , Methods in Ecology and Evolution , 2019RFree
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Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods
Bernd Hänfling, Lori Lawson Handley, Daniel S. Read, Christoph Hahn, Jianlong Li, Paul Nichols, Rosetta C. Blackman, Anna Oliver, Ian J. Winfield , Molecular Ecology , 2016RFree
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Allelic diversity for neutral markers retains a higher adaptive potential for quantitative traits than expected heterozygosity
Ana Vilas, Andrés Pérez-Figueroa, Humberto Quesada, Armando Caballero , Molecular Ecology , 2015ShellFree
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A Sparse Coding Model with Synaptically Local Plasticity and Spiking Neurons Can Account for the Diverse Shapes of V1 Simple Cell Receptive Fields
Joel Zylberberg , Jason Timothy Murphy, Michael Robert DeWeese , PLoS Computational Biology , 2011PythonFree
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Mechanistic model predicts tissue–environment relationships and trophic shifts in animal hydrogen and oxygen isotope ratios
Sarah Magozzi, Hannah B. Vander Zanden, Michael B. Wunder & Gabriel J. Bowen , Oecologia , 2019RFree
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Estimating dispersal kernels using genetic parentage data
Michael Bode, David H. Williamson, Hugo B. Harrison, Nick Outram, Geoffrey P. Jones , Methods in Ecology and Evolution , 2017MatlabFree
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A shared coevolutionary history does not alter the outcome of coalescence in experimental populations of Pseudomonas fluorescens
Meaghan Castledine, Angus Buckling, Daniel Padfield , Journal of Evolutionary Biology , 2018RFree
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Occurrence of blood feeding terrestrial leeches in a degraded forest ecosystem
Drinkwater, Rosie; Drinkwater, Rosie; Swinfield, Tom; Deere, Nicolas J , Ecological Indicators , 2019RFree
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Compendium of R code and data for Is prediction of species richness from Stacked Species Distribution Models biased by habitat saturation?.
Grenié M, Violle C, mUNOZ f. , Ecological Indicators , 2019RFree
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Niche overlap of mountain hare subspecies and the vulnerability of their ranges to invasion by the European hare; the (bad) luck of the Irish
Anthony Caravaggi, Katie Leach, Francesco Santilli, Jukka Rintala, Pekka Helle, Juha Tiainen, Francesco Bisi, Adriano Martinoli, W. Ian Montgomery & Neil Reid , Biological Invasions , 2016RFree
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Gastrointestinal ACE2, COVID-19 and IBD: Opportunity in the Face of Tragedy?
Mayur Garg, Britt Christensen, John S. Lubel , Archaea , 2020Jupyter NotebookFree
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Effect of the environment on horizontal gene transfer between bacteria and archaea
Clara A, Fuchsman, Roy Eric Collins, Gabrielle Rocap, Willian J. Brazelton , Archaea , 2017RFree
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Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis
Hajk-Georg Drost, Alexander Gabel, Ivo Grosse, Marcel Quint , Archaea , 2015PerlFree
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Ecology and mode-of-life explain lifespan variation in birds and mammals
Kevin Healy, Thomas Guillerme, Sive Finlay, Adam Kanem, Séan B. A. Kelly, Deirdre McClean, David J. Kelly, Ian Donohue, Andrew L. Jackson, Natalie Cooper , Biological Journal of the Linnean Society , 2014RFree
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Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling
Mark J. Brewer, Robert B. O'Hara, Barbara J. Anderson, Ralf Ohlemüller , Ecology and Evolution , 2016RFree
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Selective constraints on coding sequences of nervous system genes are a major determinant of duplicate gene retention in vertebrates
Julien Roux, Jialin Liu, Marc Robinson-Rechavi , Ecology and Evolution , 2016PerlFree
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Fishing degrades size structure of coral reef fish communities
James P. W. Robinson, Ivor D. Williams, Andrew M. Edwards, Jana McPherson, Lauren Yeager, Laurent Vigliola, Russell E. Brainard, Julia K. Baum , Ecology and Evolution , 2016RFree
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A simulation tool to scrutinise the behaviour of functional diversity metrics
Jana M. McPherson, Lauren A. Yeager, Julia K. Baum , Ecology and Evolution , 2017RFree
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Root microbiota assembly and adaptive differentiation among European Arabidopsis populations
Thorsten Thiergart, Paloma Durán, Thomas Ellis, Nathan Vannier, Ruben Garrido-Oter, Eric Kemen, Fabrice Roux, Carlos Alonso-Blanco, Jon Ågren, Paul Schulze-Lefert & Stéphane Hacquard , Ecology and Evolution , 2019RFree
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Imperfect pathogen detection from non-invasive skin swabs biases disease inference
Graziella V. DiRenzo, Evan H. Campbell Grant, Ana V. Longo, Christian Che-Castaldo, Kelly R. Zamudio, Karen R. Lips , Ecology and Evolution , 2017RFree
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842Metacommunity, mainland-island system or island communities? Assessing the regional dynamics of plant communities in a fragmented landscape
Felix May, Itamar Giladi, Michael Ristow, Yaron Ziv and Florian Jeltsch , Perspectives in Plant Ecology, Evolution and Systematics , 2013C++Free
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Nectar quality affects ant aggressiveness and biotic defense provided to plants
Fábio T. Pacelhe, Fernanda V. Costa, Frederico S. Neves, Judith Bronstein, Marco A. R. Mello , Biotropica , 2019RFree
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Algorithmic approaches to aid species' delimitation in multidimensional morphospace
Thomas HG Ezard, Paul N Pearson & Andy Purvis , Evolutionary Biology , 2020RFree
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Modelling coevolution in multispecies communities
Guido Caldaraelli, Paul G. Higgs, Alan J. McKane , Food Webs , 1998RFree
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Comparison of ground cover estimates from experiment plots in cotton, sorghum and sugarcane based on images and ortho-mosaics captured by UAV
Tao Duan, Bangyiu Zheng, Wei Guo, Seishi Ninomiya, Yan Guo, Scott C. Chapman , Plant Biology , 2016MATLABFree
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Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed. New Phytologist.
Dunnette, P.V., P.E. Higuera, K.K. McLauchlan, K.M. Derr, C.E. Briles, and M.H. Keefe , Fire Ecology , 2014MatlabFree
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FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild
Nhu H. Nguyen, Zewei Song, Scott T. Bates, Sara Branco, Leho Tedersoo, Jon Menke, Jonathan S. Schilling, Peter G. Kennedy , Frontiers in Ecology and Evolution , 2016PythonFree
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Quantifying the Role of Snowmelt in Stream Discharge in an Alaskan Watershed: An Analysis Using a Spatially Distributed Surface Hydrology Model
Chang Liao, Qianlai Zhuang , Arctic, Antarctic, and Alpine Research , 2017C++Free
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Occurrence of blood feeding terrestrial leeches in a degraded forest ecosystem
Drinkwater, Rosie; Swinfield,Tom; Deere, Nicolas J , Forest Ecosystems , 2019RFree
-
Validating dispersal distances inferred from autoregressive occupancy models with genetic parentage assignments
Laurie A. Hall, Nathan D. Van Schmidt, Steven R. Beissinger , Wildlife Research , 2018RFree
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Resource Allocation to Inflorescence Components Is Highly Integrated despite Differences between Allocation Currencies and Sites
Rubén Torices, Marcos Méndez , International Journal of Plant Sciences , 2014RFree
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Plastid phylogenomic analysis of green plants: A billion years of evolutionary history
Matthew A. Gitzendanner, Pamela S. Soltis, Gane K.-S. Wong, Brad R. Ruhfel, Douglas E. Soltis , Botany , 2018PerlFree
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The bias of a two-dimensional view: comparing two-dimensional and three-dimensional mesophyll surface area estimates using noninvasive imaging
Guillaume Théroux-Rancourt, J. Mason Earles, Matthew E. Gilbert, Maciej A. Zwieniecki, C. Kevin Boyce, Andrew J. McElrone, Craig R. Brodersen , Botany , 2017RFree
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Age, Growth, and Size of Lake Superior Pygmy Whitefish (Prosopium coulterii)
Taylor R. Stewart, Derek H. Ogle , American Midland Naturalist , 2016RFree
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A current affair: entanglement of humpback whales in coastal shark-control nets
Jessica A. Bolin, David S. Schoeman, Carme Pizà-Roca, Kylie L. Scales , Remote Sensing in Ecology and Conservation , 2019RFree
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A world of sequences: can we use georeferenced nucleotide databases for a robust automated phylogeography?
Paolo Gratton, Silvio Marta, Gaëlle Bocksberger, Marten Winter, Emiliano Trucchi, Hjalmar Kühl , Journal of Biogeography , 2016RFree
-
Are variations of direct and indirect plant interactions along a climatic gradient dependent on species’ strategies? An experiment on tree seedlings
Emmanuel Defossez, Benoît Courbaud, Olivier Lasbouygues, Katja Schiffers, Georges Kunstler , Oikos , 2015RFree
-
Global biosphere–climate interaction: a causal appraisal of observations and models over multiple temporal scales
Jeroen Claessen, Annalisa Molini, Brecht Martens, Matteo Detto, Matthias Demuzere,Diego G. Miralles. , Biogeosciences , 2019MATLABFree
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Among-strain consistency in the pace and shape of senescence in duckweed
Patrick M. Barks, Zach W. Dempsey, Theresa M. Burg, Robert A. Laird , Journal of Ecology , 2018RFree
-
Experimentally-constrained biophysical models of tonic and burst firing modes in thalamocortical neurons
Elisabetta Iavarone , Jane Yi, Ying Shi, Bas-Jan Zandt, Christian O’Reilly, Werner Van Geit, Christian Rössert, Henry Markram, Sean L. Hill , PLoS Computational Biology , 2019AGS ScriptFree
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Contribution of synchronized GABAergic neurons to dopaminergic neuron firing and bursting
Ekaterina O. Morozova, Maxym Myroshnychenko, Denis Zakharov , PLoS Computational Biology , 2016C++Free
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Computational Models Describing Possible Mechanisms for Generation of Excessive Beta Oscillations in Parkinson’s Disease
Alex Pavlides, S. John Hogan, Rafal Bogacz , PLoS Computational Biology , 2015MATLABFree
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Function and energy consumption constrain neuronal biophysics in a canonical computation: Coincidence detection
Michiel W. H. Remme , John Rinzel, Susanne Schreiber , PLoS Computational Biology , 2018MATLABFree
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A Sparse Coding Model with Synaptically Local Plasticity and Spiking Neurons Can Account for the Diverse Shapes of V1 Simple Cell Receptive Fields
Joel Zylberberg , Jason Timothy Murphy, Michael Robert DeWeese , PLoS Computational Biology , 2011PythonFree
-
Gap junction plasticity as a mechanism to regulate network-wide oscillations
Guillaume Pernelle, Wilten Nicola, Claudia Clopath , PLoS Computational Biology , 2018HTMLFree
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Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations
Michael D. Martin, Flora Jay, Sergi Castellano, Montgomery Slatkin , Molecular Ecology , 2017PythonFree
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Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes
Guillem Salazar, Francisco M. Cornejo-Castillo, Encarna Borrull, Cristina Díez-Vives, Elena Lara, Dolors Vaqué, Jesús M. Arrieta, Carlos M. Duarte, Josep M. Gasol, Silvia G. Acinas , Molecular Ecology , 2015RFree
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RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus)
Laura Benestan, Thierry Gosselin, Charles Perrier, Bernard Sainte-Marie, Rémy Rochette, Louis Bernatchez , Molecular Ecology , 2015HTMLFree
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Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods
Bernd Hänfling, Lori Lawson Handley, Daniel S. Read, Christoph Hahn, Jianlong Li, Paul Nichols, Rosetta C. Blackman, Anna Oliver, Ian J. Winfield , Molecular Ecology , 2016RFree
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performance: An R Package for Assessment, Comparison and Testing of Statistical Models
Daniel Lüdecke, Mattan S. Ben-Shachar, Indrajeet Patil, Philip Waggoner, and Dominique Makowski , Methods in Ecology and Evolution , 2021RFree
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Data from: A comparative analysis of common methods to identify waterbird hotspots
Allison L. Sussman, Beth Gardner, Evan M. Adams, Leo Salas, Kevin P. Kenow, David R. Luukkonen , Methods in Ecology and Evolution , 2019RFree
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A package for motif analyses of bipartite networks
Benno I. Simmons, Michelle J. M. Sweering, Maybritt Schillinger, Lynn V. Dicks, William J. Sutherland, Riccardo Di Clemente , Methods in Ecology and Evolution , 2019RFree
-
BA3-SNPs: Contemporary migration reconfigured in BayesAss for next-generation sequence data
Steven M. Mussmann, Marlis R. Douglas, Tyler K. Chafin, Michael E. Douglas , Methods in Ecology and Evolution , 2019PythonFree
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Recombination rate plasticity: revealing mechanisms by design
Laurie S. Stevison , Stephen Sefick , Chase Rushton and Rita M. Graze , Methods in Ecology and Evolution , 2017RFree
-
Point density and spatial resolution limit estimation of Leaf Area Index using discrete return LiDAR
Milodowski, David ; Swinfield, Thomas ; Coomes, David ; Williams, Mathew , Methods in Ecology and Evolution , 2018PythonFree
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