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Science NestCategoriesEvolution
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Title Title
Date Date
  • Single-cell transcriptomics unveils gene regulatory network plasticity

    Giovanni Iancono, Ramon Massoni-Badosa, Holger Heyn , Genome Biology ,  2019
    HTML

    Free

  • Comparison of computational methods for the identification of topologically assocaiting domains

    Marie Zufferey, Daniele Tavernari, Elisa Oricchio, Giovanni Ciriello , Genome Biology ,  2018
    R

    Free

  • An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BedArray

    Lucas A. Salas, Devin C. Koestler, Rondi A. Butler, Helen M.Hansen, John K. Wiencke, Karl T. Kelsey, Brock C. Christensen , Genome Biology ,  2018
    R

    Free

  • Comparative assessment of methods for aligning multiple genome sequences

    Xiaoyu Chen, Martin Tompa , Genome Biology ,  2010
    C

    Free

  • The somatic mutation landscape of the human body

    Pablo E. García-Nieto, Ashby J. Morrison, Hunter B. Fraser , Genome Biology ,  2019
    R

    Free

  • Evolution of Dosage Compensation in Anolis Carolinensis, a Reptile with XX.XY Chromosomal Sex Determination

    Shawn M.Rupp, Timothy H. Webster, Kimberly C.Olney, Elizabeth D.Hutchins, Kenro Kusumi, Melissa A. Wilson Sayres , Genome Biology ,  2016
    Python

    Free

  • Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp

    Cyril Matthey-Doret, Casper J can der Kooi, Daniel L Jeffries, Jens Bast, Alice B Dennis, Christopher Vorburger, Tanja Schwander , Genome Biology ,  2019
    Shell

    Free

  • Moderm computational approaches for analysing molecular genetic variation data

    Paul Marjoram, Simon Tavaré , Annual Review of Ecology, Evolution, and Systematics ,  2006
    Python

    Free

  • Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers

    Anne Chao, Chun-Huo Chiu, Lou Jost , Annual Review of Ecology, Evolution, and Systematics ,  2014
    R

    Free

  • Time to get moving: assisted gene flow of forest trees

    Sally N. Aitken, Jordan B. Bemmels , Annual Review of Ecology, Evolution, and Systematics ,  2015
    Rebol

    Free

  • On Fitting the Poisson Lognormal Distribution to Species-Abundance Data

    M.G. Bulmer , Annual Review of Ecology, Evolution, and Systematics ,  1974
    Pascal

    Free

  • Do baseline glucocorticoids presict fitness? Trends in Ecology and Evolution

    Frances Bonier, Paul R. Martin, Ignacio T. Moore, John C. Wingfield , Trends in Ecology and Evolution ,  2009
    HTML

    Free

  • 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 ,  2021
    R

    Free

  • Blobal photsynthetic capacity is optimized to the environment

    Nicholas G. Smith, Trevor F. Keenan, I.Colin Prentice, Han Wang , Ecology Letters ,  2019
    R

    Free

  • Abunance of common species, not species richness, drives delivery of a real-world ecosystem service

    Rachael Winfree, Jeremy W. Fox, Neal M. Williams, James R. Reilly, Daniel P.Cariveau , Ecology Letters ,  2015
    R

    Free

  • Network spandrels reflect ecological assembly

    Daniel S. Maynard, Carlos A. Serván, Stefano Allesina , Ecology Letters ,  2018
    R

    Free

  • Predicting the spread of all invasive forest pests in the United States

    Emma J. Hudgins, Andrew M. Liebhlod, Brian Leung , Ecology Letters ,  2017
    R

    Free

  • Trasnlucent windows: how uncertainty in competitive interactions impacts detection of community pattern

    Rafael D'Andrea, Annette Ostling, James P. O'Dwyer , Ecology Letters ,  2018
    R

    Free

  • Traits linked with species invasivness and community invasiblity vary with time, stage and indicator of invasion in a long-term grassland experiment

    Jane A. Catford, Annabel L. Smith, Peter D. Wragg, et al , Ecology Letters ,  2019
    R

    Free

  • The ecohydrological context of drought and classification of plant responses

    Xue Feng, David D. Sckerly, Todd E. Dawson, Stefano Manzoni, Rob P.Skelton, Giulia Vico, Sally E. Thompson , Ecology Letters ,  2018
    Python

    Free

  • Scaling metabolism from individuals to reef-fish communities at broad spatial scales

    D.R. Barneche, M.Kulbicki, S.R. Floeter, A.M. Friendlander, J.Maina, A.P Allen , Ecology Letters ,  2014
    R

    Free

  • Metabloic compensation constrains the temperature dependence of gross primary production

    Daniel Padfield, Chris Lowe, Angus Buckling, Richard Ffrench-Constant , Ecology Letters ,  2017
    R

    Free

  • Size-based ecological interactions drive food web responses to climate warming

    Max Lindmark, Jan Ohlberger, Magnus Huss, Anna Gårdmark , Ecology Letters ,  2019
    R

    Free

  • Ecology Under Lake Ice

    Stephaine E. Hamptopn, Aaron W. E. Galloway, et al , Ecology Letters ,  2016
    R

    Free

  • Linking phytoplankton community metabolism to the individual size distribution

    Daneil Padfield, Angus Buckling, Ruth Warfield, Chris Lowe, Gabriel Yvon-Durocher , Ecology Letters ,  2018
    R

    Free

  • A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences

    Tal Pupko, Itsik Pe, Ron Shamir, Dan Graur , Molecular Biology and Evolution ,  2000
    Python

    Free

  • Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens

    Jing Wang, Nathaniel R. Street, Douglas G. Scofield, Pär K. Ingvarsson , Molecular Biology and Evolution ,  2016
    Shell

    Free

  • Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata)

    Stuart V. Nielsen , Irán Andira Guzmán-Méndez , Tony Gamble , Madison Blumer , Brendan J. Pinto , Lukáš Kratochvíl, Michail Rovatsos , Molecular Biology and Evolution ,  2019
    Python

    Free

  • Accounting for Phylogenetic Uncertainty in Biogeography: A Bayesian Approach to Dispersal-Vicariance Analysis of the Thrushes

    Johan A A Nylander,Urban Olsson,Per Alström,Isabel Sanmartín , Systematic Biology ,  2008
    Perl

    Free

  • Widespread inhibition of daytime ecosystem respiration

    Trevor F. Keenan, Mirco Migliavacca, Dario Papale, Dennis Baldocchi, Markus Reichstein, Margaret Torn & Thomas Wutzler , Nature Ecology and Evolution ,  2019
    MATLAB

    Free

  • Social support drives female dominance in the spotted hyaena

    Colin Vullioud, Eve Davidian, Bettina Wachter, François Rousset, Alexandre Courtiol, Oliver P. Höner , Nature Ecology and Evolution ,  2018
    R

    Free

  • Tipping points in the dynamics of speciation

    Patrik Nosil, Jeffrey L. Feder, Samuel M. Flaxman, Zachariah Gompert , Nature Ecology and Evolution ,  2017
    Mathematica

    Free

  • Root microbiota assembly and adaptive differentiation among European Arabidopsis populations

    Thorsten Thiergart, Paloma Durán, Thomas Ellis, Nathan Vannier, Ruben Garrido-Oter, Eric Kemen , Nature Ecology and Evolution ,  2019
    R

    Free

  • Individual immune selection pressure has limited impact on seasonal influenza virus evolution

    Alvin X. Han, Sebastian Maurer-Stroh,Colin A. Russell , Nature Ecology and Evolution ,  2018
    Jupyter Notebook

    Free

  • A meta-analysis of changes in bacterial and archaeal communities with time

    Ashley Shade, J Gregory Caporaso, Jo Handelsman, Rob Knight, Noah Fierer , ISME Journal ,  2013
    R

    Free

  • Time and ecological resilience: can diurnal animals compensate for climate change by shifting to nocturnal activity?

    Ofir Levy, Tamar Dayan, Warren P. Porter, Noga Kronfeld-Schor , Ecological Monographs ,  2018
    Fortran

    Free

  • Local snow melt and temperature—but not regional sea ice—explain variation in spring phenology in coastal Arctic tundra

    Jakob J. Assmann, Isla H. Myers-Smith, Albert B. Phillimore, Anne D. Bjorkman, Richard E. Ennos, Janet S. Prevéy, Greg H. R. Henry, Niels M. Schmidt, Robert D. Hollister , Ecological Monographs ,  2019
    R

    Free

  • Disentangling herbivore impacts in primary succession by refocusing the plant stress and vigor hypotheses on phenology

    Christian Che-Castaldo, Charlie M. Crisafulli, John G. Bishop, Elise F. Zipkin, William F. Fagan , Ecological Monographs ,  2019
    HTML

    Free

  • Estimating the volume and age of water stored in global lakes using a geo-statistical approach

    Mathis Loïc Messager, Bernhard Lehner, Günther Grill, Irena Nedeva, Oliver Schmitt , Frontiers in Ecology and the Environment ,  2016
    Python

    Free

  • ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms

    William E. Peterman , Methods in Ecology and Evolution ,  2018
    R

    Free

  • Microclima: An r package for modelling meso- and microclimate

    Ilya M. D. Maclean, Jonathan R. Mosedale, Jonathan J. Bennie , Methods in Ecology and Evolution ,  2018
    R

    Free

  • A New Method for Estimation of Resource Selection Probability Function

    SUBHASH R. LELE , Methods in Ecology and Evolution ,  2010
    R

    Free

  • babette: BEAUti 2, BEAST2 and Tracer for R

    Richèl J. C. Bilderbeek, Rampal S. Etienne , Methods in Ecology and Evolution ,  2018
    R

    Free

  • Measuring microenvironments for global change: DIY environmental microcontroller units (EMUs)

    James G. Mickley, Timothy E. Moore, Carl D. Schlichting, Amber DeRobertis, Emilia N. Pfisterer, Robert Bagchi , Methods in Ecology and Evolution ,  2018
    Lua

    Free

  • Phylogenomics from low-coverage whole-genome sequencing

    Feng Zhang, Yinhuan Ding, Chao-Dong Zhu, Xin Zhou, Michael C. Orr, Stefan Scheu, Yun-Xia Luan , Methods in Ecology and Evolution ,  2019
    Shell

    Free

  • Towards an ecological trait-data standard

    Florian D. Schneider, David Fichtmueller, Martin M. Gossner, Anton Güntsch, Malte Jochum, Birgitta König-Ries, Gaëtane Le Provost, Peter Manning , Methods in Ecology and Evolution ,  2019
    R

    Free

  • A guide to the application of Hill numbers to DNA-based diversity analyses

    Antton Alberdi, M. Thomas P. Gilbert , Methods in Ecology and Evolution ,  2019
    R

    Free

  • Continuous traits and speciation rates: Alternatives to state-dependent diversification models

    Michael G. Harvey, Daniel L. Rabosky , Methods in Ecology and Evolution ,  2017
    R

    Free

  • Machine learning to classify animal species in camera trap images: Applications in ecology

    Michael A. Tabak, Mohammad S. Norouzzadeh, David W. Wolfson, Steven J. Sweeney, Kurt C. Vercauteren, Nathan P. Snow, Joseph M. Halseth, Paul A. Di Salvo , Methods in Ecology and Evolution ,  2018
    R

    Free

  • GRAPHITE: A graphical environment for scalable in situ video tracking of moving insects

    Blair J. Rossetti, Travis Dynes, Berry Brosi, Jacobus C. de Roode, Jun Kong , Methods in Ecology and Evolution ,  2017
    Matlab

    Free

  • Identifying animal species in camera trap images using deep learning and citizen science

    Marco Willi, Ross T. Pitman, Anabelle W. Cardoso, Christina Locke, Alexandra Swanson, Amy Boyer, Marten Veldthuis, Lucy Fortson , Methods in Ecology and Evolution ,  2018
    Python

    Free

  • Functional ecology and imperfect detection of species

    Tobias Roth, Eric Allan, Peter B. Pearman, Valentin Amrhein , Methods in Ecology and Evolution ,  2017
    R

    Free

  • dispRity: A modular R package for measuring disparity

    Thomas Guillerme , Methods in Ecology and Evolution ,  2019
    HTML

    Free

  • embarcadero: Species distribution modelling with Bayesian additive regression trees in r

    Colin J. Carlson , Methods in Ecology and Evolution ,  2020
    R

    Free

  • Paleontological baselines for evaluating extinction risk in the modern oceans

    Seth Dinnegan, Sean C. Anderson, Paul G. Harnik, Carl Suimpson, Derek P. Tittensor , Methods in Ecology and Evolution ,  2015
    Jupyter Notebook

    Free

  • A convolutional neural network for detecting sea turtles in drone imagery

    Patrick C. Gray, Abram B. Fleishman, David J. Klein, Matthew W. McKown, Vanessa S. Bézy, Kenneth J. Lohmann, David W. Johnston , Methods in Ecology and Evolution ,  2018
    Python

    Free

  • mfSBA: Multifractal analysis of spatial patterns in ecological communities

    Leonardo A. Saravia , Methods in Ecology and Evolution ,  2014
    C++

    Free

  • 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 ,  2018
    NetLogo

    Free

  • 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 ,  2019
    R

    Free

  • babette: BEAUti 2, BEAST2 and Tracer for R

    Richèl J. C. Bilderbeek, Rampal S. Etienne , Methods in Ecology and Evolution ,  2018
    R

    Free

  • 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 ,  2015
    R

    Free

  • babette: BEAUti 2, BEAST2 and Tracer for R

    Richèl J. C. Bilderbeek, Rampal S. Etienne , Methods in Ecology and Evolution ,  2018
    R

    Free

  • 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 ,  2017
    R

    Free

  • A quantitative framework for investigating the reliability of empirical network construction

    Alyssa R. Cirtwill, Anna Eklöf, Tomas Roslin, Kate Wootton, Dominique Gravel , Methods in Ecology and Evolution ,  2019
    R

    Free

  • 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 ,  2017
    R

    Free

  • Clustering and correlations: Inferring resilience from spatial patterns in ecosystems

    Sumithra Sankaran, Sabiha Majumder, Ashwin Viswanathan, Vishwesha Guttal , Methods in Ecology and Evolution ,  2019
    R

    Free

  • 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 ,  2017
    R

    Free

  • 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 ,  2018
    R

    Free

  • Drones and convolutional neural networks facilitate automated and accurate cetacean species identification and photogrammetry

    Patrick C. Gray, Kevin C. Bierlich, Sydney A. Mantell, Ari S. Friedlaender, Jeremy A. Goldbogen, David W. Johnston , Methods in Ecology and Evolution ,  2019
    Jupyter Notebook

    Free

  • 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 ,  2018
    R

    Free

  • Rapid spatial risk modelling for management of early weed invasions: Balancing ecological complexity and operational needs

    Jens G. Froese, Alan R. Pearse, Grant Hamilton , Methods in Ecology and Evolution ,  2019
    R

    Free

  • 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 ,  2019
    R

    Free

  • 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 ,  2019
    R

    Free

  • Using machine vision to estimate fish length from images using regional convolutional neural networks

    Graham G. Monkman, Kieran Hyder, Michel J. Kaiser, Franck P. Vidal , Methods in Ecology and Evolution ,  2019
    Python

    Free

  • Non-specific amplification compromises environmental DNA metabarcoding with COI

    Rupert A. Collins, Judith Bakker, Owen S. Wangensteen, Ana Z. Soto, Laura Corrigan, David W. Sims, Martin J. Genner, Stefano Mariani , Methods in Ecology and Evolution ,  2019
    R

    Free

  • Dealing with high uncertainty in qualitative network models using Boolean analysis

    Nadiah P. Kristensen, Ryan A. Chisholm, Eve McDonald-Madden , Methods in Ecology and Evolution ,  2019
    R

    Free

  • 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 ,  2018
    R

    Free

  • Active learning for classifying long-duration audio recordings of the environment

    Mahnoosh Kholghi, Yvonne Phillips, Michael Towsey, Laurianne Sitbon, Paul Roe , Methods in Ecology and Evolution ,  2018
    Java

    Free

  • Ecological resistance surfaces predict fine-scale genetic differentiation in a terrestrial woodland salamander

    William E. Peterman, Grant M. Connette, Raymond D. Semlitsch, Lori S. Eggert , Methods in Ecology and Evolution ,  2014
    R

    Free

  • 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 ,  2017
    R

    Free

  • Performance of multistate mark–recapture models for temporary emigration in the presence of survival costs

    Klaus Henle, Bernd Gruber , Methods in Ecology and Evolution ,  2017
    C++

    Free

  • 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 ,  2017
    R

    Free

  • Estimating recruitment from capture–recapture data by modelling spatio-temporal variation in birth and age-specific survival rates

    Richard B. Chandler, Kristin Engebretsen, Michael J. Cherry, Elina P. Garrison, Karl V. Miller , Methods in Ecology and Evolution ,  2018
    R

    Free

  • Estimating species richness and accumulation by modelling species occurrence and detectability.

    Robert M. Dorazio, J. Andrew Royle, Bo Söderström, Anders Glimskär , Methods in Ecology and Evolution ,  2016
    Python

    Free

  • momentuHMM: R package for generalized hidden Markov models of animal movement

    Brett T. McClintock, Théo Michelot , Methods in Ecology and Evolution ,  2018
    R

    Free

  • When can we trust population trends? A method for quantifying the effects of sampling interval and duration

    Hannah S. Wauchope, Tatsuya Amano, William J. Sutherland, Alison Johnston , Methods in Ecology and Evolution ,  2019
    R

    Free

  • 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 ,  2014
    R

    Free

  • 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 ,  2018
    Python

    Free

  • For everything there is a season: Analysing periodic mortality patterns with the cyclomortr package

    Eliezer Gurarie, Peter R. Thompson, Allicia P. Kelly, Nicholas C. Larter, William F. Fagan, Kyle Joly , Methods in Ecology and Evolution ,  2019
    R

    Free

  • Recombination rate plasticity: revealing mechanisms by design

    Laurie S. Stevison , Stephen Sefick , Chase Rushton and Rita M. Graze , Methods in Ecology and Evolution ,  2017
    R

    Free

  • 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 ,  2019
    R

    Free

  • 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 ,  2020
    R

    Free

  • pavo2: New tools for the spectral and spatial analysis of colour in r

    Rafael Maia, Hugo Gruson, John A. Endler, Thomas E. White , Methods in Ecology and Evolution ,  2019
    R

    Free

  • 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 ,  2019
    Python

    Free

  • 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 ,  2017
    R

    Free

  • Fast evaluation of study designs for spatially explicit capture–recapture

    Murray G. Efford, John Boulanger , Methods in Ecology and Evolution ,  2019
    R

    Free

  • Plants In Trait Analysis (PITA)

    Nicole Diaz; Jordan Holmes , Methods in Ecology and Evolution ,  2019
    Shell

    Free

  • 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 ,  2019
    R

    Free

  • Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions

    Jonathan Chang, Daniel L Rabosky, Michael E Alfaro , Methods in Ecology and Evolution ,  2019
    Python

    Free

  • 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 ,  2019
    R

    Free

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