<p>With this issue, we introduce <b>Workflows</b>—papers that describe the design, testing and analysis of novel workflows that are applicable to a broad class of problems, types of datasets or a range of experimental designs. <b>Workflows</b> adds to the existing paper types published in <i>Methods</i>: <b>Research Articles</b> that describe, test and validate new methods that are applicable to a wide range of taxa or systems; commissioned and unsolicited <b>Reviews</b> that synthesize and set benchmarks for widely used methods while offering new directions for their future development; and short <b>Applications</b> and <b>Practical Tools</b> papers that describe, respectively, new open-source software packages that advance computational methodology, and new field techniques, hardware or laboratory protocols with broad applicability. To encourage and stimulate scientific debate, the journal also publishes short <b>Perspectives</b> that identify knowledge gaps and suggest productive directions for future research, and even shorter <b>Forum</b> papers that critique or otherwise constructively respond to material that has been published recently in the journal.</p><p>We are particularly interested in two types of <b>Workflow</b> contributions: (1) papers that describe, test and analyse novel and broadly useful assemblages of new or existing software or informatic tools into pipelines that would be useful for the analysis of complex, Big datasets of demonstrable importance to ecology and evolution; and (2) papers that describe, test and analyse empirical or experimental procedures that are or could be used to generate Big datasets such as eDNA, omics, metabarcodes or varKodes, and products of continental- or larger-scale remotely sensed observations (including those collected not only by satellites but also by passive acoustic monitoring systems, telemetry and camera traps). Complete guidelines for authors and the required Checklist to accompany <b>Workflow</b> submissions are on the Methods website.</p><p>A <b>Workflow</b> manuscript will be reviewed only if it represents a substantial and quantifiable improvement over existing workflows and related methodology, and includes two other components: (1) detailed and well-commented open-source code for computational workflows, or detailed instructions for empirical/experimental workflows; and (2) a thorough analysis of error propagation illustrating how the sequential application of multiple functions or procedures in the workflow contributes to (and ideally reduces) overall uncertainty. Manuscripts describing computational workflows must also include extensive sensitivity analysis (including ablation analysis or the like for workflows that use machine- or deep-learning routines) with simulated or benchmark data and testing of the workflow on either an existing benchmarked dataset or a new Big dataset that is likely to become a benchmark dataset.</p><p>As with all the other types of papers published in
{"title":"Workflows: The latest way to publish your methods","authors":"Aaron M. Ellison","doi":"10.1111/2041-210x.70207","DOIUrl":"https://doi.org/10.1111/2041-210x.70207","url":null,"abstract":"<p>With this issue, we introduce <b>Workflows</b>—papers that describe the design, testing and analysis of novel workflows that are applicable to a broad class of problems, types of datasets or a range of experimental designs. <b>Workflows</b> adds to the existing paper types published in <i>Methods</i>: <b>Research Articles</b> that describe, test and validate new methods that are applicable to a wide range of taxa or systems; commissioned and unsolicited <b>Reviews</b> that synthesize and set benchmarks for widely used methods while offering new directions for their future development; and short <b>Applications</b> and <b>Practical Tools</b> papers that describe, respectively, new open-source software packages that advance computational methodology, and new field techniques, hardware or laboratory protocols with broad applicability. To encourage and stimulate scientific debate, the journal also publishes short <b>Perspectives</b> that identify knowledge gaps and suggest productive directions for future research, and even shorter <b>Forum</b> papers that critique or otherwise constructively respond to material that has been published recently in the journal.</p><p>We are particularly interested in two types of <b>Workflow</b> contributions: (1) papers that describe, test and analyse novel and broadly useful assemblages of new or existing software or informatic tools into pipelines that would be useful for the analysis of complex, Big datasets of demonstrable importance to ecology and evolution; and (2) papers that describe, test and analyse empirical or experimental procedures that are or could be used to generate Big datasets such as eDNA, omics, metabarcodes or varKodes, and products of continental- or larger-scale remotely sensed observations (including those collected not only by satellites but also by passive acoustic monitoring systems, telemetry and camera traps). Complete guidelines for authors and the required Checklist to accompany <b>Workflow</b> submissions are on the Methods website.</p><p>A <b>Workflow</b> manuscript will be reviewed only if it represents a substantial and quantifiable improvement over existing workflows and related methodology, and includes two other components: (1) detailed and well-commented open-source code for computational workflows, or detailed instructions for empirical/experimental workflows; and (2) a thorough analysis of error propagation illustrating how the sequential application of multiple functions or procedures in the workflow contributes to (and ideally reduces) overall uncertainty. Manuscripts describing computational workflows must also include extensive sensitivity analysis (including ablation analysis or the like for workflows that use machine- or deep-learning routines) with simulated or benchmark data and testing of the workflow on either an existing benchmarked dataset or a new Big dataset that is likely to become a benchmark dataset.</p><p>As with all the other types of papers published in","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"17 1","pages":"4-5"},"PeriodicalIF":6.3,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210x.70207","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"CMiNet: An R package and user-friendly Shiny App for constructing consensus microbiome networks","authors":"Rosa Aghdam, Claudia Solís-Lemus","doi":"10.1111/2041-210x.70198","DOIUrl":"https://doi.org/10.1111/2041-210x.70198","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"17 1","pages":"52-66"},"PeriodicalIF":6.3,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210x.70198","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145915995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Babak M. S. Arani, Egbert H. van Nes, Stephen R. Carpenter
{"title":"Reconstructing Langevin systems from high- and low-resolution time series using Euler and Hermite reconstructions","authors":"Babak M. S. Arani, Egbert H. van Nes, Stephen R. Carpenter","doi":"10.1111/2041-210x.70150","DOIUrl":"https://doi.org/10.1111/2041-210x.70150","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"17 1","pages":"85-98"},"PeriodicalIF":6.3,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210x.70150","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marius Hannes Eisele, Brendan Furneaux, Tomas Roslin, Otso Ovaskainen, Brent C. Emerson, Carmelo Andújar
{"title":"Benchmarking metabarcode sequence denoisers for improved invertebrate community diversity estimates","authors":"Marius Hannes Eisele, Brendan Furneaux, Tomas Roslin, Otso Ovaskainen, Brent C. Emerson, Carmelo Andújar","doi":"10.1111/2041-210x.70159","DOIUrl":"https://doi.org/10.1111/2041-210x.70159","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"17 1","pages":"15-32"},"PeriodicalIF":6.3,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210x.70159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Estimating scale-dependent covariate responses using two-dimensional diffusion derived from the stochastic partial differential equation method","authors":"Max Lindmark, Sean C. Anderson, James T. Thorson","doi":"10.1111/2041-210x.70177","DOIUrl":"https://doi.org/10.1111/2041-210x.70177","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"17 1","pages":"207-218"},"PeriodicalIF":6.3,"publicationDate":"2025-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210x.70177","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145915756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Fine-scale reconstruction of pelagic fish migration by iso-logging of eye lens","authors":"Jun Matsubayashi, Yutaka Osada, Katsuya Kimura, Yoshinori Aoki, Makoto Okazaki, Tetsuro Senda, Yuya Ueda, Naoto Matsubara, Yuichi Tsuda","doi":"10.1111/2041-210x.70201","DOIUrl":"https://doi.org/10.1111/2041-210x.70201","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"17 1","pages":"77-84"},"PeriodicalIF":6.3,"publicationDate":"2025-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210x.70201","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Karsten Krautwald Vesterholm, Felix T. Häfele, Florence Figeac, Lasse Jakobsen
{"title":"3D photogrammetry as a low-cost and non-invasive method for acoustic modelling of animal hearing","authors":"Karsten Krautwald Vesterholm, Felix T. Häfele, Florence Figeac, Lasse Jakobsen","doi":"10.1111/2041-210x.70197","DOIUrl":"https://doi.org/10.1111/2041-210x.70197","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"17 1","pages":"125-136"},"PeriodicalIF":6.3,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210x.70197","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145915843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
David Bolduc, Frédéric Dulude-de Broin, Gabriel Bergeron, Catherine Villeneuve, Matthieu Weiss-Blais, Clément Couloigner, Rachel Dubourg, Maxime Fraser-Franco, Francis Banville, Louis Moisan, Pierre-Olivier Montiglio, Daniel Fortin, François Thibault, Antoine Allard, Camille Gaudreau-Rousseau, Irene Roca, Audrey Durand, Clément Massé, Emmanuelle Barreau, Tamara A. Hiltunen, Emily Madsen, Mathilde Lapointe St-Pierre, Alexandra Engler, Akiko Kato, Morgane Le Goff, Maria Isabel Arce-Plata, Norma Rocio Forero-Muñoz, Sophie Gallais, Dominique Gravel, Pierre Legagneux
{"title":"Impersonating predators and prey to study trophic interactions through real-life simulations","authors":"David Bolduc, Frédéric Dulude-de Broin, Gabriel Bergeron, Catherine Villeneuve, Matthieu Weiss-Blais, Clément Couloigner, Rachel Dubourg, Maxime Fraser-Franco, Francis Banville, Louis Moisan, Pierre-Olivier Montiglio, Daniel Fortin, François Thibault, Antoine Allard, Camille Gaudreau-Rousseau, Irene Roca, Audrey Durand, Clément Massé, Emmanuelle Barreau, Tamara A. Hiltunen, Emily Madsen, Mathilde Lapointe St-Pierre, Alexandra Engler, Akiko Kato, Morgane Le Goff, Maria Isabel Arce-Plata, Norma Rocio Forero-Muñoz, Sophie Gallais, Dominique Gravel, Pierre Legagneux","doi":"10.1111/2041-210x.70180","DOIUrl":"https://doi.org/10.1111/2041-210x.70180","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"17 1","pages":"158-171"},"PeriodicalIF":6.3,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210x.70180","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145915844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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