Applications in Plant Sciences最新文献

{"title":"Applying interpretable machine learning to assess intraspecific trait divergence under landscape-scale population differentiation","authors":"Sambadi Majumder,&nbsp;Chase M. Mason","doi":"10.1002/aps3.70015","DOIUrl":"https://doi.org/10.1002/aps3.70015","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Here we demonstrate the application of interpretable machine learning methods to investigate intraspecific functional trait divergence using diverse genotypes of the wide-ranging sunflower <i>Helianthus annuus</i> occupying populations across two contrasting ecoregions—the Great Plains versus the North American Deserts.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Recursive feature elimination was applied to functional trait data from the HeliantHOME database, followed by the application of the Boruta algorithm to detect the traits that are most predictive of ecoregion. Random forest and gradient boosting machine classifiers were then trained and validated, with results visualized using accumulated local effects plots.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The most ecoregion-predictive functional traits span categories of leaf economics, plant architecture, reproductive phenology, and floral and seed morphology. Relative to the Great Plains, genotypes from the North American Deserts exhibit shorter stature, fewer leaves, higher leaf nitrogen content, and longer average length of phyllaries.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>This approach readily identifies traits predictive of ecoregion origin, and thus the functional traits most likely to be responsible for contrasting ecological strategies across the landscape. This type of approach can be used to parse large plant trait datasets in a wide range of contexts, including explicitly testing the applicability of interspecific paradigms at intraspecific scales.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel combination of in vitro propagation and hydroponic culture for hybrid cacao (Theobroma cacao) plants","authors":"Luis David Vera Pinargote,&nbsp;Elisabeth Jamet,&nbsp;Naga Raju Maddela","doi":"10.1002/aps3.70014","DOIUrl":"https://doi.org/10.1002/aps3.70014","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Currently, there is a lack of controlled cultivation methods for cacao (<i>Theobroma cacao</i>), a plant species with high commercial value. One major concern is the tendency of cacao plants to accumulate high concentrations of cadmium (Cd), a heavy metal with high toxicity to living organisms.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We describe a new two-step method for the propagation of hybrid cacao plants, consisting of (1) in vitro germination for two weeks, followed by (2) transfer to a vertical hydroponic system for growth under controlled conditions. As a test case, two new cacao hybrids were cultivated in the presence of Cd and showed different levels of tolerance.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our simple approach offers a new research direction for the controlled cultivation of cacao plants and can potentially be applied to other plants of agronomic interest. Moreover, this method allows the identification of plants that are resistant to various toxic substances, which could then be used in phytoremediation.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving computer vision for plant pathology through advanced training techniques","authors":"Jamie R. Sykes,&nbsp;Katherine J. Denby,&nbsp;Daniel W. Franks","doi":"10.1002/aps3.70010","DOIUrl":"https://doi.org/10.1002/aps3.70010","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>This study investigates advanced training techniques to improve the performance of convolutional neural networks for disease detection in cocoa, <i>Theobroma cacao</i>.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Despite recent stagnation in accuracy improvements in computer vision for image classification, our research demonstrates significant advancements in performance through semi-supervised learning, specialised loss functions, and the inclusion of a non-cocoa class.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Semi-supervised learning reduced overfitting and enhanced generalisability, particularly for subtle symptoms. The non-cocoa class exposed models to a broad range of relevant features, significantly improving model robustness and performance in difficult cases. Grad-CAM for qualitative assessment provided valuable insights into model behaviour, highlighting cases of overfitting missed by summary statistics. We also describe dynamic focal loss, a novel loss function that uses an empirical measure of difficulty to weight each image. Our results suggest that while PhytNet shows promise in terms of computational efficiency and superior handling of difficult images, ResNet18 with semi-supervised learning and dynamic focal loss emerged as the strongest contender for real-world deployment.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>This research underscores the potential of semi-supervised learning and advanced loss functions in enhancing the applicability of deep learning models in agricultural disease management. It also presents a new high-quality benchmark dataset of 7220 images of diseased and healthy cocoa trees, offering a much greater and more realistic challenge than the Plan Village dataset.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"infinitylists: A Shiny application and R package for rapid generation of place-based species checklists","authors":"Thomas Mesaglio,&nbsp;Fonti Kar,&nbsp;Hervé Sauquet,&nbsp;William K. Cornwell","doi":"10.1002/aps3.70012","DOIUrl":"https://doi.org/10.1002/aps3.70012","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Biodiversity researchers often need to answer the question: “Which species of taxon X have been documented in (or near) spatial polygon Y?” Online databases with billions of occurrence records, including vouchered specimens and citizen science records, can provide the answer; however, quick spatial processing of huge biodiversity datasets can be difficult, and many general-purpose tools are constrained by dataset size.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p><i>infinitylists</i> is a Shiny application and R package that allows users to generate species checklists for a user-specified taxon and area. It downloads taxon–country datasets (e.g., Madagascan geckos) from biodiversity data providers and uses an open source, column-oriented data file for fast retrieval and visualization. Available as a mobile-friendly web tool with preloaded data, it can also be run locally in R for very flexible applications.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p><i>infinitylists</i> is an easy-to-use tool with applications including supplementing survey data, planning collecting expeditions, and informing gap-filling. <i>infinitylists</i> is a complementary tool to existing databases to help field ecologists and naturalists globally.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144472991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using large language models to extract plant functional traits from unstructured text","authors":"Viktor Domazetoski,&nbsp;Holger Kreft,&nbsp;Helena Bestova,&nbsp;Philipp Wieder,&nbsp;Radoslav Koynov,&nbsp;Alireza Zarei,&nbsp;Patrick Weigelt","doi":"10.1002/aps3.70011","DOIUrl":"https://doi.org/10.1002/aps3.70011","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Functional plant ecology seeks to understand how functional traits govern species distributions, community assembly, and ecosystem functions. While global trait datasets have advanced the field, substantial gaps remain, and extracting trait information from text in books, research articles, and online sources via machine learning offers a valuable complement to costly field campaigns.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We propose a natural language processing pipeline that extracts traits from unstructured species descriptions by using classification models for categorical traits and question-answering models for numerical traits. The pipeline's performance is evaluated on two large databases with over 50,000 species descriptions, utilizing approaches ranging from a keyword search to large language models.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our final optimized pipeline used a transformer architecture and obtained a mean precision of 90.8% (range 81.6–97%) and a mean recall of 88.6% (77.4–97%) across five categorical traits, representing a 9.83% increase in precision and 42.35% increase in recall over a regular expression-based approach. The question-answering model yielded a normalized mean absolute error of 10.3% averaged across three numerical traits.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>The natural language processing pipeline we propose has the potential to facilitate the digitization and extraction of large amounts of plant functional trait information residing in scattered textual descriptions.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144472906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fully automatic extraction of morphological traits from the web: Utopia or reality?","authors":"Diego Marcos,&nbsp;Robert van de Vlasakker,&nbsp;Ioannis N. Athanasiadis,&nbsp;Pierre Bonnet,&nbsp;Hervé Goëau,&nbsp;Alexis Joly,&nbsp;W. Daniel Kissling,&nbsp;César Leblanc,&nbsp;André S. J. van Proosdij,&nbsp;Konstantinos P. Panousis","doi":"10.1002/aps3.70005","DOIUrl":"https://doi.org/10.1002/aps3.70005","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Plant morphological traits, their observable characteristics, are fundamental to understanding the role played by each species within its ecosystem; however, compiling trait information for even a moderate number of species is a demanding task that may take experts years to accomplish. At the same time, online species descriptions contain massive amounts of information about morphological traits, but the lack of structure makes this source of data impossible to use at scale.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>To overcome this, we propose to leverage recent advances in large language models and devise a mechanism for gathering and processing plant trait information in the form of unstructured textual descriptions, without manual curation.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We evaluate our approach by automatically replicating three manually created species–trait matrices. Our method found values for over half of all species–trait pairs, with an F1 score of over 75%.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our results suggest that large-scale creation of structured trait databases from unstructured online text is now feasible due to the information extraction capabilities of large language models. However, the process is currently limited by the availability of textual descriptions that cover all traits of interest.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144472832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome-scale reference genome of Pectocarya recurvata, the species with the smallest reported genome size in Boraginaceae","authors":"Poppy C. Northing,&nbsp;Jessie A. Pelosi,&nbsp;D. Lawrence Venable,&nbsp;Katrina M. Dlugosch","doi":"10.1002/aps3.70008","DOIUrl":"https://doi.org/10.1002/aps3.70008","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p><i>Pectocarya recurvata</i> (Boraginaceae, subfamily Cynoglossoideae), a species native to the Sonoran Desert (North America), has served as a model system for a suite of ecological and evolutionary studies. However, no reference genomes are currently available in Cynoglossoideae. A high-quality reference genome for <i>P. recurvata</i> would be valuable for addressing questions in this system and across broader taxonomic scales.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Using PacBio HiFi sequencing, we assembled a reference genome for <i>P. recurvata</i> and annotated coding regions with full-length transcripts from an Iso-Seq library. We assessed genome completeness with BUSCO and <i>k</i>-mer analysis, and estimated the genome size of six individuals using flow cytometry.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The chromosome-scale genome assembly for <i>P. recurvata</i> was 216.0 Mbp long (N50 = 12.1 Mbp). Previous observations indicated <i>P. recurvata</i> is 2<i>n</i> = 24. Our assembly included 12 primary contigs (158.3 Mbp) containing 30,655 genes with telomeres at 23 out of 24 ends. Flow cytometry measurements from the same population included two plants with 1C = 196.9 Mbp, the smallest measured for Boraginaceae, and four with 1C = 385.8 Mbp, which is consistent with tetraploidy in this population.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>The <i>P. recurvata</i> genome assembly and annotation provide a high-quality genomic resource in a sparsely represented area of the angiosperm phylogeny. This new reference genome will facilitate answering open questions in ecophysiology, biogeography, and systematics.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144472827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A low-cost protocol for the optical method of vulnerability curves to calculate P50","authors":"Georgina González-Rebeles,&nbsp;Miguel Ángel Alonso-Arevalo,&nbsp;Eulogio López,&nbsp;Rodrigo Méndez-Alonzo","doi":"10.1002/aps3.70004","DOIUrl":"https://doi.org/10.1002/aps3.70004","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The quantification of plant drought resistance, particularly embolism formation, within and across species, is critical for ecosystem management and agriculture. We developed a cost-effective protocol to measure the water potential at which 50% of hydraulic conductivity (<i>P</i>₅₀) is lost in stems, using affordable and accessible materials in comparison to the traditional optical method.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Our protocol uses inexpensive USB microscopes, which are secured along with the plants to a pegboard base to avoid movement. A Python program automatized the image acquisition. This method was applied to quantify <i>P</i>₅₀ in an exotic species (<i>Nicotiana glauca</i>) and native species (<i>Rhus integrifolia</i>) of the Mediterranean vegetation in Baja California, Mexico.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The intra- and interspecific patterns of variation in stem <i>P</i>₅₀ of <i>N. glauca</i> and <i>R. integrifolia</i> were obtained using the low-cost optical method with widely available and affordable materials that can be easily replicated for other species.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The PteridoPortal: A publicly accessible collection of over three million records of extant and extinct pteridophytes","authors":"Carl J. Rothfels,&nbsp;Jaemin Lee,&nbsp;Michael A. Sundue,&nbsp;Alan R. Smith,&nbsp;Amy Kasameyer,&nbsp;Joyce Gross,&nbsp;Garth Holman,&nbsp;Shusheng Hu,&nbsp;Matt von Konrat,&nbsp;Emily B. Sessa,&nbsp;Kimberly Watson,&nbsp;Alan Weakley,&nbsp;Libing Zhang,&nbsp;Patricia Gensel,&nbsp;Michael Hassler,&nbsp;Katelin D. Pearson,&nbsp;Ed Gilbert,&nbsp;Robyn J. Burnham,&nbsp;Richard K. Rabeler,&nbsp;Patrick Sweeney,&nbsp;Alejandra Vasco,&nbsp;Weston Testo,&nbsp;David E. Giblin,&nbsp;Stefanie M. Ickert-Bond,&nbsp;Margaret Landis,&nbsp;Melanie Link-Perez,&nbsp;Tatyana Livshultz,&nbsp;Ian Miller,&nbsp;Christopher Neefus,&nbsp;Kathleen Pigg,&nbsp;Mitchell Power,&nbsp;Alan Prather,&nbsp;Tiana Rehman,&nbsp;Lena Struwe,&nbsp;Michael Vincent,&nbsp;George Weiblen,&nbsp;Timothy Whitfeld,&nbsp;Michael D. Windham,&nbsp;George Yatskievych,&nbsp;Aaron Liston,&nbsp;Elizabeth Makings,&nbsp;Kathleen M. Pryer,&nbsp;Caroline Strömberg,&nbsp;Eve Atri,&nbsp;Jason Best,&nbsp;Ian Glasspool,&nbsp;Layne Huiet,&nbsp;Elizabeth Johnson,&nbsp;Megan R. King,&nbsp;Az Klymiuk,&nbsp;Richard Lupia,&nbsp;Lucas C. Majure,&nbsp;Carol Ann McCormick,&nbsp;Richard McCourt,&nbsp;Shanna Oberreiter,&nbsp;Kent D. Perkins,&nbsp;Yarency Rodriguez,&nbsp;Chelsea Smith,&nbsp;James Solomon,&nbsp;Jordan Teisher,&nbsp;Donna Ford-Werntz,&nbsp;Petra Fuehrding-Potschkat,&nbsp;Holly Little,&nbsp;Tom A. Ranker,&nbsp;Eric Schuettpelz,&nbsp;Carrie M. Tribble,&nbsp;Diane M. Erwin,&nbsp;Cindy V. Looy","doi":"10.1002/aps3.70003","DOIUrl":"https://doi.org/10.1002/aps3.70003","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Pteridophytes—vascular land plants that disperse by spores—are a powerful system for studying plant evolution, particularly with respect to the impact of abiotic factors on evolutionary trajectories through deep time. However, our ability to use pteridophytes to investigate such questions—or to capitalize on the ecological and conservation-related applications of the group—has been impaired by the relative isolation of the neo- and paleobotanical research communities and by the absence of large-scale biodiversity data sources.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here we present the Pteridophyte Collections Consortium (PCC), an interdisciplinary community uniting neo- and paleobotanists, and the associated PteridoPortal, a publicly accessible online portal that serves over three million pteridophyte records, including herbarium specimens, paleontological museum specimens, and iNaturalist observations. We demonstrate the utility of the PteridoPortal through discussion of three example PteridoPortal-enabled research projects.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The data within the PteridoPortal are global in scope and are queryable in a flexible manner. The PteridoPortal contains a taxonomic thesaurus (a digital version of a Linnaean classification) that includes both extant and extinct pteridophytes in a common phylogenetic framework. The PteridoPortal allows applications such as greatly accelerated classic floristics, entirely new “next-generation” floristic approaches, and the study of environmentally mediated evolution of functional morphology across deep time.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>The PCC and PteridoPortal provide a comprehensive resource enabling novel research into plant evolution, ecology, and conservation across deep time, facilitating rapid floristic analyses and other biodiversity-related investigations, and providing new opportunities for education and community engagement.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comprehensive illustrated protocol for clearing, mounting, and imaging leaf venation networks","authors":"Isabella Niewiadomski,&nbsp;Monica Antonio,&nbsp;Luiza Maria T. Aparecido,&nbsp;Mickey Boakye,&nbsp;Sonoma Carlos,&nbsp;Andrea Echevarria,&nbsp;Adrian Fontao,&nbsp;Joseph Mann,&nbsp;Ilaíne Silveira Matos,&nbsp;Norma Salinas,&nbsp;Bradley Vu,&nbsp;Benjamin Wong Blonder","doi":"10.1002/aps3.70002","DOIUrl":"https://doi.org/10.1002/aps3.70002","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Leaf venation network architecture can provide insights into plant evolution, ecology, and physiology. Venation networks are typically assessed through histological methods, but existing protocols provide limited guidance on processing large or challenging leaves.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and results</h3>\u0000 \u0000 <p>We present an illustrated protocol for visualizing whole leaf venation networks, including sample preparation, clearing, staining, mounting, imaging, and archiving steps. The protocol also includes supply lists, troubleshooting procedures, safety considerations, and examples of successful and unsuccessful outcomes. The protocol is suitable for a wide range of leaf sizes and morphologies and has been used with all major plant groups.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>We provide a workflow for obtaining high-quality mounts and images of venation networks of a wide range of species, using readily available materials.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}