Applications in Plant Sciences最新文献

{"title":"Mining buried plant trait data from the Global Biodiversity Information Facility (GBIF): Comparison and integration with multiple plant trait databases.","authors":"Takuro Katori, Michio Oguro","doi":"10.1002/aps3.70083","DOIUrl":"https://doi.org/10.1002/aps3.70083","url":null,"abstract":"<p><strong>Premise: </strong>Despite the availability of several plant trait databases, significant traits remain undocumented for a substantial number of species. To address this issue, the current study explored digital text from the Global Biodiversity Information Facility (GBIF) as an innovative source of plant trait information and evaluated its capacity to reduce existing deficiencies.</p><p><strong>Methods: </strong>Data were gathered on lifespan (<i>LS</i>), growth form (<i>GF</i>), flower color (<i>FC</i>), and maximum plant height (<i>PH</i> _<i>max</i> ) for vascular plants from GBIF and four common plant trait databases. The resulting dataset was used to evaluate the novelty and consistency of trait values derived from GBIF's digital text relative to those from other databases.</p><p><strong>Results: </strong>Incorporation of GBIF-extracted trait data led to increases of 1.2-, 1.2-, 5.5-, and 2.7-fold in the number of species with documented <i>LS</i>, <i>GF</i>, <i>FC</i>, and <i>PH</i> _<i>max</i> traits, respectively. GBIF's trait data demonstrated high congruence with other databases, except in the case of <i>FC</i>. Additionally, a comprehensive dataset compiling these trait values from GBIF and the four databases was created, offering a valuable resource for future plant trait research.</p><p><strong>Discussion: </strong>Our findings suggest that digital text in GBIF represents a significant source of plant trait information and can effectively help bridge information gaps.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":" ","pages":"e70083"},"PeriodicalIF":3.5,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13662890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149190856","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":"Scale-space image analysis for mapping spotted knapweed in grassland ecosystems.","authors":"Shohreh Sahebi, David J Hill","doi":"10.1002/aps3.70086","DOIUrl":"10.1002/aps3.70086","url":null,"abstract":"<p><strong>Premise: </strong>This study investigates the value of scale-space representations of spatial features for the identification and mapping of invasive plants using high-resolution multispectral imagery. Scale-space representations combine the two-dimensional spatial domain with a third dimension representing spatial scale, such that features can be represented across both space and image spatial resolution.</p><p><strong>Methods: </strong>Gaussian pyramids were constructed to create representations of the features across five image resolution levels (between 3 and 46 cm) within the scale space. A case study was employed to evaluate the importance of features across the scale space for the identification and mapping of spotted knapweed in a grassland ecosystem using multispectral imagery acquired using a remotely piloted aircraft system (RPAS). Classification was performed using a random forest classifier that was constructed using a process that included feature and hyperparameter optimization.</p><p><strong>Results: </strong>The results of this case study show that classifiers constructed with only high spatial resolution features were associated with better classification performance than those constructed with only lower spatial resolution features; however, the best classification is achieved by leveraging features from throughout the feature scale spaces.</p><p><strong>Discussion: </strong>These findings suggest that optimization of the spatial scale at which features are computed can substantially improve remote sensing image analysis and potentially inform RPAS flight planning to improve mission efficiency.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":" ","pages":"e70086"},"PeriodicalIF":3.5,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13669681/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149214980","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":"Petal to the metal: The slow road to automating large-scale phenology labeling for herbarium specimens.","authors":"Erin L Grady, Raphael LaFrance, Daijiang Li, Russell Dinnage, Ellen G Denny, John Deck, Robert P Guralnick","doi":"10.1002/aps3.70085","DOIUrl":"https://doi.org/10.1002/aps3.70085","url":null,"abstract":"<p><strong>Premise: </strong>Herbarium specimens represent critical historical records of plant phenology, yet automating annotation of reproductive structures remains challenging given the diversity of floral morphologies, specimen age and quality, and image quality.</p><p><strong>Methods: </strong>Here, we present a machine learning pipeline that uses an ensemble modeling approach to detect flowers on herbarium specimens and deliver these data to the phenology research community. After testing multiple strategies for generating training data, we found that in-house expert-curated annotations were essential for producing reliable results.</p><p><strong>Results: </strong>Expert validation found that the modeling pipeline detected present floral structures with relatively strong accuracy but had moderately high false negative rates. Applying the ensemble to our filtered final image dataset of 22 million records resulted in 11.1 million records labeled with flowers present. However, only 2.9 million of these contained the complete metadata necessary for downstream phenology research, highlighting the need for full label digitization efforts.</p><p><strong>Discussion: </strong>The dataset presented here represents a large compilation of historical herbarium-derived phenology records available as a resource for the phenology community. We end by demonstrating how integrating these machine-labeled records into Phenobase, a publicly available phenology database, expands taxonomic and temporal coverage for large-scale phenological analyses.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":" ","pages":"e70085"},"PeriodicalIF":3.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13628181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149103104","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":"refloraR: An R package for efficiently retrieving and analyzing plant specimen data from the Herbário Virtual Reflora.","authors":"Carlos Calderón Del Cid, Ana Flávia Alves Versiane, Paula Leitman, Fabiana Ranzato Filardi, Rafaela Campostrini Forzza, Domingos Cardoso","doi":"10.1002/aps3.70081","DOIUrl":"10.1002/aps3.70081","url":null,"abstract":"<p><strong>Premise: </strong>Advances in the digitization of herbarium collections are enabling open access to specimen data for research and conservation. In Brazil, the Herbário Virtual Reflora (HVR) hosts over 4.8 million high-resolution images of botanical specimens and their associated data from 86 national and international herbaria.</p><p><strong>Methods and results: </strong>To facilitate access and use of HVR data in biodiversity research, we developed the R package refloraR. This tool interacts with the HVR Integrated Publishing Toolkit (IPT) to download, parse, summarize, and filter herbarium records in Darwin Core Archive (DwC-A) and dataframes. It also retrieves occurrence records and indeterminate specimens for any hierarchical level. We provide a working example that combines the refloraR functions for quantifying indeterminate specimens as an indicator of taxonomic gaps within and among collections.</p><p><strong>Conclusions: </strong>The refloraR package supports reproducible workflows in systematics, conservation, and ecology. By enabling the efficient retrieval of specimen data, it integrates the HVR into modern biodiversity informatics and democratizes access to natural history collections.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":" ","pages":"e70081"},"PeriodicalIF":3.5,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13583462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148987829","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":"Herbarium-based measurements are reliable predictors of fresh plant traits in Neotropical Myrtaceae.","authors":"Yacov Kilsztajn, Lázaro Henrique Soares Moraes de Conceição, Thais Vasconcelos, Carolyn Elinore Barnes Proença, Vanessa Graziele Staggemeier","doi":"10.1002/aps3.70082","DOIUrl":"10.1002/aps3.70082","url":null,"abstract":"<p><strong>Premise: </strong>Herbarium specimens are increasingly used to extract morphological traits for ecological and evolutionary studies, yet the effects of tissue desiccation on trait measurements remain poorly understood. Here, we tested two hypotheses: (H1) whether higher tissue water content leads to greater measurement changes after herborization and (H2) whether fresh trait values can be reliably predicted from measurements of herborized specimens.</p><p><strong>Methods: </strong>We evaluated the reliability of herbarium-based measurements by comparing fresh and dried traits of leaves, flowers, fleshy fruits, and seeds across 262 individuals representing 133 Neotropical Myrtaceae species. Phylogenetic least squares models and machine learning regressions were used to test H1 and H2.</p><p><strong>Results: </strong>Leaves and flowers generally shrank after herborization, fruits size metrics tended to increase, and seeds were largely unaffected. Water content was significantly associated with the magnitude of herborization effects in flowers and some leaf and seed traits. Fresh trait values were accurately predicted from measurements of herborized specimens. Prediction errors were lowest for leaf traits, followed by fruits, flowers, and seeds.</p><p><strong>Discussion: </strong>These results partially support H1 and support H2, indicating that herborized specimens can be reliably used for trait analyses when organ-specific responses are considered, providing a practical framework to account for potential desiccation bias in functional trait research.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":" ","pages":"e70082"},"PeriodicalIF":3.5,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13576477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148975390","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":"Mapping <i>Lupinus polyphyllus</i> density and distribution along road verges using unmanned aerial vehicle (UAV)-based remote sensing.","authors":"Elin L Blomqvist, Jan-Olov Andersson, R Lutz Eckstein, Jan Haas","doi":"10.1002/aps3.70080","DOIUrl":"10.1002/aps3.70080","url":null,"abstract":"<p><strong>Premise: </strong>Road verges function as refuges for semi-natural species, but they can also facilitate the spread of non-native plants such as <i>Lupinus polyphyllus</i>. Unmanned aerial vehicle (UAV)-based remote sensing is a promising tool for mapping these species; however, its application in roadside contexts remains limited.</p><p><strong>Methods: </strong>We developed and evaluated a UAV-based workflow to detect and map lupine presence and density along roads. Red-green-blue (RGB) imagery was processed into orthomosaics and classified using object-based and pixel-based approaches with support vector machines and random forest algorithms under multiple classification schemes.</p><p><strong>Results: </strong>The highest accuracy (88.8%) was achieved using pixel-based random forest classification and a simplified scheme. Flowering purple lupine showed strong classification performance (F1 score = 96.3%), while early-stage greenish individuals were harder to detect (74.5%). Spatial heatmap comparison revealed low overestimation (1.79%) and underestimation (1.47%).</p><p><strong>Discussion: </strong>Assuming optimal phenological conditions, UAV-based mapping provides a scalable and cost-efficient complement to ground surveys for the management of <i>L. polyphyllus</i> within infrastructure areas.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":" ","pages":"e70080"},"PeriodicalIF":3.5,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13559118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148928833","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":"Rapid assessment of fern spore quality using microscale electrical conductivity testing.","authors":"Yao-Moan Huang, Chia-Wen Ko, Chin-Tzer Duh, Chu-Mei Huang, Wen-Liang Chiou, Tzu-Tong Kao","doi":"10.1002/aps3.70078","DOIUrl":"10.1002/aps3.70078","url":null,"abstract":"<p><strong>Premise: </strong>Ex situ spore banks are essential for fern conservation and research, yet traditional germination tests for assessing spore quality are time consuming and labor intensive. We explored whether electrical conductivity (EC), a rapid proxy for seed vigor, could offer an efficient alternative for evaluating fern spore quality.</p><p><strong>Methods: </strong>Using chlorophyllous spores of <i>Plenasium banksiifolium</i>, we developed a microscale EC protocol (0.01-g spores, 1-h immersion) to track EC and germination over eight weeks of storage. Spore longevity (<i>p</i> ₅₀) was estimated via probit analysis, and correlations among EC, viability, and longevity were assessed.</p><p><strong>Results: </strong>Fresh spores from different individual plants showed varied initial EC (EC₀) values, with lower EC₀ values associated with longer longevity (<i>p</i> ₅₀). During storage, EC values increased over time, while germination percentage declined. The relative EC ratio (EC_i/EC₀) showed significant negative correlations with germination percentage, with a ratio of ~2 indicating 50% viability loss and ~3 signaling complete viability loss.</p><p><strong>Discussion: </strong>The EC test presents a promising approach for rapidly assessing spore viability and longevity. Lower initial EC (EC₀) values predicted greater initial spore viability and longer longevity, likely reflecting differences in spore maturity. The relative EC_i/EC₀ ratio effectively tracked viability loss, supporting its use in improving spore bank management.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":" ","pages":"e70078"},"PeriodicalIF":3.5,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13559116/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148928826","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":"Correction to \"The challenges of growing orchids from seeds for conservation: An assessment of asymbiotic techniques\".","authors":"","doi":"10.1002/aps3.70079","DOIUrl":"https://doi.org/10.1002/aps3.70079","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1002/aps3.11496.].</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":" ","pages":"e70079"},"PeriodicalIF":3.5,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13507636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148824365","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 cost-effective DNA extraction protocol for long-read sequencing in non-model plants","authors":"Sofia Gaischuk,&nbsp;Cintia F. Marchetti,&nbsp;Ezequiel Petrillo,&nbsp;Fernando A. Rabanal,&nbsp;Detlef Weigel,&nbsp;Nicolás Bellora,&nbsp;M. Verónica Arana","doi":"10.1002/aps3.70055","DOIUrl":"https://doi.org/10.1002/aps3.70055","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Third-generation sequencing has revolutionized genomics, enabling in-depth analysis of genome sequence, structure, and epigenetic features. Yet, extracting high-quality DNA for long-read sequencing remains a bottleneck—particularly in non-model plants, such as mature trees growing in natural environments, which often contain abundant endogenous compounds that hinder extraction and downstream applications.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We developed an optimized, robust, and cost-effective DNA extraction protocol that yields high-quality DNA suitable for Oxford Nanopore Technologies and PacBio sequencing. Validation across diverse taxa—including six <i>Nothofagus</i> species, gymnosperms endemic to Andean–Patagonian forests, exotic conifers of commercial value, and model plants—demonstrated consistently high DNA purity (A₂₆₀/A₂₈₀ &gt; 1.8, A₂₆₀/A₂₃₀ &gt; 2.0) and fragment sizes ≥30 kbp. Downstream sequencing confirmed suitability for applications requiring long, intact molecules and base modification detection.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Compared to commercial kits and standard protocols, this approach achieved superior DNA integrity and yield without specialized equipment, offering an accessible solution for researchers working with challenging plant species.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 4","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70055","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148783732","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":"Pearl's causality for integrating ecological datasets: A case study on Myricaria germanica in northern Italy","authors":"Kailin Weitkämper,&nbsp;Kilian Rückschloß,&nbsp;Tommaso Sitzia,&nbsp;Bruno Michielon,&nbsp;Silke Werth,&nbsp;Felix Weitkämper","doi":"10.1002/aps3.70056","DOIUrl":"https://doi.org/10.1002/aps3.70056","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Applied ecology can significantly influence policy decisions on environmental issues. Therefore, research in this field should be as transparent and reproducible as possible. Existing expertise from a broad range of disciplines should also be integrated into ecological research to allow researchers to maximize understanding of complex systems.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We illustrate how Pearl's causality can contribute to applied ecology. We demonstrate the implications of causal diagrams for assessing the effects of anthropogenic and abiotic factors in ecological systems, using <i>Myricaria germanica</i> in Italian river systems as an example. In particular, we showcase the interplay between explicit causal modeling and classical statistical techniques.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>In our example, we find that river channel width and riverbank protections are the most important factors affecting the survival of <i>M. germanica</i> juveniles in northern Italy. Other factors such as altitude and other human activity also impact <i>M. germanica</i> survival through channel width as a mediator.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We demonstrate that causal diagrams can be an effective new language for ecological research. The causal diagram highlights that integrating hydrological, historical, or anthropological data could strengthen understanding of <i>M. germanica</i> populations in river systems. This framework facilitates interdisciplinary research and realizes the full potential of ecological datasets.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 4","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70056","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148783736","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}