Applications in Plant Sciences最新文献

{"title":"Correction to “Conservation applications of niche modeling: Native and naturalized ferns may compete for limited Hawaiian dryland habitat”","authors":"","doi":"10.1002/aps3.70052","DOIUrl":"10.1002/aps3.70052","url":null,"abstract":"<p>Edwards-Calma, K., L. Jiménez, R. Zenil-Ferguson, K. Heyduk, M. K. Thomas, and C. M. Tribble. 2024. Conservation applications of niche modeling: Native and naturalized ferns may compete for limited Hawaiian dryland habitat. <i>Applications in Plant Sciences</i> 12(3): e11598. https://doi.org/10.1002/aps3.11598</p><p>The last sentence of the original Data Availability Statement read: “The rasters with the climate variables and land-use layers can be found at their original sources using the links provided in the Methods section.” The corrected sentence reads: “The rasters with the climate variables and land-use layers can be found on Zenodo: doi.org/10.5281/zenodo.18985966.”</p><p>We apologize for this error.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147759852","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":"Procrustean pseudo-landmark methods in Python to measure massive quantities of leaf shape data","authors":"Asia Hightower,&nbsp;Svea Hall,&nbsp;Ricardo Urquidi Camacho,&nbsp;Alexandra Papamichail,&nbsp;Evan Adamski,&nbsp;Claudia Colligan,&nbsp;Aidan Deneen,&nbsp;Gabriel Dunn,&nbsp;Justine Haziza,&nbsp;Claire Henley,&nbsp;Arnan Pawawongsak,&nbsp;Lachlann Simms,&nbsp;Sean Ward,&nbsp;Manica Balant,&nbsp;Christopher Blackwood,&nbsp;Charles Cannon,&nbsp;Andrea Case,&nbsp;Aman Y. Husbands,&nbsp;Emily B. Josephs,&nbsp;Zoë Migicovsky,&nbsp;Eric Patterson,&nbsp;Yenny Alejandra Saavedra-Rojas,&nbsp;Daniel H. Chitwood","doi":"10.1002/aps3.70051","DOIUrl":"10.1002/aps3.70051","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>When examining leaf shapes that are different from one another, it can be difficult to compare both the overall leaf shape and points along the leaf margin in biologically and statistically meaningful ways.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>To address this problem, we present a simple and user-friendly leaf shape analysis method in Jupyter Notebook and Python that uses pseudo-landmarks and generalized Procrustes analysis to measure and compare the shape of any leaf. To demonstrate our analysis, we created a repository of real leaves gathered from eight experimental datasets.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Using our leaf repository, we explain how we can use pseudo-landmarks to compare all leaf shapes, both within and between species, using dimension reduction techniques like principal component analysis and can predict leaf shapes using pseudo-landmarks through linear discriminant analysis. Our leaf shape analysis also maps differences in shape as leaves grew around a rosette, showing the transition of shape across development (phyllotaxy). Finally, we showed how the relationship between leaf shape variation and genetic diversity can be investigated by combining shape with genetic data.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Through the use of generalized Procrustes analysis and pseudo-landmarks, our leaf shape analysis presents a powerful tool for examining the shape of any leaf across multiple biological, ecological, evolutionary, and developmental scales.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760092","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 two-photon fluorescence micro-spectroscopy method for chemotaxonomic characterization of fossil resins","authors":"Victoria E. McCoy,&nbsp;Michael R. Stoneman,&nbsp;Katherine M. M. Bober,&nbsp;Xavier Delclòs,&nbsp;Enrique Peñalver,&nbsp;Carole T. Gee,&nbsp;Valerică Raicu","doi":"10.1002/aps3.70053","DOIUrl":"10.1002/aps3.70053","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Amber, a fossilized chemical defensive exudate, is important for understanding ancient plant–insect/pathogen interactions, yet its botanical origins, especially for Cretaceous amber, remain enigmatic. Here, we develop and apply a fluorescence micro-spectroscopy approach within the context of a larger study on the provenance of amber.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Emission spectra were collected from 21 amber, copal, and Defaunation resin samples at six excitation wavelengths. The emission spectra at all excitation wavelengths were deconvolved using simultaneous fitting, with each emission spectrum modeled as a linear combination of four Gaussian components.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Differences between Gaussian means separated the samples into five groups. Cross-referencing these groupings with prior studies on their botanical origins indicate that they corresponded broadly to ambers from well-defined conifer families, including the Araucariaceae (group 1 associated with <i>Wollemia</i> and <i>Araucaria</i>, groups 2 and 3 associated with <i>Agathis</i>) and Cupressaceae (group 4), and Baltic amber (group 5) with unresolved taxonomic affinity.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Fluorescence micro-spectroscopy is a useful approach for characterizing fossil resin in a reproducible and nondestructive manner. Variations in the fluorescence properties of resins do not correspond to variations in age or maturity but rather to plant origin. Therefore, this approach provides an additional line of evidence for inferring the botanical origins of amber.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760375","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":"SkelPy: A graphic user interface–based approach for skeletonizing fungal networks","authors":"Melanie Madrigal,&nbsp;Aaron J. Moseley,&nbsp;Jenna C. Moseley,&nbsp;Jordan A. Dowell","doi":"10.1002/aps3.70049","DOIUrl":"10.1002/aps3.70049","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Traditional methods to quantify mycelial growth rely on destructive sampling to quantify biomass. Moreover, these approaches limit continuous observation and require a sufficient mass to measure. Recent work examines hyphal network traits by reconstructing the hyphal network from spatial coordinates via images, providing information about branching patterns and spatial growth over time.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We developed SkelPy, a Python-based graphical user interface that skeletonizes images of hyphal networks and extracts biologically relevant structural parameters such as fractal dimension, a proxy for the complexity and branching structure of the hyphal network. Using a high-throughput pipeline, we imaged three isolates of <i>Botrytis cinerea</i> grown in liquid culture for 72 h, generating a dataset of 180 time-series images.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>SkelPy enables efficient, non-destructive, and scalable quantification of hyphal growth and complexity from time-resolved image datasets, providing a powerful and user-friendly tool for studying fungal network dynamics.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760065","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":"Semi-automated assessment for NatureServe subnational conservation status ranks for state floras","authors":"Julia H. Prins,&nbsp;Joey Shaw","doi":"10.1002/aps3.70046","DOIUrl":"10.1002/aps3.70046","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Conservation status ranks measure the potential risk of extinction for species at global, national, and subnational levels, taking into account rarity, threats, and trends. These assessments are largely incomplete due to funding and resource limitations.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>This study addressed this problem by identifying five semi-automated methods to assign provisionary NatureServe subnational conservation status ranks (S-ranks) to state floras. These involved (1) estimation: (1A) calculating the mode S-rank in surrounding states and (1B) assigning an S-rank based on percentage of counties with occurrence records; and (2) calculating criteria and assigning an S-rank based on the NatureServe rank calculator using (2A) a Feature Manipulation Engine (FME) workflow, (2B) NatureServe's Rapid Analysis of Rarity and Endangerment Conservation Assessment Tool (RARECAT), and (2C) ArcGIS. S-ranks were assigned to Tennessee's native vascular flora using each method and evaluated for accuracy against published NatureServe S-ranks, human rankings, and surrounding state S-ranks.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>ArcGIS was identified as a suitable method for future ranking efforts due to its batch processing capabilities, accessibility, and agreement with NatureServe S-ranks. Therefore, a manual was created on how other states may implement this method to update and complete their S-ranks.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>By using these methods, states can more efficiently achieve comprehensive and current S-ranks, enhancing plant conservation by providing a more complete understanding of subnational extinction risk.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760143","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":"An artificial neural network–based deep learning model to predict combined stress impact and interaction in plants","authors":"Piyush Priya,&nbsp;Prachi Pandey,&nbsp;Rubi Jain,&nbsp;Manu Kandpal,&nbsp;Shradha Jain,&nbsp;Rim Chaudhury,&nbsp;Venkategowda Ramegowda,&nbsp;Muthappa Senthil-Kumar","doi":"10.1002/aps3.70047","DOIUrl":"10.1002/aps3.70047","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Plants are frequently exposed to combinations of abiotic and biotic stresses that pose a greater threat to yield and productivity than individual stresses. However, knowledge of the impact of many stress combinations in numerous plants is limited due to the lack of experimental data, which could take decades to generate. To overcome this limitation, we utilized existing literature data from various plant species and stress combinations to derive biological inferences, thereby gaining a comprehensive understanding of plant responses through a computational tool.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Public databases were used to gather literature on the impact of various abiotic and biotic stress combinations. Then, a composite artificial neural network (ANN)–based multi-target classification and regression deep learning model was developed using machine learning algorithms.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The model predicted the impact of stress interactions in plants, including the morphological parameters affected and percentage changes in those parameters, with an overall accuracy of 76.33%. Predicted reductions in yield were validated in rice under combined drought and heat stress.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>The ANN-based model developed in this study is a valuable resource for plant researchers seeking to understand the impact of stress combinations. The tool can make use of multivariate and complex combined stress datasets.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760413","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":"Assessing the viability of genebanked seeds from rare, wild plants native to the United States using the D.E.A.D. paradigm","authors":"Christina Walters,&nbsp;Lisa M. Hill,&nbsp;Katherine D. Heineman,&nbsp;Hannah M. Tetreault,&nbsp;Shaimaa Ibrahim,&nbsp;Katherine Markstein,&nbsp;Cheryl Birker,&nbsp;Kris Freitag,&nbsp;Dustin Wolkis,&nbsp;Michael Kunz,&nbsp;Sheila Murray,&nbsp;Nathaniel Kingsley,&nbsp;Alexandra Seglias,&nbsp;Nicholas Matsumoto,&nbsp;Thomas N. Kaye,&nbsp;Cheryl Peterson,&nbsp;Matthew A. Albrecht,&nbsp;Noah Dell,&nbsp;Stacy Anderson,&nbsp;Steve Blackwell,&nbsp;David Remucal,&nbsp;Wendy Gibble,&nbsp;Anita Tiller,&nbsp;Emily Coffey,&nbsp;Jason Ligon,&nbsp;Laurie Blackmore,&nbsp;Carrie Radcliffe,&nbsp;Heather E. Schneider,&nbsp;Kristen Nelson,&nbsp;David Sollenberger,&nbsp;Jessamine Finch,&nbsp;Kate Wellspring,&nbsp;Robert Jetton,&nbsp;Joyce Maschinski","doi":"10.1002/aps3.70035","DOIUrl":"10.1002/aps3.70035","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Genebanks must maintain viable seeds for decades. Seeds that germinate are clearly alive, but some seeds, often from wild populations, do not germinate because they are dormant, empty, aged, or damaged (D.E.A.D.). This work evaluates the effects of D.E.A.D. factors on genebanked seeds using a unique dataset to improve genebanking practices and standards for ex situ conservation of seed collections.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Seeds from over 100 species were recently collected from the same populations as seeds that were genebanked decades ago. Germination proportion and speed were measured after applying various temperature, chemical, or seed coat abrasion treatments. Viability was further tested using vital staining of samples with a low germination proportion. Proportions of dormant, empty, aged, and damaged seeds were compared between seed cohorts.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Germination proportion and speed varied among samples, and cues to stimulate germination of dormant seeds were identified for individual species, leading to a positive correlation between viability metrics of germination and vital staining. Empty seeds primarily contribute to low germination in this study. Aging, indicated by lower and slower germination, was evident in several of the stored samples, compared to those that had been recently harvested.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>This unique approach demonstrates the feasibility of genebanking seeds from diverse endangered plant species using freezer storage. Genebanking methods that are more relevant for crop seeds need to be modified when applied to seeds from wild populations because the sample sizes tend to be small and the seeds tend to germinate slowly and asynchronously.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760443","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148023320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148024701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148024723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}