Applications in Plant Sciences最新文献

{"title":"From theory to practice: New innovations and their application in conservation biology","authors":"Christopher P. Krieg,&nbsp;Carrie M. Tribble,&nbsp;Randall Long","doi":"10.1002/aps3.11599","DOIUrl":"10.1002/aps3.11599","url":null,"abstract":"<p>Evolution has generated an extraordinary diversity of life on Earth that drives the function of natural ecosystems (Xu et al., <span>2020</span>), human cultures (Clark et al., <span>2014</span>), and economies (Hanley and Perrings, <span>2019</span>; Paul et al., <span>2020</span>). Plants are the most dominant life form on Earth (Bar-On et al., <span>2018</span>) and the decline of plant diversity has caused drastic shifts in natural ecosystems (Pugnaire et al., <span>2019</span>), resulting in a loss of hundreds of billions of dollars (USD) per year from the global economy (Austin et al., <span>2020</span>; Diagne et al., <span>2021</span>). Plant species face unprecedented challenges to their survival, growth, and reproduction due to numerous threats, including anthropogenic factors such as land-use change, habitat destruction, climate change, and illegal poaching (IUCN, <span>2023</span>). The most urgent threats vary by region and species; thus, addressing individual threats to species survival worldwide will require broad knowledge of plant organismal function, ecology, and evolution and the creation of innovative, targeted tools and applications. This special issue features new techniques and approaches across multiple disciplines (from molecules to ecosystems) and scales of inquiry (from individual plants to global perspectives), with a central focus on the development and dissemination of new methods and perspectives in conservation biology.</p><p>Conservation biologists and practitioners around the globe are conducting research and enacting policies to conserve and preserve plant diversity at the local and regional scales. One primary obstacle to the conservation of plant diversity at larger scales has been the lack of tools that directly aid the coordination of research efforts and knowledge from around the world. Linsky et al. (<span>2024</span>) present a new collaborative framework called the Global Conservation Consortia (GCC). Under this framework, researchers and practitioners are united by a shared focus on a specific ecological or taxonomic group (e.g., trees, cycads, magnolias, oaks) to develop comprehensive conservation action plans that scaffold efforts across local, regional, and global scales. While gathering and collating data from around the globe has historically been a challenge, a new tool hosted by the Botanic Gardens Conservation International (BGCI), reported here by Quintana et al. (<span>2024</span>), aims to close knowledge gaps on the conservation status of threatened tree species across regions, increase collaboration, and provide information to decision-makers. The Conservation Action Tracker, part of the GlobalTree Portal, gathers information about the current status of threatened species, action/recovery plans, ex situ collections, species protections, and policy and outreach programs. This online database is freely available so that it can be used to guide conservation efforts and monitor their success","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11599","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141196434","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 assessment of methods to combine evolutionary history and conservation: A case study in the Brazilian campo rupestre","authors":"Raquel C. Pizzardo,&nbsp;Eimear Nic Lughadha,&nbsp;Juliana Gastaldello Rando,&nbsp;Félix Forest,&nbsp;Anselmo Nogueira,&nbsp;Luana S. Prochazka,&nbsp;Barnaby E. Walker,&nbsp;Thais Vasconcelos","doi":"10.1002/aps3.11587","DOIUrl":"10.1002/aps3.11587","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Conservation policies typically focus on biodiversity hotspots. An alternative approach involves analyzing the evolutionary history of lineages in geographic areas along with their threat levels to guide conservation efforts. Mountains exhibit high levels of plant species richness and micro-endemism, and biogeographic studies commonly point to recent and rapid evolutionary radiations in these areas. Using a nearly endemic clade of legumes, our study evaluates conservation prioritization approaches in the campo rupestre, a Neotropical ecosystem associated with mountaintops that is located between two biodiversity hotspots.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We compared the EDGE and EDGE2 metrics, which combine the evolutionary distinctiveness and the extinction risk of a species in a single value. These metrics are compared with traditional metrics used to assess conservation priority, such as phylogenetic diversity.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The EDGE values reported are lower than those of other studies using this metric, mostly due to the prevalence of threatened species with short phylogenetic branch lengths (low values of evolutionary distinctiveness). Certain areas of campo rupestre with relatively high phylogenetic diversity and EDGE values do not correspond to areas with high species richness, agreeing with previous studies on biodiversity hotspots.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our study highlights the necessity of conservation of the campo rupestres as well as advantages and disadvantages of using EDGE, EDGE2, and phylogenetic diversity for appropriate selection of conservation areas with rapid evolutionary radiations. The selection of the metrics will depend primarily on the life history of the focus group and the data availability, as well as the conservation approach.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11587","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141196449","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":"Integrated plant conservation through the Global Conservation Consortia","authors":"Jean Linsky,&nbsp;Amy Byrne,&nbsp;Vanessa Handley,&nbsp;Emily E. D. Coffey,&nbsp;Silvia Alvarez-Clare,&nbsp;Dan Crowley,&nbsp;Abby Meyer","doi":"10.1002/aps3.11586","DOIUrl":"10.1002/aps3.11586","url":null,"abstract":"<p>The 2020 State of the World's Plants and Fungi report revealed that two in five plant species are threatened with extinction. Despite their diverse ecosystem services and myriad human uses, plants receive a fraction of the conservation resources directed at animal taxa. Several existing frameworks—including International Union for Conservation of Nature (IUCN) Specialist Groups, the American Public Gardens Association Plant Collections Network, and the Center for Plant Conservation National Collection of Endangered Plants—have spurred conservation action, but there remains an urgent need to scale up conservation efforts for the world's plants. Here, a new approach to coordinated conservation action for plant taxa is described: the Global Conservation Consortia (GCC). GCC catalyze institutions and experts to collaboratively develop and implement comprehensive strategies to prevent extinction of threatened plant groups. This review focuses on three tree-focused, U.S.-led consortia: cycads, magnolias, and oaks, but the GCC framework is applicable to other taxonomic groups. This review covers consortia design and implementation, provides conservation action case studies, and shares preliminary successes and challenges as this new and exciting approach to conservation is developed.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11586","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141114532","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":"Advancing the science and practice of rare plant conservation with the Center for Plant Conservation Reintroduction Database","authors":"Joe Bellis,&nbsp;Matthew A. Albrecht,&nbsp;Joyce Maschinski,&nbsp;Oyomoare Osazuwa-Peters,&nbsp;Tina Stanley,&nbsp;Katherine D. Heineman","doi":"10.1002/aps3.11583","DOIUrl":"10.1002/aps3.11583","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Reintroductions or translocations are an increasingly important activity to recover and conserve at-risk plant species. Yet because many are not published in the scientific literature, learning from previous attempts may often require considerable time and effort. The Center for Plant Conservation Reintroduction Database (CPCRD; https://saveplants.org/reintroduction-database/), a new centralized and standardized repository of U.S.-based plant reintroductions, aims to improve the efficiency and effectiveness of accessing data on rare plant reintroductions.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The CPCRD is the product of multiple efforts to assemble information on rare plant reintroductions in the United States. The database comprises a wealth of standardized data on the key stages of a reintroduction, from the planning and implementation phases, to monitoring and management techniques.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The CPCRD is a dynamic resource, allowing data contributors to continually update their entries as projects progress. While contributions are ongoing, the CPCRD currently includes 460 projects involving 201 plant taxa, spanning diverse growth forms, ecosystems, and regions.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>The CPCRD and its well-documented and monitored projects provide a valuable practical resource for conservation practitioners, and have supported multiple scientific studies and contributed to the internationally recognized Center for Plant Conservation Best Practices Guidelines.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11583","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140975163","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":"Carbon balance: A technique to assess comparative photosynthetic physiology in poikilohydric plants","authors":"Kirsten K. Coe,&nbsp;Nicolas Neumeister,&nbsp;Maya I. Gomez,&nbsp;Niko Carvajal Janke","doi":"10.1002/aps3.11585","DOIUrl":"10.1002/aps3.11585","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Poikilohydric plants respond to hydration by undergoing dry–wet–dry cycles. Carbon balance represents the net gain or loss of carbon from each cycle. Here we present the first standard protocol for measuring carbon balance, including a custom-modified chamber system for infrared gas analysis, 12-h continuous monitoring, resolution of plant–substrate relationships, and in-chamber specimen hydration.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We applied the carbon balance technique to capture responses to water stress in populations of the moss <i>Syntrichia caninervis</i>, comparing 19 associated physiological variables. Carbon balance was negative in desiccation-acclimated (field-collected) mosses, which exhibited large respiratory losses. Contrastingly, carbon balance was positive in hydration-acclimated (lab-cultivated) mosses, which began exhibiting net carbon uptake &lt;15 min following hydration.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Carbon balance is a functional trait indicative of physiological performance, hydration stress, and survival in poikilohydric plants, and the carbon balance method can be applied broadly across taxa to test hypotheses related to environmental stress and global change.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11585","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140984408","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":"Conservation Action Tracker: A tool to identify and monitor conservation actions for tree species","authors":"Itxaso Quintana,&nbsp;Malin Rivers,&nbsp;Katharine Davies","doi":"10.1002/aps3.11579","DOIUrl":"10.1002/aps3.11579","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The GlobalTree Portal, hosted by Botanic Gardens Conservation International, provides access to information on the approximately 58,000 tree species worldwide. Included in the GlobalTree Portal is the Conservation Action Tracker, a dynamic and collaborative database to identify and monitor conservation actions for tree species globally.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The Conservation Action Tracker collates conservation action information at the species level, including species recovery/action plans, ex situ collections, propagation protocols, in situ management, species protection policy, and education/awareness campaigns.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>To date, the Conservation Action Tracker contains conservation action information for 4126 tree species, including 2161 threatened species, of which 659 are classified as Vulnerable, 783 as Endangered, and 719 as Critically Endangered. It covers conservation action information for at least one tree species in every country; however, more information is needed for 89% of Vulnerable, 87% of Endangered, and 77% of Critically Endangered tree species.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Monitoring species conservation actions can support the prioritization and scaling up of conservation practices by sharing knowledge, increasing collaboration, enabling the identification of conservation gaps, and making the information available to be used by decision-makers. Tracking conservation actions at the species level is, therefore, essential to guide future conservation efforts. Increasing the amount of data in the Conservation Action Tracker will improve the tool's ability to guide future conservation efforts and avoid the extinction of tree species.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11579","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140838485","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":"Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants","authors":"Gillian Reynolds,&nbsp;Brendan Mumey,&nbsp;Veronika Strnadova-Neeley,&nbsp;Jennifer Lachowiec","doi":"10.1002/aps3.11581","DOIUrl":"10.1002/aps3.11581","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both <i>k</i>-mer composition and frequency with a range of <i>k</i>-mer sizes. In this approach, no subgenome-specific <i>k</i>-mers are identified; rather, whole-chromosome <i>k</i>-mer subspaces were utilized.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled <i>k</i>-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global <i>k</i>-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11581","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140838533","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 roadmap of phylogenomic methods for studying polyploid plant genera","authors":"Weixuan Ning,&nbsp;Heidi M. Meudt,&nbsp;Jennifer A. Tate","doi":"10.1002/aps3.11580","DOIUrl":"10.1002/aps3.11580","url":null,"abstract":"<p>Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole-genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid-rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long-read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11580","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140672894","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 inexpensive moist chamber culture technique for finding microbiota on live tree bark","authors":"Ashley P. Bordelon,&nbsp;Harold W. Keller,&nbsp;Angela R. Scarborough","doi":"10.1002/aps3.11578","DOIUrl":"https://doi.org/10.1002/aps3.11578","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Traditional moist chamber cultures (MCs) prepared in aseptic laboratory environments using sterile Petri dishes are commonly used to quantify the microbiota of rough-bark tree species and woody vines. MCs are typically expensive and may be difficult to make, so a less expensive option made from easily available supplies was developed. These cost-friendly MCs were compared with standard laboratory methods to demonstrate their efficacy.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Modified MCs were made using inexpensive, store-bought supplies; compared to a standard laboratory setting, the modified MCs are shown to be less expensive with a faster setup time and larger size that facilitates a variety of tree and woody vine species. MC use resulted in the discovery of new species of fungi and myxomycetes with associated locality records. We provide detailed instructions for creating modified MCs, as well as a list of myxomycete species and their associated bark characteristics, pH values, and water-holding capacity.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This new, low-cost MC technique makes the study of microbiota more inclusive and accessible for those in research laboratories, classrooms, and homes, including both amateurs and professionals. MCs are easy to prepare, versatile, and applicable for many areas of botany and the biological sciences, potentially allowing exploration into unexplored areas in urban ecosystems.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11578","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140559507","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 machine learning approach to study plant functional trait divergence","authors":"Sambadi Majumder,&nbsp;Chase M. Mason","doi":"10.1002/aps3.11576","DOIUrl":"10.1002/aps3.11576","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Plant functional traits are often used to describe the spectra of ecological strategies used by different species. Here, we demonstrate a machine learning approach for identifying the traits that contribute most to interspecific phenotypic divergence in a multivariate trait space.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Descriptive and predictive machine learning approaches were applied to trait data for the genus <i>Helianthus</i>, including random forest and gradient boosting machine classifiers and recursive feature elimination. These approaches were applied at the genus level as well as within each of the three major clades within the genus to examine the variability in the major axes of trait divergence in three independent species radiations.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Machine learning models were able to predict species identity from functional traits with high accuracy, and differences in functional trait importance were observed between the genus and clade levels indicating different axes of phenotypic divergence.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Applying machine learning approaches to identify divergent traits can provide insights into the predictability or repeatability of evolution through the comparison of parallel diversifications of clades within a genus. These approaches can be implemented in a range of contexts across basic and applied plant science from interspecific divergence to intraspecific variation across time, space, and environmental conditions.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11576","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140566330","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}