Kirsten K. Coe, Nicolas Neumeister, Maya I. Gomez, Niko Carvajal Janke
Premise
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.
Methods and Results
We applied the carbon balance technique to capture responses to water stress in populations of the moss Syntrichia caninervis, 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 <15 min following hydration.
Conclusions
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.
{"title":"Carbon balance: A technique to assess comparative photosynthetic physiology in poikilohydric plants","authors":"Kirsten K. Coe, Nicolas Neumeister, Maya I. Gomez, 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 <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":"12 5","pages":""},"PeriodicalIF":2.4,"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}
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.
Methods
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.
Results
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.
Discussion
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.
{"title":"Conservation Action Tracker: A tool to identify and monitor conservation actions for tree species","authors":"Itxaso Quintana, Malin Rivers, 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":"12 3","pages":""},"PeriodicalIF":2.4,"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}
Gillian Reynolds, Brendan Mumey, Veronika Strnadova-Neeley, Jennifer Lachowiec
Premise
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.
Methods
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 k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized.
Results
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 k-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.
Discussion
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 k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.
{"title":"Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants","authors":"Gillian Reynolds, Brendan Mumey, Veronika Strnadova-Neeley, 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":"12 4","pages":""},"PeriodicalIF":2.4,"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}
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.
{"title":"A roadmap of phylogenomic methods for studying polyploid plant genera","authors":"Weixuan Ning, Heidi M. Meudt, 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":"12 4","pages":""},"PeriodicalIF":2.4,"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}
Ashley P. Bordelon, Harold W. Keller, Angela R. Scarborough
Premise
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.
Methods and Results
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.
Conclusions
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.
前提 传统的湿室培养物（MCs）是在无菌实验室环境中使用无菌培养皿制备的，通常用于量化粗皮树种和木本藤本植物的微生物区系。MC 通常价格昂贵且难以制作，因此我们开发了一种用容易获得的材料制作的价格较低的方法。将这些成本低廉的 MC 与标准实验室方法进行了比较，以证明其功效。 方法与结果 使用商店购买的廉价用品制作了改良 MC；与标准实验室设置相比，改良 MC 的成本更低，设置时间更短，体积更大，有利于多种树木和木质藤本植物的生长。使用 MC 发现了新的真菌和粘菌物种，并记录了相关地点。我们提供了制作改良 MC 的详细说明，以及木霉菌种类及其相关树皮特征、pH 值和持水能力的列表。 结论 这种新的、低成本的 MC 技术使微生物区系的研究更具包容性，更便于研究实验室、教室和家庭中的业余爱好者和专业人员使用。微生物菌群易于制备，用途广泛，适用于植物学和生物科学的许多领域，可用于探索城市生态系统中尚未开发的领域。
{"title":"An inexpensive moist chamber culture technique for finding microbiota on live tree bark","authors":"Ashley P. Bordelon, Harold W. Keller, Angela R. Scarborough","doi":"10.1002/aps3.11578","DOIUrl":"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":"12 2","pages":""},"PeriodicalIF":2.4,"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}
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.
Methods
Descriptive and predictive machine learning approaches were applied to trait data for the genus Helianthus, 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.
Results
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.
Conclusions
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.
{"title":"A machine learning approach to study plant functional trait divergence","authors":"Sambadi Majumder, 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":"12 5","pages":""},"PeriodicalIF":2.4,"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}
Gillian H. Dean, N. Ivalú Cacho, Alejandro Zuluaga Trochez, Gregory J. Pec
<p>In 2020, at the beginning of the COVID-19 pandemic, <i>Applications in Plant Sciences</i> (<i>APPS</i>) published a special issue titled “Conducting botanical research with limited resources: Low-cost methods in the plant sciences” (Dean et al., <span>2020</span>). The goal of that collection was to highlight robust, low-cost methods that could be used by researchers in under-resourced settings. Plant scientists face resource limitations for many reasons. In some countries, inadequate national funding is a major issue, as well as limited long-term investment in research infrastructure. At the same time, factors contributing to low-resource settings are also experienced by researchers in countries where research funding is more abundant. For example, although national research programs in the Global North are generally well funded, these funds may be difficult to access for investigators who hold positions at smaller institutions, such as predominantly undergraduate institutions.</p><p>Regardless of geographic location, lack of training and access to expensive and specialized equipment can be limiting, and funding to acquire expensive equipment often does not include salary for maintenance and operation by trained personnel after the initial purchase and set up. In addition, research may be performed by new investigators such as undergraduate or graduate students, or when established labs wish to explore new areas of research or techniques without committing significant resources.</p><p>Globally, substantial and significant scientific research is performed in these under-resourced settings. The COVID-19 pandemic exacerbated this situation by disrupting supply chains and forcing researchers to work from home or in isolation at their workplace, resulting in dynamic adaptations in their approaches to generating or collecting data. Suddenly confronted with an inability to travel, many scientists looked to their local environment to leverage their skills to continue research closer to home. In light of these challenges, this <i>APPS</i> special issue, titled “Resilient botany: Innovation in the face of limited mobility and resources,” showcases the creative ways that plant scientists carried on with research during a global pandemic. The papers in this issue encompass a variety of fields and scales of research, ranging from investigations of plant structure at the microscopic level to utilizing big data to understand biodiversity, but they all have one thing in common: they are all accessible to researchers and practitioners challenged by funding or travel restrictions.</p><p>It has been well documented that cataloging global biodiversity is a daunting task that will take a concerted effort by many scientists and community scientists, especially given that much of the world's biodiversity is located in areas with under-resourced research communities. A large amount of data is already contained in herbaria, and digitizing this information is an impor
{"title":"Resilient botany: Innovation in the face of limited mobility and resources","authors":"Gillian H. Dean, N. Ivalú Cacho, Alejandro Zuluaga Trochez, Gregory J. Pec","doi":"10.1002/aps3.11577","DOIUrl":"10.1002/aps3.11577","url":null,"abstract":"<p>In 2020, at the beginning of the COVID-19 pandemic, <i>Applications in Plant Sciences</i> (<i>APPS</i>) published a special issue titled “Conducting botanical research with limited resources: Low-cost methods in the plant sciences” (Dean et al., <span>2020</span>). The goal of that collection was to highlight robust, low-cost methods that could be used by researchers in under-resourced settings. Plant scientists face resource limitations for many reasons. In some countries, inadequate national funding is a major issue, as well as limited long-term investment in research infrastructure. At the same time, factors contributing to low-resource settings are also experienced by researchers in countries where research funding is more abundant. For example, although national research programs in the Global North are generally well funded, these funds may be difficult to access for investigators who hold positions at smaller institutions, such as predominantly undergraduate institutions.</p><p>Regardless of geographic location, lack of training and access to expensive and specialized equipment can be limiting, and funding to acquire expensive equipment often does not include salary for maintenance and operation by trained personnel after the initial purchase and set up. In addition, research may be performed by new investigators such as undergraduate or graduate students, or when established labs wish to explore new areas of research or techniques without committing significant resources.</p><p>Globally, substantial and significant scientific research is performed in these under-resourced settings. The COVID-19 pandemic exacerbated this situation by disrupting supply chains and forcing researchers to work from home or in isolation at their workplace, resulting in dynamic adaptations in their approaches to generating or collecting data. Suddenly confronted with an inability to travel, many scientists looked to their local environment to leverage their skills to continue research closer to home. In light of these challenges, this <i>APPS</i> special issue, titled “Resilient botany: Innovation in the face of limited mobility and resources,” showcases the creative ways that plant scientists carried on with research during a global pandemic. The papers in this issue encompass a variety of fields and scales of research, ranging from investigations of plant structure at the microscopic level to utilizing big data to understand biodiversity, but they all have one thing in common: they are all accessible to researchers and practitioners challenged by funding or travel restrictions.</p><p>It has been well documented that cataloging global biodiversity is a daunting task that will take a concerted effort by many scientists and community scientists, especially given that much of the world's biodiversity is located in areas with under-resourced research communities. A large amount of data is already contained in herbaria, and digitizing this information is an impor","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11577","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140559577","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}
Natalie N. Patten, Michelle L. Gaynor, Douglas E. Soltis, Pamela S. Soltis
Premise
Digitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs).
Methods and Results
The gatoRs workflow includes functions that streamline downloading records from the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio). We also created functions to clean downloaded specimen records. Unlike previous R packages, gatoRs accounts for differences in download structure between GBIF and iDigBio and allows for user control via interactive cleaning steps.
Conclusions
Our pipeline enables the scientific community to process biodiversity data efficiently and is accessible to the R coding novice. We anticipate that gatoRs will be useful for both established and beginning users. Furthermore, we expect our package will facilitate the introduction of biodiversity-related concepts into the classroom via the use of herbarium specimens.
前提条件数字化的生物多样性数据提供了大量信息；然而，获取和处理生物多样性数据的工作可能非常艰巨。数据清理过程中会出现一些复杂问题，如识别和删除有问题的记录。为了解决这些问题，我们创建了基于 R 的地理与分类出现清理（Geographic And Taxonomic Occurrence R-based Scrubbing，gatoRs）软件包。方法与结果 gatoRs 工作流程包括简化从全球生物多样性信息基金（GBIF）和综合数字化生物收集（iDigBio）下载记录的功能。我们还创建了清理下载标本记录的函数。与以前的 R 软件包不同，gatoRs 考虑到了 GBIF 和 iDigBio 下载结构的差异，并允许用户通过交互式清理步骤进行控制。我们预计，gatoRs 对成熟用户和初学者都很有用。此外，我们还希望我们的软件包能通过标本馆标本的使用，促进将生物多样性相关概念引入课堂。
{"title":"Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data","authors":"Natalie N. Patten, Michelle L. Gaynor, Douglas E. Soltis, Pamela S. Soltis","doi":"10.1002/aps3.11575","DOIUrl":"10.1002/aps3.11575","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Digitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>The gatoRs workflow includes functions that streamline downloading records from the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio). We also created functions to clean downloaded specimen records. Unlike previous R packages, gatoRs accounts for differences in download structure between GBIF and iDigBio and allows for user control via interactive cleaning steps.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our pipeline enables the scientific community to process biodiversity data efficiently and is accessible to the R coding novice. We anticipate that gatoRs will be useful for both established and beginning users. Furthermore, we expect our package will facilitate the introduction of biodiversity-related concepts into the classroom via the use of herbarium specimens.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11575","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140200249","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}
Hugo Jaimes, Alejandra Londoño, Carolina Saavedra-Diaz, Jhon Henry Trujillo-Montenegro, Jershon López-Gerena, John J. Riascos, Fernando S. Aguilar
Premise
Detecting single-nucleotide polymorphisms (SNPs) in a cost-effective way is fundamental in any plant breeding pipeline. Here, we compare three genotyping techniques for their ability to reproduce the allele dosage of SNPs of interest in sugarcane (Saccharum spp.).
Methods
To identify a reproducible technique to estimate allele dosage for the validation of SNP markers, the correlation between Flex-Seq, kompetitive allele-specific PCR (KASP), and genotyping-by-sequencing and restriction site–associated DNA sequencing (GBS+RADseq) was determined for a set of 76 SNPs. To find alternative methodologies for allele dosage estimation, the KASP and Flex-Seq techniques were compared for the same set of SNPs. For the three techniques, a population of 53 genotypes from the diverse sugarcane panel of the Centro de Investigación de la Caña de Azúcar (Cenicaña), Colombia, was selected.
Results
The average Pearson correlation coefficients between GBS+RADseq and Flex-Seq, GBS+RADseq and KASP, and Flex-Seq and KASP were 0.62 ± 0.27, 0.38 ± 0.27, and 0.38 ± 0.30, respectively.
Discussion
Flex-Seq reproduced the allele dosages determined using GBS+RADseq with good levels of precision because of its depth of sequencing and ability to target specific positions in the genome. Additionally, Flex-Seq outperformed KASP by allowing the conversion of a higher number of SNPs and a more accurate estimation of the allele dosage. Flex-Seq has therefore become the genotyping methodology of choice for marker validation at Cenicaña.
{"title":"Sequencing vs. amplification for the estimation of allele dosages in sugarcane (Saccharum spp.)","authors":"Hugo Jaimes, Alejandra Londoño, Carolina Saavedra-Diaz, Jhon Henry Trujillo-Montenegro, Jershon López-Gerena, John J. Riascos, Fernando S. Aguilar","doi":"10.1002/aps3.11574","DOIUrl":"10.1002/aps3.11574","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Detecting single-nucleotide polymorphisms (SNPs) in a cost-effective way is fundamental in any plant breeding pipeline. Here, we compare three genotyping techniques for their ability to reproduce the allele dosage of SNPs of interest in sugarcane (<i>Saccharum</i> spp.).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>To identify a reproducible technique to estimate allele dosage for the validation of SNP markers, the correlation between Flex-Seq, kompetitive allele-specific PCR (KASP), and genotyping-by-sequencing and restriction site–associated DNA sequencing (GBS+RADseq) was determined for a set of 76 SNPs. To find alternative methodologies for allele dosage estimation, the KASP and Flex-Seq techniques were compared for the same set of SNPs. For the three techniques, a population of 53 genotypes from the diverse sugarcane panel of the Centro de Investigación de la Caña de Azúcar (Cenicaña), Colombia, was selected.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The average Pearson correlation coefficients between GBS+RADseq and Flex-Seq, GBS+RADseq and KASP, and Flex-Seq and KASP were 0.62 ± 0.27, 0.38 ± 0.27, and 0.38 ± 0.30, respectively.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Flex-Seq reproduced the allele dosages determined using GBS+RADseq with good levels of precision because of its depth of sequencing and ability to target specific positions in the genome. Additionally, Flex-Seq outperformed KASP by allowing the conversion of a higher number of SNPs and a more accurate estimation of the allele dosage. Flex-Seq has therefore become the genotyping methodology of choice for marker validation at Cenicaña.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11574","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140148152","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}
Sara E. Hansen, Michael J. Monfils, Rachel A. Hackett, Ryan T. Goebel, Anna K. Monfils
Premise
Species distribution models (SDMs) are widely utilized to guide conservation decisions. The complexity of available data and SDM methodologies necessitates considerations of how data are chosen and processed for modeling to enhance model accuracy and support biological interpretations and ecological applications.
Methods
We built SDMs for the invasive aquatic plant European frog-bit using aggregated and field data that span multiple scales, data sources, and data types. We tested how model results were affected by five modeler decision points: the exclusion of (1) missing and (2) correlated data and the (3) scale (large-scale aggregated data or systematic field data), (4) source (specimens or observations), and (5) type (presence-background or presence-absence) of occurrence data.
Results
Decisions about the exclusion of missing and correlated data, as well as the scale and type of occurrence data, significantly affected metrics of model performance. The source and type of occurrence data led to differences in the importance of specific explanatory variables as drivers of species distribution and predicted probability of suitable habitat.
Discussion
Our findings relative to European frog-bit illustrate how specific data selection and processing decisions can influence the outcomes and interpretation of SDMs. Data-centric protocols that incorporate data exploration into model building can help ensure models are reproducible and can be accurately interpreted in light of biological questions.
{"title":"Data-centric species distribution modeling: Impacts of modeler decisions in a case study of invasive European frog-bit","authors":"Sara E. Hansen, Michael J. Monfils, Rachel A. Hackett, Ryan T. Goebel, Anna K. Monfils","doi":"10.1002/aps3.11573","DOIUrl":"10.1002/aps3.11573","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Species distribution models (SDMs) are widely utilized to guide conservation decisions. The complexity of available data and SDM methodologies necessitates considerations of how data are chosen and processed for modeling to enhance model accuracy and support biological interpretations and ecological applications.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We built SDMs for the invasive aquatic plant European frog-bit using aggregated and field data that span multiple scales, data sources, and data types. We tested how model results were affected by five modeler decision points: the exclusion of (1) missing and (2) correlated data and the (3) scale (large-scale aggregated data or systematic field data), (4) source (specimens or observations), and (5) type (presence-background or presence-absence) of occurrence data.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Decisions about the exclusion of missing and correlated data, as well as the scale and type of occurrence data, significantly affected metrics of model performance. The source and type of occurrence data led to differences in the importance of specific explanatory variables as drivers of species distribution and predicted probability of suitable habitat.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our findings relative to European frog-bit illustrate how specific data selection and processing decisions can influence the outcomes and interpretation of SDMs. Data-centric protocols that incorporate data exploration into model building can help ensure models are reproducible and can be accurately interpreted in light of biological questions.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11573","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140126498","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}
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