Embryo excision is an effective, under-described means of promoting germination in the sunflower family and may help to ensure the survival of endangered taxa or lineages with limited seed availability.
Methods and Results
We describe and illustrate a detailed method of embryo excision used successfully to stimulate germination in a diversity of composites and that requires minimal materials and expense, using Layia platyglossa as an example. We show how this procedure greatly increases germination compared to control treatments in Madia elegans, a close relative of Hawaiian silverswords that exhibits physiological dormancy.
Conclusions
This technique can be learned quickly and is highly effective. Embryo excision can aid conservation efforts dependent on minimal seed resources by enhancing germination and allowing evaluation of seed quality before or after storage, as well as synchronizing seedling development, thereby allowing for refinement of ex situ seed bank conditions and efficient use of horticultural resources.
{"title":"Embryo excision in Compositae, with implications for combating biodiversity loss","authors":"Bruce G. Baldwin, Susan Fawcett, Dustin Wolkis","doi":"10.1002/aps3.11608","DOIUrl":"10.1002/aps3.11608","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Embryo excision is an effective, under-described means of promoting germination in the sunflower family and may help to ensure the survival of endangered taxa or lineages with limited seed availability.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We describe and illustrate a detailed method of embryo excision used successfully to stimulate germination in a diversity of composites and that requires minimal materials and expense, using <i>Layia platyglossa</i> as an example. We show how this procedure greatly increases germination compared to control treatments in <i>Madia elegans</i>, a close relative of Hawaiian silverswords that exhibits physiological dormancy.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This technique can be learned quickly and is highly effective. Embryo excision can aid conservation efforts dependent on minimal seed resources by enhancing germination and allowing evaluation of seed quality before or after storage, as well as synchronizing seedling development, thereby allowing for refinement of ex situ seed bank conditions and efficient use of horticultural resources.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11608","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142199633","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}
Jacob S. Suissa, Gisel Y. De La Cerda, Leland C. Graber, Chloe Jelley, David Wickell, Heather R. Phillips, Ayress D. Grinage, Corrie S. Moreau, Chelsea D. Specht, Jeff J. Doyle, Jacob B. Landis
Premise
There is a general lack of consensus on the best practices for filtering of single-nucleotide polymorphisms (SNPs) and whether it is better to use SNPs or include flanking regions (full “locus”) in phylogenomic analyses and subsequent comparative methods.
Methods
Using genotyping-by-sequencing data from 22 Glycine species, we assessed the effects of SNP vs. locus usage and SNP retention stringency. We compared branch length, node support, and divergence time estimation across 16 datasets with varying amounts of missing data and total size.
Results
Our results revealed five aspects of phylogenomic data usage that may be generally applicable: (1) tree topology is largely congruent across analyses; (2) filtering strictly for SNP retention (e.g., 90–100%) reduces support and can alter some inferred relationships; (3) absolute branch lengths vary by two orders of magnitude between SNP and locus datasets; (4) data type and branch length variation have little effect on divergence time estimation; and (5) phylograms alter the estimation of ancestral states and rates of morphological evolution.
Discussion
Using SNP or locus datasets does not alter phylogenetic inference significantly, unless researchers want or need to use absolute branch lengths. We recommend against using excessive filtering thresholds for SNP retention to reduce the risk of producing inconsistent topologies and generating low support.
关于过滤单核苷酸多态性（SNP）的最佳方法，以及在系统发生组分析和后续比较方法中使用 SNP 还是包括侧翼区域（完整的 "位点"）更好，目前普遍缺乏共识。我们比较了 16 个数据集的分支长度、节点支持率和分化时间估计，这些数据集的缺失数据量和总规模各不相同。我们的结果揭示了系统发生组数据使用的五个方面，这些方面可能具有普遍适用性：（1）树拓扑结构在不同分析中基本一致；（2）严格筛选 SNP 保留率（如 90%-100%）会降低支持率，并且会影响树的分化时间、(3) SNP 数据集和基因座数据集的绝对分支长度相差两个数量级；(4) 数据类型和分支长度的变化对分歧时间的估计影响不大；(5) 系统图会改变对祖先状态和形态进化速率的估计。我们建议不要使用过高的 SNP 保留过滤阈值，以降低产生不一致拓扑和低支持度的风险。
{"title":"Data-driven guidelines for phylogenomic analyses using SNP data","authors":"Jacob S. Suissa, Gisel Y. De La Cerda, Leland C. Graber, Chloe Jelley, David Wickell, Heather R. Phillips, Ayress D. Grinage, Corrie S. Moreau, Chelsea D. Specht, Jeff J. Doyle, Jacob B. Landis","doi":"10.1002/aps3.11611","DOIUrl":"10.1002/aps3.11611","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>There is a general lack of consensus on the best practices for filtering of single-nucleotide polymorphisms (SNPs) and whether it is better to use SNPs or include flanking regions (full “locus”) in phylogenomic analyses and subsequent comparative methods.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Using genotyping-by-sequencing data from 22 <i>Glycine</i> species, we assessed the effects of SNP vs. locus usage and SNP retention stringency. We compared branch length, node support, and divergence time estimation across 16 datasets with varying amounts of missing data and total size.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our results revealed five aspects of phylogenomic data usage that may be generally applicable: (1) tree topology is largely congruent across analyses; (2) filtering strictly for SNP retention (e.g., 90–100%) reduces support and can alter some inferred relationships; (3) absolute branch lengths vary by two orders of magnitude between SNP and locus datasets; (4) data type and branch length variation have little effect on divergence time estimation; and (5) phylograms alter the estimation of ancestral states and rates of morphological evolution.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Using SNP or locus datasets does not alter phylogenetic inference significantly, unless researchers want or need to use absolute branch lengths. We recommend against using excessive filtering thresholds for SNP retention to reduce the risk of producing inconsistent topologies and generating low support.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11611","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141921682","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}
Arne Devriese, Gerrit Peeters, Rein Brys, Hans Jacquemyn
Premise
Plants and pollinators closely interact with each other to form complex networks of species interactions. Metabarcoding of pollen collections has recently been proposed as an advantageous method for the construction of such networks, but the extent to which diversity and community analyses depend on the extraction method and pollen concentration used remains unclear.
Methods
In this study, we used a dilution series of two pollen mixtures (a mock community and pooled natural pollen loads from bumblebees) to assess the effect of mechanical homogenization and two DNA extraction kits (spin column DNA extraction kit and magnetic bead DNA extraction kit) on the detected pollen richness and community composition.
Results
All species were successfully detected using the three methods, even in the most dilute samples. However, the extraction method had a significant effect on the detected pollen richness and community composition, with simple mechanical homogenization introducing an extraction bias.
Discussion
Our findings suggest that all three methods are effective for detecting plant species in the pollen loads on insects, even in cases of very low pollen loads. However, our results also indicate that extraction methods can have a profound impact on the ability to correctly assess the community composition of the pollen loads on insects. The choice of extraction methodology should therefore be carefully considered to ensure reliable and unbiased results in pollen diversity and community analyses.
前言植物与传粉昆虫之间密切互动，形成复杂的物种互动网络。最近有人提出，花粉采集的元条码是构建此类网络的一种有利方法，但多样性和群落分析在多大程度上取决于所使用的提取方法和花粉浓度仍不清楚。方法在这项研究中，我们使用了两种花粉混合物的稀释系列（模拟群落和来自熊蜂的汇集天然花粉量）来评估机械均质和两种 DNA 提取试剂盒（旋柱 DNA 提取试剂盒和磁珠 DNA 提取试剂盒）对检测到的花粉丰富度和群落组成的影响。讨论 我们的研究结果表明，这三种方法都能有效地检测昆虫花粉负载中的植物物种，即使在花粉负载量很低的情况下也是如此。然而，我们的研究结果也表明，提取方法会对正确评估昆虫花粉载荷群落组成的能力产生深远影响。因此，应仔细考虑提取方法的选择，以确保花粉多样性和群落分析结果的可靠性和公正性。
{"title":"The impact of extraction method and pollen concentration on community composition for pollen metabarcoding","authors":"Arne Devriese, Gerrit Peeters, Rein Brys, Hans Jacquemyn","doi":"10.1002/aps3.11601","DOIUrl":"10.1002/aps3.11601","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Plants and pollinators closely interact with each other to form complex networks of species interactions. Metabarcoding of pollen collections has recently been proposed as an advantageous method for the construction of such networks, but the extent to which diversity and community analyses depend on the extraction method and pollen concentration used remains unclear.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>In this study, we used a dilution series of two pollen mixtures (a mock community and pooled natural pollen loads from bumblebees) to assess the effect of mechanical homogenization and two DNA extraction kits (spin column DNA extraction kit and magnetic bead DNA extraction kit) on the detected pollen richness and community composition.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>All species were successfully detected using the three methods, even in the most dilute samples. However, the extraction method had a significant effect on the detected pollen richness and community composition, with simple mechanical homogenization introducing an extraction bias.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our findings suggest that all three methods are effective for detecting plant species in the pollen loads on insects, even in cases of very low pollen loads. However, our results also indicate that extraction methods can have a profound impact on the ability to correctly assess the community composition of the pollen loads on insects. The choice of extraction methodology should therefore be carefully considered to ensure reliable and unbiased results in pollen diversity and community analyses.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11601","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141932620","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}
Giancarlo M. Chiarenza, Eve Slavich, Angela T. Moles
Premise
Leaf chlorophyll is a fundamental bioindicator used in several fields; however, we lack clear guidelines for optimizing sampling efforts and producing comparable studies.
Methods
We estimated the leaf chlorophyll content of 10 plant species using nondestructive spectrometry methods. We stored half of the leaves at 4°C and half at room temperature under similar light levels to assess the role of storage in the chlorophyll degradation rate.
Results
The chilled mature leaves maintained a chlorophyll content within 5% of the original value for ~1.5 d, while the chlorophyll content of unrefrigerated mature leaves decreased rapidly, indicating that their chlorophyll content should be measured within 4 h. When refrigerated, the chlorophyll content of the expanding leaves remained within 5% of the original level for at least 5 d, but we suggest analyzing them within 3 d. In mature leaves, 73% of the variation in chlorophyll content is at the species level, 15% is between individuals, and the variation within leaves is negligible (<1%). Measuring one mature leaf from eight individuals was sufficient to provide a species chlorophyll estimate within 5% of the true value at least 80% of the time.
Discussion
We advise researchers to prioritize sampling more individuals rather than repeating measures within leaves or individuals. Our findings will help researchers to optimize their time and research efforts, and to obtain more robust ecological data.
前言叶片叶绿素是多个领域使用的基本生物指标；然而，我们缺乏明确的指导方针来优化取样工作并进行可比研究。方法我们使用无损光谱法估算了 10 种植物的叶片叶绿素含量。结果冷藏成熟叶片的叶绿素含量在约 1.5 d 内保持在原始值的 5%以内，而未冷藏成熟叶片的叶绿素含量迅速下降，这表明叶绿素含量应在 4 h 内测量。成熟叶片叶绿素含量的变化，73%在物种水平，15%在个体间，叶片内部的变化可以忽略不计（<1%）。我们建议研究人员优先对更多个体进行取样，而不是在叶片或个体内部重复测量。我们的发现将有助于研究人员优化时间和研究工作，并获得更可靠的生态数据。
{"title":"Guidelines for quantifying leaf chlorophyll content via non-destructive spectrometry","authors":"Giancarlo M. Chiarenza, Eve Slavich, Angela T. Moles","doi":"10.1002/aps3.11610","DOIUrl":"10.1002/aps3.11610","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Leaf chlorophyll is a fundamental bioindicator used in several fields; however, we lack clear guidelines for optimizing sampling efforts and producing comparable studies.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We estimated the leaf chlorophyll content of 10 plant species using nondestructive spectrometry methods. We stored half of the leaves at 4°C and half at room temperature under similar light levels to assess the role of storage in the chlorophyll degradation rate.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The chilled mature leaves maintained a chlorophyll content within 5% of the original value for ~1.5 d, while the chlorophyll content of unrefrigerated mature leaves decreased rapidly, indicating that their chlorophyll content should be measured within 4 h. When refrigerated, the chlorophyll content of the expanding leaves remained within 5% of the original level for at least 5 d, but we suggest analyzing them within 3 d. In mature leaves, 73% of the variation in chlorophyll content is at the species level, 15% is between individuals, and the variation within leaves is negligible (<1%). Measuring one mature leaf from eight individuals was sufficient to provide a species chlorophyll estimate within 5% of the true value at least 80% of the time.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We advise researchers to prioritize sampling more individuals rather than repeating measures within leaves or individuals. Our findings will help researchers to optimize their time and research efforts, and to obtain more robust ecological data.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11610","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141932621","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}
Débora C. Zuanny, Bruno Vilela, Peter W. Moonlight, Tiina E. Särkinen, Domingos Cardoso
Premise
Data on plant distribution and diversity from natural history collections and taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of the World Online (POWO) database. This growing accumulation of biodiversity information requires an advance in bioinformatic tools for accessing and processing the massive data for use in downstream science. We present herein expowo, an open-source package that facilitates extracting and using botanical data from POWO.
Methods and Results
The expowo package is implemented in R and designed to handle the entire vascular plant tree of life. It includes functions to readily distill taxonomic and distributional information about all families, genera, or species of vascular plants. It outputs a complete list of species in each genus of any plant family, with the associated original publication, synonyms, and distribution, and plots global maps of species richness at the country and botanical country levels, as well as graphs displaying species-discovery accumulation curves and nomenclatural changes over time. To demonstrate expowo's strengths in producing easy-to-handle outputs, we also show empirical examples from a set of biodiverse countries and representative species-rich and ecologically important angiosperm families.
Conclusions
By harnessing bioinformatic tools that accommodate varying levels of R programming proficiency, expowo functions assist users who have limited R programming expertise in efficiently distilling specific botanical information from online sources and producing maps and graphics for the further interpretation of biogeographic and taxonomic patterns.
{"title":"expowo: An R package for mining global plant diversity and distribution data","authors":"Débora C. Zuanny, Bruno Vilela, Peter W. Moonlight, Tiina E. Särkinen, Domingos Cardoso","doi":"10.1002/aps3.11609","DOIUrl":"10.1002/aps3.11609","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Data on plant distribution and diversity from natural history collections and taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of the World Online (POWO) database. This growing accumulation of biodiversity information requires an advance in bioinformatic tools for accessing and processing the massive data for use in downstream science. We present herein expowo, an open-source package that facilitates extracting and using botanical data from POWO.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>The expowo package is implemented in R and designed to handle the entire vascular plant tree of life. It includes functions to readily distill taxonomic and distributional information about all families, genera, or species of vascular plants. It outputs a complete list of species in each genus of any plant family, with the associated original publication, synonyms, and distribution, and plots global maps of species richness at the country and botanical country levels, as well as graphs displaying species-discovery accumulation curves and nomenclatural changes over time. To demonstrate expowo's strengths in producing easy-to-handle outputs, we also show empirical examples from a set of biodiverse countries and representative species-rich and ecologically important angiosperm families.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>By harnessing bioinformatic tools that accommodate varying levels of R programming proficiency, expowo functions assist users who have limited R programming expertise in efficiently distilling specific botanical information from online sources and producing maps and graphics for the further interpretation of biogeographic and taxonomic patterns.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11609","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141870157","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 prompt categorization of Phytophthora infestans isolates into described clonal lineages is a key tool for the management of its associated disease, potato late blight. New isolates of this pathogen are currently classified by comparing their microsatellite genotypes with characterized clonal lineages, but an automated classification tool would greatly improve this process. Here, we developed a flexible machine learning–based classifier for P. infestans genotypes.
Methods
The performance of different machine learning algorithms in classifying P. infestans genotypes into its clonal lineages was preliminarily evaluated with decreasing amounts of training data. The four best algorithms were then evaluated using all collected genotypes.
Results
mlpML, cforest, nnet, and AdaBag performed best in the preliminary test, correctly classifying almost 100% of the genotypes. AdaBag performed significantly better than the others when tested using the complete data set (Tukey HSD P < 0.001). This algorithm was then implemented in a web application for the automated classification of P. infestans genotypes, which is freely available at https://github.com/cpatarroyo/genotypeclas.
Discussion
We developed a gradient boosting–based tool to automatically classify P. infestans genotypes into its clonal lineages. This could become a valuable resource for the prompt identification of clonal lineages spreading into new regions.
前言将侵染病菌分离物迅速归类到描述的克隆系中是管理其相关病害马铃薯晚疫病的关键工具。目前，这种病原体的新分离物是通过比较其微卫星基因型和特征克隆系来进行分类的，但自动分类工具将大大改进这一过程。在此，我们为 P. infestans 基因型开发了一种灵活的基于机器学习的分类器。方法通过减少训练数据量，初步评估了不同机器学习算法在将 P. infestans 基因型归入其克隆系方面的性能。结果mlpML、cforest、nnet 和 AdaBag 在初步测试中表现最佳，几乎 100% 正确地对基因型进行了分类。在使用完整数据集进行测试时，AdaBag 的表现明显优于其他算法（Tukey HSD P < 0.001）。该算法随后被应用于一个用于自动分类 P. infestans 基因型的网络应用程序中，该程序可在 https://github.com/cpatarroyo/genotypeclas.DiscussionWe 免费获取。该程序开发了一种基于梯度提升的工具，用于将 P. infestans 基因型自动分类为其克隆系。这将成为迅速识别扩散到新地区的克隆系的宝贵资源。
{"title":"A machine learning algorithm for the automatic classification of Phytophthora infestans genotypes into clonal lineages","authors":"Camilo Patarroyo, Stéphane Dupas, Silvia Restrepo","doi":"10.1002/aps3.11603","DOIUrl":"10.1002/aps3.11603","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The prompt categorization of <i>Phytophthora infestans</i> isolates into described clonal lineages is a key tool for the management of its associated disease, potato late blight. New isolates of this pathogen are currently classified by comparing their microsatellite genotypes with characterized clonal lineages, but an automated classification tool would greatly improve this process. Here, we developed a flexible machine learning–based classifier for <i>P. infestans</i> genotypes.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The performance of different machine learning algorithms in classifying <i>P. infestans</i> genotypes into its clonal lineages was preliminarily evaluated with decreasing amounts of training data. The four best algorithms were then evaluated using all collected genotypes.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>mlpML, cforest, nnet, and AdaBag performed best in the preliminary test, correctly classifying almost 100% of the genotypes. AdaBag performed significantly better than the others when tested using the complete data set (Tukey HSD <i>P</i> < 0.001). This algorithm was then implemented in a web application for the automated classification of <i>P. infestans</i> genotypes, which is freely available at https://github.com/cpatarroyo/genotypeclas.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We developed a gradient boosting–based tool to automatically classify <i>P. infestans</i> genotypes into its clonal lineages. This could become a valuable resource for the prompt identification of clonal lineages spreading into new regions.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11603","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141778214","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}
Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.
{"title":"Variant calling in polyploids for population and quantitative genetics","authors":"Alyssa R. Phillips","doi":"10.1002/aps3.11607","DOIUrl":"10.1002/aps3.11607","url":null,"abstract":"<p>Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11607","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141738604","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}
Robert L. Baker, Grace L. Brock, Eastyn L. Newsome, Meixia Zhao
Premise
Most traits are polygenic and most genes are pleiotropic, resulting in complex, integrated phenotypes. Polyploidy presents an excellent opportunity to explore the evolution of phenotypic integration as entire genomes are duplicated, allowing for new associations among traits and potentially leading to enhanced or reduced phenotypic integration. Despite the multivariate nature of phenotypic evolution, studies often rely on simplistic bivariate correlations that cannot accurately represent complex phenotypes or data reduction techniques that can obscure specific trait relationships.
Methods
We apply network modeling, a common gene co-expression analysis, to the study of phenotypic integration to identify multivariate patterns of phenotypic evolution, including anatomy and morphology (structural) and physiology (functional) traits in response to whole genome duplication in the genus Brassica.
Results
We identify four key structural traits that are overrepresented in the evolution of phenotypic integration. Seeding networks with key traits allowed us to identify structure–function relationships not apparent from bivariate analyses. In general, allopolyploids exhibited larger, more robust networks indicative of increased phenotypic integration compared to diploids.
Discussion
Phenotypic network analysis may provide important insights into the effects of selection on non-target traits, even when they lack direct correlations with the target traits. Network analysis may allow for more nuanced predictions of both natural and artificial selection.
{"title":"Polyploidy and the evolution of phenotypic integration: Network analysis reveals relationships among anatomy, morphology, and physiology","authors":"Robert L. Baker, Grace L. Brock, Eastyn L. Newsome, Meixia Zhao","doi":"10.1002/aps3.11605","DOIUrl":"10.1002/aps3.11605","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Most traits are polygenic and most genes are pleiotropic, resulting in complex, integrated phenotypes. Polyploidy presents an excellent opportunity to explore the evolution of phenotypic integration as entire genomes are duplicated, allowing for new associations among traits and potentially leading to enhanced or reduced phenotypic integration. Despite the multivariate nature of phenotypic evolution, studies often rely on simplistic bivariate correlations that cannot accurately represent complex phenotypes or data reduction techniques that can obscure specific trait relationships.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We apply network modeling, a common gene co-expression analysis, to the study of phenotypic integration to identify multivariate patterns of phenotypic evolution, including anatomy and morphology (structural) and physiology (functional) traits in response to whole genome duplication in the genus <i>Brassica</i>.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We identify four key structural traits that are overrepresented in the evolution of phenotypic integration. Seeding networks with key traits allowed us to identify structure–function relationships not apparent from bivariate analyses. In general, allopolyploids exhibited larger, more robust networks indicative of increased phenotypic integration compared to diploids.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Phenotypic network analysis may provide important insights into the effects of selection on non-target traits, even when they lack direct correlations with the target traits. Network analysis may allow for more nuanced predictions of both natural and artificial selection.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11605","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141738603","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}
Michelle L. Gaynor, Jacob B. Landis, Timothy K. O'Connor, Robert G. Laport, Jeff J. Doyle, Douglas E. Soltis, José Miguel Ponciano, Pamela S. Soltis
Premise
Traditional methods of ploidal-level estimation are tedious; using DNA sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage sequence data for ploidy inference based on site-based heterozygosity have been developed. However, these approaches may require high-coverage sequence data, use inappropriate probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open-source R package that addresses the main shortcomings of current methods.
Methods and Results
nQuack performs model selection for improved ploidy predictions. Here, we implement expectation maximization algorithms with normal, beta, and beta-binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack.
Conclusions
Inferring ploidy based on site-based heterozygosity alone is difficult. Even though nQuack is more accurate than similar methods, we suggest caution when relying on any site-based heterozygosity method to infer ploidy.
前提传统的倍性水平估算方法非常繁琐；利用 DNA 序列数据进行细胞型估算是一种理想的替代方法。目前已开发出多种统计方法，利用序列数据进行基于位点杂合度的倍性推断。然而，这些方法可能需要高覆盖率的序列数据、使用不恰当的概率分布，或存在其他限制推断能力的统计缺陷。我们介绍了一个开源 R 软件包 nQuack，它能解决当前方法的主要缺陷。方法与结果nQuack 能进行模型选择以改进倍性预测。在这里，我们使用正态分布、贝塔分布和贝塔二叉分布实现了期望最大化算法。结论仅根据基于位点的杂合度来推测倍性是很困难的。尽管 nQuack 比类似的方法更准确，但我们建议在依赖任何基于位点的杂合度方法来推断倍性时要谨慎。
{"title":"nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity","authors":"Michelle L. Gaynor, Jacob B. Landis, Timothy K. O'Connor, Robert G. Laport, Jeff J. Doyle, Douglas E. Soltis, José Miguel Ponciano, Pamela S. Soltis","doi":"10.1002/aps3.11606","DOIUrl":"10.1002/aps3.11606","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Traditional methods of ploidal-level estimation are tedious; using DNA sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage sequence data for ploidy inference based on site-based heterozygosity have been developed. However, these approaches may require high-coverage sequence data, use inappropriate probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open-source R package that addresses the main shortcomings of current methods.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>nQuack performs model selection for improved ploidy predictions. Here, we implement expectation maximization algorithms with normal, beta, and beta-binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Inferring ploidy based on site-based heterozygosity alone is difficult. Even though nQuack is more accurate than similar methods, we suggest caution when relying on any site-based heterozygosity method to infer ploidy.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11606","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141721618","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}
Anoob Prakash, Thibaut Capblancq, Kathryn Shallows, David Saville, Deborah Landau, Chad Landress, Tal Jacobs, Stephen Keller
Premise
Global anthropogenic change threatens the health and productivity of forest ecosystems. Assisted migration and reforestation are tools to help mitigate these impacts. However, questions remain about how to approach sourcing seeds to ensure high establishment and future adaptability.
Methods
Using exome-capture sequencing, we demonstrate a computational approach to finding the best n-sets from a candidate list of seed sources that collectively achieve high genetic diversity (GD) and minimal genetic load (GL), while also increasing evolvability in quantitative traits. The benefits of this three-part strategy (diversity-load-evolvability) are to increase near-term establishment success while also boosting evolutionary potential to respond to future stressors. Members of The Nature Conservancy and the Central Appalachian Spruce Restoration Initiative planted 58,000 seedlings across 255 acres. A subset of seedlings was monitored for establishment success and variation in growth.
Results
The results show gains in GD relative to GL and increases in quantitative genetic variation in seedling growth for pooled vs. single-source restoration. No single “super source” was observed across planting sites; rather, monitoring results demonstrate that pooling of multiple sources helps achieve higher GD:GL and evolvability.
Discussion
Our study shows the potential for integrating genomics into local-scale restoration and the importance of building partnerships between academic researchers and applied conservation managers.
{"title":"Bringing genomics to the field: An integrative approach to seed sourcing for forest restoration","authors":"Anoob Prakash, Thibaut Capblancq, Kathryn Shallows, David Saville, Deborah Landau, Chad Landress, Tal Jacobs, Stephen Keller","doi":"10.1002/aps3.11600","DOIUrl":"10.1002/aps3.11600","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Global anthropogenic change threatens the health and productivity of forest ecosystems. Assisted migration and reforestation are tools to help mitigate these impacts. However, questions remain about how to approach sourcing seeds to ensure high establishment and future adaptability.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Using exome-capture sequencing, we demonstrate a computational approach to finding the best <i>n</i>-sets from a candidate list of seed sources that collectively achieve high genetic diversity (GD) and minimal genetic load (GL), while also increasing evolvability in quantitative traits. The benefits of this three-part strategy (diversity-load-evolvability) are to increase near-term establishment success while also boosting evolutionary potential to respond to future stressors. Members of The Nature Conservancy and the Central Appalachian Spruce Restoration Initiative planted 58,000 seedlings across 255 acres. A subset of seedlings was monitored for establishment success and variation in growth.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The results show gains in GD relative to GL and increases in quantitative genetic variation in seedling growth for pooled vs. single-source restoration. No single “super source” was observed across planting sites; rather, monitoring results demonstrate that pooling of multiple sources helps achieve higher GD:GL and evolvability.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our study shows the potential for integrating genomics into local-scale restoration and the importance of building partnerships between academic researchers and applied conservation managers.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11600","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441384","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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