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":null,"pages":null},"PeriodicalIF":2.7,"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":null,"pages":null},"PeriodicalIF":2.7,"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":null,"pages":null},"PeriodicalIF":2.7,"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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":2.7,"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}
Krystalyn Edwards-Calma, Laura Jiménez, Rosana Zenil-Ferguson, Karolina Heyduk, Miles K. Thomas, Carrie M. Tribble
Premise
Competition from naturalized species and habitat loss are common threats to native biodiversity and may act synergistically to increase competition for decreasing habitat availability. We use Hawaiian dryland ferns as a model for the interactions between land-use change and competition from naturalized species in determining habitat availability.
Methods
We used fine-resolution climatic variables and carefully curated occurrence data from herbaria and community science repositories to estimate the distributions of Hawaiian dryland ferns. We quantified the degree to which naturalized ferns tend to occupy areas suitable for native species and mapped the remaining available habitat given land-use change.
Results
Of all native species, Doryopteris angelica had the lowest percentage of occurrences of naturalized species in its suitable area while D. decora had the highest. However, all Doryopteris spp. had a higher percentage overlap, while Pellaea ternifolia had a lower percentage overlap, than expected by chance. Doryopteris decora and D. decipiens had the lowest proportions (<20%) of suitable area covering native habitat.
Discussion
Areas characterized by shared environmental preferences of native and naturalized ferns may decrease due to human development and fallowed agricultural lands. Our study demonstrates the value of place-based application of a recently developed correlative ecological niche modeling approach for conservation risk assessment in a rapidly changing and urbanized island ecosystem.
{"title":"Conservation applications of niche modeling: Native and naturalized ferns may compete for limited Hawaiian dryland habitat","authors":"Krystalyn Edwards-Calma, Laura Jiménez, Rosana Zenil-Ferguson, Karolina Heyduk, Miles K. Thomas, Carrie M. Tribble","doi":"10.1002/aps3.11598","DOIUrl":"https://doi.org/10.1002/aps3.11598","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Competition from naturalized species and habitat loss are common threats to native biodiversity and may act synergistically to increase competition for decreasing habitat availability. We use Hawaiian dryland ferns as a model for the interactions between land-use change and competition from naturalized species in determining habitat availability.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We used fine-resolution climatic variables and carefully curated occurrence data from herbaria and community science repositories to estimate the distributions of Hawaiian dryland ferns. We quantified the degree to which naturalized ferns tend to occupy areas suitable for native species and mapped the remaining available habitat given land-use change.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Of all native species, <i>Doryopteris angelica</i> had the lowest percentage of occurrences of naturalized species in its suitable area while <i>D. decora</i> had the highest. However, all <i>Doryopteris</i> spp. had a higher percentage overlap, while <i>Pellaea ternifolia</i> had a lower percentage overlap, than expected by chance. <i>Doryopteris decora</i> and <i>D. decipiens</i> had the lowest proportions (<i><</i>20%) of suitable area covering native habitat.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Areas characterized by shared environmental preferences of native and naturalized ferns may decrease due to human development and fallowed agricultural lands. Our study demonstrates the value of place-based application of a recently developed correlative ecological niche modeling approach for conservation risk assessment in a rapidly changing and urbanized island ecosystem.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11598","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441365","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}
Allopolyploidy—a hybridization-induced whole-genome duplication event—has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. with their homoeolog in allopolyploids varies across taxa, and methods to detect homoeologous gene flow (HGF) are needed to understand how HGF has shaped polyploid lineages.
Methods
The ABBA-BABA test represents a classic method for detecting introgression between closely related species, but here we developed a modified use of the ABBA-BABA test to characterize the extent and direction of HGF in allotetraploid Coffea arabica.
Results
We found that HGF is abundant in the C. arabica genome, with both subgenomes serving as donors and recipients of variation. We also found that HGF is highly maternally biased in plastid-targeted—but not mitochondrial-targeted—genes, as would be expected if plastid–nuclear incompatibilities exist between the two parent species.
Discussion
Together, our analyses provide a simple framework for detecting HGF and new evidence consistent with selection favoring overwriting of paternally derived alleles by maternally derived alleles to ameliorate plastid–nuclear incompatibilities. Natural selection therefore appears to shape the direction and intensity of HGF in allopolyploid coffee, indicating that cytoplasmic inheritance has long-term consequences for polyploid lineages.
{"title":"Genome-wide patterns of homoeologous gene flow in allotetraploid coffee","authors":"Andre J. Ortiz, Joel Sharbrough","doi":"10.1002/aps3.11584","DOIUrl":"https://doi.org/10.1002/aps3.11584","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Allopolyploidy—a hybridization-induced whole-genome duplication event—has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. with their homoeolog in allopolyploids varies across taxa, and methods to detect homoeologous gene flow (HGF) are needed to understand how HGF has shaped polyploid lineages.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The ABBA-BABA test represents a classic method for detecting introgression between closely related species, but here we developed a modified use of the ABBA-BABA test to characterize the extent and direction of HGF in allotetraploid <i>Coffea arabica</i>.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We found that HGF is abundant in the <i>C. arabica</i> genome, with both subgenomes serving as donors and recipients of variation. We also found that HGF is highly maternally biased in plastid-targeted—but not mitochondrial-targeted—genes, as would be expected if plastid–nuclear incompatibilities exist between the two parent species.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Together, our analyses provide a simple framework for detecting HGF and new evidence consistent with selection favoring overwriting of paternally derived alleles by maternally derived alleles to ameliorate plastid–nuclear incompatibilities. Natural selection therefore appears to shape the direction and intensity of HGF in allopolyploid coffee, indicating that cytoplasmic inheritance has long-term consequences for polyploid lineages.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11584","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142045281","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}
Alexander G. Linan, Roy E. Gereau, Rebecca Sucher, Fandey H. Mashimba, Burgund Bassuner, Andrew Wyatt, Christine E. Edwards
Premise
Although ex situ collections of threatened plants are most useful when they contain maximal genetic variation, the conservation and maintenance of genetic diversity in collections are often poorly known. We present a case study using population genomic analyses of an ex situ collection of Karomia gigas, a critically endangered tropical tree from Tanzania. Only ~43 individuals are known in two wild populations, and ex situ collections containing 34 individuals were established in two sites from wild-collected seed. The study aimed to understand how much diversity is represented in the collection, analyze the parentage of ex situ individuals, and identify efficient strategies to capture and maintain genetic diversity.
Methods
We genotyped all known individuals using a 2b-RADseq approach, compared genetic diversity in wild populations and ex situ collections, and conducted parentage analysis of the collections.
Results
Wild populations were found to have greater levels of genetic diversity than ex situ populations as measured by number of private alleles, number of polymorphic sites, observed and expected heterozygosity, nucleotide diversity, and allelic richness. In addition, only 32.6% of wild individuals are represented ex situ and many individuals were found to be the product of selfing by a single wild individual.
Discussion
Population genomic analyses provided important insights into the conservation of genetic diversity in K. gigas, identifying gaps and inefficiencies, but also highlighting strategies to conserve genetic diversity ex situ. Genomic analyses provide essential information to ensure that collections effectively conserve genetic diversity in threatened tropical trees.
{"title":"Capturing and managing genetic diversity in ex situ collections of threatened tropical trees: A case study in Karomia gigas","authors":"Alexander G. Linan, Roy E. Gereau, Rebecca Sucher, Fandey H. Mashimba, Burgund Bassuner, Andrew Wyatt, Christine E. Edwards","doi":"10.1002/aps3.11589","DOIUrl":"10.1002/aps3.11589","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Although ex situ collections of threatened plants are most useful when they contain maximal genetic variation, the conservation and maintenance of genetic diversity in collections are often poorly known. We present a case study using population genomic analyses of an ex situ collection of <i>Karomia gigas</i>, a critically endangered tropical tree from Tanzania. Only ~43 individuals are known in two wild populations, and ex situ collections containing 34 individuals were established in two sites from wild-collected seed. The study aimed to understand how much diversity is represented in the collection, analyze the parentage of ex situ individuals, and identify efficient strategies to capture and maintain genetic diversity.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We genotyped all known individuals using a 2b-RADseq approach, compared genetic diversity in wild populations and ex situ collections, and conducted parentage analysis of the collections.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Wild populations were found to have greater levels of genetic diversity than ex situ populations as measured by number of private alleles, number of polymorphic sites, observed and expected heterozygosity, nucleotide diversity, and allelic richness. In addition, only 32.6% of wild individuals are represented ex situ and many individuals were found to be the product of selfing by a single wild individual.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Population genomic analyses provided important insights into the conservation of genetic diversity in <i>K. gigas</i>, identifying gaps and inefficiencies, but also highlighting strategies to conserve genetic diversity ex situ. Genomic analyses provide essential information to ensure that collections effectively conserve genetic diversity in threatened tropical trees.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11589","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141378256","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}
Josephine Elena Reek, Janneke Hille Ris Lambers, Eléonore Perret, Alana R. O. Chin
Premise
To improve forest conservation monitoring, we developed a protocol to automatically count and identify the seeds of plant species with minimal resource requirements, making the process more efficient and less dependent on human operators.
Methods and Results
Seeds from six North American conifer tree species were separated from leaf litter and imaged on a flatbed scanner. In the most successful species-classification approach, an ImageJ macro automatically extracted measurements for random forest classification in the software R. The method allows for good classification accuracy, and the same process can be used to train the model on other species.
Conclusions
This protocol is an adaptable tool for efficient and consistent identification of seed species or potentially other objects. Automated seed classification is efficient and inexpensive, making it a practical solution that enhances the feasibility of large-scale monitoring projects in conservation biology.
为了改进森林保护监测工作，我们开发了一种自动计数和识别植物种子的方案，只需最少的资源，从而提高了工作效率，减少了对人工操作的依赖。在最成功的物种分类方法中，ImageJ 宏自动提取测量值，用于 R 软件中的随机森林分类。该方法具有很高的分类准确性，同样的过程可用于训练其他物种的模型。种子自动分类既高效又廉价，是一种实用的解决方案，提高了保护生物学大规模监测项目的可行性。
{"title":"Seed classification with random forest models","authors":"Josephine Elena Reek, Janneke Hille Ris Lambers, Eléonore Perret, Alana R. O. Chin","doi":"10.1002/aps3.11596","DOIUrl":"10.1002/aps3.11596","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>To improve forest conservation monitoring, we developed a protocol to automatically count and identify the seeds of plant species with minimal resource requirements, making the process more efficient and less dependent on human operators.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Seeds from six North American conifer tree species were separated from leaf litter and imaged on a flatbed scanner. In the most successful species-classification approach, an ImageJ macro automatically extracted measurements for random forest classification in the software R. The method allows for good classification accuracy, and the same process can be used to train the model on other species.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This protocol is an adaptable tool for efficient and consistent identification of seed species or potentially other objects. Automated seed classification is efficient and inexpensive, making it a practical solution that enhances the feasibility of large-scale monitoring projects in conservation biology.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11596","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141384729","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}
Rosa Ramirez-Castillo, Claudio Palma-Rojas, Pedro Jara Seguel, Amanda L. Grusz, Cristian Araya-Jaime
Premise
Cytotaxonomy employs chromosome visualization to study organismal relationships and evolution. Despite the critical value of cytogenetic data, cytotypes are lacking for many plant groups. Here, we present an improved approach for visualizing mitotic chromosomes in ferns, a key lineage of land plants, using the dividing cells of unfurling croziers (fiddleheads).
Methods and Results
Our modified mitotic chromosome preparation incorporates a brief pectinase–cellulase pretreatment, as well as colchicine fixation and the Feulgen reaction to improve the staining and separation of mitotic chromosomes. To demonstrate this easy and efficient assessment, we determined the sporophytic (2n) chromosome number for three fern species: Cheilanthes mollis (2n = 60), Cheilanthes hypoleuca (2n = 120), and Nephrolepis cordifolia (2n = 82).
Conclusions
The new method presented here improves visualizations of mitotic chromosomes from the dividing nuclei of young fern croziers. Fiddleheads are widely accessible in nature and in living collections worldwide, and this modified approach increases their suitability for fern cytotaxonomic studies.
{"title":"Unfurling an improved method for visualizing mitotic chromosomes in ferns","authors":"Rosa Ramirez-Castillo, Claudio Palma-Rojas, Pedro Jara Seguel, Amanda L. Grusz, Cristian Araya-Jaime","doi":"10.1002/aps3.11588","DOIUrl":"10.1002/aps3.11588","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Cytotaxonomy employs chromosome visualization to study organismal relationships and evolution. Despite the critical value of cytogenetic data, cytotypes are lacking for many plant groups. Here, we present an improved approach for visualizing mitotic chromosomes in ferns, a key lineage of land plants, using the dividing cells of unfurling croziers (fiddleheads).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Our modified mitotic chromosome preparation incorporates a brief pectinase–cellulase pretreatment, as well as colchicine fixation and the Feulgen reaction to improve the staining and separation of mitotic chromosomes. To demonstrate this easy and efficient assessment, we determined the sporophytic (2<i>n</i>) chromosome number for three fern species: <i>Cheilanthes mollis</i> (2<i>n</i> = 60), <i>Cheilanthes hypoleuca</i> (2<i>n</i> = 120), and <i>Nephrolepis cordifolia</i> (2<i>n</i> = 82)<i>.</i></p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The new method presented here improves visualizations of mitotic chromosomes from the dividing nuclei of young fern croziers. Fiddleheads are widely accessible in nature and in living collections worldwide, and this modified approach increases their suitability for fern cytotaxonomic studies.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11588","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141388056","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}
Christopher P. Krieg, Carrie M. Tribble, Randall Long
Evolution has generated an extraordinary diversity of life on Earth that drives the function of natural ecosystems (Xu et al., 2020), human cultures (Clark et al., 2014), and economies (Hanley and Perrings, 2019; Paul et al., 2020). Plants are the most dominant life form on Earth (Bar-On et al., 2018) and the decline of plant diversity has caused drastic shifts in natural ecosystems (Pugnaire et al., 2019), resulting in a loss of hundreds of billions of dollars (USD) per year from the global economy (Austin et al., 2020; Diagne et al., 2021). 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, 2023). 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.
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. (2024) 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. (2024), 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
{"title":"From theory to practice: New innovations and their application in conservation biology","authors":"Christopher P. Krieg, Carrie M. Tribble, 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}
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