Target sequence capture (Hyb-Seq) is a cost-effective sequencing strategy that employs RNA probes to enrich for specific genomic sequences. By targeting conserved low-copy orthologs, Hyb-Seq enables efficient phylogenomic investigations. Here, we present Asparagaceae1726—a Hyb-Seq probe set targeting 1726 low-copy nuclear genes for phylogenomics in the angiosperm family Asparagaceae—which will aid the often-challenging delineation and resolution of evolutionary relationships within Asparagaceae.
Methods
Here we describe and validate the Asparagaceae1726 probe set (https://github.com/bentzpc/Asparagaceae1726) in six of the seven subfamilies of Asparagaceae. We perform phylogenomic analyses with these 1726 loci and evaluate how inclusion of paralogs and bycatch plastome sequences can enhance phylogenomic inference with target-enriched data sets.
Results
We recovered at least 82% of target orthologs from all sampled taxa, and phylogenomic analyses resulted in strong support for all subfamilial relationships. Additionally, topology and branch support were congruent between analyses with and without inclusion of target paralogs, suggesting that paralogs had limited effect on phylogenomic inference.
Discussion
Asparagaceae1726 is effective across the family and enables the generation of robust data sets for phylogenomics of any Asparagaceae taxon. Asparagaceae1726 establishes a standardized set of loci for phylogenomic analysis in Asparagaceae, which we hope will be widely used for extensible and reproducible investigations of diversification in the family.
{"title":"Developing Asparagaceae1726: An Asparagaceae-specific probe set targeting 1726 loci for Hyb-Seq and phylogenomics in the family","authors":"Philip C. Bentz, Jim Leebens-Mack","doi":"10.1002/aps3.11597","DOIUrl":"10.1002/aps3.11597","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Target sequence capture (Hyb-Seq) is a cost-effective sequencing strategy that employs RNA probes to enrich for specific genomic sequences. By targeting conserved low-copy orthologs, Hyb-Seq enables efficient phylogenomic investigations. Here, we present Asparagaceae1726—a Hyb-Seq probe set targeting 1726 low-copy nuclear genes for phylogenomics in the angiosperm family Asparagaceae—which will aid the often-challenging delineation and resolution of evolutionary relationships within Asparagaceae.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here we describe and validate the Asparagaceae1726 probe set (https://github.com/bentzpc/Asparagaceae1726) in six of the seven subfamilies of Asparagaceae. We perform phylogenomic analyses with these 1726 loci and evaluate how inclusion of paralogs and bycatch plastome sequences can enhance phylogenomic inference with target-enriched data sets.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We recovered at least 82% of target orthologs from all sampled taxa, and phylogenomic analyses resulted in strong support for all subfamilial relationships. Additionally, topology and branch support were congruent between analyses with and without inclusion of target paralogs, suggesting that paralogs had limited effect on phylogenomic inference.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Asparagaceae1726 is effective across the family and enables the generation of robust data sets for phylogenomics of any Asparagaceae taxon. Asparagaceae1726 establishes a standardized set of loci for phylogenomic analysis in Asparagaceae, which we hope will be widely used for extensible and reproducible investigations of diversification in the family.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11443443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142364070","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":"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":"12 3","pages":""},"PeriodicalIF":2.4,"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":"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":"12 4","pages":""},"PeriodicalIF":2.4,"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":"12 3","pages":""},"PeriodicalIF":2.4,"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":"12 3","pages":""},"PeriodicalIF":2.4,"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":"12 4","pages":""},"PeriodicalIF":2.4,"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
<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
{"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":"12 3","pages":""},"PeriodicalIF":2.4,"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}
Raquel C. Pizzardo, Eimear Nic Lughadha, Juliana Gastaldello Rando, Félix Forest, Anselmo Nogueira, Luana S. Prochazka, Barnaby E. Walker, Thais Vasconcelos
Premise
Conservation policies typically focus on biodiversity hotspots. An alternative approach involves analyzing the evolutionary history of lineages in geographic areas along with their threat levels to guide conservation efforts. Mountains exhibit high levels of plant species richness and micro-endemism, and biogeographic studies commonly point to recent and rapid evolutionary radiations in these areas. Using a nearly endemic clade of legumes, our study evaluates conservation prioritization approaches in the campo rupestre, a Neotropical ecosystem associated with mountaintops that is located between two biodiversity hotspots.
Methods
We compared the EDGE and EDGE2 metrics, which combine the evolutionary distinctiveness and the extinction risk of a species in a single value. These metrics are compared with traditional metrics used to assess conservation priority, such as phylogenetic diversity.
Results
The EDGE values reported are lower than those of other studies using this metric, mostly due to the prevalence of threatened species with short phylogenetic branch lengths (low values of evolutionary distinctiveness). Certain areas of campo rupestre with relatively high phylogenetic diversity and EDGE values do not correspond to areas with high species richness, agreeing with previous studies on biodiversity hotspots.
Discussion
Our study highlights the necessity of conservation of the campo rupestres as well as advantages and disadvantages of using EDGE, EDGE2, and phylogenetic diversity for appropriate selection of conservation areas with rapid evolutionary radiations. The selection of the metrics will depend primarily on the life history of the focus group and the data availability, as well as the conservation approach.
{"title":"An assessment of methods to combine evolutionary history and conservation: A case study in the Brazilian campo rupestre","authors":"Raquel C. Pizzardo, Eimear Nic Lughadha, Juliana Gastaldello Rando, Félix Forest, Anselmo Nogueira, Luana S. Prochazka, Barnaby E. Walker, Thais Vasconcelos","doi":"10.1002/aps3.11587","DOIUrl":"10.1002/aps3.11587","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Conservation policies typically focus on biodiversity hotspots. An alternative approach involves analyzing the evolutionary history of lineages in geographic areas along with their threat levels to guide conservation efforts. Mountains exhibit high levels of plant species richness and micro-endemism, and biogeographic studies commonly point to recent and rapid evolutionary radiations in these areas. Using a nearly endemic clade of legumes, our study evaluates conservation prioritization approaches in the campo rupestre, a Neotropical ecosystem associated with mountaintops that is located between two biodiversity hotspots.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We compared the EDGE and EDGE2 metrics, which combine the evolutionary distinctiveness and the extinction risk of a species in a single value. These metrics are compared with traditional metrics used to assess conservation priority, such as phylogenetic diversity.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The EDGE values reported are lower than those of other studies using this metric, mostly due to the prevalence of threatened species with short phylogenetic branch lengths (low values of evolutionary distinctiveness). Certain areas of campo rupestre with relatively high phylogenetic diversity and EDGE values do not correspond to areas with high species richness, agreeing with previous studies on biodiversity hotspots.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our study highlights the necessity of conservation of the campo rupestres as well as advantages and disadvantages of using EDGE, EDGE2, and phylogenetic diversity for appropriate selection of conservation areas with rapid evolutionary radiations. The selection of the metrics will depend primarily on the life history of the focus group and the data availability, as well as the conservation approach.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11587","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141196449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jean Linsky, Amy Byrne, Vanessa Handley, Emily E. D. Coffey, Silvia Alvarez-Clare, Dan Crowley, Abby Meyer
The 2020 State of the World's Plants and Fungi report revealed that two in five plant species are threatened with extinction. Despite their diverse ecosystem services and myriad human uses, plants receive a fraction of the conservation resources directed at animal taxa. Several existing frameworks—including International Union for Conservation of Nature (IUCN) Specialist Groups, the American Public Gardens Association Plant Collections Network, and the Center for Plant Conservation National Collection of Endangered Plants—have spurred conservation action, but there remains an urgent need to scale up conservation efforts for the world's plants. Here, a new approach to coordinated conservation action for plant taxa is described: the Global Conservation Consortia (GCC). GCC catalyze institutions and experts to collaboratively develop and implement comprehensive strategies to prevent extinction of threatened plant groups. This review focuses on three tree-focused, U.S.-led consortia: cycads, magnolias, and oaks, but the GCC framework is applicable to other taxonomic groups. This review covers consortia design and implementation, provides conservation action case studies, and shares preliminary successes and challenges as this new and exciting approach to conservation is developed.
{"title":"Integrated plant conservation through the Global Conservation Consortia","authors":"Jean Linsky, Amy Byrne, Vanessa Handley, Emily E. D. Coffey, Silvia Alvarez-Clare, Dan Crowley, Abby Meyer","doi":"10.1002/aps3.11586","DOIUrl":"10.1002/aps3.11586","url":null,"abstract":"<p>The 2020 State of the World's Plants and Fungi report revealed that two in five plant species are threatened with extinction. Despite their diverse ecosystem services and myriad human uses, plants receive a fraction of the conservation resources directed at animal taxa. Several existing frameworks—including International Union for Conservation of Nature (IUCN) Specialist Groups, the American Public Gardens Association Plant Collections Network, and the Center for Plant Conservation National Collection of Endangered Plants—have spurred conservation action, but there remains an urgent need to scale up conservation efforts for the world's plants. Here, a new approach to coordinated conservation action for plant taxa is described: the Global Conservation Consortia (GCC). GCC catalyze institutions and experts to collaboratively develop and implement comprehensive strategies to prevent extinction of threatened plant groups. This review focuses on three tree-focused, U.S.-led consortia: cycads, magnolias, and oaks, but the GCC framework is applicable to other taxonomic groups. This review covers consortia design and implementation, provides conservation action case studies, and shares preliminary successes and challenges as this new and exciting approach to conservation is developed.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11586","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141114532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Joe Bellis, Matthew A. Albrecht, Joyce Maschinski, Oyomoare Osazuwa-Peters, Tina Stanley, Katherine D. Heineman
Premise
Reintroductions or translocations are an increasingly important activity to recover and conserve at-risk plant species. Yet because many are not published in the scientific literature, learning from previous attempts may often require considerable time and effort. The Center for Plant Conservation Reintroduction Database (CPCRD; https://saveplants.org/reintroduction-database/), a new centralized and standardized repository of U.S.-based plant reintroductions, aims to improve the efficiency and effectiveness of accessing data on rare plant reintroductions.
Methods
The CPCRD is the product of multiple efforts to assemble information on rare plant reintroductions in the United States. The database comprises a wealth of standardized data on the key stages of a reintroduction, from the planning and implementation phases, to monitoring and management techniques.
Results
The CPCRD is a dynamic resource, allowing data contributors to continually update their entries as projects progress. While contributions are ongoing, the CPCRD currently includes 460 projects involving 201 plant taxa, spanning diverse growth forms, ecosystems, and regions.
Discussion
The CPCRD and its well-documented and monitored projects provide a valuable practical resource for conservation practitioners, and have supported multiple scientific studies and contributed to the internationally recognized Center for Plant Conservation Best Practices Guidelines.
{"title":"Advancing the science and practice of rare plant conservation with the Center for Plant Conservation Reintroduction Database","authors":"Joe Bellis, Matthew A. Albrecht, Joyce Maschinski, Oyomoare Osazuwa-Peters, Tina Stanley, Katherine D. Heineman","doi":"10.1002/aps3.11583","DOIUrl":"10.1002/aps3.11583","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Reintroductions or translocations are an increasingly important activity to recover and conserve at-risk plant species. Yet because many are not published in the scientific literature, learning from previous attempts may often require considerable time and effort. The Center for Plant Conservation Reintroduction Database (CPCRD; https://saveplants.org/reintroduction-database/), a new centralized and standardized repository of U.S.-based plant reintroductions, aims to improve the efficiency and effectiveness of accessing data on rare plant reintroductions.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The CPCRD is the product of multiple efforts to assemble information on rare plant reintroductions in the United States. The database comprises a wealth of standardized data on the key stages of a reintroduction, from the planning and implementation phases, to monitoring and management techniques.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The CPCRD is a dynamic resource, allowing data contributors to continually update their entries as projects progress. While contributions are ongoing, the CPCRD currently includes 460 projects involving 201 plant taxa, spanning diverse growth forms, ecosystems, and regions.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>The CPCRD and its well-documented and monitored projects provide a valuable practical resource for conservation practitioners, and have supported multiple scientific studies and contributed to the internationally recognized Center for Plant Conservation Best Practices Guidelines.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11583","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140975163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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