Houyin Deng, Rong Huang, Ruping Wei, Runhui Wang, Shu Yan, Yousry A. El-Kassaby, Yuhan Sun, Yun Li, Huiquan Zheng
Premise
The impact of inbreeding on biological processes is well documented in individuals with severe inbreeding depression. However, the biological processes influencing the adaptive growth of normal selfed individuals are unknown. Here, we aimed to investigate how inbreeding affects gene expression for adaptive growth of normal selfed seedlings from a self-fertilizing parent in Chinese fir (Cunninghamia lanceolata).
Methods
Using RNA-seq data from above- and underground tissues of abnormal and normal selfed seedlings, we analyzed GO biological processes network. We also sequenced small RNAs in the aboveground tissues and measured the copy number variations (CNV) of the hub genes.
Results
Phenotypic fitness analysis revealed that the normal seedlings were better adapted than their abnormal counterparts. Upregulated differentially expressed genes (DEGs) were associated with development processes, and downregulated DEGs were mainly enriched in fundamental metabolism and stress response. Results of mRNA-miRNA parallel sequencing revealed that upregulated target genes were predominantly associated with development, highlighting their crucial role in phosphorylation in signal transduction networks. We also discovered a moderate correlation (0.1328 < R2 < 0.6257) between CNV and gene expression levels for three hub genes (TMKL1, GT2, and RHY1A).
Conclusions
We uncovered the key biological processes underpinning the growth of normal selfed seedlings and established the relationship between CNV and the expression levels of hub genes in selfed seedlings. Understanding the candidate genes involved in the growth of selfed seedlings will help us comprehend the genetic mechanisms behind inbreeding depression in the evolutionary biology of plants.
{"title":"Inbreeding in Chinese fir: Insights into the adaptive growth traits of selfed progeny from mRNA, miRNA, and copy number variation","authors":"Houyin Deng, Rong Huang, Ruping Wei, Runhui Wang, Shu Yan, Yousry A. El-Kassaby, Yuhan Sun, Yun Li, Huiquan Zheng","doi":"10.1002/ajb2.16393","DOIUrl":"10.1002/ajb2.16393","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The impact of inbreeding on biological processes is well documented in individuals with severe inbreeding depression. However, the biological processes influencing the adaptive growth of normal selfed individuals are unknown. Here, we aimed to investigate how inbreeding affects gene expression for adaptive growth of normal selfed seedlings from a self-fertilizing parent in Chinese fir (<i>Cunninghamia lanceolata</i>).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Using RNA-seq data from above- and underground tissues of abnormal and normal selfed seedlings, we analyzed GO biological processes network. We also sequenced small RNAs in the aboveground tissues and measured the copy number variations (CNV) of the hub genes.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Phenotypic fitness analysis revealed that the normal seedlings were better adapted than their abnormal counterparts. Upregulated differentially expressed genes (DEGs) were associated with development processes, and downregulated DEGs were mainly enriched in fundamental metabolism and stress response. Results of mRNA-miRNA parallel sequencing revealed that upregulated target genes were predominantly associated with development, highlighting their crucial role in phosphorylation in signal transduction networks. We also discovered a moderate correlation (0.1328 < <i>R</i><sup>2</sup> < 0.6257) between CNV and gene expression levels for three hub genes (<i>TMKL1</i>, <i>GT2</i>, and <i>RHY1A</i>).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>We uncovered the key biological processes underpinning the growth of normal selfed seedlings and established the relationship between CNV and the expression levels of hub genes in selfed seedlings. Understanding the candidate genes involved in the growth of selfed seedlings will help us comprehend the genetic mechanisms behind inbreeding depression in the evolutionary biology of plants.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":"111 9","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jessie A. Pelosi, Bethany A. Zumwalde, Weston L. Testo, Emily H. Kim, J. Gordon Burleigh, Emily B. Sessa
Premise
Reticulate evolution, often accompanied by polyploidy, is prevalent in plants, and particularly in the ferns. Resolving the resulting non-bifurcating histories remains a major challenge for plant phylogenetics. Here, we present a phylogenomic investigation into the complex evolutionary history of the vining ferns, Lygodium (Lygodiaceae, Schizaeales).
Methods
Using a targeted enrichment approach with the GoFlag 408 flagellate land plant probe set, we generated large nuclear and plastid sequence datasets for nearly all taxa in the genus and constructed the most comprehensive phylogeny of the family to date using concatenated maximum likelihood and coalescence approaches. We integrated this phylogeny with cytological and spore data to explore karyotype evolution and generate hypotheses about the origins of putative polyploids and hybrids.
Results
Our data and analyses support the origins of several putative allopolyploids (e.g., L. cubense, L. heterodoxum) and hybrids (e.g., L. ×fayae) and also highlight the potential prevalence of autopolyploidy in this clade (e.g., L. articulatum, L. flexuosum, and L. longifolium).
Conclusions
Our robust phylogenetic framework provides valuable insights into dynamic reticulate evolution in this clade and demonstrates the utility of target-capture data for resolving these complex relationships.
{"title":"All tangled up: Unraveling phylogenetics and reticulate evolution in the vining ferns, Lygodium (Schizaeales)","authors":"Jessie A. Pelosi, Bethany A. Zumwalde, Weston L. Testo, Emily H. Kim, J. Gordon Burleigh, Emily B. Sessa","doi":"10.1002/ajb2.16389","DOIUrl":"10.1002/ajb2.16389","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Reticulate evolution, often accompanied by polyploidy, is prevalent in plants, and particularly in the ferns. Resolving the resulting non-bifurcating histories remains a major challenge for plant phylogenetics. Here, we present a phylogenomic investigation into the complex evolutionary history of the vining ferns, <i>Lygodium</i> (Lygodiaceae, Schizaeales).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Using a targeted enrichment approach with the <i>GoFlag 408</i> flagellate land plant probe set, we generated large nuclear and plastid sequence datasets for nearly all taxa in the genus and constructed the most comprehensive phylogeny of the family to date using concatenated maximum likelihood and coalescence approaches. We integrated this phylogeny with cytological and spore data to explore karyotype evolution and generate hypotheses about the origins of putative polyploids and hybrids.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our data and analyses support the origins of several putative allopolyploids (e.g., <i>L. cubense, L. heterodoxum</i>) and hybrids (e.g., <i>L.</i> ×<i>fayae</i>) and also highlight the potential prevalence of autopolyploidy in this clade (e.g., <i>L. articulatum, L. flexuosum</i>, and <i>L. longifolium</i>).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our robust phylogenetic framework provides valuable insights into dynamic reticulate evolution in this clade and demonstrates the utility of target-capture data for resolving these complex relationships.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":"111 9","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ajb2.16389","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jean H. Burns, Katharine L. Stuble, Juliana S. Medeiros
<p>Combining ecological questions with evolutionary context generates novel insight into both ecology and evolution. However, our ability to draw broad inferences can be limited by the taxonomic diversity present within and across species at a site. Public gardens (including botanical gardens and arboreta) may focus solely on aesthetics in developing their gardens, but some public gardens include scientific inquiry and conservation at the core of their missions (Hohn, <span>2022</span>). These scientifically oriented public gardens follow community standards of excellence (Hohn, <span>2022</span>) to provide unique access to curated plant collections specifically designed to gather high levels of biodiversity, both among and within species, at a single geographic location. These research-grade collections include long-lived species cared for over many decades. Such public gardens have long histories of conducting and supporting research harnessing the power inherent in these diverse collections, including explorations of systematics, ecophysiology, and ecology. By bringing together species, as well as individuals within species, from across broad spatial ranges into a single site, these collections offer living repositories of diversity ripe for scientific exploration as de facto common gardens (Dosmann, <span>2006</span>; Dosmann and Groover, <span>2012</span>; Primack et al., <span>2021</span>).</p><p>The biodiversity curated by public gardens can offer a unique context for addressing questions at the intersection of ecology and evolution, such as <i>how does phylogenetic history shape plant trait evolution?</i> For example, Mason et al. (<span>2020</span>) explored seasonal trait shifts across 25 species of <i>Cornus</i> at the Arnold Arboretum (Boston, Massachusetts, USA) to ask whether there are tradeoffs among ecophysiological traits and how those traits correlate with home environment. They measured traits such as leaf chlorophyll content and leaf water content. By measuring plant traits across many species, they answered questions about ecophysiological trait evolution within a comparative phylogenetic framework. By doing so in a common garden, they controlled for much of the environmental variation that would otherwise confound a study across so many species, that occur in different habitats and locations in their native ranges. Their new analytical approaches simultaneously incorporated phylogenetic methods and within-species variation over time (Mason et al., <span>2020</span>). With this comparison, they demonstrated that traditional phylogenetic comparative approaches, which analyze a single trait mean per species, might come to erroneous conclusions about trait–trait correlations. For example, leaf nitrogen mostly declines through the growing season in <i>Cornus</i>, leading to changes in sign of correlations across the season (Mason et al., <span>2020</span>).</p><p>Plant–soil interactions are another growing area of research that
{"title":"Living collections: Biodiversity cultivated at public gardens has the power to connect ecological questions and evolutionary context","authors":"Jean H. Burns, Katharine L. Stuble, Juliana S. Medeiros","doi":"10.1002/ajb2.16394","DOIUrl":"10.1002/ajb2.16394","url":null,"abstract":"<p>Combining ecological questions with evolutionary context generates novel insight into both ecology and evolution. However, our ability to draw broad inferences can be limited by the taxonomic diversity present within and across species at a site. Public gardens (including botanical gardens and arboreta) may focus solely on aesthetics in developing their gardens, but some public gardens include scientific inquiry and conservation at the core of their missions (Hohn, <span>2022</span>). These scientifically oriented public gardens follow community standards of excellence (Hohn, <span>2022</span>) to provide unique access to curated plant collections specifically designed to gather high levels of biodiversity, both among and within species, at a single geographic location. These research-grade collections include long-lived species cared for over many decades. Such public gardens have long histories of conducting and supporting research harnessing the power inherent in these diverse collections, including explorations of systematics, ecophysiology, and ecology. By bringing together species, as well as individuals within species, from across broad spatial ranges into a single site, these collections offer living repositories of diversity ripe for scientific exploration as de facto common gardens (Dosmann, <span>2006</span>; Dosmann and Groover, <span>2012</span>; Primack et al., <span>2021</span>).</p><p>The biodiversity curated by public gardens can offer a unique context for addressing questions at the intersection of ecology and evolution, such as <i>how does phylogenetic history shape plant trait evolution?</i> For example, Mason et al. (<span>2020</span>) explored seasonal trait shifts across 25 species of <i>Cornus</i> at the Arnold Arboretum (Boston, Massachusetts, USA) to ask whether there are tradeoffs among ecophysiological traits and how those traits correlate with home environment. They measured traits such as leaf chlorophyll content and leaf water content. By measuring plant traits across many species, they answered questions about ecophysiological trait evolution within a comparative phylogenetic framework. By doing so in a common garden, they controlled for much of the environmental variation that would otherwise confound a study across so many species, that occur in different habitats and locations in their native ranges. Their new analytical approaches simultaneously incorporated phylogenetic methods and within-species variation over time (Mason et al., <span>2020</span>). With this comparison, they demonstrated that traditional phylogenetic comparative approaches, which analyze a single trait mean per species, might come to erroneous conclusions about trait–trait correlations. For example, leaf nitrogen mostly declines through the growing season in <i>Cornus</i>, leading to changes in sign of correlations across the season (Mason et al., <span>2020</span>).</p><p>Plant–soil interactions are another growing area of research that ","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":"111 9","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ajb2.16394","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Morphology has been the fundamental and most important source of information in biology. We strongly believe that in the current molecular era of biology, comparative morphology still has an important role to play in understanding life on Earth and ecosystem functioning, bridging the knowledge gap between evolution, systematics, and ecology.
{"title":"Comparative morphology at a crossroads","authors":"Julius Jeiter, Erik Smets","doi":"10.1002/ajb2.16392","DOIUrl":"10.1002/ajb2.16392","url":null,"abstract":"<p>Morphology has been the fundamental and most important source of information in biology. We strongly believe that in the current molecular era of biology, comparative morphology still has an important role to play in understanding life on Earth and ecosystem functioning, bridging the knowledge gap between evolution, systematics, and ecology.</p>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":"111 9","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ajb2.16392","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Intraspecific variation in flower microbiome composition can mediate pollination and reproduction, and so understanding the community assembly processes driving this variation is critical. Yet the relative importance of trait-based host filtering and dispersal in shaping among-species variation in floral microbiomes remains unknown.
Methods
Within two clades of Brassicaceae, we compared diversity and composition of floral microbiomes in natural populations of focal nickel and selenium hyperaccumulator species and two of their non-accumulating relatives. We assessed the relative strengths of floral elemental composition, plant phylogenetic distance (host filtering), and geography (dispersal) in driving floral microbiome composition.
Results
Species in the nickel hyperaccumulator clade had strongly divergent floral microbiomes, the most of that variation driven by floral elemental composition, followed by geographic distance between plant populations and, lastly, phylogenetic distance. Conversely, within the selenium hyperaccumulator clade, floral microbiome divergence was much lower among the species and elemental composition, geography, and plant phylogeny were far weaker determinants of microbiome variation.
Conclusions
Our results show that the strength of elemental hyperaccumulation's effect on floral microbiomes differs substantially among plant clades, possibly due to variation in elements as selective filters or in long-distance dispersal probability in different habitats.
{"title":"Hyperaccumulation of nickel but not selenium drives floral microbiome differentiation: A study with six species of Brassicaceae","authors":"Nevin P. Cullen, Tia-Lynn Ashman","doi":"10.1002/ajb2.16382","DOIUrl":"10.1002/ajb2.16382","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Intraspecific variation in flower microbiome composition can mediate pollination and reproduction, and so understanding the community assembly processes driving this variation is critical. Yet the relative importance of trait-based host filtering and dispersal in shaping among-species variation in floral microbiomes remains unknown.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Within two clades of Brassicaceae, we compared diversity and composition of floral microbiomes in natural populations of focal nickel and selenium hyperaccumulator species and two of their non-accumulating relatives. We assessed the relative strengths of floral elemental composition, plant phylogenetic distance (host filtering), and geography (dispersal) in driving floral microbiome composition.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Species in the nickel hyperaccumulator clade had strongly divergent floral microbiomes, the most of that variation driven by floral elemental composition, followed by geographic distance between plant populations and, lastly, phylogenetic distance. Conversely, within the selenium hyperaccumulator clade, floral microbiome divergence was much lower among the species and elemental composition, geography, and plant phylogeny were far weaker determinants of microbiome variation.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our results show that the strength of elemental hyperaccumulation's effect on floral microbiomes differs substantially among plant clades, possibly due to variation in elements as selective filters or in long-distance dispersal probability in different habitats.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":"111 9","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ajb2.16382","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In hermaphroditic plants, the evolution of self-fertilization is driven by two major forces; the cost of outcrossing or Fisher's automatic advantage of selfing and inbreeding depression. Seminal theoretical works have established that an inbreeding depression threshold of 0.5 governs the evolution. Below that threshold, selfing evolves, above that, outcrossing evolves. Does this threshold apply to cleistogamous plants?
Methods
I developed a model using a Lloydian approach to analyze the evolution of cleistogamy.
Results
I showed that the inbreeding depression threshold does not apply in cleistogamous species, and that because cleistogamous (closed) flowers do not export pollen, Fisher's advantage of selfing is totally cancelled.
Conclusions
In line with model predictions, I discuss the fact that cleistogamous species often exhibit low inbreeding depression in empirical studies.
{"title":"Fisher's automatic advantage of self-fertilization does not apply in cleistogamous species","authors":"Pierre-Olivier Cheptou","doi":"10.1002/ajb2.16390","DOIUrl":"10.1002/ajb2.16390","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>In hermaphroditic plants, the evolution of self-fertilization is driven by two major forces; the cost of outcrossing or Fisher's automatic advantage of selfing and inbreeding depression. Seminal theoretical works have established that an inbreeding depression threshold of 0.5 governs the evolution. Below that threshold, selfing evolves, above that, outcrossing evolves. Does this threshold apply to cleistogamous plants?</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>I developed a model using a Lloydian approach to analyze the evolution of cleistogamy.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>I showed that the inbreeding depression threshold does not apply in cleistogamous species, and that because cleistogamous (closed) flowers do not export pollen, Fisher's advantage of selfing is totally cancelled.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>In line with model predictions, I discuss the fact that cleistogamous species often exhibit low inbreeding depression in empirical studies.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":"111 9","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141981523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yu-Hsin Tseng, Li-Yaung Kuo, Israel Borokini, Susan Fawcett
Premise
Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape.
Methods
By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework.
Results
We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other.
Conclusions
The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages.
{"title":"The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae","authors":"Yu-Hsin Tseng, Li-Yaung Kuo, Israel Borokini, Susan Fawcett","doi":"10.1002/ajb2.16388","DOIUrl":"10.1002/ajb2.16388","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":"111 8","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ajb2.16388","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cameron H. Amos, Bryce A. Richardson, Sarah Barga, Francis F. Kilkenny, R. Kasten Dumroese
Premise
Intraspecific variation in drought resistance traits, such as drought escape, appear to be frequent within wild, ruderal forb species. Understanding how these traits are arrayed across the landscape, particularly in association with climate, is critical to developing forbs for wildland restoration programs. Use of forbs is requisite for maintaining biological diversity and ecological services.
Methods
Using 6074 greenhouse-grown Chaenactis douglasii seedlings from 95 wild, seed-sourced populations across the western United States, we recorded bolting phenology and estimated genome size using flow cytometry. Mixed-effects regression models were used to assess whether climate of seed origin was predictive for bolting phenology and genome size.
Results
Variation in bolting, reflecting an annual vs. perennial lifespan in this species, was observed in 8.7% of the plants, with bolting plants disproportionately occurring in locations with warm, arid climates. Populations with increasing heat and aridity were positively correlated with observed bolting (r = 0.61, p < 0.0001). About one-third (22%) of the total (61%) lifespan variation was attributed to seed source climate and annual heat moisture index, a measure of aridity. Genome size had no significant effect on bolting. Projected climate modeling for mid-century (2041–2070) supports an increasing occurrence of annual lifespan.
Conclusions
Our analyses support a drought escape, bet-hedging strategy in C. douglasii. Populations exposed to greater aridity exhibited a higher proportion of individuals with an annual lifespan. Drought escape leading to an annual lifespan can affect how seeds are propagated and deployed for climate-informed restoration.
{"title":"Annual-perennial lifespan variation in Chaenactis douglasii suggests a drought escape strategy in warm-arid environments","authors":"Cameron H. Amos, Bryce A. Richardson, Sarah Barga, Francis F. Kilkenny, R. Kasten Dumroese","doi":"10.1002/ajb2.16391","DOIUrl":"10.1002/ajb2.16391","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Intraspecific variation in drought resistance traits, such as drought escape, appear to be frequent within wild, ruderal forb species. Understanding how these traits are arrayed across the landscape, particularly in association with climate, is critical to developing forbs for wildland restoration programs. Use of forbs is requisite for maintaining biological diversity and ecological services.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Using 6074 greenhouse-grown <i>Chaenactis douglasii</i> seedlings from 95 wild, seed-sourced populations across the western United States, we recorded bolting phenology and estimated genome size using flow cytometry. Mixed-effects regression models were used to assess whether climate of seed origin was predictive for bolting phenology and genome size.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Variation in bolting, reflecting an annual vs. perennial lifespan in this species, was observed in 8.7% of the plants, with bolting plants disproportionately occurring in locations with warm, arid climates. Populations with increasing heat and aridity were positively correlated with observed bolting (<i>r</i> = 0.61, <i>p</i> < 0.0001). About one-third (22%) of the total (61%) lifespan variation was attributed to seed source climate and annual heat moisture index, a measure of aridity. Genome size had no significant effect on bolting. Projected climate modeling for mid-century (2041–2070) supports an increasing occurrence of annual lifespan.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our analyses support a drought escape, bet-hedging strategy in <i>C. douglasii</i>. Populations exposed to greater aridity exhibited a higher proportion of individuals with an annual lifespan. Drought escape leading to an annual lifespan can affect how seeds are propagated and deployed for climate-informed restoration.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":"111 9","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141911302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Silvija Milosavljevic, Felipe Kauai, Frederik Mortier, Yves Van de Peer, Dries Bonte
Premise
Whole-genome duplication (WGD, polyploidization) has been identified as a driver of genetic and phenotypic novelty, having pervasive consequences for the evolution of lineages. While polyploids are widespread, especially among plants, the long-term establishment of polyploids is exceedingly rare. Genome doubling commonly results in increased cell sizes and metabolic expenses, which may be sufficient to modulate polyploid establishment in environments where their diploid ancestors thrive.
Methods
We developed a mechanistic simulation model of photosynthetic individuals to test whether changes in size and metabolic efficiency allow autopolyploids to coexist with, or even invade, ancestral diploid populations. Central to the model is metabolic efficiency, which determines how energy obtained from size-dependent photosynthetic production is allocated to basal metabolism as opposed to somatic and reproductive growth. We expected neopolyploids to establish successfully if they have equal or higher metabolic efficiency as diploids or to adapt their life history to offset metabolic inefficiency.
Results
Polyploid invasion was observed across a wide range of metabolic efficiency differences between polyploids and diploids. Polyploids became established in diploid populations even when they had a lower metabolic efficiency, which was facilitated by recurrent formation. Competition for nutrients is a major driver of population dynamics in this model. Perenniality did not qualitatively affect the relative metabolic efficiency from which tetraploids tended to establish.
Conclusions
Feedback between size-dependent metabolism and energy allocation generated size and age differences between plants with different ploidies. We demonstrated that even small changes in metabolic efficiency are sufficient for the establishment of polyploids.
{"title":"A metabolic perspective on polyploid invasion and the emergence of life histories: Insights from a mechanistic model","authors":"Silvija Milosavljevic, Felipe Kauai, Frederik Mortier, Yves Van de Peer, Dries Bonte","doi":"10.1002/ajb2.16387","DOIUrl":"10.1002/ajb2.16387","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Whole-genome duplication (WGD, polyploidization) has been identified as a driver of genetic and phenotypic novelty, having pervasive consequences for the evolution of lineages. While polyploids are widespread, especially among plants, the long-term establishment of polyploids is exceedingly rare. Genome doubling commonly results in increased cell sizes and metabolic expenses, which may be sufficient to modulate polyploid establishment in environments where their diploid ancestors thrive.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We developed a mechanistic simulation model of photosynthetic individuals to test whether changes in size and metabolic efficiency allow autopolyploids to coexist with, or even invade, ancestral diploid populations. Central to the model is metabolic efficiency, which determines how energy obtained from size-dependent photosynthetic production is allocated to basal metabolism as opposed to somatic and reproductive growth. We expected neopolyploids to establish successfully if they have equal or higher metabolic efficiency as diploids or to adapt their life history to offset metabolic inefficiency.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Polyploid invasion was observed across a wide range of metabolic efficiency differences between polyploids and diploids. Polyploids became established in diploid populations even when they had a lower metabolic efficiency, which was facilitated by recurrent formation. Competition for nutrients is a major driver of population dynamics in this model. Perenniality did not qualitatively affect the relative metabolic efficiency from which tetraploids tended to establish.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Feedback between size-dependent metabolism and energy allocation generated size and age differences between plants with different ploidies. We demonstrated that even small changes in metabolic efficiency are sufficient for the establishment of polyploids.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":"111 8","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141900632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alberto Aleman, Maria Clara Arteaga, Jaime Gasca-Pineda, Rafael Bello-Bedoy
Premise
Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial–interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is Yucca, with Y. valida having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence.
Methods
We assembled 4411 SNPs from 147 plants of Y. valida throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species.
Results
Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of Y. valida and its sister species.
Conclusions
Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in Y. valida.
{"title":"Divergent lineages in a young species: The case of datilillo (Yucca valida), a broadly distributed plant from the Baja California Peninsula","authors":"Alberto Aleman, Maria Clara Arteaga, Jaime Gasca-Pineda, Rafael Bello-Bedoy","doi":"10.1002/ajb2.16385","DOIUrl":"10.1002/ajb2.16385","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial–interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is <i>Yucca</i>, with <i>Y. valida</i> having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We assembled 4411 SNPs from 147 plants of <i>Y. valida</i> throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of <i>Y. valida</i> and its sister species.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in <i>Y. valida</i>.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":"111 9","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141900633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号