American Journal of Botany最新文献

{"title":"Annual-perennial lifespan variation in Chaenactis douglasii suggests a drought escape strategy in warm-arid environments","authors":"Cameron H. Amos,&nbsp;Bryce A. Richardson,&nbsp;Sarah Barga,&nbsp;Francis F. Kilkenny,&nbsp;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> &lt; 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":null,"pages":null},"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}

{"title":"A metabolic perspective on polyploid invasion and the emergence of life histories: Insights from a mechanistic model","authors":"Silvija Milosavljevic,&nbsp;Felipe Kauai,&nbsp;Frederik Mortier,&nbsp;Yves Van de Peer,&nbsp;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":null,"pages":null},"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}

{"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,&nbsp;Maria Clara Arteaga,&nbsp;Jaime Gasca-Pineda,&nbsp;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":null,"pages":null},"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}

{"title":"Phylogenetic systematics of Vigna sensu stricto in the context of Physostigma and allies","authors":"Dasha M. Horton,&nbsp;Yonas Feleke,&nbsp;Remy S. Pasquet,&nbsp;Firouzeh Javadi,&nbsp;Kaycie A. Melville,&nbsp;Alfonso Delgado-Salinas,&nbsp;Mats Thulin,&nbsp;Richard F. Mithen,&nbsp;Paul Gepts,&nbsp;Ashley N. Egan","doi":"10.1002/ajb2.16381","DOIUrl":"10.1002/ajb2.16381","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p><i>Vigna</i> includes economically vital crops and wild species. Molecular systematic studies of <i>Vigna</i> species resulted in generic segregates of many New World (NW) species. However, limited Old World (OW) sampling left questions regarding inter- and intraspecific relationships in <i>Vigna</i> s.s.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>African species, including the putative sister genus <i>Physostigma</i>, were comprehensively sampled within the context of NW relatives. Maximum likelihood and Bayesian inference analyses of the chloroplast <i>matK-trnK</i> and nuclear ribosomal ITS/5.8 S (ITS) DNA regions were undertaken to resolve OW <i>Vigna</i> taxonomic questions. Divergence dates were estimated using BEAST to date key nodes in the phylogeny.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Analyses of <i>matK</i> and ITS data supported five clades of <i>Vigna</i> s.s.: subg. <i>Lasiospron</i>, a reduced subg. <i>Vigna</i>, subg. <i>Haydonia</i>, subg. <i>Ceratotropis</i>, an enlarged subg. <i>Plectrotropis</i>, and a clade including <i>V. kirkii</i> and <i>V. stenophylla</i>. Genome size estimates of 601 Mb for <i>V. kirkii</i> are near the overall mean of the genus, whereas <i>V. stenophylla</i> had a larger genome (810 Mb), similar to some <i>Vigna</i> subg. <i>Ceratotropis</i> or <i>Plectrotropis</i> species.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Former subg. <i>Vigna</i> is reduced to yellow- and blue-flowered species and subg. <i>Plectrotropis</i> is enlarged to mostly all white-, pink-, and purple-flowered species. The age of the split between NW and OW <i>Vigna</i> lineages is ~6–7 Myr. Genome size estimates cannot rule out a polyploid or hybrid origin for <i>V. stenophylla</i>, potentially involving extinct lineage ancestors of <i>Vigna</i> subg. <i>Ceratotropis</i> or <i>Plectrotropis</i>, as indicated by network and phylogenetic analyses. Taxonomic revisions are suggested based on these results.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141896551","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}

{"title":"Little evidence for homoeologous gene conversion and homoeologous exchange events in Gossypium allopolyploids","authors":"Justin L. Conover,&nbsp;Corrinne E. Grover,&nbsp;Joel Sharbrough,&nbsp;Daniel B. Sloan,&nbsp;Daniel G. Peterson,&nbsp;Jonathan F. Wendel","doi":"10.1002/ajb2.16386","DOIUrl":"10.1002/ajb2.16386","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>A complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting in either crossover (homoeologous exchanges) or non-crossover products (homoeologous gene conversion). Homoeologous gene conversion was first described in cotton by comparing SNP patterns in sequences from two diploid progenitors with those from the allopolyploid subgenomes. These analyses, however, did not explicitly consider other evolutionary scenarios that may give rise to similar SNP patterns as homoeologous gene conversion, creating uncertainties about the reality of the inferred gene conversion events.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here, we use an expanded phylogenetic sampling of high-quality genome assemblies from seven allopolyploid <i>Gossypium</i> species (all derived from the same polyploidy event), four diploid species (two closely related to each subgenome), and a diploid outgroup to derive a robust method for identifying potential genomic regions of gene conversion and homoeologous exchange.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We found little evidence for homoeologous gene conversion in allopolyploid cottons, and that only two of the 40 best-supported events were shared by more than one species. We did, however, reveal a single, shared homoeologous exchange event at one end of chromosome 1, which occurred shortly after allopolyploidization but prior to divergence of the descendant species.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Overall, our analyses demonstrated that homoeologous gene conversion and homoeologous exchanges are uncommon in <i>Gossypium</i>, affecting between zero and 24 genes per subgenome (0.0–0.065%) across the seven species. More generally, we highlighted the potential problems of using simple four-taxon tests to investigate patterns of homoeologous gene conversion in established allopolyploids.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ajb2.16386","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141896550","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}

{"title":"Early Eocene infructescences from Argentine Patagonia expand the biogeography of Malvoideae","authors":"Caroline Siegert,&nbsp;Maria A. Gandolfo,&nbsp;Peter Wilf","doi":"10.1002/ajb2.16384","DOIUrl":"10.1002/ajb2.16384","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Fossil infructescences and isolated fruits with characters of Malvoideae, a subfamily of Malvaceae (mallow family), were collected from early Eocene sediments in Chubut, Argentina. The main goals of this research are to describe and place these fossils systematically, and to explore their biogeographical implications.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Fossils were collected at the Laguna del Hunco site, Huitrera Formation, Chubut, Patagonia, Argentina. They were prepared, photographed, and compared with extant and fossil infructescences and fruits of various families using herbarium material and literature.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The infructescences are panicles with alternate arrangement of fruits. They bear the fruits on short pedicels that are subtended by a bract; the fruits display an infracarpelar disk and split to the base into five ovate sections interpreted as mericarps. Each mericarp is characterized by an acute apex and the presence of a longitudinal ridge. The isolated fruits show the same features as those on the infructescences. The fossils share unique features with members of the cosmopolitan family Malvaceae, subfamily Malvoideae.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The fossils have a unique combination of characters that does not conform to any previously described genus, justifying the erection of a new genus and species, <i>Uiher karuen</i>. This new taxon constitutes the first known Malvoideae reproductive fossils of the Southern Hemisphere, expanding the distribution of Malvoideae during the early Eocene.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141878170","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}

{"title":"The immediate metabolomic effects of whole-genome duplication in the greater duckweed, Spirodela polyrhiza","authors":"Tian Wu,&nbsp;Quinten Bafort,&nbsp;Frederik Mortier,&nbsp;Fabricio Almeida-Silva,&nbsp;Annelore Natran,&nbsp;Yves Van de Peer","doi":"10.1002/ajb2.16383","DOIUrl":"10.1002/ajb2.16383","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>In plants, whole-genome duplication (WGD) is a common mutation with profound evolutionary potential. Given the costs associated with a superfluous genome copy, polyploid establishment is enigmatic. However, in the right environment, immediate phenotypic changes following WGD can facilitate establishment. Metabolite abundances are the direct output of the cell's regulatory network and determine much of the impact of environmental and genetic change on the phenotype. While it is well known that an increase in the bulk amount of genetic material can increase cell size, the impact of gene dosage multiplication on the metabolome remains largely unknown.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We used untargeted metabolomics on four genetically distinct diploid-neoautotetraploid pairs of the greater duckweed, <i>Spirodela polyrhiza</i>, to investigate how WGD affects metabolite abundances per cell and per biomass.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Autopolyploidy increased metabolite levels per cell, but the response of individual metabolites varied considerably. However, the impact on metabolite level per biomass was restricted because the increased cell size reduced the metabolite concentration per cell. Nevertheless, we detected both quantitative and qualitative effects of WGD on the metabolome. Many effects were strain-specific, but some were shared by all four strains.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The nature and impact of metabolic changes after WGD depended strongly on the genotype. Dosage effects have the potential to alter the plant metabolome qualitatively and quantitatively, but were largely balanced out by the reduction in metabolite concentration due to an increase in cell size in this species.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141858826","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}

{"title":"Lineage diversification and rampant hybridization among subspecies explain taxonomic confusion in the endemic Hawaiian fern Polypodium pellucidum","authors":"Jonas I. Mendez-Reneau,&nbsp;Joseph L. Richards,&nbsp;Julia Hobbie,&nbsp;Emily Bollich,&nbsp;Nicholas J. Kooyers,&nbsp;Erin M. Sigel","doi":"10.1002/ajb2.16379","DOIUrl":"10.1002/ajb2.16379","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p><i>Polypodium pellucidum</i>, a fern endemic to the Hawaiian Islands, encompasses five ecologically and morphologically variable subspecies, suggesting a complex history involving both rapid divergence and rampant hybridization.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We employed a large target-capture data set to investigate the evolution of genetic, morphological, and ecological variation in <i>P. pellucidum</i>. With a broad sampling across five Hawaiian Islands, we deciphered the evolutionary history of <i>P. pellucidum</i>, identified nonhybrid lineages and intraspecific hybrids, and inferred the relative influence of geography and ecology on their distributions.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p><i>Polypodium pellucidum</i> is monophyletic, dispersing to the Hawaiian archipelago 11.53–7.77 Ma and diversifying into extant clades between 5.66 and 4.73 Ma. We identified four nonhybrid clades with unique morphologies, ecological niches, and distributions. Additionally, we elucidated several intraspecific hybrid combinations and evidence for undiscovered or extinct “ghost” lineages contributing to extant hybrid populations.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>We provide a foundation for revising the taxonomy of <i>P. pellucidum</i> to account for cryptic lineages and intraspecific hybrids. Geologic succession of the Hawaiian Islands through cycles of volcanism, vegetative succession, and erosion has determined the available habitats and distribution of ecologically specific, divergent clades within <i>P. pellucidum.</i> Intraspecific hybrids have likely arisen due to ecological and or geological transitions, often persisting after the local extinction of their progenitors. This research contributes to our understanding of the evolution of Hawai'i's diverse fern flora and illuminated cryptic taxa to allow better-informed conservation efforts.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854533","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}

{"title":"Species-tree topology impacts the inference of ancient whole-genome duplications across the angiosperm phylogeny","authors":"Michael T. W. McKibben,&nbsp;Geoffrey Finch,&nbsp;Michael S. Barker","doi":"10.1002/ajb2.16378","DOIUrl":"10.1002/ajb2.16378","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The history of angiosperms is marked by repeated rounds of ancient whole-genome duplications (WGDs). Here we used state-of-the-art methods to provide an up-to-date view of the distribution of WGDs in the history of angiosperms that considers both uncertainty introduced by different WGD inference methods and different underlying species-tree hypotheses.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We used the distribution synonymous divergences (<i>K</i>_s) of paralogs and orthologs from transcriptomic and genomic data to infer and place WGDs across two hypothesized angiosperm phylogenies. We further tested these WGD hypotheses with syntenic inferences and Bayesian models of duplicate gene gain and loss.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The predicted number of WGDs in the history of angiosperms (~170) based on the current taxon sampling is largely similar across different inference methods, but varies in the precise placement of WGDs on the phylogeny. <i>K</i>_s-based methods often yield alternative hypothesized WGD placements due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation. However, errors in species-tree inference can still produce spurious WGD hypotheses, regardless of method used.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Here we showed that different WGD inference methods largely agree on an average of 3.5 WGD in the history of individual angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the WGD inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747159","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}

{"title":"Estimates of late Early Cretaceous atmospheric CO2 from Mongolia based on stomatal and isotopic analysis of Pseudotorellia","authors":"Xiaoqing Zhang,&nbsp;Dana L. Royer,&nbsp;Gongle Shi,&nbsp;Niiden Ichinnorov,&nbsp;Patrick S. Herendeen,&nbsp;Peter R. Crane,&nbsp;Fabiany Herrera","doi":"10.1002/ajb2.16376","DOIUrl":"10.1002/ajb2.16376","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The Aptian–Albian (121.4–100.5 Ma) was a greenhouse period with global temperatures estimated as 10–15°C warmer than pre-industrial conditions, so it is surprising that the most reliable CO₂ estimates from this time are &lt;1400 ppm. This low CO₂ during a warm period implies a very high Earth-system sensitivity in the range of 6 to 9°C per CO₂ doubling between the Aptian-Albian and today.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We applied a well-vetted paleo-CO₂ proxy based on leaf gas-exchange principles (Franks model) to two <i>Pseudotorellia</i> species from three stratigraphically similar samples at the Tevshiin Govi lignite mine in central Mongolia (~119.7–100.5 Ma).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our median estimated CO₂ concentration from the three respective samples was 2132, 2405, and 2770 ppm. The primary reason for the high estimated CO₂ but with relatively large uncertainties is the very low stomatal density in both species, where small variations propagate to large changes in estimated CO₂. Indeed, we found that at least 15 leaves are required before the aggregate estimated CO₂ approaches that of the full data set.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our three CO₂ estimates all exceeded 2000 ppm, translating to an Earth-system sensitivity (~3–5°C/CO₂ doubling) that is more in keeping with the current understanding of the long-term climate system. Because of our large sample size, the directly measured inputs did not contribute much to the overall uncertainty in estimated CO₂; instead, the inferred inputs were responsible for most of the overall uncertainty and thus should be scrutinized for their value choices.</p>\u0000 </section>\u0000 </div>","PeriodicalId":7691,"journal":{"name":"American Journal of Botany","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632439","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}