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650 results for “angiosperm”
Data from: Stomatal sensitivity to CO2 diverges between angiosperm and gymnosperm tree species
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Data from: Evolutionary history of the angiosperm flora of China
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Data from: Revisiting the relative growth rate hypothesis for gymnosperm and angiosperm species co‐occurrence
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Data from: Leafing intensity and the fruit size/number trade-off in woody angiosperms
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Data from: A conifer–angiosperm divergence in the growth vs shade tolerance trade-off underlies the dynamics of a New Zealand warm-temperate rain forest
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Global distribution and evolutionary transitions of angiosperm sexual systems
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Data from: Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach
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Angiosperm to Gymnosperm host-plant switch entails shifts in microbiota of the Welwitschia bug, Probergrothius angolensis (Distant, 1902)
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High temperature frequently increases facilitation between aquatic foundation species: A global meta-analysis of interaction experiments between angiosperms, seaweeds, and bivalves
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Mitochondrial genes from eighteen angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants
<p class="Default"><span>The early diversification of angiosperms is a rapid yet complicated process and thus it renders the phylogenetic analyses of early-diverging angiosperms much difficulty. Plastid and nuclear phylogenomic studies have raised several controversial hypotheses regarding the angiosperm phylogeny, whereas mitochondrial genomes have been largely ignored. In this study, we newly sequenced mitochondrial genomes from 18 angiosperms to fill the sampling gaps in magnoliids, Austrobaileyales, Chloranthales, Ceratophyllales, and early-diverging lineages of eudicots and monocots. A data matrix of 38 mitochondrial genes from 107 taxa was assembled to address this question. Although conflicting phylogenies were recovered in this study from different datasets and analytical methods, congruence was achieved regarding the deep relationships of several major angiosperm lineages: Chloranthales always groups with Ceratophyllales, Austrobaileyales is sister to mesangiosperms, and a previously unplaced clade—Dilleniales—is consistently resolved as a sister to superasterids. Substitutional saturation, GC compositional heterogeneity, and codon-usage bias are suggested as common reasons for the noisy signals that impact phylogenetic reconstructions, and angiosperm mitochondrial genes seem to hardly suffer from these factors. In addition, the 3<sup>rd</sup> codon positions of the mitochondrial genes contained more phylogenetic signals than the 1<sup>st</sup> and 2<sup>nd</sup> codon positions, which might be responsible for the incongruent results recovered among different datasets. Due to the rapid radiation process, the relationships among these early lineages are not well resolved. Nevertheless, this study based on mitochondrial genomes provides additional evidence and alternative hypotheses for the early evolution and diversification of angiosperms.</span></p>
Data from: Ancestral polyploidy in seed plants and angiosperms
Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms1, 2, 3, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications4, 5, 6, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications—one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms.
Data from: The expression of self-incompatibility in angiosperms is bimodal
Self-incompatibility is expressed by nearly one half of all angiosperms. A large proportion of the remaining species are self-compatible, and they either outcross using various contrivances or self-fertilize to some extent. Because of the common occurrence of populations and individuals with intermediate levels of self-incompatibility, categorization of the expression of self-incompatibility as an approximately binary trait has become controversial. We collect a widely reported index (ISI) used to asses the strength and variation of self-incompatibility from over 1200 angiosperm taxa. Its distribution is bimodal and positively associated with outcrossing rate, albeit with a weak relationship within self-compatible taxa. A substantial fraction of species have intermediate mean values of ISI. Their occurrence can be caused by segregating ephemeral self-compatible mutations, averaging artifacts, and experimental biases, in addition to the often invoked stabilizing selection acting on the expression of self-incompatibility. Selection may also generally favor taxa with high ISI values through increased lineage birth and death rates, and it may counter lower-level selection advantages within taxa expressing intermediate and low values of ISI. Such a null hypothesis is nearly universally overlooked, despite the fact that it could adequately explain the observed distribution of mating and breeding systems.
Data from: Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms
Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that – at least for these genera with the currently available data – dioecy neither consistently places a strong brake on diversification nor is a strong driver.
Data from: Mating system plasticity promotes persistence and adaptation of colonizing populations of hermaphroditic angiosperms
Persistence and adaptation in novel environments are limited by small population size, strong selection, and maladaptive gene flow. Mating system plasticity is common in angiosperms and may provide both demographic and genetic benefits that promote niche evolution, including reproductive assurance and isolation from maladaptive gene flow. Yet increased self-fertilization may also cause inbreeding depression, accumulation of deleterious mutations, and reduced adaptive potential. Here we use individual-based simulations to examine the consequences of mating system plasticity for persistence and adaptation in a novel environment that imposes selection on a quantitative trait. We examine the joint evolution of local adaptation, inbreeding depression, and genetic load. We find that a plastic shift to a mixed mating system generally promotes niche evolution by decreasing the risk of extinction, providing isolation from maladaptive gene flow, and temporarily increasing genetic variance in the trait under selection, whereas obligate self-fertilization reduces adaptive potential. These effects are most pronounced under conditions of mate limitation, strong selection, or maladaptive gene flow. Our results highlight the diverse demographic and genetic consequences of self-fertilization and support the potential role for plastic shifts in mating system to promote niche evolution in flowering plants.
Data from: Evaluating the impact of genomic data and priors on Bayesian estimates of the angiosperm evolutionary timescale
The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subsampling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest divergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon sampling, significant methodological changes, and new information from the fossil record.
Data from: Salt tolerance is evolutionarily labile in a diverse set of angiosperm families
Background: Salt tolerance in plants is rare, yet they it is found across a diverse set of taxonomic groups. This suggests that, although salt tolerance involves a complex set of traits, it has evolved many times independently in different angiosperm lineages. However, the pattern of evolution of salt tolerance can vary dramatically between families. A recent phylogenetic study of the Chenopodiaceae (goosefoot family) concluded that salt tolerance has a conserved evolutionary pattern, being gained early in the evolution of the lineage then retained by most species in the family. Conversely, a phylogenetic study of the Poaceae (grass family) suggested over 70 independent origins of salt tolerance, most giving rise to only one or a few salt tolerant species. Here, we use a phylogenetic approach to explore the macroevolutionary patterns of salt tolerance in a sample of angiosperm families, in order to ask whether either of these two patterns - deep and conserved or shallow and labile - represents a common mode of salt tolerance evolution. We analyze the distribution of halophyte species across the angiosperms and identify families with more or less halophytes than expected under a random model. Then, we explore the phylogenetic distribution of halophytes in 22 families using phylogenetic comparative methods. Results: We find that salt tolerance species have been reported from over one-third of angiosperm families, but that salt tolerant species are not distributed evenly across angiosperm families. We find that salt tolerance has evolved hundreds of times over the history of the angiosperms. In a few families, we find deep and conserved origins of evolution of salt tolerance, but in the majority of families analyzed, we find that salt tolerance evolution is characterized by multiple independent origins that occur near the tips of the phylogeny and often give rise to only one or a few halophytes. Conclusions: Our results suggest that salt tolerance is evolutionarily labile in many different angiosperm families. Thus, the evolutionary pattern of many independent origins of salt tolerance near the tips of the phylogeny found previously in the grasses and observed in several other angiosperm families represents a common feature of salt tolerance evolution. Our findings add to the growing literature of the repeated evolution of complex ecological traits.
Data from: Inferring complex phylogenies using parsimony: an empirical approach using three large DNA data sets for angiosperms
To explore the feasibility of parsimony analysis for large data sets, we conducted heuristic parsimony searches and bootstrap analyses on separate and combined DNA data sets for 190 angiosperms and three outgroups. Separate data sets of 18S rDNA (1,855 bp), rbc L (1,428 bp), and atp B (1,450 bp) sequences were combined into a single matrix 4,733 bp in length. Analyses of the combined data set show great improvements in computer run times compared to those of the separate data sets and of the data sets combined in pairs. Six searches of the 18S rDNA rbc L atp B data set were conducted; in all cases TBR branch swapping was completed, generally within a few days. In contrast, TBR branch swapping was not completed for any of the three separate data sets, or for the pairwise combined data sets. These results illustrate that it is possible to conduct a thorough search of tree space with large data sets, given sufficient signal. In this case, and probably most others, sufficient signal for a large number of taxa can only be obtained by combining data sets. The combined data sets also have higher internal support for clades than the separate data sets, and more clades receive bootstrap support of 50% in the combined analysis than in analyses of the separate data sets. These data suggest that one solution to the computational and analytical dilemmas posed by large data sets is the addition of nucleotides, as well as taxa.
Phylogenomics and the rise of the angiosperms
<p>Data repository of</p> <p>Zuntini, Carruthers et al. 2024 - Phylogenomics and the rise of the angiosperms</p>
Reproductive character displacement and potential underlying drivers in a species-rich and florally diverse lineage of tropical angiosperms (Ruellia; Acanthaceae)
Reproductive character displacement is a pattern whereby sympatric lineages diverge more in reproductive character morphology than allopatric lineages. This pattern has been observed in many plant species, but comparably few have sought to disentangle underlying mechanisms. Here, in a diverse lineage of Neotropical plants (Ruellia; Acanthaceae), we present evidence of reproductive character displacement in a macroevolutionary framework (i.e., among species) and document mechanistic underpinnings. In a series of inter-specific hand pollinations in a controlled glasshouse environment, we found that crosses between species that differed more in overall flower size, particularly in style length, were significantly less likely to produce viable seeds. Further, species pairs that failed to set seed were more likely to have sympatric distributions in nature. Competition for pollinators and reinforcement to avoid costly inter-specific mating could both result in these patterns and are not mutually exclusive processes. Our results add to growing evidence that reproductive character displacement contributes to exceptional floral diversity of angiosperms.
Dated tree of 24,000 Angiosperms species incl Canary Island colonisation events
<p><span><span><span><span><span><span><span><span><span><span><span>Insular woodiness (IW), referring to the evolutionary transition from herbaceousness towards woodiness on islands, has arisen more than 30 times on the Canary Islands (Atlantic Ocean). One of the IW hypotheses suggests that drought has been a major driver of wood formation, but we do not know in which palaeoclimatic conditions the insular woody lineages originated. Therefore, we provided an updated review on the presence of IW on the Canaries, reconstructed the palaeoclimate, and estimated the timing of origin of woodiness of 24 insular woody lineages that represent a large majority of the insular woody species diversity on the Canaries. Our single, broad-scale dating analysis shows that woodiness in 60-65% of the insular woody lineages studied originated within the last 3.2 Myr during which Mediterranean seasonality (yearly summer droughts) became established on the Canaries. Consequently, our results are consistent with palaeoclimatic aridification as a potential driver of woodiness in a considerable proportion of the insular woody Canary Island lineages. However, the observed pattern between insular woodiness and palaeodrought during the last couple of million years could potentially have emerged as a result of the typically young age of the native insular flora that is characterised by a high turnover.</span></span></span></span></span></span></span></span></span></span></span></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.