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28 results for “shape assembly”
Xanthene[n]arenes: Exceptionally Large, Bowl-Shaped Macrocyclic Building Blocks Suitable for Self-Assembly
<p>Data underlying the figures in the publication “Xanthene[<em>n</em>]arenes: Exceptionally Large, Bowl-Shaped Macrocyclic Building Blocks Suitable for Self-Assembly”, published in <em>J</em><em>ACS Au</em> 2021, 1, 11, 1885–1891. <a href="https://doi.org/10.1021/jacsau.1c00343">https://doi.org/10.1021/jacsau.1c00343</a></p>
Data for "Ecosystem size filters life-history strategies to shape community assembly in lakes"
<p>Dataset 1. List of 71 fish species collected from north temperate lakes in Wisconsin USA. Data include critical life-history data used for strategy classifications according to Winemiller and Rose (1992), principal component scores, and strategy classification according to the cluster analysis.</p> <p>Dataset 2. Species occurrence data in all study lakes along with results from the 'soft classification" according to Euclidean distance.</p> <p>Dataset 3. Limnological and fish community characteristics of study lakes including species richness, lake area, estimated lake volume, and convex hull statistics for the overall fish community and each life-history strategy type.</p>
Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island
<p>Spatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche conservatism among target taxa, a broad understanding of the phenomenon requires sampling of entire communities. Species-rich groups such as arthropods are ideal case studies for understanding ecological and biodiversity dynamics along elevational gradients given their important functional role in many ecosystems, but community-level studies have been limited due to their tremendous diversity. Here, we develop a novel semi-quantitative metabarcoding approach that combines specimen counts and size-sorting to characterize arthropod community-level diversity patterns along two elevational gradients across two volcanoes on the island of Hawai`i. We find that arthropod communities between the two transects become increasingly distinct compositionally at higher elevations. Resistance surface approaches suggest that climatic differences between sampling localities are an important driver in shaping beta-diversity patterns, though the relative importance of climate varies across taxonomic groups. Nevertheless, the climatic niche position of OTUs between transects was highly correlated, suggesting that climatic filters shape the colonization between adjacent volcanoes. Taken together, our results highlight climatic niche conservatism as an important factor shaping ecological assembly along elevational gradients and suggest topographic complexity as an important driver of diversification.</p>
Functional assembly of tropical montane tree islands in the Atlantic Forest is shaped by stress-tolerance, bamboo-presence and facilitation
<p><strong>Aims</strong>: Amidst the Campos de Altitude (Highland Grasslands) in the Brazilian Atlantic Forest, woody communities grow either clustered in tree islands or interspersed within the herbaceous matrix. The functional ecology, diversity and biotic processes shaping these plant communities are largely unstudied. We characterised the functional assembly and diversity of these tropical montane woody communities and investigated how they fit within Grime's CSR (C – competitor, S – stress-tolerant, R – ruderal) scheme, what functional trade-offs they exhibit and how traits and functional diversity vary in response to bamboo presence/absence.</p> <p><strong>Methods</strong>: To characterize the functional composition of the community, we sampled five leaf traits and wood density along transects covering the woody communities both inside tree islands and outside (i.e. isolated woody plants in the grasslands community) . Then, we used Mann Whitney test, t-test and variation partitioning to determine the effects of inside vs outside tree island and bamboo presence on community weighted means, woody species diversity and functional diversity.</p> <p><strong>Results</strong>: We found a general SC/S strategy with drought-related functional trade-offs. Woody plants in tree islands had more acquisitive traits than those within the grasslands. Trait variation was mostly taxonomically than spatially driven, and species composition varied between inside and outside tree islands. Leaf thickness, wood density and foliar water uptake were unrelated to CSR-strategies, suggesting independent trait dimensions and multiple drought-coping strategies within the predominant S-strategy. Islands with bamboo presence showed lower Simpson diversity, lower functional dispersion, lower foliar water uptake and greater leaf thickness than in tree islands without bamboo.</p> <p><strong>Conclusions</strong>: The observed functional assembly hints towards large-scale environmental abiotic filtering shaping stress-tolerant community strategy, and small-scale biotic interactions driving small-scale trait variation. We recommend experimental studies with fire, facilitation treatments, eco-physiological and recruitment traits to elucidate on tree island expansion and communities response to climate change.</p>
Text-fig. 7. Cercidiphyllaceae 1–3. Trochodendroides genetrix (NEWBERRY) comb. nov. and associated reproductive structures (4, 5) from Killpecker Cr., Rock Springs, Wyoming (UF loc. 18126). 1. Twig with three attached leaves, showing variation in leaf shape and serration; composite figure assembled from images of both counterparts, UF 35427. 2. Complete leaf including petiole, UF 13243. 3. Same as 2, detail of venation. 4. Nyssidium arcticum (HEER) ILJINSKAYA fruits on an incomplete axis, UF 35454. 5. Dispersed winged seed, UF 35479. Scale = 3 cm in 1, 2; 1 cm in 3, 4; 0.5 cm in 5. in Revisions To Roland Brown'S North American Paleocene Flora
Text-fig. 7. Cercidiphyllaceae 1–3. Trochodendroides genetrix (NEWBERRY) comb. nov. and associated reproductive structures (4, 5) from Killpecker Cr., Rock Springs, Wyoming (UF loc. 18126). 1. Twig with three attached leaves, showing variation in leaf shape and serration; composite figure assembled from images of both counterparts, UF 35427. 2. Complete leaf including petiole, UF 13243. 3. Same as 2, detail of venation. 4. Nyssidium arcticum (HEER) ILJINSKAYA fruits on an incomplete axis, UF 35454. 5. Dispersed winged seed, UF 35479. Scale = 3 cm in 1, 2; 1 cm in 3, 4; 0.5 cm in 5.
Data for: Stratification and recovery time jointly shape ant functional re-assembly in a Neotropical forest
<p>Microhabitat differentiation of species communities such as vertical stratification in tropical forests contributes to species coexistence and thus biodiversity. However, little is known about how the extent of stratification changes during forest recovery and influences community reassembly. Environmental filtering determines community reassembly in time (succession) and in space (stratification), hence functional and phylogenetic composition of species communities are highly dynamic. It is poorly understood if and how these two concurrent filters – forest recovery and stratification – interact.</p> <p>In a tropical forest chronosequence in Ecuador spanning 34 years of natural recovery, we investigated the recovery trajectory of ant communities in three overlapping strata (ground, leaf litter, lower tree trunk) by quantifying 13 traits, as well as the functional and phylogenetic diversity of the ants. We expected that functional and phylogenetic diversity increase with recovery time and that each ant community within each stratum shows a distinct functional reassembly. We predicted that traits related to ant diet show divergent trajectories reflecting an increase in niche differentiation with recovery time. On the other hand, traits related to the abiotic environment were predicted to show convergent trajectories due to a more similar microclimate across strata with increasing recovery age.</p> <p>Most of the functional traits and the phylogenetic diversity of the ants were clearly stratified, confirming previous findings. However, neither functional nor phylogenetic diversity increased with recovery time. Community-weighted trait means had complex relationships to recovery time and the majority were shaped by a statistical interaction between recovery time and stratum, confirming our expectations. However, most trait trajectories converged among strata with increasing recovery time regardless of whether they were related to ant diet or environmental conditions.</p> <p>We confirm the hypothesized interaction among environmental filters during the functional reassembly in tropical forests. Communities in individual strata respond differently to recovery, and possible filter mechanisms likely arise from both abiotic (e.g., microclimate) and biotic (e.g., diet) conditions. Since vertical stratification is prevalent across animal and plant taxa, our results highlight the importance of stratum-specific analysis in dynamic ecosystems and may generalize beyond ants.</p>
Data and analysis scripts for: Co-occurrence patterns at four spatial scales implicate reproductive processes in shaping community assembly in clovers
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Data from: A fungal endophyte alters poplar leaf chemistry, deters insect feeding, and shapes insect community assembly
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Functional assembly of tropical montane tree islands in the Atlantic Forest is shaped by stress-tolerance, bamboo-presence and facilitation
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Data for: Stratification and recovery time jointly shape ant functional re-assembly in a Neotropical forest
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Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island
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The cell adhesion molecule Sdk1 shapes assembly of a retinal circuit that detects localized edges
<p>Nearly 50 different mouse retinal ganglion cell (RGC) types sample the visual scene for distinct features. RGC feature selectivity arises from its synapses with a specific subset of amacrine (AC) and bipolar cell (BC) types, but how RGC dendrites arborize and collect input from these specific subsets remains poorly understood. Here we examine the hypothesis that RGCs employ molecular recognition systems to meet this challenge. By combining calcium imaging and type-specific histological stains we define a family of circuits that express the recognition molecule Sidekick 1 (Sdk1) which include a novel RGC type (S1-RGC) that responds to local edges. Genetic and physiological studies revealed that Sdk1 loss selectively disrupts S1-RGC visual responses which result from a loss of excitatory and inhibitory inputs and selective dendritic deficits on this neuron. We conclude that Sdk1 shapes dendrite growth and wiring to help S1-RGCs become feature selective.</p>
Geology and elevation shape microbial assembly in Antarctic endolithic communities
<p>The dataset includes three table files (.csv), and one archive file (.tgz).</p> <p><strong>bacteria_summary_out3.csv: </strong>the GTDB-Tk summary for bacterial genomes</p> <p><strong>filtered_repr.tgz: </strong>filtered genomes </p> <p><strong>otu_raw3_genomes_metadata.csv:</strong> environmental data and genome abundances for each location</p> <p><strong>tax_table_otu3.csv</strong>: taxonomic table for each genome</p>
The cell adhesion molecule Sdk1 shapes assembly of a retinal circuit that detects localized edges
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Shape of AOT reverse micelles: the mesoscopic assembly is more than the sum of the parts
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Atmospheric and soil drought risks combined shape community assembly of trees in a Tropical Dry Forest
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Data from: Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Galápagos archipelago
Remote locations, such as oceanic islands, typically harbour relatively few species, some of which go on to generate endemic radiations. Species colonising these locations tend to be a non-random subset from source communities, which is thought to reflect dispersal limitation. However, non-random colonisation could also result from habitat filtering, whereby only a few continental species can become established. We evaluate the imprints of these processes on the Galápagos flora by analysing a comprehensive regional phylogeny for ~ 39 000 species alongside information on dispersal strategies and climatic suitability. We found that habitat filtering was more important than dispersal limitation in determining species composition. This finding may help explain why adaptive radiation is common on oceanic archipelagoes – because colonising species can be relatively poor dispersers with specific niche requirements. We suggest that the standard assumption that plant communities in remote locations are primarily shaped by dispersal limitation deserves reconsideration.
Data from: From ratites to rats: the size of fleshy fruits shapes species' distributions and continental rainforest assembly
Seed dispersal is a key process in plant spatial dynamics. However, consistently applicable generalisations about dispersal across scales are mostly absent because of the constraints on measuring propagule dispersal distances for many species. Here, we focus on fleshy-fruited taxa, specifically taxa with large fleshy fruits and their dispersers across an entire continental rainforest biome. We compare species-level results of whole-chloroplast DNA analyses in sister taxa with large and small fruits, to regional plot-based samples (310 plots), and whole of continent patterns for the distribution of woody species with either large (>30mm) or smaller fleshy fruits (1093 taxa). The pairwise genomic comparison found higher genetic distances between populations and between regions in the large-fruited species (Endiandra globosa), but higher overall diversity within the small-fruited species (Endiandra discolor). Floristic comparisons among plots confirmed lower numbers of large-fruited species in areas where more extreme rainforest contraction occurred, and re-colonisation by small-fruited species readily dispersed by the available fauna. Species distribution patterns showed that larger-fruited species had smaller geographic ranges than smaller-fruited species and locations with stable refugia (and high endemism) aligned with concentrations of large fleshy-fruited taxa, making them a potentially valuable conservation-planning indicator.
Data from: Multiple plant traits shape the genetic basis of herbivore community assembly
1. Community genetics research has posited a genetic basis to the assembly of ecological communities. For arthropod herbivores in particular, there is strong support that genetic variation in host plants is a key factor shaping their diversity and composition. However, the specific plant phenotypes underlying herbivore responses remain poorly explored for most systems. 2. We address this knowledge gap by examining the influence of both genetic and phenotypic variation in a dominant host-plant species, Salix hookeriana, on its associated arthropod herbivore community in a common garden experiment. Specifically, we surveyed herbivore responses among five different arthropod feeding guilds to 26 distinct S. hookeriana genotypes. Moreover, we quantified the heritability of a suite of plant traits that determine leaf quality (e.g. phenolic compounds, trichomes, specific leaf area, C : N) and whole-plant architecture, to identify which traits best accounted for herbivore community responses to S. hookeriana genotype. 3. We found that total herbivore abundance and community composition differed considerably among S. hookeriana genotypes, with strong and independent responses of several species and feeding guilds driving these patterns. We also found that leaf phenolic chemistry displayed extensive heritable variation, whereas leaf physiology and plant architecture tended to be less heritable. Of these traits, herbivore responses were primarily associated with leaf phenolics and plant architecture; however, different herbivore species and feeding guilds were associated with different sets of traits. Despite our thorough trait survey, plant genotype remained a significant predictor of herbivore responses in most trait association analyses, suggesting that unmeasured host-plant characteristics and/or interspecific interactions were also contributing factors. 4. Taken together, our results support that the genetic basis of herbivore community assembly occurs through a suite of plant traits for different herbivore species and feeding guilds. Still, identifying these phenotypic mechanisms requires measuring a broad range of plant traits and likely further consideration of how these traits affect interspecific interactions.
The dataset of the role of dormant propagule banks in shaping eco-evolutionary dynamics of community assembly
<p>Here is the dataset of the simulation data of the role of dormant propagule banks in shaping eco-evolutionary dynamics of community assembly. </p>
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