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39 results for “Community assembling process”
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: Inferring community assembly processes from mangrove species–area relationships
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Ecological network structure in response to community assembly processes over evolutionary time
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Data from: Along with intraspecific functional trait variation, individual performance is key to resolving community assembly processes
<ol> <li>Species contributing high proportions to community biomass strongly influence ecosystem processes within the community. Studies have shown that dominant species may serve as nurse plants, helping to ensure biomass stability of the subordinate species under stress conditions. The question is widely debated as to whether either niche differentiation or neutral processes drive the net outcome of plant interactions within a subordinate plant community. To answer this question, requires precise estimates of individual variation in functional traits and performance.</li> <li>In a five-year mesocosm experiment, the functional responses of a subordinate plant community to the removal of the dominant species were evaluated across two drought-stress scenarios. Small scale (i.e., large pots) wetland communities were constructed comprising one dominant species (Carex elata) and three subordinate species. Removal of the dominant species allowed evaluation of the net effects of drought and interspecific interactions. We estimated the functional divergences for three traits (specific leaf area, leaf dry matter content and height growth allocation) and compared these with performance differences quantified individually. This enabled distinctions to be made between deterministic (i.e., niche differentiation) and neutral processes driving the drought response of the subordinate community.</li> <li>We showed that the dominant species decreased relative performance differences within the subordinate plant community under conditions of permanent drought stress. These changes were associated with the convergence of traits related to resource acquisition and growth. The dominant species equalised species performance differences by supressing relatively drought-tolerant species with low competitive ability and by supporting the less drought-tolerant species with relatively high competitive ability. Meanwhile, under conditions of interannual drought, the subordinate species likely coexisted due to differentiation in resource-use strategies and the interaction with the dominant species.</li> <li>Inclusion of individual variation in performance with a functional trait approach provides valuable insights into the processes structuring plant communities. Ours is the first study to provide evidence that subordinate species exposed to drought may coexist via neutral processes arising from their interactions with the dominant species, leading to functional convergence of traits associated with the trade-off between stress tolerance and competitive ability.</li> </ol>
Integrating floral trait and flowering time distribution patterns help reveal a more dynamic nature of co-flowering community assembly processes
<p>Species' floral traits and flowering times are known to be the major drivers of pollinator-mediated plant-plant interactions in diverse co-flowering communities. However, their simultaneous role in mediating plant community assembly and plant-pollinator interactions is still poorly understood. Since not all species flower at the same time, inference of facilitative and competitive interactions based on floral trait distribution patterns should account for fine phenological structure (intensity of flowering overlap) within co-flowering communities. Such an approach may also help reveal the simultaneous action of competitive and facilitative interactions in structuring co-flowering communities.</p> <p>Here we used modularity within a co-flowering network context, as a novel approach to detect convergent and/or over-dispersed patterns in floral trait distribution and pollinator sharing. Specifically, we evaluate differences in floral trait and pollinator distribution patterns within (high temporal flowering overlap) and among co-flowering modules (low temporal flowering overlap). We further evaluate the consistency of observed floral trait and pollinator sharing distribution patterns across space (three geographic regions) and time (dry and rainy seasons).</p> <p>We found that floral trait similarity was significantly higher in plant species within co-flowering modules than in species among them. This suggests pollinator facilitation may lead to floral trait convergence, but only within co-flowering modules. However, our results also revealed seasonal and spatial shifts in the underlying interactions (facilitation or competition) driving co-flowering assembly, suggesting that the prevalent dominant interactions are not static.</p> <p>Synthesis: Overall, we provide strong evidence showing that the use of flowering time and floral trait distribution alone may be insufficient to fully uncover the role of pollinator-mediated interactions in community assembly. Integrating this information along with patterns of pollinator sharing will greatly help reveal the simultaneous action of facilitative and competitive pollinator-mediated interactions in co-flowering communities. The spatial and temporal variation in flowering and trait distribution patterns observed further emphasize the importance of adopting a more dynamic view of community assembly processes.</p>
Data and code from "A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities"
<p>Trait-based ecology suggests that abiotic filtering is the main mechanism structuring the regional species pool in different subsets of habitat-specific species. At more local spatial scales, other ecological processes may add on giving rise to complex patterns of functional diversity (FD). Understanding how assembly processes operating on the habitat-specific species pools produce the locally observed plant assemblages is an ongoing challenge. Here, we evaluated the importance of different processes to community assembly in an alpine fellfield, assessing its effects on local plant trait FD. Using classical randomization tests and linear mixed models, we compared the observed FD with expectations from three null models that hierarchically incorporate additional assembly constraints: stochastic null models (random assembly), independence null models (each species responding individual and independently to abiotic environment), and co-occurrence null models (species responding to environmental variation and to the presence of other species). We sampled species composition in 115 quadrats across 24 locations in the central Pyrenees (Spain) that differed in soil conditions, solar radiation and elevation. Overall, the classical randomization tests were unable to find differences between the observed and expected functional patterns, suggesting that the strong abiotic filters that sort out the flora of extreme regional environments blur any signal of other local processes. However, our approach based on linear mixed models revealed the signature of different ecological processes. In the case of seed mass and leaf thickness, observed FD significantly deviated from the expectations of the stochastic model, suggesting that fine-scale abiotic filtering and facilitation can be behind these patterns. Our study highlights how the hierarchical incorporation of ecological additional constraints may shed light on the dim signal left by local assembly processes in alpine environments.</p>
Data from: Tropical forest type influences community assembly processes in arbuscular mycorrhizal fungi
Aim: Plant community assembly in tropical rainforest has been shown to be largely governed by stochastic processes, but as arbuscular mycorrhizal (AM) fungi display limited host preference, they may not follow the same stochastic assembly pattern. Here, we determined the relative importance of environmental and spatial drivers responsible for the community assembly process of AM fungi in two types of tropical rainforest (semideciduous rainforest and dense ombrophilous forests). Location: Atlantic rainforest in northeastern Brazil, South America. Taxon: Arbuscular mycorrhizal fungi (Glomeromycota). Methods: We collected root samples from eight protected areas of Atlantic forest along a 700 km transect in northeastern Brazil. We measured the relative importance of deterministic and stochastic processes by redundancy analysis (RDA) and variation partitioning in comparison with null expectations using ad hoc generated neutral communities. Furthermore, we accessed species associations from co-occurrence data, at different scales using a Bayesian approach of Hierarchical Modelling of Species Communities (HMSC). Results: Overall, the extent to which stochastic and deterministic processes affected community assembly depended on the forest type and the spatial scale. Specifically, we found that abiotic and biotic predictors of AM fungal community assemblages are related to environmental homogeneity in tropical rainforests. Main conclusions: The results of the study show that dynamics in community assembly was clearly different between the two forest types, and that the difference most likely is due to differences in responses to environmental variables.
Ecoregional patterns of protist communities in mineral and organic soils: assembly processes, functional traits and diversity of testate amoebae in Northern Eurasia
<p>TA_Traits.csv file includes trait data for testate amoebae. TA_Abundance.csv file includes environmental variables (soil type and region) and relative abundance data of testate amoebae.</p>
Spatial phylogenetic and phenotypic patterns reveal ontogenetic shifts in ecological processes of plant community assembly
The analysis of spatial phylogenetic and phenotypic structure of plant communities provides insight into the underlying processes and interactions governing their assembly, and how these may change during plant ontogeny. We used point pattern analysis to find out if saplings and adult plants are surrounded by phylogenetically and phenotypically more similar or dissimilar neighbours than expected by chance, and whether these associations change from the sapling to the adult stage. To this end, we combined information on the phylogenetic structure and eight phenotypic traits of 15 woody plant species in two Mediterranean mixed forests of southeastern Spain. At the community level, we found that the sapling bank at both sites did not show phylogenetic or phenotypic spatial patterns, but adults showed phylogenetic clustering (i.e., heterospecific neighbours were more similar than expected). At the species level, we found frequently repulsive patterns in the sapling bank of less abundant species (i.e., heterospecific sapling or adult neighbours were more dissimilar than expected) in both, phylogenetic and phenotypic analyses. For the adult stage, we found phylogenetic attraction (i.e., more similar neighbours) in just one species and phenotypic clustering in four species. The processes driving the assembly of the communities of saplings and adults leave detectable signals in the spatial phylogenetic and phenotypic structure of our two forest communities. Our findings reinforce the existence of ontogenetic shifts in the mechanisms involved in plant community assembly. Facilitation between phylogenetically distant and phenotypically divergent species favours the recruitment of less abundant species. However, processes acting later in the ontogeny ameliorate the competition between close relatives and determine the spatial structure of adult plants. Nevertheless, the role of phenotype in shaping adult-adult interactions was context- and trait-dependent. The use of spatial point pattern analysis allowed a nuanced interpretation of the phylogenetic and phenotypic structures of the plant community.
Sims et al. A Tale of Two Pools: The Dynamic Influence of Subsurface Geological Processes on the Assembly and Diversification of Thermophilic Microbial Communities in Hydrothermal Systems - Supplementary Datasets
<p>These datasets comprise the supplementary datasets found in Sims et al. A Tale of Two Pools: The Dynamic Influence of Subsurface Geological Processes on the Assembly and Diversification of Thermophilic Microbial Communities in Hydrothermal Systems, <strong><em>Geochimica et Cosmiochimica Act </em></strong></p>
Warming modulates soil multifunctionality through assembly processes and co-occurrence patterns of arbuscular mycorrhizal fungal communities in drylands
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Data from: Tropical forest type influences community assembly processes in arbuscular mycorrhizal fungi
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Integrating floral trait and flowering time distribution patterns help reveal a more dynamic nature of co-flowering community assembly processes
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Data from: PER-SIMPER - a new tool for inferring community assembly processes from taxon occurrences
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Data and code from "A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities"
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Data from: Along with intraspecific functional trait variation, individual performance is key to resolving community assembly processes
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Spatial phylogenetic and phenotypic patterns reveal ontogenetic shifts in ecological processes of plant community assembly
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Data from: Life-history dimensions indicate non-random assembly processes in tropical island tree communities
<p>Community assembly processes on islands are often non-random. The mechanisms behind non-random assembly, however, are generally difficult to disentangle. Functional diversity in combination with a null model approach that accounts for differences in species richness among islands can be used to test for non-random assembly processes, but has been applied rarely to island communities. By linking functional diversity of trees on islands with a null model approach, we bridge this gap and test for the role of stochastic vs. non-random trait-mediated assembly processes in shaping communities by studying functional diversity-area relationships. We measured 11 plant functional traits linked to species dispersal and resource acquisition strategies of 57 tree species on 40 tropical islands. We grouped traits into four life-history dimensions representing (i) dispersal ability, (ii) growth strategy, (iii) light acquisition, and (iv) nutrient acquisition. To test for non-random assembly processes, we used null models that account for differences in species richness among the islands. Our results reveal contrasting responses of the four life-history dimensions to island area. The dispersal and the growth strategy dimensions were underdispersed on smaller islands, whereas the light acquisition dimension was overdispersed. The nutrient acquisition dimension did not deviate from null expectations. With increasing island area, shifts in the strength of non-random assembly processes increased the diversity of dispersal and acquisition strategies in island communities. Our results suggest that smaller islands may be more difficult to colonize and provide more limited niche space compared to larger islands, whose tree communities are likely determined by stochastic processes and higher niche diversity. Our null model approach highlights that analysing the functional diversity of different life-history dimensions provides a powerful framework to unravel community assembly processes on islands. These complex, non-random assembly processes are masked by measures of functional diversity that do not account for differences in species richness between islands.</p>
Data from: The multiple roles of β–diversity help untangle community assembly processes affecting recovery of temperate rocky shores
Metacommunity theory highlights the potential of β–diversity as a useful link to empirical research, especially in diverse systems where species exhibit a range of stage-dependent dispersal characteristics. To investigate the importance of different components and scales of β–diversity in community assembly we conducted a large-scale disturbance experiment and compared relative recovery across multiple sites and among plots within sites on the rocky shore. Six sites were spread along 80 km of coastline and, at each site, 5 plots were established, matching disturbed and undisturbed quadrats. Recovery was not complete at any of the sites after 1 year for either epibenthos (mostly composed of macroalgae and, locally, mussels) or infauna. Significant differences in recovery among sites were observed for epibenthos but not for infauna suggesting different community assembly processes were operating. This was supported by epibenthos in the recovering plots having higher species turnover than in undisturbed sediment, and recovery well predicted by local diversity, while infaunal recovery was strongly influenced by the epibenthic community's habitat complexity. However, infaunal community recovery did not simply track formation of habitat by recovering epibenthos, but appeared to be overlain by within-site and among-site aspects of infaunal -diversity. These results suggest that documenting changes in the large plants and animals alone will be a poor surrogate for rocky shore community assembly processes. No role for ecological connectivity (negative effect of among-site β–diversity) in driving recovery was observed, suggesting a low risk of effects from multiple disturbances propagating along the coast, but a limited resilience at the site scale to large-scale disturbances such as landslides or oil spills.
Data from: Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities
Environmental degradation may have strong effects on community assembly processes. We examined the assembly of bacterial and fungal communities in anthropogenically altered and near-pristine streams. Using pyrosequencing of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we specifically examined if environmental degradation deterministically decreases or increases the compositional turnover of bacterial and fungal communities. Our results showed that near-pristine streams and anthropogenically altered streams supported distinct fungal and bacterial communities. The mechanisms assembling these communities were different in near-pristine and altered environments. Environmental disturbance homogenized bacterial communities, whereas fungal communities were more dissimilar in disturbed sites than in near-pristine sites. Compositional variation of both bacteria and fungi was related to water chemistry variables in disturbed sites, further implying the influence of environmental degradation on community assembly. Bacterial and fungal communities in near-pristine streams were weakly controlled by environmental factors, suggesting that the relative importance of niche-based versus neutral processes in assembling microbial communities may strongly depend on the spatial scale and local environmental context. Our results thus suggest that environmental degradation may strongly affect the composition and β-diversity of stream microbial communities colonizing leaf litter, and that the direction of the change can be different between bacteria and fungi. A better understanding of the environmental tolerances of microbes and the mechanisms assembling microbial communities in natural environmental settings is needed to predict how environmental alteration is likely to affect microbial communities.
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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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.
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