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518 results for “community functions.”
Functional traits and habitat use: investigating community assembly in a montane community (Carabidae: Nebria)
<p>The processes that influence community assembly, such as competition for resources and environmental filtering, are often scale-dependent and vary across ecotones. Trait-based ecology provides a useful framework for testing which ecological processes most strongly influence local community composition, especially across environmental gradients where species diversity varies. Where environmental filtering dominates, species distributions are expected to be defined by strong turnover along environmental gradients, with more similar species occupying more similar habitats. Where interspecific competition dominates, species are expected to diverge in relative abundance and resource utilization at sites, so species can co-occur. Here, we integrate measurements of functional traits, microhabitat usage, isotopic composition (δ<sup>15</sup>N and δ<sup>13</sup>C), and abundance to test the importance of environmental filtering and resource/habitat partitioning in shaping a montane ground beetle species assemblage (Carabidae: Nebriini: <em>Nebria</em>) in the isolated, volcanic peaks of the northern Cascades Range, U.S.A. Across species of <em>Nebria</em>, body size, pronotal shape, temperature preference, and isotopic enrichment varied across habitats [gravel, rocks 10 cm – 50 cm in diameter), large rocks (>50 cm in diameter), vegetation-covered rocks, and alpine (snowfields and talus)], and habitat/microhabitat features were reliable predictors of species presence. Resource consumption among mid-elevation species on Mt. Rainier – the peak with the greatest species diversity – is highly overlapping. Species turnover and nestedness varied significantly across habitat gradients and peaks throughout this region and varied nearly significantly across sites. Across habitat types and sites, more similar species are more likely to coexist. These results suggest that environmental filtering is the primary process structuring this species assemblage, although we find detailed evidence for microhabitat niche partitioning among species of <em>Nebria</em> at the site-scale.</p>
Data from: Temporal changes in taxonomic and functional alpha and beta diversity across tree communities in subtropical Atlantic forests
<h2><strong>The study is published in Oikos and available at: <a href="https://doi.org/10.1111/oik.10961">https://doi.org/10.1111/oik.10961</a></strong></h2> <p>Here we aim to assess temporal taxonomic and functional alpha and beta diversity of adult and juvenile tree communities across 11 sites in the subtropical Brazilian Atlantic Forest to infer about trends and drivers of biodiversity change. The tree communities were evaluated for temporal changes in: (1) taxonomic and functional alpha diversity, (2) taxonomic and functional composition (beta diversity), and (3) identifying potential abiotic and biotic drivers of these changes, considering three censuses across a period of 10 years.</p> <p> </p> <h2>Files description:</h2> <p><strong>traits-adults.csv</strong> - adult tree species and their functional traits values.</p> <p><strong>traits-juveniles.csv</strong> - juvenile tree species and their functional trait values.</p> <p><strong>abundance-adults_synthesis.csv</strong> - adult tree species abundance over the three time periods of forest surveys (T1, T2, and T3). Raw data on tree individual level is available at ForestPlots.net database (<a href="https://forestplots.net/">https://forestplots.net/</a>) under request.</p> <p><strong>abundance-juveniles_synthesis.csv</strong> - juvenile tree species abundance over the three time periods of forest surveys (T1, T2, and T3). Raw data on tree individual level is available at ForestPlots.net database (<a href="https://forestplots.net/">https://forestplots.net/</a>) under request.</p> <p>Functional traits abbreviations are defined as follows: LA = leaf area; SLA = specific leaf area; WD = wood density; SM = seed mass; range_temp = range of mean annual temperature; range_CWD = range of climatological water deficit; and biomes_distrib = number of Brazilian biomes that the species occur according to Flora and Funga do Brazil.</p> <p> </p> <h2><strong>Acknowledgments</strong></h2> <p>This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (CAPES) – Finance Code 001, through Portal de Periódicos and scholarships granted to JMFK, JK and RCP. The fieldwork was supported by Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS grant numbers 2218 – 2551/12-2 and 19/2551-0001698-0), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq/FAPERGS/PELD number 441590/2020-9), and the Instituto Nacional de Ciência e Tecnologia (INCT) in Ecology, Evolution and Biodiversity Conservation, supported by MCTIC/CNPq (grant number 465610/2014-5). KMB gratefully acknowledge the financial support by the National Institute of Science and Technology in Low Carbon Emission Agriculture (INCT-ABC) sponsored by Brazil’s National Council for Scientific and Technological Development (CNPq, grant no. 406635/2022-6), the Foundation for Research Support of the State of Rio Grande do Sul (Fapergs, grant no. 22/2551-0000392-3), and the Ministry of Agriculture (MAPA). SCM is supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq; grant number 309659/2019-1.</p> <p> </p> <h3><strong>Please find below the data used in the study.</strong></h3>
Fig. 1 in Eukaryotic Microbial Communities Associated with Rock-dwelling Foliose Lichens: A Functional Morphological and Microecological Analysis
Fig. 1. Photograph of a portion of a Flavoparmelia thallus showing an example of a radially oriented lobe with three segments sampled in analyzing the microbial communities: A – inner, B – middle, and C – outer. Scale bar: 5 mm.
Figure 1 in sOilFauna - a global synthesis effort on the drivers of soil macrofauna communities and functioning
Figure 1. Location of the transects in the present version of the MACROFAUNA database (A) Map of the data (B) Location of the data in relation to the biomes.
Figure 3 in Impact of dike age on biodiversity and functional composition of soil macrofaunal communities in poplar forests in a reclaimed coastal area
Figure 3. PCoA ordinal configuration of soil macrofaunal communities from different habitats by Euclidean distance similarity index. In the code of the samples, the prefix means the code of the habitat, and the suffix means the number of the sample.
Figure 2 in Impact of dike age on biodiversity and functional composition of soil macrofaunal communities in poplar forests in a reclaimed coastal area
Figure 2. One-way ANOVA of taxonomic richness and abundance (A) and Margalef 's richness index R and Shannon– Weaver diversity index H' (B) across different habitats (mean ± SE). Means with different scripts are significantly different by Dunnett's T3 test (A) and LSD test (B), α = 0.05.
FIGURE 3 in Functional responses of stream fish communities to rural and urban land uses
FIGURE 3 | Flowchart of analysis. Biomass and dummy traits matrices were combined to produce functional diversity (FD) indices (FRic = functional richness, FEve = functional evenness, FDiv = functional divergence and FDis = functional dispersion) and community weight mean traits (CWM) matrices. The influences of land use/occupation (Soil matrix) over FD indices were evaluated through Pearson's correlations and over CWM through redundance analysis (RDA) and Pearson's correlations.
FIGURE 4 in Functional responses of stream fish communities to rural and urban land uses
FIGURE 4 | Ordination scores of community-weighted means (CWMs) of traits (gray bars) and proportions of land use/occupation (arrows: biplot scores for constraining variables along of the first principal axis of the redundancy analysis – RDA1) applied to 24 streams sampled in the state of Paraná, Brazil.
FIGURE 2 in Functional responses of stream fish communities to rural and urban land uses
FIGURE 2 | Ternary diagram of land use/occupation in the 24 streams sampled in the state of Paraná, Brazil.
FIGURE 1 in Functional responses of stream fish communities to rural and urban land uses
FIGURE 1 | Location of the sampling sites in the 24 streams in the state of Paraná, Brazil. Codes and names of streams in S1.
Fig. 7. Regression functions between the length and ratio L in Nematode morphometry and biomass patterns in relation to community characteristics and environmental variables in the Mekong Delta, Vietnam
Fig. 7. Regression functions between the length and ratio L/W with other characters (maturity index, feeding types) of nematodes at all stations. length L and genera richness S, maturity index MI (a); length L and percentage % of feeding type 1A and 2B (b); nematode width W with percentage of feeding type 2A (c); ratio L/W with the percentage of feeding type 2B (d).
Market forces determine the distribution of a leaky function in a simple microbial community
<p>Many biological functions are leaky, and organisms that perform them contribute some of their products to a community "marketplace" where non-performing individuals may compete for them. Leaky functions are partitioned unequally in microbial communities, and the evolutionary forces determining which species perform them and which become beneficiaries are poorly understood. Here we demonstrate that the market principle of comparative advantage determines the distribution of a leaky antibiotic resistance gene in an environment occupied by two "species" - strains of Escherichia coli growing on mutually exclusive resources and thus occupying separate niches. Communities comprised of antibiotic-resistant cells were rapidly invaded by sensitive cells of both types. While the two phenotypes coexisted stably for 500 generations, in 15/18 replicates, antibiotic sensitivity became fixed in one species. Fixation always occurred in the same species, despite both species being genetically identical except for their niche-defining mutation. In the absence of antibiotic, the fitness cost of resistance was identical in both species. However, the intrinsic resistance of the species that ultimately became the sole helper was significantly lower, and thus its reward for expressing the resistance gene was higher. Opportunity cost of resistance, not absolute cost or efficiency of antibiotic removal, determined which species became helper, consistent with the economic theory of comparative advantage. We present a model that suggests that this market-like dynamic is a general property of Black Queen systems, and in communities dependent on multiple leaky functions, could lead to the spontaneous development of an equitable and efficient division of labor.</p>
Changes in community-weighted trait mean, functional diversity, precipitation, temperature and surface area along an elevational gradient in Tenerife, Canary Islands
<p>This dataset comprises community-weighted trait means and functional diversity of leaf traits, precipitation, temperature and surface area of the elevational belt recorded in roadside (disturbed) and interior (less disturbed) plots, along an elevational gradient of 2,300 m in Tenerife, Canary Islands. The leaf traits measured were specific leaf area (SLA), nitrogen, carbon, phosphorous, nitrogen to carbon ratio, leaf dry matter content (LDMC), sodium, potassium and magnesium. The environmental variables measured are total precipitation of the growing season, mean temperature of the growing season and surface area of the elevation belt. This dataset has been used for the analysis presented in Ratier Backes et al. (in press). Mechanisms behind elevational plant species richness patterns revealed by a trait-based approach. <em>Journal of Vegetation Science</em>.</p>
Data for "Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms"
<p>This repository contains the data and external data used by teams in the Kaggle competition "HuBMAP+HPA - Hacking the Human Body" and is part of the paper "Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms".</p> <p>The directories contain:</p> <p><strong>data.zip:</strong> The training and test data, including metadata, used in the Kaggle competition "HuBMAP + HPA - Hacking the Human Body".</p> <p><strong>Team_1.zip: </strong>External data used by the first place winning solution.</p> <p><strong>Team_2.zip: </strong>External data used by the second place winning solution.</p>
Trained Models for "Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms"
<p>This repository contains the trained model weights for the baseline model and the winning solutions in the Kaggle competition "HuBMAP+HPA - Hacking the Human Body", and is part of the paper "Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms".</p> <p>The directory contains:</p> <p><strong>trained_model_1_weights.zip: </strong>Trained model weights for first place solution (Team 1).</p> <p><strong>trained_model_2_weights.zip:</strong> Trained model weights for second place solution (Team 2).</p> <p><strong>trained_model_3_weights.zip: </strong>Trained model weights for third place solution (Team 3).</p> <p><strong>trained_model_weights_baseline.zip:</strong> Trained model weights for the baseline model.</p>
Nutrient-based species selection is a prevalent driver of community assembly and functional trait space in tropical forests
<p><span>1. Soil nutrient availability and functional traits interact in complex ways during the assembly of tree communities hindering our understanding of the implications that this may have for their phylogenetic and functional diversity. </span></p> <p><span>2. We combined abundance, taxonomic, phylogenetic and functional trait data of 222 tree species distributed along nutrient concentration gradients at twenty-four plots in two tropical forest study sites. We analysed micro and macronutrient concentration in organic and topsoil horizons and tested for: (1) nutrient-based species sorting due to contrasting trait-environment relationships; (2) whether nutrient filtering has consequences for phylogenetic and functional diversity, and functional space size and occupancy; and (3) we mapped trait distributions across the phylogeny of tree species to track the evolutionary signature of nutrient availability.</span></p> <p><span>3. We found that total nitrogen (N), available phosphorus and total potassium in soil accounted for 68% of the variation in tropical tree species community composition, with strong associations with nutrient concentration for 89% of the tree species included in the analysis. This nutrient-based species selection was mediated by interactions between the three soil nutrient concentrations with leaf nitrogen, leaf thickness and wood density. Soil N concentration was positively associated with the functional space at the site level. At a plot level soil N concentration positively correlated with functional evenness and it was negatively associated with the functional space not occupied by any species in the tree community. Despite the phylogenetic conservatism of leaf N across tree lineages even when not considering legumes, many sister-species pairs show contrasting values which match with their habitat preferences thus indicating the evolutionary lability of this trait, particularly within recently diversified clades. </span></p> <p><span>4. Synthesis. Our results demonstrate that soil nutrient-based species selection is a prevalent driver of community assembly in tropical forests, a process mediated by key functional traits within the leaf and wood economics spectrum. Functional space size and its filling increase with soil nutrient concentration, whereas niche vacancy decreases. This selection process has likely influenced tropical tree species diversification patterns via habitat specialization.</span></p>
High functional diversity in deep-sea fish communities and increasing intra-specific trait variation with increasing latitude
<p>Variation in both inter- and intra-specific traits affect community dynamics, yet we know little regarding the relative importance of external environmental filters vs internal biotic interactions that shape the functional space of communities along broad-scale environmental gradients, such as latitude, elevation or depth. We examined changes in several key aspects of functional alpha-diversity for marine fishes along depth and latitude gradients by quantifying intra- and inter-specific richness, dispersion and regularity in functional trait space. We derived eight functional traits related to food acquisition and locomotion, and calculated seven complementary indices of functional diversity for 144 species of marine ray-finned fishes along large-scale depth (50 m – 1200 m) and latitudinal gradients (29° – 51° S) in New Zealand waters. Traits were derived from morphological measurements taken directly from footage obtained using Baited Remote Underwater Stereo-Video systems and museum specimens. We partitioned functional variation into intra- and inter-specific components for the first time using a PERMANOVA approach. We also implemented two tree-based diversity metrics in a functional distance-based context for the first time: namely, the variance in pairwise functional distance, and the variance in nearest-neighbour distance. Functional alpha diversity increased with increasing depth, and decreased with increasing latitude. More specifically, the dispersion and mean nearest-neighbour distances among species in trait space, and intra-specific trait variability all increased with depth, whereas functional hypervolume (richness) was stable across depth. In contrast, functional hypervolume, dispersion and regularity indices all decreased with increasing latitude; however, intra-specific trait variation increased with latitude, suggesting that intra-specific trait variability becomes increasingly important at higher latitudes. These results suggest that competition within and among species are key processes shaping functional multi-dimensional space for fishes in the deep sea. Increasing morphological dissimilarity with increasing depth may facilitate niche partitioning to promote coexistence, whereas abiotic filtering may be the dominant process structuring communities with increasing latitude.</p>
Microplastics effects on marine microbial communities and their functioning
<p><span>Microplastics pervade ocean ecosystems. Despite their effects on individuals or populations are well documented, the consequences of microplastics on ecosystem functioning, especially regarding lower trophic levels, are still largely unknown. Here we show how microplastics alter the structure and functioning of pelagic microbial ecosystems. Using experimental pelagic mesocosms, we found that microplastics indirectly affect marine productivity by changing the bacterial and phytoplankton assemblages. Specifically, the addition of microplastics increased phytoplankton biomass and shifted bacterial assemblages' composition. Such changes altered the interactions between heterotrophic and autotrophic microbes and the cycling of ammonia in the water column, which ultimately benefited photosynthetic efficiency. The effects of microplastics on marine productivity were consistent for different microplastic types. This study demonstrates that microplastics affect bacteria and phytoplankton communities and influence marine productivity, which ultimately alters the functioning of the whole ocean ecosystem.</span></p>
FIG. 4 in Lichen community assemblages and functional traits as indicators of vegetation types in central Mexico, based on herbarium specimens
FIG. 4. — Community weighted mean proportions of functional traits for each vegetation type: A, growth forms; B, substrate; C, reproductive structure types; D, photobionts.
FIG. 3 in Lichen community assemblages and functional traits as indicators of vegetation types in central Mexico, based on herbarium specimens
FIG. 3. — Ordination and clustering of lichen communities from the different vegetation types: A, non-parametric multidimensional scaling (NDMS); B, cluster analysis dendrogram. The sites Cerro el Capulín and Cerro Juan el Grande show different affinities in both analyses (part of the xerophytic shrubland in the NDMS, but more similar to the Quercus L. forest in the dendrogram, labeled as the Xerophytic-Quercus group in the latter).
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Allen Brain Atlas
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