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229 results for “community biodiversity”
Plant community responses to functional group and species removals along biodiversity experiment vegetation transects at the Jornada Basin LTER site, 1997-2002
This dataset contains vegetative cover data of plots that have had various plant functional groups or species experimentally removed at the Jornada Basin LTER site in southern New Mexico, USA. This data was collected with the objective to distinguish the differential effects of plant community biomass, functional groups, and biodiversity within functional groups on ecosystem and plant community function. To make these distinctions, treatments were established by the selective removal of plant species or functional groups within experimental plots. There are eight treatments: control (C, no removals); four functional group removal treatments (PG, perennial grass removed; S, shrubs removed; SSh, subshrubs removed; Succ, succulents removed), and three species richness manipulation treatments. Richness manipulations included a simplified treatment (Simp), where only the single most abundant species of each growth form is preserved and all other species in the growth form are removed, a reduced‐Larrea treatment (rL), where the Larrea is assumed to be the dominant and is removed while minority components remain, and a reduced-Prosopsis treatment (rP), where Prosopis rather than Larrea is removed as the shrub dominant. Following treatments, vegetative data was collected by sampling each plot along three transects twice a year (Spring and Fall) for 5 years from 1997-2002 (no data collected in 1998). This data set consists of the date of collection, plot number, treatment type, transect number, quadrat number, species codes, two diameters, height, condition, count, record IDs, and error codes. This study is complete.
Data and script: Community size can affect the signals of ecological drift and niche selection on biodiversity
<p>Updated version of the code. Data files are the same. This is the final version of the code, associated with a manuscript published in Ecology (doi: 10.1002/ecy.3014). A preprint is also available: https://www.biorxiv.org/content/10.1101/515098v1.abstract</p> <p>This is a unique dataset on insect communities sampled identically in a total of 200 streams in climatically highly different regions (100 in Brazil and 100 in Finland). The sampling design included 5 streams (communities) per watershed and provided us replicates of metacommunities (watersheds). Data also include information on in-stream variables (such as current velocity (m/s), depth (cm), stream width (cm), % of sand (0.25-2 mm), gravel (2-16 mm), pebble (16-64 mm), cobble (64-256 mm), and boulder (256-1024 mm), % of canopy cover by riparian vegetation, pH, conductivity, total nitrogen, and total phosphorus) and catchment level variables (such as average slope, % of native forest cover, pasture, agriculture, planted forests, urban areas, mining, water bodies, bare soil, secondary forest cover, and mixed land uses).</p> <p>In addition to the dataset, here we also provide and R code used to investigate the relationship between beta diversity and community size. This code calculates 4 types of beta-diversity metric for each of 100 watersheds (5 streams) in Brazil and Finland. Beta diversity: Sorensen and Bray-Curtis dissimilarity between all pairs. Beta deviation from null models: Raup-Crick (vegan version) and Bray-Curtis beta-deviation (based on the scripts by Chris Catano and Jonathan Myers). These beta diversity metrics are modelled against community size, environmental heterogeneity and spatial extent.</p> <p> </p>
Genome size influences plant growth and biodiversity responses to nutrient fertilization in diverse grassland communities
Experiments comparing diploids with polyploids and in single grassland sites show that nitrogen and/or phosphorus availability influences plant growth and community composition dependent on genome size; specifically plants with larger genomes grow faster under nutrient enrichments relative to those with smaller genomes. However, it is unknown if these effects are specific to particular site localities with speciifc plant assemblages, climates, and historical contingencies. To determine the generality of genome size dependent growth responses to nitrogen and phosphorus fertilisation, we combined genome size and species abundance data from 27 coordinated grassland nutrient addition experiments in the Nutrient Network that occur in the Northern Hemisphere across a range of climates and grassland communities. We found that after nitrogen treatment, species with larger genomes generally increased more in cover compared to those with smaller genomes, potentially due to a release from nutrient limitation. Responses were strongest for C3 grasses and in less seasonal, low precipitation environments, indicating that genome size effects on water-use-efficiency modulates genome size-nutrient interactions. Cumulatively the data suggest that genome size is informative and improves predictions of species’ success in grassland communities.
Data from: Individual energetics scale up to community coexistence: Movement, metabolism and biodiversity dynamics in fragmented landscapes
<p>Unraveling the intricate mechanisms that govern community coexistence remains a daunting challenge, particularly amidst ongoing environmental change. To understand the response of individual animals to environmental change, physiology and individual metabolism are often studied. However, this perspective is currently largely lacking in community ecology. We argue that the integration of individual metabolism into community theory can offer new insights into coexistence. We present the first individual-based metabolic community model for a terrestrial mammal community to simulate energy dynamics and home range behavior in different environments. Using this model, we investigate how ecologically similar species coexist and maintain their energy balance under food competition. Only if individuals of different species are able to balance their incoming and outgoing energy over the long-term will they be able to coexist. After thoroughly testing and validating the model against real-world patterns such as of home range dynamics and field metabolic rates, we applied it as a case study to scenarios of habitat fragmentation - a widely discussed topic in biodiversity research. First, comparing single-species simulations with community simulations, we find that the effect of habitat fragmentation on populations is strongly context-dependent. While populations of species living alone in the landscape were mostly positively affected by fragmentation, the diversity of a community of species was highest under medium fragmentation scenarios. Under medium fragmentation, energy balance and reproductive investment were also most similar among species. We therefore suggest that similarity in energy balance among species promotes coexistence. We argue that energetics should be part of community ecology theory, as the relative energetic status and reproductive investment can reveal why and under what environmental conditions coexistence is likely to occur. As a result, landscapes can potentially be protected and designed to maximize coexistence. The metabolic community model presented here can be a promising tool to investigate other scenarios of environmental change or other species communities to further disentangle global change effects and preserve biodiversity.</p>
Figure 3 in Effect of land cover on biodiversity and composition of a soil macrofauna community in a reclaimed coastal area at Yancheng, China
Figure 3. The dendrogram of cluster analysis on soil macrofauna from different habitats with Bray–Curtis similarity by paired groups method (A: Uncultivated land; B: Bulrush land; C: Wheat farm; D: Poplar forest; E: Metasequoia forest).
Figure 2 in Effect of land cover on biodiversity and composition of a soil macrofauna community in a reclaimed coastal area at Yancheng, China
Figure 2. One-way ANOVA on taxonomic richness and abundance, Margalef 's richness index (R) and Shannon-Weaver diversity index (H') among different habitats (Mean ± SE). The means with different scripts are significantly different by SNK test, α = 0.05.
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.
Data from: Biodiversity forecasting in natural plankton communities reveals temperature and biotic interactions as key predictors
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Data from: Individual energetics scale up to community coexistence: Movement, metabolism and biodiversity dynamics in fragmented landscapes
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Biodiversity facets, canopy structure and surface temperature of grassland communities
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Data from: Multi-scalar drivers of biodiversity: local management mediates wild bee community response to regional urbanization
It is critical to understand the specific drivers of biodiversity across multiple spatial scales, especially within rapidly urbanizing areas, given the distinct management recommendations that may result at each scale. However, drivers of biodiversity patterns and interactions between drivers are often only measured and modeled at a single scale. In this study, we assessed bee community composition at three time periods in 20 grassland and 20 agriculture sites located across two major metroplexes. We examined how local environmental variables and surrounding landscape composition impact bee abundance, richness, and evenness, including comparisons between groups with different nesting strategies and body sizes. We collected nearly 13,000 specimens and identified 172 species. We found that levels of regional land-use differentially impacted bee abundance and diversity depending on local habitat management. Specifically, within agriculture sites, bee richness was greater with increasing landscape-level semi-natural habitat, while in grassland sites, bee richness was similar across landscapes regardless of semi-natural habitat cover. Bee evenness at both site types declined with increasing landscape-level habitat heterogeneity, due to an increase of rare species at the grassland sites, but not in the agricultural sites; further indicating that diversity is driven by the interaction of local habitat quality and landscape-level habitat composition. We additionally found that agriculture sites supported higher abundances, but not richness, of small-bodied and below-ground nesting bees, while grassland sites supported higher abundances of above-ground nesting bees, and higher richness of large-bodied species. Increased levels of local bare ground were significantly related to multiple metrics of bee diversity, including greater below-ground nesting bee abundance and richness. Local floral richness was also significantly related to increases of overall bee abundance, as well as the abundance and richness of small bees. Overall, we suggest that local land managers can support bee abundance and diversity by conserving areas of bare soil and promoting native floral diversity, the latter especially critical in highly urban agricultural spaces. Our results provide the first documentation of significant interactions between local habitat management and landscape composition impacting insect communities in urban systems, indicating that bee conservation practices depend critically on land-use interactions across multiple spatial scales.
Data from: Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding
<p>Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focused on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic 'protists', with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro-eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro-eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods, and brings us closer to a full inventory of extant marine biodiversity.</p>
Supplementary material 2: Seu Nico Community Dynamics from: Tree Diversity and Dynamics of the Forest of Seu Nico, Viçosa, Minas Gerais, Brazil - Biodiversity Data Journal 3: e5425 (31 July 2015) https://doi.org/10.3897/BDJ.3.e5425
2868 tree occurrences from two census within 100 plots of 10x10 m in the Forest of Seu Nico (FSN), Viçosa municipality, Minas Gerais, Brazil, including measurements of each tree as well as environmental data from all 100 plots. Dataset consists of seven independent files
Rare species biodiversity, socio-demographics and local and landscape characteristics in Northern California community urban gardens
<p>Cities are sometimes characterized as homogenous with species assemblages composed of abundant, generalist species having similar ecological functions. Under this assumption, rare species, or species observed infrequently, would have especially high conservation value in cities for their potential to increase functional diversity. Management to increase the number of rare species in cities could be an important conservation strategy in a rapidly urbanizing world. However, most studies of species rarity define rarity in relatively pristine environments where human management and disturbance is minimized. We know little about what species are rare, how many species are rare, and what management practices promote rare species in urban environments. Here, we identified which plants and species of birds and bees that control pests and pollinate crops are rare in urban gardens and assessed how social, biophysical factors, and cross-taxonomic comparisons influence rare species richness. We found overwhelming numbers of rare species, with over 50% of plant cultivars observed classified as rare. Our results highlight the importance of women, older individuals, and gardeners who live closer to garden sites in increasing the number of rare plants within urban areas. Fewer rare plants were found in older gardens and gardens with more bare soil. There were more rare bird species in larger gardens and more rare bee species where canopy cover was higher. We also found that in some cases, rarity begets rarity, with positive correlations found between the number of rare plants and bee species and between bee and bird species. Overall, our results suggest that urban gardens include a high number of species existing at low frequency and that social and biophysical factors promoting rare, planned biodiversity can cascade down to promote rare, associated biodiversity.</p>
Figure 1 in Impact of dike age on biodiversity and functional composition of soil macrofaunal communities in poplar forests in a reclaimed coastal area
Figure 1. Distribution of sample sites on the reclaimed coast.
Data from: Surrogate taxa and fossils as reliable proxies of spatial biodiversity patterns in marine benthic communities
Rigorous documentation of spatial heterogeneity (β-diversity) in present-day and preindustrial ecosystems is required to assess how marine communities respond to environmental and anthropogenic drivers. However, the overwhelming majority of contemporary and palaeontological assessments have centred on single higher taxa. To evaluate the validity of single taxa as community surrogates and palaeontological proxies, we compared macrobenthic communities and sympatric death assemblages at 52 localities in Onslow Bay (NC, USA). Compositional heterogeneity did not differ significantly across datasets based on live molluscs, live non-molluscs, and all live organisms. Death assemblages were less heterogeneous spatially, likely reflecting homogenization by time-averaging. Nevertheless, live and dead datasets were greater than 80% congruent in pairwise comparisons to the literature estimates of β-diversity in other marine ecosystems, yielded concordant bathymetric gradients, and produced nearly identical ordinations consistently delineating habitats. Congruent estimates from molluscs and non-molluscs suggest that single groups can serve as reliable community proxies. High spatial fidelity of death assemblages supports the emerging paradigm of Conservation Palaeobiology. Integrated analyses of ecological and palaeontological data based on surrogate taxa can quantify anthropogenic changes in marine ecosystems and advance our understanding of spatial and temporal aspects of biodiversity.
Dataset for: Using plant traits to understand the contribution of biodiversity effects to annual crop community productivity
<p>Dataset for: Using plant traits to understand the contribution of biodiversity effects to annual crop community productivity</p>
Community biomass is driven by dominants and their characteristics –the insight from a field biodiversity experiment with realistic species loss scenario
<p>1. Revealing the role of biodiversity in ecosystem functioning (BEF) has been a major focus of ecological research over recent decades. In general, results from artificially assembled communities point to the important role of biodiversity showing that the loss of species has a negative effect on various ecosystem functions (mostly assessed by aboveground peak biomass). However, the evidence from manipulations of natural communities is scarce and results are often contradictory between these two approaches. In particular, the importance of species dominance for ecosystem functioning remains poorly understood.</p> <p>2. We created a gradient of plant species richness in a meadow community following a realistic species loss scenario (removal of less abundant species) to test the effect of diversity on community biomass and assess the importance of subordinate species compared to dominants in a five-year experiment.</p> <p>3. Contrasting with the results of BEF experiments with artificial assembly, we did not find any relationship between plant species diversity and aboveground biomass across the timeframe of the experiment. We provide evidence that dominant species' identity and traits are the main drivers of community biomass, because dominant species were able to maintain biomass production after substantial species loss. Further, dominants prevented community biomass from declining and biomass was indirectly influenced not by species richness but through differences in functional diversity. Our results support the mass ratio hypothesis, showing a much bigger effect of dominant species on community biomass production and hints at the rather minor importance of the complementarity effect between species. We emphasize that BEF research should more focus on the role of dominant species in maintaining various ecosystem functions.</p> <p>4. Synthesis. Species diversity is a poor predictor of community aboveground biomass production and dominant species can effectively compensate the total production after substantial loss of other species in a grassland community.</p>
Microevolutionary processes in a foundation tree inform macrosystem patterns of community biodiversity and structure
<p class="MDPI17abstract"><span>Despite an increased focus on multiscale relationships and interdisciplinary integration, few macroecological studies consider the contribution of genetic-based processes to landscape-scale patterns.<strong> </strong>We tested the hypothesis that tree genetics, climate, and geography jointly drive continental-scale patterns of community structure, using genome-wide SNP data from a broadly distributed foundation tree species (<a><em>Populus fremontii</em></a></span><span class="MsoCommentReference"><span> </span></span><span>S. Watson) and two dependent communities (leaf-modifying arthropods and fungal endophytes) spanning southwestern North America. Four key findings emerged: (1) Tree genetic structure was a significant predictor for both communities; however, the strength of influence was both scale- and community-dependent. (2) Tree genetics was the primary driver for endophytes, explaining 17% of variation in continental-scale community structure, whereas (3) climate was the strongest predictor of arthropod structure (24%). (4) Power to detect tree genotype<a><span>—</span></a></span><span>community phenotype associations changed with scale of genetic organization, increasing from individuals to populations to ecotypes, emphasizing the need to consider nonstationarity (i.e., changes in the effects of factors on ecological processes across scales) when inferring macrosystem properties. Our findings highlight the role of foundation tree species as drivers of macroscale community structure and provide macrosystems ecology with a theoretical framework for linking fine- and intermediate-scale genetic processes to landscape-scale patterns. Management of genetic diversity harbored within foundation species is a critical consideration for conserving and sustaining regional biodiversity.</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
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.