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88 results for “biodiversity in ecological communities”
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>
Figure 8 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation
Figure 8. Vegetation predictors of the pimpline community across traps (n = 30). (a) Epiphyte density against log richness; (b) herb ground cover against the log of inverse Simpson's Index of Diversity;
Figure 7 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation
Figure 7. Pimplinae community composition, as measured by the first axis of a Non-Metric Multidimensional Scaling analysis (NMDS1, see Figure 6) across sampling sites (n = 15), against the first Principal Component (PC1) of the habitat variables at those sites (see Table 4). The line is the linear regression (±95% CI in gray). The figure demonstrates that pimpline community composition is very strongly associated with differences in habitat characteristics across sites.
Figure 6 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation
Figure 6. An ordination using Non-metric Multidimensional Scaling (NMDS) of the pimpline community at the site level. Black numbers and points indicate the 15 sampling sites, going from the bottom of the mountain (1) to the top (15). Species are in gray, small lettering.
Figure 4 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation
Figure 4. Pimplinae wasp community metrics against elevation (altitude) across 30 traps. (a) Abundance; (b) Log10 Species Richness; (c) Log10 Simpson's Index (1/D); and (d) Shannon Index. Lines are the equations of the polynomial linear model in Table 2 with the lowest AICc, ±95%CI; (a,b): cubic models (c,d): quadratic models.
Figure 2 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation
Figure 2. Some of the Pimplinae wasp species sampled (all are females). (a) Dolichomitus megalourus (scale bar 4 mm), 10 individuals sampled; (b) Neotheronia charli (scale bar 1 mm), 24 individuals sampled; (c) Neotheronia sp. 6 (scale bar 1 mm), 26 individuals sampled; (d) Pimpla caerulea (scale bar 1 mm), 447 individuals sampled; (e) Polysphincta organensis (scale bar 2 mm), 19 individuals sampled; and (f) Polysphincta teresa (scale bar 2 mm), 8 individuals sampled.
Figure 3 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation
Figure 3. Species richness of pimplines against sampling intensity. (a) Estimates of total species richness against number of traps sampled (filled circles: observed data; open circles: bootstrap; diamonds: first-order jackknife; triangles: Chao; squares: second-order jackknife); (b) site-level rarefaction (±SD); (c) trap-level rarefaction (±SD); (d) mean individual-level rarefaction for the whole data (top line) and altitudinally-zoned subsets (from top to bottom, 332–549 m, 703–887 m, 952–1071 m, 110–150 m, and 1236–1482 m, which are superimposed, 1649–1812 m and 1935–2169 m), points are literature-based data covering the same span of sampling intensities for comparison from [45]. Note the log scale on the y-axis.
Figure 1 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation
Figure 1. (a) Location of the Serra dos Órgãos National Park (gray shaded area), a protected tropical Atlantic Rain Forest in the State of Rio de Janeiro, southeast Brazil. (b) Map of the 15 study sites and their respective altitudes along the elevational gradient in the Park, where four different phytophysiognomies are observed: (c) lower montane forest (up to 500 m), which presents a 20 m high canopy but normally no other well-defined forest layers; (d) montane forest (500 m to 1500 m), with its clear stratification into arboreal, shrub, and herb layers, and large emergent trees reaching 40 m covered with abundant lianas and epiphytes; (e) high montane forest (1500 m to 2000 m) with smaller trees of up to 10 m covered with mosses and epiphytes, and great diversity of shrubs; and (f) high-altitude grassland, also known as campos de altitude (above 2000 m), dominated by herbal vegetation growing around rocks and scattered shrubs.
Figure 5. Pimplinae wasp community metrics against mean monthly temperature across 15 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation
Figure 5. Pimplinae wasp community metrics against mean monthly temperature across 15 sites. (a) Abundance; (b) Log10 Species Richness; (c) Log10 Simpson's Index (1/D); and (d) Shannon Index. Lines are the equations of the model in Table 3 ± 95%CI. (a) cubic model; (b,d) quadratic models; and (c): linear model.
Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics
High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science.
Data from: Ecological genomics meets community-level modeling of biodiversity: mapping the genomic landscape of current and future environmental adaptation
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Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics
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Ecological interactions shape the evolution of flower colour in communities across a temperate biodiversity hotspot
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Molecular ecological network analyses: An effective conservation tool for the assessment of biodiversity, trophic interactions, and community structure
<p>Global biodiversity is threatened by the anthropogenic restructuring of animal communities, which rewires species interaction networks in real-time as individuals are extirpated or introduced. Conservation science and adaptive ecosystem management demands more rapid, quantitative, and non-invasive technologies for robustly capturing changing biodiversity and quantifying species interactions. Here we develop molecular ecological network analyses (MENA) as an ecosystem assessment tool to address these needs. To construct the ecological network, we used environmental DNA from feces to identify the plant and mammal diet of two carnivores: puma (<i>Puma concolor</i>) and bobcat (<i>Lynx rufus</i>); two omnivores: coyote (<i>Canis latrans</i>) and gray fox (<i>Urocyon cinereoargenteus</i>); and two herbivores: black-tailed deer (<i>Odocoileus hemionus</i>) and black-tailed jackrabbit (<i>Lepus californicus)</i> in a well-studied Californian reserve<i>. </i>To evaluate MENA as a comprehensive biodiversity tool, we applied our framework to identify the structure of the network, patterns of trophic interactions, key species, and to assess its utility in capturing the biodiversity of the area. The high dietary taxonomic resolution enabled the assessment of species diversity, niche breadth and overlap. The network analysis revealed a dense ecological network with a high diversity of weakly connected species and a community that is highly modular and non-nested. The significant prevalence of tri-trophic chain and exploitative competition patterns indicates (i) the removal or reintroduction of a top predator would trigger a trophic cascade within this community, directly affecting their prey and indirectly the plant communities, and (ii) the potential impact of indirect effects between two predators that consume the same prey. These results suggest that the recent resurgence of puma in the study area may impact the herbaceous and woody vegetation and the population size of other predators. This effect of fluctuating predator populations and plant communities could be predicted through MENA's fine-scale assessment of the diet selection and the identified keystone species. Although just using a subset of species, MENA more rapidly, accurately, and effectively captured the broader biodiversity of the area in comparison to other methodologies. MENA reconstructed and unveiled the hidden complexity in trophic structure and interaction networks within the community, providing a promising toolkit for biodiversity and ecosystem management.</p>
Figure 9 from: Perissinotto R, Bird MS, Bilton DT (2016) Predaceous water beetles (Coleoptera, Hydradephaga) of the Lake St Lucia system, South Africa: biodiversity, community ecology and conservation implications. ZooKeys 595: 85-135. https://doi.org/10.3897/zookeys.595.8614
Figure 9 - Peltodytes sp. 4.10 mm, iSimangaliso Wetland Park, Western Shores (site 6), February 2015 DT Bilton, MS Bird & R Perissinotto leg.
Figure 8 from: Perissinotto R, Bird MS, Bilton DT (2016) Predaceous water beetles (Coleoptera, Hydradephaga) of the Lake St Lucia system, South Africa: biodiversity, community ecology and conservation implications. ZooKeys 595: 85-135. https://doi.org/10.3897/zookeys.595.8614
Figure 8 - Haliplus natalenis Wehncke, 1880 3.72 mm, iSimangaliso Wetland Park, False Bay (site 27), January 2015 DT Bilton, MS Bird & R Perissinotto leg.
Figure 71 from: Perissinotto R, Bird MS, Bilton DT (2016) Predaceous water beetles (Coleoptera, Hydradephaga) of the Lake St Lucia system, South Africa: biodiversity, community ecology and conservation implications. ZooKeys 595: 85-135. https://doi.org/10.3897/zookeys.595.8614
Figure 71 - Laccophilus cryptos Biström, Nilsson & Bergsten, 2015 2.5 mm, iSimangaliso Wetland Park, Western Shores (site 2), July 2014 MS Bird leg.
Figure 70 from: Perissinotto R, Bird MS, Bilton DT (2016) Predaceous water beetles (Coleoptera, Hydradephaga) of the Lake St Lucia system, South Africa: biodiversity, community ecology and conservation implications. ZooKeys 595: 85-135. https://doi.org/10.3897/zookeys.595.8614
Figure 70 - Laccophilus canthydroides Omer-Cooper, 1957 3.24 mm, iSimangaliso Wetland Park, Eastern Shores (site 23), February 2015 DT Bilton, MS Bird & R Perissinotto leg.
Figure 73 from: Perissinotto R, Bird MS, Bilton DT (2016) Predaceous water beetles (Coleoptera, Hydradephaga) of the Lake St Lucia system, South Africa: biodiversity, community ecology and conservation implications. ZooKeys 595: 85-135. https://doi.org/10.3897/zookeys.595.8614
Figure 73 - Laccophilus simplicistriatus Gschwendtner, 1932 3.8 mm, iSimangaliso Wetland Park, Eastern Shores (site 21), February 2015 DT Bilton, MS Bird & R Perissinotto leg.
Figure 72 from: Perissinotto R, Bird MS, Bilton DT (2016) Predaceous water beetles (Coleoptera, Hydradephaga) of the Lake St Lucia system, South Africa: biodiversity, community ecology and conservation implications. ZooKeys 595: 85-135. https://doi.org/10.3897/zookeys.595.8614
Figure 72 - Laccophilus contiro Guignot, 1952 3.30 mm, iSimangaliso Wetland Park, Eastern Shores (site 14), February 2015 DT Bilton, MS Bird & R Perissinotto leg.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
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.