Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
79
datasets available to search
ShareScore release 0.7.1
Dataset results
79 results for “environmental filtering”
Dataset and R code used in "Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes"
<p>Dataset and R code used for the manuscript:</p> <p>Von Eggers, J. M., Wisnoski, N. I., Calder, J. W., Capo, E., Groff, D. V., Krist, A. C., & Shuman, B. (2024). Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes. <em>Environmental Microbiology</em>, 26(3), e16607.</p> <p>This dataset and code are also available on GitHub (<a href="https://github.com/jvoneggers/WYLakeSedMicrobes">https://github.com/jvoneggers/WYLakeSedMicrobes</a>).</p>
Data and scripts for: Idiosyncratic responses to biotic and environmental filters in wood-inhabiting fungal communities
<p>These files include the data, the scripts, and the pipeline for bioinformatic analyses for reproducing the results presented in the manuscript "<em>Idiosyncratic responses to biotic and environmental filters in wood-inhabiting fungal communities</em>".</p> <p>Description of the files can be found from the README.docx file.</p>
FIGURE 3 in Habitat modification driven by land use as an environmental filter on the morphological traits of neotropical stream fish fauna
FIGURE 3 | Representation of significant associations (p <0.05) identified by the fourth-corner method in the factorial map of the RLQ analysis. Red denotes a positive relationship between morphological traits and environmental variables, blue indicates a negative relationship, and grey represents nonsignificant relationships. Codes: Cond: Conductivity, Rock: Rocky substrate, Woody: Woody debris, Turb: Turbidity, Backw: Backwater, DO: Dissolved Oxygen, Temp: Temperature. See acronyms for the morphological traits in Tab. S3.
FIGURE 1 in Habitat modification driven by land use as an environmental filter on the morphological traits of neotropical stream fish fauna
FIGURE 1 | Study area. Location of sampling sites according with land use covers: S1 -Manoel Gomes, S2 - Pedregulho, S3 - Arquimedes, S4 - Bom Retiro, S5 - Rio da Paz, S6 - Nene, S7 - Cascavel, S8 - Afluente do Quati, and S9 - Quati.
FIGURE 2 in Habitat modification driven by land use as an environmental filter on the morphological traits of neotropical stream fish fauna
FIGURE 2 | Relationship between morphological traits and environmental variables of the first two axes of the RLQ of the species along the lower Iguaçu River. The figures of the fish were added to illustrate the species. Codes: Woody: Woddy debris, Cond: Conductivity, Rocky: Rocky substrate, Turb: Turbidity, Backw: Backwater, DO: Dissolved Oxygen, Temp: Temperature, Anc: Ancystrus sp., Syn: Synbranchus sp., Hyp: Hypostomus sp., Hep: Heptapterus sp., Cam: Cambeva sp., Cor: Corydoras sp., Rha: Rhamdia sp., Geo: Geophagus sp., Ast: Astyanax sp., Psa: Psalidodon sp., Bry: Bryconamericus sp., Gym: Gymnotus sp., Hop: Hoplias sp., Pha: Phalloceros sp., Poe: Poecilia sp.
Environmental vs. biotic filtering: what if species traits contribute to both?
Open the record for dataset details and reuse information.
Data from: Floral organs act as environmental filters and interact with pollinators to structure the yellow monkeyflower (Mimulus guttatus) floral microbiome
Open the record for dataset details and reuse information.
Trait coordination and environmental filters shape functional trait distributions of forest understory herbs
We test the importance of environmental filtering and trait covariance for structuring the functional traits of understory herbaceous communities.
Data from: Spatially-explicit depiction of a floral epiphytic bacterial community reveals role for environmental filtering within petals
<p>The microbiome of flowers (anthosphere) is an understudied compartment of the plant microbiome. Within the flower, petals represent a heterogeneous environment for microbes in terms of resources and environmental stress. Yet little is known of drivers of structure and function of the epiphytic microbial community at the within-petal scale. We characterized the petal microbiome in two co-flowering plants that differ in pattern of ultraviolet (UV) absorption along their petals. Bacterial communities were similar between plant hosts, with only rare phylogenetically distant species contributing to differences. The epiphyte community was highly culturable (75% of families) lending confidence to the spatially-explicit isolation and characterization of bacteria. In one host, petals were heterogeneous in UV absorption along their length and in these there was a negative relationship between growth rate and position on the petal, as well as lower UV tolerance in strains isolated from the UV absorbing base than from UV reflecting tip. A similar pattern was not seen in microbes isolated from a second host whose petals had uniform patterning along their length. Across strains, variation in carbon utilization and chemical tolerance followed common phylogenetic patterns. This work highlights the value of petals for spatially-explicit explorations of bacteria of the anthosphere.</p>
Data from: Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales
Whether niche processes, like environmental filtering, or neutral processes, like dispersal limitation, are the primary forces driving community assembly is a central question in ecology. Here, we use a natural experimental system of isolated tree "islands" to test whether environment or geography primarily structures fungal community composition at fine spatial scales. This system consists of isolated pairs of two distantly-related, congeneric pine trees established at varying distances from each other and the forest edge, allowing us to disentangle the effects of geographic distance versus host and edaphic environment on associated fungal communities. We identified fungal community composition with Illumina sequencing of ITS amplicons, measured all relevant environmental parameters for each tree - including tree age, size, and soil chemistry - and calculated geographic distances from each tree to all others and to the nearest forest edge. We applied generalized dissimilarity modeling to test whether total and ectomycorrhizal fungal (EMF) communities were primarily structured by geographic or environmental filtering. Our results provide strong evidence that, as in many other organisms, niche and neutral processes both contribute significantly to turnover in community composition in fungi, but environmental filtering plays the dominant role in structuring both free-living and symbiotic fungal communities at fine spatial scales. In our study system, we found pH and organic matter primarily drive environmental filtering in total soil fungal communities and that pH and cation exchange capacity – and, surprisingly, not host species - were the largest factors affecting EMF community composition. These findings support an emerging paradigm that pH may play a central role in the assembly of all soil mediated systems.
Data from: Environmental filtering structures fungal endophyte communities in tree bark
<p>The factors that control the assembly and composition of endophyte communities across plant hosts remains poorly understood. This is especially true for endophyte communities inhabiting inner tree bark, one of the least studied components of the plant microbiome. Here, we test the hypothesis that bark of different tree species acts as an environmental filter structuring endophyte communities, as well as the alternative hypothesis, that bark acts as a passive reservoir that accumulates a diverse assemblage of spores and latent fungal life stages. We develop a means of extracting high‐quality DNA from surface sterilized tree bark to compile the first culture‐independent study of inner bark fungal communities. We sampled a total of 120 trees, spanning five dominant overstorey species across multiple sites in a mixed temperate hardwood forest. We find that each of the five tree species harbour unique assemblages of inner bark fungi and that angiosperm and gymnosperm hosts harbour significantly different fungal communities. Chemical components of tree bark (pH, total phenolic content) structure some of the differences detected among fungal communities residing in particular tree species. Inner bark fungal communities were highly diverse (mean of 117–171 operational taxonomic units per tree) and dominated by a range of Ascomycete fungi living asymptomatically as putative endophytes. Together, our evidence supports the hypothesis that tree bark acts as an environmental filter structuring inner bark fungal communities. The role of these potentially ubiquitous and plant‐specific fungal communities remains uncertain and merits further study.</p>
Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests
<p><span><span><span><span><span><span><span><span><span><span><span>Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical datasets are required to account for taxon- and context-dependency but relevant research in understudied areas is often compromised by the taxonomic impediment<span><span>. </span></span>We here employed haplotype-level community DNA metabarcoding, enabled by stringent filtering of Amplicon Sequence Variants (ASVs), to characterize metacommunity structure of soil microarthropod assemblages across a mosaic of five forest habitats on the Troodos mountain range in Cyprus. We found similar β diversity patterns at ASV and species (OTU, Operational Taxonomic Unit) levels, which pointed to a primary role of habitat filtering resulting in the existence of largely distinct metacommunities linked to different forest types. Within-habitat turnover was correlated to topoclimatic heterogeneity, again emphasizing the role of environmental filtering. However, when integrating landscape matrix information for the highly fragmented <i>Quercus alnifolia</i> habitat, we also detected a major role of spatial isolation determined by patch connectivity, indicating that stochastic and niche-based processes synergistically govern community assembly. Alpha diversity patterns varied between ASV and OTU levels, with OTU richness decreasing with elevation and ASV richness following a longitudinal gradient, potentially reflecting a decline of genetic diversity eastwards due to historical pressures. Our study demonstrates the utility of haplotype-level community metabarcoding for characterising metacommunity structure of complex assemblages and improving our understanding of biodiversity dynamics across mountainous landscapes worldwide.</span></span></span></span></span></span></span></span></span></span></span></p>
Habitat area and environmental filters determine avian richness along an elevation gradient in mountain peatlands
<p>Globally, relationships between avian richness and elevation in mountain ecosystems typically reflect one of four well-documented patterns, but the mechanisms responsible for these patterns are poorly understood. We investigated which pattern best described bird species richness in peatlands of the Upper Bow Basin of the Canadian Rocky Mountains (1300 to 2000 m a.s.l.) and used a model competition framework to investigate possible mechanisms. Avian richness displayed a plateauing (cubic) relationship in response to increasing elevation (AICc weight = 0.48). Log richness was significantly positively related to log peatland area (R<sup>2</sup> = 0.42, p = 0.001); however, once we accounted for the richness-area relationship (area was not related to elevation (R<sup>2</sup> = 0.13, p = 0.083)), the richness-elevation relationship was best described by a negative linear model rather than a cubic model (AICc weight = 0.69, R<sup>2</sup> = 0.39). Consequently, we reject the neutral model of the mid-domain effect and conclude that peatland area and one or more environmental filters are simultaneously driving relationships between avian richness and elevation in Rocky Mountain peatlands. Multi-causality likely explains why researchers in different geographies observe inconsistent patterns between richness and elevation: drivers and interactions among drivers may vary spatially. Importantly, Natural Subregion was a stronger predictor of avian species richness than elevation per se (AICc weight = 0.96), suggesting that the responsible environmental filter(s) is relatively homogenous within ecological land classes (e.g., primary productivity) rather than directly variable with elevation (e.g., temperature). The results also lend insight into priorities for future research on richness-elevation patterns in mountain birds.</p>
Nuanced qualitative trait approaches reveal environmental filtering and phylogenetic constraints on lichen communities
<p>We propose that a qualitative trait approach based on more detailed nuanced traits may reveal previously overlooked patterns, especially when combined with phylogenetic perspectives. By sampling epiphytic lichens and using a functional approach based on nuanced qualitative traits, such as a much greater resolution over photobiont identity, type of cortex and chemical compounds, we evaluated the effects of environmental filtering and phylogenetic constraints on community assembly along natural succession of Atlantic rainforest. We found changes in taxonomic, functional and phylogenetic composition, structure and diversity. Functional traits such as photobiont genera, type of cortex, reproductive structures, propagule size and protection strategies showed strong responses to succession. Mature forests with a closed canopy impose strong environment filtering that is reflected in lichen species turnover, limiting diversity, but also holding different functional and phylogenetic composition. The use of a nuanced qualitative trait approach may overcome some of the limitations of using this type of traits and show the importance of often overlooked key lichen functional traits, including presence of carbon concentrating mechanisms in photobionts and cortex properties. Furthermore, this is the first study showing how patterns of phylogenetic assembly along forest succession structure lichen communities.</p>
Partner fidelity and environmental filtering preserve stage-specific turtle ant gut symbioses for over 40 million years
<p><span>Sustaining beneficial gut symbioses presents a major challenge for animals, Including holometabolous insects. Social insects may meet such challenges through behavioral symbiont transfer and transgenerational inheritance through colony founders. We address such potential through colony-wide explorations across 13 eusocial, holometabolous ant species in the genus <em>Cephalotes</em>. Through amplicon sequencing and qPCR, we show that previously characterized worker microbiomes are largely conserved across adult castes, that adult microbiomes exhibit strong trends of phylosymbiosis, and that <em>Cephalotes</em> cospeciate with their most abundant adult symbionts. We find, also, that winged queens harbor worker-like microbiomes prior to colony founding, suggesting that vertical inheritance promotes ancient partner fidelity. While some adult-abundant symbionts colonize guts of larvae, microbiomes from this stage are by environmental bacteria from the Enterobacteriales, Lactobacillales, and Actinobacteria. Re-acquisition of such bacteria, each generation, for >40 million years suggests conserved environmental filtering and, hence, a second mechanism behind distinct symbioses divided by metamorphosis.</span></p>
Data from: Environmental filtering of macroinvertebrate traits influences ecosystem functioning in a large river floodplain
<p>The Biodiversity-Ecosystem Function hypothesis postulates that higher biodiversity is correlated with faster ecosystem process rates and increased ecosystem stability in fluctuating environments. Exhibiting high spatio-temporal habitat diversity, floodplains are highly productive ecosystems, supporting communities that are naturally resilient and highly diverse. </p> <p>We examined linkages among floodplain wetland habitats, invertebrate communities and their associated traits, and ecosystem function across 60 sites within the floodplain wetlands of the lower Wolastoq | Saint John River, New Brunswick, using structural equation modelling and Threshold Indicator Taxa ANalysis (TITAN2). </p> <p>We identified key environmental filters structuring invertebrate communities, by linking increased niche differentiation through shoreline change, flood pulse dynamics, and macrophyte bed complexity with increased taxa and functional diversity. </p> <p>Examination of traits linked to ecosystem functions revealed that more resilient wetlands with balance between primary productivity and decomposition as carbon sources were associated with greater functional evenness and richness, while habitat patches with elevated decomposition rates had lower functional richness, reflecting a simplified, more disturbed habitat. </p> <p>While our more complex overarching SEM model was ultimately compromised by an overspecified number of pathways, our results nevertheless are indicative of a divergence between wetland and riverine ecosystems in their relationships linking biodiversity and ecosystem function, illustrating how to define ecosystem health in wetland habitats, and demonstrating how critical functions support healthy wetland habitats by providing increased resilience to disturbance.</p>
Do large-scale associations in birds imply biotic interactions or environmental filtering?
<p><strong>Aim</strong>: There has been a wide interest in the effect of biotic interactions on species' occurrences and abundances at large spatial scales, coupled with a vast development of the statistical methods to study them. Still, the evidence whether the effects of within-trophic level biotic interactions (e.g. competition and heterospecific attraction) are discernible beyond local scales remains inconsistent. Here, we present a novel hypothesis-testing framework based on joint dynamic species distribution models (JDSDMs) and functional trait similarity to dissect between environmental filtering and biotic interactions. </p> <p><strong>Location</strong>: France and Finland. </p> <p><strong>Taxon</strong>: Birds. </p> <p><strong>Methods</strong>: We estimated species-to-species associations within a trophic level, independent of the main environmental variables (mean temperature and total precipitation) for common species at large spatial scale with joint dynamic species distribution models (VAST). We created hypotheses based on species' functionality (morphological and/or diet dissimilarity) and habitat preferences about the sign and strength of the pairwise spatio-temporal associations to estimate the extent to which they result from biotic interactions (competition, heterospecific attraction) and/or environmental filtering. </p> <p><strong>Results</strong>: Spatio-temporal associations were mostly positive (80%), followed by random (15%), and only 5% were negative. Negative spatio-temporal associations in different communities were due to a few species when they existed. The relationship between spatio-temporal association and functional dissimilarity among species was negative, which fulfills the predictions of both environmental filtering and heterospecific attraction. </p> <p><strong>Main conclusions: </strong>We showed that processes leading to species aggregation (mixture between environmental filtering and heterospecific attraction) seem to dominate assembly rules, and we did not find evidence for competition. Altogether, hypothesis-testing framework based on joint dynamic species distribution models and functional trait similarity is beneficial in ecological interpretation of species-to-species associations from the long-term large-scale data. </p>
Can short-term data accurately model long-term environmental exposures? Investigating the multigenerational adaptation potential of Daphnia magna to environmental concentrations of organic ultraviolet filters
<p>Organic ultraviolet filters (UVFs) are contaminants of concern, ubiquitously found in many aquatic environments due to their use in personal care products to protect against ultraviolet radiation. Research regarding the toxicity of UVFs such as avobenzone, octocrylene and oxybenzone indicates that these chemicals may pose a threat to invertebrate species; however, minimal long-term studies have been conducted to determine how these UVFs may affect continuously exposed populations. The present study modeled the effects of a 5-generation exposure of <em>Daphnia</em> <em>magna</em> to these UVFs at environmental concentrations. Avobenzone and octocrylene resulted in minor, transient decreases in reproduction and wet mass. Oxybenzone exposure resulted in > 40% mortality, 46% decreased reproduction and 4-fold greater reproductive failure over the F0 and F1 generations; however, normal function was largely regained by the F2 generation. These results indicate that <em>Daphnia</em> are able to acclimate over long-term exposures to concentrations of 6.59 μg/L avobenzone, ~0.6 μg/L octocrylene or 16.5 μg/L oxybenzone. This suggests that short-term studies indicating high toxicity may not accurately represent long-term outcomes in wild populations, adding additional complexity to risk assessment practices at a time when many regions are considering or implementing UVF bans in order to protect these most sensitive invertebrate species.</p>
Large-scale restoration of species-rich dry grasslands on arable land: Environmental filtering drives successful species establishment over a period of 10 years
<p>Sowing of regionally specific seed mixtures on former arable land is increasingly used to restore species-rich grasslands, but it often faces important obstacles in environmental conditions and colonisation from preserved surrounding grasslands. Long-term landscape scale studies, which explore the processes governing plant establishment from seed mixtures and later colonisation from the surrounding landscape are scarce. We studied the species and functional trait composition of 32 grasslands restored 1–11 years before the first sampling by sowing regional seed mixtures in the White Carpathian Mts (SE Czech Republic). We compared them with 23 well-preserved permanent grasslands in their surroundings. In each grassland we estimated plant species cover in three plots of 25 m<sup>2</sup>, in restored grasslands in 2009, 2014 and 2019, in permanent grasslands in 2009. The species composition of the restored grasslands converged towards the permanent grasslands due to expansion of dry grassland species and retreat of mesic grassland and weed species. The majority (60–71%) of the vegetation cover of restored grasslands was formed by sown species, while the species number was mainly determined by colonising unsown species (61–63%). The species number of restored grasslands remained lower than that in permanent grasslands. Functional trait composition (Community Weighted Mean) of the sown seed mixtures, permanent grasslands and restored grasslands overlapped in all three samplings. With increasing grassland age, species with resource-retaining traits of low specific leaf area and high leaf dry matter content, lower stature, higher seed mass, and lower capacity for clonal reproduction expanded. Functional trait diversity of the plots was mostly lower than expected by null model randomisations of community, which indicates strong environmental filtering. Comparison of newly colonising species and extinct species indicated that mainly species with traits similar to the rest of the community are able to colonise the grasslands successfully. Synthesis and applications. Sowing of regionally specific seed mixtures was successful and demonstrated to be a fast way of grassland restoration, particularly in terms of functional trait composition. The resulting species diversity depended on the colonisation processes, which are controlled by the functional composition of the local communities.</p>
Data from: leaf functional diversity and environmental filtering in a tropical dry forest: comparison between two geological substrates
<p><span>The role of geological substrate in shaping plant community functional diversity remains poorly understood. Considering the involvement of leaves in the energy, water and nutrient economics of plants, we hypothesized that leaves experience geology-related filtering, impacting functional attributes and functional leaf community diversity on different substrates. We studied tropical dry forest communities on limestone and siliciclastic phyllite-derived soils, comparing their functional diversity and soil physico-chemical properties. We predicted the most benign habitat (less severe filter) to be associated with higher leaf functional diversity and an acquisitive strategy prevalence, while the more stressful habitat should show conservative leaf traits and lower leaf functional diversity. We measured six traits in 31 common tree species (representing ~80% of community crown cover): leaf area, specific leaf area, leaf thickness, leaf dry matter content, petiole length, and leaf blade narrowness. Leaf functional diversity was assessed through the functional trait dispersion metric. Intraspecific functional variation was examined in 25 species shared between substrates. The limestone substrate was more fertile (higher phosphorous) with higher water retention, while phyllite had higher nitrogen and lower humidity. Principal component analysis segregated plots by substrate, with limestone plots being more clustered. Community leaf functional diversity was higher in the limestone forest. Most species examined showed inter-substrate trait differences in at least one leaf functional trait. The two substrates constituted distinct growth environments, with the more benign substrate associated to higher community functional leaf diversity. The intraspecific analysis revealed the prevalence of acquisitive traits in the more benign and more conservative traits in the more stressful habitat. This study advances our understanding of the role of geological substrate as an environmental filter in tropical dry forest, influencing leaf functional responses and emphasizing the importance of intraspecific functional variation.</span></p>
ScienceDex guides
Understand access before you commit
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.