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.
4,034
datasets available to search
ShareScore release 0.7.1
Dataset results
4,034 results for “Species associations”
Data from: Species abundance fluctuations over 31 years are associated with plant-soil feedback in a species-rich mountain meadow
<p>1. Increasing evidence suggest that plant-soil interactions play an essential role in plant community assembly processes. Empirical investigations show that plant species abundance in the field is often related to plant-soil biota interactions, however, the direction of these relations have yielded inconsistent results.</p> <p>2. We combined unique 31-year long field data on species abundances from a species-rich mountain meadow with single time point plant-soil feedback greenhouse experiments of 24 co-occurring plant species. We tested whether these relations were dynamic in time, whether coupled increases and decreases in abundance between years were related to plant-soil feedback and whether these changes were underlain by years in which manuring was applied.</p> <p>3. The prevailingly negative relationship between plant-soil feedback and plant relative abundance in the field was significantly time-dependent, which may reconcile the contrasting results in literature. Furthermore, significant coupled oscillations appeared between species relative abundance changes and plant-soil feedback, which were likely moderated by years in which manuring was applied. Our results are consistent with the notion that the more abundant species are stabilised by negative plant-soil feedback, and the less abundant species co-vary with the fluctuations of these more competitive species.</p> <p>4. Synthesis: Our results project plant-soil feedback as an important regulatory mechanism in plant communities, operating in conjunction with a species' competitive ability and soil nutrient availability. We suggest that negative feedback is particularly prominent in more abundant plant species that profit from more readily available soil nutrients than less abundant species with positive feedback. Negative plant-soil feedback may thus prevent more abundant plant species from outcompeting less abundant plant species, facilitating stable species co-existence.</p>
Closely related tree species support distinct communities of seed-associated fungi in a lowland tropical forest
<p>Previous theoretical work has highlighted the potential for natural enemies to mediate the coexistence of species with similar life-histories via density-dependent effects on survivorship. For plant pathogens to play this role, they must differ in their ability to infect or induce disease in different host plant species. In tropical forests characterized by high diversity, these effects must extend to phylogenetically closely related species pairs. Mortality at the seed and seedling stage strongly influences the abundance and distribution of tropical tree species, but the host preferences and spatial distributions of fungi are rarely determined.</p> <p>We examined how host species identity, relatedness, and seed viability influence the composition of fungal communities associated with seeds of four co-occurring pioneer trees (<em>Cecropia insignis</em>, <em>C. longipes</em>, <em>C. peltata</em>, and <em>Jacaranda copaia</em>). Seeds were buried in mesh bags in five common gardens in the understory of a lowland tropical forest in Panama and retrieved at intervals from 1-30 months. A subset of the seeds in each bag was used to determine germination success. One half of each remaining seed was tested for viability; the other half was used to culture and identify seed-infecting fungi.</p> <p>Seeds were infected by fungi after burial. Although fungal communities differed in viable vs. dead seeds, and across burial locations, community composition primarily varied as a function of plant species identity (30.7% of variation in community composition vs. 4.5% for viability and location together), even for congeneric <em>Cecropia</em> species. Phylogenetic reconstruction showed that relatedness of fungi mostly reflected differences between <em>Jacaranda</em> (Bignoniaceae) and <em>Cecropia</em> (Urticaceae).</p> <p>Although the proportion of germinable seeds decreased gradually over time for all species, intraspecific variation in survival was high at the same location (e.g., ranging from 0-100% for <em>C. peltata</em>) suggesting variable exposure or susceptibility to seed pathogens.</p> <p>Synthesis: Our study provides evidence under field conditions that congeneric tree species with similar life-history differ markedly in seed-associated fungal communities when exposed to the same soilborne fungi. This is a critical first step supporting pathogen mediated coexistence of closely related tree species.</p>
Figure 5 in A new species and new record of Agistemus Summers (Acari: Stigmaeidae) associated withCapsicum annuum L. var.glabriusculum (Solanaceae) from Northeastern of Mexico
Figure 5 Agistemus piquinnusn. sp. (male); A – Leg I, B – Leg II, C – Leg III, D – Leg IV.
Figure 2 in A new species and new record of Agistemus Summers (Acari: Stigmaeidae) associated withCapsicum annuum L. var.glabriusculum (Solanaceae) from Northeastern of Mexico
Figure 2 Agistemus piquinnusn. sp. Gnathosoma; A – Female, B – Male.
Figure 3 in A new species and new record of Agistemus Summers (Acari: Stigmaeidae) associated withCapsicum annuum L. var.glabriusculum (Solanaceae) from Northeastern of Mexico
Figure 3 Agistemus piquinnusn. sp. (female); A – Leg I, B Leg II, C – Leg III, D – Leg IV.
Drought survival is positively associated with high turgor loss points in temperate perennial grassland species
<p>1. Turgor loss point (π<sub>tlp</sub>) has been suggested to be a key trait for drought resistance in woody species. In herbaceous grassland species the role of π<sub>tlp</sub> for species drought survival has not yet been tested, although grasslands are projected to experience more frequent and intense droughts with climate change.</p> <p>2. To gain insights into the role of π<sub>tlp</sub> for drought resistance of temperate perennial grassland species, we assessed π<sub>tlp</sub> of 41 species common in Germany (20 forbs, 21 grasses). We directly related them to the species' comparative whole-plant drought survival and midday leaf water potentials under drought (Ψ<sub>MD</sub>) assessed in a common garden drought experiment, and to species moisture association.</p> <p>3. Species drought survival increased with increasing π<sub>tlp</sub> across all species as well as within forbs or grasses separately. Ψ<sub>MD</sub> was positively related to π<sub>tlp</sub> and drought survival. Our results imply that high π<sub>tlp</sub> promotes drought survival of common perennial European temperate mesic grassland species by enabling them to maintain high leaf water potentials under drought, i.e., a desiccation avoidance strategy. However, π<sub>tlp</sub> was not related to species moisture association.</p> <p>4. The positive relationship between π<sub>tlp</sub> and drought survival in herbaceous grassland species was opposite to the negative relationship previously established in woody plants, implying that mechanisms of drought resistance differ between woody and herbaceous species. Our results highlight the necessity of directly testing the relationship of functional traits to whole-plant drought survival in different plant life forms, before using trait assessments for predicting plant responses to drought.</p>
Data from: Evidence for facilitation among avian army-ant attendants: specialization and species associations across elevations
Mixed-species assemblages can involve positive and negative interactions, but uncertainty about high-value patchy resources can increase the value of information sharing among heterospecific co-foragers. I sampled species composition of bird-flocks attending army-ant raids in three adjacent elevation zones in Costa Rica, across multiple years, to test for positive and negative associations among raid-attending bird species. My goal was to test whether the most frequent and specialized raid-attending species showed evidence of facilitating or excluding other bird species. I quantified elevational variation in avian community composition at raids, then asked whether species composition was associated with variation in flock characteristics (flock size and species richness). I identified the most frequent raid-attending species (those that attended raids most frequently relative to their mist-net capture rates), and bird species that performed specialized army ant-following behavior (bivouac-checking, which allows birds to memorize and track mobile army-ant colonies). There was significant turnover of bird species among zones (including the frequent and specialized attendants); patterns of species overlap suggested a gradual transition from a Pacific-slope to an Atlantic-slope raid-attending bird fauna. Raid-attendance frequency was positively correlated with bivouac-checking behavior. With few exceptions, the most frequent raid-attending bird species, and the bivouac-checking species, also participated in the most species-rich flocks. High species-gregariousness suggests many of the frequently attending and/or bivouac-checking species functioned as core flock members. However, some bird species pairs were significantly negatively associated at raids. Despite species turnover, per-flock numbers of birds at raids did not differ among geographic zones, but flocks on the Pacific-slope were heavier because larger bodied bird species attended raids. Previous studies showed that the size (biomass) of bird-flocks corresponds to the amount of food the birds kleptoparasitize from ant raids, and the heavier Pacific-slope bird-flocks could have greater negative kleptoparasitic impacts.
Data from: Architectural differences associated to functional traits among 45 coexisting tree species in central Africa
1. Architectural traits that determine the light captured in a given environment are an important aspect of the life-history strategies of tropical tree species. In this study, we examined how interspecific variation in architectural traits is related to the functional traits of 45 coexisting tree species in central Africa. 2. At the tree level, we measured tree diameter, total height and crown dimensions for an average of 30 trees per species (range 14–72, total 968 trees) distributed over a large range of diameters (up to 162 cm). Using log-log models, we fitted species-specific allometric relationships between tree diameter, height and crown dimensions. At the species level, we derived architectural traits (height and crown dimensions) at 15 cm and maximum diameters from species-specific allometries. The architectural traits were then related to functional traits, including light requirements, wood density, leaf habit, and dispersal mode. 3. Among the 45 coexisting tree species, we identified strong variations in height and crown allometries, along with architectural traits derived from these species-specific allometries. There was a positive correlation among architectural traits, suggesting that large-statured canopy species were taller and had larger and deeper crowns than small-statured understory species at all ontogenic stages. The relationships between architectural and functional traits highlighted a continuum of species between the large-statured canopy species and the small-statured understory species. In this moist and seasonal forest, large-statured canopy species tended to be light-demanding, wind-dispersed, deciduous and large contributors to forest biomass (high basal area), while small-statured understory species tended to be shade-tolerant, animal-dispersed, evergreen and most abundant in terms of stem density. 4. Our results highlighted strong architectural differences among coexisting tropical tree species in central Africa. The relationships between architectural and functional traits provided insights into the life-history strategy of tropical tree species.
Hierarchical multi-grain models improve descriptions of species' environmental associations, distribution, and abundance
<p>The characterization of species' environmental niches and spatial distribution predictions based on them are now central to much of ecology and conservation, but implicitly requires decisions about the appropriate spatial scale (i.e. <i>grain</i>) of analysis. Ecological theory and empirical evidence suggest that range-resident species respond to their environment at two characteristic, hierarchical spatial grains: (i) <i>response grain</i>, the (relatively fine) grain at which an individual uses environmental resources, and (ii) <i>occupancy grain</i>,<i> </i>the (relatively coarse) grain equivalent to a typical home range. We use a multi-grain (MG) occupancy model, aided by fine-grain remotely sensed imagery, to simultaneously estimate species-environment associations at both grains, conduct grain optimization to measure response grain, and apply this analysis framework to an example species: a medium-sized bird (<i>Tockus deckeni</i>) in a heterogeneous East African landscape. Based on home range analysis of movement data, we calculate an occupancy grain of 1km for <i>T. deckeni</i>. Using a grain optimization procedure across 32 grains from 10m to 500m, we identify 60m as the most strongly supported response grain for a suite of environmental variables, slightly coarser than opportunistic behavioral observations would have suggested. Validation confirms that the accuracy of the optimized MG occupancy model substantially exceeds that of equivalent single-grain (SG) occupancy models. We further use a simulation approach to assess the potential impacts of accounting for the multi-scale structure of species' environmental requirements on estimates of population size. We find that the more strongly supported MG approach consistently predicts a minimum population sizes in the study landscape that is much lower than that provided by the SG model. This suggests that SG approaches commonly used in conservation applications could lead to overly optimistic abundance and population estimates and that the MG approach may be more appropriate for supporting species conservation goals. More generally, we conclude that multi-grain approaches of the sort presented, and increasingly enabled by growing high-resolution remotely sensed data, hold great promise for offering a more mechanistic framework for assessing the appropriate grain(s) for population monitoring and management and enable more reliable estimates of abundances and species' distributions.</p>
Figure 1 in Bat species composition associated with restinga lagoons from the Paulo César Vinha State Park, Espírito Santo, Brazil
Figure 1. Location of the Paulo Cesar Vinha State Park – PEPCV within Brazil, State of Espírito Santo and Guarapari. Latter A and B are the Sampled point one (P1) and two (P2), letter C and D are Feia and Vermelha lagoon, respectively.
Figure 4 in Bat species composition associated with restinga lagoons from the Paulo César Vinha State Park, Espírito Santo, Brazil
Figure 4. Principal Component Analyses of the bat composition in the Paulo CesarVinha State Park – PEPCV,Espírito Santo,Brazil.Ordination was performed by species abundance and the matrix was transformed by Hellinger procedure.
Figure 3 in Bat species composition associated with restinga lagoons from the Paulo César Vinha State Park, Espírito Santo, Brazil
Figure 3. Observed and estimated bat species richness in the tree lagoons sampled in the Paulo Cesar Vinha State Park – PEPCV, Espírito Santo, Brazil. (A) 'Caraís' lagoon, (B) 'Feia' lagoon, (C) 'Vermelha' lagoon, and (D) Final observed and estimated species richness. Vertical bars represent 95% confidence intervals.
Figure 3 in Diversity of Diptera species associated with pig carcasses in a Brazilian city exposed to high rates of homicide
Figure 3. Similarity analysis (Clusters dendrogram) of the diversity of necrophagous Diptera species between decomposition stages: (A) in the season dry and (B) season rainy.
Figure 1 in Diversity of Diptera species associated with pig carcasses in a Brazilian city exposed to high rates of homicide
Figure 1. (A) Location of sample sites in the Dois Irmãos State Park in Recife and (B) structure used in the attraction and collection of insects.
Data from: Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste
A citizen science project found that the greenhouse camel cricket (Diestrammena asynamora) is common in North American homes. Public response was to wonder "what good are they anyway?" and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical, and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, a hide beetle (Dermestes maculatus) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified capable of growth on lignocellulosic components, including lignin. Cedecea lapagei was selected for further study due to growth on most lignocellulose components. The C. lapagei secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically-guided discovery of novel organisms.
Genotypic variation in an ecologically important parasite is associated with host species, lake, and spore size
<p>Genetic variation in parasites has important consequences for host-parasite interactions. Prior studies of the ecologically important parasite <i>Metschnikowia bicuspidata</i> have suggested low genetic variation in the species. Here, we collected <i>M. bicuspidata</i> from two host species (<i>Daphnia dentifera</i> and <i>Ceriodaphnia dubia</i>) and two regions (Michigan and Indiana, USA). Within a lake, outbreaks tended to occur in one host species but not the other. Using microsatellite markers, we identified six parasite genotypes grouped within three distinct clades, one of which was rare. Of the two main clades, one was generally associated with <i>D. dentifera,</i> with lakes in both regions containing a single genotype. The other <i>M. bicuspidata</i> clade was mainly associated with <i>C. dubia</i>, with a different genotype dominating in each region. Despite these associations, both <i>D. dentifera-</i> and <i>C. dubia</i>-associated genotypes were found infecting both hosts in lakes. However, in lab experiments, the <i>D. dentifera</i>-associated genotype infected both <i>D. dentifera</i> and <i>C. dubia</i>, but the <i>C. dubia</i>-associated genotype, which had spores that were approximately 30% smaller, did not infect <i>D. dentifera. </i>We hypothesize that variation in spore size might help explain patterns of cross-species transmission. Future studies exploring the causes and consequences of variation in spore size may help explain patterns of infection and the maintenance of genotypic diversity in this ecologically important system.</p>
Data from: Impact of the invasive alien topmouth gudgeon (Pseudorasbora parva) and its associated parasite Sphaerothecum destruens on native fish species
<p>Two datasets belonging to the paper "Impact of the invasive alien topmouth gudgeon (<i>Pseudorasbora parva</i>) and its associated parasite <i>Sphaerothecum destruens</i> on native fish species" published in Biological Invasions (https://doi.org/10.1007/s10530-019-02114-6), is provided here. The first dataset consists of individual measured and weighed fish per sampled water body. In case a large number (>50) of the same species and length were encountered, a representative number was weighed and measured, and the remaining individuals were only counted. The second dataset consists of parameters related to morphology and water quality, and number of specimens found per fish species, of each sampled water body. Below, methodological information is provided on the study site, the sampling process, and the water sample analysis. For references, see the published paper in Biological Invasions.</p><p> </p><p>Study site</p><p>We selected 54 water bodies (oxbow lakes, shallow lakes and ponds) in river floodplains of the IJssel, Meuse, Nederrijn and Waal River. These water bodies were selected using the following criteria: a) Potential presence of <i>P. parva</i> according to the Dutch National Database Flora and Fauna, b) No permanent hydrological connection with the main stream or a side channel, c) Similarity in habitat characteristics (e.g., depth and surface area, for habitat characteristics per sampling site), d) Suitability for sampling with a seine net. These criteria were set to reduce variance in the fish species composition created by habitat variables, as our aim was to detect effects caused by <i>P. parva</i>. The areas of sampled water bodies ranged from 100 to 80,000 m2. In total 54 sites located in the floodplains were visited and sampled using a seine net (21 m long, 2.4 m high, mesh size 4x4 to 10x10 mm). Fifteen sites could not be sampled sufficiently with this gear type due to high vegetation cover and/or water depth. Hence, 39 sites were included in the analyses of effect on fish assemblages and body condition. The coordinate system used here concerns Amersfoort RD (EPSG: 28992). </p><p> </p><p>Sampling</p><p>Sampling of the fish populations was carried out from October to December 2015. The seine net was used while wading and provided adequate data on juvenile and small fishes in shallow habitats. The sampling area ranged from 0.04 to 82.35% of the surface area of water bodies and was used to calculate fish densities (number of fish m-2). All caught fishes were identified, weighed (accuracy 0.05 g) and their total lengths (TL, from tip of snout to longer caudal fin lobe, accuracy 1 mm) measured in the field. Young of the year (YOY) were distinguished, based on length. Each individual was assigned to being a YOY, based on known YOY thresholds in the Netherlands. Small fishes (<35 mm) were pooled for weighting. In case a large number (>50) of the same species and length were encountered, a representative number was weighed and measured, and the remaining individuals were only counted. Subsequently, the fishes were released. </p><p>Habitat and soil parameters which included coverage percentage of aquatic vegetation, littoral vegetation, and substrate (mud, sand, gravel and rocks), and tree branches in the water were visually estimated. The water transparency (cm) was determined using a Secchi disk (measured vertically). Water temperature (°C), conductivity (μS cm-1) and salinity (PSU) were measured at the site with the use of a Model 30 meter (YSI incorporated). A water sample was taken and at the same day pH and alkalinity (eq l-1) were measured in the laboratory. Water samples in polyethylene bottles were stored in the freezer at a maximum storage time of 75 days until analysis. Metal ions were analysed using an ICP analyser (Thermo Electron corporation IRIS Intrepid ΙΙ XDL). Concentrations of nitrate (NO3-), ammonium (NH4+), phosphate (PO43-), chloride (Cl-) and potassium (K+) were determined using an Auto Analyzer 3 system (Bran and Luebbe, Norderstedt Germany). Physico-chemical data is missing for site 39 due to loss of the sample.</p><p> </p><p>Abstract</p><p>The Asian cyprinid <i>Pseudorasbora parva</i> is considered to be a major threat to native fish communities and listed as an invasive alien species of European Union concern. Our study aims to gain evidence-based knowledge on the impact of both <i>P. parva</i> and it parasite <i>Sphaerothecum destruens</i> on native fish populations by analysing fish assemblages and body condition of individuals of native fish species in floodplain water bodies that were invaded and uninvaded by <i>P</i>. <i>parva</i>. We explored the use of environmental DNA (eDNA) techniques to detect <i>S. destruens</i>. Prevalence of <i>S. destruens</i> in native fish species was assessed. Fish samplings showed significantly negative correlations between the abundance of <i>P. parva</i> and the native <i>Leucaspius delineatus</i>, and <i>Pungitius pungitius</i> and three biodiversity indices of the fish assemblages (Simpson's diversity index, Shannon-Wiener index and evenness). Contrastingly, the abundances of the native <i>Gasterosteus aculeatus</i> and <i>P. parva</i> were positively related. In nearly all isolated water bodies with <i>P. parva</i>, this species is outnumbering native fish species. No effect of <i>P. parva</i> presence was found on body condition of native fish species. <i>Sphaerothecum destruens</i> was demonstrated to occur in both <i>P. parva</i> and <i>G. aculeatus</i>. <i>Gasterosteus aculeatus</i> is suggested to be an asymptomatic carrier that can aid the further spread of <i>S. destruens,.</i> Analysis of eDNA proved to be a promising method for early detection of <i>S. destruens</i>, here showing that <i>S. destruens</i> presence coincided with <i>P. parva</i> presence. The ongoing invasion of both <i>P. parva</i> and <i>S. destruens</i> is predicted to pose a significant risk to native fish communities.</p>
Fig. 12 in New Genera and Species of Oak-Associated Phylini (Heteroptera: Miridae: Phylinae) from Western North America
Fig. 12. Distribution of species of the genera Crassomiris, Phallospinophylus, and Pygovepres.
Fig. 13 in New Genera and Species of Oak-Associated Phylini (Heteroptera: Miridae: Phylinae) from Western North America
Fig. 13. Distribution of species of the genera Quercophylus, Rubellomiris, and Rubeospineus.
Fig. 3 in New Genera and Species of Oak-Associated Phylini (Heteroptera: Miridae: Phylinae) from Western North America
Fig. 3. Head and male genitalic structures of Crassomiris spp. and Phallospinophylus setosus.
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.