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.
129
datasets available to search
ShareScore release 0.9.0
Dataset results
129 results for “Diversity dependence”
Diversity loss from multiple interacting disturbances is regime-dependent
<p>Data and R code for 'Diversity loss from multiple interacting disturbances is regime-dependent'.</p> <p>Information about the files can be found in the ._README.txt file.</p>
Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification
One of the primary goals of macroevolutionary biology has been to explain general trends in long-term diversity patterns, including whether such patterns correspond to an up-scaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity-dependent diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time-dependence without diversity-dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time-dependent, but diversity-independent model that matches the expected diversity through time of a diversity-dependent model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity-dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity-dependence. We advocate that tests encompassing additional data, e.g., traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.
Supporting data: Grain-dependent responses of mammalian diversity to land-use and the implications for conservation set-aside
<p>Camera trap and live trap datasets underlying the analyses in an <em>Ecological Applications </em>paper (http://onlinelibrary.wiley.com/doi/10.1890/15-1363/abstract), provided in .csv format. Each row consists of a single trap night at a given location, with species in different columns. Old-growth forest, logged forest and oil palm plantation locations have the prefixes "Old", "Log" and "Palm", respectively. Values in each cell are the number of independent captures, as defined in the paper. </p>
Research data supporting "Sequence-Dependent Self-Assembly and Structural Diversity of Islet Amyloid Polypeptide-Derived β-Sheet Fibrils"
<p>Research data supporting the publication:</p> <p>Wang, S.-T. et al., 2017, Sequence-Dependent Self-Assembly and Structural Diversity of Islet Amyloid Polypeptide-Derived β-Sheet Fibrils, ACS Nano, http://dx.doi.org/10.1021/acsnano.7b02325</p>
Native plant diversity creates microbial legacies that either promote or suppress non-natives, depending on drought history
<p>High-diverse native plant communities resist non-native plants more strongly than low-diverse communities, in part through resource competition. Yet, the role of soil biota is largely unknown, although non-native plants interact with soil biota. Here, we tested the responses of non-native plants to soil conditioned by different native plant diversities. We applied well-watered and dry treatments in the conditioning and response phases to explore the effects of historical and contemporary environmental stresses. Historical water conditions determined the effects of native diversity via soil biota on responding non-natives grown in well-watered environments. Non-native growth decreased with native species richness for well-watered soil inocula but increased for dry soil inocula. However, non-native growth in dry environments did not depend on conditioning native species richness of soil inocula. We provide a new understanding of mechanisms behind diversity-invasibility relationships and demonstrate that temporal variation in environmental stress shapes relationships among native plant diversity, soil biota, and non-native plants.</p>
Fig 5 in Species Diversity Of Wetland Birds, Depending On Area, Overgrowth Of Water Bodies On The Example Of Sovskie Ponds (Ukraine)
Fig 5. Percentage of species under conditions of overgrowth of a reservoir with macrophytes, a - 5% overgrowth, b - 90% overgrowth, c - 45% overgrowth, d - 55% overgrowth, e - 65% overgrowth.
Fig. 3 in Diversity and density-dependence relationship between hymenopteran egg parasitoids and the corn leafopper (Hemiptera: Cicadellidae) in maize agroecosystem vs. teosinte wild habitat
Fig. 3. Relationship between the number of exposed Dalbulus maidis eggs and number of Anagrus virlai within the crop maize habitat on (A) maize sentinel plants, and (B) teosinte sentinel plants.
Fig. 1 in Diversity and density-dependence relationship between hymenopteran egg parasitoids and the corn leafopper (Hemiptera: Cicadellidae) in maize agroecosystem vs. teosinte wild habitat
Fig. 1. Relationship between the number of exposed Dalbulus maidis eggs and number of adult parasitoids (of any species) found in the crop maize habitat on (A) maize sentinel plants, and (B) teosinte sentinel plants.
Scale-dependent diversity-biomass relationships can be driven by tree mycorrhizal association and soil fertility
<p><span>Diversity–biomass relationships (DBRs) often vary with spatial scale in terrestrial ecosystems, but the mechanisms driving these scale-dependent patterns remain unclear, especially for highly heterogeneous forest ecosystems. This study explores how mutualistic associations between trees and different mycorrhizal fungi (i.e., arbuscular mycorrhizal (AM) vs. ectomycorrhizal (EM) association) modulate scale-dependent DBRs. We hypothesized that in soil-heterogeneous forests with a mixture of AM and EM tree species, (i) AM and EM tree species respond in contrasting ways (i.e., positively vs. negatively respectively) to increasing soil fertility, (ii) AM tree dominance contributes to higher tree diversity and EM tree dominance contributes to greater standing biomass and that as a result, (iii) mycorrhizal associations exert an overall negative effect on DBRs across spatial scales. To empirically test these hypotheses, we collected </span><span>detailed tree distribution and soil information (nitrogen, phosphorus, organic matter, pH, etc.) from seven temperate and subtropical AM-EM mixed forest mega-plots (16–50 ha). Using spatial codispersion null model and structural equation modeling, we identified the relationships among AM or EM tree dominance, soil fertility, tree species diversity and biomass, and thus DBRs across 0.01–1 ha scales. We found first evidence overall supporting the above three hypotheses in these AM-EM mixed forests: (i) In most forests, with increasing soil fertility tree communities changed from EM-dominated to AM-dominated. (ii) Increasing AM tree dominance had an overall positive effect on tree diversity and a negative effect on biomass, even after controlling for soil fertility and number of trees. Together, (iii) the changes in mycorrhizal dominance along soil fertility gradients weakened the positive DBR observed at 0.01–0.04 ha scales in nearly all forests and drove negative DBRs at 0.25–1 ha scales in four out of seven forests. Hence, this study highlights a soil-related mycorrhizal dominance mechanism that could partly explain why in many natural forests, biodiversity-ecosystem functioning (BEF) relationships shift from positive to negative with increasing spatial scale.</span></p>
Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification
Open the record for dataset details and reuse information.
Scale-dependent diversity-biomass relationships can be driven by tree mycorrhizal association and soil fertility
Open the record for dataset details and reuse information.
Native plant diversity generates microbial legacies that either promote or suppress non-natives, depending on drought history
Open the record for dataset details and reuse information.
Resolving the context-dependency of local heterogeneity-diversity relationships across rocky reefs worldwide
Open the record for dataset details and reuse information.
Weed dataset - Crop diversity Experiment - Crop-weed relationships are context-dependent and cannot fully explain the positive effects of intercropping on yield
<p>This shows the weed mass per species and crop yield per species of each plot described in the experiment. </p>
Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
<pre>This repository contains data related to: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels Amanda J. Lea, Julie Peng, Julien F. Ayroles A preprint of this work can be found here: https://www.biorxiv.org/content/10.1101/2021.11.04.467311v2 Specifically, the filtered, normalized, and batch corrected gene expression data file (31Mar21_all_runs_voom_resid.txt) is provided along with the metadata. We also provide the output from matrix eQTL that was used as input for mashR. Scripts used to generate and analyze these data are provided here: https://github.com/AmandaJLea/LCLs_gene_exp</pre>
Cell size-dependent species sensitivity to nanoparticles underlies changes in phytoplankton diversity and productivity
<p>Nanoparticle pollution has been shown to affect various organisms. However, the effects of nanoparticles on species interactions, and the role of species traits, such as body size, in modulating these effects, are not well understood. We addressed this issue using competing freshwater phytoplankton species exposed to copper oxide nanoparticles. Increasing nanoparticle concentration resulted in decreased phytoplankton species growth rates and community productivity (both abundance and biomass). Importantly, we consistently found that nanoparticles had greater negative effects on species with smaller cell sizes, such that nanoparticle pollution weakened the competitive dominance of smaller species and promoted species diversity. Moreover, nanoparticles reduced the growth rate differences and competitive ability differences of competing species, while having little effect on species niche differences. Consequently, nanoparticle pollution reduced the selection effect on phytoplankton community abundance but increased the selection effect on community biomass. Our results suggest cell size as a key functional trait to consider when predicting phytoplankton community structure and ecosystem functioning in the face of increasing nanopollution.</p>
Fungal symbiont diversity drives growth of Holcus lanatus depending on soil nutrient availability
<ol> <li>Arbuscular mycorrhizal (AM) fungi frequently colonise plant roots and can affect plant morphology and physiology through their contribution to plant nutrition. However, the functional role of AM fungi in the presence of other microbial symbionts, including widespread Mucoromycotina 'fine root endophytes' (MFRE) fungi, remains largely unknown.</li> <li>While both AM fungi and MFRE transfer nutrients, including nitrogen, from inorganic and organic sources to host plants, their combined effects on co-colonised plants have only been investigated in liverworts. Here, we compare the morphology and physiology of the grass <em>Holcus lanatus</em> grown with an AM fungal community versus a more diverse symbiotic fungal community containing both AM fungi and MFRE. </li> <li> <em>Holcus lanatus</em> plants were grown in the presence of either a diverse MFRE+AM fungi soil inoculum or a multi-species AM fungal inoculum. Plant traits associated with growth were quantified, along with fungal transfer of <sup>15</sup>N tracer to plants from a variety of sources (ammonium chloride, alanine, glycine, algal necromass). </li> <li> <em>Holcus lanatus</em> grown with the AM fungal community had greater root and shoot growth during early development and prior to the addition of <sup>15</sup>N-labelled sources, compared to plants grown with the more diverse symbiotic fungal community. When nitrogen sources were made available to the fungal symbionts in the pot microcosms, plants growing with the MFRE+AM fungi soil inoculum had a faster growth rate than plants growing with the AM fungal community. At harvest, <em>H. lanatus</em> grown with the AM fungal community had a larger biomass and there were no differences in <sup>15</sup>N tracer assimilation in plants across the two fungal community treatments.</li> <li>Our results demonstrate that the diversity of fungal inocula in conjunction with soil nutrient availability determines the benefits derived by plants from diverse fungal symbionts. Our research contributes to understanding host plant outcomes in diverse multi-symbiont scenarios.</li> </ol>
Non-native species drive biotic homogenization, but it depends on the realm, beta diversity facet and study design: A meta-analytic systematic review
<p>While reducing the species richness of invaded communities is a well-known consequence of biological invasions, non-native species can also reduce variability between communities over time (i.e., beta diversity) in a process known as biotic homogenization. Although biotic homogenization due to non-native species is a common topic of theoretical reviews, we believe no global meta-analysis on the effect of non-native species on beta diversity has been carried out yet. Here, we systematically show that non-native species drive biotic homogenization, but it depends on the realm, beta diversity facet and study design. Biotic homogenization was more intense in marine and freshwater ecosystems than in terrestrial ecosystems. We also found that non-native species reduced both taxonomic and phylogenetic beta diversity, but not the functional beta diversity. Finally, we observed more intense effects using "before vs. after invasion" followed by "uninvaded vs. invaded sites" while the effect size of studies using "communities associated with native vs. non-native species" did not differ from zero. Our findings highlight that non-native species contribute to biotic homogenization as a prevalent pattern in communities worldwide, and that biodiversity conservation strategies should go beyond investigating the reduction in the number of species by also taking into account beta diversity in its multiple facets.</p>
Eco-evolutionary dynamics modulate plant responses to global change depending on plant diversity and species identity
Global change has dramatic impacts on grassland diversity. However, little is known about how fast species can adapt to diversity loss and how this affects their responses to global change. Here, we performed a common garden experiment testing whether plant responses to global change are influenced by their selection history and the conditioning history of soil at different plant diversity levels. Using seeds of four grass species and soil samples from a 14-year-old biodiversity experiment, we grew the offspring of the plants either in their own soil or in soil of a different community, and exposed them either to drought, increased nitrogen input, or a combination of both. Under nitrogen addition, offspring of plants selected at high diversity produced more biomass than those selected at low diversity, while drought neutralized differences in biomass production. Moreover, under the influence of global change drivers, soil history, and to a lesser extent plant history, had species-specific effects on trait expression. Our results show that plant diversity modulates plant-soil interactions and growth strategies of plants, which in turn affects plant eco-evolutionary pathways. How this change affects species' response to global change and whether this can cause a feedback loop should be investigated in more detail in future studies.
Impacts of flowering density on pollen dispersal and gametic diversity are scale dependent
<p>Pollen dispersal is a key evolutionary and ecological process, but the degree to which variation in the density of concurrently flowering conspecific plants (i.e., co-flowering density) shapes pollination patterns remains understudied. We monitored co-flowering density and corresponding pollination patterns of the insect-pollinated palm <em>Oenocarpus bataua</em> in northwestern Ecuador and found that the influence of co-flowering density on these patterns was scale-dependent: high neighborhood densities were associated with reductions in pollen dispersal distance and gametic diversity of progeny arrays, whereas we observed the opposite pattern at the landscape scale. In addition, neighborhood co-flowering density also impacted forward pollen dispersal kernel parameters, suggesting that low neighborhood densities encourage pollen movement and may promote gene flow and genetic diversity. Our work reveals how co-flowering density at different spatial scales influences pollen movement, which in turn informs our broader understanding of the mechanisms underlying patterns of genetic diversity and gene flow within populations of plants.</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.