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.
552
datasets available to search
ShareScore release 0.7.1
Dataset results
552 results for “species abundance”
Data from: Sharing detection heterogeneity information among species in community models of occupancy and abundance can strengthen inference
<p>1. The estimation of abundance and distribution and factors governing patterns in these parameters is central to the field of ecology. The continued development of hierarchical models that best utilize available information to inform these processes is a key goal of quantitative ecologists. However, much remains to be learned about simultaneously modeling true abundance, presence, and trajectories of ecological communities.</p> <p>2. Simultaneous modeling of the population dynamics of multiple species provides an interesting mechanism to examine patterns in community processes and, as we emphasize herein, to improve species-specific estimates by leveraging detection information among species. Here we demonstrate a simple but effective approach to share information about observation parameters among species in hierarchical community abundance and occupancy models, where we use shared random effects among species to account for spatiotemporal heterogeneity in detection probability.</p> <p>3. We demonstrate the efficacy of our modeling approach using simulated abundance data, where we recover well our simulated parameters using N-mixture models. Our approach substantially increases precision in estimates of abundance compared to models that do not share detection information among species. We then expand this model, and apply it to repeated detection/non-detection data collected on six species of tits (Paridae) breeding at 119 1 km<sup>2</sup> sampling sites across a <em>P. montanus</em> hybrid zone in northern Switzerland (2004-2020). We find strong impacts of forest cover and elevation on population persistence and colonisation in all species. We also demonstrate evidence for interspecific competition on population persistence and colonization probabilities, where the presence of marsh tits reduces population persistence and colonisation probability of sympatric willow tits, potentially decreasing gene flow among willow tit subspecies.</p> <p>4. While conceptually simple, our results have important implications for the future modeling of population abundance, colonization, persistence, and trajectories in community frameworks. We suggest potential extensions of our modeling in this paper, and discuss how leveraging data from multiple species can improve model performance and sharpen ecological inference.</p>
Congeneric predators fill discrete niches created by the relative abundances of their prey species
To what degree is niche partitioning driven by underlying patterns in resources such as food, rather than by competition itself? Do discrete niches exist? We address these questions in the context of Cooper's and Sharp-shinned Hawks, two broadly sympatric, North American, bird-eating raptors in the genus Accipiter. We find that the resource base, as quantified by body masses of birds at bird feeders, is approximately lognormal (smallest birds are most abundant), with lesser modes (peaks) in abundance at larger body mass. The predators appear to exploit peaks in the resource base, with Sharp-shinned Hawks focusing on small prey items (median of 26.5 g), and Cooper's Hawks taking prey from the two most abundant peaks (both the small body mass peak and a lesser peak at medium body mass ~90g). We tested the ability of citizen scientists to distinguish these notoriously similar species, and we determined the influence of potential false positive detections on our conclusions. We find that citizen scientists struggle to distinguish these predators from one another, and 18% of Cooper's Hawks were identified as Sharp-shinned Hawks, while 27% of Sharp-shinned Hawks were identified as Cooper's Hawks. Yet, simulations show that this uncertainty did not jeopardize our qualitative conclusions.
Avian species richness and abundance shows stronger response to bison grazing intensity than to ecosystem productivity
Temperate grassland ecosystems are one of the most threatened ecosystems worldwide, and their loss endangers the grassland songbirds that rely upon them. This guild of birds has shown long-term declines in North America. At the same time, American bison (Bison bison) are becoming more common through reintroductions, and they may make significant modifications to grassland songbird habitat. To support conservation for this guild, we sought to understand the importance of bison grazing and ecosystem productivity to the species richness, occupancy, and abundance of this avian community. We conducted dependent double-observer bird counts, measured bison grazing intensity with patty counts, and used remote-sensed Normalized Difference Vegetation Index (NDVI) data to measure ecosystem productivity. Our work took place in the National Bison Range near Moiese, Montana and in Yellowstone National Park in Wyoming. We found that species richness was positively correlated with patty counts, and had a weak negative correlation with NDVI. Occupancy probability for six of seven grassland songbird species was positively correlated with patty counts, and for six of seven species was negatively correlated with NDVI. Abundance of vesper sparrow (Pooecetes graminueus) and western meadowlark (Sturnella neglecta) were positively correlated with patty counts, although for western meadowlark, this trend became less positive with increasing patty counts. Our work suggests that managers may want to encourage a broad range of bison grazing intensities to ensure that vegetative conditions related to bison grazing are present for all species.
Estimation of species abundance based on the number of segregating sites using environmental DNA (eDNA)
<p>The advancement of environmental DNA (eDNA) has enabled rapid and non-invasive species detection in aquatic environments. While most studies focus on detecting species presence or absence, recent research has explored using eDNA data to quantify species abundance. This estimation usually is based on the concentration of targeted eDNA. However, eDNA concentration can be influenced by various factors, both biotic and abiotic, which can obscure the relationship between concentration and species abundance. In this study, we suggest using the number of segregating sites as a proxy for estimating species abundance. We investigated this relationship in silico, in vitro, and in situ (mesocosm experiments) using two brackish goby species, <em>Acanthogobius hasta</em> and <em>Tridentiger bifasciatus</em>. Analysis of simulated and in vitro data, where DNA was mixed from a known number of individuals, revealed a strong correlation between the number of segregating sites and species abundance (R<sup>2</sup> > 0.9; P < 0.01). Results from the mesocosm experiment confirmed this correlation (R<sup>2</sup> = 0.70, P < 0.01). This correlation remained consistent despite biotic factors such as body size and feeding behavior of the fish (P > 0.05). Cross-validation tests demonstrated that the number of segregating sites predicts species abundance more accurately and reliably than eDNA concentration. In conclusion, the number of segregating sites is a precise and robust indicator of species abundance compared to eDNA concentration, offering a significant enhancement to the quantitative capabilities of eDNA technology.</p>
Data from: Among-species variation in six decades of changing migration timings explained through ecology, life-history and abundance
<p>Species utilising seasonal environments must now alter timings of key life-history events in response to large-scale climatic changes, thereby maintaining trophic synchronies. Yet substantial among-species variation in cross-decadal phenological changes is observed. Transitioning from basic description of such variation towards prediction of future phenological responses now requires standardised studies that rigorously quantify and explain variation in the direction, magnitude and form of changing timings across diverse species in relation to key ecological and life-history variables. Accordingly, we fitted multi-quantile regressions to 59 years of high-quality multi-species data on spring and autumn bird migration timings through northern Scotland. We demonstrate substantial variation in cross-decadal changes in timings among 72 species, and quantify the degree to which variation can be explained through differences in species ecology, life-history and population trajectories. Consistent with predictions, species with seasonal diets, narrower breeding habitat breadths, shorter generation lengths and capability to produce multiple offspring broods per year advanced their migration timing in one or both seasons. In contrast, species with less seasonal diets, and that produce single annual offspring broods, showed no change. Meanwhile, contrary to prediction, long-distance migrants advanced their migration timings as much as short-distance migrants. Changes in migration timing also varied with changes in local migratory abundance, such that species with increasing seasonal abundance apparently altered their migration timing, whilst species with decreasing abundance did not. These patterns concur with expectation if changing migration timing is adaptive. However, we demonstrate that similar patterns can be generated through numerical sampling processes given changing abundances, implying that apparent phenology-abundance relationships should be carefully validated and interpreted. Overall, our results show that migrant bird species with differing ecologies and life-histories have shown systematically differing phenological changes over six decades contextualised by large-scale environmental changes, potentially facilitating future predictions and altering temporal dynamics of seasonal species co-occurrences.</p>
Figure 3 in Population abundance and growth parameters of an exotic bivalve species, Anadara kagoshimensis, in the Southwestern Black Sea
Figure 3. Distribution of biomass CPUA (kg km–2) A. kagoshimensis in 2011.
Figure 2 in Population abundance and growth parameters of an exotic bivalve species, Anadara kagoshimensis, in the Southwestern Black Sea
Figure 2. Sampling gear (hydroulic dredge).
Figure 6 in Population abundance and growth parameters of an exotic bivalve species, Anadara kagoshimensis, in the Southwestern Black Sea
Figure 6. Shell length–weight relationship of A. kagoshimensis by years.
Figure 1 in Population abundance and growth parameters of an exotic bivalve species, Anadara kagoshimensis, in the Southwestern Black Sea
Figure 1. Map showing the study areas and sampling stations in the Southwestern Black Sea
Figure 5 in Population abundance and growth parameters of an exotic bivalve species, Anadara kagoshimensis, in the Southwestern Black Sea
Figure 5. Change of per haul biomass by subarea and year.
Figure 4 in Population abundance and growth parameters of an exotic bivalve species, Anadara kagoshimensis, in the Southwestern Black Sea
Figure 4. Distribution of biomass A. kagoshimensis CPUA (kg km–2) in 2012.
Species abundance information improves sequence taxonomy classification accuracy - Qiita data
<p><a href="https://qiime2.org">QIIME 2</a> Artifacts containing microbiome samples, organised by EMPO 3 classification.</p> <p>Used to test <a href="https://library.qiime2.org/plugins/q2-clawback/">q2-clawback</a>.</p> <p>Downloaded from <a href="https://qiita.ucsd.edu">Qiita</a>. Draws from the following Qiita study ids:</p> <p>11113[1], 11444, 1716, 10369[2], 990[3], 2080, 1713, 894, 1289, 1883, 1673, 1288, 10353, 2192[4], 10323, 678, 1773, 662, 1799, 864, 1481, 1024[5], 1064, 2182, 10934, 1674, 1795[6], 10273, 10283[7], 10422[8], 804, 10308, 1056[9], 2382[5], 1240, 889, 1041, 1717, 1222, 11149, 11669, 807[10], 10245, 1711, 1721, 910, 1001, 895, 550[11], 1747[12], 713[13], 755, 861, 958[14], 11161[15], 11154[16], 945, 723, 1715, 1714, 10798.</p> <p>References<br> 1. Schulfer, A. F. et al. Nat Microbiol 3, 234–242 (2017).<br> 2. Ruhe, J. et al. Front Plant Sci 7 (2016).<br> 3. O'Brien, S. L. et al. Environ Microbiol 18, 2039–2051 (2016).<br> 4. Lax, S. et al. Science 345, 1048–1052 (2014).<br> 5. Zarraonaindia, I. et al. mBio 6 (2015).<br> 6. Navas-Molina, J. A. et al. in Methods Enzymol 371–444 (2013).<br> 7. Fang, X. et al. Front Microbiol 9 (2018).<br> 8. Tripathi, A. et al. mSystems 3 (2018).<br> 9. Delsuc, F. et al. Mol Ecol 23, 1301–1317 (2013).<br> 10. Gibbons, S. M. et al. PLoS ONE 9, e97435 (2014).<br> 11. Caporaso, J. G. et al. Genome Biol 12, R50 (2011).<br> 12. Hyde, E. R. et al. mSystems 1 (2016).<br> 13. Brazelton, W. J., Nelson, B. & Schrenk, M. O. Front Microbiol 2 (2012).<br> 14. Vitaglione, P. et al. Am J Clin Nutr 101, 251–261 (2014).<br> 15. Spirito, C. M., Marzilli, A. M. & Angenent, L. T. Environ Sci Technol 52, 13438–13447 (2018).<br> 16. Pham, V. T. H. et al. Sci Rep 7 (2017).</p>
Species abundance information improves sequence taxonomy classification accuracy - HMP and NCBI data
<p>Data used to test <a href="https://library.qiime2.org/plugins/q2-clawback/">q2-clawback</a> using taxonomic weights derived from shotgun sequencing experiments.</p> <p>Includes reference sequences and taxonomies derived from the NCBI RefSeq database[1] and paired amplicon and shotgun sequencing results downloaded from the Human Microbiome Project[2].</p> <p>References<br> 1. O’Leary, N. A. et al. en. Nucleic Acids Res. 44, D733–45 (2016).<br> 2. Huttenhower, C. et al. Nature 486, 207 (2012).</p>
Figure S1 in The amount of mulch increases the abundance, and its composition the species diversity of springtails in crop rotation on chernozem soils
Figure S1. Residual plots for GLMM
Figure 1 in Spatiotemporal distribution, abundance, and species-environment relationships of Scyphozoa (Cnidaria) species in Hisarönü, Marmaris, and Fethiye bays (Muğla, Turkey
Figure 1. Sampling stations on the coast of Muğla.
Figure. Relative abundance of species in the Phyllonorycter parasitoid complex. in Hymenopterous parasitoids associated with Phyllonorycter coryli (Nic.) and Phyllonorycter nicellii (Stt.) on hazel in Poland
Figure. Relative abundance of species in the Phyllonorycter parasitoid complex.
Dataset showing species abundance in each subplot. ("teste_Rhill.xlsx")
<p>This dataset is the general spreadsheet of grassland species abundance obtained using the Londo scale. The data have been compartmentalized according to the analysis focus into tabs by region (HG and PG) or sites (ACE, ALE, ARA, LAV, TAI, TAV, VAC). The treatments are defined as CONV (CG - Continuous grazing), CONS (DG - Deferred grazing), and EXCL (GE - Grazing exclosure).</p>
Data from: Plant community responses to long-term fertilization: changes in functional group abundance drive changes in species richness
Declines in species richness due to fertilization are typically rapid and associated with increases in aboveground production. However, in a long-term experiment examining the impacts of fertilization in an early successional community, we found it took 14 years for plant species richness to significantly decline in fertilized plots, despite fertilization causing a rapid increase in aboveground production. To determine what accounted for this lag in the species richness response, we examined several potential mechanisms. We found evidence suggesting the abundance of one functional group—tall species with long-distance (runner) clonality—drove changes in species richness, and we found little support for other mechanisms. Tall runner species initially increased in abundance due to fertilization, then declined dramatically and were not abundant again until later in the experiment, when species richness and the combined biomass of all other functional groups (non-tall runner) declined. Over 86 % of the species found throughout the course of our study are non-tall runner, and there is a strong negative relationship between non-tall runner and tall runner biomass. We therefore suggest that declines in species richness in the fertilized treatment are due to high tall runner abundance that decreases the abundance and richness of non-tall runner species. By identifying the functional group that drives declines in richness due to fertilization, our results help to elucidate how fertilization decreases plant richness and also suggest that declines in richness due to fertilization can be lessened by controlling the abundance of species with a tall runner growth form.
Data from: Global warming will affect the maximum potential abundance of boreal plant species
<p>Forecasting the impact of future global warming on biodiversity requires understanding how temperature limits the distribution of species. Here we rely on Liebig's Law of Minimum to estimate the effect of temperature on the maximum potential abundance that a species can attain at a certain location. We develop 95%-quantile regressions to model the influence of effective temperature sum on the maximum potential abundance of 25 common understory plant species of Finland, along 868 nationwide plots sampled in 1985. Fifteen of these species showed a significant response to temperature sum that was consistent in temperature-only models and in all-predictors models, which also included cumulative precipitation, soil texture, soil fertility, tree species and stand maturity as predictors. For species with significant and consistent responses to temperature, we forecasted potential shifts in abundance for the period 2041–2070 under the IPCC A1B emission scenario using temperature-only models. We predict major potential changes in abundance and average northward distribution shifts of 6–8 km yr−1. Our results emphasize inter-specific differences in the impact of global warming on the understory layer of boreal forests. Species in all functional groups from dwarf shrubs, herbs and grasses to bryophytes and lichens showed significant responses to temperature, while temperature did not limit the abundance of 10 species. We discuss the interest of modelling the 'maximum potential abundance' to deal with the uncertainty in the predictions of realized abundances associated to the effect of environmental factors not accounted for and to dispersal limitations of species, among others. We believe this concept has a promising and unexplored potential to forecast the impact of specific drivers of global change under future scenarios.</p>
Data from: The biogeographical patterns of species richness and abundance distribution in stream diatoms are driven by climate and water chemistry
In this inter-continental study of stream diatoms, we asked three important but still unresolved ecological questions: 1) What factors drive the biogeography of species richness and species abundance distribution (SAD); 2) Are climate-related hypotheses, which have dominated the research on the latitudinal and altitudinal diversity gradients, adequate in explaining spatial biotic variability; and 3) Is the SAD response to the environment independent of richness? We tested a number of climatic theories and hypotheses (i.e., the species-energy and the metabolic theory; and the energy variability and the climatic tolerance hypothesis) but found no support for any of these concepts as the relationships of richness with explanatory variables were non-existent, weak or unexpected. Instead, we demonstrated that diatom richness and SAD evenness generally increased with temperature seasonality and at mid- to high total phosphorus concentrations. The spatial patterns of diatom richness and the SAD—mainly longitudinal in the US, but latitudinal in Finland—were defined primarily by the covariance of climate and water chemistry with space. The SAD was not entirely controlled by richness, emphasizing its utility for ecological research. Thus, we found support for the operation of both climate and water chemistry mechanisms in structuring diatom communities, which underscores their complex response to the environment and the necessity for novel predictive frameworks.
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.