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.
2,603
datasets available to search
ShareScore release 0.9.0
Dataset results
2,603 results for “Ecological data”
Data from publication: Castillioni, K., & Isbell, F. (2023). Early positive spatial selection effects of beta-diversity on ecosystem functioning. Landscape Ecology, 1-15.
Data from publication: Castillioni, K., & Isbell, F. (2023). Early positive spatial selection effects of beta-diversity on ecosystem functioning. Landscape Ecology, 1-15. Spatial beta-diversity may increase landscape productivity if there are positive spatial selection effects. Alternatively, dominant species in mixtures might not be the most productive species in monoculture leading to negative or neutral spatial selection effects. However, these hypotheses remain untested experimentally. Seedling survival can determine species establishment, influencing productivity later. To address this knowledge gap, we experimentally tested whether transplanted seedlings of dominant species optimally sort among habitat types (grassland dominated by Andropogon gerardii, savanna by Quercus macrocarpa, deciduous forest by Acer rubrum, coniferous forest by Pinus strobus, bog by Larix laricina), creating positive effects of landscape diversity on seedling survival and net biodiversity effects at Cedar Creek Ecosystem Science Reserve (CCESR) in Minnesota, USA. The study is named BetaDIV and consists of 100 plots (20 plots per habitat × 5 habitats). Each of the five habitats includes two true replicate monocultures for each of the five species and two true replicates for each of the five possible mixture compositions of four species (leaving each one out in turn to eventually explore the effect of species identity). Each plot is 1.5 by 1.5 m, with 12 seedlings planted 0.5 m apart in a 4 × 4 square grid, except in the plot corners. In the early June 2022, we tagged and planted all seedlings (i.e., bareroot seedlings for trees and plugs for the grass A. gerardii). Two weeks after the initial transplanting, we started tracking seedling survival (presented here) to investigate how seedlings responded to local habitat conditions. We conducted a seedling census for each of the 1200 tagged seedlings (12 seedlings per plot×100 plots), in early September 2022, which was two months at the end
Lake ice surveys, 1874-2022, Adirondack Long-Term Ecological Monitoring Program Project No. 8 by Adirondack Ecological Center of the State University of New York College of Environmental Science and Forestry, Newcomb, New York. Environmental Data Initiative.
The objective of this dataset is to document ice-in and ice-out dates on several lakes on the State University of New York College of Environmental Science and Forestry's Huntington Wildlife Forest (HWF). Lakes include: Arbutus, Catlin, Deer, Military, Rich, Wolf and Lodo Pond; some records exist for Long Pond and other water bodies but they are not included here except in some comment fields.
Ecology and Evolutionary Biology Field Trip at the Coweeta Hydrologic Laboratory (Watershed 18) in 2004: Aquatic Invertebrates (Adult) data
As part of an educational project, we intend to conduct a short "bioblitz" that will focus on 4 major groups of organisms: (1) vertebrates, especially birds and salamanders; (2) the local flora, especially fungi, trees, and any herbaceous species present this early; (3) aquatic invertebrates; (4) terrestrial invertebrates. Data will be compared to available lists of taxa from Coweeta and Great Smoky Mountains National Park.
Optimizing sampling across methods improves the power of ecological monitoring data
Transect-based monitoring has long been a valuable tool in ecosystem monitoring. These transects are often used to measure multiple ecosystem attributes. The line-point intercept (LPI), vegetation height, and canopy gap intercept methods comprise a set of core methods, which provide indicators of ecosystem condition. However, users struggle to design a sampling strategy that optimizes the ability to detect ecological change using transect-based methods. We assessed the sensitivity of these core methods on a one-hectare plot to transect length, number, and sampling interval to determine: 1) minimum sampling required to describe ecosystem characteristics and detect change for each method and 2) optimal transect length and number for all three methods to make recommendations for future analyses and monitoring efforts. We used data from 13 National Wind Erosion Research Network locations spanning the western US, which included 151 measurements over time across five biomes. We found that longer and increased numbers of transects were more important for reducing sampling error than increased sample intensity along transects. For all methods and indicators across plots, three 100-m transects reduced sampling error so that indicator estimates fall within an 95% confidence interval of +/- 5% for canopy gap intercept and LPI-total foliar cover, +/- 5 cm for height and +/- two species for LPI-species counts. For the same criteria at 80% confidence intervals, two 100-m transects are needed. Site-scale inference was strongly affected by sample design, consequently our understanding of ecological dynamics may be influenced by sampling decisions.
MCR LTER: Coral Reef: Density-dependence data for Edmunds, et al., Ecology 2018
This dataset contains coral cover data describing the context within which denisty-dependence (DD) was measured on the island of Moorea, French Polynesia, including data describing the benthic community, diameters of Pocillopora spp. measured in photoquadrats, surveys of corals and recruits. These data correspond to figures 1 through 3 in the manuscript by PJ Edmunds, L. Bramanti, and H.R. Nelson, 'Density-dependence mediates coral community structure', Ecology, 99(11), 2018, pp. 2605-2613. This ata set was revised on 27 November 2018. The data managed for Fig. 3 were missing values for two quadrats used in the analysis (quadrats 24 and 9). In this data revision, the values from the missing quadrats have been included. The reefs of Mo’orea, French Polynesia, provide the opportunity to study DD of coral population growth, because coral assemblages in this location responded to declines in abundance with high recruitment and an increase in cover during which recruitment of pocilloporid corals was inversely associated with density. This study tests for DD in this system, first, by describing the context within which it operates: coral cover changed from 46% in 2005, to less than 1% in 2010 following an outbreak of a corallivorous sea star and a cyclone, and then increased to 74% by 2017, in large part through inverse density- associated pocilloporid recruitment. Second, a test for DD of recruitment was conducted by decreasing Pocillopora spp. cover from 33% to 19%: one year later, the density of Pocillopora spp. recruits was 1.65-fold higher in the low versus high cover treatment. Finally, the effects of DD were investigated by comparing simulated and empirical distributions of pocilloporid colonies: as predicted by DD, small colonies were randomly distributed, while large colonies were uniformly distributed. Together these results demonstrate DD of population regulation for Pocillopora spp. corals, thus revealing the potential importance of this ecological principle i
They Came From The Pacific: How changing Arctic currents could contribute to an ecological regime shift in the Atlantic Ocean - Lagrangian Data 1990-2002 (2 of 2)
<p>Supporting data for Kelly et al.: They Came From The Pacific: How changing Arctic currents could contribute to an ecological regime shift in the Atlantic Ocean (Earth's Future, submitted)<br> <br> Trajectories saved by year of release in the Bering Strait. All months from that year are included in the same file, with the first 1000 trajectories corresponding to January release, second 1000 from February release, and so on. <br> <br> Due to the size of files, this is split into two uploads. Part 1 covers 1970-1989 releases, 1990 onward is saved in Part 2. </p>
They Came From The Pacific: How changing Arctic currents could contribute to an ecological regime shift in the Atlantic Ocean - Lagrangian Data 1970-1989 (1 of 2)
<p>Supporting data for Kelly et al.: They Came From The Pacific: How changing Arctic currents could contribute to an ecological regime shift in the Atlantic Ocean (Earth's Future, submitted)<br> <br> Trajectories saved by year of release in the Bering Strait. All months from that year are included in the same file, with the first 1000 trajectories corresponding to January release, second 1000 from February release, and so on. <br> <br> Due to the size of files, this is split into two uploads. Part 1 covers 1970-1989 releases, 1990 onward is saved in Part 2. </p>
FIG. 3. — Navicordulia pascali n in The genus Navicordulia Machado & Costa, 1995 (Insecta, Odonata, Corduliidae s.str.): new species, identification key for males and data on ecology and distribution
FIG. 3. — Navicordulia pascali n. sp., holotype: A, S10 and anal appendages in dorsal view; B, part of S9, S10 and anal appendages in left lateral view. Scale bars: 1 mm.
FIG. 1. — Navicordulia pascali n in The genus Navicordulia Machado & Costa, 1995 (Insecta, Odonata, Corduliidae s.str.): new species, identification key for males and data on ecology and distribution
FIG. 1. — Navicordulia pascali n. sp., holotype: A, general habitus; B, head in dorsal view and part of thorax in right lateral view.Scale bars: A, 10 mm; B, 1 mm.
FIG. 6 in The genus Navicordulia Machado & Costa, 1995 (Insecta, Odonata, Corduliidae s.str.): new species, identification key for males and data on ecology and distribution
FIG. 6. — "Savane-roche" in the Barruol Mounts, locus typicus of Navicordulia pascali n. sp. Photo by Stéphane Brûlé.
Data from: Breaking Barriers? Ethnicity and socioeconomic background impact on early career progression in the fields of ecology and evolution
<p>The academic disciplines of Science, Technology, Engineering and Mathematics (STEM) have long suffered from a lack of diversity. While in recent years there has been some progress in addressing the underrepresentation of women in STEM subjects, other characteristics that have the potential to impact on equality of opportunity have received less attention. In this study, we surveyed 188 early career scientists (ECRs), defined as within ten years of completing their PhD, in the fields of ecology, evolutionary biology, behaviour, and related disciplines. We examined associations between ethnicity, age, sexual orientation, sex, socioeconomic background, and disability, with measures of career progression, namely publication record, number of applications made before obtaining a postdoc, type of contract, and number of grant applications made. We also queried respondents on perceived barriers to progression, and potential ways of overcoming them. Our key finding was that socioeconomic background and ethnicity were associated with measures of career progression. While there was no difference in the number of reported first-authored papers on PhD completion, ethnic minority respondents reported fewer other-authored papers. In addition, ECRs from a lower socioeconomic background were more likely to report being in teaching and research positions, rather than research only positions, the latter being perceived as more prestigious by some institutions. We discuss our findings in the context of possible inequality of opportunity. We hope that this study will stimulate wider discussion, and help to inform strategies to address the underrepresentation of minority groups in the fields of ecology and evolution, and STEM subjects more widely.</p>
Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis
<p>Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether host-related selection on diapause timing anticipates genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of <i>Rhagoletis pomonella </i>to their sibling species <i>R. mendax</i> that attacks blueberries. The responses of 57,857 single nucleotide polymorphisms in a diapause study on the hawthorn race strongly predicted the direction and magnitude of genomic divergence among the three flies at a field site in Fennville, Michigan, USA. As anticipated, the apple race and <i>R. mendax</i> show parallel changes in the frequencies of putative inversions on three chromosomes associated with the earlier fruiting times of apples and blueberries compared to hawthorns. A diapause experiment on <i>R. mendax</i> revealed compensatory mutations throughout the genome accounting for the earlier eclosion of blueberry, but not apple flies. Thus, a degree of predictability, although not complete, exists in the genomics of diapause across the ecological speciation continuum in <i>Rhagoletis</i>. The generality of this result is placed in the context of other similar systems.</p>
Data from: Linking land use and the nutritional ecology of herbivores: a case study with the Senegalese locust
1) Access to high-quality food is a main driver of population dynamics. For herbivores protein and carbohydrates are key nutrients that are notoriously variable in plants and are affected by land use. However, few studies have linked foraging decisions and performance in the laboratory to the nutritional landscape available in the field. 2) <i>Oedaleus senegalensis</i> is a nonmodel locust, a grass-feeder, and the main pest of millet, a subsistence crop in the Sahel. In this study, we examined dietary preference and locust performance across a range of protein:carbohydrate ratios using the Geometric Framework methodology. We then applied a fitness landscape approach to visualize these results with the plant nutrient contents available across four land-use types: millet, groundnut, fallow, and grazed fields. Finally, we contrasted our results with locust distribution in the field. Several locust species (<i>O. senegalensis</i> included) exhibit density dependent color polymorphism thus we also reported individual coloration (brown or green). 3) We found that <i>O. senegalensis</i> preferred moderately carbohydrate-biased food 1:1.6 protein: carbohydrate ratio. All traits recorded (mass gain, development time, growth rate, molt success, and performance index) were best near that ratio and declined on either side presenting a "hump-shape". Fallow fields contained more plants, particularly grasses, that were both abundant and closer to the optimal protein:carbohydrate ratio recorded from the lab experiments. 4) When we surveyed <i>O. senegalensis</i> abundance and proportion, we found that they were more numerous in the fallow fields. Brown morph individuals, the ones associated with high density, were proportionally more abundant in fallow fields than green individuals. 5) Our study provides evidence that variation in nutritional landscapes—relative to an herbivore's optimal nutrient balance—is a key driver of herbivore population distribution and abundance, and can be used to predict bottom-up effects on herbivore species. protein:carbohydrate ratio recorded from the lab experiments.
Data from: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.
Data from: Species distribution models of the Spotted Wing Drosophila (Drosophila suzukii, Diptera: Drosophilidae) in its native and invasive range reveal an ecological niche shift
<p>The Spotted Wing Drosophila (<em>Drosophila</em> <em>suzukii</em>) is native to Southeast Asia. Since its first detection in 2008 in Europe and North America, it has been a pest to the fruit production industry as it feeds and oviposits on ripening fruit. Here we aim to model the potential geographical distribution of <em>D. suzukii</em>. We performed an extensive literature review to map the current records. In total, 517 documented occurrences (96 native and 421 invasive) were identified spanning 52 countries. Next, we constructed three species distribution models (SDMs) based on occurrence records in: 1) the native range (SDMnative), 2) the invasive range in Europe (SDMEurope) and 3) a global model of all records (SDMglobal). The models aimed to investigate, whether this species will be able to occupy additional ecological niches beyond its native range and expand its current geographic distribution both globally and in Europe. The SDMs were generated using Maximum Entropy algorithms (Maxent) based on present occurrence records and bioclimatic variables (WorldClim). Predictions of habitat suitability vary greatly depending on the origins of occurrence records. According to all models, precipitation and low temperatures were key limiting factors for the distribution of <em>D. suzukii</em>, which suggests that this species requires a humid environment with mild winters in order to establish a permanent population in its invasive range. Several regions in the invasive range, not presently occupied by this species, were predicted highly suitable, especially in northern Europe, suggesting that <em>D. suzukii</em> is not occupying its full fundamental niche yet. Synthesis and applications. Based on these models of potential geographic distribution of the Spotted Wing Drosophila (<em>Drosophila</em> <em>suzukii</em>), we show a shift in the ecological niche in <em>D. suzukii</em> populations, emphasizing the importance of using presence and local environmental data. Further investigation regarding new occurrences is recommended to secure optimal pest management. Despite a continuing expansion, many countries still lack proper surveillance schemes, and we urge policymakers to initiate appropriate management programs.</p>
Data and plot scripts for "Rising complexity and falling explanatory power in ecology"
<p>Analyses of published research can provide a realistic perspective on the progress of science. By analyzing more than 18 000 articles published by the preeminent ecological societies, we found that (1) ecological research is becoming increasingly statistically complex, reporting a growing number of <em>P</em> values per article and (2) the value of reported coefficient of determination (<em>R</em>2) has been falling steadily, suggesting a decrease in the marginal explanatory power of ecology. These trends may be due to changes in the way ecology is studied or in the way the findings of investigations are reported. Determining the reason for increasing complexity and declining marginal explanatory power would require a critical review of the scientific process in ecology, from research design to dissemination, and could influence the public interpretation and policy implications of ecological findings.<br /> <br /> <br /> Read More: http://www.esajournals.org/doi/abs/10.1890/130230</p>
Supporting Data from Ecological Opportunities and Constraints in the Evolution of Diatoms
<p>2016-02-01<br /> Teofil Nakov</p> <p>Data and code for Nakov, Ruck, Alverson: Ecological opportunities and constraints in the evolution of diatom</p> <p>This packet contains the following files:</p> <p>1. Sequence alignment for 540 diatoms and 2 Bolidomonas: Nakov-etal-542-taxon-alignment-clean.fasta<br /> 2. The constraint topology used in tree searches: Nakov-etal-constraint-small-clades.phylip<br /> 3. Alignment partition file: Nakov-etal-tiger-partitions-rax<br /> 4. Character data for 540 diatoms and 2 Bolidomonas: Nakov-etal-542-taxon-discrete-characters.csv<br /> 5. The best tree from 420 RAxML optimizations: Nakov-etal-RAxML_bestTree.opt_89<br /> 6. 99 additional trees used in the analyses: Nakov-etal-99-randomly-sampled-unique-trees.newick<br /> 7. All 100 trees converted into chronograms: Nakov-etal-100-chronograms-smooth-1000.newick<br /> 8. Script with random seeds for RAxML optimizations: Nakov-etal-RAxML-calls-for-420-optimizations<br /> 9. R scripts with random seeds: Nakov-etal-R-scripts.zip (three scripts: equal-rates, independent, and coordinated + paint regimes models)<br /> 10. TreePL control file: Nakov-etal-TreePL-control-file.txt</p>
Survey data for "Remote Sensing & GIS Training in Ecology and Conservation"
<p>This file provides the raw data of an online survey intended at gathering information regarding remote sensing (RS) and Geographical Information Systems (GIS) for conservation in academic education. The aim was to unfold best practices as well as gaps in teaching methods of remote sensing/GIS, and to help inform how these may be adapted and improved. A total of 73 people answered the survey, which was distributed through closed mailing lists of universities and conservation groups.</p>
Data from: Elucidating the morphology and ecology of Eoandromeda octobrachiata from the Ediacaran of South Australia
<p><em>Eoandromeda octobrachiata</em> is a poorly understood Ediacaran organism, with spiral-octoradial arms, found in South Australia and South China. The informal Nilpena member of the Rawnsley Quartzite, Flinders Ranges in South Australia preserves more than 200 specimens of <em>Eoandromeda</em>. Here we use the novel application of rotational geometric morphometrics together with palaeoenvironmental information to provide a better insight into their palaeobiology and ecology and to address conflicting hypotheses regarding mode of life and taxonomic affinity. We find that <em>Eoandromeda</em> likely had a radially symmetrical shape in life, was cone-shaped and had a high relief off the microbial mat. Analysis of the symmetric and asymmetric shape components revealed they deform strongly in the direction of palaeocurrent, therefore are thought to be made of a flexible material. Almost all specimens are compressed flat. Specimens that appear to have not fully collapsed support the idea that <em>Eoandromeda</em> was likely cone-shaped and further suggest that they possibly collapsed spirally. Our shape analysis along with observed morphological features support the benthic mode of life hypothesis rather than pelagic. Morphological and ecological inconsistencies do not fully support the hypothesis of a Ctenophora taxonomic affinity.</p>
Data for: Pollinator and habitat-mediated selection as potential contributors to ecological speciation in two closely related species
<p>In ecological speciation, incipient species diverge due to natural selection that is ecologically based. In flowering plants, different pollinators could mediate that selection (pollinator-mediated divergent selection) or other features of the environment that differ between habitats of two species could do so (environment-mediated divergent selection). Although these mechanisms are well understood, they have received little rigorous testing, as few studies of divergent selection across sites of closely related species include both floral traits that influence pollination and vegetative traits that influence survival. This study employed common gardens in sites of the two parental species and a hybrid site, each containing advanced generation hybrids along with the parental species, to test these forms of ecological speciation in plants of the genus <em>Ipomopsis</em>. Three vegetative traits (specific leaf area, leaf trichomes, and photosynthetic water-use efficiency) and five floral traits (corolla length and width, anther insertion, petal color, nectar production) were analyzed for impacts on fitness components (survival to flowering and seeds per flower, respectively). These traits exhibited strong clines across the elevational gradient in the hybrid zone, with narrower clines in theory reflecting stronger selection or higher genetic variance. Plants with long corollas and inserted anthers had higher seeds per flower at the <em>I. tenuituba </em>site, whereas selection favored the reverse condition at the <em>I. aggregata</em> site, a signature of divergent selection. In contrast, no divergent selection due to variation in survival was detected on any vegetative trait. Selection within the hybrid zone most closely resembled selection within the <em>I. aggregata</em> site. Across traits, the strength of divergent selection was not significantly correlated with width of the cline, which was better predicted by evolvability (standardized genetic variance). These results support the role of pollinator-mediated divergent selection in ecological speciation and illustrate the importance of genetic variance in determining divergence across hybrid zones.</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.