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.
332
datasets available to search
ShareScore release 0.9.0
Dataset results
332 results for “Ecological niches”
Data from: Correlation between genetic diversity and environmental suitability: taking uncertainty from ecological niche models into account
The hindcast of shifts in the geographical ranges of species as estimated by ecological niche modelling (ENM) has been coupled with phylogeographical patterns, allowing the inference of past processes that drove population differentiation and genetic variability. However, more recently, some studies have suggested that maps of environmental suitability estimated by ENM may be correlated to species' abundance, raising the possibility of using environmental suitability to infer processes related to population demographic dynamics and genetic variability. In both cases, one of the main problems is that there is a wide variation in ENM development methods and climatic models. In this study, we analyse the relationship between heterozygosity (He) and environmental suitability from multiple ENMs for 25 population estimates for Dipteryx alata, a widely distributed, endemic tree species of the Cerrado region of central Brazil. We propose a new approach for generating a statistical distribution of correlations under randomly generated ENM. The confidence intervals from these distributions indicate how model selection with different properties affects the ability to detect a correlation of interest (e.g. the correlation between He and suitability). Additionally, our approach allows us to explore which particular ensemble of ENMs produces the better result for finding an association between environmental suitability and He. Caution is necessary when choosing a method or a climatic data set for modelling geographical distributions, but the new approach proposed here provides a conservative way to evaluate the ability of ensembles to detect patterns of interest.
Data from: Ecological niche modeling for a cultivated plant species: a case study on taro (Colocasia esculenta) in Hawai'i
Under the threat of ongoing and projected climate change, communities in the Pacific Islands face challenges of adapting culture and lifestyle to accommodate a changing landscape. Few models can effectively predict how biocultural livelihoods might be impacted. Here, we examine how environmental and anthropogenic factors influence an ecological niche model (ENM) for the realized niche of cultivated taro (Colocasia esculenta) in Hawai'i. We created and tuned two sets of ENMs: one using only environmental variables, and one using both environmental and cultural characteristics of Hawa'i. These models were projected under two different Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathways (RCPs) for 2070. Models were selected and evaluated using average omission rate and area under the receiver operating characteristic curve (AUC). We compared optimal model predictions by comparing the percentage of taro plots predicted present and measured ENM overlap using Schoener's D-statistic. The model including only environmental variables consisted of 19 Worldclim bioclimatic variables, in addition to slope, altitude, distance to perennial streams, soil evaporation, and soil moisture. The optimal model with environmental variables plus anthropogenic features also included a road density variable (which we assumed as a proxy for urbanization) and a variable indicating agricultural lands of importance to the State of Hawai'i. The model including anthropogenic features performed better than the environment-only model based on omission rate, AUC, and review of spatial projections. The two models also differed in spatial projections for taro under anticipated future climate change. Our results demonstrate how ENMs including anthropogenic features can predict which areas might be best suited to plant cultivated species in the future, and how these areas could change under various climate projections. These predictions might inform biocultural conservation priorities and initiatives. In addition, we discuss the incongruences that arise when traditional ENM theory is applied to species whose distribution has been significantly impacted by human intervention, particularly at a local scale relevant to biocultural conservation initiatives.
Data from: A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)
The central-marginal hypothesis (CMH) predicts that population size, genetic diversity, and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core-to-edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size, and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core-to-edge genetic patterns. These results suggest that multiple processes may influence a species' distribution based on the heterogeneity of habitat across a species' range and that replicated sampling may be needed to accurately test the CMH. Our work also emphasizes the importance of identifying the geographic range core with methods other than using the Euclidean center on a map, which may help to explain discrepancies among other empirical tests of the CMH. Assessing core to edge population genetic patterns across an entire species' range accompanied with ENM can inform our general understanding of the mechanisms leading to species' geographic range limits.
Data from: Environmental filtering improves ecological niche models across multiple scales
1. A clear challenge for ecological niche modeling is determining how to best mitigate the effects of sampling bias from commonly collected biodiversity data. Recent approaches have focused on filtering occurrences in overrepresented regions based on geographic or environmental proximity. 2. We tested the efficacy of filtering in geographic and environmental space using occurrence data from four species. Our evaluation strategies examined 14 distance measures in geographic and environmental spaces and eight combinations of environmental variables and their ordinations. This resulted in 78 datasets for each species, which we evaluated using area under the curve (AUC), the difference between training and testing AUC, omission rate, the true skill statistic, and Schoener's D to examine the effects of different filtering schemes. 3. The degree of change produced by filtering on predicted suitability and evaluation statistics increased with increasing range size. Environmental filtering resulted in higher model fit at larger extents and retained more occurrences than geographic filtering. 4. Our results indicate that models should be evaluated using multiple evaluation statistics at multiple thresholds. The use of bin sizes when filtering in environmental space allows for simple comparison between species and filter types and makes for an easily reportable and repeatable distance metric. We specifically recommend that ecological niche models using natural history collection data filter in environmental space with variables derived from permutation importance or the first few axes of a principal components ordination.
Figure 3 in Natural history and ecological niche modelling of coastal Atyphella Olliff Larvae (Lampyridae: Luciolinae) in Vanuatu
Figure 3. Distributions of pronotal widths and resulting predicted instars in two species of coastal Atyphella.
Figure 2 in Natural history and ecological niche modelling of coastal Atyphella Olliff Larvae (Lampyridae: Luciolinae) in Vanuatu
Figure 2. (a) Collection site of coastal Atyphella. Yellow dots indicate locations specimens were collected in 2018. (b) Predictive model for possible localities of coastal Atyphella in Vanuatu. White squares indicate locations Atyphella was collected in 2018.
Figure 1 in Natural history and ecological niche modelling of coastal Atyphella Olliff Larvae (Lampyridae: Luciolinae) in Vanuatu
Figure 1. (a) Typical habitat of coastal Atyphella (Efate, Vanuatu). (b) Typical habitat of coastal Atyphella (Malekula, Vanuatu). (c) Experimental setup of submersion experiment. (d) Captive coastal Atyphella feeding on snail.
Reassessing the taxonomy of Libidibia ferrea complex, the iconic Brazilian tree "pau-ferro" using morphometrics and ecological niche modeling
Open the record for dataset details and reuse information.
Ecological niche modelling to project past, current and future distributional shift of black ebony tree (Diospyros melanoxylon Roxb.) in India
<p>The present study utilized an ensemble modelling approach to predict the distribution of <em>D. melanoxylon</em> under present, past (Last Glacial Maximum, ~22,000 cal yr BP, Middle Holocene ~6000 cal yr BP) and future climate change scenarios (RCP 2.6 and 8.5 for 2050s and 2070s). The annual mean temperature, mean temperature of the wettest quarter and annual precipitations were the most critical parameters that chiefly influence the distribution of <em>D. melanoxylon</em>. The ensemble model rendered high accuracy with AUC=0.93, TSS=0.74, and Kappa=0.71. Past projections of <em>D. melanoxylon</em> indicated a widespread distribution during the Last Glacial Maximum and Middle Holocene suggesting its adaptability to semi-dry as well as warm and humid climates, respectively. The presence of fossil pollen evidence of <em>D. melanoxylon</em> in the suitable habitats derived through past projections in this study complements the model results and marks occurrences of the species during the Last Glacial Maximum and Middle Holocene. By 2050s and 2070s (RCP 8.5), there would be a decline in the distribution by only 0.4% (13622 km2) and 0.2% (6842 km2) of the extremely habitat suitable, respectively. The main factor leading to reduced habitat suitability is the anticipated rise in temperature and variations in seasonal precipitation patterns. Our findings, help in identifying the parts of the country which would be severely affected by future climate change scenarios and plan conservation strategies for this commercially important species to facilitate its growth in suitable habitats which are likely to sustain under future climatic conditions.</p>
Fig. 2 in Climatic Niche Conservatism and Ecological Diversification in the Holarctic Cold-Dwelling Butterfly Genus Erebia
Fig. 2. Illustrative figures of European and Asian mountains (panels A, B) and ancestral reconstruction of climatic traits (panels C–G) for species-specific average values of WorldClim variables.The ancestral reconstructions are based on OU model of evolution in the butterfly genus Erebia.
Fig. 3 in Climatic Niche Conservatism and Ecological Diversification in the Holarctic Cold-Dwelling Butterfly Genus Erebia
Fig. 3. The relationships between climatic and elevation niche widths and niche position along the gradient of conditions occupied by the butterfly genus Erebia. The points correspond to the niche width (y-axis) and average value of a climate variable or elevation for individual species (x-axis).The best fit of generalized additive models (GAM) is shown by lines (separately for species of the European and the Asian clade). Statistical significance of the model fit is also shown. edf denotes the estimated degrees of freedom, which indicates the complexity of the nonlinear relationship (edf = 1 corresponds to a linear relationship).
Fig. 1 in Climatic Niche Conservatism and Ecological Diversification in the Holarctic Cold-Dwelling Butterfly Genus Erebia
Fig. 1. Phylogenetic relationships and divergence time estimates for the butterfly genus Erebia. The European clade diversified mainly in Europe, the Asian clade in Asia, although the geographic distribution of several species is not restricted to a single region (see Supp Fig. 3 [online only]). The full biogeographic reconstruction is shown in the Supp Figs. 3–5 (online only). Climatic PCA displays the distribution-based climatic data for all species of the European and the Asian clades.The polygons show the full extent of the conditions occupied by each clade (dotted lines) and the core 50% of the climatic niche (solid lines). The inset shows the correlation of individual bioclimatic variables with the first and second PCA axes.The bioclimatic variables (bio1, bio4, bio12, and bio15) displayed significant phylogenetic signal (Table 3).The European clade inhabits warmer, more humid, and less seasonal climate compared to the Asian clade.
Hell ant ecological niche prediction dataset
<p><strong>Data S1.</strong> Supplementary Data_Fossil Morphometrics (separate file)</p> <p>All fossil morphometric data for all fossil specimens included in this study. The Excel file has four tabs: one with all raw trait measurements measured in a functional morphological framework (“raw functional”); one with all raw trait measurements measured in a homologous morphological framework (“raw homologous”); one with all size-corrected ratio trait measurements measured in a functional morphological framework (“ratio functional”); and one with all size-corrected ratio trait measurements measured in a homologous morphological framework (“raw homologous”). </p> <p> </p> <p><strong>Data S2.</strong> Supplementary Data_ Trap Jaw Ecomorphospace (separate file)</p> <p>All body size and ecological niche data used for calculating ecomorphospace occupation in extinct and extant trapjaw ant taxa. The Excel file has tabs for each genus of trapjaw ants, which were combined for cases where multiple genera were treated as one lineage. “MinHaidomyrmecinae” is collated solely from predictions estimated under a raw trait measurement functional morphology framework, while “MaxHaidomyrmecinae” is collated from predictions estimated using all models.</p> <p> </p> <p><strong>Data S3.</strong> Supplementary Data_Random Forest Code (separate file)</p> <p>R code that may be used to reproduce the Random Forest analyses, commented for clarity. </p>
Raw coordinates and measurements from: Like parent, like child -Ontogenetic development of claws of intertidal arthropods (Acari, Oribatida) from different ecological niches
<p>The shape of claws of adult air-breathing intertidal oribatid mites shows a strong correlation with ecology. As nothing is known about juvenile characteristics of this trait, the ontogenetic development of these attachment devices was studied for the first time with comprehensive geometric morphometric methods. In nine investigated species, claws of immature stages can be classified into the same ecological categories as adults, i.e. juveniles of several rock-dwelling species already show higher and stronger curved claw shapes with smaller claw angles, while juvenile instars of the single investigated mangrovedwelling species possess lower and less curved claws with wider claw angles. For each species, claw curvature is almost static during the complete development and claw length grows directly proportional with increasing body size. Developmental changes in body size and weight are thus mainly compensated by a simple relative growth in size. Despite the finding that claw shapes of early developmental stages are already classifiable into ecological categories, their shapes also change slightly during development to become more 'rock', 'mix' or 'mangrove'-like, respectively. The present results demonstrate that ecology is also the most important factor in shaping the claws of immatures and that attachment in the intertidal environment is vital for the survival of each mobile stage.</p>
FIGURE 6 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 6. MaxEnt model outputs for Ampedus samedovi. Minimum Training Presence threshold is applied to outputs.
FIGURE 5 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 5. MaxEnt model outputs for Ampedus platiai. Minimum Training Presence threshold is applied to outputs.
FIGURE 2 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 2. Distributions and collecting localities of Ampedus platiai and Ampedus samedovi. Red: Distribution of only A. platiai in the provinces, Blue: Distribution of only A. samedovi in the provinces, Yellow: Distribution of A. platiai and A. samedovi in the provinces (The map is designed in ArcGis 10.2).
FIGURE 1 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 1. Habitus and aedeagi photos of examined species. A–B. Ampedus platiai, C–D. A. samedovi, E–F. A. pomonae (Aedeagi of A. platiai and A. samedovi are redrawn from Kabalak 2010 and aedeagus of A. pomonae is redrawn from Platia 1994.). BML: Basal struts of median lobe, BP: Basal piece, ML: Median Lobe, PDT: Paramere distal tooth, PR: Paramere.
Sexual dimorphism in an adaptive radiation: Does intersexual niche differentiation result in ecological character displacement?
<p>Evolutionary radiations are one plausible explanation for the rich biodiversity on Earth. Adaptive radiations are the most studied form of evolutionary radiations and ecological opportunity has been identified as one factor permitting them. Competition among individuals is supposedly highest in populations of conspecifics. Divergent modes of resource use might minimize trophic overlap, and thus intersexual competition, resulting in ecological character displacement between sexes. However, the role of intersexual differentiation in speciation processes is insufficiently studied. The few studies available suggest that sexual niche differentiation exists in adaptive radiations, but their role within the radiation, and the extent of differentiation within the organism itself, remains largely unexplored. Here, we test the hypothesis that multiple morphological structures are affected by sexual niche differentiation in "roundfin" <i>Telmatherina</i>, the first case where sexual niche differentiation was demonstrated in an adaptive fish radiation. We show that sexes of two of the three morphospecies differ in several structural components of the head, all of these are likely adaptive. Sexual differentiation is linked to the respective morphospecies-specific ecology and affects several axes of variation. Trait variation translates into different feeding modes, processing types and habitat usages that add to interspecific variation in all three morphospecies. Intrasexual selection, i.e. male-male competition, may contribute to variation in some of the traits, but appears unlikely in internal structures which are invisible for other individuals. We conclude that intersexual variation adds to the adaptive diversity of roundfins, and might play a key role in minimizing intersexual competition in emerging radiations.</p>
Figure 6 in Ecological niche overlap of two allopatric karst-adapted tiger geckos (Goniurosaurus) from northern Vietnam: microhabitat use and implications for conservation
Figure 6. (a) Scatterplots of all variable groups on coordinates of (1) Dim1–Dim2, (2) Dim3–Dim4 axes in the multiple factor analysis (MFA); (b) the first four important variables contributing to (1) Dim1, (2) Dim2, (3) Dim3, (4) Dim4; (c) scatter diagrams illustrating ecological spaces of Goniurosaurus huuliensis and Goniurosaurus luii on coordinates of (1) Dim1–Dim2, (2) Dim3–Dim4 axes.
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.