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.
491
datasets available to search
ShareScore release 0.9.0
Dataset results
491 results for “population modelling”
Data from: Population genomic tests of models of adaptive radiation in Lake Victoria region cichlid fish.
Adaptive radiation is usually thought to be associated with speciation, but the evolution of intraspecific polymorphisms without speciation is also possible. The radiation of cichlid fish in Lake Victoria is perhaps the most impressive example of a recent rapid adaptive radiation, with 600+ very young species. Key questions about its origin remain poorly characterized, such as the importance of speciation versus polymorphism, whether species persist on evolutionary time scales, and if speciation happens more commonly in small isolated or in large connected populations. We used 320 individuals from 105 putative species from Lakes Victoria, Edward, Kivu, Albert, Nabugabo and Saka, in a radiation-wide AFLP genome scan to address some of these questions. We demonstrate pervasive signatures of speciation supporting the classical model of adaptive radiation associated with speciation. A positive relationship between the age of lakes and the average genomic differentiation of their species, and a significant fraction of molecular variance explained by above-species level taxonomy suggest the persistence of species on evolutionary time scales, with radiation through sequential speciation rather than a single starburst. Finally the large gene diversity retained from colonization to individual species in every radiation suggests large effective population sizes and makes speciation in small geographical isolates unlikely.
Data from: A dynamical model for invasive round goby populations reveals efficient and effective management options
1. When prevention of invasive species' introductions fails, society faces the challenge to manage these invasive species in an effective and efficient way. The success of this depends on biological aspects and on cooperation between decision makers and scientists. Using the case of the round goby Neogobius melanostomus, one of Europe's worst invasive species, we propose an approach guiding scientists to co-produce effective and efficient population control measures in collaboration with decision makers. 2. We surveyed the effectiveness, urgency and simplicity perceived by decision makers as well as the support of two population control options: removal of eggs and/or adults. Using a field study and a dynamical population model, we investigated the effectiveness and efficiency for both options in different population contexts. 3. Decision makers initially seemed to lack a clear preference for either control option. After being presented with preliminary field and modelling results, decision makers mostly approved measures being developed to implement the two control options. 4. Starting population control early after detecting the species requires in total fewer years for eradication than controlling an established population: to reach an eradication success rate of 95%, 13 years for early start vs. 18 years for late start are needed when removing eggs and adults; when removing adults only, 20 vs. 29 years are needed. Removing eggs and adults combined results in a yearly effort of 5.01 h m-2, while removing adults only results in a yearly effort of 1.76 h m-2. Thus, removing adults only proved to be the most efficient option to eradicate the population. Nonetheless, considerable effort is needed: when removing less than 57% of the adult population, eradication is not feasible, even assuming low survival and fecundity rates for the population. Further, inflow of new propagules renders eradication efforts ineffective. 5. Synthesis and applications. Scientists who aim to support decision makers in finding an optimal control strategy for invasive species need to be able to provide scientific knowledge on effectiveness and efficiency of different options. For round goby and most non-native species, eradication is only feasible if started early in recently arrived populations and if inflow of new propagules can be prevented.
Data from: Using a full annual cycle model to evaluate long-term population viability of the conservation-reliant Kirtland's warbler after successful recovery
Long-term management planning for conservation-reliant migratory songbirds is particularly challenging because habitat quality in different stages and geographic locations of the annual cycle can have direct and carry-over effects that influence the population dynamics. The Neotropical migratory songbird Kirtland's warbler Setophaga kirtlandii (Baird 1852) is listed as endangered under the U.S. Endangered Species Act and Near Threatened under the IUCN Red List. This conservation-reliant species is being considered for U.S. federal delisting because the species has surpassed the designated 1000 breeding pairs recovery threshold since 2001. To help inform the delisting decision and long-term management efforts, we developed a population simulation model for the Kirtland's warbler that incorporated both breeding and wintering grounds habitat dynamics, and projected population viability based on current environmental conditions and potential future management scenarios. Future management scenarios included the continuation of current management conditions, reduced productivity and carrying capacity due to the changes in habitat suitability from the creation of experimental jack pine Pinus banksiana (Lamb.) plantations, and reduced productivity from alteration of the brown-headed cowbird Molothrus ater (Boddaert 1783) removal programme. Linking wintering grounds precipitation to productivity improved the accuracy of the model for replicating past observed population dynamics. Our future simulations indicate that the Kirtland's warbler population is stable under two potential future management scenarios: (i) continuation of current management practices and (ii) spatially restricting cowbird removal to the core breeding area, assuming that cowbirds reduce productivity in the remaining patches by ≤41%. The additional future management scenarios we assessed resulted in population declines. Synthesis and applications. Our study indicates that the Kirtland's warbler population is stable under current management conditions and that the jack pine plantation and cowbird removal programmes continue to be necessary for the long-term persistence of the species. This study represents one of the first attempts to incorporate full annual cycle dynamics into a population viability analysis for a migratory bird, and our results indicate that incorporating wintering grounds dynamics improved the model performance.
Two new hybrid populations expand the swordtail hybridization model system
<p>Natural hybridization events provide unique windows into the barriers that keep species apart as well as the consequences of their breakdown. Here we characterize hybrid populations formed between the northern swordtail fish Xiphophorus cortezi and X. birchmanni from collection sites on two rivers. We use simulations and new genetic reference panels to develop sensitive and accurate local ancestry calling in this novel system. Strikingly, we find that hybrid populations on both rivers consist of two genetically distinct subpopulations: a cluster of pure X. birchmanni individuals and one of phenotypically intermediate hybrids that derive ~85-90% of their genome from X. cortezi. Simulations suggest that initial hybridization occurred ~150 generations ago at both sites, with little evidence for contemporary gene flow between subpopulations. This population structure is consistent with strong assortative mating between individuals of similar ancestry. The patterns of population structure uncovered here mirror those seen in hybridization between X. birchmanni and its sister species, X. malinche, indicating an important role for assortative mating in the evolution of hybrid populations. Future comparisons will provide a window into the shared mechanisms driving the outcomes of hybridization not only among independent hybridization events between the same species but also across distinct species pairs.</p>
Protected by dragons: density surface modeling confirms large population of the critically endangered Yellow-crested Cockatoo on Komodo island
<p>Intense trapping of the critically endangered Yellow-crested Cockatoo <em>Cacatua sulphurea</em> for the International pet trade has devastated its populations across Indonesia such that populations >100 individuals remain at only a handful of sites. We combined distance sampling with density surface modeling (DSM) to predict local densities and estimate total population size for one of these areas, Komodo Island, part of Komodo National Park (KNP) in Indonesia. We modeled local density based on topography (topographic wetness index) and habitat types (percentage of palm savanna and deciduous monsoon forest). Our population estimate of 1,113 (95% CI: 587–2,109) individuals on Komodo Island was considerably larger than previous conservative estimates. Our density surface maps showed cockatoos to be absent over much of the island, but present at high densities in wooded valleys. Coincidence between our DSM and a set of independent cockatoo observations was high (93%).<br> Standardized annual counts by KNP staff in selected areas of the island showed increases in cockatoo records from <400 in 2011 to ~650 in 2017. Taken together, our results indicate that KNP, alongside and indeed because of preserving its iconic Komodo Dragons <em>Varanus komodoensis</em>, is succeeding in protecting a significant population of Indonesia's rarest cockatoo species. To our knowledge this is the first time DSM has been applied to a Critically Endangered species. Our findings highlight the potential of DSM for locating abundance hotspots, identifying habitat associations, and estimating global population size in a range of threatened taxa, especially if independent datasets can be used to validate model predictions.</p>
Fig. 6. Maximum entropy models for A in Weak Genetic Differentiation among Populations of the Andean Ground Beetle Pelmatellus columbianus (Reiche, 1843) (Coleoptera: Carabidae)
Fig. 6. Maximum entropy models for A) the past (21,000 years) and B) present distribution of Pelmatellus columbianus, using five bioclimatic variables. Maps show the limit of the montane forest (above 2,450 m) in green and páramo (above 3,000 m) in light brown.
Figure 3 in Distribution modelling of the rare stink bug Ceratozygum horridum (Germar, 1839): isolated in small spots across the Neotropics or a continuous population?
Figure 3. Maps of occurrence probability of stink bug Ceratozygum horridum transferred to different biomes; 1: Continuous values of median occurrence probability resulting from an ensemble of all models performed with different numbers of background points; 2: mask showing areas with dissimilar environments recovered from multivariate environmental similarity surface (MESS). (a) Amazon; (b) Dry diagonal; (c) Atlantic Forest.
Figure 2 in Distribution modelling of the rare stink bug Ceratozygum horridum (Germar, 1839): isolated in small spots across the Neotropics or a continuous population?
Figure 2. (a) Occurrence data of Ceratozygum horridum; highlighted in light grey the convex hull polygon comprising the 10 records in Amazon forest used to train the models; in dark grey a 100 km buffer; (b) continuous values of median occurrence probability resulting from an ensemble with all cross-validations predictions of each model performed with different numbers of background points.
Figure 1 in Distribution modelling of the rare stink bug Ceratozygum horridum (Germar, 1839): isolated in small spots across the Neotropics or a continuous population?
Figure 1. (a) Distribution map of Ceratozygum horridum; B, C Habitus of C. horridum. (b) Dorsal; (c): Lateral. Scale bar: 0.5 mm.
Optimization used in in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>OptimizationResults contain the expanded input model for each data set, in the C field are the indices of the core reactions in the expanded input model used to build the multi-cell population for the 121 different parameters, A contains the indices of reaction in the multi-cell population model for the 121 runs, thresh the parameter setting for the cover and REI. The REI is given in %. So 5 REI means 0.05. While A might change because of alternative optimals when run on a different computer, C and the expanded Input model will remain unchanged.</p> <p> </p> <p>Multi_cell_population_CRC and Multi_cell_population_NM are the models obtained by scFASTCORMICS with the optimal setting for Dataset1 and Dataset2, respectively. </p> <p>Please, check the publication (scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data) for more details.</p>
Golden-cheeked warbler Integrated Population Model (IPM) data in Austin, TX (2011–2019)
<p>These data and code are associated with the publication in Ecosphere entitled "Urban land cover and El Nino events negatively impact population viability of an endangered North American songbird." We performed an integrated population model to evaluate the effect of climate patterns and urban land cover on the viability of an endangered wood-warbler breeding in central Texas. We used territory monitroing data from 2011–2019 to predict viability of the population 25 years into the future.</p>
Validation of Existing Diabetes Risk Models in a Swedish Population
ClinicalTrials.gov study NCT05609266. IPD Sharing: NO. Countries: 0. Publications: 30.
Validation of a Red Blood Cell Transfusion Prediction Model in a Low Transfusion Rate Population.
ClinicalTrials.gov study NCT05581238. IPD Sharing: YES. Countries: 1. Publications: 7.
The Investigation of the Prediction Model and Prevention Strategy of Serious Pregnancy Complications in Hypertensive Disorders of Pregnancy Based on the Chinese Population
ClinicalTrials.gov study NCT05089175. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Duet 2.0 Starting the Conversation: A New Intervention Model to Stimulate Language Growth in Underserved Populations
ClinicalTrials.gov study NCT04692519. IPD Sharing: NO. Countries: 1. Publications: 23.
High-quality Image (NIR and RGB) Dataset Synchronized With Contact Vital Sings Recordings and Clinical Data of Stratified Healthy Population. Algorithms and AI Models to Obtain a Set of Vital Signs Im
ClinicalTrials.gov study NCT05947721. IPD Sharing: NO. Countries: 1. Publications: 2.
Comparative Population Pharmacodynamic Modeling for Sevoflurane Effects Using ADMS and Bispectral Index
ClinicalTrials.gov study NCT03069456. IPD Sharing: NO. Countries: 1. Publications: 3.
Impact of Predictive Modeling on Time to Palliative Care in an Outpatient Primary Care Population
ClinicalTrials.gov study NCT04604457. IPD Sharing: NO. Countries: 1. Publications: 1.
Nomograms for Optimization of Amikacin First Dose in Critically Ill Patients Using a Population Pharmacokinetics Model
ClinicalTrials.gov study NCT03683511. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Artificial Intelligence/Machine Learning Modeling on Time to Palliative Care Review in an Inpatient Hospital Population
ClinicalTrials.gov study NCT03976297. IPD Sharing: NO. Countries: 1. Publications: 1.
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.