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3,585 results for “Population study”
Bioinformatic pipeline from: Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River
<p>Community composition data are essential for conservation management, facilitating identification of rare native and invasive species, along with abundant ones. However, traditional capture-based morphological surveys require considerable taxonomic expertise, are time consuming and expensive, can kill rare taxa and damage habitats, and often are prone to false negatives. Alternatively, metabarcode assays can be used to assess the genetic identity and compositions of entire communities from environmental samples, comprising a more sensitive, less damaging, and relatively time- and cost-efficient approach. However, there is a trade-off between the stringency of bioinformatic filtering needed to remove false positives and the potential for false negatives. The present investigation thus evaluated use of four mitochondrial (mt) DNA metabarcode assays and a customized bioinformatic pipeline to increase confidence in species identifications by removing false positives, while achieving high detection probability. Positive controls were used to calculate sequencing error, and results that fell below those cutoff values were removed, unless found with multiple assays. The performance of this approach was tested to discern and identify North American freshwater fishes using lab experiments (mock communities and aquarium experiments) and processing of a bulk ichthyoplankton sample. The method then was applied to field environmental (e)DNA water samples taken concomitant with electrofishing surveys and morphological identifications. This protocol detected 100% of species present in concomitant electrofishing surveys in the Wabash River and an additional 21 that were absent from traditional sampling. Using single 1 L water samples collected from just four locations, the metabarcoding assays discerned 73% of the total fish species that were discerned in comparison to four months of an extensive electrofishing river survey in the Maumee River, along with an additional nine species. In both rivers, total fish species diversity was best resolved when all four metabarcode assays were used together, which identified 35 additional species missed by electrofishing. Ecological distinction and diversity levels among the fish communities also were better resolved with the metabarcode assays than with morphological sampling and identifications, especially with the combined assays. At the population-level, metabarcode analyses targeting the invasive round goby <i>Neogobius melanostomus</i> and the silver carp <i>Hypophthalmichthys molitrix</i> identified all population haplotype variants found using Sanger sequencing of morphologically sampled fish, along with additional intra-specific diversity, meriting further investigation. Overall findings demonstrated that the use of multiple metabarcode assays and custom bioinformatics that filter potential error from true positive detections improves confidence in evaluating biodiversity.</p>
Data from: Bayesian quantification of ecological determinants of outcrossing in natural plant populations: computer simulations and the case study of biparental inbreeding in English yew
The mating system is a central parameter of plant biology because it shapes their ecological and evolutionary properties. Therefore, determining ecological variables that influence the mating system is important for a deeper understanding of the functioning of plant populations. Here, using old concepts and recent statistical developments, we propose a new statistical tool to make inferences about ecological determinants of outcrossing in natural plant populations. The method requires co-dominant genotypes of seeds collected from maternal plants within different locations. Using extensive computer simulations, we demonstrated that the method is robust to the issues expected for real-world data, including the Wahlund effect, inbreeding and genotyping errors such as allele dropout and allele misclassification. Furthermore, we showed that the estimates of ecological effects and outcrossing rates can be severely biased if genotyping errors and genetic differentiation are not treated explicitly. Application of the new method to the case study of a dioecious tree (Taxus baccata) allowed revealing that female trees that grow in lower local densities have a greater tendency towards mating with relatives. Moreover, we also demonstrated that biparental inbreeding is higher in populations that are characterised by a longer mean distance between trees and a smaller mean trunk perimeter. We found these results to agree with both the theoretical predictions and the history of English yew.
Data from: Is MHC diversity a better marker for conservation than neutral genetic diversity? a case study of two contrasting dolphin populations
Genetic diversity is essential for populations to adapt to changing environments. Measures of genetic diversity are often based on selectively neutral markers, such as microsatellites. Genetic diversity to guide conservation management, however, is better reflected by adaptive markers, including genes of the major histocompatibility complex (MHC). Our aim was to assess MHC and neutral genetic diversity in two contrasting bottlenose dolphin (Tursiops aduncus) populations in Western Australia—one apparently viable population with high reproductive output (Shark Bay) and one with lower reproductive output that was forecast to decline (Bunbury). We assessed genetic variation in the two populations by sequencing the MHC class II DQB, which encompasses the functionally important peptide binding regions (PBR). Neutral genetic diversity was assessed by genotyping twenty‐three microsatellite loci. We confirmed that MHC is an adaptive marker in both populations. Overall, the Shark Bay population exhibited greater MHC diversity than the Bunbury population—for example, it displayed greater MHC nucleotide diversity. In contrast, the difference in microsatellite diversity between the two populations was comparatively low. Our findings are consistent with the hypothesis that viable populations typically display greater genetic diversity than less viable populations. The results also suggest that MHC variation is more closely associated with population viability than neutral genetic variation. Although the inferences from our findings are limited, because we only compared two populations, our results add to a growing number of studies that highlight the usefulness of MHC as a potentially suitable genetic marker for animal conservation. The Shark Bay population, which carries greater adaptive genetic diversity than the Bunbury population, is thus likely more robust to natural or human‐induced changes to the coastal ecosystem it inhabits.
Figure 3. from: A first integrative study of the identity and origins of the British Dwarf Pill Millipede populations, Trachysphaera cf. lobata (Diplopoda, Glomerida, Glomeridae) - Biodiversity Data Journal 3: e5176 (09 June 2015) https://doi.org/10.3897/BDJ.3.e5176
Figure 3. - TW18: T.lobata, female, Isle of Wight
Data from: Relict stands of Central European oaks: unravelling autochthony and genetic structure based on a multi-population study
<p><span>Central European white oaks expanded rapidly after the last glacial period and reached their current distribution range during the early Holocene. They have been an important resource of timber, fuelwood and animal feed for humans, who actively promoted their presence in forests and other landscape types at least since the early historical times. Besides stands with intensive management, putatively relict populations of three native oak species can be found on unproductive sites with restricted accessibility. Here, we apply chloroplast and nuclear microsatellite markers in order to address the autochthony of relict and managed stands and compare the spatial distribution of genetic variation between them. Based on data from more than 150 populations, we demonstrate that oak autochthony was preserved throughout historical times which is likely the result of traditional silvicultural treatment. This is supported by the fact that the spatial pattern of chloroplast haplotype distribution still reflects the post-glacial recolonization in both relict and old managed stands. We observed significant admixture of haplotypes only in stands established after the Second World War, which is attributable to the transfer of reproductive material used for afforestation. In terms of nuclear genetic variation, we observed marked differences among species. <em>Quercus</em> <em>pubescens</em> exhibited a pronounced genetic structure. Genetic drift and limited gene flow among its small and isolated populations in our study area might have contributed to this pattern. Varying extent of genetic introgression with other sympatric oak species could offer an additional explanation. On the contrary, the gene pools of <em>Q. petraea </em>and<em> Q. robur</em> are highly homogenous, displaying only weak isolation-by-distance. We found no significant differences of genetic diversity and differentiation between relict and managed stands. This suggests that seed transfer mostly occurred within our study area, even in those stands established in post-war times, verifying previous findings that point out limited human interference. We recommend consideration of population genetic structure for gene conservation, with a finer resolution of gene conservation units needed for <em>Q. pubescens </em>due to its spatial genetic structure. Both relict and old managed stands, species-pure or mixed, are suitable for conservation, as they host autochthonous gene pools. Coppice-with-standard management could contribute to preservation of autochthony. In the face of climate change, it is also important to maintain the evolutionary potential of the stands, by facilitating generative reproduction and allowing for hybridization in mixed stands.</span></p>
Fig. 1. a in Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms
Fig. 1. a) Temperature and b) photosynthetically active radiation profiles in Lake Alchichica.
Fig. 11 in Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms
Fig. 11. Spirostomum teres occurrence (%) in habitats defined by DO concentration (mgL–1).
A NATIONAL STUDY OF SEROPREVALENCE OF COVID-19 INFECTION IN THE POPULATION OF THE REPUBLIKA SRPSKA
<p>Results of population-based age stratified seroepidemiological investigation in the Republika Srpska.</p>
Fig. 1 in Scale-Morphometry Study To Discriminate Gibel Carp (Carassius Gibelio) Populations In The Balaton-Catchment (Hungary)
Fig. 1. Overlooking map of sampling areas
Population-based, Age- and Gender- Stratified Sero-Survey Study for SARS-CoV-2 in Uganda
<p>Results of population-based age stratified seroepidemiological investigation in Uganda</p>
Can fire-age mosaics really deal with conflicting needs of species? A study using population hotspots of multiple threatened birds
<p> Locations that support high densities of a species ("population hotspots") have a disproportionate influence on species' persistence. In fire-prone ecosystems, managers attempting to promote population hotspots of multiple species must understand how hotspot locations might shift with post-fire succession and how much overlap exists in the locations of population hotspots for multiple species. Mangers are then tasked with resolving fire-management conflicts in overlapping locations.</p> <p>We studied three co-occurring threatened bird species in a fire-prone 'mallee' region of south-eastern Australia. We undertook field surveys for each species (1508 surveys; 540 sites; 9-ha each). We used N-mixture models to determine (a) what factors affect species' density (including post-fire succession); (b) species' population sizes; (c) locations of species' current population hotspots and locations that may become population hotspots in the future as the post-fire successional state changes and (d) the degree of overlap in the current and possible future hotspots of species.</p> <p>We found substantial variation in the densities of the three species across the study area, with roughly half of each species' population occurring in only 20 percent of potential habitat (i.e. population hotspots). All species shared a preference for subtle depressions in the landscape, resulting in substantial overlap in their population hotspots. Two species had contrasting responses to post-fire succession in the subtle depressions. As a result, there was only a narrow post-fire period that supported population hotspots of both species, creating a challenge for fire managers in these shared locations.</p> <p><em>Synthesis and Applications.</em> Many studies make vague recommendations for fire-age mosaics that do not provide managers with the detail they need to implement appropriate fire-age mosaics. By contrast, we explicitly quantify, then balance the conflicting post-fire needs of species in locations that support population hotspots of multiple species. Using this approach, we develop principles to guide the implementation of fire-age mosaics in such locations. This approach represents a step towards applying fire-age mosaic theory to support effective species conservation.</p>
Dataset to study the population genomics of introduced Nile tilapia (Oreochromis niloticus (Linnaeus, 1758)) in the Democratic Republic of the Congo: repeated introductions since colonial times with multiple sources
<p>During colonial times, Nile tilapia <em>Oreochromis niloticus</em> (Linnaeus, 1758) was introduced in non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focussing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridisation. Using RAD sequencing (27 611 SNPs), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, stressing their ability to interbreed and the potential threat they cause to the genetic integrity of native tilapias. Populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity with Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge to avoid introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.</p>
ASreml code and Data from the study "Between-population differences in the genetic and maternal components of body mass in roe deer"
<p>This repository contains the source code (ASremL input files) and the data used to perform the QG analyses (univariate, bivariate, random regression animal models) in the study "Between-population differences in the genetic and maternal components of body mass in roe deer". Quéméré E et al.</p> <p> </p>
Study on the mating systems of wild rice Oryza rufipogon and O. nivara and their effects on population genetic variation
<p>As the wild ancestors of Asian cultivated rice,<em> Oryza rufipogon</em> Griff. and <em>O. nivara</em> Sharma et Shastry serve as valuable germplasms for rice breeding. Mating systems are important in shaping the level and pattern of population genetic variation, and are crucial for germplasm conservation. We genotyped 12 simple sequence repeats (SSR) markers for a large number of maternal plants and seeds collected from <em>O</em>.<em> rufipogon</em> and <em>O. nivara</em> populations distributed in Southeast Aisa and South China. Based on the 12 SSR markers, we estimated the outcrossing rates and other parameters of the mixed-mating model for the two wild rice species. We also assessed the level of genetic diversity and population structure for parental populations of <em>O</em>.<em> rufipogon</em> and <em>O. nivara</em>. Our study could facilitate <em>in situ</em> and <em>ex situ</em> conservation, and the utilization of these valuable germplasm resources.</p>
Figure 2. – The18 in Fishers' perceptions of river resources: case study of French Guiana native populations using contextual cognitive mapping
Figure 2. – The18 concepts that fishers mentioned most frequently.
Figure 6 in Fishers' perceptions of river resources: case study of French Guiana native populations using contextual cognitive mapping
Figure 6. – Cognitive maps of threats of fishing practices on the fish resource and environment.
Figure 8 in Fishers' perceptions of river resources: case study of French Guiana native populations using contextual cognitive mapping
Figure 8. – Potential chains of events caused by the Westernization process.
Figure 4 in First data on population estimates and dispersal of Montenegrina subcristata - a field study at Virpazar, Montenegro
Figure 4. Sum of individuals counted at each observation date at site A (above) and site B (below).
Fig. 5 in A review of Sciurus Group studies on the red squirrel (Sciurus vulgaris): presence, population density and colour phases in Lombardy (Italy)
Fig. 5 - Orientation of the red squirrel dreys per study area.
Fig. 3 in A review of Sciurus Group studies on the red squirrel (Sciurus vulgaris): presence, population density and colour phases in Lombardy (Italy)
Fig. 3 - Study areas in Lombardy. Box: geographic position of Lombardy (black) in Italy.
ScienceDex guides
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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.