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Dataset results
5,538 results for “Population data”
Genotype data of 10 nuclear microsatellite loci for 30 Quercus acutissima populations in China
<p>This dataset includes genotype data of 10 nuclear microsatellite loci for 707 individuals of Quercus acutissima from 30 natural populations in China.</p>
nSSR genotype data for 30 Quercus acutissima populations and 18 Quercus chenii populations in China
<p>This dataset includes genotype data of seven nSSR loci for 696 individuals of Quercus acutissima from 30 natural populations, and 415 individuals of Quercus chenii from 18 natural populations in China.</p>
Zea mays MAGIC RIL population - field trial phenotyping data
<p>MIAPPE compliant ISA-tab files of the Zea mays MAGIC RIL population derived from eight genetically diverse founder lines.</p>
Zea mays MAGIC RIL population - growth chamber phenotyping data
<p>MIAPPE compliant ISA-tab files of 197 recombinant inbred lines of two different maize (Zea mays) populations including indepth phenotyping of the fourth leaf at later stages of development.</p>
Fig. 1 in Unpublished population data of Dendrobates azureus Hoogmoed 1969 obtained in 1968 and 1970, and its historical and current taxonomic status
Fig. 1. Dendrobates "azureus" (= tinctorius).
Silva, Harder et al. Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history Data
<p>Dataset used in the "Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history" paper by Silva, Harder et al.</p> <p>This dataset includes Fasta files for Simulated dataset and VCF files for both Empirical and Simulated datasets.</p>
Open dataset for the research of "Assessing accuracy improvement of integrating digital footprints into gridded population mapping: spatiotemporal variations and data bias"
<p>Result datasets for "Assessing accuracy improvement of integrating digital footprints into gridded populationmapping:spatiotemporal variations and data bias":</p> <ol> <li> S1 is the results for gridded population mapping using different methods.</li> <li> S2 is the aggregate results of population mapping at county level.</li> <li> S3 is the results for intraday variation of population disaggregation accuracy,</li> <li> S4 is the data bias of different digital footprints.</li> </ol>
Model results and data associated with "Antecedent effect models as an exploratory tool to link climate drivers to herbaceous perennial population dynamics data"
<p>Model results and data (including Bayesian posteriors) associated with "Antecedent effect models as an exploratory tool to link climate drivers to 3 herbaceous perennial population dynamics data".</p> <p>This is a repository created to store the posteriors of the models fit within this project. Because these occupy so much space, it makes sense to store them in a separate repository.</p> <p>There are two directories:</p> <ul> <li><em>model_results/</em> contains all of the posteriors (files with character pattern <em>main_posterior_#.csv</em>). The three types of files contained in this directory are described in <em>metadata_model_results.xlsx</em>. The number # corresponds to column "index" in file <em>raw_data/design_insample.csv</em>.</li> <li><em>raw_data/</em> is mostly not essential: it contains the raw data to fit models, and it replicates folder <em>data/</em> in repository https://dx.doi.org/10.5281/zenodo.13909628.</li> </ul>
Geospatial micro-estimates of slum populations in 129 Global South countries using machine learning and public data
<p><span>Reliable estimation of populations living in slums or slum-like conditions is crucial for urban planning, humanitarian resource allocation, and human well-being improvement. We generate the micro-estimate of slum population at a neighborhood level (~</span><span>3.63 arc-minutes</span><span>, preserving the privacy of vulnerable people) for 129 Global South countries in 2018. The estimates are built based on the Sustainable Development Goals 11.1 indicator framework and machine learning algorithms to heterogeneous data from household-based surveys and satellite images, as well as grided population data. Our integrated regional models show strong predictive capabilities for cluster-level slums proxy, explaining 82% to 96% of the variation in ground-truth surveys conducted in Global South countries, with root mean squared error ranging from 4.85% to 10.47%. The models perform match or surpass benchmarks established by previous studies.</span><span> </span><span>Cross-comparison with independent data sources at multi-scales suggest that our approach can yield reliable and consistent slum population estimates.</span></p>
Data and codes for "Habitat structural complexity increases age-class coexistence and population growth rate through relaxed cannibalism in medaka fish"
<p>The zip file contains readme files, as well as data and codes to reproduce results and figures from the paper.</p>
Data from: Environmental heterogeneity and not vicariant biogeographic barriers generate community wide population structure in desert adapted snakes
Genetic structure can be influenced by local adaptation to environmental heterogeneity and biogeographic barriers, resulting in discrete population clusters. Geographic distance among populations, however, can result in continuous clines of genetic divergence that appear as structured populations. Here we evaluate the relevant importance of these three factors over a landscape characterized by environmental heterogeneity and the presence of a hypothesized biogeographic barrier in producing population genetic structure within 13 codistributed snake species using a genomic dataset. We demonstrate that geographic distance and environmental heterogeneity across western North America contribute to population genomic divergence. Surprisingly, landscape features long thought to contribute to biogeographic barriers play little role in divergence community wide. Our results suggest that isolation by environment is the most important contributor to genomic divergence. Furthermore, we show that models of population clustering that incorporate spatial information consistently outperform nonspatial models, demonstrating the importance of considering geographic distances in population clustering. We argue that environmental and geographic distances as drivers of community-wide divergence should be explored before assuming the role of biogeographic barriers.
Data from: Population-based screening for hepatitis C antibodies and active infection using a point-of-care test in a low prevalence area
<p><span><span><span><span><span><span><span><span><span><span><span><b>Background.</b> Data on the true prevalence of hepatitis C virus (HCV) infection in the </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>general population is essential to health policies. We evaluated a program implementing free universal HCV screening using a non-invasive point-of-care test (POCT) (OraQuick-HCV rapid test) in oral fluid in an urban area in Valencia, South-Eastern Spain. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methods.</b> A cross-sectional study was performed during 2015-2017. Free HCV screening was offered by regular mail to 11,500 individuals aged 18 and over, randomly selected from all census residents in the Health Department. All responding participants filled in a questionnaire about HCV infection risk factors and were tested in their tertiary Hospital. In those with a positive POCT, results were confirmed by enzyme-immunoassay and HCV-RNA.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Results.</b> 1,206 persons agreed to participate (response rate: 11.16%). HCV antibodies were detected in 19 (1.60%) cases (age-sex standardized rate: 1.31%; 95%CI: 0.82-2.07), but only 8 showed positive HCV-RNA (age-sex standardized rate: 0.56%; 95%CI: 0.28-1.14). The majority (89%) of the cases were born before 1965 and 74% had at least one known risk factor for HCV infection. All anti-HCV positive individuals were already aware of their infection, and no undiagnosed cases were detected. The performance of the POCT was excellent for detecting active infection. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Conclusions.</b> These preliminary data suggest that HCV population screening with a POCT is feasible but, in our setting, mailing recruiting is not effective (11% response rate). The low prevalence of HCV antibodies and active infection in the participant population (with no new diagnoses made) suggests that, in our setting, underdiagnosis may be uncommon.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Files uploaded include the study database (Stata v.13) and the do.file of the study.</b></span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis, in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia.
Data from: Local prey community composition and genetic distance predict venom divergence among populations of the northern Pacific rattlesnake (Crotalus oreganus)
Identifying the environmental correlates of divergence in functional traits between populations can provide insights into the evolutionary mechanisms that generate local adaptation. Here, we assess patterns of population differentiation in expressed venom proteins in Northern Pacific rattlesnakes (Crotalus oreganus) from 13 locations across California. We evaluate the relative importance of major biotic (prey species community composition), abiotic (temperature, precipitation, and elevation) and genetic factors (genetic distance based on RADseq loci) as correlates of population divergence in venom phenotypes. We found that over half of the variation in venom composition is associated with among-population differentiation for genetic and environmental variables, and that this variation occurred along axes defining previously observed functional trade-offs between venom proteins that have neurotoxic, myotoxic and hemorrhagic effects. Surprisingly, genetic differentiation among populations was the best predictor of venom divergence, accounting for 46% of overall variation, whereas differences in prey community composition and abiotic factors explained smaller amounts of variation (23% and 19%, respectively). The association between genetic differentiation and venom composition could be due to an isolation by distance effect or, more likely it may reflect an isolation-by-environment effect where selection against recent migrants is strong, producing a correlation between neutral genetic differentiation and venom differentiation. Our findings suggest that even coarse estimates of prey community composition can be useful in understanding the selection pressures acting on patterns of venom protein expression. Additionally, our results suggest that factors other than adaptation to spatial variation in prey need to be considered when explaining population divergence in venom.
Data from: Intraspecific variation and symmetry of the inner-ear labyrinth in a population of wild turkeys: implications for paleontological reconstructions
The cochlea and semicircular canals of the inner ear are vital neurosensory devices. There are associations between the anatomy of these sensorineural structures, their function, and the function of related biological systems, e.g., hearing ability, gaze stabilization, locomotor agility, and posture. The endosseous labyrinth is frequently used as a proxy to infer the performance of the hearing and vestibular systems, locomotor abilities, and ecology of extinct species. Such fossil inferences are often based on single specimens or even a single ear, representing an entire species. To address whether a single ear is representative of a population, we used geometric morphometrics to quantitatively assess the variation in shape and symmetry in a sample of endosseous labyrinths of wild turkeys Meleagris gallopavo of southern Ohio. We predicted that ears would be symmetrical both within individuals and across the sample; that labyrinth shape and size would covary; that labyrinth shape would vary with the size of the brain, measured as width of the endocranium at the cerebellum; and that labyrinths would be morphologically integrated. To test these predictions, we microCT-scanned the heads of 26 cadaveric turkeys, digitally segmented their endosseous labyrinths in Avizo, and assigned 15 manual landmarks and 20 sliding semilandmarks to each digital model. Following Procrustes alignment, we conducted an analysis of bilateral symmetry, a Procrustes regression analysis for allometry and other covariates including side and replicate, and analyses of global integration and modularity. Based on Procrustes distances, no individual's left and right ears were clearly different from each other. When comparing the ears of different specimens, statistically clear differences in shape were found in only 66 of more than 1300 contrasts. Moreover, effects of both directional and fluctuating asymmetry were very small—generally, two orders of magnitude smaller than the variance explained by individual variation. Statistical tests disagreed on whether these asymmetric effects crossed the threshold of significance, possibly due to non-isotropic variation among landmarks. Regardless, labyrinths appeared to primarily vary in shape symmetrically. Neither labyrinth size nor endocranial width was correlated with labyrinth shape, contrary to our expectations. Finally, labyrinths were found to be moderately integrated in a global sense, but four weakly separated modules—the three semicircular canals and cochlea—were recovered using a maximum-likelihood analysis. The results show that both fluctuating and directional asymmetry play a larger role in shape variation than expected—but nonetheless, endosseous labyrinths are symmetrical within individuals and at the level of the population, and their shape varies symmetrically. Thus, inferences about populations, and very possibly species, may be confidently made when only a single specimen, or even a single ear, is available for study.
Data from: Selection for life-history traits to maximize population growth in an invasive marine species
Species establishing outside their natural range, negatively impacting local ecosystems, are of increasing global concern. They often display life-history features characteristic for r-selected populations with fast growth and high reproduction rates to achieve positive population growth rates (r) in invaded habitats. Here, we demonstrate substantially earlier maturation at a 2 orders of magnitude lower body mass at first reproduction in invasive compared to native populations of the comb jelly Mnemiopsis leidyi. Empirical results are corroborated by a theoretical model for competing life-history traits that predicts maturation at the smallest possible size to optimize r, while individual lifetime reproductive success (R0), optimized in native populations, is near constant over a large range of intermediate maturation sizes. We suggest that high variability in reproductive tactics in native populations is an underappreciated determinant of invasiveness, acting as substrate upon which selection can act during the invasion process.
Data from: Old-growth forests buffer climate-sensitive bird populations from warming
Aim: Habitat loss and climate change constitute two of the greatest threats to biodiversity worldwide, and theory predicts that these factors may act synergistically to affect population trajectories. Recent evidence indicates that structurally complex old-growth forest can be cooler than other forest types during spring and summer months, thereby offering potential to buffer populations from negative effects of warming. Old growth may also have higher food and nest-site availability for certain species, which could have disproportionate fitness benefits as species approach their thermal limits. Location: Pacific Northwestern United States. Methods: We predicted that negative effects of climate change on 30-year population trends of old-growth-associated birds should be dampened in landscapes with high proportions of old-growth forest. We modelled population trends from Breeding Bird Survey data for 13 species as a function of temperature change and proportion old-growth forest. Results: We found a significant negative effect of summer warming on only two species. However, in both of these species, this relationship between warming and population decline was not only reduced but reversed, in old-growth-dominated landscapes. Across all 13 species, evidence for a buffering effect of old-growth forest increased with the degree to which species were negatively influenced by summer warming. Main conclusions: These findings suggest that old-growth forests may buffer the negative effects of climate change for those species that are most sensitive to temperature increases. Our study highlights a mechanism whereby management strategies to curb degradation and loss of old-growth forests—in addition to protecting habitat—could enhance biodiversity persistence in the face of climate warming.
Data from: RAD sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for non-model organisms, potentially revolutionising the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (1) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci, and; (2) quantify error rates for loci, alleles and SNPs. As an empirical example we use a double digest RAD dataset of a non-model plant species, Berberis alpina, collected from high altitude mountains in Mexico.
Data from: The laboratory domestication of zebrafish: from diverse populations to inbred substrains
<p>We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of 'personalized medicine'. Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behaviour and physiology, for modelling diseases, and for testing pharmaceutic compounds in vivo. However, all of these strains are derived from artificial bottleneck events and therefore are likely to represent only a fraction of the genetic diversity present within the species.</p> <p>Here we use Restriction site-Associated DNA sequencing (RAD-seq) to genetically characterize wild populations of zebrafish from India, Nepal and Bangladesh, and to compare them to previously published data on four common laboratory strains. We measured nucleotide diversity, heterozygosity and allele frequency spectra, and find that wild zebrafish are much more diverse than laboratory strains. Further, in wild zebrafish there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are most distinct from all other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic, physiological, pharmaceutic and evolutionary studies in Danio rerio.</p>
Data from: The socially parasitic ant Polyergus mexicanus has host-associated genetic population structure and related neighboring nests
<p>The genetic structure of populations can be both a cause and a consequence of ecological interactions. For parasites, genetic structure may be a consequence of preferences for host species or of mating behavior. Conversely, genetic structure can determine where conspecific interactions among parasites lay on a spectrum from cooperation to conflict. We used microsatellite loci to characterize the genetic structure of a population of the socially parasitic dulotic (aka "slave-making") ant (<i>Polyergus mexicanus</i>), which is known for its host-specificity and conspecific aggression. First, we assessed whether the pattern of host species use by the parasite has influenced parasite population structure. We found that host species use was correlated with subpopulation structure, but this correlation was imperfect: some subpopulations used one host species exclusively, while others used several. Second, we examined the viscosity of the parasite population by measuring the relatedness of pairs of neighboring parasitic ant nests at varying distances from each other. Although natural history observations of local dispersal by queens suggested the potential for viscosity, there was no strong correlation between relatedness and distance between nests. However, 35% of nests had a closely related neighboring nest, indicating that kinship could potentially affect the nature of some interactions between nests of this social parasite. Our findings confirm that ecological forces like host species selection can shape the genetic structure of parasite populations, and that such genetic structure has the potential to influence parasite-parasite interactions in social parasites via inclusive fitness.</p>
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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.