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5,538 results for “Population data”
Data from: Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads
<p>Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (<i>Spea multiplicata</i>). <i>Spea</i> tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 12 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.</p>
Population abundance data and species range maps
<p><b>Aim </b>–<b> </b>The abundant-center hypothesis (ACH) predicts a negative relationship between species abundance and the distance to geographic range center. Since its formulation, empirical tests of the ACH have involved different settings (e.g. the distance to the ecological niche or to the geographic range center), but studies found contrasting support for this hypothesis. Here, we evaluate whether these discrepancies might stem from differences regarding the context in which the ACH is tested (geographical or environmental), how distances are measured, how species envelopes are delineated, how the relationship is evaluated and which data are used.</p> <p><b>Location</b> – Americas.</p> <p><b>Time Period </b>– 1800-2017.</p> <p><b>Major taxa studied</b> – mammal, bird, fish and tree seedlings.</p> <p><b>Methods</b> – Using published abundance data for 801 species, together with species range maps, we tested the ACH using three distance metrics in both environmental and geographical spaces with range and niche envelopes delineated using two different algorithms, totaling 12 different settings. We then evaluated the distance-abundance relationship using correlation coefficients (traditional approach) and mixed-effect models to reduce the effect of sampling noise on parameter estimates.</p> <p><b>Results</b> – Similar to previous studies, correlation coefficients indicated an absence of effect of distance on abundance for all taxonomic groups and settings. In contrast, mixed-effect models highlighted relationships of various strengths and shapes, with a tendency for more theoretically-supported settings to provide stronger support for the ACH. The relationships were however not consistent across taxonomic groups and settings, and were sometimes even opposite to ACH expectations.</p> <p><b>Main conclusions</b> – We found mixed and inconclusive results regarding the ACH. These results corroborate recent findings, and suggest either that our ability to predict abundances from the location of populations within geographical or environmental spaces is low, or that the data used here have a poor signal-to-noise-ratio. The latter calls for further testing on other datasets using the same range of settings and methodological framework.</p>
Population Dynamics of the date palm mite, Oligonychus afrasiaticus over 4 years data
<p>The data uploaded in MS Excel is related to the population dynamics of the date palm mite, Oligonychus afrasiaticus. This field study was conducted in 02 regions of Saudi Arabia. The duty was collected over 04 years.</p>
Breeding system data for populations of T. perfoliata
<p><span>Both intrinsic and extrinsic forces work together to shape connectivity and genetic variation in populations across the landscape. Here we explored how geography, breeding system traits, and environmental factors influence the population genetic patterns of <em>Triodanis perfoliata</em>, a widespread mix-mating annual plant in the contiguous US. By integrating population genomic data with spatial analyses and modeling the relationship between breeding system and genetic diversity, we illustrate the complex ways in which these forces shape genetic variation. Specifically, we used 4,705 single nucleotide polymorphisms to assess genetic diversity, structure, and evolutionary history among 18 populations. Populations with more obligately selfing flowers harbored less genetic diversity (π: R2 = 0.63, P = 0.01, n = 9 populations), and we found significant population structuring (FST = 0.48). Both geographic isolation and environmental factors played significant roles in predicting the observed genetic diversity: we found that corridors of suitable environment appear to facilitate gene flow between populations, and that environmental resistance is correlated with increased genetic distance between populations. Last, we integrated our genetic results with species distribution modeling to assess likely patterns of connectivity among our study populations. Our landscape and evolutionary genetic results suggest that <em>T. perfoliata</em> experienced a complex demographic and evolutionary history, particularly in the center of its distribution. As such, there is no singular mechanism driving this species' evolution. Together, our analyses support the hypothesis that breeding system, geography, and environmental variables shape the patterns of diversity and connectivity of T. perfoliata in the US.</span></p>
Data from: Breeding system and geospatial variation shape the population genetics of Triodanis perfoliata
<p><span>Both intrinsic and extrinsic forces work together to shape connectivity and genetic variation in populations across the landscape. Here we explored how geography, breeding system traits, and environmental factors influence the population genetic patterns of <em>Triodanis perfoliata</em>, a widespread mix-mating annual plant in the contiguous US. By integrating population genomic data with spatial analyses and modeling the relationship between breeding system and genetic diversity, we illustrate the complex ways in which these forces shape genetic variation. Specifically, we used 4,705 single nucleotide polymorphisms to assess genetic diversity, structure, and evolutionary history among 18 populations. Populations with more obligately selfing flowers harbored less genetic diversity (π: R<sup>2</sup> = 0.63, P = 0.01, n = 9 populations), and we found significant population structuring (F<sub>ST</sub> = 0.48). Both geographic isolation and environmental factors played significant roles in predicting the observed genetic diversity: we found that corridors of suitable environment appear to facilitate gene flow between populations, and that environmental resistance is correlated with increased genetic distance between populations. Last, we integrated our genetic results with species distribution modeling to assess likely patterns of connectivity among our study populations. Our landscape and evolutionary genetic results suggest that <em>T. perfoliata</em> experienced a complex demographic and evolutionary history, particularly in the center of its distribution. As such, there is no singular mechanism driving this species' evolution. Together, our analyses support the hypothesis that breeding system, geography, and environmental variables shape the patterns of diversity and connectivity of <em>T. perfoliata</em> in the US. </span></p>
Supplemental data for: Development and validation of a polygenic risk score for stroke in the Chinese population
<div class="WordSection1"> <div class="WordSection1"> <strong>Objective</strong>: To construct a polygenic risk score (PRS) for stroke and evaluate its utility in risk stratification and primary prevention for stroke.</div> <div class="WordSection1"> </div> <div class="WordSection1"> <strong>Methods</strong>: Using meta-analytic approach and large genome-wide association results for stroke and stroke-related traits in East Asians, we generated a combined PRS (metaPRS) by incorporating 534 genetic variants in a training set of 2,872 patients with stroke and 2,494 controls. We then validated its association with incident stroke using Cox regression models in large Chinese population-based prospective cohorts comprising 41,006 individuals.</div> <div class="WordSection1"> </div> <div class="WordSection1"> <strong>Results</strong>: During a total of 367,750 person-years (mean follow-up 9.0 years), 1,227 participants developed stroke before age of 80 years. Individuals with high polygenic risk had an about 2-fold higher risk of incident stroke compared with those with low polygenic risk (HR: 1.99, 95% CI: 1.66-2.38), with the lifetime risk of stroke being 25.2% (95% CI: 22.5%-27.7%) and 13.6% (95% CI: 11.6%-15.5%), respectively. Individuals with both high polygenic risk and family history displayed the lifetime risk as high as 41.1% (95% CI: 31.4%-49.5%). Moreover, individuals with high polygenic risk achieved greater benefits in terms of absolute risk reductions from adherence to ideal fasting blood glucose and total cholesterol than those with low polygenic risk. Maintaining favorable cardiovascular health (CVH) profile could substantially mitigate the increased risk conferred by high polygenic risk to the level of the low polygenic risk (from 34.6 % to 13.2%).</div> <div class="WordSection1"> </div> <div class="WordSection1"> <strong>Conclusions</strong>: Our metaPRS has great potential for risk stratification of stroke and identification of individuals who may benefit more from maintaining ideal CVH. </div> <div class="WordSection1"> </div> <div class="WordSection1"> <strong>Classification of Evidence</strong>: This study provides Class I evidence that a meta-polygenic risk score is predictive of stroke risk.</div> <p> </p> </div>
Data for: Relationships between reproductive character displacement in genital morphology and the population-level cost of interspecific mating: Implications for the Templeton effect
<p><span>Natural selection against maladaptive interspecific reproductive interactions may cause greater divergence in mating traits between sympatric populations than between allopatric populations in a pair of species, known as reproductive character displacement (RCD), evidence for the lock-and-key hypothesis of genital evolution. However, the relative importance of various processes contributing to RCD in genital morphology (e.g., reinforcement, reproductive interference, and population filtering or the Templeton effect) is not clear. Here, we examined hypotheses for RCD in genital morphology, with a special focus on the Templeton effect (which predicts that only highly differentiated populations can exist in sympatry). We examined population-level fitness costs in interspecific mating between <em>Carabus maiyasanus</em> and <em>C. iwawakianus</em> with RCD in genital morphology. A mating experiment using populations with various degrees of RCD in genital morphology showed no evidence for consistently lower interspecific mating costs in <em>C. maiyasanus</em> populations in contact with displacement in genital morphology than in remote populations, contrary to the predictions of the Templeton effect. Alternatively, interspecific mating costs varied among populations. Observed relationships between the sizes of genital parts concerning isolation and interspecific mating costs across populations suggested that population-level fitness costs do not necessarily decrease during the process leading to RCD. Our results provide insight into ecological and evolutionary processes during secondary contact in closely related species.</span></p>
21 autosomal STR marker data for Roma population in Serbia
<p>Here we present the data for 21 autosomal STR markers, included in The Investigator 24plex QS kit (Qiagen, Germany), for Roma population in Serbia. </p>
The data for Reconstruction of Cosmic Black Hole Growth and Mass Distribution from Quasar Luminosity Functions at z>4: Implications for Faint and Low-mass Populations in JWST
<p>The data for Figure 1 in the AAS article: Reconstruction of Cosmic Black Hole Growth and Mass Distribution from Quasar Luminosity Functions at z>4: Implications for Faint and Low-mass Populations in JWST</p> <p>in each file, the column heads are x: M1450; y_f0: total Phi(Mpc^-3 mag^-1) for f_seed=1.0 y1_f0: unobscured Phi for f_seed=1.0 y_f1: total Phi for f_seed=0.1 y1_f1: unobscured Phi for f_seed=0.1</p>
Data used for analysis in "Calibrating tropical forest coexistence in ecosystem demography models using multi-objective optimization through population-based parallel surrogate search"
Open the record for dataset details and reuse information.
Data from "A population of neurons selective for human voice in the monkey brain"
<p>Preprocessed datasets associated to the research article "A population of neurons selective for human voice in the monkey brain", PNAS.</p>
Data associated with the publication 'Population-level coding of avoidance learning in medial prefrontal cortex' by Benjamin Ehret et al.
<p>This repository contains data for the following publication:</p> <p>Population-level coding of avoidance learning in medial prefrontal cortex</p> <p>Ehret B., Boehringer R., Amadei E. A., Cervera M. R., Henning C., Galgali A., Mante V., Grewe, B. F.</p> <p>Nature Neuroscience 2024</p> <p> </p> <p>The associated analysis code is published here:</p> <p>https://github.com/behret/paper_code_active_avoidance</p> <p> </p> <p>This repository contains 1) source data to reproduce all figures and 2) processed data to reproduce most analyses. </p> <p>A small subset requires access to the raw data, which is too extensive to be published online. However, raw data can be made available upon request.</p>
Data from "Population genomic structure of Lemna minor and the cryptic species L. japonica in Switzerland"
<p>SNP data and sample annotation:</p> <ul> <li>sampleTab.csv contains the sample annotation (species and population)</li> <li>L.minor.reference.bcftools.snps.vcf.gz(.tbi) contains SNPs from all samples using the L. minor reference genome (Lm7210)</li> <li>L.japonica.reference.bcftools.snps.vcf.gz(.tbi) contains SNPs from all samples using the L. japonica reference genome (Lj9421)</li> </ul>
Population synthesis data of massive binaries: NS/BH-core mergers and double compact objects formation and mergers
<p><span>Binary population synthesis data generated using the rapid population synthesis code COMPAS.</span></p> <p><span>Contains:</span></p> <p><span>1. Full COMPAS output in (.csv format) for running massive binaries varying the common envelope efficiency parameter and the metallicity.</span></p> <p><span>2. Identifying seeds of systems that result in neutron star (NS)/black hole (BH)-core mergers, binary NSs, binary BHs and NS-BH binaries. </span></p>
Data for: Genetic relatedness shapes social dynamics in a threatened finch: Implications for population assessment
<p>Tropical granivorous finches often form large flocks around resources. The composition of these flocks, whether they are random groups of individuals or comprise related birds travelling together, is currently unknown. Understanding this distinction would aid in assessing the accuracy of population counts. To bridge this knowledge gap, we combined high-frequency location tracking with comprehensive genetic sequencing to investigate the relationship between pairwise association strength and genetic relatedness in Gouldian finches (<em>Erythrura gouldiae</em>). Our study revealed that birds captured near each other were more inclined to travel together, and their relatedness was significantly linked to the strength of their association. These findings suggest that within-flock associations are influenced by genetic relatedness, contributing to the stability of the flock size. We propose that juvenile kin associations play a pivotal role in this dynamic, potentially enhancing survival rates by forming sibling subgroups. The consistent flock sizes of Gouldian finches during movement have implications for estimating population sizes from waterhole counts, allowing flocks to be considered as distinct units for concurrent counts at multiple waterholes. This approach would offer a reasonably accurate method for estimating local populations, and conducting repeated counts on consecutive days could provide reliable and replicable results.</p>
Data for: Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales
<p>House mice (<em>Mus musculus</em>) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely-used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure, and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of <em>Mus</em>, with a focus on <em>M. m. domesticus</em>. We find that the major axis of genetic variation in <em>M. m. domesticus</em> is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand, and various small offshore islands is of northern European origin. Next, we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.</p>
Data from: High nest failure in a zebra finch population and persistent predation of a nest by a monitor lizard
<p>Predation is well known to have substantial effects on behaviour and fitness in many animals. In songbirds, nest predation is rarely observed directly, so that research focusses primarily on the consequences of predation and less on the behaviour of the predator. Here, we report predation data in a zebra finch (<em>Taeniopygia catanosis</em>) nest box population, highlighting a 22-min-long sequence, captured on video, of a sand goanna (<em>Varanus gouldii</em>) predating a zebra finch nest in the wild. This monitor lizard appeared to be extremely persistent with climbing and jumping up to the next box nine times, including three successive unsuccessful attempts that lead to a change in approach strategy. It removed all six nestlings from the nest box during those repeated approaches and consumed them. In combination with overall high predation rates in the study population we document here, the findings highlight the role that a single predator species can have on nest success and, thus potentially also breeding decisions and social organisation of the prey population. Specifically so in a species like the zebra finch which synchronises reproductive attempts through the use of social information acquired through nest inspections and which uses social hotspots where they could gather information on changes in local social composition due to the individualised signals they use.</p>
Microsatellite data for Prosopis species sampled from different non-native populations in Kenya and Ethiopia
<p>Microsatellite data for seven loci and 711 individuals of <em>P. juliflora</em> and <em>P. pallida</em> sampled from non-native populations from Kenya and Ethiopia.</p>
Double Trouble : Multiple infections and the coevolution of virulence-resistance in structured host-parasite populations - Scripts, Data and Supplementary Material
<p>Supplementary material</p> <p> </p> <p>Contains the Mathematica notebook for analytical and numerical computations, and figure generation.</p> <p>An Rscript used to reproduce the coevolutionary figures from section "Coevolution"</p> <p>The set of appendices in a .pdf file.</p>
Data from: Phenotypic correlates between clock genes and phenology among populations of Diederik cuckoo, Chrysococcyx caprius
<p>Dataset of Clock genes for Diederik Cuckoos collected as part of a migration genetics study.</p>
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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.