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5,538 results for “population data”
A Genetic Algorithm Approach to Regenerate Image from a Reduce Scaled Image Using Bit Data Count-Figure 11. Initial population
<p>In figure 11 it is the initial population showed and figure 12 the population started to change and figure 13 we reached a convergence.</p>
SNP call data for: The current epidemic of the barley pathogen Ramularia collo-cygni derives from a recent population expansion and shows global admixture
<p>Ramularia Leaf Spot is becoming an ever increasing problem in main barley growing regions since the 1980s, causing up to 70% yield loss in extreme cases. Yet, the causal agent <em>Ramularia collo-cygni</em>, remains poorly studied. The diversity of the pathogen in the field thus far remains unknown. Furthermore, it is unknown to which extend the pathogen has a sexual reproductive cycle. To date, the teleomorph of <em>R. collo-cygni</em> has not been observed.</p> <p>To study the genetic diversity of <em>R. collo-cygni </em>and to get more insights into its biology, we sequenced the genomes of 19 <em>R. collo-cygn</em>i isolates from multiple geographic locations and diverse hosts. Here we share the SNP call data as well as the reference genome.</p> <p>The reference genome files and assembly can be found on ENI: GCA_900074925.1</p> <p>https://www.ebi.ac.uk/ena/data/view/GCA_900074925.1</p> <p>The raw sequence data is also available through ENI: ERX2296228</p> <p>https://www.ebi.ac.uk/ena/data/view/ERX2296228</p>
data for the PCI publication "New insights into the population genetics of partially clonal organisms: when seagrass data meet theoretical expectations"
<p><strong>Data analyzed int he article "New insights into the population genetics of partially clonal organisms: when seagrass data meet theoretical expectations", doi </strong> <a href="https://arxiv.org/abs/1902.10240v5">https://arxiv.org/abs/1902.10240v5</a> <strong> doi of the PCI recommandation: </strong>https://doi.org/10.24072/pci.evolbiol.100083</p>
Figure 2 in Investigation of genetic variation among Turkish populations of Andricus lignicola using mitochondrial cytochrome b gene sequence data
Figure 2. Bayesian analysis tree. Posterior probability values are given on the branches. Outgroup haplotypes: Ac (Andricus caliciformis) and Ak (Andricus kollari).
MANET: uncertainty in demographics – data on population projections
<p>This is a repository of global and regional human population data collected from: the databases of scenarios assessed by the Intergovernmental Panel on Climate Change (Sixth Assessment Report, Special Report on 1.5 C; Fifth Assessment Report), multi-national databases of population projections (World Bank, International Database, United Nation population projections), and other very long-term population projections (Resources for the Future).</p> <p>More specifically, it contains:</p> <p>- in `other_pop_data` folder files from <a href="https://databank.worldbank.org/source/population-estimates-and-projections">World Bank,</a> the <a href="https://www.census.gov/data-tools/demo/idb/#/dashboard?COUNTRY_YEAR=2023&COUNTRY_YR_ANIM=2023">International Database</a> from the US Census, and from <a href="https://ghdx.healthdata.org/record/ihme-data/global-population-forecasts-2017-2100">IHME</a></p> <p>- in the `SSP` folder, the Shared Socioeconomic Pathways, as in the version 2.0 downloaded from <a href="https://tntcat.iiasa.ac.at/SspDb/dsd?Action=htmlpage&page=10">IIASA</a> and as in the version 3.0 downloaded from <a href="https://data.ece.iiasa.ac.at/ssp/#/workspaces">IIASA workspace</a></p> <p>- in the `UN` folder, the demographic projections from <a href="https://population.un.org/wpp/Download/Standard/Population/">UN</a></p> <p>- `IAMstat.xlsx`, an overview file of the metadata accompanying the scenarios present in the IPCC databases</p> <p>- `RFF.csv`, an overview file containing the population projections obtained by <a href="../record/6016583#.Y42iFuzP2rP">Resources For the Future</a> </p> <p>'- the remaining `.csv` files with names `AR6#`, `AR5#`, `IAMC15#` contain the IPCC scenarios assessed by the IPCC for preparing the IPCC assessment reports. They can be downloaded from <a href="https://tntcat.iiasa.ac.at/AR5DB">AR5</a>, <a href="https://data.ene.iiasa.ac.at/iamc-1.5c-explorer/#/downloads">SR 1.5</a>, and <a href="https://data.ene.iiasa.ac.at/ar6/#/workspaces">AR6</a></p> <p>This data in intended to be downloaded for use together with the package downloadable <a href="https://github.com/sgiarols/Climate_Scenario_Data_Science">here</a>.</p> <p>The dataset was used as a supporting material for the paper "Underestimating demographic uncertainties in the synthesis process of the IPCC" accepted on npj Climate Action (DOI : 10.1038/s44168-024-00152-y).</p>
Linked collectors and determiners for: Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status.
Natural history specimen data linked to collectors and determiners held within, "Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d">https://bionomia.net/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d">https://gbif.org/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d</a>. Formatted as a Frictionless Data package.
Genome streamlining: effect of mutation rate and population size on genome size reduction: simulated data
<p>Lineages data of populations simulated with Aevol (<a href="https://gitlab.inria.fr/aevol/aevol">https://gitlab.inria.fr/aevol/aevol</a>), and the Wild-Types sequences used for that.</p> <p>Conditions: change of mutation rate, population size, or both.<br>Mutational bias: none, insertion bias or deletion bias</p>
Data from: Difference in reproductive mode rather than ploidy explains niche differentiation in sympatric sexual and apomictic populations of Potentilla puberula
Apomicts tend to have larger geographical distributional ranges and to occur in ecologically more extreme environments than their sexual progenitors. However, the expression of apomixis is typically linked to polyploidy. Thus, it is a priori not clear whether intrinsic effects related to the change in the reproductive mode or rather in the ploidy drive ecological differentiation. We used sympatric sexual and apomictic populations of Potentilla puberula to test for ecological differentiation. To distinguish the effects of reproductive mode and ploidy on the ecology of cytotypes, we compared the niches (i) of sexuals (tetraploids) and autopolyploid apomicts (penta-, hepta- and octoploids) and (ii) of the three apomictic cytotypes. We based comparisons on a ploidy screen of 238 populations along a latitudinal transect through the Eastern European Alps and associated bioclimatic, soil and topographic data. Sexual tetraploids preferred primary habitats at drier, steeper, more south-oriented slopes, while apomicts mostly occurred in human-made habitats with higher water availability. Contrariwise, we found no or only marginal ecological differentiation among the apomictic higher ploids. Based on the pronounced ecological differences found between sexuals and apomicts, in addition to the lack of niche differentiation among cytotypes of the same reproductive mode, we conclude that reproductive mode rather than ploidy is the main driver of the observed differences. Moreover, we compared our system with others from the literature, to stress the importance of identifying alternative confounding effects (such as hybrid origin). Finally, we underline the relevance of studying ecological parthenogenesis in sympatry, to minimise the effects of differential migration abilities
Data from: When the "selfish herd" becomes the "frozen herd": spatial dynamics and population persistence in a colonial seabird
Aggregations are common in ecological systems at a range of scales and may be driven by exogenous constraints such as environmental heterogeneity and resource availability or by 'self-organizing' interactions among individuals. One mechanism leading to self-organized animal aggregations is captured by Hamilton's 'selfish herd' hypothesis, which suggests that aggregations may be driven by an individual's effort to minimize their risk of predation by surrounding themselves with conspecifics. We demonstrate that aggregations observed in Adélie penguin (Pygoscelis adeliae) colonies are a convolution of both self-organized dynamics and external forcing arising from landscape terrain. In fluid, highly mobile aggregations, individuals are constantly moving in response to changing environmental conditions, the locations of predators, or the movements of conspecifics. However, when the ability to rearrange is limited and spatial reconfiguration occurs on slower time scales than changes in population size, systems may become trapped in sub-optimal arrangements. We use simulated annealing to demonstrate that Adélie penguin colonies are frozen in sub-optimal spatial arrangements, and employ an individual-based modelling approach to demonstrate that this sub-optimal spatial configuration is driven by a convolution of nest site fidelity and stochastic events at the level of individual nests. The resulting spatial dynamics are responsible for a hysteretic response to long-term changes in abundance. We find that declining abundance leads to fragmentation even in a homogeneous environment, which has population-level consequences for reproductive success because predation is biased towards colony edges. Strong edge effects from heterogeneous predation coupled with fragmentation in response to population declines creates a positive feedback cycle that can accelerate population decline. This work provides a mechanistic understanding of complex spatial structuring in penguin colonies, provides a link between current spatial patterning and past dynamics, and suggests the possibility of critical collapse in seabird populations.
Data from: Intraspecific correlations between growth and defense vary with resource availability and differ within- and among-populations
<p>A paradigm in the plant defense literature is that defending against herbivores comes at a cost to growth, resulting in a growth-defense tradeoff. However, while there is strong evidence for growth-defense tradeoffs across species, evidence is mixed within species. Several mechanisms can account for this equivocal support within species, but teasing them apart requires examining growth-defense relationships both within and among populations, an approach seldom employed. We examined correlations between plant biomass (growth) and terpene production (defense) within and among populations of Monarda fistulosa, a perennial herb. We sampled populations from Montana and Wisconsin, regions that differ in resource availability characterized by different summer precipitation and associated abiotic conditions that influence plant productivity. We found negative, neutral, and positive growth-defense correlations, depending on the scale examined. Negative correlations occurred across populations originating from divergent regions, positive correlations occurred across populations originating from within the high-resource region, and neutral correlations were found within single populations. Collectively, these results challenge the general expectation of ubiquitous tradeoffs and support emerging views that resource availability (as it affects productivity) shapes the evolution of defense at different scales.</p>
Code and data associated with Christiansen et al. 2021 "Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing"
<p>All code and data input and output files (except reference genome and raw sequencing data) needed to reproduce the results of Christiansen et al. 2021 as released on <a href="https://github.com/notothen/radpilot">https://github.com/notothen/radpilot</a> alongside journal publication. See published paper:</p> <p>Christiansen, H., Heindler, F.M., Hellemans, B. <em>et al.</em> Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. <em>BMC Genomics</em> <strong>22, </strong>625 (2021). <a href="https://doi.org/10.1186/s12864-021-07917-3">https://doi.org/10.1186/s12864-021-07917-3</a></p>
SNP Data for Aedes aegypti populations in Florida and southern California
<p>In the affiliated paper we compare likely the oldest populations of <i>Aedes aegypti</i> in continental North America with some of the newest to illuminate the range of genetic diversity and structure that can be found within the invasive range of this important disease vector. <i>Aedes aegypti</i> populations in Florida have likely persisted since the 1600-1700s, while populations in southern California derive from new invasions that occurred in the last ten years. For this comparison, we genotyped 1,193 individuals from 29 sites at 12 highly variable microsatellites and a subset of these individuals at 23,961 single nucleotide polymorphisms (SNPs). This dataset contains the SNP genetic information.</p>
Microsatellite data for Aedes aegypti populations in Florida and southern California
<p>In the affiliated paper we compare likely the oldest populations of <i>Aedes aegypti</i> in continental North America with some of the newest to illuminate the range of genetic diversity and structure that can be found within the invasive range of this important disease vector. <i>Aedes aegypti</i> populations in Florida have likely persisted since the 1600-1700s, while populations in southern California derive from new invasions that occurred in the last ten years. For this comparison, we genotyped 1,193 individuals from 29 sites at 12 highly variable microsatellites and a subset of these individuals at 23,961 single nucleotide polymorphisms (SNPs).</p>
Disk population synthesis data for the article: "Large gaps and high accretion rates in photoevaporative transition disks with a dead zone"
<p>We make available here the results of our gas evolution simulations for the article "Large gaps and high accretion rates in photoevaporative transition disks with a dead zone".</p> <p>We include the result of our population synthesis study, consisting in 10 tables corresponding to 9 models including both dead zone and photoevaporation, and 1 control model including photoevaporation only. The results can be plotted using the "Plotting-PopulationSynthesisModels.ipynb" jupyter notebook.</p> <p>The tables including a dead zone are named as: Macc_Rhole_Pop_AD(X)_RD(Y).txt, where (X)*1.e-4 corresponds to the turbulence in the dead zone, and (Y)*AU corresponds to the dead zone radial extent.</p> <p>The tables include the following fields: Simulation ID, Time [Myr] at which the snapshot was taken, Gap size [AU] measured at the outer edge, Accretion rate log[Msun/yr], and Gas disk mass. We also include a table called "LxRc_Distribution.txt", that indicates the X-ray luminosity log[erg/s] and initial disk characteristic radius [AU] used for the corresponding Simulation ID.</p> <p> </p> <p>We also include the gas surface density evolution of a Control simulation, with photoevaporation only (with Lx = 1.e30 erg/s), and a Dead Zone + Photoevaporation simulation (with dead zone turbulence 1.e-4, and dead zone radial extend 10 AU). These can be plotted using the "Plotting-SingleGasEvolution.ipynb" jupyter notebook.</p>
Fig. 3. Land use and land cover data for 2014 in Population trends and conservation status of proboscis monkeys (Nasalis larvatus) in the face of habitat change in the Klias Peninsula, Sabah, Borneo, Malaysia
Fig. 3. Land use and land cover data for 2014/2015 within the 1-km buffer distance from surveyed rivers, overlaid with proboscis monkey sightings from the 2004/2005 and 2014 surveys, Protected Areas, and Production Forest Reserve boundaries.
Text-fig. 3 Ternary diagram of the relative abundance (in %) of juvenile, prime adult, and old adult specimens in samples of Castor fiber (data from Table 3). The red dots indicate the Pleistocene samples of Bilzingsleben II (B), Weimar- Ehringsdorf (E), and Weimar-Taubach (T), the black dot represents an extant population from Telemark in Norway (data from Campbell 2009). Abbreviations of zones (after Discamps and Costamagno 2015): JOP – Juveniles-Old-Prime dominated zone, JPO – Juveniles-Prime-Old dominated zone, O – Old dominated zone, P – Prime dominated zone. The diagram shows the position of all three fossil samples in the prime dominated zone. in Mortality Profiles Of Castor And Trogontherium (Mammalia: Rodentia, Castoridae), With Notes On The Site Formation Of The Mid-Pleistocene Hominin Locality Bilzingsleben Ii (Thuringia, Central Germany)
Text-fig. 3 Ternary diagram of the relative abundance (in %) of juvenile, prime adult, and old adult specimens in samples of Castor fiber (data from Table 3). The red dots indicate the Pleistocene samples of Bilzingsleben II (B), Weimar- Ehringsdorf (E), and Weimar-Taubach (T), the black dot represents an extant population from Telemark in Norway (data from Campbell 2009). Abbreviations of zones (after Discamps and Costamagno 2015): JOP – Juveniles-Old-Prime dominated zone, JPO – Juveniles-Prime-Old dominated zone, O – Old dominated zone, P – Prime dominated zone. The diagram shows the position of all three fossil samples in the prime dominated zone.
Data from: Floral scents of a deceptive plant are hyperdiverse and under population-specific phenotypic selection
<p>Floral scent is a key mediator in plant–pollinator interactions; however, little is known to what extent intraspecific scent variation is shaped by phenotypic selection, with no information yet in deceptive plants. We recorded 289 scent compounds in deceptive moth fly-pollinated <i>Arum maculatum </i>from various populations north vs. south of the Alps, the highest number so far reported in a single plant species. Scent and fruit set differed between regions, and some, but not all differences in scent could be explained by differential phenotypic selection in northern vs. southern populations. Our study is the first to provide evidence that phenotypic selection is involved in shaping geographic patterns of floral scent in deceptive plants. The hyperdiverse scent of <i>A. maculatum</i> might result from the plant's imitation of various brood substrates of its pollinators.</p>
Data from: Dinosaurian survivorship schedules revisited: new insights from an age-structured population model
<p>Little is known on dinosaur population biology due to insufficient information on age-dependent fecundities and mortalities. So far, survivorship curves (hereafter SC) of only six dinosaurs (four tyrannosaurs, one ceratopsian, one hadrosaur) were erected from bone assemblages of aged specimens. They indicate high survival throughout most of their life with presumable higher mortalities after hatching and increasing mortalities towards its end. However, all studies ignored that assemblages must preserve stationary age distributions (i.e., the population's age distribution is stable and its size is constant over time as overall population fecundities match mortalities, hereafter SAD population) to infer a reliable SC for a taxon.</p> <p>To assess SCs of these dinosaurs, I built a simple population model with age-dependent fecundities and survival rates. Its few input parameters are maximum longevity, age at sexual maturation and maximum annual offspring number, on which information exists in these dinosaurs. As bone histological studies and scaling relationships provide estimates on its three parameters, my model is also applicable to other extinct taxa.</p> <p> Modelling suggests that bone assemblages did not preserve SAD populations. SCs determined for SAD populations of <i>Albertosaurus sarcophagus</i>,<i> Gorgosaurus libratus</i>, <i>Dasplatosaurus torosus</i> and <i>Tyrannosaurus rex</i> indicated that low mortalities follow high mortalities early in their life or that mortalities were rather constant throughout their life. In <i>Psittacosaurus lujiatuensis</i> modelling suggests low mortalities throughout most of its life that increase towards its end. The SC of <i>Maiasaura peeblesorum</i> was not questioned by my model as it is unable to capture sigmoidal or other composite SCs.</p>
Populations of local direction-selective cells encode global motion patterns generated by self-motion. Data, Code and Model.
<p>Directional tuning of the population of local motion detectors T4/T5 in the visual system of the fruit fly <em>Drosophila melanogaster</em>. Direction tuning and receptive field location was measured by recording responses to visual stimuli containing dark or bright edges/stripes moving into 8 directions. All provided MATLAB scripts were used to analyze and illustrate data show in the manuscript 'Populations of local direction-selective cells encode global motion patterns generated by self-motion.'</p> <p>All data were obtained using <em>in vivo </em>two photon microscopy. Image time series were preprocessed using SIMA python software for motion alignment and further processed using custom written matlab or python code.</p> <p>Please find all relevant information to use the code in the README file.</p>
Data and code for: Plastic and quantitative genetic divergence mirror environmental gradients among wild, fragmented populations of Impatiens capensis
<p><strong>Premise of the study:</strong> Habitat fragmentation generates molecular genetic divergence among isolated populations but few studies have assessed phenotypic divergence and fitness in populations where the genetic consequences of habitat fragmentation are known. Phenotypic divergence could reflect plasticity, local adaptation, and/or genetic drift.</p> <p><strong>Methods:</strong> We examined patterns and potential drivers of phenotypic divergence among 12 populations of jewelweed (<em>Impatiens capensis </em>Meerb.) that show strong molecular genetic signals of isolation and drift among fragmented habitats. We measured morphological and reproductive traits in both maternal plants within natural populations and their self-fertilized progeny grown together in a common garden. We also quantified environmental divergence between home sites and the common garden.</p> <p><strong>Key results: </strong>Populations with less molecular genetic variation expressed less maternal phenotypic variation. Progeny in the common garden converged in phenotypes relative to their wild mothers but retained among-population differences in morphology, survival, and reproduction. Among-population phenotypic variance was 3-10x greater in home sites than in the common garden for 6 of 7 morphological traits measured. Patterns of phenotypic divergence paralleled environmental gradients in ways suggestive of adaptation. Progeny resembled their mothers less as the environmental distance between their home site and the common garden increased.</p> <p><strong>Conclusions: </strong>Despite strong molecular signatures of isolation and drift, phenotypic differences among these <em>Impatiens </em>populations appear to reflect both adaptive quantitative genetic divergence and plasticity. Quantifying the extent of local adaptation and plasticity and how these covary with molecular and phenotypic variation help us predict when populations may lose their adaptive capacity. </p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.