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333 results for “population level”
Rural population count at 1 km for 2000-2020 based on WorldPop and GHS-SMOD urbanization level
<p>Rural population count at 1 km grid in EPSG:4326 for 2000-2020 (annual). This is only an estimate of the rural population. This probably misses many rural areas, especially in the tropics. The maps were derived using two data sources:</p> <ol> <li><a href="https://hub.worldpop.org/geodata/listing?id=64">WorldPop population counts at 1 km</a>;</li> <li><a href="https://human-settlement.emergency.copernicus.eu/download.php?ds=smod">GHS-SMOD urbanization levels at 1 km</a>;</li> </ol> <p>Rural population is estimated using the following translation rules for GHS-SMOD (note: these are arbitrary rules based on the GHS-SMOD documentation):</p> <ul> <li>Class 30: “Urban Centre grid cell” = 0% rural</li> <li>Class 23: “Dense Urban Cluster grid cell” = 0.5% rural</li> <li>Class 22: “Semi-dense Urban Cluster grid cell” = 2% rural</li> <li>Class 21: “Suburban or per-urban grid cell” = 15% rural</li> <li>Class 13: “Rural cluster grid cell” = 95% rural</li> <li>Class 12: “Low Density Rural grid cell” = 100% rural</li> <li>Class 11: “Very low density rural grid cell” = 100% rural</li> </ul> <p>The nighttime images are based on: <a href="https://doi.org/10.5281/zenodo.7750174">https://doi.org/10.5281/zenodo.7750174</a></p> <ul> <li>Schiavina, Marcello; Melchiorri, Michele; Pesaresi, Martino (2023): GHS-SMOD R2023A - GHS settlement layers,<br>application of the Degree of Urbanisation methodology (stage I) to GHS-POP R2023A and GHS-BUILT-S R2023A,<br>multitemporal (1975-2030). European Commission, Joint Research Centre (JRC) [Dataset] doi:<br>10.2905/A0DF7A6F-49DE-46EA-9BDE-563437A6E2BA PID: <a href="http://data.europa.eu/89h/a0df7a6f-49de-46ea-%209bde-563437a6e2ba">http://data.europa.eu/89h/a0df7a6f-49de-46ea-</a><br><a href="http://data.europa.eu/89h/a0df7a6f-49de-46ea-%209bde-563437a6e2ba">9bde-563437a6e2ba</a></li> </ul>
The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high-levels of lineage-specific diversity driven by recombination
<p><em>Aspergillus fumigatus </em>is a deadly agent of human fungal disease, where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on <em>de novo</em> assemblies offer a promising alternative to reference-based genomics, with the potential to address the full genetic repertoire of a species. Here, we use a combination of population genomics, phylogenomics, and pan-genomics to assess population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes in <em>A. fumigatus</em>. We provide evidence for three distinct populations of <em>A. fumigatus</em>, structured by both gene variation (SNPs and indels) and distinct gene presence-absence variation with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism, hinting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Despite low levels of outcrossing, <em>A. fumigatus</em> demonstrated a large pan-genome including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference based approach for evaluating intraspecific variation, and the power of combined genomic approaches to elucidate population structure, genetic diversity, and the putative ecological drivers of clinically relevant fungi.</p> <p>Accompanying manuscript is available as preprint at <a href="https://dx.doi.org/10.1101/2021.12.12.472145">https://dx.doi.org/10.1101/2021.12.12.472145</a> </p> <p>Lotus A. Lofgren, Brandon S. Ross, Robert A. Cramer, Jason E. Stajich. Combined Pan-, Population-, and Phylo-Genomic Analysis of <em>Aspergillus fumigatus</em> Reveals Population Structure and Lineage-Specific Diversity bioRxiv 2021.12.12.472145; doi: https://doi.org/10.1101/2021.12.12.472145</p>
Gene co-ordinates, expression levels; SNP identifiers and functions for Drosophila melanogaster (Sussex LHM population)
<p>Data for SNP context information to add to GWAS results. Specifically, SNP functions, sex-bias in gene expression, official SNP idenfiers from NCBI dbSNP, and gene positions and names (from UCSC Genome Browswer). Most of the input files are on-line and their URLs are stated in the code (make_dmel_accessory_data.sh). Also includes code, logs, and exploratory graphs.</p>
Variant dataset and code for "Population-level whole genome sequencing of Ascochyta rabiei identifies genomic loci associated with isolate aggressiveness"
<p>This dataset contains genetic variants (SNPs) of <em>Ascochyta rabiei</em> isolates and the R code used in their analysis to generate the results and figures described in the manuscript "<strong>Population-level whole genome sequencing of <em>Ascochyta rabiei</em> identifies genomic loci associated with isolate aggressiveness</strong>".</p> <div> <div> </div> </div>
The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover
<p>Zenodo deposit for Pozzi et al (2024) AJB</p> <p>The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover</p> <p><strong> _____________________________________________________________________________________________________________________________________</strong></p> <p><strong>The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover</strong></p> <p>Adrien C.M. Pozzi<sup>1,2</sup>, Ruth G. Shaw<sup>1</sup>, Georgiana May<sup>1,3</sup></p> <p><sup>1</sup> Department of Ecology, Evolution and Behavior, University of Minnesota Twin-Cities, St Paul, MN 55108. <sup>2</sup> Current affiliation: Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622 Villeurbanne, France. ORCID: 0000-0001-6765-4293. <sup>3</sup> Correspondence: Georgiana May (gmay@umn.edu)</p> <p><em><strong>Keywords:</strong></em></p> <p>conservation; <em>Dalea</em> spp.; habitat fragmentation; mutualism; nitrogen-fixing symbiosis; population level variation; native prairie legume; restoration; rhizobia</p> <p><em><strong>Description:</strong></em></p> <p>This Zenodo deposit is part of the MN LCCMR Healthy Prairies project granted to R. Shaw and G. May, UMN Twin-Cities. It contains the following files:</p> <p><span><span>·<span> </span></span></span>“Metadata & data” spreadsheet. <em>Contains metadata and data about the Twin Valley experiment (including the position of plants, an intermediary census, growth and nodulation traits for harvested plants, data on bacterial isolates from root nodules, and source modifiers for GenBank accessions OQ732394-OQ732572).</em></p> <p><span><span>·<span> </span></span></span>“Blast alignments output.txt” text file. <em>Contains ouput of Blastn alignements for the 16S rRNA genes of bacterial isolates against the rRNA_typestrains/16S_ribosomal_RNA 16S ribosomal RNA (Bacteria and Archaea type strains) database, to determine the genus as recommended by GenBank during sequence submission.</em></p> <p><span><span>·<span> </span></span></span>“General script.R”. <em>R script of the general statistical analyses produced for publication.</em></p> <p><span><span>·<span> </span></span></span>“General environment.RData”.<em> The companion RData (environment) of the above R script.</em></p> <p><span><span>·<span> </span></span></span>“Trait model script.R”. <em>R script of the plant trait models produced for publication</em></p> <p><span><span>·<span> </span></span></span>“Trait model environment.RData”. <em>The companion RData (environment) of the above R script.</em></p> <p><strong><em>Acknowledgments:</em></strong></p> <p>The authors thank members of the May Lab (Mai Beauclaire, Em Daily, Mara Demers, Kane Keller, Cedric Ndinga-Muniania, Liam Vertal, Monica Watson) for their help in field and lab work. We thank members of the Healthy Prairies project (Shelby Flint, Anna Peschel, Bill Peterson) who provided much of the infrastructure that made this project possible, as well as help in setting up field experiments. We also thank volunteer undergrads from University of Minnesota Morris (Amelia Nelson, Emily Job, Lily Fulton) for assistance in measuring harvested plants and counting nodules. Funding for this project was provided by the Minnesota Environment and Natural Resources Trust Fund as recommended by the Legislative-Citizen Commission on Minnesota Resources (LCCMR) Project 00086965, Healthy Prairies.</p> <p> </p>
Population-level health and economic impacts of introducing Vaccae vaccination in China: A modeling study
<p>Supplementary to "Population-level health and economic impacts of introducing Vaccae vaccination in China: A modeling study"</p>
Datasets, reproducible codes, and results for evaluating differential expression analysis methods on population-level RNA-seq data
<p>This upload contains the necessary R codes and data to reproduce the FDR and Power results described in our correspondence "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" to Li Y, Ge X, Peng F, Li W, Li JJ, Exaggerated false positives by popular differential expression methods when analyzing human population samples, <em>Genome Biology</em> 23, 79, 2022, DOI: 10.1186/s13059-022-02648-4.</p>
A scalable, accurate, and universal analysis framework using individual-level allele frequency for large-scale genetic association studies in an admixed population
<p>Inclusion of individuals with diverse or admixed genetic ancestries is crucial to discover novel findings that may be missed by genomics analyses rooted solely in Caucasian population. Here, we present an analysis framework, SPAmix, which is scalable to a large-scale biobank data analysis including hundreds of thousands of admixed individuals and is universally applicable to various types of complex traits including binary trait, quantitative trait, time-to-event trait, longitudinal traits, etc. For each genetic variant, SPAmix uses genotype data and genetic principal components (PCs) to estimate individual-level allele frequency, which is subsequently used to calibrate p values via a retrospective analysis. A hybrid strategy including saddlepoint approximation (SPA) can greatly increase the accuracy to analyze rare genetic variants, especially if the phenotypic distribution is unbalanced or extremely unbalanced. Compared to Tractor, SPAmix does not require local ancestry information and can be straightforwardly applicable to a multi-way admixed population. Meanwhile, SPAmix can also be extended to SPAmix<sub>local</sub> in which the local ancestry can be incorporated if available. In addition, we propose SPAmix<sub>CCT</sub> to combine the p values of SPAmix and SPAmix<sub>local</sub> via Cauchy combination (CCT). SPAmix<sub>local</sub> performs close to Tractor when analyzing quantitative traits and is more accurate when analyzing binary traits with an unbalanced case-control ratio. And SPAmix<sub>CCT </sub>is an optimal unified approach for various cross-ancestry genetic architectures. Extensive simulation studies and real data analyses of 369,314 UK Biobank individuals from multiple ancestries demonstrated that SPAmix is scalable and can discover novel hits while controlling type I error rates well.</p>
Bonanza Creek Experimental Forest Defoliating Insect Population Levels Per Leaf 1975-2012 - Werner
Defoliating insect population levels were monitored at Bonanza Creek Experimental Forest, Fairbanks, Alaska, USA from 1976 to 202012. Total number of insects per square meter of foliage is archived in this dataset.
Data 1 for "Population- and age-specific patterns of haemosporidian assemblages and infection levels in European Bee-eaters (Merops apiaster)"
<p>Data related to the article "Population- and age-specific patterns of haemosporidian assemblages and infection levels in European Bee-eaters (<em>Merops apiaster</em>)" in the format .xlsx. The 1st sheet contains all variables for analyses done with the R script (see 10.5281/zenodo.3968360). The 2nd sheet contains explanations about the variables in sheet 1.</p>
New genetic markers for Sapotaceae phylogenomics: more than 600 nuclear genes applicable from family to population levels
<p>Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short tandem repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from<em>Capurodendron delphinense</em> and <em>Bemangidia lowryi</em>, both from the Tseboneae tribe, as well as the published <em>Manilkara zapota</em> transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (<em>C. delphinense</em>) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. All together, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.</p>
Simulated Herbarium data for testing the accuracy with which specimen data can predict the timing and duration of population-level flowering displays
<p>This dataset provides code and example data for simulating specimen collections of flowering plants across North America, and for developing phenological predictions of population-level flowering onset and termination for these data. It further presents code for assessing the accuracy of these predictions relaticve to known (simulated) population-level flowering dates at the location of each collection.</p>
Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions
<p>Polysaccharide utilization loci (PULs) in the human gut microbiome have critical roles in shaping human health and ecological dynamics. We develop a CRISPR-FnCpf1-RecT genome-editing tool to study 23 PULs in the highly abundant species <em>B. uniformis</em> (BU). We identify the glycan-degrading functions of multiple PULs and elucidate transcriptional coordination between PULs that enables the population to adapt to the loss of PULs. Exploiting a pooled BU mutant barcoding strategy, we demonstrate that the <em>in vitro</em> fitness and the colonization ability of BU in the murine gut is enhanced by deletion of specific PULs and modulated by glycan availability. We show that BU PULs can mediate complex glycan-dependent interactions with butyrate producers that depend on the mechanism of degradation and the butyrate producer glycan utilizing ability. In sum, PULs are major determinants of community dynamics and butyrate production and can provide a selective advantage or disadvantage depending on the nutritional landscape. </p>
Data from: Environmental drivers of population-level variation in the migratory and diving ontogeny of an Arctic top predator
<p>The development of migratory strategies that enable juveniles to survive to recruitment is critical for species that exploit seasonal niches. For animals that forage via breath-hold diving this requires a combination of both physiological and foraging skill development. Here, we assess how migratory and dive behaviour develop over the first months of life for a migratory Arctic top predator, the harp seal, tracked using animal-borne satellite relay data loggers. We reveal similarities in migratory movements and differences in diving behaviour between juveniles from breeding populations in the Northwest Atlantic and Greenland Sea. In both regions, periods of resident and transient behaviour during migration were associated with proxies for food availability; sea ice concentration and water depth. However, while ontogenetic development of dive behaviour was similar for both groups of juveniles over the first 25 days, after this time Greenland Sea animals performed shorter and shallower dives and were more closely associated with sea ice than Northwest Atlantic animals. Together, these results highlight the role of both intrinsic and extrinsic factors in shaping early-life behaviour. Differences in the environmental conditions experienced during early-life may shape how populations respond to the rapid changes occurring in the Arctic ocean ecosystem.</p>
Code: A model of wild bee populations accounting for spatial heterogeneity and climate induced temporal variability of food resources at the landscape level
<p><span>The viability of wild bee populations and the pollination services that they provide are driven by the availability of food resources during their activity period and within the surroundings of their nesting sites. Changes in climate and land use influence the availability of these resources and are major threats to declining bee populations. Because wild bees may be vulnerable to interactions between these threats, spatially explicit models of population dynamics that capture how bee populations jointly respond to land use at a landscape scale and weather are needed. Here, we developed a spatially and temporally explicit theoretical model of wild bee populations aiming for a middle ground between the existing mapping of visitation rates using foraging equations and more refined agent-based modelling. The model is developed for <em>Bombus</em> sp. and captures within-season colony dynamics. The model describes mechanistically foraging at the colony level and temporal population dynamics for an average colony at the landscape level. Stages in population dynamics are temperature-dependent triggered with a theoretical generalized seasonal progression, which can be informed by growing degree days (GDD). The purpose of the LandscapePhenoBee model is to evaluate the impact of systematic changes and within-season variability in resources on bee population sizes and crop visitation rates. In a simulation study, we used the model to evaluate the impact of the shortage of food resources in the landscape arising from extreme drought events in different types of landscapes (ranging from different proportions of semi-natural habitats and early and late flowering crops) on bumblebee populations.</span></p>
Figure 2. Flufenacet degradation 24 h in Flufenacet activity is affected by GST inhibitors in blackgrass (Alopecurus myosuroides) populations with reduced flufenacet sensitivity and higher expression levels of GSTs
Figure 2. Flufenacet degradation 24 h after treatment with different inhibitors in the sensitive Alopecurus myosuroides population Herbiseed-S (A) and population Kehdingen1 with reduced flufenacet efficacy (B). Different letters indicate significant differences in flufenacet degradation between treatments,and asterisks (*) indicate significant differences between the two populations for each treatment (P ≤ 0.05).
Figure 4 in Flufenacet activity is affected by GST inhibitors in blackgrass (Alopecurus myosuroides) populations with reduced flufenacet sensitivity and higher expression levels of GSTs
Figure 4. Expression of three tau-class glutathione transferases (GST1, GST2,GST3), two phi-class GSTs (GST4, GST5), and a theta-class isoform (GST6) differentially expressed in the sensitive Alopecurus myosuroides populations Herbiseed-S and Appel-S and the populations Kehdingen1 and Kehdingen2 with reduced flufenacet efficacy. Different letters indicate significant differences between populations (false discovery rate ≤ 0.05). TMM, trimmed mean of M values.
Figure 1 in Flufenacet activity is affected by GST inhibitors in blackgrass (Alopecurus myosuroides) populations with reduced flufenacet sensitivity and higher expression levels of GSTs
Figure 1. Dose–response analysis of the fresh weight of four Alopecurus myosuroides populations treated with different dose rates of flufenacet estimated using a threeparameter log-logistic model (see Equation 1).
Fig. 2 in What drives population-level effects of parasites? Meta-analysis meets life-history
Fig. 2. Funnel plot of effect size (Hedges' g) by standard error (SE). The white circles represent studies included in the meta-analysis. The black circles represent missing imputed studies. The white diamond represents overall effect size as calculated in the meta-analysis, and the black diamond represents the corrected effect size.
Fig. 1 in What drives population-level effects of parasites? Meta-analysis meets life-history
Fig. 1. Forest plot of effect sizes (rectangles) and confidence intervals (bars) for each study and the effect averaged across all studies (diamond).
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.