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19,493 results for “Populism”
Figure 5 in Longterm study in Leucoptera coffeella population from southern Minas Gerais, Brazil
Figure 5: Correlation between the number of predated larvae and the number of attacled leaves between January 2015 and December 2019 (F = 57.68, p <0.01) (MP: predated mines; FM: mined leaves).
Placental Expression Quantitative Trait Loci In An East Asian Population
<p>Analysis script, full eQTL summary statistics, and fine-mapping statistics of article "Placental Expression Quantitative Trait Loci In An East Asian Population". This data contains workflow and result of 102 East Asian placental expression quantitative trait loci analysis.</p><p>Genotype from 102 cord blood used in the analysis is also included. Variants with minor allele frequencies less than 0.01 was filtered out to prevent personnel identification.</p>
Fig. 1 in Population viability analysis of the population of Raffles' banded langurs Presbytis femoralis in Singapore
Fig. 1. Top left: baseline scenario shown with threat and management scenarios found to markedly impact upon population growth, run for 500 iterations over a 50-year period and showing the mean number of extant individuals for each. Top right: a retrospective analysis using parameters from the baseline scenario with estimates of 40 individuals in 2010 to predict the current population in 2021. Bottom right: a retrospective analysis using parameters from the baseline scenario with estimates of 10–14 individuals in 1990 to predict the current population in 2021. Bottom left: The Raffles' banded langur. Photos: Sabrina Jabbar.
FIG. 1 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 1.—Map of the Hawaiian Islands with collection sitesfor Hawaiian hoary bat tissues used inthis study. Sites with n> 1 are denoted with an asterisk.
FIG. 2 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 2.—PCA result plot showing clustering of individual bats from four Hawaiian Islands using 21,808,031 SNPs. Sample information included in supplementary table S4, Supplementary Material online.
FIG. 4 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 4.—SNAPP-based phylogenetic tree inference. (A) The maximum clade credibility or consensus tree, showing approximate divergence of hoary bats across the Hawaiian archipelago. The axis on the bottom of the figure corresponds to million years before present (Ma), using the emergence of Hawai'i (~0.43 Ma) as a calibration point (95% confidence intervals were given in square brackets). (B) The drawing of all sampled trees showing all ingroup nodes were supported by maximum posterior probabilities (1.00).
Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies
<p>Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence PCR amplicons derived from cDNA templates tagged with universal molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR and the use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Handling of the large datasets produced from SMRT-UMI sequencing was facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline), that automatically filters and parses reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination or early cycle PCR errors, resulting in highly accurate sequence datasets. The optimized SMRT-UMI sequencing method presented here represents a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus (HIV) quasispecies.</p>
An exposome atlas of serum reveals risk of chronic diseases in Chinese population
<p>Although adverse environmental exposures are considered to be a major cause to chronic diseases, current studies have provided limited knowledge on real-world chemical exposures and related risks. Here, we collected serum samples from 5696 healthy people and patients, including 12 chronic diseases in China, and completed serum biomonitoring containing 267 chemicals using gas and liquid chromatography-tandem mass spectrometry. 74 high-frequently detected exposures were used for exposure characterization and risk analysis. Results showed that region was the most critical factor influencing human exposure levels, followed by age. Organochlorine pesticides and perfluoroalkyl substances were associated with multiple chronic diseases, and some of them exceeded safe ranges. Mixture effect models showed significant risk effects of exposure on hyperlipidemia, metabolic syndrome and hyperuricemia. Overall, this study provided a comprehensive human serum exposure atlas and its disease risk, which could guide subsequent more in-depth cause-and-effect studies between environmental exposures and human health. The R codes and related example data for statistical analysis and figure production have been deposited to the GitHub (https://github.com/youlei2023/ExposomeAtlas).</p>
The Helicobacter pylori Genome Project (HpGP) Phase1 dataset and 255 H. pylori population reference dataset
<p>This repository holds the HpGP Phase 1 genomic dataset for Hp26695 and 1011 study samples. All 1012 genomic sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline(PGAP). Also, it has 255 curated public available H. pylori genomic sequences used for population structure analysis in Thorell et al. Nature Communications, 14:8184 (2023).</p> <p>You can check the NCBI BioProject website for the latest annotation and sequence updates.</p> <p>https://www.ncbi.nlm.nih.gov/bioproject/?term=HpGP</p> <p>Please cite the above-mentioned paper if you use the data.</p>
Unravelling the mystery of endemic versus translocated populations of the endangered Australian lungfish (Neoceratodus forsteri)
<p><strong>RADseq dataset of the Australian lungfish (</strong><em><strong>Neoceratodus forsteri).</strong></em></p> <p>The dataset is constituted of 100 samples and 5,196 nuclear SNPs. There are five populations each with 20 samples. IDs: BUR (Burnett River), MRY (Mary River), TIN (Tinana River), NPD (North Pine River), BNE (Brisbane River).</p> <p>The dataset is in VCF format.</p> <p> </p> <p><strong>Scripts for statistical calculations and demographic simulations.</strong></p>
Genomic footprints of (pre) colonialism: Population declines in urban and forest túngara frogs coincident with historical human activity
<p>Urbanisation is rapidly altering ecosystems, leading to profound biodiversity loss. To mitigate these effects, we need a better understanding of how urbanisation impacts dispersal and reproduction. Two contrasting population demographic models have been proposed that predict that urbanisation either promotes (facilitation model) or constrains (fragmentation model) gene flow and genetic diversity. Which of these models prevails likely depends on the strength of selection on specific phenotypic traits that influence dispersal, survival, or reproduction. Here, we a priori examined the genomic impact of urbanisation on the Neotropical túngara frog (<em>Engystomops pustulosu</em>s), a species known to adapt its reproductive traits to urban selective pressures. Using whole-genome resequencing for multiple urban and forest populations we examined genomic diversity, population connectivity and demographic history. Contrary to both the fragmentation and facilitation models, urban populations did not exhibit substantial changes in genomic diversity or differentiation compared to forest populations, and genomic variation was best explained by geographic distance rather than environmental factors. Adopting an a posteriori approach, we additionally found both urban and forest populations to have undergone population declines. The timing of these declines appears to coincide with extensive human activity around the Panama Canal during the last few centuries rather than recent urbanisation. Our study highlights the long-lasting legacy of past anthropogenic disturbances in the genome and the importance of considering the historical context in urban evolution studies as anthropogenic effects may be extensive and impact non-urban areas on both recent and older timescales. </p>
Mixed population trends inside a California protected area: Evidence from long-term community science monitoring
<p><span>Protected areas are one of the most widespread and accepted conservation interventions, yet their population trends are rarely compared to regional trends to gain insight into their effectiveness. Here, we leverage two long-term community science datasets to demonstrate mixed effects of protected areas on long-term bird population trends. We analyzed 31 years of bird transect data recorded by community volunteers across all major habitats of Stanford University's Jasper Ridge Biological Preserve to determine the population trends for a sample of 66 species. We found that nearly a third of species experienced long-term declines, and on average, all species declined by 12%. Further, we averaged species trends by conservation status and key life history attributes to identify correlates and possible drivers of these trends. Observed increases in some cavity-nesters and declines of scrub-associated species suggest that long-term fire suppression may be a key driver, reshaping bird communities through changes in forest and chaparral structure and composition. Additionally, we compared our results to those of the North American Breeding Bird Survey's Central California Coast region (n = 55 species) to place Jasper Ridge in a broader context. Most species experienced similar directional population trends inside vs. outside of the preserve, and only eight species (14.5%) did better inside this small, protected area. Therefore, we must identify relevant management strategies for declining populations and explicitly consider how existing protected areas target and manage each species. Further, this analysis underscores the importance of local and national community science for revealing nuanced long-term bird population trends.</span></p>
Dataset for paper "Freihardt (2025): Environmental shocks and migration among a climate-vulnerable population in Bangladesh. Population and Environment. DOI 10.1007/s11111-025-00478-7"
<p>This is the dataset underlying the paper: </p> <p>Freihardt, J. (2025): Environmental shocks and migration among a climate-vulnerable population in Bangladesh. Population and Environment, 47, 6. DOI: 10.1007/s11111-025-00478-7.</p>
Thermal performance of Aedes sierrensis life history traits for populations collected across the species range
<p>How mosquitoes may respond to rapid climate warming remains unknown for most species, but will have major consequences for their future distributions, with cascading impacts on human well-being, biodiversity, and ecosystem function. We investigated the adaptive potential of a wide-ranging mosquito species, <em>Aedes sierrensis</em>, across a large climatic gradient by conducting a common garden experiment measuring the thermal limits of mosquito life history traits. Although field-collected populations originated from vastly different thermal environments that spanned over 1,200 km, we found limited variation in upper thermal tolerance between populations. In particular, the upper thermal limits of all life history traits varied by <3°C across the species range and, for most traits, did not differ significantly between populations. For one life history trait—pupal development rate—we did detect significant variation in upper thermal limits between populations, and this variation was strongly correlated with source temperatures, providing evidence of local thermal adaptation for pupal development. However, we found that maximum environmental temperatures across most of the species' range already regularly exceed the highest upper thermal limits estimated under constant temperatures. This result suggests that strategies for coping with and/or avoiding thermal extremes are likely key components of current and future mosquito thermal tolerance.</p>
Figure 3 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats
Figure 3. – Projection of Procrustes coordinates and scores of canonical variate on Aphanius fasciatus shape analysis (A) and comparative transformation grids (B). LM: Mellah lagoon, M: Mellah marsh, BZ: Lagoon of Bizerte, LA: Ayata Lake.
Figure 2 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats
Figure 2. – Landmarks distribution on fish body of Aphanius fasciatus. 1: Eye position, 2: Dorsal opercular limit, 3: Beginning of dorsal fin, 4: End of dorsal fin, 5: Dorsal limit of caudal peduncle, 6: Median limit of caudal peduncle, 7: Ventral limit of caudal peduncle, 8: End of anal fin, 9: Beginning of anal fin, 10: Pelvic fin insertion, 11: Ventral opercula limit, 12: Dorsal limit of pectoral fin, 13: Ventral limit of pectoral fin, 14: Mouth.
Figure 1 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats
Figure 1. – Map of the west Mediterranean basin with North African sample sites. 1: Mellah lagoon (LM), 2: Mellah marsh (M), 3: Lagoon of Bizerte (BZ), 4: Ayata Lake (LA).
Figure 2 in Extant because important or important because extant? On the scientific importance and conservation of a genetically pure Sicilian population of the threatened Salmo cettii Rafinesque, 1810
Figure 2. – Individual Salmo cettii from Tellesimo Stream (for the morphological and phenotypical characteristics of Sicilian trout see: Duchi, 1988; Fruciano et al., 2014; Duchi, 2018).
An inbreeding perspective on the effectiveness of wildlife population defragmentation measures: A case study on wild boar (Sus scrofa) of Veluwe, The Netherlands
<p>Pervasive inbreeding is a major genetic threat of population fragmentation and can undermine the efficacy of population connectivity measures. Nevertheless, few studies have evaluated whether wildlife crossings can alleviate the frequency and length of genomic autozygous segments. Here, we provided a genomic inbreeding perspective on the potential effectiveness of mammal population defragmentation measures. We applied a SNP-genotyping case study on the ~2500 wild boar Sus scrofa population of Veluwe, The Netherlands, a 1000-km<sup>2 </sup>Natura 2000 protected area with many fences and roads but also, increasingly, fence openings and wildlife crossings. We combined a 20K genotyping assessment of genetic status and migration rate with a simulation that examined the potential for alleviation of isolation and inbreeding. We found that Veluwe wild boar subpopulations are significantly differentiated (FST-values of 0.02-0.07) and have low levels of gene flow. One noteworthy exception was the Central and Southeastern subpopulation, which were nearly panmictic and appeared to be effectively connected through a highway wildlife overpass. Estimated effective population sizes were at least 85 for the meta-population and ranging from 31 to 52 for the subpopulations. All subpopulations, including the two connected subpopulations, experienced substantial inbreeding, as evidenced through the occurrence of many long homozygous segments. Simulation output indicated that whereas one or few migrants per generation could undo genetic differentiation and boost effective population sizes rapidly, genomic inbreeding was only marginally reduced. The implication is that ostensibly successful connectivity restoration projects may fail to alleviate genomic breeding of fragmented mammal populations. We put forward that defragmentation projects should allow for (i) monitoring of levels of differentiation, migration and genomic inbreeding, (ii) anticipation of the inbreeding status of the meta-population, and, if inbreeding levels are high and/or haplotypes have become fixed, (iii) consideration of enhancing migration and gene flow among meta-populations, possibly through translocation.</p>
An integrated population model reveals source-sink dynamics for competitively subordinate African wild dogs linked to anthropogenic prey depletion
<ol> <li>Many African large carnivore populations are declining due to decline of the herbivore populations on which they depend. The densities of apex carnivores like the lion and spotted hyena correlate strongly with prey density, but competitive subordinates like the African wild dog benefit from competitive release when the density of apex carnivores is low, so the expected effect of a simultaneous decrease in resources and dominant competitors is not obvious. </li> <li>Wild dogs in Zambia's Luangwa Valley Ecosystem occupy four ecologically similar areas with well-described differences in the densities of prey and dominant competitors, due to spatial variation in illegal offtake.</li> <li>We used long-term data to fit a Bayesian integrated population model (IPM) of the demography and dynamics of wild dogs in these four regions. The IPM used Leslie projection to link a Cormack-Jolly-Seber model of area-specific survival (allowing for individual heterogeneity in detection), a zero-inflated Poisson model of area-specific fecundity, and a state-space model of population size that used estimates from a closed mark-capture model as the counts from which (latent) population size was estimated.</li> <li>The IPM showed that both survival and reproduction were lowest in the region with the lowest density of preferred prey (puku, <em>Kobus vardonii</em>, and impala, <em>Aepyceros</em> <em>melampus</em>), despite little use of this area by lions. Survival and reproduction were highest in the region with the highest prey density, and intermediate in the two regions with intermediate prey density. The population growth rate (λ) was positive for the population as a whole, strongly positive in the region with the highest prey density, and strongly negative in the region with the lowest prey density.</li> <li>It has long been thought that the benefits of competitive release protect African wild dogs from the costs of low prey density. Our results show that the costs of prey depletion overwhelm the benefits of competitive release and cause local population decline where anthropogenic prey depletion is strong. Because competition is important in many guilds and humans are affecting resources of many types, it is likely that similarly fundamental shifts in population limitation are arising in many systems.</li> </ol>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.