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424 results for “population differentiation”
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>
Geographical gradients of genetic diversity and differentiation among the southernmost marginal populations of Abies sachalinensis revealed by EST-SSR polymorphism
Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than do central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and methods: A total of 1,189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations; namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were highly differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido.
Data from: Drift happens: molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests
Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus FST = 0.32, FST' = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R2 = 0.51) and higher local inbreeding (R2 = 0.22). Populations varied greatly in levels of local inbreeding (FIS = 0.2 to 0.9) and FIS declined in smaller, more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.
Mountain landscape connectivity and subspecies appurtenance shape genetic differentiation in natural plant populations of the snapdragon (Antirrhinum majus L.)
<p>This dataset provides the raw data for the population genetic analyses for the article: "Mountain landscape connectivity and subspecies appurtenance shape genetic differentiation in natural plant populations of the snapdragon (Antirrhinum majus L.)" by Benoit Pujol; Juliette Archambeau; Aurore Bontemps; Mylène Lascoste; Sara Marin; and Alexandre Meunier found in the journal "Botany Letters", Vol 164 pp. 111-119 (DOI: 10.1080/23818107.2017.1310056).</p> <p>Link to journal open access article: http://www.tandfonline.com/doi/pdf/10.1080/23818107.2017.1310056</p> <p>Link to Zenodo article reporsitory: https://zenodo.org/record/801169</p> <p>The datafile includes three data sheets:</p> <p>Data, which contains for each plant : the name of the population, the name of the sampled individual, the subspecies, the latitude of the population, the longitude of the population, the altitudinal elevation of the population in meters, and the microsatellite genotype of each plant. Genotype data is recorded by locus (two columns for the two alleles at one locus). Locus name is found as the title of the column. The record for each allele is its allele size.</p> <p>valleys 1 and valleys 2, which contains the association between populations and valleys following the two scenarios that we analyzed in the paper.</p> <p>Microsatelite loci were developed during previous work: see the following paper for more details: Debout, G., E. Lhuillier, P.-J. Malé, B. Pujol, and C. Thébaud. 2012. Development and characterization of 24 polymorphic microsatellite loci in two Antirrhinum majus subspecies (Plantaginaceae) using pyrosequencing technology. Conservation Genetics Resources 4:75-79.</p>
Fig. 2. A in Genetic differentiation in populations of Aedes aegypti (Diptera, Culicidae) dengue vector from the Brazilian state of Maranhão
Fig. 2. A priori estimate of the probable groups of populations produced by the BAPS (Bayesian Analysis of Population Structure v 6.0) program, indicating a total of two groups.
Dataset: Measuring stimulus-evoked neurophysiological differentiation in distinct populations of neurons in mouse visual cortex
<p>This dataset contains the calcium imaging and behavioral data analyzed in our paper, "Measuring stimulus-evoked neurophysiological differentiation in distinct populations of neurons in mouse visual cortex".</p> <p>These data were obtained at the Allen Brain Observatory as part of the <em>OpenScope</em> project, which is operated by the Allen Institute.</p> <p>Analysis code is available at <a href="https://github.com/wmayner/openscope-differentiation">https://github.com/wmayner/openscope-differentiation</a>.</p>
Differential changes in lifecycle-event phenology provide a window into regional population declines
<p class="MsoNormal"><span>Climate change affects the phenology of annual lifecycle events of organisms, such as reproduction and migration. Shifts in the timing of these events could have important population implications directly, or provide information about the mechanisms driving population trajectories, especially if they differ between lifecycle event. We examine if such shifts occur in a declining migratory passerine bird (Willow Warbler, <em>Phylloscopus trochilus</em>), which exhibits latitudinally diverging population trajectories. We find evidence of phenological shifts in breeding initiation, breeding progression and moult that differ across geographic and spring temperature gradients. Moult initiation following warmer springs advances faster in the south than in the north, resulting in proportionally shorter breeding seasons, reflecting higher nest failure rates in the south and in warmer years. Tracking shifts in multiple lifecycle events allowed us to identify points of failure in the breeding cycle in regions where the species has negative population trends, thereby demonstrating the utility of phenology analyses for illuminating mechanistic pathways underlying observed population trajectories.</span></p>
Data from: Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation
<p class="MsoNormal"><span>Comparing divergence in quantitative tr</span><span>aits and neutral m</span><span>olecular markers, such as <em>Q</em><sub>ST</sub><em>–F</em><sub>ST</sub> comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. </span><em>Onithochiton neglectus</em> (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into two geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesised to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (<em><span>F<sub>ST</sub></span></em><span>)</span> with an index of phenotypic differentiation (<em>P<sub>ST</sub></em>). We used 7,562 putatively neutral single nucleotide polymorphisms (SNPs) across 15 populations and three clades of <em>O. neglectus</em> throughout New Zealand to infer <em><span>F<sub>ST</sub></span></em>. <em>P<sub>ST</sub></em> was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades and shape groups. By systematically comparing <em>P<sub>ST</sub></em> with <em>F<sub>ST</sub></em><sub>,</sub> we identified evidence of local adaptation in a number of the <em>O. neglectus </em>shell shape traits. This <span>supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.</span></p>
Fig. 2 in Genetic Differentiation And Linkage Disequilibrium In A Spatially Fragmented Population Of Cheilosia Vernalis (Diptera: Syrphidae) From The Balkan Peninsula
Fig. 2. Standardized variance of allelic frequencies FST (open symbols) and genetic distance D (NEI 1978) (filled symbols) plotted against corresponding geographic distance between subpopulation pairs of Cheilosia vernalis: Durmitor-Morinj (75 km), Fruška Gora- Durmitor (240 km), and Fruška Gora-Morinj (306 km). Pearson correlation coefficients between geographic distance and FST and D
Fig. 1 in Genetic Differentiation And Linkage Disequilibrium In A Spatially Fragmented Population Of Cheilosia Vernalis (Diptera: Syrphidae) From The Balkan Peninsula
Fig. 1. Map of Serbia and Montenegro showing sampling sites for the studied subpopulations of Chelosia vernalis, and genotype distribution at the Pgm locus. The Pgm locus was the most variable locus in the surveyed subpopulations, and along with differences of allele frequency variances at the
Fig. 4 in MORPHOLOGICALAND GENETIC DIFFERENTIATION OF SAXIFRAGA HIRCULUS L. (SAXIFRAGACEAE) POPULATIONS IN LITHUANIA Edita Meškauskaitė, Donatas Naugžemys, Donatas Žvingila, Jonas Remigijus
Fig. 4. UPGMA dendrogram of genetic relationships among 20 S. hirculus individuals from Merkinė population
Figure 11 in Pleistocene population differentiation in the ant Myrmica scabrinodis (Hymenoptera: Formicidae) - a taxonomic borderline case
Figure 11. Discriminant values separating the western (white rhombs) and eastern population (black dots) of Myrmica scabrinodis showing a strong morphological convergence in the allopatric range. Geographic longitude in logarithmic scale.
Figure 4 in Pleistocene population differentiation in the ant Myrmica scabrinodis (Hymenoptera: Formicidae) - a taxonomic borderline case
Figure 4. View along the axis of scape with definition of standard viewing positions and the slope angle of basal scape lobe.
Fig. 2 in Genetic and morphological differentiation among populations of the narrowly endemic and karst forest-adapted Pilea pteridophylla (Urticaceae)
Fig. 2 Morphological variation among individuals of Pilea pteridophylla sampled along its distribution range in the tropical karst forest of southern Mexico. Plot of individual scores for the first two components of the principal component analysis using morphological data. Coloured symbols represent the two populations recognized for the species: red circles, Tabasco; and blue circles, Chiapas. Ellipses correspond to the 95% confidence intervals estimated for each population. The lines represent the dispersion of the individuals within each population
Fig. 3 in Genetic and morphological differentiation among populations of the narrowly endemic and karst forest-adapted Pilea pteridophylla (Urticaceae)
Fig. 3 Statistical parsimony networks of rps16-trnQ, trnL-trnF and rps16-trnQ + trnL-trnF dataset using the gaps as missing data. Coloured symbols represent the two populations recognized for the species: red circles, Tabasco; and blue circles, Chiapas. Open-white circles represent the number of mutational steps between haplotypes. The size of the circles is proportional to the frequency of each haplo-
Fig. 1 in Genetic and morphological differentiation among populations of the narrowly endemic and karst forest-adapted Pilea pteridophylla (Urticaceae)
Fig. 1 Mountain karst forests of Mexico and the studied species Pilea pteridophylla A. K. Monro (Urticaceae). A Geographic distribution of the Mountain karst forests of Mexico. B Individual from the Chiapas population. C Individual from the Tabasco population
Fig. 2 in Sexual dimorphism and population differentiation in the Chilean Neotropical moth Macaria mirthae (Lepidoptera, Geometridae): a wing geometric morphometric example
Fig. 2. Benítez et al. (2015), representation of the 13 morphological landmarks identified in the forewings of Macaria mirthae.
Fig. 3 in Sexual dimorphism and population differentiation in the Chilean Neotropical moth Macaria mirthae (Lepidoptera, Geometridae): a wing geometric morphometric example
Fig. 3. PCA analysis of the sexual shape dimorphism of Macaria mirthae: the figure shows the first two orthogonal PC components' axes that represent the shape space dimensions, also a decomposition of shape variation between sexes. *Each point represents a different shape.
Fig. 5 in Sexual dimorphism and population differentiation in the Chilean Neotropical moth Macaria mirthae (Lepidoptera, Geometridae): a wing geometric morphometric example
Fig. 5. Multivariate regression of the wing shape on the wing centroid size of Macaria mirthae. Grey points represent female wings and black points represent male wings.
Fig. 1 in Sexual dimorphism and population differentiation in the Chilean Neotropical moth Macaria mirthae (Lepidoptera, Geometridae): a wing geometric morphometric example
Fig. 1. Graphical scheme of the location of the two Valleys in Atacama Desert in the north of Chile.
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.