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88 results for “parallel adaptation”
Continuously fluctuating selection reveals extreme granularity and parallelism of adaptive tracking
<p>Temporally fluctuating environmental conditions are a ubiquitous feature of natural habitats. Yet, how finely natural populations adaptively track fluctuating selection pressures via shifts in standing genetic variation is unknown. We generated high-frequency, genome-wide allele frequency data from a genetically diverse population of Drosophila melanogaster in extensively replicated field mesocosms from late June to mid-December, a period of ~12 generations. Adaptation throughout the fundamental ecological phases of population expansion, peak density, and collapse was underpinned by extremely rapid, parallel changes in genomic variation across replicates. Yet, the dominant direction of selection fluctuated repeatedly, even within each of these ecological phases. Comparing patterns of allele frequency change to an independent dataset procured from the same experimental system demonstrated that the targets of selection are predictable across years. In concert, our results reveal fitness-relevance of standing variation that is likely to be masked by inference approaches based on static population sampling, or insufficiently resolved time-series data. We propose such fine-scaled temporally fluctuating selection may be an important force maintaining functional genetic variation in natural populations and an important stochastic force affecting levels of standing genetic variation genome-wide.</p>
Data from: Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?
<p>When populations colonise new environments they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes, and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (> 22X coverage) in Berthelot's pipit (<em>Anthus berthelotii</em>), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. Firstly, we quantify how genomic divergence accumulates across the speciation continuum, i.e., among Berthelot's pipit populations, between subspecies across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (<em>Anthus campestris</em>). Across these colonisation timeframes (2.1 million – <em>ca.</em> 8,000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism, and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism, and immune defence.</p>
Data from: Local adaptation to seasonal cues at the fronts of two parallel, climate-induced butterfly range expansions
<p>Climate change allows species to expand polewards, but non-changing environmental features may limit expansions. Daylength is unaffected by climate and drives life cycle timing in many animals and plants. Because daylength varies over latitudes, poleward-expanding populations must adapt to new daylength conditions. We studied local adaptation to daylength in the butterfly <em>Lasiommata megera</em>, which is expanding northwards along several routes in Europe. Using common garden laboratory experiments with controlled daylengths, we compared diapause induction between populations from the southern-Swedish core range and recently established marginal populations from two independent expansion fronts in Sweden. Caterpillars from the northern populations entered diapause in clearly longer daylengths than those from southern populations, with the exception of caterpillars from one geographically isolated population. The northern populations have repeatedly and rapidly adapted to their local daylengths, indicating that the common use of daylength as seasonal cue need not strongly limit climate-induced insect range expansions.</p>
Analyses for: Genome-wide parallelism underlies contemporary adaptation in urban lizards
<p>R scripts and data files for all analyses and visualizations in "Genome-wide parallelism underlies contemporary adaptation in urban lizards" (Winchell et al., 2023, PNAS)</p> <p>R scripts as R-markdown code files in 3 parts are executable with files in datafiles compressed folder. R markdown files also exported as PDF's in 3 parts with code output.</p>
Starspot mapping with adaptive parallel tempering. II. Application to TESS data for M-dwarf flare stars, AU Microscopii, YZ Canis Minoris, and EV Lacertae (Flare Tables)
<p>For TESS PDC-SAP data of AU Mic (Sector 1 and 27), YZ CMi (Sector 7 and 34), and EV Lac (Sector 16), detected flare properties are listed: the peak time (BJD-2745000), amplitude, equivalent duration (sec), and e-folding time (day).</p>
Data from: Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?
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Data from: Local adaptation to seasonal cues at the fronts of two parallel, climate-induced butterfly range expansions
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Continuously fluctuating selection reveals extreme granularity and parallelism of adaptive tracking
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Data from: Parallel changes in gut microbiome composition and function during colonization, local adaptation and ecological speciation
<p>The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.</p>
In-memory integration of existing software components for parallel adaptive unstructured mesh workflows: PHASTA 3D dam break
<p>Input mesh, solution field, configuration files, and job scripts for running the adaptive PHASTA-Chef 3D dam break case.</p> <p>Data stream, POSIX file, and ramdisk results are also included. The python scripts used to generate the bandwidth and open/close time plots are included.</p>
Numerical data set belonging to: 'A Finite Volume Parallel Adaptive Mesh Refinement Method for Solid-Liquid Phase'
<p>This data set corresponds to the paper 'A Finite Volume Parallel Adaptive Mesh Refinement Method for Solid-Liquid Phase Change', submitted to Numerical Heat Transfer, Part A: Applications. The numerical data is included in VTK format (to be read by paraView) for the following cases:</p><p>1) 2D Gallium melting in a rectangular cavity (70x50 elements, 140x100 elements, 280x200 elements, 560x400 elements, 1120x800 elements and adaptive mesh)</p><p>2) 3D Gallium melting in a hexagonal cavity (adaptive mesh)</p><p>3) 2D freeze-plug (both steady-state and melting transient): 110x300 elements, 220x600 elements, 440x1200 elements and adaptive mesh)</p><p>Due to the size of the data-set, the data has been split over 8 tar archives featuring a gzip compression. To unpack the data, run the command: cat paper_<i>amr</i>_<i>data.</i>tar.gz.* | tar xzvf -</p><p> </p>
Real-Time Motor Unit Tracking from sEMG Signals with Adaptive ICA on a Parallel Ultra-Low Power Processor
<p>Dataset and code to replicate the paper:</p> <p>Orlandi et al., "Real-Time Motor Unit Tracking from sEMG Signals with Adaptive ICA on a Parallel Ultra-Low Power Processor"</p>
Data from: Annual and perennial Medicago show signatures of parallel adaptation to climate and soil in highly conserved genes
<p class="AbstractSummary">Human induced environmental change may require rapid adaptation of plant populations and crops, but the genomic basis of environmental adaptation remain poorly understood. We analyzed polymorphic loci from the perennial crop <i>Medicago sativa </i>(alfalfa or lucerne) and the annual legume model species <i>M. truncatula </i>to search for a common set of candidate genes that might contribute to adaptation to abiotic stress in both annual and perennial <i>Medicago</i> species.</p> <p class="AbstractSummary">We identified a set of candidate genes of environmental adaptation associated with environmental gradients along the distribution of the two <i>Medicago</i> species. Candidate genes for each species were detected in homologous genomic linkage blocks using genome-environment (GEA) and genome-phenotype association analyses.</p> <p>Hundreds of GEA candidate genes were species-specific, of these, 13.4% (<i>M. sativa</i>) and 24% (<i>M. truncatula</i>) were also significantly associated with phenotypic traits. A set of 168 GEA candidates were shared by both species, which was 25.4% more than expected by chance. When combined, they explained a high proportion of variance for certain phenotypic traits associated with adaptation. Genes with highly conserved functions dominated among the shared candidates and were enriched in Gene Ontology terms that have shown to play a central role in drought avoidance and tolerance mechanisms by means of cellular shape modifications and other functions associated with cell homeostasis.</p> <p class="AbstractSummary">Our results point to the existence of a molecular basis of adaptation to abiotic stress in <i>Medicago</i> determined by highly conserved genes and gene functions. We discuss these results in light of the recently proposed omnigenic model of complex traits.</p>
Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects
<p>Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar, because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental, and phenotypic data with Bayesian modeling and randomization tests to quantify the degree of parallelism and its relationship with ecology and genetics. Our results show that the extent to which genomic regions associated with climate are parallel among species of <em>Timema</em> stick insects is shaped collectively by shared ecology and genomic background. Specifically, the extent of genomic parallelism decays with divergence in climatic conditions (i.e., habitat or ecological similarity) and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits, and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.</p>
Data from: Parallel shifts in trout feeding morphology suggest rapid adaptation to alpine lake environments
<p>Eco-evolutionary interactions following ecosystem change provide critical insight into the ability of organisms to adapt to shifting resource landscapes. Here we explore evidence for the rapid parallel evolution of trout feeding morphology following eco-evolutionary interactions with zooplankton in alpine lakes stocked at different points in time in the Wind River Range (Wyoming, USA). In this system, trout predation has altered the zooplankton species community and driven a decrease in average zooplankton size. In some lakes that were stocked decades ago, we find shifts in gill raker traits consistent with the hypothesis that trout have rapidly adapted to exploit available smaller-bodied zooplankton more effectively. We explore this morphological response in multiple lake populations across two species of trout (cutthroat trout, Oncorhynchus clarkii, and golden trout Oncorhynchus aguabonita) and examine the impact of resource availability on morphological variation in gill raker number among lakes. Furthermore, we present genetic data to provide evidence that historically stocked cutthroat trout populations likely derive from multiple population sources, and incorporate variation from genomic relatedness in our exploration of environmental predictors of feeding morphology. These findings describe rapid adaptation and eco-evolutionary interactions in trout and document an evolutionary response to novel, contemporary ecosystem change.</p>
A Multicenter, Randomized, Double-blind, Placebo-controlled, Parallel-group, Bayesian Adaptive Randomization Design, Dose Response Study of the Efficacy of E2006 in Adults and Elderly Subjects With Ch
ClinicalTrials.gov study NCT01995838. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Parallel polygenic urban adaptation despite high gene flow in a coastal marine invertebrate
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Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects
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Scripts from: Ancient stickleback genomes reveal the early stages of parallel adaptation
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Data from: Does the genomic landscape of species divergence in Phaseolus beans coerce parallel signatures of adaptation and domestication?
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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)
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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.