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188 results for “rapid adaptation”
Data from Neutral genetic structuring of pathogen populations during rapid adaptation
<p><strong>Datasets and temporary dataframes relating to the article "Neutral genetic structuring of pathogen populations during rapid adaptation".</strong></p> <p>These datasets and temporary dataframes are necessary to run the scripts from the public GitLab repository: <a href="https://gitlab.com/saubin.meline/neutral-genetic-structuring-adaptation">https://gitlab.com/saubin.meline/neutral-genetic-structuring-adaptation</a>. Please refer to this public GitLab repository for the latest version of the codes and to perform all analyses presented in the article.</p> <p>Original datasets from the demogenetic model:</p> <ul> <li>Output_RandomDesign.txt</li> <li>Output_RegularDesign_With_host_alternation.txt</li> <li>Output_RegularDesign_Without_host_alternation.txt</li> <li>Output_RandomDesign_Mnull_Medoid_With_host_alternation.txt</li> <li>Output_RandomDesign_Mnull_Medoid_Without_host_alternation.txt</li> </ul> <p>All remaining files correspond to temporary dataframes generated by the scripts in the GitLab repository, provided here for reproducibility of the results and to save time at certain time-consuming scripts.</p>
Data from: Padfield et al. (2016) Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters.
<p>This repository provides the data from the TPC and logistic growth curves from the paper:</p> <p>Padfield, D., Yvon‐Durocher, G., Buckling, A., Jennings, S., & Yvon‐Durocher, G. (2016). Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters, 19(2), 133-142.</p> <p>metadata.pdf gives a more detailed explanation of the data.</p>
Rapid sensorimotor adaptation to auditory midbrain silencing in free-flying bats
<p>This dataset accompanies the manuscript entitled "Rapid sensorimotor adaptation to auditory midbrain silencing in free-flying bats".<br>The structures contain the preprocessed data for each bat (individual structures for vocal and flight trajectory, or an overall structure for behavior). <br>The original code that allows for the figure generation associated with this manuscript is included. <br>The data for the audiograms and ABRs is also provided in csv format.</p>
On the genetic architecture of rapidly adapting and convergent life history traits in guppies
<p>The genetic basis of traits shapes and constrains how adaptation proceeds in nature; rapid adaptation can be facilitated by polygenic traits, which subsequently provide multiple, redundant, genetic routes to adaptive phenotypes, reducing re-use of the same genes (genetic convergence). Guppy life history traits evolve rapidly and convergently among natural high- (HP) and low-predation (LP) environments in northern Trinidad. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use an F2 QTL design to examine the genetic basis of seven (five female, two male) guppy life history phenotypes to assess whether the genetic architecture of these traits reflects theoretical predictions. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL ma pping (single-locus associations). Our results are consistent with architectures of many-loci of small effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but these could fuel redundancy and limit gene re-use across populations, in agreement with an absence of strong signatures of genetic convergence from recent population genomic analyses of wild HP-LP guppies.</p>
Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability
<p>While selfing populations harbor little genetic variation limiting evolutionary potential, the causes are unclear. We experimentally evolved large, replicate populations of <em>Mimulus guttatus </em>for nine generations in greenhouses with or without pollinating bees and studied DNA polymorphism in descendants. Populations without bees adapted to produce more selfed seed yet exhibited striking reductions in DNA polymorphism despite large population sizes. Importantly, the genome-wide pattern of variation cannot be explained by a simple reduction in effective population size, but instead reflects the complicated interaction between selection, linkage, and inbreeding. Simulations demonstrate that the spread of favored alleles at few loci depresses neutral variation genome-wide in large populations containing fully selfing lineages. It also generates greater heterogeneity among chromosomes than expected with neutral evolution in small populations. Genome-wide deviations from neutrality were documented in populations with bees, suggesting widespread influences of background selection. After applying outlier tests to detect loci under selection, two genome regions were found in populations with bees, yet no adaptive loci were otherwise mapped. Large amounts of stochastic change in selfing populations compromise evolutionary potential and undermine outlier tests for selection. This occurs because genetic draft in highly selfing populations makes even the largest changes in allele frequency unremarkable.</p>
Large effect loci mediate rapid adaptation of salmon body size after river regulation
<p>Understanding the potential of natural populations to adapt to altered environments is becoming increasingly relevant in evolutionary research. Currently, our understanding of adaptation to human alteration of the environment is hampered by lack of knowledge on the genetic basis of traits, lack of time series, and little or no information on changes in optimal trait values. Here we used time series data spanning nearly a century to investigate how body mass of Atlantic salmon (<em>Salmo salar</em>) adapts to river regulation. We found that the change in body mass followed the change in waterflow, both decreasing to ~1/3 of their original values. Allele frequency changes at two loci in the regions of <em>vgll3</em> and <em>six6 </em>predicted more than 80% of the observed body mass reduction. Modelling the adaptive dynamics revealed that the population mean lagged behind its optimum before catching up ~6 salmon generations after the initial waterflow reduction. Our results demonstrate rapid adaptation mediated by large effect loci and provide insight into the temporal dynamics of evolutionary rescue following human disturbance.</p>
Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails
<p>Scripts and data used in the research study <strong>Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails</strong>.</p> <p><a href="https://doi.org/10.1101/2023.09.27.559715" target="_blank" rel="noopener">https://doi.org/10.1101/2023.09.27.559715</a></p>
Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive pest fly
<p><span>Both local adaptation and adaptive phenotypic plasticity can influence the match between phenotypic traits and local environmental conditions. Theory predicts that environments stable for multiple generations promote local adaptation, while highly heterogeneous environments favor adaptive phenotypic plasticity. However, when environments have periods of stability mixed with heterogeneity, the relative importance of local adaptation and adaptive phenotypic plasticity is unclear. Here, we used <em>Drosophila suzukii</em> as a model system to evaluate the relative influence of genetic and plastic effects on the match of populations to environments with periods of stability from three to four generations. This invasive pest insect can develop within different fruits, and persists throughout the year in a given location on a succession of distinct host fruits, each one being available for only a few generations. Using reciprocal common environment experiments of natural <em>D. suzukii</em> populations collected from cherry, strawberry and blackberry, we found that both oviposition preference and offspring performance were higher on medium made with the fruit from which the population originated, than on media made with alternative fruits. This pattern, which remained after two generations in the laboratory, was analyzed using a statistical method we developed to quantify the contributions of local adaptation and adaptive plasticity in determining fitness. Altogether, we found that genetic effects (local adaptation) dominate over plastic effects (adaptive phenotypic plasticity). Our study demonstrates that spatially and temporally variable selection does not prevent the rapid evolution of local adaptation in natural populations. The speed and strength of adaptation may be facilitated by several mechanisms including a large effective population size and strong selective pressures imposed by host plants.</span></p>
Data: "Happy new ears: rapid adaptation to novel spectral cues in vertical sound localization."
<p>Data related to the manuscript entitled: "Happy new ears: rapid adaptation to novel spectral cues in vertical sound localization.". For more information, read the README file.</p>
Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive pest fly
Open the record for dataset details and reuse information.
Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability
Open the record for dataset details and reuse information.
On the genetic architecture of rapidly adapting and convergent life history traits in guppies
Open the record for dataset details and reuse information.
Ecophysiological and behavioral adaptations of birds to rapid urbanization of a desert environment in central Arizona-Phoenix, from 2006 to 2008.
We used Sonoran desert species that have adapted to urbanization to various degrees to investigate relations between endocrine parameters, in particular plasma corticosterone in response to acute stress, and aspects of the immune system, parasite infections, and body condition. Desert residents generally suppressed their endocrine response to acute stress during the breeding season and underwent marked seasonal changes in body condition. By contrast, conspecific urban residents tended to maintain an acute stress response throughout the year and showed subdued seasonal changes in body condition. We surmise that this difference is related to differences between desert and urban environments in food resources that birds use to sustain themselves. The goal of upcoming studies will be to test this hypothesis. In addition, we are carrying out studies aimed at elucidating the neuroendocrine mechanisms that mediate differential stress responses seen in birds residing in rural vs. urban habitats. We are also developing experiments examining relation between the stress response and the activity of the immune and reproductive system. The data that we have already collected, and those to be collected in the coming year, will provide the most extensive set of data to date on effects of urbanization on wild vertebrates and on the mechanisms that are responsible for these effects.
Rapid adaptive evolution of the diapause program during range expansion of an invasive mosquito
<p>In temperate climates, the recurring seasonal exigencies of winter represent a fundamental physiological challenge for a wide range of organisms. In response, many temperate insects enter diapause, an alternative developmental program, including developmental arrest, that allows organisms to synchronize their life cycle with seasonal environmental variation. Geographic variation in diapause phenology contributing to local climatic adaptation is well documented. However, few studies have examined how the rapid evolution of a suite of traits expressed across the diapause program may contribute to climatic adaptation on a contemporary timescale. Here, we investigate the evolution of the diapause program over the past 35 years by leveraging a "natural experiment" presented by the recent invasion of the Asian tiger mosquito, <i>Aedes albopictus,</i> across the eastern United States. We sampled populations<i> </i>from two distinct climatic regions separated by six degrees of latitude (~700 km). Using common-garden experiments, we identified regional genetic divergence in diapause-associated cold tolerance, diapause duration, and post-diapause starvation tolerance. We also found regional divergence in non-diapause thermal performance. In contrast, we observed minimal regional divergence in non-diapause larval growth traits and at neutral molecular marker loci. Our results demonstrate rapid evolution of the diapause program and imply strong selection caused by differences in winter conditions.</p>
Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation
Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.
Data from: The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish
Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor–based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediating genes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversity has likely been a crucial substrate for selective sweeps to propel rapid adaptation.
Rapid adaptation (or not) in restored plant populations
<p>Mismatches between the traits of a colonizing population and a novel habitat can generate strong selection, potentially resulting in rapid adaptation. However, for most colonization events, it can be difficult to detect rapid adaptation or distinguish it from non-adaptive evolutionary changes. Here I take advantage of a replicated prairie restoration experiment to compare recently established plant populations in two closely-located restored prairies to each other and to their shared source population to test for rapid adaptation. Using a reciprocal transplant experiment six years after the populations were established, I found that one restored plant population showed evidence of adaptation, outperforming the other restored population when grown at its home site. In contrast, I detected no evidence for adaptation at the other site. These findings demonstrate that while rapid adaptation can occur in colonizing plant populations, it may not be the rule. Better understanding of when adaptation may or may not occur in these contexts may help us use evolution to our advantage, potentially improving establishment of desirable species in restored habitats.</p>
Rapid evolution and local adaptation of urban aphids
<p>Publication in preparation: R Scripts and data for analyses and results of an aphid common garden experiment conducted in summer 2019 in Berlin, Germany. This repository is a work in progress.</p>
Dataset for Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic
<p><strong>Dataset for Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic</strong></p> <p>Code used for plotting of main figures and quantifying allelic shifts attached in the GitHub repository CareyMetheringham/MardenPark. Additional files for analysis of GEBV shifts between adults and juveniles, estimation of heritability, trends in green up and simulations of allelic shifts included as:</p> <ul> <li>GEBV-regression.Rmd</li> <li>heritabilityEst.R</li> <li>GreeningAnalysis.R</li> <li>Simulated_selection_analysis.Rmd</li> <li>Distinguishing the effects of selection from genetic drift.pdf</li> </ul> <p>Data files:</p> <ul> <li>S1 - phenotypic measurements for adult and juvenile trees</li> <li>S2 - Effect sizes for SNPs used to calculate GEBV</li> <li>S3 - Allelic frequencies of sites used to calculate GEBV</li> <li>related_trees.csv - Predicted parentage of trees</li> <li>gebv_model_df.csv - Data used for greenup calculations in GreeningAnalysis.R</li> <li>maf1.pass2.miss25.snps.only.LD.vcf - Filtered file of high MAF SNPs used for parentage estimation</li> <li>unlinked_sites.csv - unlinked sites used in GEBV-regression.Rmd</li> <li>ebv_table_10000_250 - table of estimated breeding values in field trial populatio, used for heritability estimation</li> <li>MP_eefects_MIA_and_MAA.csv - Data for plotting Figure 3 - Estimated effect size of the major and minor allele, plus standard error on the estimate</li> </ul>
Data from: Thyroid hormone tinkering elicits integrated phenotypic changes potentially explaining rapid adaptation of color vision in cichlid fish
Vision is critical for most vertebrates, including fish. One challenge that aquatic habitats pose is the high variability in spectral properties depending on depth, turbidity and composition of the water body. By altering opsin gene expression and chromophore usage, cichlid fish modulate visual sensitivities to maximize sensory input from the available light in their respective habitat. Thyroid hormone (TH) has been proposed to play a role in governing adaptive diversification in visual sensitivity in Nicaraguan Midas cichlids, which evolved in less than ~3,100 generations. As suggested by indirect measurements of TH levels (i.e., expression of deiodinases), populations adapted to short wavelength light in clear lakes have lower TH levels than ones inhabiting turbid lakes enriched in long-wavelength light. We experimentally manipulated TH levels by exposing two-week-old Midas cichlids to exogenous TH or a TH-inhibitor and measured opsin gene expression and chromophore usage (via cyp27c1 expression). Whereas exogenous TH induces long-wavelength sensitivity by changing opsin gene expression and chromophore usage in a concerted manner, TH-inhibited fish exhibit a visual phenotype with sensitivities shifted to shorter-wavelengths. Tinkering with TH levels in eyes results in concerted phenotypic changes that can provide a rapid mechanism of adaptation to novel light environments. --
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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)
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.