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145 results for “Adaptation by time”
Genetic architecture and adaptation of flowering time among environments
<p>1. The genetic basis of flowering time changes across environments, and pleiotropy may limit adaptive evolution of populations in response to local conditions. However, little is known about how genetic architecture changes among environments.</p> <p>2. We used genome-wide association studies (GWAS) in <i>Boechera stricta</i> (Graham) Al-Shehbaz, a relative of <i>Arabidopsis</i>, to examine flowering variation among environments and associations with climate conditions in home environments. Also, we used molecular population genetics to search for evidence of historical natural selection.</p> <p>3. GWAS found 47 significant quantitative trait loci (QTLs) that influence flowering time in one or more environments, control plastic changes in phenology between experiments, or show associations with climate in sites of origin. Genetic architecture of flowering varied substantially among environments. We found that some pairs of QTLs showed similar patterns of pleiotropy across environments. A large-effect QTL showed molecular signatures of adaptive evolution and is associated with climate in home environments. The derived allele at this locus causes later flowering and predominates in sites with greater water availability.</p> <p>4. This work shows that GWAS of climate associations and ecologically important traits across diverse environments can be combined with molecular signatures of natural selection to elucidate ecological genetics of adaptive evolution.</p>
Data from: Influence of range position on locally adaptive gene-environment associations in Populus flowering time genes
Local adaptation is pervasive in forest trees, which are characterized by large effective population sizes spanning broad climatic gradients. In addition to having relatively contiguous populations, many species also form isolated populations along the rear edge of their range. These rear-edge populations may contain unique adaptive diversity reflecting a history of selection in marginal environments. Thus, discovering genomic regions conferring local adaptation in rear edge populations is a key priority for landscape genomics to ensure conservation of genetic resources under climate change. Here, we report on adaptive gene-environment associations in SNPs from 27 genes in the Populus flowering time gene network, analyzed on a range-wide collection of >1000 balsam poplar trees, including dense sampling of the southern range edge. We use a combined approach of local adaptation scans to identify candidate SNPs, followed by modeling the compositional turnover of adaptive SNPs along multivariate climate gradients using Gradient Forests (GF). Flowering time candidate genes contained extensive evidence of climate adaptation, namely outlier population structure and gene-environment associations, along with allele frequency divergence between the core and edge of the range. GF showed strong allele frequency turnover along gradients of elevation and diurnal temperature variability, as well as threshold responses to summer temperature and precipitation, with turnover especially strong in edge populations that occur at high elevation but southerly latitudes. We discuss these results in light of how climate may disrupt locally adaptivegene-environment relationships, and suggest that rear edge populations hold climate-adaptive variants that should be targeted for conservation.
Principal component decomposition of acoustic and neural representations of time-varying pitch reveals adaptive efficient coding of speech covariation patterns
<p>Data and scripts reported by Llanos and colleagues in their Brain and Language study </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>
Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation : simulated data
<p>Data simulated with Aevol (<a href="http://www.aevol.fr">www.aevol.fr</a>), a software available on gitlab ( <a href="https://gitlab.inria.fr/aevol/aevol">https://gitlab.inria.fr/aevol/aevol</a> ), for our paper submitted to Molecular Ecology entitled "Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation".</p>
Time Course Adaptations Using Deuterated Creatine (D3Cr) Method
ClinicalTrials.gov study NCT03573583. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Real-time Adaptation to Changes in Insulin Sensitivity
ClinicalTrials.gov study NCT01261052. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Development and Testing of a Just-in-Time Adaptive Smart Phone Intervention to Reduce Drinking Among Homeless Adults
ClinicalTrials.gov study NCT03746808. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Genetic architecture and adaptation of flowering time among environments
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Data from: Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: estimates of selection and QTL mapping
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Sensory-motor tuning allows generic features of conspecific acoustic scenes to guide rapid, adaptive, call-timing responses in Túngara frogs
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Parallel flowering time clines in native and introduced ragweed populations are likely due to adaptation
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Data from: Influence of range position on locally adaptive gene-environment associations in Populus flowering time genes
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Local adaptation from afar: migratory bird populations diverge in the initiation of reproductive timing while wintering in sympatry
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Lineage-specific adaptation to climate involves flowering time in North American Arabidopsis lyrata
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Species differences in reproductive timing and egg load in two fly species adapted to different host plants
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Delayed adaptive radiation among New Zealand stream fishes: joint estimation of divergence time and trait evolution in a newly delineated island species flock
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Data for: Deep-time demographic inference suggests ecological release as driver of Neoavian adaptive radiation
<p>Data for:</p> <p>Houde P, Braun EL, Zhou L. 2020. Deep-time demographic inference suggests ecological release as driver of Neoavian adaptive radiation. Diversity, in review</p> <p>**************************************************<br> The .tar.gz file will expand to yield a directory named "Houde_Braun_Zhou_data_files". That directory has three subdirectories:</p> <p>1. alignments<br> 2. indel_matrices<br> 3. trees</p> <p>The Houde_Braun_Zhou_data_files directory also includes a README.txt file with complete details regarding the contents of each subdirectory.</p>
Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster
<p>Organisms living in seasonally variable environments utilize cues such as light and temperature to induce plastic responses, enabling them to exploit favorable seasons and avoid unfavorable ones. Local adapation can result in variation in seasonal responses, but the genetic basis and evolutionary history of this variation remains elusive. Many insects, including <i>Drosophila melanogaster,</i> are able to undergo an arrest of reproductive development (diapause) in response to unfavorable conditions. In <i>D. melanogaster</i>, the ability to diapause is more common in high latitude populations, where flies endure harsher winters, and in the spring, reflecting differential survivorship of overwintering populations. Using a novel hybrid swarm-based genome wide association study, we examined the genetic basis and evolutionary history of ovarian diapause. We exposed outbred females to different temperatures and day lengths, characterized ovarian development for over 2800 flies, and reconstructed their full phased genomes. We found that diapause scored at two different developmental cutoffs has modest heritability, and we identified hundreds of SNPs associated with each of the two phenotypes. Alleles associated with one of the diapause phenotypes tend to be more common at higher latitudes, but these alleles do not show predictable seasonal variation. The collective signal of many small-effect, clinally varying SNPs can plausibly explain latitudinal phenotypic variation seen in North America. SNPs associated with diapause do not exhibit signs of recent selective sweeps, but most are segregating at relatively high frequencies in Africa, suggesting that variation in diapause relies on ancestral polymorphisms. Finally, we utilized outdoor mesocosms to track diapause under natural conditions. We found that hybrid swarms reared outdoors evolved increased propensity for diapause in late fall, whereas indoor control populations experienced no such change. Our results indicate that diapause is a complex, quantitative trait with different evolutionary patterns across time and space.</p>
Increased time sampling in an evolve-and-resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change
<p>"Evolve and resequence" (E&R) studies combine experimental evolution and whole-genome sequencing to interrogate the genetics underlying adaptation. Due to ease of handling, E&R work with asexual organisms like bacteria can employ optimized experimental design, with large experiments and many generations of selection. By contrast, E&R experiments with sexually reproducing organisms are more difficult to implement, and design parameters vary dramatically among studies. Thus, efforts have been made to assess how these differences, such as number of independent replicates, or size of experimental populations, impact inference. We add to this work by investigating the role of time sampling – the number of discrete timepoints sequence data is collected from evolving populations. Using data from an E&R experiment with outcrossing <i>Saccharomyces cerevisiae </i>in which populations were sequenced 17 times over ~540 generations, we address the following questions: (i) do more timepoints improve the ability to identify candidate regions underlying selection? And (ii) does high-resolution sampling provide unique insight into evolutionary processes driving adaptation? We find that while time sampling does not improve the ability to identify candidate regions, high-resolution sampling does provide valuable opportunities to characterize evolutionary dynamics. Increased time sampling reveals three distinct trajectories for adaptive alleles: one consistent with classic population genetic theory (i.e. models assuming constant selection coefficients), and two where trajectories suggest more context-dependent responses (i.e. models involving dynamic selection coefficients). We conclude that while time sampling has limited impact on candidate region identification, sampling 8 or more timepoints has clear benefits for studying complex evolutionary dynamics.</p>
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.