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9 results for “models of rate variation”
Open-population SCR model to estimate spatiotemporal variation in individual birth locations, detection rates, and survival
<p>This is an open population SCR model developed by R. Chandler and K. Engebretsen. The full model incorporates 4 spatial covariates in birth location density submodel, 3 location-specific, temporal covariates in the detection submodel, and 4 spatial covariates in the survival submodel. </p> <p>Formatted data is provided for the 2015 and 2016 fawning season in south Florida and the model can be fit using the script fitFawnModel.R.</p>
Open-population SCR model to estimate spatiotemporal variation in individual birth locations, detection rates, and survival
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Data from: On the Mkv model with among-character rate variation
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Data from: Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants
Because novel environmental conditions alter the selection pressure on genes or entire subgenomes, adaptive and nonadaptive changes will leave a measurable signature in the genomes, shaping their molecular evolution. We present herein a model of the trajectory of plastid genome evolution under progressively relaxed functional constraints during the transition from autotrophy to a nonphotosynthetic parasitic lifestyle. We show that relaxed purifying selection in all plastid genes is linked to obligate parasitism, characterized by the parasite's dependence on a host to fulfill its life cycle, rather than the loss of photosynthesis. Evolutionary rates and selection pressure coevolve with macrostructural and microstructural changes, the extent of functional reduction, and the establishment of the obligate parasitic lifestyle. Inferred bursts of gene losses coincide with periods of relaxed selection, which are followed by phases of intensified selection and rate deceleration in the retained functional complexes. Our findings suggest that the transition to obligate parasitism relaxes functional constraints on plastid genes in a stepwise manner. During the functional reduction process, the elevation of evolutionary rates reaches several new rate equilibria, possibly relating to the modified protein turnover rates in heterotrophic plastids.
Data from: A Poissonian model of indel rate variation for phylogenetic tree inference
While indel rate variation has been observed and analyzed in detail, it is not taken into account by current indel-aware phylogenetic reconstruction methods. In this work, we introduce a continuous time stochastic process, the geometric Poisson indel process, that generalizes the Poisson indel process by allowing insertion and deletion rates to vary across sites. We design an efficient algorithm for computing the probability of a given multiple sequence alignment based on our new indel model. We describe a method to construct phylogeny estimates from a fixed alignment using neighbor joining. Using simulation studies, we show that ignoring indel rate variation may have a detrimental effect on the accuracy of the inferred phylogenies, and that our proposed method can sidestep this issue by inferring latent indel rate categories. We also show that our phylogenetic inference method may be more stable to taxa subsampling than methods that either ignore indels or indel rate variation.
Data from: A Poissonian model of indel rate variation for phylogenetic tree inference
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Data from: How does evolutionary variation in basal metabolic rates arise? A statistical assessment and a mechanistic model
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Data from: Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants
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Catalogs and stress history for "stress dependent b value variations in a heterogeneous rate-and-state fault model"
<p>Catalogs of synthetic seismicity and stress history used in the manuscrit "stress dependent b value variations in a heterogeneous rate-and-state fault model".</p>
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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.