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138 results for “population coding”
Data and code to replicate the analyses in "Interpopulation differences in male reproductive effort drive the population dynamics of a host exposed to an emerging fungal pathogen"
<p>Data and code used to run the analyses presented in the article "Interpopulation differences in male reproductive effort drive the population dynamics of a host exposed to an emerging fungal pathogen" published in Journal of Animal Ecology. Please cite this article if you use the data or write to the authors for a potential collaboration. If you require further details about the data please write to: andresvalenzuela.zoo@gmail or avalenzuela@ranitadedarwin.org.</p> <p>This study is part of an ongoing long-term monitoring program focused on the threatened Southern Darwin's frog (<em>Rhinoderma darwinii</em>), led by the Chilean non-profit organization ONG Ranita de Darwin (www.ranitadedarwin.org/monitoreo). This project has been funded by Zoo Leipzig, The National Geographic Society, Rufford Foundation, Weeden Foundation, Mohamed Bin Zayed Species Conservation Fund, VONA, Fundación Huilo Huilo, and Fundación MERI. We want to thank to the many volunteers that have kindly participated during this project.</p>
Code from: A theoretical framework for trait-based eco-evolutionary dynamics: population structure, intraspecific variation, and community assembly
<p>How is trait diversity in a community apportioned between and within co-evolving species? Disruptive selection may result in either a few species with large intraspecific trait variation (ITV) or many species with different mean traits but little ITV. Similar questions arise in spatially structured communities: heterogeneous environments could result in either a few species that exhibit local adaptation or many species with different mean traits but little local adaptation. To date, theory has been well-equipped to either include ITV or to dynamically determine the number of coexisting species, but not both. Here, we devise a theoretical framework that combines these facets, and apply it to the above questions of how trait variation is apportioned within and between species in unstructured and structured populations, using two simple models of Lotka-Volterra competition. For unstructured communities, we find that as the breadth of the resource spectrum increases, ITV goes from being unimportant to crucial for characterizing the community. For spatially structured communities on two patches, we find no local adaptation, symmetric local adaptation, or asymmetric local adaptation depending on how much the patches differ. Our framework provides a general approach to incorporate ITV in models of eco-evolutionary community assembly.</p>
Matlab code for " Prior expectation enhances sensorimotor behavior by modulating population tuning and subspace activity in sensory cortex"
<p>Here are the data and code supporting the findings of the paper, 'Prior expectation enhances sensorimotor behavior by modulating population tuning and subspace activity in sensory cortex.'</p>
Simulation code for: Effects of population size change on the genetics of adaptation following an abrupt change in environment
<p>Since the rediscovery of Mendelian genetics over a century ago, there has been much debate about the evolutionary importance of mutations with large phenotypic effects. While population genetic models predict that large-effect mutations will typically contribute to adaptation following an abrupt change in environment, the prediction applies to populations of stable size and overlooks effects of population size change on adaptation (e.g., population decline following habitat loss; growth during range expansion). We evaluate the phenotypic and fitness effects of mutations contributing to adaptation immediately following an abrupt environmental shift that alters both selection and population size dynamics. We show that large-effect mutations are likely to contribute to adaptation in populations declining to a new carrying capacity, somewhat smaller-effect mutations contribute to evolutionary rescue, and small-effect mutations predominate in growing populations. We also show that the relative contributions of positively selected and overdominant mutations to adaptation depend on interactions between the phenotypic effect size distribution for new mutations and the specific form of population size change during adaptation (i.e., growth, decline, or evolutionary rescue). Our results illustrate how population size dynamics can shape the genetic basis of adaptation, which should motivate empirical comparisons of populations adapting in different demographic contexts.</p>
Code and data for: Demographic resilience may sustain significant coral populations in a 2°C-warmer world.
<p>Data and Matlab code produced for the manuscript: Mason, R. A. B., Bozec, Y.-M., & Mumby, P. J. (2023). Demographic resilience may sustain significant coral populations in a 2°C-warmer world. <em>Global Change Biology</em>, 29(14): 4152-4160. <a href="https://doi.org/10.1111/gcb.16741">https://doi.org/10.1111/gcb.16741</a></p> <p>For questions about the contents of this repository, please contact robert.mason1@uqconnect.edu.au</p>
Data and code for: Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells
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Data from: Error-robust modes of the retinal population code
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Data from: Population and individual identification of Coho Salmon in British Columbia through parentage-based tagging and genetic stock identification: an alternative to coded-wire tags
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Data and statistical code from: Population differences in the effect of context on personality in an invasive lizard
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Simulation code for: Effects of population size change on the genetics of adaptation following an abrupt change in environment
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R code and data for running models in "Rapid Growth of the Swainson’s Hawk Population in California since 2005"
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Data from: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies
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Data and code for Heterogeneous selection on exploration behavior within and among West European populations of a passerine bird
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Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history
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R code, spatial and tabular data to fully reproduce STEPS simulations of population change for common brushtail possum, grassland melomys and northern brown bandicoot in northern Australia
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Code from: A theoretical framework for trait-based eco-evolutionary dynamics: population structure, intraspecific variation, and community assembly
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Data and code from: Landscape-driven isolation among, but high genetic diversity within, peripheral populations of a threatened frog
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Code for Individual Based Model to assess impact of KHV release on carp population
<p><b>1: </b>Common carp (<i>Cyprinus carpio</i>) is one of the top global invasive vertebrates and can cause significant ecological damage. The Australian Government's National Carp Control Program (NCCP) proposes to release Koi Herpesvirus (KHV) to eradicate feral carp in one of the largest ecological interventions ever attempted. Ecological and human health risks have been highlighted regarding the release of a highly pathogenic viral biocontrol for an aquatic species. The efficacy of KHV has also been questioned, and it has not been demonstrated to produce lasting population reductions.</p> <p> </p> <p>2. We developed an individual-based model (IBM) to examine the ecological and evolutionary response of a carp population after KHV release. This simulated the interaction between fish life history, viral epidemiology, host genetic resistance and population demography to critically evaluate the impact of KHV release under optimal conditions and a "best case scenario" for disease transmission.</p> <p> </p> <p>3. KHV will rarely result in prolonged reductions or population extinctions. Crucially, realistic scenarios result in a rapidly rebounding population of resistant individuals. Additional measures aimed to reduce carp population recovery rate (e.g. with genetic engineering) require rapid efficacy to significantly reduce carp numbers alongside KHV.<br> </p> <p>4. Fish fecundity has an overwhelming influence on viral efficacy as a biocontrol agent when combined with genetic resistance within a population. A high probability of population extinction is only met when carp fecundity is reduced to 1% of biological observations.<br> </p> <p><span>5.<i> Synthesis and applications. </i></span>We use an individual-based model to evaluate the efficacy of Koi Herpesvirus biocontrol in Common <a>Ca</a>rp, and find that high host fecundity combined with genetic resistance results in rapid population rebound after initial large fish-kills. Biocontrol approaches relying on natural selection lose efficacy over successive generations as resistance genes increases in frequency. Given the intense logistical effort and risks to ecosystems and human health associated with large fish kills after viral release, we suggest that sustained manual removal, alongside ecological restoration to favour recovery of native species, provides a risk-free approach to reducing populations.<br> </p>
Data and code for: Dietzel et al. Long-term shifts in the colony size structure of coral populations along the Great Barrier Reef
<p>The age or size structure of a population has a marked influence on its demography and reproductive capacity. While declines in coral cover are well documented, concomitant shifts in the size frequency distribution of coral colonies are rarely measured at large spatial scales. Here we document major shifts in the colony size structure of coral populations along the 2,300km length of the Great Barrier Reef over the past two decades. Coral colony abundances on reef crests and slopes have declined sharply across all colony size classes and in all coral taxa compared to historical baselines. Declines were particularly pronounced in the Northern and Central regions of the Great Barrier Reef, following mass coral bleaching in 2016 and 2017. The relative abundances of large colonies remained relatively stable, but this apparent stability masks steep declines in absolute abundance. The potential for recovery of older fecund corals is uncertain given the increasing frequency and intensity of disturbance events. The systematic decline in smaller colonies across regions, habitats and taxa, suggests that a decline in recruitment has further eroded the recovery potential and resilience of coral populations.</p>
Data and code for paper "Reciprocal interactions between tumour cell populations enhance growth and reduce radiation sensitivity in prostate cancer."
<p>This repository contains raw data and code for the manuscript with DOI: 10.1038/s42003-020-01529-5.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.