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100 results for “genetic code”
Code and initial metapopulation data for model construction and simulation analyses for: Genetic rescue from protected areas is modulated by migration, hunting rate and timing of harvest
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Dataset and R code: Genetic diversity of lion populations in Kenya: evaluating past management practices and recommendations for future conservation actions by Chege M et.al
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Data and code for: Multiple genetic impacts of immigration interact to shape local population persistence versus extinction
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Data and coding files for: Within population plastic responses to combined thermal-nutritional stress differ from those in response to single stressors, and are genetically independent across traits in both males and females
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The Structural Basis of the Genetic Code: Amino Acid Recognition by Aminoacyl-tRNA Synthetases
<p>Data sets for the characterization of amino acid recognition in aminoacyl-tRNA synthetases:</p> <ul> <li>multiple-sequence alignment files in FASTA format</li> <li>Excel tables to infer original sequence positions from renumbered positions</li> </ul> <p>Accompanying the paper: <a href="https://www.biorxiv.org/content/10.1101/606459v1">https://www.biorxiv.org/content/10.1101/606459v1</a></p>
Data and Code: No support for the genetic hypothesis of the Black-white achievement gap using polygenic scores and tests for divergent selection
<p>Data and Code for article "No support for the genetic hypothesis of the Black-white achievement gap using polygenic scores and tests for divergent selection"</p>
Data and code for: Species-specific effects of production practices on genetic diversity in plant reintroduction programs
<p class="MsoNormal"><span>Plant production practices can influence the genetic diversity of cultivated plant materials and, ultimately, their potential to adapt to a reintroduction site. A common step in the plant production process is the application of seed pre-treatment to alleviate physiological seed dormancy and successfully germinate seeds. In production settings, the seeds that germinate more rapidly may be favored in order to fill plant quotas. In this study, we investigated how the application of cold-moist stratification treatments with different durations can lead to differences in the genetic diversity of the propagated plant materials. Specifically, we exposed seeds of three <em>Viola</em> species to two different cold stratification durations, and then we analyzed the genetic diversity of the resulting subpopulations through </span><span>double-digestion restriction site-associated sequencing (ddRADseq). Our results show that, in two out of three species, utilizing a short stratification period will decrease the genetic diversity of neutral and expressed loci, likely due to the imposition of a genetic bottleneck and artificial selection. We conclude that, in some species, the use of minimal stratification practices in production may jeopardize the adaptive potential and long-term persistence of reintroduced populations and suggest that practitioners carefully consider the evolutionary implications of their production protocols. We highlight the need to consider the germination ecology of target species when selecting the length of dormancy-breaking pre-treatments.</span></p>
Code & data of the paper "Data sampling via Active Learning in Cartesian Genetic Programming for Biomedical Data"
<p>Code & data of the paper "Data sampling via Active Learning in Cartesian Genetic Programming for Biomedical Data"</p> <p> </p>
Data and code for: Does the definition of a novel environment affect the ability to detect cryptic genetic variation?
<p>Anthropogenic change exposes populations to environments that have been rare or entirely absent from their evolutionary past. Such novel environments are hypothesised to release cryptic genetic variation, a hidden store of variance that can fuel evolution. However, support for this hypothesis is mixed. One possible reason is a lack of clarity in what is meant by 'novel environment', an umbrella term encompassing conditions with potentially contrasting effects on the exposure or concealment of cryptic variation. Here, we use a meta-analysis approach to investigate changes in the total genetic variance of multivariate traits in ancestral versus novel environments. To determine whether the definition of a novel environment could explain the mixed support for a release of cryptic genetic variation, we compared absolute novel environments, those not represented in a population's evolutionary past, to extreme novel environments, those involving frequency or magnitude changes to environments present in a population's ancestry. Despite sufficient statistical power, we detected no broadscale pattern of increased genetic variance in novel environments, finding the type of novel environment did not explain any significant variation in effect sizes. When effect sizes were partitioned by experimental design, we found increased genetic variation in studies based on broad-sense measures of variance, and decreased variation in narrow-sense studies, in support of previous research. Therefore, the source of genetic variance, not the definition of a novel environment, was key to understanding environment-dependant genetic variation, highlighting non-additive genetic variance as an important component of cryptic genetic variation and avenue for future research.</p>
Data and R codes from: Exploring the effect of 195 years-old locks on species movement: Landscape genetics of painted turtles in the Rideau Canal, Canada
<p>Aquatic systems have been extensively altered by human structures (e.g., construction of dams/canals) and these have major impacts on the connectivity of wildlife populations through the loss and isolation of suitable habitats. Habitat loss and isolation affect gene flow and influence the persistence of populations in time and space by restricting movements. Isolation can result in higher inbreeding, lower genetic diversity, and greater genetic structure, which may render populations more vulnerable to environmental changes, and thus to extinction. Given the ubiquity and the persistence of dams and canals in space and time, it is crucial to understand their effects on the population genetics of aquatic species. Here, we documented the genetic diversity and structure of painted turtle (<em>Chrysemys picta</em>) populations in the Rideau Canal, Ontario, Canada. More specifically, we used 13 microsatellites to evaluate the influence of locks on genetic variation in 822 painted turtles from 22 sites evenly distributed along the 202-km canal. Overall, we found low, but significant, genetic differentiation suggesting that some dispersal is occurring throughout the canal. In addition, we showed that locks contribute to the genetic differentiation observed in the system. Clustering analysis revealed two distinct genetic groups whose boundary is associated with a series of six locks. Our results illustrate how artificial waterways, such as canal systems, can influence population genetic structure. We highlight the importance of adopting management plans that can mitigate the impacts of human infrastructure and preserve gene flow across the landscape to maintain viable populations.</p>
Supporting data and code for: Host plant and insecticides shape the evolution of genetic and clonal diversity in a major aphid crop pest
<p>This is the first release of the final data and code for the article accepted for publication in <em>Evolutionary Applications</em> journal. It contains the necessary scripts to produce most of the analyses and figures of the manuscript. All the necessary data can be found in the 'data' folder.</p>
ASreml code and Data from the study "Between-population differences in the genetic and maternal components of body mass in roe deer"
<p>This repository contains the source code (ASremL input files) and the data used to perform the QG analyses (univariate, bivariate, random regression animal models) in the study "Between-population differences in the genetic and maternal components of body mass in roe deer". Quéméré E et al.</p> <p> </p>
Data and code for phenotypic, genetic and distribution analyses of the parthenogenetic grasshopper Warramaba virgo and its sexual progenitors
<p>Includes raw data on phenotypic traits (critical thermal maximum, chill coma recovery, water loss and metabolic rate vs. temperature, mass of eggs, hatchlings and females, clutch sizes and lifetime reproductive output, development time, time to maturity, longevity), molecular traits (SNP, COI and microsatellite data) and distribution as well as code to analyse them.</p>
Code for the population genetic models of the evolution of preference strength
<p>Sexual selection has a rich history of mathematical models that consider why preferences favor one trait phenotype over another (for population genetic models) or what specific trait value is preferred (for quantitative genetic models). Less common is exploration of the evolution of choosiness or preference strength: that is, by how much a trait is preferred. We examine both population and quantitative genetic models of the evolution of preferences, specifically developing "baseline models" of the evolution of preference strength during the Fisher process. Using a population genetic approach based on the classic model of Kirkpatrick (1982), we find selection for stronger and stronger preferences when trait variation is maintained by mutation. However, this force is quite weak and likely to be swamped by drift in moderately-sized populations. In a quantitative genetic model based on Lande (1981), unimodal preferences will generally not evolve to be increasingly strong without bounds when male traits are under stabilizing viability selection, but evolve to extreme values when viability selection is directional. Our results highlight that different shapes of fitness and preference functions lead to qualitatively different trajectories for preference strength evolution ranging from no evolution to extreme evolution of preference strength.</p>
Code and source data for the paper: "Heat over heritability: increasing body size in response to global warming is not stabilized by genetic effects in Bechstein's bats"
<p>The first two script include code for the model building testing different fixed effect strucutes.</p> <p>The next two script includes all code for the descriptive analysis, all figures, as well as the animal models that compare heritabilty between the different environments (Q1-Q4) as well as between the birth environments differentials of mothers and daughters.</p> <p>Data contain the pedigree ('pedigree_Model_cod.csv'), further information ('pedigree_information_cod.csv) and weather data ('Weather_summer.csv')</p>
Additional data and code for "You can move, but you can't hide: identification of mobile genetic elements with geNomad"
<ul> <li><strong>benchmark_data:</strong> Data used to train and evaluate the classification models.</li> <li><strong>giant_virus_data:</strong> Sequences and metadata of giant viruses identified in public metagenomes.</li> <li><strong>neural_network_training:</strong> Code used to train geNomad's neural network-based classification model.</li> <li><strong>provirus_data:</strong> Data used to train and evaluate the conditional random field model employed by geNomad to identify provirus regions.</li> <li><strong>reference_sequences:</strong> Sequences of chromosomes, plasmids, and viruses that were used to build geNomad's marker dataset and to generate the training data for the classification models.</li> </ul>
Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails
<p>This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode</p>
Data and Code for: Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia
<p><span>Differences in reproductive strategies can have important implications for macro- and micro-evolutionary processes. We used a comparative approach through a population genetics lens to evaluate how three distinct reproductive strategies shape patterns of divergence among as well as gene flow and genetic diversity within three closely related taxa in the genus <em>Clarkia</em>. One taxon is a predominantly autonomous self-fertilizer and the other two taxa are predominantly outcrossing but vary in the primary pollinator they attract. In genotyping populations using genotyping-by-sequencing and comparing loci shared across taxa, our results suggest that differences in reproductive strategies in part promote evolutionary divergence among these closely related taxa. Contrary to expectations, we found that the selfing taxon had the highest levels of heterozygosity but a low rate of polymorphism. The high levels of fixed heterozygosity for a subset of loci suggests this pattern is driven by the presence of structural rearrangements in chromosomes common in other <em>Clarkia </em>taxa. In evaluating patterns within taxa, we found a complex interplay between reproductive strategy and geographic distribution. Differences in the mobility of primary pollinators did not translate to a difference in rates of genetic diversity and gene flow within taxa – a pattern likely due to one taxon having a patchier distribution and a less temporally and spatially reliable pollinator. Taken together, this work advances our understanding of the factors that shape gene flow and the distribution of genetic diversity within and among closely related taxa.</span></p>
Code for the population genetic models of the evolution of preference strength
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Data From: Parentage‐based tagging combined with genetic stock identification is a cost‐effective and viable replacement for coded‐wire tagging in large‐scale assessments of marine Chinook salmon fisheries in British Columbia, Canada
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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.