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100 results for “genetic code”
Data and code from: Predicting population genetic change in an autocorrelated random environment: insights from a large automated experiment
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Data and code for: Does the definition of a novel environment affect the ability to detect cryptic genetic variation?
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Data and code for: Decline in offspring quantity but not quality from successive matings in male rainforest <em>Drosophila</em>, with no evidence for genetic divergence in male mating behaviour along climatic and density gradients
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Data and Code for: Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia
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Data and code for: Species-specific effects of production practices on genetic diversity in plant reintroduction programs
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Stan code from: Simulation modeling reveals the evolutionary role of landscape shape and species dispersal on genetic variation within a metapopulation
Different shapes of landscape boundaries can affect the habitat networks within them and consequently the spatial genetic-patterns of a metapopulation. In this study, we used a mechanistic framework to evaluate the effects of landscape shape, through watershed elongation, on genetic divergence among populations at the metapopulation scale. Empirical genetic data from four, sympatric stream-macroinvertebrates having aerial adults were collected from streams in Japan to determine the roles of species-specific dispersal strategies on metapopulation genetics. Simulation results indicated that watershed elongation allows the formation of river networks with fewer branches and larger topographic constraints. This results in decreased interpopulation connectivity but a lower level of spatial isolation of distal populations (e.g., those found in headwaters) occurring in the landscapes examined. Distal populations had higher genetic divergence when their downstream-biased dispersal (relative to upstream- and/or overland-biased dispersal) was high. This underscores the importance of distal populations influencing genetic divergence at the metapopulation scale for species having downstream-biased dispersal. In turn, lower genetic divergence was observed under watershed elongation when the genetic isolation of distal populations was decreased in such species. This strong association between landscape shape and evolutionary processes highlights the importance of natural, spatial architecture in assessing the effectiveness of conservation and management strategies.
Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens - Data table and code for data analysis
<p>We provide data and code needed to re-do the analyses and figures presented in our preprint <em>Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent </em>Trichogramma evanescens (DOI : 10.1101/2020.08.21.257881 ):</p> <p>- data table : <em>data_repetition01.xls</em>, with informations about each column in the file <em>data_repetition_info.pdf</em></p> <p>- data table : <em>data_individual01.xls</em>, with informations about each column in the file <em>data_indivdual_info.pdf</em></p> <p><em>- </em>The R code used to do the analyses : <em>Rscript-Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens.R</em></p> <p><br> </p> <p> </p> <p> </p> <p> </p>
Data from: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies
Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.
Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history
Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029), and this heterogeneity could not be explained by differences in substitution rates. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history.
Data from: Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada
Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage-based tagging (PBT) may overcome problems associated with coded-wire tag-based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded-wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774–individual, 267–population baseline available for assignment. Coho salmon from un-CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT-GSI system of identification to individuals in 2017 fisheries and escapements provided high-resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian-origin coho salmon relative to CWTs, and an opportunity for a genetic-based system to replace the current CWT system for coho salmon assessment.
Canadian Arctic whale genomic data and code to estimate genetic offsets
<div>This is a repository for code and data used in estimating genetic offsets in Arctic whales in the eastern Canadian Arctic. See README.md file for details.</div> <div><br>Associated publication:</div> <div>de Greef, E., Müller, C., Snead A., Rivkin, L. R., Ferguson, S. H., Watt, C. A., Marcoux, M., Petersen, S. D., and Garroway, C. J. (2025). Identifying areas of potential risk based on future genetic adaptability in three Arctic whale species. <em>The American Naturalist.</em></div> <div> </div>
Data and Code for "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic"
<p>Please see the README.md file for a detailed description of each of the code and data files in this dataset.</p>
Stan code from: Branching networks can have opposing influences on genetic variation in riverine metapopulations
Aim: Fractal networks, represented by branching complexity in rivers, are ubiquitous in nature. In rivers, the number of either distal (e.g., in headwater streams) or confluent (e.g., in mainstems) locations can be increased along with their branching complexity. Distal- or confluent-spatial locations can result in fewer or greater corridor linkages that can alter genetic divergence at the metapopulation scale. These mechanisms underlying the resulting genetic structuring remain poorly understood at the metapopulation scale, particularly in terms of the roles of species-specific dispersal traits. The objective of this study is to mechanistically understand how branching complexity can simultaneously influence genetic divergence in opposite directions. Location: Northeastern Japan Methods: To evaluate the integrated influences of network complexity and species dispersal on genetic divergence among populations at the catchment scale, we modelled metapopulation genetic dynamics under a Bayesian inference framework by adapting empirical genetic data from four macroinvertebrate species. Simulations were then performed using empirical and virtual species-characteristics on virtual river networks. Results: Our simulation experiments showed that both greater landscape connectivity (resulting from shorter watercourse distance) and greater isolation of distal locations occurred in the more-branched river networks. These two spatial features have negative and positive influences on genetic divergence, with their relative importance varying among different species and dispersal characteristics. Specifically, genetic divergence at the metapopulation scale increased for species having higher downstream-biased dispersal but decreased for species having higher upstream-biased dispersal. Distal populations (e.g., in headwaters) have higher genetic independence when downstream-biased asymmetry is higher. Main conclusions: We found a strong association between species dispersal and evolutionary processes such as gene flow and genetic drift. This association mediates the pervasive influences of branching complexity on genetic-divergence in the metapopulation. It also highlights the importance of considering species dispersal-patterns when developing management strategies in the face of rapid environmental-change scenarios.
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>
Data, Code and Computational Environment for: Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion
<p><strong>Data</strong></p> <p>The csv file "2023-06-27_data.csv" contains genetic profiles for all olive trees analyzed in the publication: Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion". The genotypes are provided in the GenAlEx format.</p> <p> </p> <p><strong>Code</strong></p> <p>Code is provided in the compressed folder "Tourvas_et_al_Olive". It is structured as a R project and can easily be opened, after decompressing, from the Rstudio interface. If you prefer to review and/or reuse code you can access it from the "analysis" folder inside the "Tourvas_et_al_Olive" folder.</p> <p> </p> <p><strong>Computational Environment</strong></p> <p>A tarball for the Docker image "tourvas_et_al_olive" is also provided. This is the recommended way to reproduce the results of the publication: "Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion".</p> <p>It is assumed that you already have Docker installed on your system. If not, please visit <a href="https://docs.docker.com/get-started/">https://docs.docker.com/get-started/</a></p> <p>To use it:</p> <ul> <li>download the image file tourvas_et_al_olive.tar</li> <li>load it with docker with the command:</li> </ul> <pre><code class="language-bash">docker load --input tourvas_et_al_olive.tar</code></pre> <ul> <li>then launch the Docker container with the command:</li> </ul> <pre><code class="language-bash">docker run --name popgen --rm -dp 8787:8787 -e ROOT=TRUE -e DISABLE_AUTH=true -v "`pwd`":/home/rstudio/working nikostourvas/tourvas_et_al_olive</code></pre> <ul> <li>start your favorite web browser and go to: http://localhost:8787/</li> <li>from the bottomright pane of the Rstudio server click on the directory "Tourvas_et_al_Olive" and open the project by clicking on the "Tourvas_et_al_Olive.Rproj" file</li> <li>launch the scripts inside the "analysis" directory and run them to reproduce results</li> </ul>
Files and code to replicate the analyses and figures in the manuscript "Genetics, energetics, and allostery in proteins with randomized cores and surfaces"
<p>Welcome to the Zenodo repository for the following publication: Genetics, energetics, and allostery in proteins with randomized cores and surfaces by Escobedo, Voigt, Faure and Lehner, Science 2025.</p> <p>This repository contains all files and code to replicate the analyses and figures associated with the publication. Code is also available at <a href="https://github.com/lehner-lab/combinatorialcores" target="_new" rel="noopener">GitHub</a>. Raw NGS fastq files are available at Gene Expression Omnibus [GEO: GSE266299] (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE266299" rel="nofollow">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE266299</a>)</p>
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 from: Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada
Open the record for dataset details and reuse information.
Simulation code for: Effects of population size change on the genetics of adaptation following an abrupt change in environment
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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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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.