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5,538 results for “population data”
Data from: Sexual selection on male but not female function in monoecious and dioecious populations of broadleaf arrowhead (Sagittaria latifolia)
<p class="MsoNormal">Direct measures of sexual selection in plants are rare and complicated by modular growth. Because of modularity, instantaneous measures of fitness scale with size, but size variation in plants is largely non-heritable, obscuring patterns of selection on heritable variation. We measured the magnitude of sexual selection in a monoecious and a dioecious population of the clonal plant <em>Sagittaria latifolia</em> using Bateman gradients (<em>ß<sub>ss</sub></em>). These gradients were calculated using parentage analysis and residual regression to account for the effects of shoot and clone size on mating and reproductive success. In both populations: (i) mating via male function was associated with greater promiscuity; and (ii) <em>ß</em><sub>ss</sub> were positive, with significant associations between mating and reproductive success for male but not female function. Moreover, estimated <em>ß</em><sub>ss</sub> were similar for the monoecious and dioecious populations, possibly because non-overlapping female and male sex phases in hermaphroditic <em>S. latifolia </em>reduces the scope for interference between sex functions during mating. This study builds on previous studies of selection on plant mating traits, and of sexual selection under experimental conditions by showing that sexual selection can operate in natural populations of plants, including populations of hermaphrodites.</p>
Data from: Spatial consistency in drivers of population dynamics of a declining migratory bird
<p>1. Many migratory species are in decline across their geographical ranges. Single-population studies can provide important insights into drivers at a local scale, but effective conservation requires multi-population perspectives. This is challenging because relevant data are often hard to consolidate, and state-of-the-art analytical tools are typically tailored to specific datasets.</p> <p>2. We capitalized on a recent data harmonization initiative (SPI-Birds) and linked it to a generalized modeling framework to identify the demographic and environmental drivers of large-scale population decline in migratory pied flycatchers (<em>Ficedula</em> <em>hypoleuca</em>) breeding across Britain.</p> <p>3. We implemented a generalized integrated population model (IPM) to estimate age-specific vital rates, including their dependency on environmental conditions, and total and breeding population size of pied flycatchers using long-term (34–64 years) monitoring data from seven locations representative of the British breeding range. We then quantified the relative contributions of different vital rates and population structures to changes in short- and long-term population growth rates using transient life table response experiments (LTREs).</p> <p>4. Substantial covariation in population sizes across breeding locations suggested that change was the result of large-scale drivers. This was supported by LTRE analyses, which attributed past changes in short-term population growth rates and long-term population trends primarily to variation in annual survival and dispersal dynamics, which largely act during migration and/or non-breeding season. Contributions of variation in local reproductive parameters were small in comparison, despite sensitivity to local temperature and rainfall within the breeding period.</p> <p>5. We show that both short- and longer-term population changes of British-breeding pied flycatchers are likely linked to factors acting during migration and in non-breeding areas, where future research should be prioritized. We illustrate the potential of multi-population analyses for informing management at (inter)national scales and highlight the importance of data standardization, generalized and accessible analytical tools, and reproducible workflows to achieve them.</p>
Data for: Population niche width is driven by within-individual niche expansion and individual specialization in introduced brook trout in mountain lakes
<p><span>The width of a population's resource use niche is determined by individual diet breadth ("within-individual component") and the degree of niche partitioning between individuals ("between-individual component"). The balance between these two factors affects ecological stability and evolutionary trajectories, and may shift as ecological opportunity permits broader population niches. Lakes in California's Sierra Nevada Mountains vary in resource diversity for introduced brook trout (<em>Salvelinus fontinalis</em>) due to elevation, lake morphometry, and watershed features. We compared the relative contributions of within- and between-individual niche components to two measures of the dietary niches of thirteen populations of brook trout: prey taxonomic composition and prey size distribution. For both taxonomic and size diversity of fish diets, population niche width was positively related to both the within- and between-individual components. For taxonomic diversity, the two components increased in parallel, while for size diversity, the between-individual component became more important relative to the within-individual component in populations with the greatest niche widths. Our results support the Niche Variation Hypothesis that populations with broader niches are more heterogeneous among individuals and show that individual niche width and individual specialization can operate in parallel to expand the population niche.</span></p>
Code and data for: Emergence of spatially structured populations by area-concentrated search
<p>The idea that populations are spatially structured has become a very powerful concept in ecology, raising interest in many research areas. However, despite dispersal being a core component of the concept, it typically does not consider the movement behavior underlying any dispersal. Using individual-based simulations in continuous space, we investigate the emergence of a spatially structured population in landscapes with spatially heterogeneous resource distribution and with organisms following simple area-concentrated search (ACS); individuals do not, however, perceive or respond to any habitat attributes per se but only to their foraging success. We investigated effects of different resource clustering patterns in landscapes (single large cluster vs. many small clusters) and different resource densities on spatial structure of populations and movement between resource clusters of individuals. As the results, we found that foraging success increased with increasing resource density and decreasing number of resource clusters. In a wide parameter space, the system exhibited attributes of a spatially structured population with individuals concentrated in areas of high resource density, searching within areas of resources, and 'dispersing' in a straight line between resource patches. 'Emigration' was more likely from patches that were small or of low quality (low resource density), but we observed an interaction effect between these two parameters. With the ACS implemented, individuals tended to move deeper into a resource cluster in scenarios with moderate resource density than in scenarios with high resource density. 'Looping' from patches was more likely if patches were large and of high quality. Our simulations demonstrate that spatial structure in populations may emerge if critical resources are heterogeneously distributed and if individuals follow simple movement rules (such as ACS). Neither the perception of habitat nor an explicit decision to emigrate from a patch on the side of acting individuals is necessary for the emergence of spatial structure.</p>
Data for: Inferring population connectivity in Eastern Massasauga Rattlesnakes (Sistrurus catenatus) using landscape genetics
<p>Assessing the environmental factors that influence the ability of a threatened species to move through the landscape can be used to identify conservation actions that connect isolated populations. However, direct observations of species' movement are often limited making the development of alternate approaches necessary. Here we use landscape genetic analyses to assess the impact of landscape features on the movement of individuals between local populations of a threatened snake, the Eastern Massasauga Rattlesnake (<em>Sistrurus catenatus</em>). We linked connectivity data with habitat information from two landscapes of similar size: a large region of unfragmented habitat and a previously studied fragmented landscape consisting of isolated patches of habitat. We used this analysis to identify features of the landscape where modification or acquisition would enhance population connectivity in the fragmented region. We found evidence that current connectivity is impacted by both contemporary landcover features, especially roads, and inherent landscape features such as elevation. Next, we derived estimates of expected movement ability using a recently developed pedigree-based approach and Least Cost Paths through the unfragmented landscape. We then used our pedigree and resistance map to estimate resistance polygons of the potential extent for <em>S. catenatus</em> movement in the fragmented landscape. These polygons identify possible sites for future corridors connecting currently isolated populations in this landscape by linking the impact of future habitat modification or land acquisition to dispersal ability in this species. Overall, our study shows how modeling landscape resistance across differently fragmentated landscapes can identify habitat features that affect contemporary movement in threatened species in fragmented landscapes and how this information can be used to guide mitigation actions whose goal is to connect isolated populations.</p>
single-cell RNAseq data (data set 1) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>The present dataset (dataset1) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from CRC samples downloaded from the GEO website (<strong>GSE81861). </strong></p> <p>see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data</p> <p>and github: https://github.com/sysbiolux/scFASTCORMICS</p> <p>For more information, version updates of the scFASTCORMICS. </p>
Data from: Cost-saving population genomic investigation of Daphnia longispina complex resting eggs using whole genome amplification and pre-sequencing screening
<p>This dataset contains all paired MiSeq sequences that were generated for the study "Cost-saving population genomic investigation of<em> Daphnia longispina</em> complex resting eggs using whole genome amplification and pre-sequencing screening" by Nickel and Cordellier.</p> <p>The sample names used in the study and the associated file names are explained in the table<strong> </strong>"Study_sample_names.xlsx"</p> <p> </p>
Data from: Range-edge populations of seaweeds show niche unfilling and poor adaptation to increased temperatures
<p>Data used for the study entitled "Range-edge populations of seaweeds show niche unfilling and poor adaptation to increased temperatures". These are the distribution data collected from literature and personal communications to complete the GBIF and OBIS distributional records of the Atlantic European coast, the weekly growth data taken from the study individuals as well as the binomial survival data used for the graphs of the last week of the experiment.</p>
Temperature data of the 2022 MHW and underwater pictures of impacts on bath sponge populations
<p>July-to-August seawater temperature recorded at 18 m depth at the “3PP” station, La Ciotat, near Marseille, South of France (43.163°N; 5.599°E) using <em>in situ</em> autonomous sensors during the 2022 MHW, in the two previous years (grey dotted lines), and during the reference 2003 MHW (orange dotted line). Only one record per day is shown;</p> <p>IMG 1467: Two living sponge species, <em>Ircinia oros</em> and the bath sponge <em>Spongia officinalis</em>, the latter with necrotic spots on its surface (September 7, 2022) - Author Thierry Pérez</p> <p>IMG 1688: The same two sponges after five days (September 12, 2022), <em>S. officinalis</em> is dying, covered by a white bacterial veil. Author Thierry Pérez</p> <p> P9216598: A once rich and healthy population of <em>S. officinalis</em> at 10 m depth, September 21, 2022; Arrows point to <em>S. officinalis</em> dead skeletons left attached to the rocky wall; Author Pierre Chevaldonné</p>
Data for: Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia
<p>Genomic diversity is a fundamental component of Earth's total biodiversity and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (<em>Mesembriomys</em> <em>gouldii</em>), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.</p>
Cover Your Basis: Comprehensive Data-Driven Characterization of the Binary Black Hole Population
<p>The accompanying data and code release for the analyses presented in "Cover Your Basis: Comprehensive Data-Driven Characterization of the Binary Black Hole Population". See the github paper repository at https://github.com/bruce-edelman/CoveryingYourBasis and the arxiv release of the paper at: https://arxiv.org/abs/2210.12834</p>
Data and code for paper "Freihardt (2024): Perceptions of environmental changes among a climate-vulnerable population from Bangladesh. Climatic Change. DOI 10.1007/s10584-024-03678-6"
<p>This dataset contains the temperature, precipitation, erosion, and perception data, as well as the analysis code in R necessary to replicate the results of the paper:</p> <p>Freihardt, J. (2024): Perceptions of environmental changes among a climate-vulnerable population from Bangladesh. Climatic Change, 177, 25. DOI: 10.1007/s10584-024-03678-6.</p>
Data from: Genomics reveals the role of admixture in the evolution of structure among sperm whale populations within the Mediterranean Sea
<p>In oceanic ecosystems, the nature of barriers to gene flow, and the processes by which populations may become isolated are different from the terrestrial environment, and less well understood. In this study, we investigate a highly mobile species (the sperm whale, <em>Physeter macrocephalus</em>) that is genetically differentiated between an open North Atlantic population and the populations in the Mediterranean Sea. We apply high-resolution single nucleotide polymorphisms (SNP) analysis to study the nature of barriers to gene flow in this system, comparing gene flow across the putative boundary into the Mediterranean (Strait of Gibraltar and Alboran Sea region) with novel analyses on structuring among sperm whale populations within the Mediterranean basin. Our data support a recent founding of the Mediterranean, around the time of the last glacial maximum, and shows concerted historical demographic profiles in both the Atlantic and the Mediterranean. In each region, there is evidence for a population decline around the time of the founder event, more extreme within the Mediterranean Sea where effective population size is substantially lower. While differentiation is strongest at the Atlantic/Mediterranean boundary, there is also significant differentiation between the Eastern and Western basins of the Mediterranean Sea. We propose, however, that the mechanisms are different. While post-founding gene flow was reduced between the Mediterranean and Atlantic populations, within the Mediterranean an important factor differentiating the basins is likely a greater degree of admixture between the Western basin and the North Atlantic.</p>
Data for: Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow
<p>Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gene flow. Comparative studies of population genetic data from species with differing life histories provide opportunities to tease apart the role of dispersal in shaping gene flow and population genetic structure. Here, we examine population genetic data from sets of bird species specialized on a series of Amazonian habitat types hypothesized to filter for species with dramatically different dispersal abilities: stable upland forest, dynamic floodplain forest, and highly dynamic riverine islands. Using genome-wide markers, we show that habitat type has a significant effect on population genetic structure, with species in upland forest, floodplain forest, and riverine islands exhibiting progressively lower levels of structure. Although morphological traits used as proxies for individual-level dispersal ability did not explain this pattern, population genetic measures of gene flow are elevated in species from more dynamic riverine habitats. Our results suggest that the habitat in which a species occurs drives the degree of population genetic structuring via its impact on long-term fluctuations in levels of gene flow, with species in highly dynamic habitats having particularly elevated gene flow. These differences in genetic variation across taxa specialized in distinct habitats may lead to disparate responses to environmental change or habitat-specific diversification dynamics over evolutionary time scales.</p>
[Dataset] Data for the course "Population Genomics" at Aarhus University
<p>Datasets, conda environments and Softwares for the course "Population Genomics" of Prof Kasper Munch. This course material is maintained by the <a href="https://hds-sandbox.github.io/">health data science sandbox</a>. This <a href="https://hds-sandbox.github.io/PopulationGenomicsCourse/">webpage</a> shows the latest version of the course material.</p> <ol> <li> Data.tar.gz Contains the datasets and executable files for some of the softwares<br> You can unpack by simply doing<br> tar -zxf Data.tar.gz -C ./<br> This will create a folder called Data with the uncompressed material inside</li> <li>Course_Env.packed.tar.gz Contains the conda environment used for the course. This needs to be unpacked to adjust all the prefixes (Note this environment is created on Ubuntu 22.10). You do this in the command line by <ol> <li>creating the folder Course_Env: mkdir Course_Env</li> <li>untar the file: tar -zxf Course_Env.packed.tar.gz -C Course_Env</li> <li>Activate the environment: conda activate ./Course_Env</li> <li>Run the unpacking script (it can take quite some time to get it done): conda-unpack</li> </ol> </li> <li>Course_Env.unpacked.tar.gz The same environment as above, but will work only if untarred into the folder /usr/Material - so use the version above if you are using it in another folder. This file is mostly to execute the course in our own cloud environment.</li> <li>environment_with_args.yml The file needed to generate the conda environment. Create and activate the environment with the following commands: <ol> <li>conda env create -f environment_with_args.yml -p ./Course_Env</li> <li>conda activate ./Course_Env</li> </ol> </li> </ol> <p> </p> <p>The data is connected to the following repository:<a href="https:// github.com/hds-sandbox/Popgen_course_aarhus."> https://github.com/hds-sandbox/Popgen_course_aarhus.</a> The original course material from Prof Kasper Munch is at <a href="https://github.com/kaspermunch/PopulationGenomicsCourse">https://github.com/kaspermunch/PopulationGenomicsCourse</a>.</p> <p> </p> <p><strong>Description</strong></p> <p>The participants will after the course have detailed knowledge of the methods and applications required to perform a typical population genomic study.</p> <p>The participants must at the end of the course be able to:</p> <ul> <li>Identify an experimental platform relevant to a population genomic analysis.</li> <li>Apply commonly used population genomic methods.</li> <li>Explain the theory behind common population genomic methods.</li> <li>Reflect on strengths and limitations of population genomic methods.</li> <li>Interpret and analyze results of population genomic inference.</li> <li>Formulate population genetics hypotheses based on data</li> </ul> <p>The course introduces key concepts in population genomics from generation of population genetic data sets to the most common population genetic analyses and association studies. The first part of the course focuses on generation of population genetic data sets. The second part introduces the most common population genetic analyses and their theoretical background. Here topics include analysis of demography, population structure, recombination and selection. The last part of the course focus on applications of population genetic data sets for association studies in relation to human health.</p> <p>Curriculum</p> <p>The curriculum for each week is listed below. "Coop" refers to a set of <a href="https://github.com/cooplab/popgen-notes/releases/download/v1.2/minicoop.pdf">lecture notes by Graham Coop</a> that we will use throughout the course.</p> <p>Course plan</p> <ol> <li>Course intro and overview: <ul> <li>Coop chapters 1, 2, 3, <a href="https://www.nature.com/articles/nature18964">Paper: Genome Diversity Project</a></li> </ul> </li> <li>Drift and the coalescent: <ul> <li>Coop chapter 4; <a href="https://www.nature.com/articles/ng.3036">Paper: Platypus</a></li> <li>Exercise: Read mapping and base calling</li> </ul> </li> <li>Recombination: <ul> <li>Lecture: <a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2016.0455">Review: Recombination in eukaryotes</a>, <a href="https://www.nature.com/articles/s41576-020-0240-1">Review: Recombination rate estimation</a></li> <li>Exercise: Phasing and recombination rate</li> </ul> </li> <li>Population strucure and incomplete lineage sorting: <ul> <li>Lecture: Coop chapter 6, <a href="https://doi.org/10.1146/annurev-genet-120213-092532">Review: Incomplete lineage sorting</a></li> <li>Exercise: Working with VCF files</li> </ul> </li> <li>Hidden Markov models: <ul> <li>Lecture: Durbin chapter 3, <a href="https://www.nature.com/articles/nature07331">Paper: population structure</a></li> <li>Exercise: Inference of population structure and admixture</li> </ul> </li> <li>Ancestral recombination graphs: <ul> <li>Lecture: <a href="https://bmcgenomdata.biomedcentral.com/articles/10.1186/1471-2156-7-16">Paper: Approximating the ARG</a>, <a href="https://www.nature.com/articles/s41588-019-0484-x">Paper: Tree inference</a></li> <li>Exercise: ARG dashboard exercises + Inference of trees along sequence</li> </ul> </li> <li>Past population demography: <ul> <li>Lecture: Coop chapter 4, <a href="https://www.nature.com/articles/nature10231">Paper: PSMC</a>, revisit <a href="https://www.nature.com/articles/s41588-019-0484-x">Paper: Tree inference</a></li> <li>Exercise: Inferring historical populations</li> </ul> </li> <li>Direct and linked selection: <ul> <li>Lecture: Coop chapters 12, 13, revisit <a href="https://www.nature.com/articles/s41588-019-0484-x">Paper: Tree inference</a></li> </ul> </li> <li>Admixture: <ul> <li>Lecture: <a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007349">Review: Admixture</a>, <a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007641">Paper: Admixture inference</a></li> <li>Exercise: Detecting archaic ancestry in modern humans</li> </ul> </li> <li>Genome-wide association study (GWAS): <ul> <li>Lecture: <a href="https://github.com/cooplab/popgen-notes/releases/download/v1.2/release_popgen_notes.pdf">Coop lecture notes</a> 99-120</li> <li>Exercise: GWAS quality control</li> </ul> </li> <li>Heritability: <ul> <li>Lecture: Coop Lecture notes Sec. 2.2 (p23-36) + Chap. 7 (p119-142)</li> <li>Exercise: Association testing</li> </ul> </li> <li>Evolution and disease: <ul> <li>Lecture: Coop Lecture notes Sec. 11.0.1 (p217-221)</li> <li>Exercise: Estimating heritability</li> </ul> </li> </ol>
Data and code for: Failure to purge: Population and individual inbreeding effects on fitness across generations of wild Impatiens capensis
<p>Inbreeding exposes deleterious recessive alleles in homozygotes, lowering fitness and generating inbreeding depression (ID). Both purging (via selection) and fixation (via drift) should reduce segregating deleterious mutations and ID in more inbred populations. These theoretical predictions are not well-tested in wild populations, which is concerning given purging/fixation have opposite fitness outcomes. We examined how individual- and population-level inbreeding and genomic heterozygosity affected maternal and progeny fitness within and among 12 wild populations of <em>Impatiens capensis</em>. We quantified maternal fitness in home sites, maternal multilocus heterozygosity (using 12,560 SNPs), and lifetime fitness of selfed and predominantly outcrossed progeny in a common garden. These populations spanned a broad range of individual- (<span class="s1"><em>f</em></span><span class="s2"><sub>i</sub></span><em> </em>= -0.17–0.98) and population-level inbreeding (<span class="s1"><em>F</em></span><span class="s2"><sub>IS</sub></span> = 0.25–0.87). More inbred populations contained fewer polymorphic loci, less fecund mothers, and smaller progeny, suggesting higher fixed loads. However, despite appreciable ID (mean: 8.8 lethal equivalents per gamete), ID did not systematically decline in more inbred population. More heterozygous mothers were more fecund and produced fitter progeny in outcrossed populations, but this pattern unexpectedly reversed in highly inbred populations. These observations suggest that persistent overdominance or some other force acts to forestall purging and fixation in these populations.</p>
VCF files of ddRAD seq data of Bermuda petrel population
<p>Two VCF files resulted from two different filtering and analyses of ddRAD sequencing data of the endangered Bermuda petrel. The one_snp VCF contains only one snp per RAD locus, while the all_snps contained all SNPs in a RAD locus.</p>
Data for: Genetic control of grain amino acid composition in a UK soft wheat mapping population
<p>Wheat is a major source of nutrients for populations across the globe, but the amino acid composition of wheat grain does not provide optimal nutrition. The nutritional value of wheat grain is limited by low concentrations of lysine (the most limiting essential amino acid) and high concentrations of free asparagine (precursor to the processing contaminant acrylamide). There are currently few available solutions for asparagine reduction and lysine biofortification through breeding. In this study, we investigated the genetic architecture controlling grain-free amino acid composition and its relationship to other traits in a Robigus × Claire doubled haploid population. Multivariate analysis of amino acids and other traits showed that the two groups are largely independent of one another, with the largest effect on amino acids being from the environment. Linkage analysis of the population allowed the identification of QTL controlling free amino acids and other traits, and this was compared against genomic prediction methods. Following the identification of a QTL controlling free lysine content, wheat pangenome resources facilitated analysis of candidate genes in this region of the genome. These findings can be used to select appropriate strategies for lysine biofortification and free asparagine reduction in wheat breeding programmes.</p>
Data from: Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth
<p>This dataset supports the article "Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth", which is under minor revision in Journal of Experimental Botany. The study addresses the combined effects of and plant population origin, drought and heat stress on plant growth, plant morphology and the leaf metabolome. The data were assessed in Northern and Southern European individuals of <em>Cakile maritma</em> (See Rocket). An R-script containing all statistical analyses that have been implemented with these data is also provided.</p>
Data from: Additive genetic and environmental variation interact to shape the dynamics of seasonal migration in a wild bird population
<p><span>Dissecting joint micro-evolutionary and plastic responses to environmental perturbations requires quantifying interacting components of genetic and environmental variation underlying expression of key traits. This ambition is particularly challenging for phenotypically discrete traits where multiscale decompositions are required to reveal non-linear transformations of underlying genetic and environmental variation into phenotypic variation, and when effects must be estimated from incomplete field observations. We devised a joint multistate capture-recapture and quantitative genetic animal model and fitted this model to full-annual-cycle resighting data from partially-migratory European shags (<em>Gulosus</em> <em>aristotelis</em>) to estimate key components of genetic, environmental and phenotypic variance in the ecologically critical discrete trait of seasonal migration versus residence. We demonstrate non-negligible additive genetic variance in latent liability for migration, resulting in detectable micro-evolutionary responses following two episodes of strong survival selection. Further, liability-scale additive genetic effects interacted with substantial permanent individual and temporary environmental effects to generate complex non-additive effects on expressed phenotypes, causing substantial intrinsic gene-by-environment interaction variance on the phenotypic scale. Our analyses therefore reveal how temporal dynamics of partial seasonal migration arise from combinations of instantaneous micro-evolution and within-individual phenotypic consistency, and highlight how intrinsic phenotypic plasticity could expose genetic variation underlying discrete traits to complex forms of selection.</span></p>
ScienceDex guides
Understand access before you commit
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.