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356 results for “heritability”
Data to support: Moving beyond heritability in the search for coral adaptive potential
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Further evidence from common garden rearing experiments of heritable traits separating lean and siscowet lake charr (Salvelinus namaycush) ecotypes
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Rhesus macaque cone ratio heritability
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Data from: Telomere heritability and parental age at conception effects in a wild avian population
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Vitamin D status is heritable and under environment-dependent selection in the wild
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The heritability of size in a wild annual plant population with hierarchical size structure
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Data from: Ant collective behavior is heritable and shaped by selection
Collective behaviors are widespread in nature and usually assumed to be strongly shaped by natural selection. However, the degree to which variation in collective behavior is heritable and has fitness consequences -- the two prerequisites for evolution by natural selection -- is largely unknown. We used a new pharaoh ant ( Monomorium pharaonis ) mapping population to estimate the heritability, genetic correlations, and fitness consequences of three collective behaviors (foraging, aggression, and exploration) as well as body size, sex ratio, and caste ratio. Heritability estimates for the collective behaviors were moderate, ranging from 0.17 to 0.32, but lower than our estimates for the heritability of caste ratio, sex ratio, and the body size of new workers, queens, and males. Moreover, variation among colonies in collective behaviors was phenotypically correlated, suggesting that selection may shape multiple colony collective behaviors simultaneously. Finally, we found evidence for directional selection that was similar in strength to estimates of selection in natural populations. Altogether, our study begins to elucidate the genetic architecture of collective behavior and is one of the first studies to demonstrate that it is shaped by selection.
Short-term heritable variation overwhelms two hundred generations of mutational variance for metabolic traits in Caenorhabditis elegans
<p>Metabolic disorders have a large heritable component, and have increased markedly in human populations over the past few generations. Genome-wide association studies of metabolic traits typically find a substantial unexplained fraction of total heritability, suggesting an important role of spontaneous mutation. An alternative explanation is that epigenetic effects contribute significantly to the heritable variation. Here we report a study designed to quantify the cumulative effects of spontaneous mutation on adenosine metabolism in the nematode <i>Caenorhabditis elegans</i>, including both the activity and concentration of two metabolic enzymes and the standing pools of their associated metabolites. The only prior studies on the effects of mutation on metabolic enzyme activity, in <i>Drosophila melanogaster</i>, found that total enzyme activity presents a mutational target similar to that of morphological and life-history traits. However, those studies were not designed to account for short-term heritable effects. We find that the short-term heritable variance for most traits is of similar magnitude as the variance among MA lines. This result suggests that the potential heritable effects of epigenetic variation in metabolic disease warrant additional scrutiny.</p>
m6A-TWAS weights for "Genetic Analyses Support the Contribution of mRNA N6-methyladenosine (m6A) Modification to Human Diseases Heritability"
<p>We included the m6A-TWAS weights (trained using FUSION) for our manuscript "Genetic Analyses Support the Contribution of mRNA <em>N</em>6-methyladenosine (m6A) Modification to Human Diseases Heritability". </p> <p>This dataset is a supplement to the m6A QTL summary statistics data and imputed genotype data at https:// doi.org/10.5281/zenodo.3870952.</p>
Data from: A heritable symbiont and host-associated factors shape fungal endophyte communities across spatial scales
1. Although microbial ecologists are intensely interested in the processes governing microbial community assembly, progress has been limited by a lack of studies that span multiple geographical scales and levels of biological organization. 2. We used high throughput sequencing to characterize foliar fungal endophyte communities and host plant genetic structure both within, and among, 24 populations of spotted locoweed (Astragalus lentiginosus) across the Great Basin Desert. 3. Across the Great Basin, both within, and among populations of the host plant, fungal endophyte richness was predicted by plant size and variation in the seed-borne, heritable fungus, Alternaria fulva, which produces the bioactive alkaloid swainsonine. 4. The degree of between-plant turnover in the endophyte community was inversely related to host plant inbreeding and average plant size, and positively related to the relative abundance of A. fulva. Plant size was inversely related to endophyte community richness, both among, and within populations. The genetic and physical distance between host populations was not predictive of differences in fungal community structure. 5. Synthesis: Through pairing intensive local- and regional sampling, we uncovered a primacy of deterministic forces imposed by a heritable symbiont on the community structure of locoweed endophytes.
Data from: Heritable variation in circulating glucocorticoids and endocrine flexibility in a free-living songbird
Phenotypic flexibility is a central way that organisms cope with challenging and changing environments. As endocrine signals mediate many phenotypic traits, heritable variation in hormone levels, or their context-dependent flexibility, could present an important target for selection. Several studies have estimated the heritability of circulating glucocorticoid levels under acute stress conditions, but little is known about the potential for either baseline hormone levels or rapid endocrine flexibility to evolve. Here we assessed the potential for selection to operate on the elevation (circulating hormone levels) and flexibility of glucocorticoid reaction norms to acute restraint stress. Multivariate animal models revealed low but significant heritability in baseline (h2=0.13-0.14) and stress-induced glucocorticoids (h2=0.18), and moderate heritability in glucocorticoid flexibility in response to acute stress (h2=0.38) in free-living juvenile tree swallows (Tachycineta bicolor; n=408). Baseline glucocorticoids were not genetically correlated with either stress-induced glucocorticoids or glucocorticoid flexibility. These findings indicate that baseline glucocorticoids and the acute stress response are distinct traits that can be independently shaped by selection. Microevolutionary changes that influence the expression or flexibility of these endocrine mediators of phenotype may be an important way that populations adapt to changing environments and novel threats.
The c-Abl inhibitor IkT-148009 therapeutically suppresses neurodegeneration in models of heritable and sporadic Parkinson's Disease
<p>Parkinson's Disease (PD) is the second most prevalent neurodegenerative disease of the central nervous system, with an estimated 5,000,000 cases worldwide. PD pathology is characterized by the accumulation of misfolded a-synuclein, which is thought to play a critical role in the etiopathogenesis of the disease. Animal models of PD suggest that activation of the Abelson Tyrosine Kinase, or c-Abl, plays an essential role in the initiation and progression of a-synuclein pathology and initiates processes leading to the degeneration of dopaminergic and non-dopaminergic neurons. Given the essential role of c-Abl in the disease, a proprietary c-Abl inhibitor library was developed to identify potent, orally bioavailable c-Abl inhibitors capable of crossing the blood-brain barrier based on pre-defined characteristics, leading to the discovery of IkT-148009. IkT-148009 is a selective, potent, brain-penetrant c-Abl inhibitor with a favorable toxicology profile that was analyzed for therapeutic potential in animal models of slowly progressive, a-synuclein-dependent disease. In models of both inherited and sporadic Parkinson's disease in the mouse, IkT-148009 suppressed c-Abl activation to baseline and substantially protected neurons from degeneration when administered therapeutically by once daily oral gavage beginning four weeks after disease initiation. Recovery of normal behavioral function in diseased mice occurred within 8 weeks of initiating treatment and occurred concomitantly with a substantial reduction of a-synuclein pathology in the brain. These disease-modifying outcomes in mice suggest IkT-148009 has the potential to be a disease-modifying therapy in human disease.</p>
Heritability and genome-wide association study of vaccine-induced immune response in Beagles: A pilot study
<p>Both genetic and non-genetic factors contribute to individual variation in the immune response to vaccination. Understanding how genetic background influences variation in both the magnitude and persistence of vaccine-induced immunity is vital for improving vaccine development and identifying possible causes of vaccine failure. Dogs provide a relevant biomedical model for investigating mammalian vaccine genetics; canine breed structure and long linkage disequilibrium simplify genetic studies in this species compared to humans. The objective of this study was to estimate the heritability of the antibody response to vaccination against viral and bacterial pathogens and to identify genes driving variation of the immune response to vaccination in Beagles. Sixty puppies were immunized following a standard vaccination schedule with an attenuated combination vaccine containing antigens for canine adenovirus type 2, canine distemper virus, canine parainfluenza virus, canine parvovirus, and four strains of <em>Leptospira</em> bacteria. Serum antibody measurements for each viral and bacterial component were measured at multiple time points. Heritability estimations and GWAS were conducted using SNP genotypes at 279,902 markers together with serum antibody titer phenotypes. The heritability estimates were: (1) to <em>Leptospira</em> antigens, ranging from 0.178 to 0.628; and (2) to viral antigens, ranging from 0.199 to 0.588. There was not a significant difference between the overall heritability of vaccine-induced immune response to <em>Leptospira</em> antigens compared to viral antigens. Genetic architecture indicates that SNPs of low to high effect contribute to immune response to vaccination. GWAS identified two genetic markers associated with vaccine-induced immune response phenotypes. Collectively, these findings indicate that genetic regulation of the immune response to vaccination is antigen-specific and influenced by multiple genes of small effect.</p>
Genetic architecture of heritable leaf microbes
<p><em>Background</em></p> <p>Host-associated microbiomes are shaped by both their environment and host genetics, and often impact host performance. The scale of host genetic variation important to microbes is largely unknown, yet fundamental to the community assembly of host-associated microbiomes, and with implications for the eco-evolutionary dynamics of microbes and hosts. Using <em>Ipomoea hederacea</em>, Ivy-leaved morning glory, we generated matrilines differing in quantitative genetic variation and leaf shape, which is controlled by a single Mendelian locus. We then investigated the relative roles of Mendelian and quantitative genetic variation in structuring the leaf microbiome, and how these two sources of genetic variation contributed to microbe heritability.</p> <p><em>Results</em></p> <p>We found that despite large effects of the environment, both Mendelian and quantitative genetic host variation were important in contributing to microbe heritability, and that the cumulative small effect genomic differences due to matriline explained as much or more microbial variation than a single large effect locus. Furthermore, our results are the first to suggest that leaf shape itself contributes to variation in the abundances of some microbes in the leaf microbiome.</p> <p><em>Conclusions</em></p> <p>The genetic architecture of plant-associated microbiomes depends on both quantitative genetic variation and Mendelian traits, with similar contributions to microbe heritability. Our results demonstrate the roles of different scales of host genetic variation in the assembly of a natural microbiome. The genetic basis and heritability of a host's microbial phenotype is important for host evolution and ecology because microbes can affect host fitness, and because it can influence reciprocal selection between hosts and microbiomes. Additionally, when host-associated microbiomes have heritability, then this suggests they have the capacity to evolve as other host traits might, with potentially adaptive functions.</p>
Data from: Heritability of growth and leaf loss compensation in a long-lived tropical understorey palm
<p>Data from: Heritability of growth and leaf loss compensation in a long-lived tropical understorey palm, PLOS ONE.</p> <p>Quantitative genetic data related to growth parameters and leaf loss compensation of 1402 <em>Chamaedorea elegans</em> seedlings. Data was collected in a greenhouse experiment performed at the Unifarm experimental facilities of Wageningen University between January 2013 and July 2014, in which a defoliation treatment was applied. Seeds were collected in the Montes Azules Biosphere Reserve in Chiapas, Mexico. See PLOS ONE publication for more details.</p> <p>The file contains a separate "read me" tab in which the meaning of the variable codes is explained. </p> <p> </p>
Data from: Experimental evidence of rapid heritable adaptation in the absence of initial standing genetic variation
<p>The success of genetically depauperate populations in the face of environmental change is contrary to the expectation that high genetic diversity is required for rapid adaptation. Alternative pathways such as environmentally induced genetic modifications and non-genetic heritable phenotypes have been proposed mechanisms for heritable adaptation within an ecologically relevant timeframe. However, experimental evidence is currently lacking to establish if, and to what extent, these sources of phenotypic variation can produce a response.<br> <br> To test if adaptation can rapidly occur in the absence of initial standing genetic variation and recombination in small populations, we (i) exposed replicate monoclonal populations of the microzooplankton <em>Brachionus calyciflorus</em> to a culturing regime that selected for phenotypic variants with elevated population growth with either high or low phosphorus food for a period of 55 days and (ii) examined population-level response in two fully factorial common garden experiments at day 15 and 35 of the exposure experiment.<br> <br> Within six generations, we observed heritable local adaptation to nutrient limitation. More specifically, populations with a history of exposure to P-limited food exhibited higher population growth rates under low P food conditions than populations with a high P exposure history. However, the capacity for such a response was found to vary among clones.<br> <br> Our study finds that although standing genetic variation is considered essential for rapid heritable adaptation, the rapid emergence of <em>de novo</em> genetic variation or alternative sources of phenotypic variation could aid in the establishment and persistence of low diversity populations.</p>
Dataset 2: The plant response to high CO2 levels is heritable and orchestrated by DNA methylation
<p>This is a supporting dataset from the manuscript “The plant response to high CO<sub>2</sub> levels is heritable and orchestrated by DNA methylation” by Panda et al. This dataset was used to study trans-generational growth responses to environments with contrasting CO<sub>2</sub> levels.</p> <p>Raspberry Pi computers and cameras were used to image <em>Arabidopsis thaliana</em> wild-type (Columbia) and mutant (<em>ago1-27</em>, <em>cmt2-7/cmt3-11t</em>, <em>ddm1-2</em>, <em>met1</em>, <em>pol IV</em>, <em>suvh4/suvh5/suvh6</em>, and <em>ubp1b</em>) plants growing under ambient (450-500 ppm) and high (1000 ppm) CO<sub>2</sub> conditions. Imaging was done hourly from overhead beginning on the 8th day after sowing and continued until the 25th day after sowing.</p> <p>Dataset 2 contains images of plants grown in the second round of the experiment under ambient and high CO<sub>2</sub> conditions.</p>
Dataset 1: The plant response to high CO2 levels is heritable and orchestrated by DNA methylation
<p>This is a supporting dataset from the manuscript “The plant response to high CO<sub>2</sub> levels is heritable and orchestrated by DNA methylation” by Panda et al. This dataset was used to study trans-generational growth responses to environments with contrasting CO<sub>2</sub> levels.</p> <p>Raspberry Pi computers and cameras were used to image <em>Arabidopsis thaliana</em> wild-type (Columbia) and mutant (<em>ago1-27</em>, <em>cmt2-7/cmt3-11t</em>, <em>ddm1-2</em>, <em>met1</em>, <em>pol IV</em>, <em>suvh4/suvh5/suvh6</em>, and <em>ubp1b</em>) plants growing under ambient (450-500 ppm) and high (1000 ppm) CO<sub>2</sub> conditions. Imaging was done hourly from overhead beginning on the 8th day after sowing and continued until the 25th day after sowing.</p> <p>Dataset 1 contains images of plants grown in the first round of the experiment under ambient and high CO<sub>2</sub> conditions.</p>
Dataset 3: The plant response to high CO2 levels is heritable and orchestrated by DNA methylation
<p>This is a supporting dataset from the manuscript “The plant response to high CO<sub>2</sub> levels is heritable and orchestrated by DNA methylation” by Panda et al. This dataset was used to study trans-generational growth responses to environments with contrasting CO<sub>2</sub> levels.</p> <p>Raspberry Pi computers and cameras were used to image <em>Arabidopsis thaliana</em> wild-type (Columbia) and mutant (<em>ago1-27</em>, <em>cmt2-7/cmt3-11t</em>, <em>ddm1-2</em>, <em>met1</em>, <em>pol IV</em>, <em>suvh4/suvh5/suvh6</em>, and <em>ubp1b</em>) plants growing under ambient (450-500 ppm) and high (1000 ppm) CO<sub>2</sub> conditions. Imaging was done hourly from overhead beginning on the 8th day after sowing and continued until the 25th day after sowing.</p> <p>Dataset 3 contains images of the plants grown in the third round of the experiment under ambient and high CO<sub>2</sub> conditions. Plants were the progeny of plants from the first and second rounds.</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>
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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.