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97 results for “genetic variance”
Data from: No additive genetic variance for tolerance to ethynylestradiol exposure in natural populations of brown trout (Salmo trutta)
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Genomic prediction with non-additive effects in beef cattle: Stability of variance component and genetic effect estimates against population size
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Data from: Female and male genetic effects on offspring paternity: additive genetic (co)variances in female extra-pair reproduction and male paternity success in song sparrows (Melospiza melodia)
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Data for "Accurate Estimation of Marker-Associated Genetic Variance and Heritability in Complex Trait Analyses"
<p>This data is associated with the manuscript titled "Accurate Estimation of Marker-Associated Genetic Variance and Heritability in Complex Trait Analyses".</p> <p>9 files are contained. These files contain the summary statistics from the linear mixed model analyses in the simulations</p> <p>data_fig1a - all data for recreating Figure 1A</p> <p>data_fig1b - all data for recreating Figure 1B</p> <p>data_fig1c - all data for recreating Figure 1C</p> <p>data_fig1d - all data for recreating Figure 1D</p> <p>data_fig1e - all data for recreating Figure 1E</p> <p>data_fig1f - all data for recreating Figure 1F</p> <p>data_fig2 - all data for recreating Figure 2</p> <p>data_fig3 - all data for recreating Figure 3</p> <p>data_fig4 - all data for recreating Figure 4</p>
Data from: High-dimensional variance partitioning reveals the modular genetic basis of adaptive divergence in gene expression during reproductive character displacement
Although adaptive change is usually associated with complex changes in phenotype, few genetic investigations have been conducted of adaptations that involve sets of high dimensional traits. Microarrays have supplied high-dimensional descriptions of gene expression, and phenotypic change resulting from adaptation often results in large-scale changes in gene expression. We demonstrate how genetic analysis of large-scale changes in gene expression generated during adaptation can be accomplished by determining by high-dimensional variance partitioning within classical genetic experimental designs. A microarray experiment conducted on a panel of recombinant inbred lines (RILs) generated from two populations of Drosophila serrata that have diverged in response to natural selection, revealed genetic divergence in 10.6% of 3762 gene products examined. Over 97% of the genetic divergence in transcript abundance was explained by only 12 genetic modules. The two most important modules, explaining 50% of the genetic variance in transcript abundance, were genetically correlated with the morphological traits that are known to be under selection. The expression of three candidate genes from these two important genetic modules was assessed in an independent experiment using qRT-PCR on 430 individuals from the panel of RILs, and confirmed the genetic association between transcript abundance and morphological traits under selection.
Data from: Quantitative genetic variance in experimental fly populations evolving with or without environmental heterogeneity
Heterogeneous environments are typically expected to maintain more genetic variation in fitness within populations than homogeneous environments. However, the accuracy of this claim depends on the form of heterogeneity as well as the genetic basis of fitness traits and how similar the assay environment is to the environment of past selection. Here we measure quantitative genetic variance for three traits important for fitness using replicated experimental populations of Drosophila melanogaster evolving under four selective regimes: constant salt-enriched medium (Salt), constant cadmium-enriched medium (Cad), and two heterogeneous regimes that vary either temporally (Temp) or spatially (Spatial). As theory predicts, we found that Spatial populations tend to harbor more genetic variation than Temp populations or those maintained in a constant environment that is the same as the assay environment. Contrary to expectation, Salt populations tend to have more genetic variation than Cad populations in both assay environments. We discuss the patterns for quantitative genetic (QG) variances across regimes in relation to previously reported data on genome-wide sequence diversity. For some traits, the QG patterns are similar to the diversity patterns of ecological selected SNPs whereas the QG patterns for some other traits resembled that of neutral SNPs.
Data from: Very low levels of direct additive genetic variance in fitness and fitness components in a red squirrel population
A trait must genetically correlate with fitness in order to evolve in response to natural selection, but theory suggests that strong directional selection should erode additive genetic variance in fitness and limit future evolutionary potential. Balancing selection has been proposed as a mechanism that could maintain genetic variance if fitness components trade off with one another and has been invoked to account for empirical observations of higher levels of additive genetic variance in fitness components than would be expected from mutation–selection balance. Here, we used a long-term study of an individually marked population of North American red squirrels (Tamiasciurus hudsonicus) to look for evidence of (1) additive genetic variance in lifetime reproductive success and (2) fitness trade-offs between fitness components, such as male and female fitness or fitness in high- and low-resource environments. "Animal model" analyses of a multigenerational pedigree revealed modest maternal effects on fitness, but very low levels of additive genetic variance in lifetime reproductive success overall as well as fitness measures within each sex and environment. It therefore appears that there are very low levels of direct genetic variance in fitness and fitness components in red squirrels to facilitate contemporary adaptation in this population.
Data from: Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea
Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range.
Data from: Environmental stress correlates with increases in both genetic and residual variances: a meta-analysis of animal studies
Adaptive evolutionary responses are determined by the strength of selection and the amount of genetic variation within traits, however, both are known to vary across environmental conditions. As selection is generally expected to be strongest under stressful conditions, understanding how the expression of genetic variation changes across stressful and benign environmental conditions is crucial for predicting the rate of adaptive change. While theory generally predicts increased genetic variation under stress, previous syntheses of the field has found limited support for this notion. These studies have focused on heritability, which is dependent on other environmentally sensitive, but non-genetic, sources of variation. Here, we aim to complement these studies with a meta-analysis where we examine changes in coefficient of variation (CV) in maternal, genetic, and residual variances across stressful and benign conditions. Confirming previous analyses, we did not find any clear direction in how heritability changes across stressful and benign conditions. However, when analyzing CV, we found higher genetic and residual variance under highly stressful conditions in life-history traits but not in morphological traits. Our findings are of broad significance to contemporary evolution suggesting that rapid evolutionary adaptive response may be mediated by increased evolutionary potential in stressed populations.
Data from: Reduced genetic variance among high fitness individuals: inferring stabilizing selection on male sexual displays in D. serrata
Directional selection is prevalent in nature yet phenotypes tend to remain relatively constant, suggesting a limit to trait evolution. However, the genetic basis of this limit is unresolved. Given widespread pleiotropy, opposing selection on a trait may arise from the effects of the underlying alleles on other traits under selection, generating net stabilizing selection on trait genetic variance. These pleiotropic costs of trait exaggeration may arise through any number of other traits, making them hard to detect in phenotypic analyses. Stabilizing selection can be inferred, however, if genetic variance is greater among low compared to high fitness individuals. We extend a recently suggested approach to provide a direct test of a difference in genetic variance for a suite of cuticular hydrocarbons (CHCs) in Drosophila serrata. Despite strong directional sexual selection on these traits, genetic variance differed between high and low fitness individuals and was greater among the low fitness males for seven of eight CHCs, significantly more than expected by chance. Univariate tests of a difference in genetic variance were non-significant but likely have low power. Our results suggest that further CHC exaggeration in D. serrata in response to sexual selection is limited by pleiotropic costs mediated through other traits.
Data from: Sexually antagonistic genetic variance for fitness in an ancestral and a novel environment
The intersex genetic correlation for fitness (rwfm), a standardized measure of the degree to which male and female fitness covary genetically, has consequences for important evolutionary processes, but few estimates are available and none have explored how it changes with environment. Using a half-sibling breeding design, we estimated the genetic (co)variance matrix (G) for male and female fitness, and the resulting rwfm,in Drosophila serrata. Our estimates were performed in two environments: the laboratory yeast food to which the population was well adapted and a novel corn food. The major axis of genetic variation for fitness in the two environments, accounting for 51.3 per cent of the total genetic variation, was significant and revealed a strong signal of sexual antagonism, loading negatively in both environments on males but positively on females. Consequently, estimates of rwfm were negative in both environments (-0.34 and -0.73, respectively), indicating that the majority of genetic variance segregating in this population has contrasting effects on male and female fitness. The possible strengthening of the negative rwfm in this novel environment may be a consequence of no history of selection for amelioration of sexual conflict. Additional studies from a diverse range of novel environments will be needed to determine the generality of this finding.
Data from: Genetic regulatory network motifs constrain adaptation through curvature in the landscape of mutational (co)variance
Systems biology is accumulating a wealth of understanding about the structure of genetic regulatory networks, leading to a more complete picture of the complex genotype-phenotype relationship. However, models of multivariate phenotypic evolution based on quantitative genetics have largely not incorporated a network-based view of genetic variation. Here we model a set of two-node, two-phenotype genetic network motifs, covering a full range of regulatory interactions. We find that network interactions result in different patterns of mutational (co)variance at the phenotypic level (the M-matrix), not only across network motifs but also across phenotypic space within single motifs. This effect is due almost entirely to mutational input of additive genetic (co)variance. Variation in M has the effect of stretching and bending phenotypic space with respect to evolvability, analogous to the curvature of space-time under general relativity, and similar mathematical tools may apply in each case. We explored the consequences of curvature in mutational variation by simulating adaptation under divergent selection with gene flow. Both standing genetic variation (the G-matrix) and rate of adaptation are constrained by M, so that G and adaptive trajectories are curved across phenotypic space. Under weak selection the phenotypic mean at migration-selection balance also depends on M.
Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression
<p><span>The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some threats are well known and have clear methods of prevention (e.g., habitat loss can be reduced with stronger land-clearing control), whereas others are less easily addressed. One of the major current threats to koalas is chlamydial disease, which can have major impacts on individual survival and reproduction rates and can translate into population declines. Effective management strategies for the disease in the wild are currently lacking, and to date we know little about the determinants of individual susceptibility to disease. Here we investigated the genetic basis of variation in susceptibility to chlamydia using one of the most intensively studied wild koala populations. We combined data from veterinary examinations, chlamydia testing, genetic sampling and movement monitoring. Out of our sample of </span><span>342 wild koalas, 60 were found to have chlamydia.</span><span> Using genotype information on 5007 SNPs to investigate the role of genetic variation in determining disease status, we found no evidence of inbreeding depression, but a heritability of 0.11 (95%CI = 0.05 – 0.23) for the probability that koalas had chlamydia. Heritability of susceptibility to chlamydia could be relevant for future disease management, as it suggests adaptive potential for the population.</span></p>
Data from: Additive genetic variance in polyandry enables its evolution, but polyandry is unlikely to evolve through sexy or good sperm processes
Polyandry is widespread despite its costs. The sexually selected sperm hypotheses ('sexy' and 'good' sperm) posit that sperm competition plays a role in the evolution of polyandry. Two poorly studied assumptions of these hypotheses are the presence of additive genetic variance in polyandry and sperm competitiveness. Using a quantitative genetic breeding design in a natural population of Drosophila melanogaster, we first established the potential for polyandry to respond to selection. We then investigated whether polyandry can evolve through sexually selected sperm processes. We measured lifetime polyandry and offensive sperm competitiveness (P2) while controlling for sampling variance due to male x male x female interactions. We also measured additive genetic variance in egg-to-adult viability and controlled for its effect on P2 estimates. Female lifetime polyandry showed significant and substantial additive genetic variance and evolvability. In contrast, we found little genetic variance or evolvability in P2 or egg-to-adult viability. Additive genetic variance in polyandry highlights its potential to respond to selection. However, the low levels of genetic variance in sperm competitiveness suggest the evolution of polyandry may not be driven by sexy sperm or good sperm processes.
Rapid evolution of sexual size dimorphism facilitated by Y-linked genetic variance data set
<p>The three datasets were collected to study the genetic architecture of sexual size dimorphism in the seed beetle <i>Callosobruchus maculatus</i> (Quantitative_genetics_data_set), the response of sexual dimorphism to artificial selection (artificial_selection_data_set) and to isolate and quantify the effect of Y haplotypes on male body size (Y_introgression_data_set).</p> <p><u>Quantitative genetics:</u> A four generation breeding design with pedigree information for 8022 individuals and body size measurements for 7356 individuals. The breeding design and sample size of the study allows to partition genetic variances into additive autosomal, additive sex-linked, autosomal dominance and X-linked dominance variance.</p> <p><u>Artificial selection:</u> Family level phenotypic data over 10 generations of artificial selection using direct progenitors of the quantitative genetics experiment in 5 different selection regimes (random selection [C], sexually antagonistic selection, for increased sexual dimorphism [SA], sex limited selection; for small males [SL1], for large females [SL2], for large males [SL3]), each selection regime was replicated by two replicate lines, resulting in 10 selection lines.</p> <p><u>Y introgression:</u> We followed the Y lineage (paternal founder line) from the quantitative genetics experiment over the course of the artificial selection, and after the selection we introgressed each remaining Y lineage into an isogenic background, by 13 generations of backcrossing of males with the isogenic females in order to isolate the Y-linked effect on male body size.</p>
Milieu Intérieur Collection - Genetic & Environmental Determinants Of Immune Phenotype Variance
ClinicalTrials.gov study NCT03905993. IPD Sharing: YES. Countries: 0. Publications: 4.
Data from: Sexually antagonistic genetic variance for fitness in an ancestral and a novel environment
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Data from: An experimental test of the mutation-selection balance model for the maintenance of genetic variance in fitness components
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Data from: Low genetic variance in the duration of the incubation period in a collared flycatcher (Ficedula albicollis) population
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Data from: Male-bias in distributions of additive genetic, residual, and phenotypic variances of shared traits
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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.