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187 results for “genetic correlations”
Spatial genetic differentiation correlates with species assemblage turnover across tropical reef fish lineages
<p><strong>Aim:</strong> Evaluating the similarity of diversity patterns across micro- to macroevolutionary scales in natural communities, such as species-genetic diversity correlations (SGDC), may inform on processes shaping community assembly. However, whether SGDCs not only hold across communities but also across lineages has never been explored so far. Here we investigated SGDCs across co-distributed taxa for different spatial components (α, β, γ), and formally tested the influence of dispersal traits on β SGDCs. <strong>Location:</strong> Western Indian Ocean</p> <p><strong>Time period:</strong> 2016–2017</p> <p><strong>Major taxa studied:</strong> Tropical reef fish species with contrasting dispersal traits</p> <p><strong>Methods:</strong> Using ddRADseq single nucleotide polymorphism (SNP) data for 20 tropical reef fishes and distribution data of 2,446 species belonging to 12 families, we analysed the correlations between within-species genetic diversity and within-family species diversity (i.e., lineage diversity) for the three spatial components (α, β, γ SGDCs). We then related the strength of β-SGDCs per species to proxies of larval dispersal abilities.</p> <p><strong>Results:</strong> We detected positive and significant lineage-based SGDC only for the β component, i.e., the families showing the greatest level of species turnover among sites contains the species with the greatest levels of genetic differentiation. We showed that the Monsoon drift mainly explained the β diversity patterns at both intraspecific and interspecific levels. Higher β-SGDCs were found for species with short pelagic larval duration and weak larval swimming capacity.</p> <p><strong>Main conclusions:</strong> Our study reveals a strong correlation between genetic and species β diversity, a result explained by the presence of a 'soft' barrier and mediated by larval dispersal processes. This suggests that vicariance and dispersal limitation are major processes shaping β-diversity patterns from microevolutionary to macroevolutionary scales in tropical reef fishes.</p>
Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake
<p class="MsoNormal">Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation reflecting long-term impacts of genetic drift, yet this widely used approach has been questioned in the genomics era. Here we leverage a chromosome-level assembly and whole genome resequencing data (N=110 individuals) from an endangered rattlesnake (<em>Sistrurus catenatus</em>) to evaluate the relationship between genome-wide neutral and functional diversity over long- and short-term timescales. As predicted for populations at long-term equilibrium, we found a positive correlation between population-level estimates of neutral genetic diversity (π) and the mean number of highly detrimental loss-of-function mutations, and a negative relationship between neutral genetic diversity and an estimate of genetic load. In contrast, we found only a weak, non-significant positive correlation between levels of neutral and adaptive variation. Additional analyses using estimates of drift at more recent time scales (> 100 generations) show expected correlations between both measures of genetic load, but a lack of a significant correlation with levels of adaptive variation. Individual-based demographic metrics that capture drift impacts over recent time scales confirm these results. Broadly, our results confirm that estimates of diversity and demography based on neutral genetic variation provide an accurate measure of a key component of genetic erosion – genetic load – in populations of a threatened vertebrate. Our findings also provide nuance to the neutral-functional diversity controversy by demonstrating that neutral genetic diversity is useful in predicting some, but not all, components of functional genetic diversity.</p>
Association of Host Genetics With Vaccine Efficacy and Study of Immune Correlates of Risk From a Tetravalent Dengue Vaccine
ClinicalTrials.gov study NCT02827162. IPD Sharing: YES. Countries: 1. Publications: 2.
Data from: Extra-pair paternity correlates with genetic diversity, but not breeding density, in a Neotropical passerine, the Black Catbird
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Data from: Genetic independence of naturally correlated variation in resistance to endemic and novel pathogens
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Data for: Limited host availability disrupts the genetic correlation between virulence and transmission
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Data from: Enhanced correlations of EST-SSR based genetic distance with hybrid performance, specific hybridizing ability and heterosis using effect-increasing and effect-decreasing alleles: a case study in Eucalyptus L'Hér
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An ecological-evolutionary investigation of phenotypic, genetic, and environmental variation and correlations among reproductive traits of tall goldenrod (<em>Solidago altissima</em>)
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Leg length and bristle density both necessary for water surface locomotion are genetically correlated in water striders
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Spatial genetic differentiation correlates with species assemblage turnover across tropical reef fish lineages
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Data from: Correlations among genetic, epigenetic, and phenotypic variation of Phragmites australis along latitudes
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Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake
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Data from: Genetic correlations among developmental and contextual behavioral plasticity in Drosophila melanogaster
Correlations among traits, including behaviors, are important because traits that are genetically correlated may not evolve independently. Recently, behavioral correlations research has expanded to include correlations not only in mean-level behaviors, but also in behavioral plasticity, i.e., the degree to which individuals change their behavior in response to environmental stimuli. Positive correlations among behavioral plasticities would imply that individuals or genotypes that are behaviorally plastic in one way may also be plastic in other ways; negative correlations could imply tradeoffs. Here, we examine aversive odor conditioning (learning) at two time points, and plasticity in pupation site selection behavior across substrates, in a panel of Drosophila genotypes. These behaviors represent different types of behavioral plasticity: contextual plasticity describes behavioral responses to stimuli that are currently present, while developmental plasticity describes behavioral responses to remembered experiences with stimuli in the recent past. We find that learning scores and plasticity in pupation site selection behavior are positively genetically correlated, representing the first example of a genetic correlation between developmental and contextual plasticity. These findings imply that ecological and evolutionary theories focusing on variation in a single dimension of behavioral plasticity may be incomplete.
Strong and weak cross-sex correlations govern the quantitative-genetic architecture of social group choice in Drosophila melanogaster
<p><span><span><span><span><span><span><span><span><span><span><span>When genotypes differ in niche-constructing traits, genotypes are expected to differ in which environments they experience, providing a novel causal relationship between genotypes, environments, and behavior. Such genetic variation in niche construction (or, more precisely, environment construction) is predicted to be especially important for social environments, yet the quantitative-genetic parameters governing such variation is still poorly understood. Here, we examine genetic variation and cross-sex genetic correlations for social environment-constructing behaviors. We focus on whether genetic variation in patch use—the tendency to spend time near food patches where conspecifics may be present—and group-size preference—the specific group size chosen when individuals are affiliating—is correlated or decoupled across sexes in the fruit fly, <i>Drosophila melanogaster</i>. Across three choice treatments, we find genotype and sex differences in how much time individuals spend near patches, and which group sizes they prefer. We find that the genetic basis of patch use is strongly coupled across sexes, whereas the genetic basis of group-size preference is completely <i>de</i>coupled across sexes. We discuss how these findings augment and complicate our understanding of the evolutionary genetics of social behaviors.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Oceanographic connectivity and environmental correlates of genetic structuring in Atlantic herring in the Baltic Sea
Marine fish often show little genetic structuring in neutral marker genes, and Atlantic herring (Clupea harengus) in the Baltic Sea are no exception; historically, very low levels of population differentiation (FST ≈ 0.002) have been found, despite a high degree of interpopulation environmental heterogeneity in salinity and temperature. Recent exome sequencing and SNP studies have however shown that many loci are under selection in this system. Here, we combined population genetic analyses of a large number of transcriptome-derived microsatellite markers with oceanographic modelling to investigate genetic differentiation and connectivity in Atlantic herring at a relatively fine scale within the Baltic Sea. We found evidence for weak but robust and significant genetic structuring (FST = 0.008) explainable by oceanographic connectivity. Genetic differentiation was also associated with site differences in temperature and salinity, with the result driven by the locus Her14 which appears to be under directional selection (FST = 0.08). The results show that Baltic herring are genetically structured within the Baltic Sea, and highlight the role of oceanography and environmental factors in explaining this structuring. The results also have implications for the management of herring fisheries, the most economically important fishery in the Baltic Sea, suggesting that the current fisheries management units may be in need of revision.
Data from: Genetic correlations and little genetic variance for reaction norms may limit potential for adaptation to pollution by ionic and nanoparticulate silver in a whitefish (Salmonidae)
For natural populations to adapt to anthropogenic threats, heritable variation must persist in tolerance traits. Silver nanoparticles, the most widely used engineered nanoparticles, are expected to increase in concentrations in freshwaters. Little is known about how these particles affect wild populations, and whether genetic variation persists in tolerance to permit rapid evolutionary responses. We sampled wild adult whitefish and crossed them in vitro full factorially. In total, 2896 singly raised embryos of 48 families were exposed to two concentrations (0.5 μg/L; 100 μg/L) of differently sized silver nanoparticles or ions (silver nitrate). These doses were not lethal; yet higher concentrations prompted embryos to hatch earlier and at a smaller size. The induced hatching did not vary with nanoparticle size and was stronger in the silver nitrate group. Additive genetic variation for hatching time was significant across all treatments, with no apparent environmental dependencies. No genetic variation was found for hatching plasticity. We found some treatment-dependent heritable variation for larval length and yolk volume, and one instance of additive genetic variation for the reaction norm on length at hatching. Our assessment suggests that the effects of silver exposure on additive genetic variation vary according to trait and silver source. While the long-term fitness consequences of low-level silver exposure on whitefish embryos must be further investigated to determine whether it is, in fact, detrimental, our results suggest that the evolutionary potential for adaptation to these types of pollutants may be low.
Data from: Intralocus tactical conflict: genetic correlations between fighters and sneakers of the dung beetle Onthophagus taurus
Males and females differ in their phenotypic optima for many traits, and since the majority of genes are expressed in both sexes, some alleles can be beneficial to one sex but harmful to the other (intralocus sexual conflict; ISC). ISC theory has recently been extended to intrasexual dimorphisms, where certain alleles may have opposite effects on the fitness of males of different morphs that employ alternative reproductive tactics (intralocus tactical conflict; ITC). Here we use a half-sib breeding design to investigate the genetic basis for ISC and ITC in the dung beetle Onthophagus taurus. We found positive heritabilities and intersexual genetic correlations for almost all traits investigated. Next, we calculated the intrasexual genetic correlation between males of different morphs for horn length, a sexually selected trait, and compared it to intrasexual correlations for naturally selected traits in both sexes. Intrasexual genetic correlations did not differ significantly between the sexes or between naturally and sexually selected traits, failing to support the hypothesis that horns present a reduction of intrasexual genetic correlations due to ITC. We discuss the implications for the idea of developmental reprogramming between male morphs, and emphasize the importance of genetic correlations as constraints for the evolution of dimorphisms.
Data from: A meta-analysis reveals a positive correlation between genetic diversity metrics and environmental status in the long-lived seagrass Posidonia oceanica
The seagrass Posidonia oceanica is a key engineering species structuring coastal marine systems throughout much of the Mediterranean basin. Its decline is of concern, leading to the search for short- and long-term indicators of seagrass health. Using ArcGIS maps from a recent, high-resolution (1–4 km) modelling study of 18 disturbance factors affecting coastal marine systems across the Mediterranean (Micheli et al. 2013, http://globalmarine.nceas.ucsb.edu/mediterranean/), we tested for correlations with genetic diversity metrics (allelic diversity, genotypic/clonal diversity and heterozygosity) in a meta-analysis of 56 meadows. Contrary to initial predictions, weak but significantly positive correlations were found for commercial shipping, organic pollution (pesticides) and cumulative impact. This counterintuitive finding suggests greater resistance and resilience of individuals with higher genetic and genotypic diversity under disturbance (at least for a time) and/or increased sexual reproduction under an intermediate disturbance model. We interpret the absence of low and medium levels of genetic variation at impacted locations as probable local extinctions of individuals that already exceeded their resistance capacity. Alternatively, high diversity at high-impact sites is likely a temporal artefact, reflecting the mismatch with pre-environmental impact conditions, especially because flowering and sexual recruitment are seldom observed. While genetic diversity metrics are a valuable tool for restoration and mitigation, caution must be exercised in the interpretation of correlative patterns as found in this study, because the exceptional longevity of individuals creates a temporal mismatch that may falsely suggest good meadow health status, while gradual deterioration of allelic diversity might go unnoticed.
Data from: Developmental instability is genetically correlated with phenotypic plasticity, constraining heritability, and fitness
Although adaptive plasticity would seem always to be favored by selection, it occurs less often than expected. This lack of ubiquity suggests that there must be trade-offs, costs, or limitations associated with plasticity. Yet, few costs have been found. We explore one type of limitation, a correlation between plasticity and developmental instability, and use quantitative genetic theory to show why one should expect a genetic correlation. We test that hypothesis using the Landsberg erecta × Cape Verde Islands recombinant inbred lines (RILs) of Arabidopsis thaliana. RILs were grown at four different nitrogen (N) supply levels that span the range of N availabilities previously documented in North American field populations. We found a significant multivariate relationship between the cross-environment trait plasticity and the within-environment, within-RIL developmental instability across 13 traits. This genetic covariation between plasticity and developmental instability has two costs. First, theory predicts diminished fitness for highly plastic lines under stabilizing selection, because their developmental instability and variance around the optimum phenotype will be greater compared to nonplastic genotypes. Second, empirically the most plastic traits exhibited heritabilities reduced by 57% on average compared to nonplastic traits. This demonstration of potential costs in inclusive fitness and heritability provoke a rethinking of the evolutionary role of plasticity.
Data from: Deciphering the drivers of negative species-genetic diversity correlation in Alpine amphibians
The evolutionary and ecological importance of neutral and adaptive genetic diversity is widely recognized. Nevertheless, genetic diversity is rarely assessed for conservation planning, which often implicitly assumes a positive correlation between species and genetic diversity. Multiple drivers can cause the co-variation between the genetic diversity of one species and the richness of the whole communities, and explicit tests are needed to identify the processes that can determine species-genetic diversity correlations (SGDC). Here we tested whether intrapopulation genetic diversity (at neutral loci) and species richness co-vary in the amphibian communities of a southern Alpine region (Trentino, Italy), using the common frog (Rana temporaria) as focal species for the study of genetic diversity. We also analyzed ecological similarity, niche overlap and interspecific interactions between the species, to unravel the processes determining SGDC. The neutral genetic diversity of common frogs was negatively related to species richness. The negative SGDC was probably due to an opposite influence of environmental gradients on the two levels of biodiversity, since the focal species and the other amphibians differ in ecological preferences, particularly in terms of thermal optimum. Conversely, we did not find evidence for a role of interspecific interactions in the negative SGDC. Our findings stress that species richness cannot be used as a universal proxy for genetic diversity, and only combining SGDC with analyses on the determinants of biodiversity can allow to identify the processes determining the relationships between genetic and species diversity.
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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.