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4,563 results for “correlations”
Data from: Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass
<p><span>Germplasm from perennial ryegrass (<i>Lolium perenne</i> L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking.</span></p> <p><span>We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by <i>de novo</i> gene prediction and functional annotation of 39,967 genes.</span></p> <p><span>GEA-GWAS revealed eight outlier loci associated with both an environmental variable and a phenotypic trait. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold-dry vs mild-wet winter and long rainy season vs long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co-association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations.</span></p> <p><span>The CANCOR test provides an integrated framework to analyze adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change.</span></p>
Correlation Analysis and Simulation Modeling of Land use Land Cover change and its Link with Land surface temperature
<p>The uploaded data is related to LULC modeling. Data consist of driving variables and correlation analysis between LST and NDVI in different LULC classes.</p>
Stability of elemental content correlates with plant resistance to soil impoverishment
<p><i>Aims</i> We investigated whether plant resistance to soil impoverishment would depend on their flexibility in taking up nutrients and on maintaining elemental stoichiometry.</p> <p><i>Methods</i> We mixed sand with grassland soil in mass proportions of 0, 10, 30, 50 and 70% to simulate soil impoverishment as caused by a gradient of desertification intensity and examined how plant nitrogen (N) uptake (<sup>15</sup>NH<sub>4</sub>NO<sub>3</sub> and NH<sub>4</sub><sup>15</sup>NO<sub>3</sub> labelling) and nutrient stoichiometry were associated with plant growth responses of a sedge (<i>Carex duriuscula</i>) and a forb (<i>Potentilla chinensis</i>).</p> <p><i>Results</i> With increasing intensity of soil impoverishment, plant biomass, cover and density decreased for <i>C. duriuscula</i>, but not for <i>P. chinensis</i>. Interestingly, uptake of both <sup>15</sup>NO<sub>3</sub><sup>-</sup> and <sup>15</sup>NH<sub>4</sub><sup>+</sup> increased for the sedge but not for the forb, with the former species showing stronger preference of NO<sub>3</sub><sup>-</sup>. However, the sedge showed decreasing nutrient contents and concentrations of phosphorus (P) and magnesium (Mg), and thus increasing stoichiometric ratios of N:P and calcium (Ca):Mg. In contrast,<i> </i>the forb maintained its biomass by showing strong stability in nutrient content, concentration and stoichiometry.</p> <p><i>Conclusions</i> Stability of N uptake and nutrient stoichiometry were associated with higher resistance to soil impoverishment of<i> </i>the forb<i> </i>than the sedge. Our study highlights the importance of stability in nutrient uptake and stoichiometry for determining plant-species resistance to nutrient-poor conditions.</p>
Evolution in alternating environments with tunable inter-landscape correlations
<p>Natural populations are often exposed to temporally varying environments. Evolutionary dynamics in varying environments have been extensively studied, though understanding the effects of varying selection pressures remains challenging. Here we investigate how cycling between a pair of statistically related fitness landscapes affects the evolved fitness of an asexually reproducing population. We construct pairs of fitness landscapes that share global fitness features but are correlated with one another in a tunable way, resulting in landscape pairs with specific correlations. We find that switching between these landscape pairs, depending on the ruggedness of the landscape and the inter-landscape correlation, can either increase or decrease steady-state fitness relative to evolution in single environments. In addition, we show that switching between rugged landscapes often selects for increased fitness in both landscapes, even in situations where the landscapes themselves are anti-correlated. We demonstrate that positively correlated landscapes often possess a shared maximum in both landscapes that allows the population to step through sub-optimal local fitness maxima that often trap single landscape evolution trajectories. Finally, we demonstrate that switching between anti-correlated paired landscapes leads to ergodic-like dynamics where each genotype is populated with nonzero probability, dramatically lowering the steady-state fitness in comparison to single landscape evolution.</p>
Taxus genotype data for "Trunk perimeter correlates with genetic bottleneck intensity and the level of genetic diversity in populations of Taxus baccata L."
<p>The data set contains microsatellite genotypes (18 loci) of Taxus baccata trees, together with the information about sampling sites.</p>
Digital image correlation (DIC) measurement of contact stiffness
<p>Measurements with digital image correlation of normal and tangential contact stiffness for ground Ti-6Al-4V interfaces suggest a linear relationship between normal contact stiffness and normal load and a linear relationship between tangential contact stiffness and tangential load. The normal contact stiffness for these surfaces is observed approximately to be inversely proportional to an equivalent surface roughness parameter, defined for two surfaces in contact. The ratio of the tangential contact stiffness to the normal contact stiffness at beginning of a load step is seen to be given approximately by the Mindlin ratio. A simple empirical model is proposed to estimate both normal and tangential contact stiffness at different loads for ground Ti-6Al-4V surfaces of known surface roughness and coefficient of friction.</p>
Cell Volume (3D) Correlative Microscopy Facilitated by Intra-Cellular Fluorescent Nanodiamonds as Multi-Modal Probes
<p>RAW files</p>
Supplementary material 1 from: Lach L, Hoffmann BD, Moir ML (2020) Native and non-native sources of carbohydrate correlate with abundance of an invasive ant. NeoBiota 63: 155-175. https://doi.org/10.3897/neobiota.63.57925
Tables S1–S6
Macroevolution of flower color patterning: biased transition rates and correlated evolution with flower size
<p>Floral pigmentation patterns can both mediate plant-pollinator interactions and modify the abiotic environment of reproductive structures. To date there have been no inquiries into the rate and directionality of macroevolutionary transitions between patterned and non-patterned petals despite their ecological importance and ubiquity across angiosperms. Petals in the Potentilleae tribe (Rosaceae) display color patterns in the ultraviolet (UV) and human-visible spectrum, or can be uniform in color (i.e., patternless). Using a phylogeny of Potentilleae, I test whether evolutionary transition rates between patterned and non-patterned petals are biased in either direction. I then examine whether UV and human-visible patterns are phylogenetically correlated and test the prediction that color patterns will evolve in concert with larger flowers if they function as guides to orient pollinators to floral rewards. I found that transition rates were biased toward petals that were uniform in color. Transition rates from patterned to uniformly-colored petals were two and six times higher than the reverse for UV and human-visible pattern, respectively. The presence of UV and human-visible pattern evolved independently from one another. However, the evolution of human-visible pattern was associated with the evolution of larger flowers but the evolution of UV pattern was correlated with the evolution of smaller flowers. I posit that the transition bias towards non-patterned flowers may reflect developmental constraints on spatial regulation of pigments required to produce floral color patterning. The correlated evolution of larger flowers and human-visible pigmentation patterns support the hypothesis that nectar or pollen guides are more likely to evolve in larger-flowered species. This work provides insight into how transition rate bias and trait correlations can shape phylogenetic patterns of floral color pattern diversity.</p>
Perceptual correlates of homosynaptic long term potentiation in human nociceptive pathways: a replication study
<p>Animal studies have shown that high-frequency stimulation (HFS) of peripheral C-fibers induces long-term potentiation (LTP) within spinal nociceptive pathways. The aim of this replication study was to assess if a perceptual correlate of LTP can be observed in humans. In 20 healthy volunteers we applied HFS to the left or right volar forearm. Before and after applying HFS we delivered single electrical test stimuli through the HFS electrode while a second electrode at the contralateral arm served as control condition. Moreover, to test the efficacy of the HFS protocol we quantified changes in mechanical pinprick sensitivity before and after HFS of the skin surrounding both electrodes. The perceived intensity was collected for both electrical and mechanical stimuli. After HFS, the perceived pain intensity elicited by the mechanical pinprick stimuli applied on the skin surrounding the HFS-treated site was significantly higher compared to control site (heterotopic effect). Furthermore, we found a higher perceived pain intensity for single electrical stimuli delivered to the HFS-treated site compared to the control site (homotopic effect). Whether the homotopic effect reflects a perceptual correlate of homosynaptic LTP remains to be elucidated.</p>
Data from: Evaluating the role of inbreeding depression in heterozygosity-fitness correlations: how useful are tests for identity disequilibrium?
Heterozygosity-fitness correlations (HFCs) have been observed for several decades, but their causes are often elusive. Tests for identity disequilibrium (ID, correlated heterozygosity between loci) are commonly used to determine if inbreeding depression is a possible cause of HFCs. We used computer simulations to determine how often ID is detected when HFCs are caused by inbreeding depression. We also used ID in conjunction with HFCs to estimate the proportion of variation (r2) in fitness explained by the individual inbreeding coefficient (F). ID was not detected in a large proportion of populations with statistically significant HFCs (sample size = 120 individuals) unless the variance of F was high (σ2(F) ≥ 0.005) or many loci were used (100 microsatellites or 1000 SNPs). For example, with 25 microsatellites, ID was not detected in 49% of populations when HFCs were caused by six lethal equivalents and σ2(F) was typical of vertebrate populations (σ2(F) ≈ 0.002). Estimates of r2 between survival and F based on ID and HFCs were imprecise unless ID was strong and highly statistically significant (P ≈ 0.01). These results suggest that failing to detect ID in HFC studies should not be taken as evidence that inbreeding depression is absent. The number of markers necessary to simultaneously detect HFC and ID depends strongly on σ2(F). Thus the mating system and demography of populations, which influence σ2(F), should be considered when designing HFC studies. ID should be used in conjunction with HFCs to estimate the correlation between fitness and F, because HFCs alone reveal little about the strength of inbreeding depression.
Data from: What drives selection on flowering time? An experimental manipulation of the inherent correlation between genotype and environment
The optimal timing of the seasonal switch from somatic growth to reproduction can depend on an individual's condition at reproduction, the quality of the environment in which it will reproduce, or both. In annual plants, vegetative size (a function of age at flowering) affects resources available for seed production, while exposure to mutualists, antagonists, and abiotic stresses in the environment (functions of Julian date of flowering), influences success in converting resources into offspring. The inherent tight correlation between age, size, and environment obscures their independent fitness contributions. We isolated the fitness effects of these factors by experimentally manipulating the correlation between age at flowering and date of flowering in Brassica rapa. We staggered the planting dates of families with differing ages at flowering to produce experimental populations in which age at flowering and date of flowering were positively-, negatively-, or uncorrelated. In all populations, plants with an early date of flowering produced more seed than those flowering late, regardless of age or size at flowering onset. The temporal environment was thus the principal driver of selection on flowering time, but its importance relative to that of age and size varied with the presence/absence of herbivores and seed predators.
Data from: Individual correlates of infectivity of influenza A virus infections in households
Background: Identifying individual correlates of infectivity of influenza virus is important for disease control and prevention. Viral shedding is used as a proxy measure of infectivity in many studies. However, the evidence for this is limited. Methods: In a detailed study of influenza virus transmission within households in 2008–12, we recruited index cases with confirmed influenza infection from outpatient clinics, and followed up their household contacts for 7–10 days to identify secondary infections. We used individual-based hazard models to characterize the relationship between individual viral shedding and individual infectivity. Results: We analyzed 386 households with 1147 household contacts. Index cases were separated into 3 groups according to their estimated level of viral shedding at symptom onset. We did not find a statistically significant association of virus shedding with transmission. Index cases in medium and higher viral shedding groups were estimated to have 21% (95% CI: -29%, 113%) and 44% (CI: -16%, 167%) higher infectivity, compared with those in the lower viral shedding group. Conclusions: Individual viral load measured by RT-PCR in the nose and throat was at most weakly correlated with individual infectivity in households. Other correlates of infectivity should be examined in future studies.
Data from: Non-invasive monitoring of temporal and spatial blood flow during bone graft healing using diffuse correlation spectroscopy
Vascular infiltration and associated alterations in microvascular blood flow are critical for complete bone graft healing. Therefore, real-time, longitudinal measurement of blood flow has the potential to successfully predict graft healing outcomes. Herein, we non-invasively measure longitudinal blood flow changes in bone autografts and allografts using diffuse correlation spectroscopy in a murine femoral segmental defect model. Blood flow was measured at several positions proximal and distal to the graft site before implantation and every week post-implantation for a total of 9 weeks (autograft n = 7 and allograft n = 10). Measurements of the ipsilateral leg with the graft were compared with those of the intact contralateral control leg. Both autografts and allografts exhibited an initial increase in blood flow followed by a gradual return to baseline levels. Blood flow elevation lasted up to 2 weeks in autografts, but this duration varied from 2 to 6 weeks in allografts depending on the spatial location of the measurement. Intact contralateral control leg blood flow remained at baseline levels throughout the 9 weeks in the autograft group; however, in the allograft group, blood flow followed a similar trend to the graft leg. Blood flow difference between the graft and contralateral legs (ΔrBF), a parameter defined to estimate graft-specific changes, was elevated at 1–2 weeks for the autograft group, and at 2–4 weeks for the allograft group at the proximal and the central locations. However, distal to the graft, the allograft group exhibited significantly greater ΔrBF than the autograft group at 3 weeks post-surgery (p < 0.05). These spatial and temporal differences in blood flow supports established trends of delayed healing in allografts versus autografts.
Data from: Ornament complexity is correlated with sexual selection: (a comment on Raia et al., "Cope's rule and the universal scaling law of ornament complexity")
Raia et al. propose that the evolution of the shape and complexity of animal ornaments (e.g., deer antlers) can be explained by interspecific variation in body size and is not influenced by sexual selection. They claim to show that ornament complexity is related to body size by an 0.25-power law and argue that this finding precludes a role for sexual selection in the evolution of ornament complexity. However, their study does not test alternative hypotheses and mismeasures antler shape allometry by omitting much of the published data. We show that an index of sexual selection (sexual size dimorphism) is positively correlated with size-corrected antler complexity and that the allometric slope of complexity is substantially greater than 0.25, contra Raia et al. We conclude that sexual selection and physical constraints both affect the evolution of antler shape.
Data from: Impacts of genetic correlation on the independent evolution of body mass and skeletal size in mammals
Mammals show a predictable scaling relationship between limb bone size and body mass. This relationship has a genetic basis which likely evolved via natural selection but it is unclear how much the genetic correlation between these traits in turn impacts their capacity to evolve independently. We selectively bred laboratory mice for increases in tibia length independent of body mass to test the hypothesis that a genetic correlation with body mass constrains evolutionary change in tibia length. Over 14 generations we produced mean tibia length increases of 11-12% while mean body mass was unchanged in selectively bred mice and random-bred controls. Using evolutionary scenarios with different selection and quantitative genetic parameters we also found that this genetic correlation impedes the rate of evolutionary change in both traits slowing increases in tibia length while preventing decreases in body mass despite the latter's negative effect on fitness. Overall results from this ongoing selection experiment suggest that parallel evolution of relatively longer hind limbs among rodents for example in the context of strong competition for resources and niche partitioning in heterogeneous environments may have occurred very rapidly on geological timescales in spite of the genetic correlation between tibia length and body mass.
Data from: The response of correlated traits following cessation of fishery-induced selection
The application of evolutionary principles to the management of fisheries has gained considerable attention recently. Harvesting of fish may apply directional or disruptive selection to key life history traits and evidence for fishery-induced evolution is growing. The traits that are directly selected upon are often correlated (genetically or phenotypically) with a suite of interrelated physiological, behavioral, and morphological characters. A question that has received comparatively little attention is whether or not, after cessation of fishery-induced selection, these correlated traits revert back to previous states. Here, we empirically examine this question. In experiments with the Atlantic silverside, Menidia menidia, we applied size-selective culling for 5 generations and then maintained the lines a further 5 generations under random harvesting. We found that some traits do return to pre-harvesting levels (e.g., larval viability), some partially recover (e.g., egg volume, size at hatch), and others show no sign of change (e.g., food consumption rate, vertebral number). Such correlations among characters could, in theory, greatly accelerate or decelerate the recovery of fish populations. These results may explain why some fish stocks fail to recover after fishing pressure is relaxed.
Data from: Population demography and heterozygosity-fitness correlations in natural guppy populations: an examination using sexually selected fitness traits
Heterozygosity-fitness correlations (HFCs) have been examined in a wide diversity of contexts, and the results are often used to infer the role of inbreeding in natural populations. Although population demography, reflected in population-level genetic parameters such as allelic diversity or identity disequilibrium, is expected to play a role in the emergence and detectability of HFCs, direct comparisons of variation in HFCs across many populations of the same species, with different genetic histories, are rare. Here, we examined the relationship between individual microsatellite heterozygosity and a range of sexually selected traits in 660 male guppies from 22 natural populations in Trinidad. Similar to previous studies, observed HFCs were weak overall. However, variation in HFCs among populations was high for some traits (although these variances were not statistically different from zero). Population-level genetic parameters, specifically genetic diversity levels (number of alleles, observed/expected heterozygosity) and measures of identity disequilibrium (g2 and heterozygosity-heterozygosity correlations) were not associated with variation in population-level HFCs. This latter result indicates that these metrics do not necessarily provide a reliable predictor of HFC effect sizes across populations. Importantly, diversity and identity disequilibrium statistics were not correlated, providing empirical evidence that these metrics capture different essential characteristics of populations. A complex genetic architecture likely underpins multiple fitness traits, including those associated with male fitness, which may have reduced our ability to detect HFCs in guppy populations. Further advances in this field would benefit from additional research to determine the demographic contexts in which HFCs are most likely to occur.
Data from: Inference of adaptive shifts for multivariate correlated traits
To study the evolution of several quantitative traits, the classical phylogenetic comparative framework consists of a multivariate random process running along the branches of a phylogenetic tree. The Ornstein-Uhlenbeck (OU) process is sometimes preferred to the simple Brownian Motion (BM) as it models stabilizing selection toward an optimum. The optimum for each trait is likely to be changing over the long periods of time spanned by large modern phylogenies. Our goal is to automatically detect the position of these shifts on a phylogenetic tree, while accounting for correlations between traits, which might exist because of structural or evolutionary constraints. We show that, in the presence shifts, phylogenetic Principal Component Analysis (pPCA) fails to decorrelate traits efficiently, so that any method aiming at finding shift needs to deal with correlation simultaneously. We introduce here a simplification of the full multivariate OU model, named scalar OU (scOU), which allows for noncausal correlations and is still computationally tractable. We extend the equivalence between the OU and a BM on a re-scaled tree to our multivariate framework. We describe an Expectation Maximization algorithm that allows for a maximum likelihood estimation of the shift positions, associated with a new model selection criterion, accounting for the identifiability issues for the shift localization on the tree. The method, freely available as an R-package (PhylogeneticEM) is fast, and can deal with missing values. We demonstrate its efficiency and accuracy compared to another state-of-the-art method (l1ou) on a wide range of simulated scenarios, and use this new framework to re-analyze recently gathered datasets on New World Monkeys and Anolis lizards.
Data from: Evolutionary history and genetic parallelism affect correlated responses to evolution
We investigated the relationship between genomic and phenotypic evolution among replicate populations of Escherichia coli evolved for 1000 generations in four different environments. By re-sequencing evolved genomes, we identified parallel changes in genes encoding transcription regulators within and between environments. Depending on both the environment and the altered gene, genetic parallelism at the gene level involved mutations that either repeatedly affected identical codons or domains or were more widely distributed within the relevant genes. Evolved clones were characterized by parallel phenotypic changes in their respective evolution environments but also in the three alternative environments. Phenotypic parallelism for both traits was high for clones that evolved in the same environment, even in the absence of genetic parallelism. By contrast, clones that evolved in different environments revealed a higher parallelism in correlated responses when they shared mutated genes. Altogether, this work shows that after an environmental change or the colonization of a new habitat, similar ecological performances might be expected for individuals that shared mutated genes or experienced similar past selective pressures.
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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.