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188 results for “explained variation”
Five genetic variants explain over 70% of hair coat pheomelanin intensity variation in purebred and mixed breed domestic dogs - Supporting information
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Data from: Variation in plant functional traits is best explained by the species identity: stability of trait based species ranking across meadow management regimes
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Isolation by geographical distance after release from Pleistocene refugia explains genetic and phenotypic variation in Xylotrupes siamensis (Coleoptera: Scarabaeidae)
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Host energetics explain variation in parasite productivity across hosts and ecosystems
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Data from: Host sex and age typically explain variation in parasitism of Rock Ptarmigan: implications for identifying determinants of exposure and susceptibility
<p>Measures of parasitism often differ between hosts. This variation is thought due in part to age or sex differences in exposure to parasites and/or susceptibility to parasitism. We assessed how often age or sex biases in parasitism were found using a large, multi-year (2006 – 2017) dataset of 12 parasite species of Icelandic Rock Ptarmigan (<em>Lagopus muta</em>). We found host traits (i.e. age and/or sex) accounted for significant variation in abundance of 11 of the 12 parasite species. We often found increased abundance among juvenile hosts, although significant adult biases were observed for three parasite species. Additionally, higher levels of parasitism by many species were observed for female hosts, contrary to frequent male biases in parasitism reported for other vertebrates. Abundance of six parasite species was best explained by interactions between host age and sex; some degree of decrease in abundance with host age was present for both male and female hosts for four of those parasite species. We consider various host and parasite traits that could account for observed singular and repeated patterns of age and/or sex biases in parasitism (e.g. age- and sex-related grouping behaviours, age-specific mortality in relation to parasitism, acquisition of greater immunity with age). This work provides a foundation for future studies investigating age-related differences in acquired immunity and age-specific parasite-mediated mortality for males and females, as well as studies on interactions between co-infecting parasite species.</p>
Data from: Plant host identity and soil macronutrients explain little variation in sapling endophyte community composition: is disturbance an alternative explanation?
1. Bacterial endophytes may be fairly host specific; nonetheless, an important subset of taxa may be shared among numerous host species forming a community-wide core microbiome. Moreover, other key factors, particularly the supply of limiting macronutrients and disturbances, may supersede the importance of host identity. 2. We tested the following four non-mutually exclusive hypotheses: 1. The Host Identity Hypothesis: endophytes vary substantially among different host plant species. 2. The Core Microbiome Hypothesis: a subset of microbial taxa will be shared among all host plant species. 3. The Soil Resource Supply Hypothesis: endophytes vary substantially among habitats with experimentally elevated levels of macronutrients. 4. The Disturbance-Disruption Hypothesis: disturbances created by the periodic application of antibiotics structure bacterial endophyte communities. 3. We tested these hypotheses by characterizing endophytes using high-throughput sequencing among seedlings of five phylogenetically diverse tree species nested within a long-term, full factorial nitrogen, phosphorus, and potassium soil fertilization experiment. We artificially disturbed one of our focal species by applying antibiotics every 10-14 days for 29 months within the soil (N,P,K) fertilization experiment. 4. While we detected a significant effect of host identity and soil nutrient additions, together they explained little variation in endophyte community composition (< 10%). We found unequivocal evidence for a core microbiome shared by all species. Specifically, we found nine OTUs were present among 95% or more of all control saplings, representing a third of the total reads. These bacterial taxa belonged to the Actinobacteria. 5. In contrast, disturbance (antibiotics) explained more endophyte variation than all nutrient addition combinations combined and twice the variation explained by host identity for all five tree species. Synthesis: Our results challenge the idea that host identity is a primary filter shaping bacterial endophyte communities; this suggests that many of the same bacterial taxa occur inside plant hosts even if those host plants are phylogenetically diverse. Moreover, we documented a distinct core microbiome shared among our five focal tree species. Finally, we found that disturbance was an important driver of microbial community composition, which parallels the importance of disturbance in other areas of community ecology.
Data from: Can variation in standard metabolic rate explain context-dependent performance of farmed salmon offspring?
Escaped farmed Atlantic salmon interbreed with wild Atlantic salmon, leaving offspring that often have lower success in nature than pure wild salmon. On top of this, presence of farmed salmon descendants can impair production of wild type recruits. We hypothesize that both these effects connect with farmed salmon having acquired higher standard metabolic rates (SMR, the energetic cost of self-maintenance) during domestication. Furthermore, fitness related advantages of phenotypic traits associated with both high SMR and farmed salmon (e.g. social dominance) depend on environmental conditions, such as food availability. We hypothesize that farmed offspring have an advantage at high food availability due to e.g. dominance behavior but suffer increased risks of starvation when food is scarce because this behavior is energy-demanding. To test these hypotheses, we first compare embryo SMR of pure farmed, farmed-wild hybrids and pure wild offspring. Next, we test early life performance (in terms of survival and growth) of hybrids relative to that of their wild half-siblings, as well as their competitive abilities, in semi-natural conditions of high and low food availability. Finally, we test how SMR affects early life performance at high and low food availability. We find inconclusive support for the hypothesis that domestication has induced increased SMR. Further, wild and hybrid juveniles had similar survival and growth in the semi-natural streams. Yet, the presence of hybrids led to decreased survival of their wild half-siblings. Contrary to our hypothesis about context-dependency, these effects were not modified by food availability. However, wild juveniles with high SMR had decreased survival when food was scarce, but there was no such effect at high food availability. This study provides further proof that farmed salmon introgression may compromise the viability of wild salmon populations. We cannot, however, conclude that this is connected to alterations in the metabolic phenotype of farmed salmon.
Data from: A novel nonparametric measure of explained variation for survival data with an easy graphical interpretation
Introduction: For survival data the coefficient of determination cannot be used to describe how good a model fits to the data. Therefore, several measures of explained variation for survival data have been proposed in recent years. Methods: We analyse an existing measure of explained variation with regard to minimisation aspects and demonstrate that these are not fulfilled for the measure. Results: In analogy to the least squares method from linear regression analysis we develop a novel measure for categorical covariates which is based only on the Kaplan-Meier estimator. Hence, the novel measure is a completely nonparametric measure with an easy graphical interpretation. For the novel measure different weighting possibilities are available and a statistical test of significance can be performed. Eventually, we apply the novel measure and further measures of explained variation to a dataset comprising persons with a histopathological papillary thyroid carcinoma. Conclusion: We propose a novel measure of explained variation with a comprehensible derivation as well as a graphical interpretation, which may be used in further analyses with survival data.
Data from: Functional traits explain variation in plant life history strategies
Ecologists seek general explanations for the dramatic variation in species abundances in space and time. An increasingly popular solution is to predict species distributions, dynamics and responses to environmental change based on easily measured anatomical and morphological traits. Trait-based approaches assume that simple functional traits influence fitness and life history evolution, but rigorous tests of this assumption are lacking because they require quantitative information about the full life-cycles of many species representing different life histories. Here we link a global traits database with empirical matrix population models for 222 species and report strong relationships between functional traits and plant life histories. Species with large seeds, long-lived leaves, or dense wood have slow life histories, with mean fitness (i.e. population growth rates) more strongly influenced by survival than by growth or fecundity, compared to fast life history species with small seeds, short-lived leaves, or soft wood. In contrast to measures of demographic contributions to fitness based on whole life-cycles, analyses focused on raw demographic rates may underestimate the strength of association between traits and mean fitness. Our results help establish the physiological basis for plant life history evolution and show the potential for trait-based approaches in population dynamics.
Data from: Genetic diversity does not explain variation in extra-pair paternity in multiple populations of a songbird
Many songbirds are socially monogamous but genetically polyandrous, mating with individuals outside their pair bonds. Extra-pair paternity (EPP) varies within and across species, but reasons for this variation remain unclear. One possible source of variation is population genetic diversity, which has been shown in interspecific meta-analyses to correlate with EPP but which has limited support from intraspecific tests. Using eight populations of the genetically polyandrous red-winged blackbird (Agelaius phoeniceus), including an island population, we investigated whether population-level differences in genetic diversity led to differences in EPP. We first measured genetic diversity over ten microsatellite loci and found, as predicted, low genetic diversity in the island population. Additional structure analyses with multilocus genotypes and mtDNA showed the island population to be distinct from the continental populations. However, the island population's EPP rate fell in the middle of the continental populations' distribution, while the continental populations themselves showed significant variation in EPP. This result suggests that genetic diversity by itself is not a predictor of EPP rate. We discuss reasons for the departure from previous results, including hypotheses for EPP that do not solely implicate female-driven behavior.
Data from: Linking genetic merit to sparse behavioral data: does behavior explain genetic variation for maternal care in Soay sheep?
Wild quantitative genetic studies have focused on a subset of traits (largely morphological and life-history), with others, such as behaviors, receiving much less attention. This is because it is challenging to obtain sufficient data, particularly for behaviors involving interactions between individuals. Here, we explore an indirect approach for pilot investigations of the role of genetic differences in generating variation in parental care. Variation in parental genetic effects for offspring performance is expected to arise from among-parent genetic variation in parental care. Therefore, we used the animal model to predict maternal breeding values for lamb growth and used these predictions to select females for field observation, where maternal and lamb behaviors were recorded. Higher predicted maternal breeding value for lamb growth was associated with greater suckling success, but not with any other measures of suckling behavior. Though our work cannot explicitly estimate the genetic basis of the specific traits involved, it does provide a strategy for hypothesis generation and refinement, that we hope could be used to justify data collection costs needed for confirmatory studies. Here results suggest that behavioral genetic variation is involved in generating maternal genetic effects on lamb growth in Soay sheep. Though important caveats and cautions apply, our approach may extend the ability to initiate more genetic investigations of difficult-to-study behaviours and social interactions in natural populations.
Data from: Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics
Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity, and persistence. We used riverscape genetics modeling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population specific and pairwise FST) within five metapopulations (79 populations, 4,583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events, and summer mean flow) often explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g., basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.
Data from: Nest shape explains variation in sexual dichromatism in New World blackbirds
Following Charles Darwin, research on sexual dichromatism has long focused on sexual selection driving ornamentation in males. However, Alfred Russel Wallace proposed another explanation – that dichromatism evolves as a result of selection favoring crypsis in incubating females. Many recent studies suggest that evolutionary changes in sexual dichromatism often result from changes in female, in addition to male, plumage, yet the evolutionary mechanisms driving changes in female plumage remain largely unexplained. To test Wallace's hypothesis, we examined variation in sexual dichromatism and nest shape, a proxy for predation risk, among New World blackbirds (Aves: Icteridae). Phylogenetic models reveal an evolutionary correlation between sexual dichromatism and nest exposure. Specifically, we found that transitions in monochromatic lineages with exposed nests toward either concealed nests or dichromatism were common. Although this evidence supports Wallace's hypothesis that female incubation leads to selection for crypsis or concealment, we also found that transitions to monomorphism were common, even in lineages with exposed nests – a result suggestive of a role for positive selection on female ornamentation. These patterns of plumage evolution support a growing body of work emphasizing the importance of developing and testing hypotheses to explain evolutionary changes in female, as well as male, ornamentation.
Data from: Dispersal propensity, but not flight performance, explains variation in dispersal ability
Enhanced dispersal ability may lead to accelerated range expansion and increased rates of population establishment, thereby affecting population genetic structure and evolutionary potential. Morphological, behavioural and physiological traits that characterize dispersive individuals from residents are poorly understood for many invertebrate systems, especially in non-polymorphic pterygote species. Here we examined phenotypic differences between dispersal-prone and philopatric individuals from repeated mark-release-recapture (MRR) experiments using an invasive agricultural pest, Ceratitis capitata. Comprehensive morphometric assessment and subsequent minimal adequate modelling using an information theoretic approach identified thorax mass : body mass ratio as a key predictor of disperser flies under semi-natural conditions. Performance differences in flight ability were then examined under controlled laboratory conditions to assess whether greater thorax mass : body mass ratio was associated with enhanced flight ability. The larger thorax : body mass ratio was associated with measurable differences in mean flight duration, most predominantly in males, and also by their willingness to disperse, scored as the number and duration of voluntary flights. No other measures of whole-animal flight performance (e.g. mean and peak vertical force, total or maximum flight duration) differed. Variation in voluntary behaviour may result in significant alterations of movement behaviour and realized dispersal in nature. This phenomenon may help explain intraspecific variation in the dispersal ability of insects.
Data from: Broad-scale variation in sexual dichromatism in songbirds is not explained by sex differences in exposure to predators during incubation
The evolution of sexual dichromatism provoked one of the greatest disagreements between Charles Darwin and Alfred Russel Wallace. According to Darwin the main driving force is sexual selection, whereby choosy females prefer showy males, leading to the evolution of conspicuous male plumage. On the other hand, Wallace suggested that dichromatism may arise because nest predation favors more cryptic females. To test the role of natural selection in the evolution of dichromatism we combined quantitative data on differences in parental share in nest attentiveness (representing the strength of natural selection on males vs. females) with spectrophotometric measurements of dichromatism in 412 species of songbirds from 69 families. We expected to find stronger dichromatism in open-nesting species with more divergent parental roles and in body parts exposed during incubation. Dichromatism was not related to the differences in parental share during incubation, but it was most pronounced in lekking species, migrants, and small species. Our results thus suggest that Wallace's hypothesis is not able to explain broad-scale variation in the dichromatism of songbirds, but point to a role for sexual selection, mutual mate choice, and migration strategy in shaping the extraordinary variation in dichromatism exhibited by songbirds.
Data from: Does multiple paternity explain phenotypic variation among offspring in wild boar?
During pregnancy, littermates compete to extract maternal resources from the placenta. Unequal extraction of resources leads to developmental differences among offspring and thus within-litter variation in offspring mass. Because competition among littermates can be stronger among half-sibs, multiple paternity may represent an adaptive strategy allowing females to increase within-litter phenotypic variation among offspring when facing variable environments. Wild boar (Sus scrofa) females produce large litters with diversified offspring in terms of body mass. Additionally, multiple paternity within a litter has been observed in this promiscuous species. One can hypothesize that multiple paternity represents the mechanism by which females increase within-litter phenotypic variation. Combining long-term monitoring data with paternity analyses in a wild boar population, we tested whether the increase in the number of fathers within a litter explained the increase in within-litter variation in offspring mass observed in large litters. We showed that heavy females mated earlier during the rut, produced larger litters with a higher number of fathers and more variable fetus mass than lighter females. Within-litter variation of offspring mass increased with gestation stage and litter size, suggesting differential allocation of maternal resource among offspring in utero. However, we found only a weak paternal effect on offspring mass and no direct effect of the number of fathers on the within-litter variation in offspring mass. These results indicate that differential maternal allocation to offspring during pregnancy is unlikely related to paternal identity in this species.
Data from: Density-mediated carry-over effects explain variation in breeding output across time in a seasonal population
In seasonal environments, where density dependence can operate throughout the annual cycle, vital rates are typically considered to be a function of the number of individuals at the beginning of each season. However, variation in density in the previous season could also cause surviving individuals to be in poor physiological condition, which could carry over to influence individual success in the following season. We examine this hypothesis using replicated populations of Drosophila melanogaster, the common fruitfly, over 23 non-overlapping generations with distinct breeding and non-breeding seasons. We found that the density at the beginning of the non-breeding season negatively affected the fresh weight of individuals that survived the non-breeding season and resulted in a 25% decrease in per capita breeding output among those that survived to the next season to breed. At the population level, per capita breeding output was best explained by a model that incorporated density at the beginning of the previous non-breeding season (carry-over effect, COE) and density at the beginning of the breeding season. Our results support the idea that density-mediated COEs are critical for understanding population dynamics in seasonal environments.
Morphology of the limb, shell, and head explain the variation in performance and ecology across 14 turtle taxa (12 species)
<p>Because morphology directly influences an organism's ability to utilize its habitat and dietary resources, it also influences fitness. Comparing the relationship between morphology, performance, and ecology is fundamental to understand how organisms evolve to occupy a wide range of habitats and diets. In turtles, studies have documented important relationships between morphology, performance, and ecology, but none were field based or considered limb, shell, and head morphology simultaneously. We compare morphology, performance, and ecology of 14 turtle taxa (12 species) in Mexico that range in their affinity to water and in their diet. We took linear measurements of limb, shell, and head variables, measured maximum swimming speed, maximum bite force, how often turtles were encountered on land, and used stable isotopes to assess trophic position. We use these data to test three hypotheses. The first, that morphology, performance, and ecology covary. The second, that limb and shell variables, like hand length, correlate to swim speed and the percent time spent on land. The third, was that that head variables, like head width, correlate to bite force and stable isotopes. We find support for these hypotheses and provide the first evidence that morphology influences performance and ecology in turtles in the field.</p>
Data from: Can variation in standard metabolic rate explain context-dependent performance of farmed salmon offspring?
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Data from: Broad-scale variation in sexual dichromatism in songbirds is not explained by sex differences in exposure to predators during incubation
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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.