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118 results for “Environmental selection”
Data from: Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation
Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates.
Data from: The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales
The evaluation of the molecular signatures of selection in species lacking an available closely related reference genome remains challenging, yet it may provide valuable fundamental insights into the capacity of populations to respond to environmental cues. We screened 25 native populations of the tree species Frangula alnus subsp. alnus (Rhamnaceae), covering three different geographical scales, for 183 annotated single-nucleotide polymorphisms (SNPs). Standard population genomic outlier screens were combined with individual-based and multivariate landscape genomic approaches to examine the strength of selection relative to neutral processes in shaping genomic variation, and to identify the main environmental agents driving selection. Our results demonstrate a more distinct signature of selection with increasing geographical distance, as indicated by the proportion of SNPs (i) showing exceptional patterns of genetic diversity and differentiation (outliers) and (ii) associated with climate. Both temperature and precipitation have an important role as selective agents in shaping adaptive genomic differentiation in F. alnus subsp. alnus, although their relative importance differed among spatial scales. At the 'intermediate' and 'regional' scales, where limited genetic clustering and high population diversity were observed, some indications of natural selection may suggest a major role for gene flow in safeguarding adaptability. High genetic diversity at loci under selection in particular, indicated considerable adaptive potential, which may nevertheless be compromised by the combined effects of climate change and habitat fragmentation.
Selection and application of agri-environmental indicators to assess potential technologies for nutrient recovery in agriculture (Data Sets)
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Data for: Estimating density dependence, environmental variance and long-term selection on a stage-structured life history
<p>We model growth of a density-dependent stage-structured population undergoing small or moderate fluctuations around a deterministically stable equilibrium in a stochastic environment, assuming that a weighted sum of stage abundances, N, exerts density dependence on the stage-specific vital rates of survival and reproduction. We approximate the dynamics of N as a onedimensional stochastic process with three key parameters: the density-independent growth rate and the net density dependence and environmental variance in the life history. Comparisons of populations and species with different life histories are facilitated using the key parameters, which we show how to estimate from long-term demographic data on fluctuations in the vital rates. We also show that life history evolution is a stochastic maximization of a simple function of the key parameters. Elements in the long-term selection gradient acting on the life history can be expressed as sensitivities of this function with respect to density-independent, density-dependent, and stochastic components of the vital rates. Using years of demographic data on a great tit population, we estimate the key demographic parameters, which accurately predict the observed mean, coefficient of variation, and fluctuation rate of N, and also evaluate the long-term selection gradient on the population.</p>
Supplementary material 2 from: Nkuna KV, Visser V, Wilson JRU, Kumschick S (2018) Global environmental and socio-economic impacts of selected alien grasses as a basis for ranking threats to South Africa. NeoBiota 41: 19-65. https://doi.org/10.3897/neobiota.41.26599
Figure S2 : Explanation note: The impact magnitude of the 48 studied alien grasses across different habitats. The impact magnitudes on the x-axis are the least-square means of the impact scores as derived from a cumulative link mixed effects model. On the y-axis are the habitat types impacted by alien grasses and in brackets is the number of species with records in that habitat. The points represent the impact magnitudes and the error bars represent 95 % confidence intervals. Letters on the right side of the confidence intervals are level groupings indicating no significant differences among the habits. Comparisons are Tukey adjusted.
Supplementary material 1 from: Nkuna KV, Visser V, Wilson JRU, Kumschick S (2018) Global environmental and socio-economic impacts of selected alien grasses as a basis for ranking threats to South Africa. NeoBiota 41: 19-65. https://doi.org/10.3897/neobiota.41.26599
Supplementary material 1 from: Nkuna KV, Visser V, Wilson JRU, Kumschick S (2018) Global environmental and socio-economic impacts of selected alien grasses as a basis for ranking threats to South Africa. NeoBiota 41: 19-65. https://doi.org/10.3897/neobiota.41.26599
Data from: What determines prey selection in owls? Roles of prey traits, prey class, environmental variables, and taxonomic specialization
Ecological theory suggests that prey size should increase with predator size, but this trend may be masked by other factors affecting prey selection, such as environmental constraints or specific prey preferences of predator species. Owls are an ideal case study for exploring how predator body size affects prey selection in the presence of other factors due to the ease of analyzing their diets from owl pellets and their widespread distributions, allowing interspecific comparisons between variable habitats. Here, we analyze various dimensions of prey resource selection among owls, including prey size, taxonomy (i.e., whether or not particular taxa are favored regardless of their size), and prey traits (movement type, social structure, activity pattern, and diet). We collected pellets of five sympatric owl species (Athene noctua, Tyto alba, Asio otus, Strix aluco, and Bubo bubo) from 78 sites across the Mediterranean Levant. Prey intake was compared between sites, with various environmental variables and owl species as predictors of abundance. Despite significant environmental impacts on prey intake, some key patterns emerge among owl species studied. Owls select prey by predator body size: Larger owls tend to feed on wider ranges of prey sizes, leading to higher means. In addition, guild members show both specialization and generalism in terms of prey taxa, sometimes in contrast with the expectations of the predator–prey body size hypothesis. Our results suggest that while predator body size is an important factor in prey selection, taxon specialization by predator species also has considerable impact.
Data from: Fine-scale genetic structure in a wild bird population: the role of limited dispersal and environmentally-based selection as causal factors
Individuals are typically not randomly distributed in space; consequently ecological and evolutionary theory depends heavily on understanding the spatial structure of populations. The central challenge of landscape genetics is therefore to link spatial heterogeneity of environments to population genetic structure. Here, we employ multivariate spatial analyses to identify environmentally induced genetic structures in a single breeding population of 1174 great tits Parus major genotyped at 4701 single-nucleotide polymorphism (SNP) loci. Despite the small spatial scale of the study relative to natal dispersal we found multiple axes of genetic structure. We built distance-based Moran's eigenvector maps to identify axes of pure spatial variation, which we used for spatial correction of regressions between SNPs and various external traits known to be related to fitness components (avian malaria infection risk, local density of conspecifics, oak tree density and altitude). We found clear evidence of fine-scale genetic structure, with 21, 7 and 9 significant SNPs respectively associated with infection risk by two species of avian malaria (Plasmodium circumflexum and P. relictum) and local conspecific density. Such fine-scale genetic structure relative to dispersal capabilities suggests ecological and evolutionary mechanisms maintain within-population genetic diversity in this population with the potential to drive micro-evolutionary change.
Data and scripts from: Experimental evidence of size-selective harvest and environmental stochasticity effects on population demography, fluctuations, and nonlinearity
<p class="MsoNormal">Theory and analyses of fisheries datasets indicate that harvesting can alter population structure and destabilize nonlinear processes, which increases population fluctuations. We conducted a factorial experiment on the population dynamics of <em>Daphnia magna</em> in relation to size-selective harvesting and stochasticity of food supply. Harvesting and stochasticity treatments both increased population fluctuations. Timeseries analysis indicated that fluctuations in control populations were nonlinear, and nonlinearity increased substantially in response to harvesting. Both harvesting and stochasticity induced population juvenescence, but harvesting did so via depletion of adults whereas stochasticity increased the abundance of juveniles. A fitted fisheries model indicated that harvesting shifted populations towards higher reproductive rates and larger-magnitude damped oscillations that amplify demographic noise. These findings provide experimental evidence that harvesting increases nonlinearity of population fluctuations and that both harvesting and stochasticity increase population variability and juvenescence.</p>
Fig. 1 in Quantitative variations of usnic acid and selected elements in terricolous lichen Cladonia mitis Sandst., with respect to different environmental factors - A chemometric approach
Fig. 1. Relationship between usnic acid content in Cladonia mitis and the latitude of the collection sites (R = 0.547, p =0.019). The circles denote samples from open area, while squares denote samples from forest area.
Fig. 4 in Quantitative variations of usnic acid and selected elements in terricolous lichen Cladonia mitis Sandst., with respect to different environmental factors - A chemometric approach
Fig. 4. The projection of samples on the plane defined by the first two latent components of the PLS model. The circles denote samples from open area, while squares denote samples from forest area.
Fig. 2 in Quantitative variations of usnic acid and selected elements in terricolous lichen Cladonia mitis Sandst., with respect to different environmental factors - A chemometric approach
Fig. 2. Relationship between usnic acid content in Cladonia mitis and the altitude (in the range of 50 and 500 m above sea level) of the collection sites (n = 13). The circles denote samples from open area, while squares denote samples from forest area.
Fig. 3 in Quantitative variations of usnic acid and selected elements in terricolous lichen Cladonia mitis Sandst., with respect to different environmental factors - A chemometric approach
Fig. 3. The weights of the first two latent components of the partial least square model. Usnic acid and Pb concentrations are response parameters, all other parameters are predictors.
Data from: Natural selection on a measure of parasite resistance varies across ages and environmental conditions in a wild mammal
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Data from: The evolution of male-biased dispersal under the joint selective forces of inbreeding load, and demographic and environmental stochasticity
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Data from: Selective increases in inter-individual variability in response to environmental enrichment in female mice
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Data from: Relationships between spatio-temporal environmental and genetic variation reveal an important influence of exogenous selection in a pupfish hybrid zone
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Data for: Estimating density dependence, environmental variance and long-term selection on a stage-structured life history
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Data from: Signatures of selection for environmental adaptation and zebu x taurine hybrid fitness in East African Shorthorn Zebu
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Data from: When Bergmann's rule fails: evidences of environmental selection pressures shaping phenotypic diversification in a widespread seabird
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.