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44 results for “environmental stability”
Data from "Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar"
<p><strong>Data from : 'Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar'</strong></p> <p>An Vanden Broeck*, Tim Meese*, Pieter Verschelde, Karen Cox, Berthold Heinze, Dieter Deforce, Ellen De Meester and Filip Van Nieuwerburgh</p> <p> </p> <p>Related publication: Vanden Broeck, A.*, Meese, T.*, Verschelde, P. <em>et al.<strong> Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar</strong></em>. <em>BMC Biol</em> <strong>22</strong>, 30 (2024). https://doi.org/10.1186/s12915-024-01816-1</p> <ul> <li>* These authors contributed equally.</li> </ul> <p>--------------------------------------------------</p> <p><strong>Background: </strong>Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar (<em>Populus nigra</em> cv. 'Italica' Duroi) offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome.</p> <p><strong>Results: </strong>We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe any biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring's' phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment.</p> <p><strong>Conclusions: </strong>Genome-wide cytosine methylation patterns in symmetrical GC-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in GC-context can be used as bio-markers to infer a common ancestor and thus to investigate the environmental history of a specific Lombardy poplar on short time-scales. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.</p> <p> </p> <p><strong>ADDITIONAL FILES</strong></p> <p><strong>Additional file 1.</strong> CSV-file with information on the Lombardy poplar trees samples used for whole genome bisulfite sequencing (WGBS) in the two methylome experiments (<em>metadata</em>). The raw fastq datafiles obtained by whole genome bisulfite sequencing (WGBS) are available at the <a href="https://www.ncbi.nlm.nih.gov/geo/">Gene Expression Omnibus (GEO) database</a> (submission GSE225596).</p> <p><strong>Additional file 2.</strong> CSV-file with mapping statistics, bisulfite conversion rates and percentages of cytosine methylation for each DNA-sample analyzed by whole genome bisulfite sequencing (WGBS). (<em>processed data</em>).</p> <p><strong>Additional file 3</strong>. CSV-file with the total list of GO terms that were enriched in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (<em>processed data</em>).</p> <p><strong>Additional file 4. </strong>POWERPOINT-file. Heatmaps with GO terms over-represented in promoters containing DMRs in CpG-context per between-group pairwise comparison. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively). A. HUN4 versus ITS3; B. HUN4 versus UKD2, C; ITS3 versus SPC1; D. HUN4 versus SCP1, E. SPC1 versus UKD2</p> <p><strong>Additional file 5. </strong>CSV-file with the raw data of the bud set observations in the common garden experiment (<em>raw data</em>).</p> <p><strong>Additional file 6. </strong>HTML-file with the R source codes to reproduce the results of the bud set analysis (<em>code,</em> <em>R script</em>).</p> <p><strong>Additional file 7. </strong>A text-file representing the Snakefile (i.e. a readable Python-based workflow) including the different steps and rules of the bioinformatics of the WGBS data analyses (<em>code, Snakefile</em>).</p> <p><strong>Additional file 8. </strong>RMD-file<strong> </strong>with the code to reproduce the analyses to identify differential methylated predefined regions (<em>code,</em> <em>R script</em>).</p> <p><strong>Additional file 9. </strong>R-script with the code to reproduce the clustering and visualizing of the GO enrichment results (<em>code,</em> <em>R script</em>).</p> <p><strong>Supporting files 1</strong>. Zip-folder with: i) excel-files listing the genes in DMRs, and ii) PNG-files with the ‘Biological Coefficient of Variation (BCV)’-plots between any of the six pairwise comparisons of Lombardy poplars grouped per ortet and identified with Bioconductor package edgeR. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (<em>processed data</em>).</p> <p><strong>Supporting files 2</strong>. Zip-folder with PNG-files representing heatmaps and excel-files with clustered GO terms significant over-represented in promoters and gene regions located in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively. The files were obtained with the Bioconductor package simplifyEnrichment (<em>processed data</em>).</p> <p>---------------------------------------------------------</p> <p>Version 3:</p> <ul> <li>Renaming of file names according to the publisher's guidelines</li> <li>Additional file 2 includes also bisulfite conversion rates per sample</li> </ul>
Figure 1 in Using of fluctuating asymmetry in adult Pelophylax ridibundus (Amphibia: Anura: Ranidae) meristic traits as a method for assessing developmental stability of population and environmental quality of their habitat: industrial area in southern Bulgaria
Figure 1. An indicative map of the sites in southern Bulgaria where P. ridibundus individuals were captured in 2019.
Figure 2 in Using of fluctuating asymmetry in adult Pelophylax ridibundus (Amphibia: Anura: Ranidae) meristic traits as a method for assessing developmental stability of population and environmental quality of their habitat: industrial area in southern Bulgaria
Figure 2. Photos of some asymmetric P. ridibundus individuals from site 1: the Chaya River in southern Bulgaria. Legend: a–d: asymmetric morphological traits on the back of the body and hind limbs of frogs, e–f: asymmetric morphological traits on the fingers of frogs. Trait 1 – number of stripes on the dorsal side of the thigh (femur); trait 2 – number of spots on the dorsal side of the thigh; trait 3 – number of stripes on the dorsal side of the shank (crus); trait 4 – number of spots on the dorsal side of the shank; trait 5 – number of stripes on the foot (pes); trait 6 – number of spots on the foot; trait 7 – number of stripes and spots on the back (dorsum); trait 8 – number of white spots on the ventral side of the second finger of the hind leg; trait 9 – number of white spots on the ventral side of the third finger of the hind leg; trait 10 – number of white spots on the ventral side of the fourth finger of the hind leg.
Spatial, environmental, and functional distances among temporal ponds attenuate synchronization, stabilizing plant richness and biomass dynamics
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Evaluation of Sustainable and Environmentally Friendly Stabilization of Cohesionless Sandy Soil for Transportation Infrastructure
<p>Ordinary Portland cement (OPC) is generally used to stabilize cohesionless sandy soils that are often found in coastal areas. Due to its high carbon footprint, many studies are being conducted to identify a suitable green alternative for stabilizing cohesionless soils. Previous studies have shown that partially replacing OPC with waste materials such as nano-silica and coal waste reduces the overall carbon footprint without significantly impacting the performance. Geopolymer (GP) received a lot of attention in the past few decades owing to its similar properties to that of OPC yet with a lower carbon footprint. This study investigated the feasibility of stabilizing cohesionless sandy soils with metakaolin-based GP. Engineering and characterization tests such as shrinkage, strength, pH, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS) were performed to evaluate various characteristics of the stabilized mixes with different dosages of geopolymer and relate them to microstructural changes. Notably, GP-treated soils did not deteriorate during the durability tests, whereas the OPC-treated soil only retained about 75% of its strength. This is an indication that GP could be a better choice than OPC in coastal areas where cohesionless soils often experience heavy rainfall and flooding. Overall, an optimum dosage of GP improved both the mechanical properties and durability of cohesionless soils.</p>
Data from: Linking environmental stability with genetic diversity and population structure in two Atlantic Forest palm trees
<p><span>Spatial patterns of biodiversity in the Atlantic Forest of Brazil are well characterized. However, there is no consensus on the biological processes underlying these patterns, and multiple competing hypotheses have been proposed, several of which center on climatic stability. Here, we ask if Late Quaternary climatic stability predicts contemporary population structure and genomic-level diversity in two palm species: </span><span>Syagrus botryophora </span><span>and S. pseudococos (Arecaceae)</span></p> <p><span>We first use species occurrence data to model the distribution of suitable environments in 62 time-slice climate projections over the last 120 thousand years, and summarize stability over that period. We then use >25,000 RADseq-generated SNPs to i) describe the spatial patterns of genomic variation in both species, ii) test how well genomic variation is explained by isolation by distance and by the environmental resistance imposed by historical instability (isolation by resistance) and iii) test for a correlation between genetic diversity and historical stability.</span></p> <p><span>The contemporary range of S. botryophora has been relatively stable over the last 30 thousand years and there are two isolated regions of high stability for S. pseudococos. The genomic data recovers a clear pattern of isolation by distance in S. botryophora and two structured populations in S. pseudococos. Consequently, the contribution of isolation by resistance to overall genetic structure is much higher in S. pseudococos. Genetic diversity is not significantly correlated with historical stability in either species.</span></p> <p><span>Based on the concordance between historical stability and genetic structure, Late Quaternary climate stability may have maintained population connectivity within S. botryophora and promoted intraspecific divergence in S. pseudococos. Conversely, historical stability does not seem to be driving spatial patterns of genetic diversity. This study supports the primary role of climatic stability in determining spatial population structure, but not genetic diversity, in the Atlantic Forest.</span></p>
Data from: Associations between developmental stability, canalization and phenotypic plasticity in plants with temporally heterogeneous environmental experience
<p>We subjected eight plant species to a first round of alternating inundation and drought vs. constantly moderate water treatments and a second round of water conditions. Fluctuating asymmetry (FA), intra- and inter-individual variations (CV<sub>intra</sub> and CV<sub>inter</sub>), and plasticity in traits were measured and correlations between variables were calculated for each species. Early temporally heterogeneous experience decreased the leaf size of half of the species, but had complex effects on leaf fluctuating asymmetry (FA) and inter-individual variation (CV<sub>inter</sub>) in traits immediately or in late conditions, with little effects on intra-individual variation (CV<sub>intra</sub>). There were several positive correlations between FA and CV<sub>inter</sub>, while there were correlations between CV<sub>inter</sub> and plasticity in early treatments, but negative ones in late treatments.</p>
Development of Environmentally-Friendly Stabilization Methods for Transportation Infrastructure Based on Geopolymers
<p>Corresponding data set for Tran-SET Project No. 17GTTAM02. Abstract of the final report is stated below for reference:</p> <p>"Geopolymers (GPs) have received much attention as an eco-friendly and sustainable alternative to conventional chemical additives, since they can be processed at room temperatures from aqueous solutions by utilizing waste materials (e.g. fly ash) or abundant natural sources (e.g. clay). A collaborative research study is carried out by teams from Texas A&M University (TAMU) and University of Texas at Arlington (UTA) to investigate the effectiveness of GPs for stabilizing base and subgrade materials by considering the strength and shrink-swell characteristics. Two types of clay, obtained from the North Dallas area, were mixed with a potassium-based GP synthesized from metakaolin and silica fume, at a ratio of 8 wt% of dry geopolymer to dry soil, and cured for a period of 7 days. Moisture-density relationship tests conducted show that treated soils have a higher optimum moisture content and lower maximum dry density as compared to untreated soils. Treated soils exhibited significant reduction in shrinkage and swell properties as compared to untreated soils. Additionally, unconfined compression strength tests also show an increase in strength of treated soils."</p>
Genetic differences in the temporal and environmental stability of transgenerational environmental effects
<p><span><span><span><span><span><span><span><span><span><span><span>Environments influence the expression of phenotypes of individuals, their progeny, and even their grandprogeny. The duration of environmental effects and how they are modified by subsequent environments are predicted to be targets of natural selection in variable environments. However, little is known about the genetic basis of the temporal persistence of environmental effects and their stability of expression across subsequent environments, or even the extent to which natural genotypes differ in these attributes of environmental effects. We factorially manipulated the thermal environment experienced in three successive generations, to quantify the temporal persistence and environmental stability of temperature effects in contrasting genotypes of <i>Arabidopsis thaliana</i>. We found that genotypes differed in the manner in which environmental effects dissipated across successive generations, the manner in which responses to ancestral environments were stably expressed in present environments, the manner in which ancestral environments altered responses to present environments, and in the manner in which ancestral environments altered fitness in present conditions. Genetic variation exists in nature for these trait-specific environmental responses, suggesting that the temporal persistence and stability of environmental effects in variable environments have the potential to evolve in response to natural selection imposed by different environments and sequences of environments.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Freshwater fishes maintain multi-trait phenotypic stability across an environmental gradient in aqueous calcium
<p>Reductions in a limiting nutrient might be expected to necessitate compromises in the functional traits that depend on that nutrient; yet populations existing in locations with low levels of such nutrients often do not show the expected degradation of functional traits. Indeed, we previously found that fish of three species, Logperch (<em>Percina caprodes</em>),Pumpkinseed Sunfish (<em>Lepomis gibbosus</em>), and Yellow Perch (<em>Perca flavescens</em>) residing in low-calcium water in the Upper St. Lawrence River nevertheless maintained levels of scale calcium comparable to those of conspecific populations in high-calcium water. However, it remains possible that the maintenance of one functional trait under nutrient-limited conditions could come at the expense of maintaining other functional traits that depend on that same nutrient. Hence, we here extend prior work by examining other calcium-dependent traits: skeletal element sizes and bone densities in the same fish species in the same area. Using radiographs of 101 fish from the three species across four locations (two in high-calcium water and two in low-calcium water), we document multi-trait "homeostasis" along the gradient of water calcium. That is, we did not detect any effect of calcium regime (low-calcium versus high-calcium) on any of the measured variables. Further, effect sizes for the skeletal traits were very low – lower even than effect sizes previously documented for scale calcium. Our results thus show that native fishes maintain phenotype stability across a suite of functional traits linked to calcium regulation, perhaps pointing to an "organismal-level homeostasis" scenario rather than a "trait-level homeostasis" scenario. </p>
Data from: Linking environmental stability with genetic diversity and population structure in two Atlantic Forest palm trees
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Data from: Plants and soil biota co-regulate stability of ecosystem multifunctionality under multiple environmental changes
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Data from: Freshwater fishes maintain multi-trait phenotypic stability across an environmental gradient in aqueous calcium
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Data from: Stability of environmental DNA methylation and its utility in tracing spawning of fish
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Data for: Long-term environmental stability does not erode plasticity in nest building repsonses to changing ambient conditions
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Genetic differences in the temporal and environmental stability of transgenerational environmental effects
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Data from: Associations between developmental stability, canalization and phenotypic plasticity in plants with temporally heterogeneous environmental experience
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Environmental heterogeneity, rather than stability, explains spider assemblage differences between ecosystems
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Data from: Environmental DNA metabarcoding reveals temporal dynamics but functional stability of arthropod communities in cattle dung
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Data from: Effects of vicariant barriers, habitat stability, population isolation and environmental features on species divergence in the south-western Australian coastal reptile community
Identifying explicit hypotheses regarding the factors determining genetic structuring within species can be difficult, especially in species distributed in historically dynamic regions. To contend with these challenges, we use a framework that combines species distribution models, environmental data and multi-locus genetic data to generate and explore phylogeographic hypotheses for reptile species occupying the coastal sand-dune and sand-plain habitats of the south-western Australian biodiversity hotspot; a community which has both a high diversity of endemics and has varied dramatically in spatial extent over time. We use hierarchical AMOVA, summary statistic and distance-based analyses to explicitly test specific phylogeographic hypotheses. Namely, we test if biogeographic vicariance across barriers, habitat stability, population isolation along a linear habitat or fragmentation across different environments can explain genetic divergence within five co-distributed squamate reptile species. Our results show that patterns of genetic variation reflect complex and species-specific interactions related to the spatial distribution of habitats present currently and during repeated glacial minima, as opposed to being associated with historical factors such as habitat stability between glacial and inter-glacial periods or vicariant barriers. We suggest that the large impact of habitat characteristics over time (i.e., relative levels of habitat connectivity, climatic gradients and spatial heterogeneity of soil types) reflects the ecological restrictions of the sand-dune and sandplain reptile communities and may explain the lack of concordance across taxa. The study demonstrates the general utility of the approach for assemblage-level, as well as single species, phylogeographic study, including its usefulness for exploring biologically-informed hypotheses about what factors have influenced patterns of genetic variation.
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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)
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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.