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215 results for “environmental adaptation”
Survey instrument, data, and code for paper "Freihardt, Buntaine, Bernauer (2024): Choosing to protect: Public support for flood defense over relocation in climate change adaptation. Environmental Research Letters. DOI 10.1088/1748-9326/ad6781"
<p>This is the survey instrument, data, and code underlying the manuscript:</p> <p>"Freihardt, Buntaine, Bernauer (2024): Choosing to protect: Public support for flood defense over relocation in climate change adaptation. Environmental Research Letters. DOI 10.1088/1748-9326/ad6781"</p>
Datasets belonging to the publication "Allelic variants confer Arabidopsis adaptation to small regional environmental differences".
<p>Datasets belonging to the publication "Allelic variants confer Arabidopsis adaptation to small regional environmental differences".</p> <p>A short description of each file is found below. Samples in the Variant Call Format (VCF) files are named according to how they are stored in the National Center for Biotechnology Information (NCBI) BioSample database. Detailed descriptions of how each file was generated are found in the manuscript.</p> <p><strong>Dartmap_Dutch_1001G_nuclear.vcf.gz</strong></p> <p>2,712,612 bi-allelic SNPs and 353,974 bi-allelic small indels called in the DartMap panel and the Dutch 1001G accessions (collectively referred to as DartMap + 1001G panel for brevity) relative to the <em>Arabidopsis thaliana</em> Col-0 nuclear genome reference sequence.</p> <p><strong>Dartmap_Dutch_1001G_mitochondrial.vcf.gz</strong></p> <p>231 bi-allelic SNPs and 23 bi-allelic small indels called in the DartMap panel and the Dutch 1001G accessions (collectively referred to as DartMap + 1001G panel for brevity) relative to the <em>A. thaliana</em> Col-0 mitochondrial genome reference sequence.</p> <p><strong>Dartmap_Dutch_1001G_chloroplast.vcf.gz</strong></p> <p>400 bi-allelic SNPs and 79 bi-allelic small indels called in the DartMap panel and the Dutch 1001G accessions (collectively referred to as DartMap + 1001G panel for brevity) relative to the <em>A. thaliana</em> Col-0 chloroplast genome reference sequence.</p> <p><strong>Dartmap_CNVs.vcf.gz</strong></p> <p>29,155 copy number variants (CNVs) called in the DartMap panel relative to the <em>A. thaliana</em> Col-0 reference genome.</p> <p><strong>Dartmap_Dutch_1001G_neighbouring_countries_nuclear.vcf.gz</strong></p> <p>Filtered VCF file containing variants of the DartMap + 1001G panel and that of neighbouring countries relative to the <em>A. thaliana</em> Col-0 nuclear genome reference sequence. Used for population structure analysis in the manuscript.</p> <p><strong>Dartmap_Dutch_1001G_neighbouring_countries_mitochondrial.vcf.gz</strong></p> <p>Filtered VCF file containing variants of the DartMap + 1001G panel and that of neighbouring countries relative to the <em>A. thaliana</em> Col-0 mitochondrial genome reference sequence. Used for population structure analysis in the manuscript.</p> <p><strong>Dartmap_Dutch_1001G_neighbouring_countries_chloroplast.vcf.gz</strong></p> <p>Filtered VCF file containing variants of the DartMap + 1001G panel and that of neighbouring countries relative to the <em>A. thaliana</em> Col-0 chloroplast genome reference sequence. Used for population structure analysis in the manuscript.</p> <p><strong>Dartmap_GWAS_GEA.vcf.gz</strong></p> <p>Filtered VCF file containing all variants of the DartMap panel that were used for all genome-wide association (GWA) and genome-environment association (GEA) analyses.</p> <p><strong>DartMap_phenotypical_data.xlsx</strong></p> <p>All relevant phenotypical data of the DartMap panel. </p> <p><strong>Dartmap_sample_ids_NCBI_sample_names.csv</strong></p> <p>Table showing which numerical ID of each DartMap sample corresponds to which NCBI BioSample ID. </p>
Data from: Helophyte Glyceria spiculosa adapts to environmental changes by adjusting bud bank dynamics
<p>Exploring plant adaptation strategies under habitat variations from the perspective of bud banks is essential for understanding vegetation regeneration under global changes. To date, less attention has been paid to how bud banks respond to environmental changes. In this study, Glyceria spiculosa was selected as the subject. Field bud bank surveys were conducted in three vegetation zones: wet meadow, tussock marsh, and marsh. A pot experiment containing three flooding periods (no flooding, flooding for 1-5 weeks, and flooding for 6-10 weeks), four nitrogen levels (1, 10, 30, and 100 mg/L), and two nitrogen forms (ammonium nitrogen and nitrate nitrogen) was carried out to further investigate the relationship between bud banks and environmental factors. Rhizome internode buds dominated in the natural vegetation zone, with their density peaking in the marsh zone and minimizing in the tussock marsh zone. Soil nutrients and water depth impacted tiller bud density. Tiller bud density was highest in pot experiment. Both ammonium nitrogen and elevated nitrogen levels promoted bud bank densities, and ammonium nitrogen further enhanced the tiller bud density increase induced by higher nitrogen levels. Nitrogen level was the primary factor influencing total, tiller, and rhizome internode bud densities, whereas flooding period was the most crucial determinant of rhizome apical bud density. Our results reveal that the adjustment of bud bank type and density is a crucial strategy for plants to adapt to environmental changes, emphasizing the significance of nutrient and water variations in shaping plant reproductive strategies and adaptive capacity.</p> <p> </p> <p>The data included different types of bud bank density, soil and water nutrient data from field investigation, corresponding different types of bud bank density and initial plant height extracted from pot experiment.</p> <h3>Variables</h3> <ul> <li>site: site</li> <li>plot: plot</li> <li>quadrat: quadrat</li> <li>wetland.type: wetland type</li> <li>Tzongya: density of the total buds</li> <li>Tfennieya: density of the tiller buds (buds growing vertically upward from the base of the plant)</li> <li>Tgenjingjieya: density of the rhizome internode buds (buds located on the rhizome internodes)</li> <li>Tgenjingdingya: density of the rhizome apical buds (buds located at the tip of the rhizome)</li> <li>WTN: water total nitrogen</li> <li>WTP: water total phosphorus</li> <li>WNO3: water nitrate nitrogen</li> <li>WNH4: water ammonium nitrogen</li> <li>STN: soil total nitrogen</li> <li>STP: soil total phosphorus</li> <li>SNO3-N: soil nitrate nitrogen</li> <li>SNH4-N: soil ammonium nitrogen</li> <li>water.depth: water depth</li> <li>Nform: nitrogen form(AN:ammonium nitrogen; NN:nitrate nitrogen)</li> <li>Flooding: flooding periods (ck: no flooding throughout; F1: flooding in weeks 1-5, F2: flooding in weeks 6-10)</li> <li>Nlevel: nitrogen levels (N1:1; N2: 10;N3: 30; N4: 100 mg/L)</li> <li>zongya: density of the total buds</li> <li>fennieya: density of the tiller buds (buds growing vertically upward from the base of the plant)</li> <li>genjingjieya: density of the rhizome internode buds (buds located on the rhizome internodes)</li> <li>genjingdingya: density of the rhizome apical buds (buds located at the tip of the rhizome)</li> <li>InitialH: Initial height</li> </ul>
Data from: Environmental heterogeneity and not vicariant biogeographic barriers generate community wide population structure in desert adapted snakes
Genetic structure can be influenced by local adaptation to environmental heterogeneity and biogeographic barriers, resulting in discrete population clusters. Geographic distance among populations, however, can result in continuous clines of genetic divergence that appear as structured populations. Here we evaluate the relevant importance of these three factors over a landscape characterized by environmental heterogeneity and the presence of a hypothesized biogeographic barrier in producing population genetic structure within 13 codistributed snake species using a genomic dataset. We demonstrate that geographic distance and environmental heterogeneity across western North America contribute to population genomic divergence. Surprisingly, landscape features long thought to contribute to biogeographic barriers play little role in divergence community wide. Our results suggest that isolation by environment is the most important contributor to genomic divergence. Furthermore, we show that models of population clustering that incorporate spatial information consistently outperform nonspatial models, demonstrating the importance of considering geographic distances in population clustering. We argue that environmental and geographic distances as drivers of community-wide divergence should be explored before assuming the role of biogeographic barriers.
Divergent response and adaptation of specific leaf area to environmental change at different spatio-temporal scales jointly improve plant survival
<p><span>Specific leaf area (SLA) is one of the most important plant functional traits. </span><span>It </span><span>integrates multiple functions and reflects strategies of plants to obtain resources. </span><span>How plants employ different strategies (e.g., through SLA) to respond to dynamic environmental conditions remains poorly understood.This study aimed to </span><span>explore the s</span><span>patial variation in SLA and divergent adaptation of plants by changing SLA </span><span>through the lens of biogeographic patterns, evolutionary history, and short-term responses. SLA data for 5424 plant species from 76 natural communities in China were systematically measured and integrated with meta-analysis of field experiments (i.e., global warming, drought, and nitrogen addition). The mean value of SLA across all species was 21.8 m2 kg–1, ranging from 0.9 to 110.2 m2 kg–1. SLA differed among different ecosystems, temperature zones, vegetation types, and functional groups. Phylogeny had a weak effect on SLA, but plant species evolved toward higher SLA. Furthermore, plants responded nonlinearly to environmental change by changing SLA. Unexpectedly, radiation was one of the main factors determining the spatial variation in SLA on a large scale. Conversely, short-term manipulative experiments showed that SLA increased with increased resource availability and tended to stabilize with treatment duration. However, different species exhibited varying response patterns. Overall, long-term adaptation of plants to environmental gradients and its short-term response to resource pulses through variation in SLA jointly improve plant adaptability to a changing environment. Overall SLA-environment relationships should be emphasized as a multidimensional strategy for elucidating environmental change in future research. </span></p>
Can short-term data accurately model long-term environmental exposures? Investigating the multigenerational adaptation potential of Daphnia magna to environmental concentrations of organic ultraviolet filters
<p>Organic ultraviolet filters (UVFs) are contaminants of concern, ubiquitously found in many aquatic environments due to their use in personal care products to protect against ultraviolet radiation. Research regarding the toxicity of UVFs such as avobenzone, octocrylene and oxybenzone indicates that these chemicals may pose a threat to invertebrate species; however, minimal long-term studies have been conducted to determine how these UVFs may affect continuously exposed populations. The present study modeled the effects of a 5-generation exposure of <em>Daphnia</em> <em>magna</em> to these UVFs at environmental concentrations. Avobenzone and octocrylene resulted in minor, transient decreases in reproduction and wet mass. Oxybenzone exposure resulted in > 40% mortality, 46% decreased reproduction and 4-fold greater reproductive failure over the F0 and F1 generations; however, normal function was largely regained by the F2 generation. These results indicate that <em>Daphnia</em> are able to acclimate over long-term exposures to concentrations of 6.59 μg/L avobenzone, ~0.6 μg/L octocrylene or 16.5 μg/L oxybenzone. This suggests that short-term studies indicating high toxicity may not accurately represent long-term outcomes in wild populations, adding additional complexity to risk assessment practices at a time when many regions are considering or implementing UVF bans in order to protect these most sensitive invertebrate species.</p>
Convergent genomic signatures of local adaptation across a continental-scale environmental gradient
<p><span>Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in adaptive evolution, in particular the extent to which similar genetic mechanisms drive adaptation to common selective forces. Here, we investigated the genomics of local adaptation in two non-sister woodpeckers that are co-distributed across an entire continent and exhibit remarkably convergent patterns of geographic variation. We sequenced the genomes of 140 individuals of Downy (<em>Dryobates</em> <em>pubescens</em>) and Hairy (<em>D</em>. <em>villosus</em>) woodpeckers and employed a suite of genomic approaches to identify loci under selection. We showed evidence that convergent genes have been targeted by selection in response to shared environmental pressures, such as temperature and precipitation. Among candidates, we found multiple genes putatively linked to key phenotypic adaptations to climate, including differences in body size (e.g., <em>IGFPB</em>) and plumage (e.g., <em>MREG</em>). These results are consistent with genetic constraints limiting the pathways of adaptation to broad climatic gradients, even after genetic backgrounds diverge.</span></p>
Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing
<p>Antarctica poses numerous challenges to life such as cold shock, low nutrient concentrations and periodic desiccation over a wide range of extreme temperatures. Cyanobacteria survive this harsh environment having evolved adaptive metabolic plasticity to become the dominant primary producers. The type strain cyanobacterium <em>Halotia branconii</em> CENA392 was isolated from an Antarctic intertidal seashore. The complete circular genome of this strain is presented herein, which was assembled using long sequence reads. The genome encoded some stress-related genes associated with low-temperature adaptation and biosynthesis of mycosporine-like amino acid (MAA) photoprotective compounds. Empirical experimentation demonstrated constitutive production of the MAA porphyra-334 and total carotenoids without exposure to low temperatures or ultraviolet radiation stress. Phylogenetic analysis provided insights on the taxonomic placement and the evolutionary history of some annotated genes. These data exemplify the importance of generating complete quality genome sequences of microorganisms isolated from extreme intertidal environments, facilitating in-depth evaluation of ecological and taxonomic inferences.</p>
Rapid hyperthyroidism-induced adaptation of Salmonid fish in response to environmental pollution
<p><span>The streams draining volcanic landscapes are often characterized by a complex of factors that negatively affect hydrobionts and lead to a decline of their populations. However, in a number of cases, hydrobionts ensure the resilience of populations througth a range of rapid adaptive changes. Here, we present both field and experimental data shedding light on the physiological basis of adaptation in populations of Dolly Varden charr (<em>Salvelinus malma</em>) differing in the duration of isolation in volcanic streams contaminated with heavy metals. The study reveals that isolated populations have a physiological phenotype that distinguishes them from the populations inhabiting clean waters. They are characterized by a hyperthyroid status accompanied by an increased metabolic rate, elevated activity of antioxidant enzymes, decreased ionic conductivity of tissues and reduced stored energetic reserves. The experimental data elucidate that hyperthyroidism is an adaptive characteristic enhancing the resistance to heavy metal contamination and shaping the evolution of these populations. The similarity of physiological, developmental and morphological changes in isolated populations suggests a common source and mechanisms underpinning their "evolutionary rescue". Thus, populations of <em>S. malma</em> trapped in volcanic streams represent a genuine case of a rapid neuroendocrine-driven adaptation to changing environmental stimuli.</span></p>
Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplant
<p><span>Crop wild relatives possess desirable traits that confer resilience to various environmental stresses. We applied landscape genomics, that associates environment with genomic variation to understand the genetic basis of their adaptation. <br></span></p> <p> </p> <p><span>In this study, we applied landscape genomics to examine the differences in allele frequency of 15,416 Single Nucleotide Polymorphisms (SNPs) among 153 accessions of wild eggplant relatives from Africa, the principal hotspot of these wild relatives. Further, we explored the correlation between the genetic variations and the bio-climatic and soil conditions at their collection sites.</span></p> <p> </p> <p><span><span>Our results showed that the environment has a greater impact on the genetic variation in the eggplant wild relative populations compared to the geographical distances between collection sites while controlling for population structure. These findings indicate the relevance of the environment in shaping genetic variation in eggplant relatives over time. We detected also candidate SNPs associated with ten environmental factors. Some of these SNPs signal genes involved in pathways that help with adaptation to environmental stresses such as drought, heat, cold, salinity, pests, and diseases. </span><br></span></p>
Overcoming the congenitally disadvantageous mutation through adaptation to environmental UV exposure in land snails
<p>Congenital fitness-disadvantageous mutations are not maintained in the population; they are purged from the population through processes such as purifying selection. However, these mutations could persist in the population as polymorphisms when it is advantageous for the individuals carrying them to adapt to a specific external environment. We tested this hypothesis using the dimorphic land snail <em>Euhadra peliomphala simodae</em> in Japan; these snails have dark or bright-coloured shells. The survival rate of dark snails at hatching was lower than that of the bright ones, as observed in the F1 progenies produced through crossing. Dark snails have a congenital fitness-disadvantageous mutation; however, they also have protection against ultraviolet radiation. They have a higher survival rate than the bright snails in a UV environment, as observed using the UV exposure experiments and UV transmittance measurements. This is a good example of a congenitally disadvantageous mutation that is advantageous for adapting to the external environment. These results explain the maintenance of polymorphism and highlight the genotypic and phenotypic diversity in the wild population.</p>
Intraspecific variation among Chinook salmon populations indicates physiological adaptation to local environmental conditions
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Data from: Environmental heterogeneity and not vicariant biogeographic barriers generate community wide population structure in desert adapted snakes
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Data from: Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients
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Environmental predictability drives different routes to adaptation
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Rapid hyperthyroidism-induced adaptation of Salmonid fish in response to environmental pollution
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Environmental data provide marginal benefit for predicting climate adaptation
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Can short-term data accurately model long-term environmental exposures? Investigating the multigenerational adaptation potential of Daphnia magna to environmental concentrations of organic ultraviolet filters
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Data from: Disentangling evolutionary, environmental and morphological drivers of plant anatomical adaptations to drought and cold in Himalayan graminoids
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Limited divergent adaptation despite a substantial environmental cline in wild pea
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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
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.