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215 results for “environmental adaptation”
Anticipatory plasticity: frog embryos respond to environmental cues by producing an adaptive phenotype at hatching
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Data from: Genetic, phenotypic, and environmental drivers of local adaptation and climate-change induced maladaptation in yellow warblers
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Environmental effects on genetic variance are likely to constrain adaptation in novel environments
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Data from: An adaptive biomolecular condensation response is conserved across environmentally divergent species
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Data from: Avoiding dead ends: the experimental evolution of constraint as adaptation to environmental variation
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Limited divergent adaptation despite a substantial environmental cline in wild pea
<p><span><span>Isolation by environment (IBE) is a wide spread phenomenon in nature. It is commonly expected that the degree of differences among environments is proportional to the level of divergence between populations in these environments. Consequentially, it is assumed that species' genetic diversity displays pattern of IBE in the presence of a strong environmental cline if geneflow does not mitigate isolation. We tested this common assumption by analyzing the genetic diversity and demographic history of <i>Pisum fulvum. P. fulvum </i>inhabits very contrasting habitats in the southern Levant and is expected to display only minor migration rates between populations what makes it an ideal test case. Ecogeographic and subpopulation structure was analyzed and compared. Correlation of genetic with environmental distances was calculated to test the effect of IBD and IBE and detect the main drivers of these effects. Historic effective population size was estimated using stairwayplots. Limited overlap of ecogeographic and genetic clustering was observed, and correlation of genetic with environmental distances was statistically significant yet small. We detected a sharp decline of effective population size during the last glacial period. The low degree of IBE <span>may be</span> the result of genetic drift due to the past bottleneck. Our findings contradict the expectation that strong environmental clines cause IBE in the absence of extensive geneflow.</span></span></p>
Data from: Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes
Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and assess whether temperature and precipitation were associated with genetic differentiation. We found that S. brevipes exhibited overall strong population differentiation, with potential admixture in Canadian populations. This species also displayed genomic signatures of positive selection as well as genomic sites significantly associated with distinct climatic regimes and abiotic environmental parameters. These genomic regions included genes involved in transmembrane transport of substances and helicase activity potentially involved in cold stress response. Our study sheds light on large-scale environmental adaptation in fungi by identifying putative adaptive genes and providing a framework to further investigate the genetic basis of fungal adaptation.
Data from: Genetic by environmental variation but no local adaptation in oysters (Crassostrea virginica)
Functional trait variation within and across populations can strongly influence population, community, and ecosystem processes, but the relative contributions of genetic vs. environmental factors to this variation are often not clear, potentially complicating conservation and restoration efforts. For example, local adaptation, a particular type of genetic by environmental (G*E) interaction in which the fitness of a population in its own habitat is greater than in other habitats, is often invoked in management practices, even in the absence of supporting evidence. Despite increasing attention to the potential for G*E interactions, few studies have tested multiple populations and environments simultaneously, limiting our understanding of the spatial consistency in patterns of adaptive genetic variation. In addition, few studies explicitly differentiate adaptation in response to predation from other biological and environmental factors. We conducted a reciprocal transplant experiment of first-generation eastern oyster (Crassostrea virginica) juveniles from six populations across three field sites spanning 1000 km in the southeastern Atlantic Bight in both the presence and absence of predation to test for G*E variation in this economically valuable and ecologically important species. We documented significant G*E variation in survival and growth, yet there was no evidence for local adaptation. Condition varied across oyster cohorts: Offspring of northern populations had better condition than offspring from the center of our region. Oyster populations in the southeastern Atlantic Bight differ in juvenile survival, growth, and condition, yet offspring from local broodstock do not have higher survival or growth than those from farther away. In the absence of population-specific performance information, oyster restoration and aquaculture may benefit from incorporating multiple populations into their practices.
Data from: Disentangling evolutionary, environmental and morphological drivers of plant anatomical adaptations to drought and cold in Himalayan graminoids
Understanding what determine plants ability to survive drought and cold is crucial for predicting how plants may respond to ongoing climate change. Plant survival strategies are usually characterized by morphological and physiological adaptations, while their underlying anatomical settings are largely unknown. Woody angiosperms and herbaceous dicots have repeatedly evolved small water transporting conduits and large storage parenchyma tissues at colder or drier places to cope with freezing- and drought-induced damages. However, whether these adaptations are also valid for graminoids remains unclear. Here we show that stem anatomical variations in grasses, sedges and rushes dominating in western Himalayan grasslands are driven by elevation and soil moisture via control over aboveground plant stature and belowground clonal growth, while phylogenetic constraints have only a weak effect. Phylogenetic comparative analyses controlling for confounding factors showed that the elevation-related cooling controls the conductive system through reduced vessel diameter and extended assimilatory and storage tissues with more chlorenchyma and less sclerenchyma around vessels. The soil moisture deficit, on the other hand, determines stabilization structures by promoting short-rhizomatous turf graminoids with hollow stems, thicker epidermis and deep adventitious roots in dry steppes and semi-deserts. Saline wetlands and moist alpine pastures promote long-rhizomatous short-stature plants with lower need for mechanical support (absence of hollow stem) and exposure to high evaporative forcing (thinner epidermis). Observed trends of decreasing vessel sizes and lignification rate with elevation supports the existing knowledge that narrower vessels and extensive parenchyma assist plants to grow in cold environments by avoiding freezing-induced cavitation. Our results bring novel information on ecological drivers influencing the evolution of anatomical adaptations in high mountain graminoids. Distinct grassland types, covering elevations from 2650 to 6150 m, harbor unrelated species with different evolutionary histories that have converged towards similar anatomical structures.
Data from: Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees
<p>The <em>Asian honeybee</em>, <em>Apis cerana</em>, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories, and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger-scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group of<em> A. cerana</em>. Integrating this with 525 resequencing datasets, we constructed the first pan-genome of <em>A. cerana</em>, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions, however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novel <em>A. cerana</em> ecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in the Atpalpha gene, indicated that this SV may promote the cold adaptation of <em>A. cerana</em> by altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation of <em>A. cerana</em>.</p>
Data from: Combining the resurrection approach with transplant experiments to investigate adaptation of plant populations to environmental change
<p>Recent climatic changes, such as more frequent droughts and heatwaves, can lead to rapid evolutionary adaptations in plant populations. Such rapid evolution can be investigated using the resurrection approach by comparing plants raised from stored ancestral and contemporary seeds from the same population. This approach has so far only been used in common garden experiments, allowing it to reveal genetic differentiation but not adaptation. In this study, we performed a novel approach by testing for evolutionary adaptation in natural plant populations using a resurrection study in combination with in situ transplantations. We cultivated seedlings from ancestors (23–26 years old) and contemporary descendants of three perennial species (<em>Melica ciliata, Leontodon hispidus</em> and <em>Clinopodium vulgare</em>) from calcareous grasslands in the greenhouse and transplanted them back to their collection sites. In addition, we sowed seeds of ancestors and descendants of two species (<em>L. hispidus</em> and <em>C. vulgare</em>) to the collection sites in order to investigate germination rates. In transplanted <em>M. ciliata</em> seedlings, we observed lower mortality and larger plant size in descendants compared to ancestors. This indicates that descendants are better adapted than ancestors to the current environmental conditions, which proved to be exceptionally hot and dry during the study period. Descendants of <em>C. vulgare</em> seedlings tended to be smaller and descendants of <em>L. hispidus</em> seedlings produced fewer leaves compared to their ancestors in their contemporary environmental conditions. In <em>C. vulgare</em> and <em>L. hispidus</em>, we found evolution towards faster germination, and especially descendant seeds of <em>C. vulgare</em> were better adapted to the unfavourable conditions during the experimental period. Concluding, we demonstrate that our novel approach to combine resurrection ecology with transplant experiments is a promising avenue to rigorously test for evolutionary adaptations in changing environments.</p>
Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation
<p>Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary aDNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms, and to thereby potentially provide an understanding of the evolutionary histories of past populations. To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than one gram of sediment. Here we maximise sequence coverage by extracting DNA from ~50x more sediment per sample than the majority of previous studies, to achieve genotype resolution. From a time-series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of threespine stickleback at key time points of this transition. We find a staggered temporal dynamic, in which freshwater alleles at known loci of large effect in marine-freshwater divergence of threespine stickleback (e.g. <em>EDA</em>) were already established during the brackish phase of the formation of the isolation basin. Yet marine alleles were still detected across the majority of marine-freshwater divergence associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of threespine sticklebacks at the end of the last glacial period complements contemporary experimental approaches and highlights the untapped potential for retrospective 'evolve-and-resequence' natural experiments using sedaDNA.</p>
Immigration delays but does not prevent adaptation following environmental change: experimental evidence
<p>In today's rapidly changing world, it is critical to examine how animal populations will respond to severe environmental change. Following events such as pollution or deforestation that cause populations to decline, extinction will occur unless populations can adapt in response to natural selection, a process called evolutionary rescue. Theory predicts that immigration can delay extinction and provide novel genetic material that can prevent inbreeding depression and facilitate adaptation. However, when potential source populations have not experienced the new environment before (<em>i.e.,</em> are naive), immigration can counteract selection and constrain adaptation. This study evaluated the effects of immigration of naive individuals on evolutionary rescue using the red flour beetle, <em>Tribolium castaneum, </em>as a model system. Small populations were exposed to a challenging environment, and three immigration rates (zero, one, or five migrants per generation) were implemented with migrants from a benign environment. Following an initial decline in population size across all treatments, populations receiving no immigration gained a higher growth rate one generation earlier than those with immigration, illustrating the constraining effects of immigration on adaptation. After seven generations, a reciprocal transplant experiment found evidence for adaptation regardless of immigration rate. Thus, while the immigration of naive individuals briefly delayed adaptation, it did not increase extinction risk or prevent adaptation following environmental change.</p>
Data from: Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients
<p>Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (<em>Ochotona princeps</em>) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism (SNP)-based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37-193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (<em>n</em>=158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair, some of which have been previously linked to putative high elevation and/or climate adaptation that may serve as important targets in future studies.</p>
FIGURE 2 in Environmental correlates of adaptive diversification in postglacial freshwater fishes
FIGURE 2 Legend on next page.
Data from: Diversity and molecular evolution of non-visual opsin genes across environmental, developmental, and morphological adaptations in frogs
<p>Dataset for the article Diversity and molecular evolution of non-visual opsin genes across environmental, developmental, and morphological adaptations in frogs. Includes non-visual opsin coding sequences from frogs, sequence alingments, phylogenetics trees, and raw PAML results files.</p>
Physiological and environmental data from: Are you ready for the heat? Plasticity vs adaptation of heat tolerance in three-spined stickleback
<p>Heat waves constitute a challenge for aquatic ectotherms. However, the thermal tolerance of animals and their individual phenotypic plasticity to respond to heat waves may be influenced by thermal history. We tested these hypotheses by comparing the upper thermal tolerance and the individual capacities of three-spined sticklebacks from populations with different thermal histories to respond to heat waves. Two populations originated from thermally polluted nuclear power plant (NPP) habitats, while four locations represented geographically adjacent control areas. To disentangle the genetic adaptation from the phenotypic plastic response, we measured the individual upper thermal tolerance and the responses at molecular level in common garden conditions before and after a laboratory-mimicked heat wave. We found that the sticklebacks exhibit considerable phenotypic plasticity in thermal tolerance since the heat wave increased fish upper thermal tolerance significantly. The individual plasticity to respond to the heat wave was also negatively correlated to initial thermal tolerance. On the other hand, neither the thermal tolerance nor the plastic responses differed between NPP and control sites despite detection of significant but low genome-wide divergence in 10 out of 15 pairwise comparisons. Our results suggest that five decades of nuclear power plant activity with warmer water has not resulted in a detectable evolutionary change in either the upper thermal tolerance or its plasticity in three-spined sticklebacks potentially rendering them sensitive to frequent heat waves.</p>
Environmental variation and biotic interactions limit adaptation at ecological margins: lessons from rainforest Drosophila and European butterflies
<p>Models of local adaptation to spatially varying selection predict that maximum rates of evolution are determined by the interaction between increased adaptive potential owing to increased genetic variation, and the cost genetic variation brings by reducing population fitness. We discuss existing and new results from our laboratory assays and field transplants of rainforest Drosophila and UK butterflies along environmental gradients, which try to test these predictions in natural populations. Our data suggest that: (i) local adaptation along ecological gradients is not consistently observed in time and space, especially where biotic and abiotic interactions affect both gradient steepness and genetic variation in fitness; (ii) genetic variation in fitness observed in the laboratory is only sometimes visible to selection in the field, suggesting that demographic costs can remain high without increasing adaptive potential; and (iii) antagonistic interactions between species reduce local productivity, especially at ecological margins. Such antagonistic interactions steepen gradients and may increase the cost of adaptation by increasing its dimensionality. However, where biotic interactions do evolve, rapid range expansion can follow. Future research should test how the environmental sensitivity of genotypes determines their ecological exposure, and its effects on genetic variation in fitness, to predict the probability of evolutionary rescue at ecological margins. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.</p>
Data for: (Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions
<p><span>Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (<em>Ciona intestinalis</em>) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of </span><span>divergent selection</span><span>. </span><span>In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, gene ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.</span></p>
Beyond cyanogenesis: Temperature gradients drive environmental adaptation in North American white clover (Trifolium repens L.)
<p>Species that repeatedly evolve phenotypic clines across environmental gradients have been highlighted as ideal systems for characterizing the genomic basis of local environmental adaptation. However, few studies have assessed the importance of observed phenotypic clines for local adaptation: conspicuous traits that vary clinally may not necessarily be the most critical in determining local fitness. The present study was designed to fill this gap, using a plant species characterized by repeatedly-evolved adaptive phenotypic clines. White clover is naturally polymorphic for its chemical defense cyanogenesis (HCN release with tissue damage); climate-associated cyanogenesis clines have evolved throughout its native and introduced range worldwide. We performed landscape genomic analyses on 415 wild genotypes from 43 locations spanning much of the North American species range to assess the relative importance of cyanogenesis loci vs. other genomic factors in local climatic adaptation. We find clear evidence of local adaptation, with temperature-related climatic variables best describing genome-wide differentiation between sampling locations. The same climatic variables are also strongly correlated with cyanogenesis frequencies and gene copy number variations (CNVs) at cyanogenesis loci. However, landscape genomic analyses indicate no significant contribution of cyanogenesis loci to local adaptation. Instead, several genomic regions containing promising candidate genes for plant response to seasonal cues are identified — some of which are shared with previously-identified QTLs for locally-adaptive fitness traits in North American white clover. Our findings suggest that local adaptation in white clover is likely determined primarily by genes controlling the timing of growth and flowering in response to local seasonal cues. More generally, this work suggests that caution is warranted when considering the importance of conspicuous phenotypic clines as primary determinants of local adaptation.</p>
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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.