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86 results for “Novel Environment”
Coral thermotolerance retained following year-long exposure to a novel environment
<p>Description of datasets:</p> <h4>HTSeqCounts</h4> <p>Raw HTSeq count data used for downstream RNA sequencing analyses and visualisations including Principal Component Analysis and Differential Gene Expression analysis of the four habitat groups (mangrove to reef, reef to reef, wild mangrove and wild reef).</p> <h4>GO enriched gene results:</h4> <p>GO enriched genes summarised by broad categories of GO Slims for <em>Pocillopora acuta</em> corals originating from a mangrove system vs colonies from an adjacent reef site, translocated to a reef environment for one year. Samples for gene expression were collected during an acute heat stress assay to assess differentially enriched genes between mangrove and reef corals under 36 ºC. Enriched GO terms were grouped into broader functional categories using the “goSlim” function in the GSEABase R package with GOslim generic obo as the reference database to allow for a summary of key functions enriched in groups under heat stress. See manuscript methods for further detail on differential gene expression analysis.</p> <h4>2022-2023 mangrove/reef temperature and pH</h4> <p>Temperature and pH data measured in the Low Isles mangrove lagoon and reef habitat using HOBO MX2510 loggers deployed from February 2022 - February 2023. </p> <h4>Methylated DNA data</h4> <p>Percent DNA methylation relative to total DNA of mangrove to reef, reef to reef and wild mangrove groups under acute temperature stress during the February 2023 CBASS experiment.</p> <h4>Analysis code.zip</h4> <p>A copy of all R code used in the data analysis of this project</p> <p> </p>
Environmental effects on genetic variance are likely to constrain adaptation in novel environments
<p>Adaptive plasticity allows populations to cope with environmental variation but is expected to fail as conditions become unfamiliar. In novel conditions, populations may instead rely on rapid adaptation to increase fitness and avoid extinction. Adaptation should be fastest when both plasticity and selection occur in directions of the multivariate phenotype that contain abundant genetic variation. However, tests of this prediction from field experiments are rare. Here, we quantify how additive genetic variance in a multivariate phenotype changes across an elevational gradient, and test whether plasticity and selection align with genetic variation. We do so using two closely related, but ecologically distinct, sister species of Sicilian daisy (Senecio, Asteraceae) adapted to high and low elevations on Mount Etna. Using a paternal half-sibling breeding design, we generated and then reciprocally planted c.19,000 seeds of both species, across an elevational gradient spanning each species' native elevation, and then quantified mortality and five leaf traits of emergent seedlings. We found that genetic variance in leaf traits changed more across elevations than between species. The high-elevation species at novel lower elevations showed changes in the distribution of genetic variance among the leaf traits, which reduced the amount of genetic variance in the directions of selection and the native phenotype. By contrast, the low-elevation species mainly showed changes in the amount of genetic variance at the novel high elevation, and genetic variance was concentrated in the direction of the native phenotype. For both species, leaf trait plasticity across elevations was in a direction of the multivariate phenotype that contained a moderate amount of genetic variance. Together, these data suggest that where plasticity is adaptive, selection on genetic variance for an initially plastic response could promote adaptation. However, large environmental effects on genetic variance are likely to reduce adaptive potential in novel environments.</p>
Genetic background and thermal regime influence adaptation to novel environment in the seed beetle, Callosobruchus maculatus
<p>Climate change is associated with the increase in both mean and variability of thermal conditions. Therefore, the use of more realistic fluctuating thermal regimes is the most appropriate laboratory method for predicting population responses to thermal heterogeneity. However, the long- and short-term implications of evolving under such conditions are not well understood. Here, we examined differences in key life history traits among populations of seed beetles (<em>Callosobruchus</em> <em>maculatus</em>) that evolved under either constant control conditions or in an environment with fluctuating daily temperatures. Specifically, individuals from two distinct genetic backgrounds were kept for 19 generations at one of two temperatures, a constant temperature (T=29°C) or a fluctuating daily cycle (T<sub>mean</sub>=33°C, T<sub>max</sub>=40°C, and T<sub>min</sub>=26°C), and were assayed either in their evolved environment or in the other environment. We found that beetles that evolved in fluctuating environments but were then switched to constant 29°C conditions had far greater lifetime reproductive success compared to beetles that were kept in their evolved environments. This increase in reproductive success suggests that beetles raised in fluctuating environments may have evolved greater thermal breadth than control condition beetles. In addition, the degree of sexual dimorphism in body size and development varied as a function of genetic background, evolved thermal environment, and current temperature conditions. These results highlight not only the value of incorporating diel fluctuations into climate research but also suggest that populations that experience variability in temperature may be better able to respond to both short- and long-term changes in environmental conditions.</p>
A novel flow chamber for biodegradable alloy assessment in physiologically realistic environments: Supporting Data
<p>Experimental data including Excel analysis and microscopy supporting the publication 'A novel flow chamber for biodegradable alloy assessment in physiologically realistic environments' <a href="https://doi.org/10.1063/1.4821498" target="_blank" rel="noopener">https://doi.org/10.1063/1.4821498</a></p>
Genetic background and thermal regime influence adaptation to novel environment in the seed beetle, Callosobruchus maculatus
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Data from: Distinct catecholaminergic pathways projecting to hippocampal CA1 transmit contrasting signals during navigation in familiar and novel environments
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Environmental effects on genetic variance are likely to constrain adaptation in novel environments
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Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment
Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.
Data from: Behavioural and fitness effects of translocation to a novel environment: whole-lake experiments in two aquatic top predators
<p>Translocation into a novel environment through common fisheries-management practices, such as fish stocking, provides opportunities to study behavioural and fitness impacts of translocations at realistic ecological scales. The process of stocking, as well as the unfamiliarity with novel ecological conditions and the interactions with resident fish may affect translocated individuals, leading to alterations of behaviours and causing fitness impacts.</p> <p>Our objectives were to investigate how aquatic top-predators behaviourally establish themselves and compete with resident individuals following introduction in a novel lake environment and to investigate the resulting fitness consequences.</p> <p>Using high-resolution acoustic telemetry, we conducted whole-lake experiments and compared the activity, activity-space size and fate of translocated and resident individuals in two model top predators, northern pike (Esox lucius, n = 160) and European catfish (Silurus glanis, n = 33). Additionally, we compared the reproductive fitness of translocated and resident northern pike. The experiment was conducted with large (adult) individuals of different origins, resilient to predation, but subject to agonistic interactions and competition with resident fish.</p> <p>Over a period of several months, the translocated catfish exhibited consistently larger activity-space sizes than resident catfish, but did not differ from residents in activity and survival. The pike from one of the two translocated origins we tested also showed elevated space-use, and both translocated origins revealed higher mortality rates than their resident conspecifics, indicating maladjustment to their novel environment. When non-resident pike reproduced, they overwhelmingly produced hybrid offspring with resident fish, indicating that introductions fostered gene flow of non-native genes.</p> <p>Our study indicates that fish introductions result in behavioural and fitness impacts even in large-bodied top predators that experience low levels of natural predation risk. </p>
Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments
<p>Phenotypic reaction norms are often shaped and constrained by selection and are important for allowing organisms to respond to environmental change. However, selection cannot constrain reaction norms for environmental conditions that populations have not experienced. This may allow cryptic neutral genetic variation for the reaction norm to accumulate such that a release of phenotypic variation occurs when it is exposed to novel conditions. Most genomic diversity behaves as if functionally neutral. Genome-wide diversity metrics may therefore correlate with levels of cryptic genetic variation and, as a result, could exhibit a positive relationship with a release of phenotypic variation in novel environments. To test this hypothesis, we conducted translocations of juvenile brook trout (Salvelinus fontinalis) from 12 populations to novel uninhabited ponds that represented a gradient of environmental conditions. We assessed reaction norms for morphological traits (body size and four morphometric relative warps) across pond environmental gradients and evaluated the effect of genome-wide heterozygosity on phenotypic variability. All traits displayed plastic reaction norms. Overall, we found some evidence that a release of phenotypic variation consistent with cryptic genetic variation can occur in novel environmental conditions. However, the extent to which this release was correlated with average genome-wide diversity was limited to only one of five morphological traits examined. Our results suggest that the link between genomic diversity and the accumulation of cryptic genetic variation in reaction norms may be limited. Similarly, reaction norms were constrained for many of the morphological traits examined. Past conditions may have constrained reaction norms in the putatively novel environments despite significant deviations from contemporary source population habitat. Additionally, as a generalist colonizing species brook trout may exhibit plastic phenotypes across a wide range of environmental conditions.</p>
Comparing raccoon MHC diversity in native and introduced ranges: evidence for the importance of functional immune diversity for adaptation and survival in novel environments.
<p>The adaptive potential of invasive species is related to the genetic <span class="il">diversity</span> of the invader, which is influenced by genetic drift and natural selection. Typically, the genetic <span class="il">diversity</span> of invaders is studied with neutral genetic markers, however, the expectation of reduced <span class="il">diversity</span> has not been consistently supported by empirical studies. Here, we describe and interpret genetic <span class="il">diversity</span> at both neutral microsatellite loci and the immune related <span class="il">MHC</span>-DRB locus of <span class="il">native</span> and invasive populations of <span class="il">raccoon</span> to better understand of how drift and selection impact patterns of genetic <span class="il">diversity</span> during the invasion process. We found that despite the loss of many <span class="il">MHC</span> alleles in comparison with <span class="il">native</span> populations, functional <span class="il">MHC</span> supertypes are preserved in the invasive region. In the <span class="il">native</span> <span class="il">raccoon</span> population the number of supertypes within individuals was higher than expected under a neutral model. The high level of individual functional divergence may facilitate the adaptation to local conditions in the invasive range. These results suggest that selection is driving divergent allele combinations despite drift causing allelic loss. In the invasive populations, we also detected increased population structure at microsatellites compared to the <span class="il">MHC</span> locus, further suggesting that balancing selection is acting on adaptively important regions of the <span class="il">raccoon</span> genome. Finally, we found that alleles known to exhibit resistance to rabies in the <span class="il">native</span> range, Prlo-DRB*4, Prlo-DRB*16 and Prlo-DRB*102, were the most common alleles in the European populations, suggesting directional selection is acting on this locus. Our research shows empirical support for the importance of functional immune <span class="il">diversity</span> for adaptation and survival in novel environments.</p>
Data from: Phenotypic plasticity facilitates initial colonization of a novel environment
Phenotypic plasticity can allow organisms to respond to environmental changes by producing better matching phenotypes without any genetic change. Because of this, plasticity is predicted to be a major mechanism by which a population can survive the initial stage of colonizing a novel environment. We tested this prediction by challenging wild Drosophila melanogaster with increasingly extreme larval environments and then examining expression of alcohol dehydrogenase (ADH) and its relationship to larval survival in the first generation of encountering a novel environment. We found that most families responded in the adaptive direction of increased ADH activity in higher alcohol environments and families with higher plasticity were also more likely to survive in the highest alcohol environment. Thus, plasticity of ADH activity was positively selected in the most extreme environment and was a key trait influencing fitness. Furthermore, there was significant heritability of ADH plasticity which can allow plasticity to evolve in subsequent generations after initial colonization. The adaptive value of plasticity, however, was only evident in the most extreme environment and had little impact on fitness in less extreme environments. The results provide one of the first direct test of the adaptive role of phenotypic plasticity in colonizing a novel environment.
Data and code for: Does the definition of a novel environment affect the ability to detect cryptic genetic variation?
<p>Anthropogenic change exposes populations to environments that have been rare or entirely absent from their evolutionary past. Such novel environments are hypothesised to release cryptic genetic variation, a hidden store of variance that can fuel evolution. However, support for this hypothesis is mixed. One possible reason is a lack of clarity in what is meant by 'novel environment', an umbrella term encompassing conditions with potentially contrasting effects on the exposure or concealment of cryptic variation. Here, we use a meta-analysis approach to investigate changes in the total genetic variance of multivariate traits in ancestral versus novel environments. To determine whether the definition of a novel environment could explain the mixed support for a release of cryptic genetic variation, we compared absolute novel environments, those not represented in a population's evolutionary past, to extreme novel environments, those involving frequency or magnitude changes to environments present in a population's ancestry. Despite sufficient statistical power, we detected no broadscale pattern of increased genetic variance in novel environments, finding the type of novel environment did not explain any significant variation in effect sizes. When effect sizes were partitioned by experimental design, we found increased genetic variation in studies based on broad-sense measures of variance, and decreased variation in narrow-sense studies, in support of previous research. Therefore, the source of genetic variance, not the definition of a novel environment, was key to understanding environment-dependant genetic variation, highlighting non-additive genetic variance as an important component of cryptic genetic variation and avenue for future research.</p>
On the fast track: Hybrids adapt more rapidly than parental populations in a novel environment
<p>Rates of hybridization are predicted to increase due to climate change and human activity that cause redistribution of species and bring previously isolated populations into contact. At the same time, climate change leads to rapid changes in the environment, requiring populations to adapt rapidly in order to survive. A few empirical cases suggest hybridization can facilitate adaptation despite its potential for incompatibilities and deleterious fitness consequences. Here we use simulations and Fisher's Geometric model to evaluate the conditions and time frame of adaptation via hybridization in both diploids and haplodiploids. We find that hybrids adapt faster to new environments compared to parental populations in nearly all simulated scenarios, generating a fitness advantage that can offset intrinsic incompatibilities and last for tens of generations, regardless of whether the population was diploid or haplodiploid. Our results highlight the creative role of hybridization and suggest that hybridization may help contemporary populations adapt to the changing climate. However, adaptation by hybrids may well happen at the cost of reduced biodiversity, if previously isolated lineages collapse into one.</p>
Novel environments induce variability in fitness-related traits
<p class="MsoNormal">Environmental change from anthropogenic activities threatens individual organisms, the persistence of populations, and entire species. Rapid environmental change puts organisms in a double bind, they are forced to contend with novel environmental conditions but with little time to respond. Phenotypic plasticity can act quickly to promote establishment and persistence of individuals and populations in novel or altered environments. In typical environmental conditions, fitness-related traits can be buffered, reducing phenotypic variation in expression of traits, and allowing underlying genetic variation to accumulate without selection. In stressful conditions, buffering mechanisms can break down, exposing underlying phenotypic variation and permitting the expression of phenotypes that may allow populations to persist in the face of altered or otherwise novel environments. Using reciprocal transplant experiments of freshwater snails, we demonstrate that novel conditions induce higher variability in growth rates and, to a lesser degree, morphology (area of the shell opening) relative to natal conditions. Our findings suggest a potentially important role of phenotypic plasticity in population persistence as organisms face a rapidly changing, human-altered world.</p>
Novel Methods for Implementing Measurement-Based Care for Youth in Low-resource Environments
ClinicalTrials.gov study NCT05644756. IPD Sharing: NO. Countries: 1. Publications: 2.
Novel Training Environment to Normalize Altered Finger Force Direction Post Stroke
ClinicalTrials.gov study NCT03995069. IPD Sharing: YES. Countries: 1. Publications: 2.
Assessing a Novel Virtual Environment That Assists With Activities of Daily Living
ClinicalTrials.gov study NCT05418296. IPD Sharing: NO. Countries: 1. Publications: 3.
Data from: Genetic monitoring of brown trout released into a novel environment: Establishment and genetic impact on natural populations
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Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments
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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.