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231 results for “adaptive plasticity”
Data from: Adaptive developmental plasticity in a butterfly: mechanisms for size and time at pupation differ between diapause and direct development
Diapause (overwintering) and direct development are alternative developmental pathways in temperate insects. Diapause necessitates physiological preparations for dormancy, while direct development is associated with strong time constraints, resulting in selection for fast development under the direct development pathway. Physiological and behavioural preparations for pupation contribute to development time, so divergent selection in them is expected between the alternative developmental pathways. Critical mass for pupation induction is a central physiological parameter for the pupation process. Here, we compare the critical masses and the characteristics of the wandering stage – wandering taking place after the cessation of growth and before pupation – between diapausing and directly developing larvae in the butterfly Pieris napi. Critical mass estimation succeeded only for diapausing individuals, among which it was lower in females than in males, indicating an inter-pathway difference in the physiology of critical mass. Directly developing individuals wandered for a shorter time and distance and lost less mass before pupation than diapausing individuals. These physiological and behavioural differences represent adaptive phenotypic plasticity and contribute to fast development under direct development. Thus, the observed developmental plasticity in physiology offers a mechanistic explanation for adaptive life-history variation between alternative developmental pathways and sexual dimorphism.
Data from: Trait specific consequences of inbreeding on adaptive phenotypic plasticity
Environmental changes may stress organisms and stimulate an adaptive phenotypic response. Effects of inbreeding often interact with the environment and can decrease fitness of inbred individuals exposed to stress more so than that of outbred individuals. Such an interaction may stem from a reduced ability of inbred individuals to respond plastically to environmental stress; however, this hypothesis has rarely been tested. In this study, we mimicked the genetic constitution of natural inbred populations by rearing replicate Drosophila melanogaster populations for 25 generations at a reduced population size (10 individuals). The replicate inbred populations, as well as control populations reared at a population size of 500, were exposed to a benign developmental temperature and two developmental temperatures at the lower and upper margins of their viable range. Flies developed at the three temperatures were assessed for traits known to vary across temperatures, namely abdominal pigmentation, wing size, and wing shape. We found no significant difference in phenotypic plasticity in pigmentation or in wing size between inbred and control populations, but a significantly higher plasticity in wing shape across temperatures in inbred compared to control populations. Given that the norms of reaction for the noninbred control populations are adaptive, we conclude that a reduced ability to induce an adaptive phenotypic response to temperature changes is not a general consequence of inbreeding and thus not a general explanation of inbreeding–environment interaction effects on fitness components.
Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum
Gene expression is known to be highly responsive to the environment and important for adjustment of metabolism but there is also growing evidence that differences in gene regulation contribute to species divergence and differences among locally adapted populations. However, most studies so far investigated populations when divergence had already occurred. Selection acting on expression levels at the onset of adaptation to an environmental change has not been characterized. Understanding the mechanisms is further complicated by the fact that environmental change is often multivariate, meaning that organisms are exposed to multiple stressors simultaneously with potentially interactive effects. Here we use a novel approach by combining fitness and whole-transcriptome data in a large-scale experiment to investigate responses to drought, heat and their combination in Tribolium castaneum . We found that fitness was reduced by both stressors and their combined effect was almost additive. Expression data showed that stressor responses were acting independently and did not interfere physiologically. Since we measured expression and fitness within the same individuals, we were able to estimate selection on gene expression levels. We found that variation in fitness can be attributed to gene expression variation and that selection pressures were environment dependent and opposite between control and stress conditions. We could further show that plastic responses of expression were largely adaptive, i.e. in the direction that should increase fitness.
Data from: Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod
Organisms may respond to changing environments through phenotypic plasticity or adaptive evolution. These two processes are not mutually exclusive and may either dampen or strengthen each other's effects, depending on the genetic correlation between trait values and the slopes of their norms of reaction. To examine the effect of adaptation to heat stress on the plasticity of heat tolerance, we hybridized populations of the crustacean Tigriopus californicus that show divergent phenotypes for heat tolerance. We then selected for increased heat tolerance in hybrids and measured heat tolerance and the phenotypic plasticity of heat tolerance in both selected lines and unselected controls. To test whether the changes in phenotypic plasticity were associated with changes in the plasticity of gene expression, we also sequenced transcriptomes of selected and unselected lines, both under heat shock and at ambient temperatures. We observed increased heat tolerance in selected lines, but also lower phenotypic and transcriptional plasticity in response to heat stress. The plastic response to heat stress was highly enriched for hydrolytic and catalytic activities, suggesting a prominent role for degradation of misfolded proteins. Our findings have important implications for biological responses to climate change: if adaptation to environmental stress reduces plasticity, then plasticity and adaptive evolution will make overlapping, rather than additive contributions to buffering populations from environmental change.
Intraspecific variation of Phragmites australis: Clinal adaption of functional traits and phenotypic plasticity vary with latitude of origin
<p>1. Widespread plant species generally have high intraspecific variation in functional traits, which is reflected in their great variety of phenotypes. This variety can result from both genetic differences due to local adaptation and phenotypic plasticity. With high intraspecific variation and nearly global distribution, the common reed <i>Phragmites australis</i> is a suitable model species for studying the underlying mechanisms of intraspecific trait variation. </p> <p>2. In this study, 71 genotypes of <i>P. australis</i> from seven phylogeographic groups were transplanted into two replicate common gardens located in very different climates: northern Europe and mid-east Asia. We measured seven functional traits of all these genotypes over the growing season, including shoot height, maximum biomass per shoot, shoot density, node number per stem, leaf lifespan, flowering occurrence and flowering date. Our aim was to assess the relative effects of genetic (phylogeographic origin) and environmental (common garden) status, and interactions between them, on intraspecific variation in functional traits of <i>P. australis</i>. </p> <p>3. We found common garden having the strongest influence on most functional traits studied. All traits except flowering occurrence varied significantly across gardens, revealing the important role of phenotypic plasticity on trait variation of <i>P. australis</i>. We also found significant differences in trait variation among the different phylogeographic groups of <i>P. australis</i> and, thus, evidence for genetically determined intraspecific variation in the morphological and life-history traits addressed in this study. All functional traits showed significant (p≤0.0054), albeit minor to moderately explained (<i>R</i><sup>2</sup> ≤0.57), latitudinal patterns in both gardens. Covariation of multiple traits was similar in the two gardens. Phenotypic plasticity was trait-specific, and the plasticity of shoot height and maximum biomass per shoot increased towards higher latitude of genotypic origin. Our results indicate that the latitude of origin affects the evolution of functional traits, as well as their phenotypic plasticity. </p> <p>4. Since phenotypic plasticity is a crucial mechanism for acclimation and evolution, our findings support the role of gene-based adaptive phenotypic plasticity in plant evolution. The intraspecific spatial variation of functional traits and their phenotypic plasticity can help predict species distribution, persistence and invasion under global climate change.</p>
Data from: Plastic and evolutionary gene expression responses are correlated in European grayling (Thymallus thymallus) sub-populations adapted to different thermal environments
Understanding how populations adapt to changing environmental conditions is a long-standing theme in evolutionary biology. Gene expression changes have been recognized as an important driver of local adaptation, but relatively little is known regarding the direction of change and in particular, about the interplay between plastic and evolutionary gene expression. We have previously shown that the gene expression profiles of European grayling (Thymallus thymallus) populations inhabiting different thermal environments include both plastic and evolutionary components. However, whether the plastic and evolutionary responses were in the same direction was not investigated in detail, nor was the identity of the specific genes involved. In this study, we show that the plastic changes in protein expression in response to different temperatures are highly correlated with the evolutionary response in grayling subpopulations adapted to different thermal environments. This finding provides preliminary evidence that the plastic response most likely facilitates adaptation during the early phases of colonization of thermal environments. The proteins that showed significant changes in expression level between warm and cold temperature treatments were mostly related to muscle development, which is consistent with earlier findings demonstrating muscle mass differentiation between cold and warm grayling populations.
Dataset from the Am J Bot 2016 103(9) paper: "Disentangling plasticity of serotiny, a key adaptive trait in a Mediterranean conifer"
<p>Raw data from the American Journal of Botany paper: "Disentangling plasticity of serotiny, a key adaptive trait in a Mediterranean conifer" Am J Bot. 2016 Sep;103(9):1582-91. doi: 10.3732/ajb.1600199</p>
Supplementary material 1 from: Muraro M, Romagnoli S, Barzaghi B, Falaschi M, Manenti R, Ficetola GF (2021) Invasive predators induce plastic and adaptive responses during embryo development in a threatened frog. NeoBiota 70: 69-86. https://doi.org/10.3897/neobiota.70.65454
Geographic coordinates of the monitored sites and the significance of the independent variables in the three parental investment mixed models.
Genomic data from: Are you ready for the heat? Phenotypic 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>
Male adaptive plasticity can explain the evolution of sexual perception costs
<p>Sensory perception of environmental cues has been shown to trigger plastic responses that can induce important fitness costs, including the dramatic modulation of ageing across distant taxa. For example, male Drosophila melanogaster suffer a marked decrease in fitness, including faster reproductive and actuarial ageing, if they perceive female cues but fail to mate shortly after (ageing via sexual perception). While this has been a breakthrough for our understanding of the mechanisms of ageing, it poses the question as to why such plastic responses evolved. Here, we used D. melanogaster to ask whether sexual perception costs may be a by-product of plastic adaptive responses to female cues. We found that: a) short-term (1 day) perception of female cues prior to mating opportunities increases male relative lifetime reproductive success in a competitive environment, b) medium-term (3-7 days) perception is neutral, and c) long-term (15 days) perception leads to reproductive costs. We then ran mathematical simulations under a wide range of socio-sexual and demographic scenarios to show that such plastic male responses can be adaptive whenever mating rates fluctuate within the range experienced by D. melanogaster and other insects in the wild, suggesting this may be a widespread strategy in nature. Finally, we show that, because the short-term benefits of plastic responses will be mostly acquired by high-quality males while long-term costs will be mostly paid by low-quality males, sexual perception can significantly magnify sexual selection (15-27% average increase in the opportunity for selection).</p>
Data from: Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads
<p>Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (<i>Spea multiplicata</i>). <i>Spea</i> tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 12 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.</p>
Dataset of Rapid adaptive responses of rosette-type macrophyte Vallisneria natans juveniles to varying water depths: The role of leaf trait plasticity
<p>Rosette-type submerged macrophytes are widely distributed across a range of water depths in shallow lakes and play a key role in maintaining ecosystem structures and functions. However, little is known about the rapid adaptive responses of such macrophytes to variations in water depth, especially at the juvenile stage. Here, we conducted a short term <i>in situ</i> mesocosm experiment, in which the juveniles of <i>Vallisneria natans</i> were exposed to a water depth gradient ranging from 20 to 360 cm. Twenty-two leaf-related traits were examined after four weeks of growth in a shallow lake. Most (18) traits of <i>V. natans</i> generally showed high plasticity in relation to water depth. Specifically, juveniles allocated more biomass to leaves, and had higher specific leaf area, leaf length to width ratio, chlorophyll content, and carotenoids content in deep waters, displaying trait syndrome associated with high resource acquisition. In contrast, <i>V. natans</i> juveniles in shallow waters had higher leaf dry matter content, leaf soluble carbohydrate content, carotenoids per unit chlorophyll, and peroxidase activity, pertaining to resource conservation. Notably, underwater light intensity was found to be the key factor explaining the trait plasticity along the water depth gradient, and 1.30 mol photons m<sup>–2</sup> d<sup>–1 </sup>(at 270 cm) could be the optimal irradience level based on the total biomass of <i>V. natans</i> juveniles. The present study highlights the significance of leaf trait plasticity for rosette-type macrophytes in response to variations in water depth, and sheds new light on the differences between trade-offs in deep- and shallow-water areas.</p>
Phenotypic Plasticity Structure of Metasequoia glyptostroboides (Taxodiaceae) Fine Adventitious Roots Adapt to Aquatic and Terrestrial Environments
<p>Supplement 1. Phellogen close to the remnant exodermis and under lysigenous primary phloem. Match to Fig. 2C, D, secondary xylem, vascular cambium (below arrowhead), phellogen (arrows), lysigenous primary phloem (black arrow), phloem aerenchyma, dilated parenchyma (*), phloem fibers, remnant exodermis (ex), staining: TBO; scale bars = 50 μm;</p> <p> </p> <p>Supplement 2. Phellogen under lysigenous primary phloem. Match to Fig. 2C, D, secondary xylem, vascular cambium (below arrow), phellogen (arrows), lysigenous primary phloem (black arrow), cortical aerenchyma, dilated parenchyma (*), phloem fibers, remnant exodermis (ex), staining: TBO; scale bars = 50 μm;</p>
Data from: Niche specialization influences adaptive phenotypic plasticity in threespine stickleback
Phenotypic plasticity may be favored in generalist populations if it increases niche width, even in temporally constant environments. Phenotypic plasticity can increase the frequency of extreme phenotypes in a population and thus allow it to make use of a wide resource spectrum. Here we test the prediction that generalist populations should be more plastic than specialists. In a common-garden experiment, we show that solitary, generalist populations of threespine sticklebacks inhabiting small coastal lakes of British Columbia have a higher degree of morphological plasticity than the more specialized sympatric limnetic and benthic species. The ancestral marine stickleback showed low levels of plasticity similar to those of sympatric sticklebacks, implying that the greater plasticity of the generalist population has evolved recently. Measurements of wild populations show that those with mean trait values intermediate between the benthic and limnetic values indeed have higher morphological variation. Our data indicate that plasticity can evolve rapidly after colonization of a new environment in response to changing niche use.
Data from: Dissecting the contributions of plasticity and local adaptation to the phenology of a butterfly and its host plants
Phenology affects the abiotic and biotic conditions that an organism encounters and consequently its fitness. For populations of high latitude species, spring phenology often occurs earlier in warmer years and regions. Here we apply a novel approach to decompose spatiotemporal covariation between spring temperature and the phenology of two flowering plants, Cardamine pratensis and Alliara petiolata, and a Lepidopteran herbivore, Anthocharis cardamines, across the UK, into the contributions of plasticity and local adaptation. All three species overlap in the time-window over which mean temperatures best predict variation in phenology and we find little evidence that the position of time-windows varies latitudinally, as expected if they were initiated by day-length. The focal species show pronounced temperature-mediated phenological plasticity of similar magnitude. While we find no evidence for local adaptation in the flowering times of the plants, geographic variation in the phenology of the butterfly reveals countergradient local adaptation. Geographic variation in the butterfly's phenology appears to be more sensitive to variation in temperature than the flowering times of the host plants and we find no evidence that coevolution has generated geographic variation in adaptive phenological plasticity.
Data from: Adaptive maternal behavioral plasticity and developmental programming mitigate the transgenerational effects of temperature in dung beetles
Phenotypic plasticity allows organisms to cope with rapid environmental change. Yet exactly when during ontogeny plastic responses are elicited, whether plastic responses produced in one generation influence phenotypic variation and fitness in subsequent generations, and the role of plasticity in shaping population divergences, remains overall poorly understood. Here, we use the dung beetle <i>Onthophagus taurus</i> to assess plastic responses to temperature at several life stages bridging three generations and compare these responses across three recently diverged populations. We find that beetles reared at hotter temperatures grow less than those reared at mild temperatures, and that this attenuated growth has transgenerational consequences by reducing offspring size and survival in subsequent generations. However, we also find evidence that plasticity may mitigate these consequences in two ways: (i) mothers modify the temperature of their offspring's developmental environment via behavioral plasticity and (ii) in one population, offspring exhibit accelerated growth when exposed to hot temperatures during very early development ("developmental programming"). Lastly, our study reveals that offspring responses to temperature diverged among populations in fewer than 100 generations, possibly in response to range-specific changes in climatic or social conditions.
Data from: Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads
<p>Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (<i>Spea multiplicata</i>). <i>Spea</i> tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (<i>Spea multiplicata</i>). <i>Spea</i> tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.</p>
Larval development and poor food availability: Local adaptations and plasticity in a widespread amphibian species
<p>Data of fire salamander larvae reared under rich and poor food conditions. Data include also length, growth rate and number of prey attacked by the same larvae for 30 days after metamorphosis.</p> <p>In this study, we considered two extrinsic factors such as food availability and altitude and we examined their effects on larval growth, timing of metamorphosis and survival in fire salamander larvae. We also investigated whether larval diet has repercussions on growth rate of juvenile salamanders in the month following metamorphosis.</p> <p>Our experimental study was conducted on 150 newborn fire salamander larvae from 15 epigean sites at different altitudes (ranging between 250 and 1491 m a.s.l.). The larvae of each site were divided into two treatment groups: "poor" and "rich" food conditions. </p>
Plasticity and the adaptive evolution of switchlike reaction norms under environmental change
<p>Phenotypic plasticity is often posited as an avenue for adaptation to environmental change, whereby environmental influences on phenotypes could shift trait expression toward new optimal values. Conversely, plastic trait expression may inhibit adaptation to environmental change by reducing selective pressure on ill-adapted traits. While plastic responses are often assumed to be linear, non-linear phenotype-environment relationships are common, especially in thermally-sensitive traits. Here we examine non-linear plasticity in a trait with great ecological and evolutionary significance: sexual phenotype in species with environmental sex determination (ESD). In species with ESD development switches between male and female at an environmental threshold (the inflection point). The inflection point is a key trait for adaptive responses to changing environments and should evolve toward the new optimum in order to maintain evolutionarily stable sex ratios. We used an individual-based theoretical model to investigate how two forms of plasticity in the ESD reaction norm – the non-linear slope of the reaction norm and a linear shift in the inflection point – influence the evolution of the inflection point under climate warming. We found that steeper reaction norm slopes (high non-linear plasticity) promoted evolution toward new optimal phenotypes (higher inflection points). In contrast, increased linear plasticity in the inflection point (shift) hindered adaptive evolution. Additionally, populations in moderate warming scenarios showed greater adaptive evolution of the inflection point compared with extreme warming scenarios, suggesting that the proximity of existing phenotypes to new optimal phenotypes influences evolutionary outcomes. Unexpectedly, we found greater population persistence under high climate variability, due to the increased production of rare-sex individuals in unusually cold years. Our results demonstrate that different forms of phenotypic plasticity have crucially different effects on adaptive evolution. Plasticity that prevented sex ratio bias hindered the evolution of the inflection point, while plasticity that exacerbated sex ratio bias promoted adaptation to environmental change. </p>
Data and Code for: Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America
<p>This submission contains all the code and data necessary for reproducing 1) the dataset, 2) the main results, and 3) all supplemental analyses appearing in the manuscript titled: <em>Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America</em> (Ramirez-Parada, Park, Record, Davis, Ellison, and Mazer, 2023). A preprint of this manuscript can be accessed at: https://doi.org/10.21203/rs.3.rs-3131821/v1.</p> <p> </p> <p>Extracting the compressed file will generate a folder titled "Project folder", containing sub-folders named "Data" and "R code". In order for the code to work, users need to preserve the folder structure of the code and data, as the R Markdown files in the "R code" folder have relative file paths that read and write data within the "Data" folder. Moving either would require re-writing the filepaths across Rmds for the code to run.</p> <p><br> To replicate the results, the following R Markdowns must be run in sequence (once they have been run, the Rmds for supplemental analyses can be used in any order):</p> <p><br> <em>"1. Subsetting Dataset.Rmd"</em></p> <p>This file processes a specimen dataset of ca. 2.3 million specimens that we assembled for this project (publicly available on Dryad: <a href="https://doi.org/10.25349/D9WP6S">https://doi.org/10.25349/D9WP6S</a>), filtering out duplicates, specimens out of the spatial scope of the PRISM data used for all analyses, and subsetting to only those species represented by a minimum of 300 specimens. This filtering yields a dataset of 1,038,047 specimens in flower across 1,605 species.</p> <p>For an in-depth description of the starting dataset, please refer to the "READ ME.txt" file within the "Project folder", and visit its corresponding Dryad repository (linked above).</p> <p><br> <em>"2. Main Analysis - Estimating S_space, S_time, and S_diff.Rmd"</em></p> <p>This file uses the subset dataset produced by the previous Rmd to fit the varying-intercepts, varying-slopes model that produced the estimates of apparent plasticity and apparent adaptation underlying all main analyses. This Rmd exports a dataset of species-specific estimates of S<sub>space</sub>, S<sub>time</sub>, and S<sub>space</sub> - S<sub>time</sub> that is used to recreate Figures 2, 3, and 4 of the main text in the next step. This is the most time consuming R Markdown file to run, as each MCMC chain used to fit the model in Stan must be run on a dedicated processor (limiting the usefulness of parallel computation). Fitting the model using 3 MCMC chains, 1000 iterations for warmup, and 4000 iterations for sampling, took approximately 24 hours using an Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz processor. </p> <p> </p> <p><em>"3. Main Analysis - Figures 2, 3, and 4.Rmd"</em></p> <p>Finally, this Rmd uses the dataset of species-specific estimates to conduct all analyses underlying Figures 2, 3, and 4, recreating each of these figures.</p> <p><strong><em>For detailed descriptions of all materials (code and data) and instructions for using them, please refer to the "READ ME.txt" file within "Project folder". </em></strong></p> <p> </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.