Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
829
datasets available to search
ShareScore release 0.9.0
Dataset results
829 results for “Evolvability”
Can disease resistance evolve independently at different ages? Genetic variation in age-dependent resistance to disease in three wild plant species
Open the record for dataset details and reuse information.
Data for: Eco-evolutionary interactions with multiple evolving species reveal both antagonistic and additive effects
Open the record for dataset details and reuse information.
Do animal personality components independently evolve and develop in response to environmental complexity?
Open the record for dataset details and reuse information.
Aphid male wing polymorphisms are transient and have evolved repeatedly
Open the record for dataset details and reuse information.
Genetic, developmental and neural changes underlying evolving butterfly mate preference
Open the record for dataset details and reuse information.
Data from: Responses of activity rhythms to temperature cues evolve in Drosophila populations selected for divergent timing of eclosion
Even though the rhythm in adult emergence and rhythm in locomotor activity are two different rhythmic phenomena that occur at distinct life-stages of the fly life cycle, previous studies have hinted at similarities in certain aspects of the organisation of the circadian clock driving these two rhythms. For instance, the period gene plays an important regulatory role in both rhythms. In an earlier study, we have shown that selection on timing of adult emergence behaviour in populations of Drosophila melanogaster leads to the co-evolution of temperature sensitivity of circadian clocks driving eclosion. In this study, we were interested in asking if temperature sensitivity of the locomotor activity rhythm has evolved in our populations with divergent timing of adult emergence rhythm, with the goal of understanding the extent of similarity (or lack of it) in circadian organisation between the two rhythms. We found that in response to simulated jetlag with temperature cycles, late chronotypes (populations selected for predominant emergence during dusk) indeed re-entrain faster than early chronotypes (populations selected for predominant emergence during dawn) to 6-h phase-delays, thereby indicating enhanced sensitivity of the activity/rest clock to temperature cues in these stocks (entrainment is the synchronisation of internal rhythms to cyclic environmental time-cues). Additionally, we found that late chronotypes show higher plasticity of phases across regimes, day-to-day stability in phases and amplitude of entrainment, all indicative of enhanced temperature sensitive activity/rest rhythms. Our results highlight remarkably similar organisation principles between emergence and activity/rest rhythms.
Data from: A rapidly evolved shift in life history timing during ecological speciation is driven by the transition between developmental phases
<p>For insect species in temperate environments, seasonal timing is often governed by the regulation of diapause, a complex developmental program that allows insects to weather unfavorable conditions and synchronize their lifecycles with available resources. Diapause development consists of a series of distinct phases including initiation, maintenance, termination, and post-diapause development. The evolution of insect seasonal timing depends in part on how these phases of diapause development and post-diapause development interact to affect variation in phenology. Here, we dissect the physiological basis of a recently evolved phenological shift in Rhagoletis pomonella (Diptera: Tephritidae), a model system for ecological divergence. A recently derived population of R. pomonella shifted from specializing on native hawthorn fruit to earlier fruiting introduced apples, resulting in a 3-4 week shift in adult emergence timing. We tracked metabolic rates of individual flies across post-winter development to test which phases of development may act either independently or in combination to contribute to this recently evolved divergence in timing. Apple and hawthorn flies differed in a number of facets of their post-winter developmental trajectories. However, divergent adaptation in adult emergence phenology in these flies was due almost entirely to the end of the pupal diapause maintenance phase, with post-diapause development having a very small effect. The relatively simple underpinnings of variation in adult emergence phenology suggest that further adaptation to seasonal change in these flies for this trait might be largely due to the timing of diapause termination unhindered by strong covariance among different components of post-diapause development.</p>
Floral signals evolve in a predictable way under artificial and pollinator selection in Brassica rapa
<p>You find here the R scripts and data necessary to reproduce the results published in "Floral signals evolve in a predictable way under artificial and pollinator selection in Brassica rapa" by Zu et al. 2020 BMC Evolutionary Biology.</p> <p>The whole analysis is in the script "G-analysis.R". The associated data is loaded from the ".Rdata" and ".txt" files associated. The scripts "randG...R" are required to generate bootstrap replicates of G-matrix estimates. This is best done on an HPC cluster. To avoid having to run those randomizations, we provide the summary data we have generated from randomizations to run the full analysis.</p> <p>In Zu et al., we used data from an artificial selection and a pollinator (bumblebee, hoverfly) evolution experiment with fast cycling <em>Brassica rapa </em>plants to predict evolutionary changes of 12 floral volatiles and 4 morphological floral traits in response to selection. Using the observed selection gradients and the genetic variance-covariance matrix (G-matrix) of the traits, we showed that the observed responses of most floral traits including volatiles were predicted in the right direction in both artificial- and bumblebee-selection experiment. Genetic covariance had a mix of constraining and facilitating effects on evolutionary responses. We further revealed that G-matrices also evolved in the selection processes.</p> <p>We are depositing here the raw phenotypic data used to estimate the G-matrices in the artificial selection experiment along with the R scripts used to run the analyses.</p> <p>The phenotypic data of the pollinator experimental evolution experiment have been published elsewehere (Gervasi & Schiestl, 2017, Nature Communications 8:14691; doi:10.1038/ncomms14691).</p>
Data from: Selfing ability and drift load evolve with range expansion
Colonization at expanding range edges often involves few founders, reducing effective population size. This process can promote the evolution of self-fertilization, but implicating historical processes as drivers of trait evolution is often difficult and requires an explicit model of biogeographic history. In plants, contemporary limits to outcrossing are often invoked as evolutionary drivers of self-fertilization, but historical expansions may shape mating system diversity, with leading-edge populations evolving elevated selfing ability. In a widespread plant, Campanula americana, we identified a glacial refugium in the southern Appalachian Mountains from spatial patterns of genetic drift among 24 populations. Populations farther from this refugium have smaller effective sizes and fewer rare alleles. They also displayed elevated heterosis in among-population crosses, reflecting the accumulation of deleterious mutations during range expansion. While populations with elevated heterosis had reduced segregating mutation load, the magnitude of inbreeding depression lacked geographic pattern. The ability to self-fertilize was strongly positively correlated with the distance from the refugium and mutation accumulation—a pattern that contrasts sharply with contemporary mate and pollinator limitation. In this and other species, diversity in sexual systems may reflect the legacy of evolution in small, colonizing populations, with little or no relation to the ecology of modern populations.
Association between susceptibility of Thrips palmi to spinetoram and frequency of G275E mutation provides basis for molecular diagnostics of field-evolved resistance
<p><b><span>Background</span></b><span>: Spinosyn resistance is an increasing problem in field control of targeted pests. While putative mechanisms underlying spinosyn resistance have been identified in controlled studies on many species, mechanisms underlying field-evolved resistance and the development of a molecular diagnostic method for monitoring field resistance have lagged behind. Here, we examined levels of resistance of melon thrips, <i>Thrips palmi,</i> to spinetoram as well as target site mutations in field populations across China to identify potential mechanisms and useful molecular markers for diagnostic purposes.</span></p> <p><b><span>Results</span></b><span>: LC<sub>50</sub> </span><span>of 16 field-collected populations to the spinetoram varied from 0.12 to 759.34 </span>mg L<sup>-1</sup><span>. In resistant populations, we identified the G275E mutation, which has previously been linked to spinosyns resistance, as well as another nonsynonymous mutation, F314V, both located in the <i>α</i>6 subunit of the nicotinic acetylcholine receptor. There was a strong correlation between levels of spinetoram resistance and allele frequency of G275E mutation in field-collected populations (<i>r<sup>2</sup></i> = 0.84) and those reared under laboratory conditions for two to five generations (<i>r<sup>2</sup></i> = 0.91). LC<sub>50</sub> ranged from 0.12 to 0.66 </span>mg L<sup>-1</sup><span> in populations without </span><span>G275E mutation, while it ranged from </span>33.12<span> to 39.91</span> mg L<sup>-1</sup><span> in most populations with a </span><span>G275E mutation frequency > 90%, with the exception of one field-collected population which had an G275E frequency of 92% and a very high LC<sub>50</sub> value of 759.34</span> mg L<sup>-1</sup><span>, suggesting additional mechanisms.</span></p> <p><b><span>Conclusions: </span></b><span>Our results indicate that field-evolved resistance of <i>T. palmi</i> to spinetoram in China is mainly conferred by the G275E mutation, with other mechanisms contributing to a higher level of resistance. The frequency of the G275E mutation provides a useful diagnostic for quantifying resistance levels in field populations of <i>T. palmi</i>.</span></p>
The Life Cycle of Features in Highly-Configurable Software Systems Evolving in Space and Time
<p>Dataset covering the entire development history of four open-source systems from different domains, covering a total of 37500 commits from up to 20 years of development, which can serve as a source of information for new studies on the evolution of systems in space and time.</p>
Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation
Body size plays a key role in the ecology and evolution of all organisms. Therefore, quantifying the sources of morphological (co)variation, dependent and independent of body size, is of key importance when trying to understand and predict responses to selection. We combine structural equation modeling with quantitative genetics analyses to study morphological (co)variation in a meta-population of house sparrows (Passer domesticus). As expected, we found evidence of a latent variable 'body size', causing genetic and environmental covariation between morphological traits. Estimates of conditional evolvability show that allometric relationships constrain the independent evolution of house sparrow morphology. We also found spatial differences in general body size and its allometric relationships. On islands where birds are more dispersive and mobile, individuals were smaller and had proportionally longer wings for their body size. While in islands where sparrows are more sedentary and nest in dense colonies, individuals were larger and had proportionally longer tarsi for their body size. We corroborated these results using simulations and show that our analyses produce unbiased allometric slope estimates. This study highlights that in the short term allometric relationships may constrain phenotypic evolution, but that in the long term selection pressures can also shape allometric relationships.
Detecting selected haplotype blocks in evolve and resequence experiments
Shifting from the analysis of single nucleotide polymorphisms to the reconstruction of selected haplotypes greatly facilitates the interpretation of Evolve and Resequence (E&R) experiments. Merging highly correlated hitchhiker SNPs into haplotype blocks reduces thousands of candidates to few selected regions. Current methods of haplotype reconstruction from Pool-Seq data need a variety of data-specific parameters that are typically defined ad hoc and require haplotype sequences for validation. Here, we introduce haplovalidate, a tool which detects selected haplotypes in Pool-seq time series data without the need for sequenced haplotypes. Haplovalidate makes data-driven choices of two key parameters for the clustering procedure, the minimum correlation between SNPs constituting a cluster and the window size. Applying haplovalidate to simulated and experimental E&R data reliably detects selected haplotype blocks with low false discovery rates. Importantly, our analyses identified a restriction of the haplotype block-based approach to describe the genomic architecture of adaptation. We detected a substantial fraction of haplotypes containing multiple selection targets. These blocks were considered as one region of selection and therefore led to under-estimation of the number of selection targets. We demonstrate that the separate analysis of earlier time points can significantly increase the separation of selection targets into individual haplotype blocks. We conclude that the analysis of selected haplotype blocks has great potential for the characterisation of the adaptive architecture with E&R experiments.
Data from: Evolvability and craniofacial diversification in genus Homo
There is abundant theoretical and empirical evidence for the influence of variational properties of populations on microevolution, and more limited support for their lasting impact during macroevolution. This study applies evolutionary quantitative genetic approaches to assess the long-term impact of within-population phenotypic variation and covariation (the P matrix) on population divergence in recent humans and species diversification in genus Homo. Similarity between the primary axes of within- and between-population craniofacial variation confirms a role for pmax in human population divergence, although diversification is not constrained to be unidimensional. The long term impact of the P matrix on craniofacial evolution is supported by higher-than-average evolvabilities along most branches of the Homo tree, but statistical uncertainty inherent in the data reduce confidence in this conclusion. Higher evolvability is not statistically correlated with increased rate of evolution, although the relationship is in the predicted direction. This is due in part to the high evolutionary rate on the early modern human branch despite its moderate level of evolvability. There was evidence for neutral evolution as well as directional and stabilizing selection over the Plio-Pleistocene using generalized genetic distance as a test statistic.
Environment dependent costs and benefits of recombination in independently evolved populations of Escherichia coli
Understanding of the causes by which reproductive isolation arises remains limited. We examine the role of adaptation in driving reproductive isolation among 12 Escherichia coli populations evolved in two different environments. We found that, regardless of whether parents were selected in the same or different environments, the average fitness of recombinants was lower than the expected, consistent with a prevailing influence of incompatibility between independently accumulated mutations. Exceptions to this pattern occurred among recombinants of some parents evolved in different environments. These recombinants were less fit than expected in the selective environment of one parent, but more fit than expected in the selective environment of the other parent. Our results indicate that both parallel and divergent adaptation can quickly lead to intrinsic genetic barriers contributing to the initial stages of speciation and show that these barriers can be complex, for example, depending on the environment in which recombinant offspring are tested.
Migratory lineages rapidly evolve larger body sizes than non-migratory relatives in ray-finned fishes
<p><span>Migratory animals respond to environmental heterogeneity by predictably moving long distances in their lifetime. Migration has evolved repeatedly in animals, and many adaptations are found across the tree of life that increase migration efficiency. Life history theory predicts that migratory species should evolve a larger body size than non-migratory species and some empirical studies have shown this pattern. A recent study analyzed the evolution of body size between diadromous and non-diadromous </span>shads, herrings, anchovies and allies<span>, finding that species evolved larger body sizes when adapting to a diadromous lifestyle. It remains unknown whether different fish clades adapt to migration similarly. We used an adaptive landscape framework to explore body size evolution for over 4500 migratory and non-migratory species of ray-finned fishes. By fitting models of macroevolution, we show that migratory species are evolving towards a body size that is larger than non-migratory species. Furthermore, we find that migratory lineages evolve towards their optimal body size more rapidly than non-migratory lineages, indicating body size is a key adaption for migratory fishes. Our results show, for the first time, that the largest vertebrate radiation on the planet exhibited strong evolutionary determinism when adapting to a migratory lifestyle.</span></p>
Phylogenetic distribution of regeneration and asexual reproduction in Annelida: fission evolves in regenerative clades
<p>Supplementary Data</p> <p>Invertebrate Biology 2016</p> <p>Includes annelid regeneration and fission database (comma separated text table), 2 PDF documents containing field descriptions and full references, 1 Nexus formatted file containing multiple-sequence alignment and RAxML tree, and 1 Geneious formatted file containing multiple-sequence alignment and RAxML tree</p>
Data from: Repeated divergence in opsin genes expression mirrors photic habitat changes in rapidly evolving crater lake cichlid fishes
<div> <div> <div class="msocomtxt"> <p class="MsoNormal"><span>Selection pressures differ along environmental gradients and organisms' phenotypes. Traits tightly linked to fitness (e.g., the visual system) are expected to closely track environmental variation along gradients. Within such gradients, adaptation to local conditions might be due to heritable and non-heritable, environmentally induced variation. Disentangling these sources of phenotypic variation requires studying, in nature and the laboratory, closely related populations experiencing different environments. The Nicaraguan great and crater lakes show an environmental gradient in photic conditions extending from clear crater lakes to very turbid great lakes. From two old, turbid great lakes, Midas cichlid fish (<em>Amphilophus </em>cf.<em> citrinellus</em>) independently colonized seven isolated crater lakes of varying light conditions, resulting in a small adaptive radiation. We estimated the variation in visual sensitivities along this photic gradient by measuring differential cone opsin gene expression among populations from different lakes. The visual sensitivities observed in all seven derived crater lake populations have not changed randomly but shifted predictably in direction and magnitude, repeatedly mirroring changes in photic conditions. Intrapopulation phenotypic variation decreases as environments become spectrally narrower suggesting different selective landscapes within the gradient. Comparing wild-caught and lab-reared fish revealed that 48% of this phenotypic variation is genetically determined and evolved rapidly. Our results demonstrate deterministic, rapid phenotypic evolution that fine-tunes visual sensitivity to fine-scale environmental variation.</span></p> <p class="MsoCommentText"><span> </span></p> </div> </div> </div>
Data from: Plant pathogenic bacterium Ralstonia solanacearum can rapidly evolve tolerance to antimicrobials produced by Pseudomonas biocontrol bacteria
<p>Soil-borne plant pathogens significantly threaten crop production due to lack of effective control methods. One alternative to traditional agrochemicals is microbial biocontrol, where pathogen growth is suppressed by naturally occurring bacteria that produce antimicrobial chemicals. However, it is still unclear if pathogenic bacteria can evolve tolerance to biocontrol antimicrobials and if this could constrain the long-term efficacy of biocontrol strategies. Here we used an <em>in vitro</em> experimental evolution approach to investigate if the phytopathogenic <em>Ralstonia solanacearum </em>bacterium, which causes bacterial wilt disease, can evolve tolerance to antimicrobials produced by <em>Pseudomonas</em> bacteria. We further asked if tolerance was specific to pairs of <em>R. solanacearum</em> and <em>Pseudomonas</em> strain and certain antimicrobial compounds produced by <em>Pseudomonas</em>. We found that while all <em>R. solanacearum</em> strains could initially be inhibited by <em>Pseudomonas</em> strains, this inhibition decreased following successive subculturing with or without <em>Pseudomonas</em> supernatants. Using separate tolerance assays, we show that the majority of <em>R. solanacearum </em>strains evolved increased tolerance to multiple <em>Pseudomonas</em> strains. Mechanistically, evolved tolerance was most likely linked to reduced susceptibility to orfamide lipopeptide antimicrobials secreted by <em>Pseudomonas</em> strains in our experimental conditions. Some levels of tolerance also evolved in the control treatments, which was likely correlated response due to adaptations to the culture media. Together, these results suggest that plant-pathogenic bacteria can rapidly evolve increased tolerance to bacterial antimicrobial compounds, which could reduce the long-term efficacy of microbial biocontrol.</p>
Thermal modeling of subduction zones with prescribed and evolving 2D and 3D slab geometries data
<p>Deforming subduction zone finite element model temperature, velocity, surface and flux field data as reported in the work:</p> <p>N. Sime, C. R. Wilson and P. E. van Keken<br> Thermal modeling of subduction zones with prescribed and evolving 2D and 3D slab geometries.</p>
ScienceDex guides
Understand access before you commit
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.