Find research datasets worth reusing

opencc-by-4.0Aug 2003View details →

Fig. 1 in Peripatopsidae (Onychophora) from New Zealand - observations on selected morphs of the 'Peripatoides novaezealandiae-complex' in culture: morphological and reproductive aspects

Fig. 1: New Zealand localities of observed Peripatopsidae: the abbreviations are for Mount Auckland, Boundary Stream, Paengaroa Mataroa, Mohi Bush, Monckton, Woodville Gorge, Kapiti Island, and Ngapaerera. Part of 'base-map': Modified after Crosby et al. (1976).

opencc-zeroFeb 2023View details →

Nutrient-based species selection is a prevalent driver of community assembly and functional trait space in tropical forests

1. Soil nutrient availability and functional traits interact in complex ways during the assembly of tree communities hindering our understanding of the implications that this may have for their phylogenetic and functional diversity. 2. We combined abundance, taxonomic, phylogenetic and functional trait data of 222 tree species distributed along nutrient concentration gradients at twenty-four plots in two tropical forest study sites. We analysed micro and macronutrient concentration in organic and topsoil horizons and tested for: (1) nutrient-based species sorting due to contrasting trait-environment relationships; (2) whether nutrient filtering has consequences for phylogenetic and functional diversity, and functional space size and occupancy; and (3) we mapped trait distributions across the phylogeny of tree species to track the evolutionary signature of nutrient availability. 3. We found that total nitrogen (N), available phosphorus and total potassium in soil accounted for 68% of the variation in tropical tree species community composition, with strong associations with nutrient concentration for 89% of the tree species included in the analysis. This nutrient-based species selection was mediated by interactions between the three soil nutrient concentrations with leaf nitrogen, leaf thickness and wood density. Soil N concentration was positively associated with the functional space at the site level. At a plot level soil N concentration positively correlated with functional evenness and it was negatively associated with the functional space not occupied by any species in the tree community. Despite the phylogenetic conservatism of leaf N across tree lineages even when not considering legumes, many sister-species pairs show contrasting values which match with their habitat preferences thus indicating the evolutionary lability of this trait, particularly within recently diversified clades. 4. Synthesis. Our results demonstrate that soil nutrient-based species selection is a prevalent driver of community assembly in tropical forests, a process mediated by key functional traits within the leaf and wood economics spectrum. Functional space size and its filling increase with soil nutrient concentration, whereas niche vacancy decreases. This selection process has likely influenced tropical tree species diversification patterns via habitat specialization.

opencc-zeroFeb 2023View details →

Data from: Disruptive selection and the evolution of discrete color morphs in Timema stick insects

A major unresolved issue in biology is why phenotypic and genetic variation is sometimes continuous, yet other times packaged into discrete units of diversity, such as morphs, ecotypes, and species. In theory, ecological discontinuities can impose strong disruptive selection that promotes the evolution of discrete forms, but direct tests of this hypothesis are lacking. Here we show that Timema stick insects exhibit genetically-determined color morphs that range from weakly to strongly discontinuous. Color data from nature and a manipulative field experiment demonstrate that greater morph differentiation is associated with shifts from host plants exhibiting more continuous color variation to those exhibiting greater coloration distance between green leaves and brown stems, the latter of which generates strong disruptive selection. Our results show how ecological factors can promote discrete variation, and we further present results on how this can have variable effects on the genetic differentiation that promotes speciation.

opencc-zeroMar 2023View details →

Selection on offspring size and contemporary evolution under ocean acidification

Ocean acidification may have deleterious effects on many species, but anticipating long-term changes in the abundance of populations will require an understanding of ocean acidification as an evolutionary force. Here I show that ocean acidification alters natural selection on offspring size and is likely to drive contemporary evolution. In a detailed study of a coastal fish species (California Grunion), I demonstrate that larval mortality is highly sensitive to ocean acidification and that mortality rates are lower for larger larvae. However, these effects are countered by tradeoffs between offspring size and number, suggesting that measurements of <a>maternal </a>fitness are critical for quantifying selection through ocean acidification. Measurements of selection and genetic variation were used to project the evolution of larval size as seawater conditions changed incrementally over many decades. Results for California Grunion suggest that contemporary evolution may offset the projected decline in reproductive success by about 50%.

opencc-by-4.0Apr 2022View details →

Scripts of data selection and analysis: role of community size in driving spatial variation in riverine fish metacommunities around the world

Here we describe how we obtained and analyzed data for the manuscript: High compositional dissimilarity among small communities is decoupled from environmental variation, accepted for publication in Oikos. (10.1111/oik.09802). A preprint is also available: https://doi.org/10.32942/osf.io/vngse We investigated the role of community size in mediate the strength of ecological drift and environmental selection in driving community spatial variation in metacommunities.

Evidence for stronger sexual selection in males than females using an adapted method of Bateman's classic study of Drosophila melanogaster

Bateman’s principle, originally a test of Darwin’s theoretical ideas, has since become fundamental to sexual selection theory and vital to contextualising the role of anisogamy and the operational sex ratio in sex differences in both reproductive competition and precopulatory sexual selection. Despite this, Bateman’s principle has received substantial criticism, and researchers have highlighted both statistical and methodological errors, suggesting that Bateman’s original experiment contains too much sampling bias for there to be any evidence of sexual selection. This study uses Bateman’s original method as a template, accounting for two fundamental flaws in his original experiments, (i) viability effects and (ii) a lack of mating behaviour observation. Experimental populations of Drosophila melanogaster consisted of wild-type focal individuals and non-focal individuals established by backcrossing the brown eye (bw-) eye-colour marker. Mating assays included direct observation of mating behaviour and subsequently, total number of offspring were counted, to obtain measures of mating success, reproductive success, and standardised variance measures based on Bateman’s principle. The results provide observational support for Bateman’s principle, particularly that (i) males had significantly more variation in number of mates compared to females and (ii) males had significantly more individual variation in total number of offspring. We also find significantly steeper Bateman gradient for males compared to females, suggesting that sexual selection is operating more intensely in males. However, female remating was limited, providing the opportunity for future study to further explore female reproductive success in correlation with higher levels of remating.

Spring temperature drives phenotypic selection on plasticity of flowering time

Data on field observations of flowering time and fitness of the perennial forest herb Lathyrus vernus and on spring temperature from weather station data. The dataset includes 22 years of data (1987–1996 and 2006–2017) from a L. vernus population located in a deciduous forest in Tullgarn, SE Sweden (58.9496 N, 17.6097 E). It includes records from 837 individuals (607 from 1987 to 1996, and 230 from 2006 to 2017), and from 2478 flowering events. The dataset includes the following variables: year: year of the recording id_nr: numeric plant id id: unique plant id (combination of numeric plant id and period) fcode: flowering code (1 if the plant flowered on that year, 0 if not) FFD: First Flowering Date n_fl: number of flowers n_fr: number of fruits totseed: total number of seeds intactseed: total number of intact seeds (not damaged by seed predator beetles) shoot_vol: shoot volume period: old (1987–1996) or new (2006–2017) n_years_fl_fitness: number of years when data on flowering and fitness is available n_years_study: number of years when the plant was included in the study mean_4: Average daily mean temperature of April (calculated from nearby meteorological station data) cmean_4: Mean-centred average daily mean temperature of April

Data set for article "Selective deuteration as a tool for resolving autoxidation mechanisms in a-pinene ozonolysis"

The data set for publication  "Selective deuteration as a tool for resolving autoxidation mechanisms in a-pinene ozonolysis" (preprint https://doi.org/10.5194/egusphere-2022-1131). Contains raw data files for the CI-orbitrap mass spectrometer (.raw files), preprocessed files used in data analysis and creating the figures in the publication, and measurement diaries for the experiments.

opencc-zeroMar 2023View details →

Data for: Outcomes of multifarious selection on the evolution of visual signals

Multifarious sources of selection shape visual signals and can produce phenotypic divergence. Theory predicts variance in warning signals should be minimal due to purifying selection, yet polymorphism is abundant. While in some instances divergent signals can evolve into discrete morphs, continuously variable phenotypes are also encountered in natural populations. Notwithstanding, we currently have an incomplete understanding of how combinations of selection shape fitness landscapes, particularly those which produce polymorphism. We modeled how combinations of natural and sexual selection act on aposematic traits within a single population to gain insights into what combinations of selection favor the evolution and maintenance of phenotypic variation. With a rich foundation of studies on selection and phenotypic divergence, we reference the poison frog genus Oophaga to model signal evolution. Multifarious selection on aposematic traits created the topology of our model's fitness landscape by approximating different scenarios found in natural populations. Combined, the model produced all types of phenotypic variation found in frog populations, namely monomorphism, continuous variation, and discrete polymorphism. Our results afford advances into how multifarious selection shapes phenotypic divergence, which, along with additional modelling enhancements, will allow us to further our understanding of visual signal evolution.

Insights into Batch Selection for Event-camera Motion Estimation - Datasets

See <a href="https://github.com/event-driven-robotics/batch-selection-experiments">https://github.com/event-driven-robotics/batch-selection-experiments</a> for examples on how to read and process the data. Simulated datasets were used to accurately have a ground-truth of 3 DoF camera rotation, for valid training and evaluation. Four photo-realistic simulated environments from UnrealCV Zoo were selected as they are publicly available indoor scenes and include diverse lighting textures, shadows, reflections and object clutter. The camera was positioned inside the virtual room and rotated along all its three axes randomly at a variety of speeds. Frames were generated at >1 kHz from which the event-stream is generated using log-image-difference  techniques. Five velocity trajectories were used for arch1, four velocity trajectories were used for arch2, and three trajectories for arch3. Including the final room dataset, a total of 13 different datasets (each with a different velocity trajectory) cover a total of 190 seconds of data. Note: room is split into 3 archived files. Please cite: <blockquote> Valerdi, J.L., Bartolozzi, C. and Glover, A., 2023. Insights into Batch Selection for Event-Camera Motion Estimation. Sensors, 23(7), p.3699. </blockquote> <pre><code>@article{valerdi2023insights, title={Insights into Batch Selection for Event-Camera Motion Estimation}, author={Valerdi, Juan L and Bartolozzi, Chiara and Glover, Arren}, journal={Sensors}, volume={23}, number={7}, pages={3699}, year={2023}, publisher={MDPI} }</code></pre>

opencc-by-4.0Sep 2022View details →

EEG Dataset for 'Decoding of selective attention to continuous speech from the human auditory brainstem response' and 'Neural Speech Tracking in the Theta and in the Delta Frequency Band Differentially Encode Clarity and Comprehension of Speech in Noise'.

The repository contains the unprocessed EEG data recorded for the publications [1, 2]. For convenience, the onsets of the EEG data provided here are time-aligned with the onsets of the audio books in the 'audiobooks' folder, and the EEG data are provided in HDF5 format. Please refer to the original version of this dataset for more details. More details, as well as the original data files, are available at the original repository <a href="https://doi.org/10.5281/zenodo.7086209">here</a>. Examples of using these data (preprocessing, fitting linear models) can be found <a href="https://github.com/Mike-boop/trf-examples">here</a>. The English conditions (clean, lb, mb, hb, fM, fW) comprised a single recording session. The Dutch conditions (cleanDutch, lbDutch, mbDutch, hbDutch) comprised a separate recording session. You see which participants took part in each session in session_info.json. Please note some details about the stimulus presentation for the various listening conditions: <ul> <li>English speech-in-babble-noise (lb, mb, hb): babble noise was played by itself for one second before the audiobook track began. The babble noise was also played for one second after the audiobook track ended. Therefore, you should discard the first second and the last second from these trial during your analysis.</li> <li>Dutch speech-in-babble-noise (lbDutch, mbDutch, hbDutch): the story (narrated in Dutch) was played by itself for one second before the babble noise track began. Then, the babble noise was increased linearly in amplitude for one second. Therefore, you should discard the first two seconds from these trials during your analysis.</li> <li>Dutch in quiet, and Dutch-in-babble-noise (cleanDutch, lbDutch, mbDutch, hbDutch): some English sentences were embedded in the Dutch narratives in order to encourage attention. You should crop these from your analysis. The onsets and offsets of the English sentences (in samples, at 44100Hz) are provided in the audiobooks/*Dutch/english_onsets_info.json files.</li> <li>Competing-speakers conditions (fM, fW): sometimes the attended track is longer than the unattended track, or vice-versa. The onsets of both tracks are aligned. You should crop the trial to the length of the shortest track for your analysis.</li> </ul> If you use this data, please cite the original publications, as well as this repository [1,2,3]. [1] Etard O, Kegler M, Braiman C, Forte A E and Reichenbach T. “Decoding of selective attention to continuous speech from the human auditory brainstem response” 2019. NeuroImage 200 1–11 [2] Etard O and Reichenbach T. “Neural speech tracking in the theta and in the delta frequency band differentially encode clarity and comprehension of speech in noise” 2019. J. Neurosci. 39 5750–9 [3] Etard O and Reichenbach T. "EEG Dataset for 'Decoding of selective attention to continuous speech from the human auditory brainstem response' and 'Neural Speech Tracking in the Theta and in the Delta Frequency Band Differentially Encode Clarity and Comprehension of Speech in Noise". Doi: 10.5281/zenodo.7086208

Selected simulation input and output for patchoulol synthase and germacradien-11-ol synthase

Files related to the biomolecular simulations in the following publication: Active site loop engineering abolishes water capture in hydroxylating sesquiterpene synthases Prabhakar L. Srivastava,[a] Sam T. Johns,[b] Rebecca Walters,[b] David J. Miller,[a] Rudolf K. Allemann*[a] and Marc W. Van der Kamp*[b]   [a]School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom [b]School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom See the README.docx document for details.

DIETxPOSOME - Selection of potentially useful papers from literature mining and machine learning protocols

DIETxPOSOME database concerning literature selection of potentially useful papers retrieved from PubMed search API, concerning contaminants quantification in food items of worldwide highest supply and using FoodMine code (text matching filter) and machine learning (ML) protocols. A list of 2,442 papers that potentially contained relevant information, covering the period between 2000 and 2022, was compiled from an initial number of 1,932,345 papers.

Size-selective harvesting impacts learning and decision-making in zebrafish

Size-selective harvesting common to fisheries is known to evolutionarily alter life-history and behavioural traits in exploited fish populations. Changes in these traits may in turn modify learning and decision-making abilities through energetic trade-offs with brain investment that can vary across development or via correlations with personality traits. We examined the hypothesis of size-selection-induced alteration of learning performance in three selection lines of zebrafish (Danio rerio) generated through intensive harvesting for large, small and random body-size for five generations followed by no further selection for ten generations that allowed examining evolutionarily fixed outcomes. We tested associative learning ability throughout ontogeny in fish groups using a colour-discrimination paradigm with a food reward, and the propensity to make group decisions in an associative task. All selection lines showed significant associative abilities that improved across ontogeny. The large-harvested line fish showed a significantly slower associative learning speed as subadults and adults than the controls. We found no evidence of memory decay as a function of size-selection. Decision-making speed did not vary across lines, but the large-harvested line made faster decisions during the probe trial. Collectively, our results show that size-selective harvesting evolutionarily alters associative and decision-making abilities in zebrafish, which could affect resource acquisition and survival in exploited fish populations.

GWAS results of selected binarized neurocognitive task performances from Philadelphia Neurodevelopmental Cohort

This archive contains analysis results associated with the publication: Shraddha Pai, Shirley Hui, Philipp Weber, Soumil Narayan, Owen Whitley, Peipei Li, Viviane Labrie, Jan Baumbach, Anne L Wheeler, Gary D Bader. (2023). Multi-scale systems genomics analysis predicts pathways, cell types and drug targets involved in normative variation in peri-adolescent human cognition. Cerebral Cortex. ----------------------------------------------------------- *loco.mlma files:  Univariate GWAS summary statistics for binarized performance of computerized neurocognitive tests in the Philadelphia Neurodevelopmental Cohorts. GWAS was performed on individuals ascertained to be of European genetic ancestry. For methods, please refer to the publication above. Phenotype codes: lnb_tp2    Working memory    LNB: Number of Correct Responses to 2-Back Trials (TP) pcpt_t_tp    Attention    PCPT: Total of Correct Responses to Number Trials (TP) and Letter Trials (TP) peit_cr    Emotion identification    PEIT: Total Correct Responses for All Test Trials, by genus pfmt_ifac_tot    Face memory    PFMT: Total Correct Responses for All Test Trials plot_tc    Spatial reasoning    PLOT: Total Correct Responses for All Test Trials, by genus pmat_pc    Nonverbal reasoning    PMAT: Percent of Correct Responses for All Test Trials, by genus pvrt_cr    Verbal reasoning    PVRT: Total Correct Responses for All Test Trials, by genus pwmt_kiwrd_tot    Word memory    PWMT: Total Correct Responses for All Test Trials volt_svt    Object memory    VOLT: Total Correct Responses for All Test Trial

Spatio-temporal change of selected soil physico-chemical properties in grevillea-banana agroforestry systems

This is a data base containin raw data (soil and litter data) as well as the R scripts used for their analyses

Data from: Strong selection is poorly aligned with genetic variation in Ipomoea hederacea

The multivariate evolution of populations is the result of the interactions between natural selection, drift, and the underlying genetic structure of the traits involved. Covariances among traits bias responses to selection, and the multivariate axis which describes the greatest genetic variation is expected to be aligned with patterns of divergence across populations. An exception to this expectation is when selection acts on trait combinations lacking genetic variance, which limits evolutionary change. Here we used a common garden field experiment of individuals from 57 populations of Ipomoea hederacea to characterize linear and nonlinear selection on five quantitative traits in the field. We then formally compare patterns of selection to previous estimates of within-population genetic covariance structure (the G-matrix) and population divergence in these traits. We found that selection is poorly aligned with previous estimates of genetic covariance structure and population divergence. In addition, the trait combinations favoured by selection were generally lacking genetic variation, possessing approximately 15-30% as much genetic variation as the most variable combination of traits. Our results suggest that patterns of population divergence are likely the result of the interplay between adaptive responses, correlated response, and selection favoring traits lacking genetic variation.

Data for: Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution in Arabidopsis thaliana

Differential gene expression between environments often underlies phenotypic plasticity. However, environment-specific expression patterns are hypothesized to relax selection on genes, and thus limit plasticity evolution. We collated over 27 terabases of RNA-sequencing data on Arabidopsis thaliana from over 300 peer-reviewed studies and 200 treatment conditions to investigate this hypothesis. Consistent with relaxed selection, genes with more treatment-specific expression have higher levels of nucleotide diversity and divergence at nonsynonymous sites but lack stronger signals of positive selection. This result persisted even after controlling for expression level, gene length, GC content, the tissue specificity of expression, and technical variation between studies. Overall, our investigation supports the existence of a hypothesized trade-off between the environment specificity of a gene's expression and the strength of selection on said gene in A. thaliana. Future studies should leverage multiple genome-scale datasets to tease apart the contributions of many variables in limiting plasticity evolution.

Herbivorous dietary selection shown by hawfinch (Coccothraustes coccothraustes) within mixed woodland habitats

Knowledge of diet and dietary selectivity is vital, especially for the conservation of declining species. Accurately obtaining this information, however, is difficult, especially if the study species feeds on a wide range of food items within heterogeneous and inaccessible environments, such as the tree canopy. Hawfinches ( Coccothraustes coccothraustes ), like many woodland birds, are declining for reasons that are unclear. We investigated the possible role that dietary selection may have in these declines in the UK. Here, we used a combination of high-throughput sequencing of 261 hawfinch faecal samples assessed against tree occurrence data from quadrats sampled in three hawfinch population strongholds in the UK to test for evidence of selective foraging. This revealed that hawfinches show selective feeding and consume certain tree genera disproportionally to availability. Positive selection was shown for beech (Fagus), cherry (Prunus), hornbeam (Carpinus), maples (Acer) and oak (Quercus), while Hawfinch avoided ash (Fraxinus), birch (Betula), chestnut (Castanea), fir (Abies), hazel (Corylus), rowan (Sorbus) and lime (Tilia). This approach provided detailed information on hawfinch dietary choice and may be used to predict the effects of changing food resources on other declining passerine populations in the future.

Supplementary data for: Selection on visual opsin genes in diurnal Neotropical frogs and loss of the SWS2 opsin in poison frogs

Amphibians are ideal for studying visual system evolution because their biphasic (aquatic and terrestrial) life history and ecological diversity expose them to a broad range of visual conditions. Here we evaluate signatures of selection on visual opsin genes across Neotropical anurans and focus on three diurnal clades that are well-known for the concurrence of conspicuous colors and chemical defense (i.e., aposematism): poison frogs (Dendrobatidae), Harlequin toads (Bufonidae: Atelopus), and pumpkin toadlets (Brachycephalidae: Brachycephalus). We found evidence of positive selection on 44 amino acid sites in LWS, SWS1, SWS2, and RH1 opsin genes, of which one in LWS and two in RH1 have been previously identified as spectral tuning sites in other vertebrates. Given that anurans have mostly nocturnal habits, the patterns of selection revealed new sites that might be important in spectral tuning for frogs, potentially for adaptation to diurnal habits and for color-based intraspecific communication. Furthermore, we provide evidence that SWS2, normally expressed in rod cells in frogs and some salamanders, has likely been lost in the ancestor of Dendrobatidae, suggesting that under low-light levels, dendrobatids have inferior wavelength discrimination compared to other frogs. This loss might follow the origin of diurnal activity in dendrobatids and could have implications for their chemical ecology, biodiversity, and behavior. Our analyses show that assessments of opsin diversification in understudied groups could expand our understanding of the role of sensory system evolution in ecological adaptation.