Find research datasets worth reusing

opencc-zeroOct 2022View details →

Data from: Sexual selection on male but not female function in monoecious and dioecious populations of broadleaf arrowhead (Sagittaria latifolia)

Direct measures of sexual selection in plants are rare and complicated by modular growth. Because of modularity, instantaneous measures of fitness scale with size, but size variation in plants is largely non-heritable, obscuring patterns of selection on heritable variation. We measured the magnitude of sexual selection in a monoecious and a dioecious population of the clonal plant Sagittaria latifolia using Bateman gradients (ßss). These gradients were calculated using parentage analysis and residual regression to account for the effects of shoot and clone size on mating and reproductive success. In both populations: (i) mating via male function was associated with greater promiscuity; and (ii) ßss were positive, with significant associations between mating and reproductive success for male but not female function. Moreover, estimated ßss were similar for the monoecious and dioecious populations, possibly because non-overlapping female and male sex phases in hermaphroditic S. latifolia reduces the scope for interference between sex functions during mating. This study builds on previous studies of selection on plant mating traits, and of sexual selection under experimental conditions by showing that sexual selection can operate in natural populations of plants, including populations of hermaphrodites.

opencc-zeroDec 2021View details →

Evolutionary responses of energy metabolism, development, and reproduction to artificial selection for increasing heat tolerance in Drosophila subobscura

Adaptation to warming conditions involves increased heat tolerance and metabolic changes to reduce maintenance costs and maximize biological functions close to fitness. Evidence shows that energy metabolism evolves in response to warming conditions, but we know little about how heat stress intensity determines the evolutionary responses of metabolism and life history traits. Here, we evaluated the evolutionary responses of energy metabolism and life-history traits to artificial selection for increasing heat tolerance in Drosophila subobscura, using two protocols to measure and select heat tolerance: slow and fast ramping protocols. We found that the increase in heat tolerance was associated with reduced activity of the enzymes involved in the glucose-6-phosphate branchpoint, but no changes in the metabolic rate in selected lines. We also found that the evolution of increased heat tolerance increased the early fecundity in selected lines and increased the egg-to-adult viability only in the slow-ramping selected lines. This work shows heat tolerance can evolve under different thermal scenarios but with different evolutionary outcomes on associated traits depending on the heat stress intensity. Therefore, spatial and temporal variability of thermal stress intensity should be taken into account to understand and predict the adaptive response to ongoing and future climatic conditions.

Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species

Pathogen-mediated selection and sexual selection are important drivers of evolution. Both processes are known to target genes of the major histocompatibility complex (MHC), a gene family encoding cell-surface proteins that display pathogen peptides to the immune system. The MHC is also a model for understanding processes such as gene duplication and trans-species allele sharing. The class II MHC protein is a heterodimer whose peptide-binding groove is encoded by an MHC-IIA gene and an MHC-IIB gene. However, our literature review found that class II MHC papers on infectious disease or sexual selection included IIA data only 18% and 9% of the time, respectively. To assess whether greater emphasis on MHC-IIA is warranted, we analyzed MHC-IIA sequence data from 50 species of vertebrates (fish, amphibians, birds, mammals) to test for polymorphism and positive selection. We found that the number of MHC-IIA alleles within a species was often high, and covaried with sample size and number of MHC-IIA genes assayed. While MHC-IIA variability tended to be lower than that of MHC-IIB, the difference was only ~25%, with ~3 fewer IIA alleles than IIB. Furthermore, the unexpectedly high MHC-IIA variability showed clear signatures of positive selection in most species, and positive selection on MHC-IIA was stronger in fish than in other surveyed vertebrate groups. Our findings underscore that MHC-IIA can be an important target of selection. Future work should therefore expand the characterization of MHC-IIA at both allelic and genomic scales, and incorporate MHC-IIA into models of fitness consequences of MHC variation.

The opportunity for selection: an important but slippery concept in ecology and evolution.

1. The concept of the opportunity for selection (I), measured as the variance in relative fitness, is over 60 years old, yet remains poorly understood by, or even unknown to, many ecologists and evolutionary biologists. This essay aims to clarify key conceptual and practical issues concerning use and estimation of I, which represents a theoretical upper limit on the rate of evolutionary adaptation. 2. The component of I caused by linear selection on a single trait is equal to the square of its standardised selection differential i. Even if no phenotypic selection occurs (i=0), however, realised I will typically be nonzero, owing to environmental or stochastic variation in fitness. 3. The opportunity for viability selection depends only on the mean survival rate, but selective mortality will typically account for only a small fraction of total mortality. 4. Fecundity selection is accompanied by expected overdispersion in reproductive success (variance > mean), but overdispersion can also occur for reasons unrelated to phenotype, or by chance. The estimated opportunity for fecundity selection can also vary independently of i if estimated mean reproductive success is affected by study design, e.g. offspring are counted at different life stages or a variable fraction are missed. 5. For these reasons, I alone should not be used to make inferences about selection in progress and its drivers. Nevertheless, some empirical studies have documented weak to moderate correlations between I and phenotypic selection, so variation in I or related metrics across ecological contexts might provide clues that unmeasured traits are under variable selection. 20-Oct-2022 --

Simulations for pre-industrial climate using EC-Earth3-LR model — selected data for a study on AMOC

A long-term control simulation of pre-industrial period (1850 CE) climates were performed by the EC-Earth3-LR climate model with a horizontal resolution of ~1.125°. The dataset contains selected output data from the simulations. In total, a 2000-year long control simulation was made, which has pre-industrial orbital boundary conditions, initialized by a pre-run steady restart file (the output of approximately 500-year pre-industrial control simulation). This dataset is used to investigate internal climate variability without external forcing changes under pre-industrial climate conditions. The dataset contains Earth system model results from EC-Earth3 presented in the study by Cao et al. (2022). Model configuration Time periods: Pre-Industrial (2000-year time slice) ESM configuration: EC-Earth3-LR Horizontal resolution: ~1.125° (~125 km) Available data Annual mean data for standard oceanographic and meteorological variables.

opencc-by-4.0Oct 2022View details →

Systematic Literature Mapping - Selected Articles Data Extraction

- CSV with the raw data extracted from abstract + full-text review from the selected articles. - CSV with normalized data. - CSV with the normalized data after being a feature engineering step in which some columns have been deleted. - CSV with formal context to extract the concepts lattice.

Data from: "Influence of natal habitat preference on habitat selection during extra-home range movements in a large ungulate"

Secondary dataset used for analysis in "Influence of natal habitat preference on habitat selection during extra-home range movements in a large ungulate". Raw GPS relocation data are not publicly available due to potential ethical implications but are available from the corresponding author (Nathan Hooven, nathan.d.hooven@gmail.com) upon reasonable request. Files include: deer_data_6.csv: Sampled covariate values for each used and available location used in SSF analysis Metadata: Metadata information for deer_data_6.csv

Balancing selection at a wing pattern locus is associated with major shifts in genome-wide patterns of diversity and gene flow

Selection shapes genetic diversity around target mutations, yet little is known about how selection on specific loci affects the genetic trajectories of populations, including their genome-wide patterns of diversity and demographic responses. Here we study the patterns of genetic variation and geographic structure in a neotropical butterfly, Heliconius numata, and its closely related allies in the so-called melpomene-silvaniform clade. H. numata is known to have evolved an inversion supergene which controls variation in wing patterns involved in mimicry associations with distinct groups of co-mimics. Butterflies show disassortative mate preferences and heterozygote advantage at this locus. We contrasted patterns of genetic diversity and structure 1) among extant polymorphic and monomorphic populations of H. numata, 2) between H. numata and its close relatives, and 3) between ancestral lineages. We show that H. numata populations which carry the inversions as a balanced polymorphism show markedly distinct patterns of diversity compared to all other taxa. They show the highest genetic diversity and effective population size estimates in the entire clade, as well as a low level of geographic structure and isolation by distance across the entire Amazon basin. By contrast, monomorphic populations of H. numata as well as its sister species and their ancestral lineages all show lower effective population sizes and genetic diversity, and higher levels of geographical structure across the continent. One hypothesis is that the large effective population size of polymorphic populations could be caused by the shift to a regime of balancing selection due to the genetic load and disassortative preferences associated with inversions. Testing this hypothesis with forward simulations supported the observation of increased diversity in populations with the supergene. Our results are consistent with the hypothesis that the formation of a supergene triggered a change in gene flow, causing a general increase in genetic diversity and the homogenisation of genomes at the continental scale.

SYNTHETIC dataset attached to the paper "Grasp Pre-shape Selection by Synthetic Training: Eye-in-hand Shared Control on the Hannes Prosthesis"

SYNTHETIC dataset to replicate the results in "Grasp Pre-shape Selection by Synthetic Training: Eye-in-hand Shared Control on the Hannes Prosthesis", accepted to IEEE/RSJ IROS 2022. In order to fully reproduce the experiments, download also the REAL dataset.  To automatically download the REAL and SYNTHETIC dataset, run the script provided at the link below. Code to replicate the results available at: https://github.com/hsp-iit/prosthetic-grasping-experiments

REAL dataset attached to the paper "Grasp Pre-shape Selection by Synthetic Training: Eye-in-hand Shared Control on the Hannes Prosthesis"

REAL dataset to replicate the results in "Grasp Pre-shape Selection by Synthetic Training: Eye-in-hand Shared Control on the Hannes Prosthesis", accepted to IEEE/RSJ IROS 2022. In order to fully reproduce the experiments, download also the SYNTHETIC dataset.  To automatically download the REAL and SYNTHETIC dataset, run the script provided at the link below. Code to replicate the results available at: https://github.com/hsp-iit/prosthetic-grasping-experiments

Simulated pollinator decline has similar effects on seed production of female and hermaphrodite Lobelia siphilitica, but different effects on selection on floral traits

PREMISE: Pollinator decline, by reducing seed production, is predicted to strengthen natural selection on floral traits. However, the effect of pollinator decline on gender dimorphic species (such as gynodioecious species, where plants produce female or hermaphrodite flowers) may differ between the sex morphs: if pollinator decline reduces the seed production of females more than hermaphrodites, then it should also have a larger effect on selection on floral traits in females than in hermaphrodites. RESULTS: Experimentally reducing pollination decreased seed production of both females and hermaphrodites by ~21%. Reducing pollination also strengthened selection on floral traits, but this effect was not larger in females than in hermaphrodites. Instead, reducing pollination intensified selection for taller inflorescences in hermaphrodites, but did not intensify selection on any floral trait in females. CONCLUSIONS: Our results suggest that pollinator decline will not have a larger effect on either seed production or selection on floral traits of female plants. As such, any effect of pollinator decline on seed production may be similar for gender dimorphic and monomorphic species. However, the potential for floral traits of females (and thus of gender dimorphic species) to evolve in response to pollinator decline could be limited.

Pre- and post-copulatory sexual selection increase offspring quality but impose survival costs to female field crickets

Whether sexual selection increases or decreases fitness is under ongoing debate. Sexual selection operates before and after mating. Yet, the effects of each episode of selection on individual reproductive success remain largely unexplored. We ask how disentangled pre- and post-copulatory sexual selection contribute to fitness of field crickets Gryllus bimaculatus. Treatments allowed exclusively for i) pre-copulatory selection, with males fighting and courting one female, and the resulting pair breeding monogamously, ii) post-copulatory selection, with females mating consecutively to multiple males, and iii) relaxed selection, with enforced pair monogamy. While standardizing the number of matings, we estimated a number of fitness traits across treatments and show that females experiencing sexual selection were more likely to reproduce, their offspring hatched sooner, developed faster and had higher body mass at adulthood, but females suffered survival costs. Interestingly, we found no differences in fitness of females or their offspring from pre- and post-copulatory sexual selection treatments. Our findings highlight the potential for sexual selection in enhancing indirect female fitness while concurrently imposing direct survival costs. By potentially outweighing these costs, increased offspring quality could lead to beneficial population-level consequences of sexual selection.

Data from: Prior associations affect bumblebees' generalization performance in a tool-selection task

A small brain and short life allegedly limit cognitive abilities. Our view of invertebrate cognition may also be biased by the choice of experimental stimuli. Here, the stimuli (color) pairs in Match-To-Sample (MTS) tasks affected the performance of buff-tailed bumblebees (Bombus terrestris). We trained the bees to roll a tool, ball, to a goal that matched its color. Color-matching performance was slower with yellow-and-orange/red than with blue-and-yellow stimuli. When assessing the bees' concept learning in a transfer test with a novel color, the bees trained with blue-and-yellow (novel color: orange/red) were highly successful, the bees trained with blue-and-orange/red (novel color: yellow) did not differ from random, and those trained with yellow-and-orange/red (novel color: blue) failed the test. These results highlight that stimulus salience can affect the conclusions on test subjects' cognitive ability. Therefore, we encourage paying attention to stimulus salience (among other factors) when assessing invertebrate cognition.

SNAPPING PSI surface motion measurements over selected sites presented in MDPI Remote Sensing paper "SNAPPING Services on the Geohazards Exploitation Platform for Copernicus Sentinel-1 Surface Motion Mapping"

SNAPPING PSI surface motion measurements over selected sites as presented in the paper with the title "SNAPPING Services on the Geohazards Exploitation Platform for Copernicus Sentinel-1 Surface Motion Mapping"  by Michael Foumelis, Jose Manuel Delgado Blasco, Fabrice Brito, Fabrizio Pacini, Elena Papageorgiou, Panteha Pishehvar and Philippe Bally on Remote Sensing Open Access Journal. Whenever using this dataset, please cite its original paper (<a href="https://doi.org/10.3390/rs14236075">https://doi.org/10.3390/rs14236075</a>) and include the reference to this dataset (<a href="https://doi.org/10.5281/zenodo.7369653">https://doi.org/10.5281/zenodo.7369653</a>). This dataset includes average Line-of-Sight velocities for the following sites and dates: <table> <tbody> <tr> <td>Site name</td> <td>Country</td> <td>Period</td> <td>Relative orbit</td> <td>Orbit direction</td> </tr> <tr> <td>Cap-Haïtien</td> <td>Haiti</td> <td>Jan-2017 / Dec-2019</td> <td>106</td> <td>ascending</td> </tr> <tr> <td>Gran Renaissance Ethiopian Dam</td> <td>Ethiopia</td> <td>Jan-2019 / Jun-2021</td> <td>50</td> <td>descending</td> </tr> <tr> <td>La Palma Volcano</td> <td>Spain</td> <td>Jun-2019 / Dec-2021</td> <td>169</td> <td>descending</td> </tr> <tr> <td>Santorini Volcano</td> <td>Greece</td> <td>Apr-2015 / May-2021</td> <td>29</td> <td>ascending</td> </tr> <tr> <td>San Francisco</td> <td>USA</td> <td>Jan-2016 / Dec-2020</td> <td>115</td> <td>descending</td> </tr> <tr> <td>Thessaloniki International Airport (SKG)</td> <td>Greece</td> <td>Apr-2015 / Dec-2020</td> <td>102</td> <td>ascending</td> </tr> </tbody> </table>

Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks

This release includes the different genomic datasets used in the article entitled "Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks " by Ramírez-Valiente et al., File description: Samples.xlsx: Description of individual and population codes used in the different analyses and genomic datasets. Quercus_faginea_p12r05m05minMAF001_all_loci.str: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for Quercus faginea including all loci. Quercus_faginea_p12r05m05minMAF001_neutral_loci.str: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for Quercus faginea excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN. Quercus_lusitanica_p7r05m05minMAF001_all_loci.str: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for Quercus lusitanica including all loci. Quercus_ lusitanica_p7r05m05minMAF001_neutral_loci.str: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for Quercus lusitanica excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN. Quercus_faginea_p12r05m05minMAF001_BAYESCAN.txt: Input file used to perform BAYESCAN analyses for Quercus faginea. Quercus_lusitanica_p7r05m05minMAF001_BAYESCAN.txt: Input file used to perform BAYESCAN analyses for Quercus lusitanica. Quercus_faginea_p12r05m05minMAF001_ARLEQUIN.arp: Input file used to perform ARLEQUIN analyses for Quercus faginea. Quercus_lusitanica_p7r05m05minMAF001_ARLEQUIN.arp: Input file used to perform ARLEQUIN analyses for Quercus lusitanica. Quercus_faginea_p12r05m05minMAF001_all_loci.vcf: Variant call format (VCF) file for Quercus faginea including all loci. Quercus_faginea_p12r05m05minMAF001_neutral_loci.vcf: Variant call format (VCF) file for Quercus faginea excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN. Quercus_lusitanica_p7r05m05minMAF001_all_loci.vcf: Variant call format (VCF) file for Quercus lusitanica including all loci. Quercus_ lusitanica_p7r05m05minMAF001_neutral_loci.vcf: Variant call format (VCF) file for Quercus lusitanica excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN. Quercus_faginea_Greenhouse_DRIFTSEL.txt: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for Quercus faginea under common garden greenhouse experiments. Quercus_faginea_Outdoor_DRIFTSEL.txt: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for Quercus faginea under common garden outdoor experiments. Quercus_lusitanica_Greenhouse_DRIFTSEL.txt: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for Quercus lusitanica under common garden greenhouse experiments.

opencc-by-4.0Dec 2022View details →

Restricted language access during childhood affects adult brain structure in selective language regions

Anatomical measurements data and analysis codes in R used in manuscript 'Restricted language access during childhood affects adult brain structure in selective language regions'.

opencc-zeroDec 2022View details →

Glue genes are subjected to diverse selective forces in Drosophila during Drosophila development

Molecular evolutionary studies usually focus on genes with clear roles in adult fitness or on developmental genes expressed at multiple time points during the life of the organism. Here, we examine the evolutionary dynamics of Drosophila glue genes, a set of eight genes tasked with a singular primary function during a specific developmental stage: the production of glue that allows animal pupa to attach to a substrate for several days during metamorphosis. Using phenotypic assays and available data from transcriptomics, PacBio genomes, and genetic variation from global populations, we explore the selective forces acting on the glue genes within the cosmopolitan D. melanogaster species and its five closely related species, D. simulans, D. sechellia, D. mauritiana, D. yakuba, and D. teissieri. We observe a three-fold difference in glue adhesion between the least and the most adhesive D. melanogaster strain, indicating a strong genetic component to phenotypic variation. These eight glue genes are among the most highly expressed genes in salivary glands yet they display no notable codon bias. New copies of Sgs3 and Sgs7 are found in D. yakuba and D. teissieri with the Sgs3 coding sequence evolving rapidly after duplication in the D. yakuba branch. Multiple sites along the various glue genes appear to be constrained. Our population genetics analysis in D. melanogaster suggests signs of local adaptive evolution for Sgs3, Sgs5 and Sgs5bis and traces of recent selection for Sgs1, Sgs3, Sgs7 and Sgs8. Our work shows that stage-specific genes can be subjected to various dynamic evolutionary forces.

opencc-by-4.0Dec 2022View details →

Lack of pollinators selects for increased selfing, restricted gene flow and resource allocation in the rare Mediterranean sage Salvia brachyodon

Salvia brachyodon (Lamiaceae): raw data on flower morphometry, nectar concentration and volume and seed weight according various pollination treatments.

opencc-zeroJan 2023View details →

Data and Code for: Resistance is futile: Weaker selection for resistance by abundant parasites increases prevalence and depresses host density

We model host evolution of costly resistance to infection and its dependence on environmental factors, such as nutrients. We find that higher nutrients can increase infection prevalence AND select for lower resistance. In turn, the model predicts that lower resistance drives infection prevalence even higher while depressing host density. The attached code performs the model analysis, produces the published figures, and conducts statistical analysis on the data (described below). We conducted a mesocosm experiment with mixtures of zooplankton host (Daphnia dentifera) genotypes, algal resources (Ankistrodesmus falcatus), and fungal parasites (Metschnikowia bicuspidata). Mesocosm populations were supplied with low or high nutrients (5 or 50 ug/L phosphorus and 100 or 1000 ug/L nitrogen). We measured densities of hosts along with age class (juvenile or adult), sex, infections status, and egg number and chlorophyll densities; these data are a subset of data published previously Walsman et al. Functional Ecology (<a href="https://doi.org/10.1111/1365-2435.14030">https://doi.org/10.1111/1365-2435.14030</a>; data at <a href="https://doi.org/10.5061/dryad.mw6m905zg">https://doi.org/10.5061/dryad.mw6m905zg</a>). For the first time, we also report genotype frequencies for the mixed genotype treatments. Importantly, we found that high nutrients increased infection prevalence as well as selecting for the host genotype less resistant to infection; the resulting host evolution increased infection prevalence further and depressed host density. These data and code may be reused with citation of the corresponding publication ("'Resistance is futile': Weaker selection for resistance by abundant parasites increases prevalence and depresses host density" in The American Naturalist).