Find research datasets worth reusing

Different adaptation error types in affective computing have different effects on user experience: a Wizard-of-Oz study

The record consists of one Excel file that contains individual participant data for the study "Different adaptation error types in affective computing have different effects on user experience: a Wizard-of-Oz study". The study included 97 participants who were randomly divided into five groups corresponding to five adaptation behaviors (SingleSmall, SingleModerate, ImmediateLow, ImmediateHigh, IrreversibleHigh). Each participant took part in three 11-minute intervals. Difficulty changed every 60 seconds in each 11-minute interval, and there are thus 11 difficulty values per interval. At the end of each interval, participants self-reported their experience using the NASA Task Load Index (6 items) and Intrinsic Motivation Inventory (8 items). After the third interval, participants were asked to rate how much they liked the 3 intervals on a visual analog scale that was converted to 1-100 numerical scores.

opencc-by-4.0Sep 2021View details →

Assessing Nitrogen Availability in Biobased Fertilizers: Effect of Vegetation on Mineralization Patterns

Biobased nitrogen (N) fertilizers derived from animal manure can substitute synthetic mineral N fertilizer and contribute to more sustainable agriculture. Practitioners need to obtain a reliable estimation of the biobased fertilizers’ N value. This study compared the estimates for pig slurry (PS) and liquid fraction of digestate (LFD) using laboratory incubation and plant-growing experiments. A no-N treatment was used as control and calcium ammonium nitrate (CAN) as synthetic mineral fertilizer. After 100 days of incubation, the addition of PS and LFD resulted in a net N mineralization rate of 10.6 ± 0.3% and 20.6 ± 0.4% of the total applied N, respectively. The addition of CAN showed no significant net mineralization or immobilization (net N release 96 ± 6%). In the pot experiment under vegetation, all fertilized treatments caused N immobilization with a negative net N mineralization rate of −51 ± 11%, −9 ± 4%, and −27 ± 10% of the total applied N in CAN, PS, and LFD treatments, respectively. Compared to the pot experiment, the laboratory incubation without vegetation may have overestimated the N value of biobased fertilizers. Vegetation resulted in a lower estimation of available N from fertilizers, probably due to intensified competition with soil microbes or increased N loss via denitrification.

Survey Results - User Accuracy Effects on Algorithmic Accuracy

The survey was hosted on Qualtrics and participants recruited via Cloud Research. Participants are US-only. The data includes those who did not finish. No PII data was collected. The survey included a deception scenario for a mortgage application followed by a battery of questions to assess ratings of the algorithm, assess participant honesty, and assess algorithmic awareness.

openmit-licenseNov 2023View details →

Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex

When using the data or code from this manuscript, please cite it as:Leiva FP, Santos M, Rezende E, & Verberk WCEP. 2021. Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex. Zenodo. <a href="https://doi.org/10.5281/zenodo.5120028">https://doi.org/10.5281/zenodo.5120028</a>.

opengpl-3.0-or-laterNov 2023View details →

Replication data for An Empirical Approximation of the Effects of Trade Sanctions with an Application to Russia

This is the dataset to replicate all the tables and figures in the paper <a href="https://doi.org/10.1093/epolic/eiad027">"An Empirical Approximation of the Effects of Trade Sanctions with an Application to Russia"</a>, published in Economic Policy, 2023, by Jean Imbs and Laurent Pauwels. All data manipulations and programming are detailed on the GitHub site:<a href="https://github.com/laurentpauwels/sanctionpaper"> https://github.com/laurentpauwels/sanctionpaper</a>. The raw and processed data are in this sanctionpaperdata_v1/matlab/data folder. For convenience the simulation output (simulationoutput.txt) required to build the scatter plots in Figure 1 with STATA is available in sanctionpaperdata_v1/matlab/output.Instructions  If you clone the GitHub repository:1. Place the downloaded data folder (located in sanctionpaperdata_v1/matlab/) in the matlab folder of the GitHub repository. 2. Place the downloaded simulation_output.txt I(located in sanctionpaperdata_v1/matlab/output/) in the matlab/output folder of the GitHub repository if you do not want to run the simulations as detailed on GitHub.DescriptionThe matlab/data/raw folder contains an ICIO21 folder with the ICIO21 data, and a WIOD folder with the SEA16 data (in data/raw/WIOD/SEA16) and the WIOT16 data in CSV format (in data/raw/WIOD/WIOT16).NOTE: WIOD provides the data in XLSB format. The XLSB WIOD data is in the WIOT_in_EXCEL.zip located in the matlab/data/raw/WIOD/. Python is used to convert XLSB into CSV files. See python code in GitHub repository for unzipping and conversion to CSV. The converted CSV files are provided for convenience.The parsed and pre-processed ICIO21, SEA16, and WIOT16 data are stored in the /matlab/data/processed folder into three separate .mat structure files:icio21_strc.mat contains:<ul><li>the meta data (icio21_text), i.e., the information about the structure of the numerical data such as lists of countrycode, countries, industrycode, industries, isic_rev4 codes, years covered, name of final categories, etc.</li><li>the numerical data (icio21_data):<ul><li>Z (icio21_data.Z), the intermediate IO data for the listed industries (R), countries (N), and years (T). Its structure is 3-dimensionsal: (NxR)x(NxR)xT.</li><li>F (icio21_data.F), the final demand data for the same countries, industries and years. Its structure is 3-dimension: (NxR)x(NxC)xT. The columns are NxC where C are the number of final demand categories.</li></ul></li></ul> wiod16_strc.mat has the same structure as icio21_strc.mat with the meta data in wiot16_text and the numerical data in wiot16_data.sea16_strc.mat has the meta data in sea16_text and the numerical data in sea16_data. SEA16 contains 16 variables instead of Input-Output type data. The country, industry, and year coverage is not the same as ICIO21.NOTE: matlab/scripts/convertMatlabStruc2data.m in the GitHub repository converts MATLAB v7.3 format ("structure data") to an updated format without structure so that it is more easily compatible with other software. All data parsing and preprocessing are done with MATLAB, see GitHub repository for details.SourcesThe raw data come from these sources:1. OECD Inter-Country Input-Output (ICIO) data November 2021 release (downloaded on 2 July 2023)- Source: OECD-ICIO 2021 release data is available at <a href="http://oe.cd/icio">http://oe.cd/icio</a>2.  WIOD Socio-Economic Accounts (SEA) data 2016 release (downloaded on 30 May 2023)- Source: <a href="https://www.rug.nl/ggdc/valuechain/wiod/wiod-2016-release">https://www.rug.nl/ggdc/valuechain/wiod/wiod-2016-release</a>3. WIOD World Input-Output Tables (WIOT) data November 2016 (downloaded on 23 June 2023)- Source: <a href="https://www.rug.nl/ggdc/valuechain/wiod/wiod-2016-release">https://www.rug.nl/ggdc/valuechain/wiod/wiod-2016-release</a>

opencc-by-4.0Jul 2023View details →

Supplementary material (part 2) for "On the effect of tributary valleys on thermally driven winds in the main valley: a case study in the Inn Valley"

Part 2 of the supplementary material for the master's thesis "On the effect of tributary valleys on thermally driven winds in the main valley: a case study in the Inn Valley." (Deidda 2023, available at <a href="https://resolver.obvsg.at/urn:nbn:at:at-ubi:1-134436">https://resolver.obvsg.at/urn:nbn:at:at-ubi:1-134436</a>). The supplementary material consists in two parts: part 1 includes scripts, datasets, model setup files and figures (available at <a href="https://zenodo.org/records/8089010">https://zenodo.org/records/8089010</a>), while part 2 includes the model output needed to create the figures (see description below).This directory contains part of the model output used for the thesis. The model used is WRF-ARW version 4.4 (Skamarock et al. 2021). Information on the model setup is available in the thesis, Section 2.2. For storage limitations, only the files needed to create the graphs presented in the thesis are available.The file format is type_domain_date.nc where domain is "d01" or "d02" (respectively for the outer or inner domain, see Section 2.2 in the thesis), while type is "wrfout", "mean_out", or "Averaged", where:<ul><li>"wrfout" is the instantaneous WRF output;</li><li>"mean_out" is the time-averaged WRF output, computed using the fork <a href="https://github.com/matzegoebel/WRFlux">WRFlux</a>.</li><li>"Averaged" is a combination of time-averaged and instantaneous outputs. These files were created using the the script Create_intermediate_files.py, available in the <a href="https://zenodo.org/records/8089010">software directory </a>(in Scripts.zip). These files were computed to have a lighter and WRF-like formatted data containing the averaged fields needed for the analysis.</li></ul>

Data repository accompanying "Flux-tunable Josephson Effect in a Four-Terminal Junction"

Open the record for dataset details and reuse information.

Data from: Mechanical soil disturbance in a pine savanna has multi-year effects on plant species composition

Data used in the manuscript Mechanical soil disturbance in a pine savanna has multi-year effects on plant species composition accepted for publication in Ecosphere. Data included are species lists for all plots and years, percent cover of species in each plot in 2021, and life-history characteristics (life span, dispersal mechanism, seed bank persistence) of all species. See manuscript for site description and data collection methodology.

opencc-by-4.0Jan 2023View details →

Figure 1 in Effects of commercial oils on the camel tick, Hyalomma dromedarii (Acari: Ixodidae) and their enzyme activities

Figure 1. Mortality percentages of Hyalomma dromedarii semi-engorged females treated with different concentrations of four oils at five successive days after treatment – A. Rosemary; B. Garlic; C. Neem; D. Cyperus. a, b, … etc. indicate significant differences between concentrations (%) of each oil for each day according to Tukey test (P <0.001).

Dataset from : Effects of inlet guide vanes on the performance and stability of an aeronautical centrifugal compressor

This dataset pertains to the publication 'Effects of inlet guide vanes on the performance and stability of an aeronautical centrifugal compressor', N. Poujol,  P. Duquesne, I. Trébinjac. Journal of turbomachinery. ASME (2021)These data were obtained from the figures in the article.Where possible, each figure is provided in CSV format.

Ripple effects in a communication network: Anti-eavesdropper defence elicits elaborated sexual signals in rival males

Emitting conspicuous signals into the environment to attract mates comes with the increased risk of interception by eavesdropping enemies. As a defence, a commonly described strategy is for signallers to group together in leks, diluting each individual's risk. Lekking systems are often highly social settings in which competing males dynamically alter their signalling behaviour to attract mates. Thus, signalling at the lek requires navigating fluctuations in risk, competition, and reproductive opportunities. Here, we investigate how behavioural defence strategies directed at an eavesdropping enemy have cascading effects across the communication network. We investigated these behaviours in the túngara frog (Engystomops pustulosus), examining how a calling male's swatting defence directed at frog-biting midges indirectly affects the calling behaviour of his rival. We found that the rival responds to swat-induced water ripples by increasing his call rate and complexity. Then, performing phonotaxis experiments, we found that eavesdropping fringe-lipped bats (Trachops cirrhosus) do not exhibit a preference for a swatting male compared to his rival, but females strongly prefer the rival male. Defences to minimize attacks from eavesdroppers thus shift the mate competition landscape in favour of rival males. By modulating the attractiveness of signalling prey to female receivers, we posit that eavesdropping micropredators likely have an unappreciated impact on the ecology and evolution of sexual communication systems.

Lake effect on summer cooling of shorelines and adjacent inland forests on Lake Superior's north shore

Climate refugia, or areas that are projected to remain relatively stable under climate change, can serve as remnant habitat or steeping stones for species dispersal. The largest freshwater lake in the world by surface area, Lake Superior, serves as a model system for understanding cooling-mediated local refugia, as its cool summer water temperatures and wave action have maintained shoreline habitats suitable for disjunct opulations for arctic-alpine plants since deglaciation. It is known to affect local climates by providing a summer cooling effect near its shorelines, however, the inland gradient of change and spatial patterns of cooling has not been quantified. Here, we describe the extent of the inland cooling gradient, the degree of temperature buffering, and patterns of cooling for Lake Superior's north shore over a 3-year period. Specifically, we established 7 transects along Lake Superior's north shore, with temperature data loggers placed at 10 m, 100 m, 1 km, 10 km, and 100 km inland. We analyzed temperature data by year, month, summer maximum, and growing degree days (GDD0) for each site. Summertime cooling at shore sites (10m) was ~5 °C cooler than inland control sites (100 km), while sites 10 km from the shore were still 1.6 °C cooler than control sites. Magnitude of cooling varied geographically, with sites further west and southeast showing little to no cooling effect. Site on the exposed north and northeast shore where disjunct arctic-alpine plants are most common showed the highest degree of temperature buffering. We also found that shoreline sites on the north and northeast shore had shorter growing seasons compared to inland control sites. Finally, the number of days per year warmer than 16 °C, a maximum temperature threshold associated with arctic-alpine plant occurrences, averaged 65 days per year at 10 m sites and 82 days per year at control sites. The north shore of Lake Superior serves as a transition zone between temperate deciduous forests and boreal forests and is predicted to transition to deciduous forests under climate change. An understanding of the extent of lake-mediated cooling on adjacent forests can better inform risk to arctic-alpine disjunct species, inland forests, and overall vegetation transition models on Lake Superior's north shore.

Characterization and effect of biomimetic surfaces based on the topography of a self-cleaning leaf on bacterial binding

Four self-cleaning leaves (Tenderheart, Cauliflower, White cabbage, and Leek) and the corresponding biomimetic surfaces were analyzed for their properties (water contact angle, surface hydrophobicity and roughness). The antifouling behavior was assessed by bacterial attachment, adhesion, and retention assays.

Perturbative effective field theory expansions for cosmological phase transitions, dataset

This dataset is the work of Oliver Gould and Tuomas V.I. Tenkanen. It collects the numerical data from the paper <a href="https://arxiv.org/abs/2309.01672">"Perturbative effective field theory expansions for cosmological phase transitions"</a> (2023). It primarily contains data from perturbative calculations of the thermal evolution of the real-triplet extended Standard Model at two benchmark parameter points.In addition, for comparison to the perturbative results, we have included data of the scalar quadratic condensates as a function of temperature from the lattice Monte-Carlo simulations of Lauri Niemi, Michael J. Ramsey-Musolf, Tuomas V.I. Tenkanen and David J. Weir, from the paper <a href="https://doi.org/10.1103/PhysRevLett.126.171802">"Thermodynamics of a Two-Step Electroweak Phase Transition"</a> (2020). We thank the authors for granting permission to reproduce this data here.Everything is contained within the archive file <a href="https://zenodo.org/api/records/10353066/draft/files/triplet_two_step_data.tar.gz/content">triplet_two_step_data.tar.gz</a>, a tarball compressed with Gzip. For further details and for the context of this dataset, see the above papers. Details of the conventions used in the dataset can be found in the accompanying README.md file.

Effects of nutrient enrichment on freshwater macrophyte and invertebrate abundance: A meta-analysis

The zip-file contains the data and code accompanying the paper 'Effects of nutrient enrichment on freshwater macrophyte and invertebrate abundance: A meta-analysis'. Together, these files should allow for the replication of the results. The 'raw_data' folder contains the 'MA_database.csv' file, which contains the extracted data from all primary studies that are used in the analysis. Furthermore, this folder contains the file 'MA_database_description.txt', which gives a description of each data column in the database. The 'derived_data' folder contains the files that are produced by the R-scripts in this study and used for data analysis. The 'MA_database_processed.csv' and 'MA_database_processed.RData' files contain the converted raw database that is suitable for analysis. The 'DB_IA_subsets.RData' file contains the 'Individual Abundance' (IA) data subsets based on taxonomic group (invertebrates/macrophytes) and inclusion criteria. The 'DB_IA_VCV_matrices.RData' contains for all IA data subsets the variance-covariance (VCV) matrices. The 'DB_AM_subsets.RData' file contains the 'Total Abundance' (TA) and 'Mean Abundance' (MA) data subsets based on taxonomic group (invertebrates/macrophytes) and inclusion criteria. The 'output_data' folder contains maps with the output data for each data subset (i.e. for each metric, taxonomic group and set of inclusion criteria). For each data subset, the map contains random effects selection results ('Results1_REsel_<subset>.csv'), the fixed effects selection results ('Results2_FEsel_<subset>.csv'), the random variance components and R^2 values for the best models subset ('Results3_BestModels_<subset>.csv'), the parameter value estimations for the fixed effects ('Results4_Parameters_<subset>.csv'), the standard errors for the estimated parameter values ('Results5_SE_<subset>.csv'), and the consensus model parameter values ('Results6_ConsensusModel_<subset>.csv'). Furthermore, each map contains a file with the best-selected random effects model structure ('BestRanEf_<subset>.RData'), the model with the best-selected random effects structure without moderators (only for IA) ('BestRanEfModel_<subset>.RData'), and a file with the consensus model ('ConsensusModel_<subset>.RData'). The 'scripts' folder contains all R-scripts that we used for this study. The 'PrepareData.R' script takes the database as input and adjusts the file so that it can be used for data analysis. The 'PrepareDataIA.R' and 'PrepareDataAM.R' scripts make subsets of the data and prepare the data for the meta-regression analysis and mixed-effects regression analysis, respectively. The regression analyses are performed in the 'SelectModelsIA.R' and 'SelectModelsAM.R' scripts to calculate the regression model results for the IA metric and MA/TA metrics, respectively. These scripts require the 'RandomAndFixedEffects.R' script, containing the random and fixed effects parameter combinations, as well as the 'Functions.R' script. The 'CreateMap.R' script creates a global map with the location of all studies included in the analysis (figure 1 in the paper). The 'CreateForestPlots.R' script creates plots showing the IA data distribution for both taxonomic groups (figure 2 in the paper). The 'CreateHeatMaps.R' script creates heat maps for all metrics and taxonomic groups (figure 3 in the paper, figures S11.1 and S11.2 in the appendix). The 'CalculateStatistics.R' script calculates the descriptive statistics that are reported throughout the paper, and creates the figures that describe the dataset characteristics (figures S3.1 to S3.5 in the appendix). The 'CreateFunnelPlots.R' script creates the funnel plots for both taxonomic groups (figures S6.1 and S6.2 in the appendix) and performs Egger's tests. The 'CreateControlGraphs.R' script creates graphs showing the dependency of the nutrient response to control concentrations for all metrics and taxonomic groups (figures S10.1 and S10.2 in the appendix). The 'figures' folder contains all figures that are included in this study.

Functional traits—not nativeness—shape the effects of large mammalian herbivores on plant communities

Large mammalian herbivores (megafauna) have experienced extinctions and declines since prehistory. Introduced megafauna have partly counteracted these losses yet are thought to have unusually negative effects compared to native megafauna. Using a meta-analysis of 3,995 plot-scale plant abundance and diversity responses from 221 studies, we found no evidence that megafauna impacts were shaped by nativeness, 'invasiveness', 'feralness', coevolutionary history, or functional and phylogenetic novelty. Nor was there evidence that introduced megafauna facilitate introduced plants more than native megafauna. Instead, we found strong evidence that functional traits shaped megafauna impacts, with larger-bodied and bulk-feeding megafauna promoting plant diversity. Our work suggests that trait-based ecology provides better insight into interactions between megafauna and plants than concepts of nativeness.

Environmental effects on genetic variance are likely to constrain adaptation in novel environments

Adaptive plasticity allows populations to cope with environmental variation but is expected to fail as conditions become unfamiliar. In novel conditions, populations may instead rely on rapid adaptation to increase fitness and avoid extinction. Adaptation should be fastest when both plasticity and selection occur in directions of the multivariate phenotype that contain abundant genetic variation. However, tests of this prediction from field experiments are rare. Here, we quantify how additive genetic variance in a multivariate phenotype changes across an elevational gradient, and test whether plasticity and selection align with genetic variation. We do so using two closely related, but ecologically distinct, sister species of Sicilian daisy (Senecio, Asteraceae) adapted to high and low elevations on Mount Etna. Using a paternal half-sibling breeding design, we generated and then reciprocally planted c.19,000 seeds of both species, across an elevational gradient spanning each species' native elevation, and then quantified mortality and five leaf traits of emergent seedlings. We found that genetic variance in leaf traits changed more across elevations than between species. The high-elevation species at novel lower elevations showed changes in the distribution of genetic variance among the leaf traits, which reduced the amount of genetic variance in the directions of selection and the native phenotype. By contrast, the low-elevation species mainly showed changes in the amount of genetic variance at the novel high elevation, and genetic variance was concentrated in the direction of the native phenotype. For both species, leaf trait plasticity across elevations was in a direction of the multivariate phenotype that contained a moderate amount of genetic variance. Together, these data suggest that where plasticity is adaptive, selection on genetic variance for an initially plastic response could promote adaptation. However, large environmental effects on genetic variance are likely to reduce adaptive potential in novel environments.

opencc-by-4.0Dec 2022View details →

Data from "Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar"

Data from : 'Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar' An Vanden Broeck*, Tim Meese*, Pieter Verschelde, Karen Cox, Berthold Heinze, Dieter Deforce, Ellen De Meester and Filip Van Nieuwerburgh   Related publication: Vanden Broeck, A.*, Meese, T.*, Verschelde, P. et al. Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar. BMC Biol 22, 30 (2024). https://doi.org/10.1186/s12915-024-01816-1 <ul> <li>* These authors contributed equally.</li> </ul> -------------------------------------------------- Background: Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar (Populus nigra cv. 'Italica' Duroi) offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. Results: We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe any biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring's' phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment. Conclusions: Genome-wide cytosine methylation patterns in symmetrical GC-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in GC-context can be used as bio-markers to infer a common ancestor and thus to investigate the environmental history of a specific Lombardy poplar on short time-scales. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.   ADDITIONAL FILES Additional file 1. CSV-file with information on the Lombardy poplar trees samples used for whole genome bisulfite sequencing (WGBS) in the two methylome experiments (metadata). The raw fastq datafiles obtained by whole genome bisulfite sequencing (WGBS) are available at the <a href="https://www.ncbi.nlm.nih.gov/geo/">Gene Expression Omnibus (GEO) database</a> (submission  GSE225596). Additional file 2. CSV-file with mapping statistics, bisulfite conversion rates and percentages of cytosine methylation for each DNA-sample analyzed by whole genome bisulfite sequencing (WGBS). (processed data). Additional file 3. CSV-file with the total list of GO terms that were enriched in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (processed data). Additional file 4. POWERPOINT-file. Heatmaps with GO terms over-represented in promoters containing DMRs in CpG-context per between-group pairwise comparison. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively). A. HUN4 versus ITS3; B. HUN4 versus UKD2, C; ITS3 versus SPC1; D. HUN4 versus SCP1,  E. SPC1 versus UKD2 Additional file 5. CSV-file with the raw data of the bud set observations in the common garden experiment (raw data). Additional file 6. HTML-file with the R source codes to reproduce the results of the bud set analysis (code, R script). Additional file 7. A text-file representing the Snakefile (i.e. a readable Python-based workflow) including the different steps and rules of the bioinformatics of the WGBS data analyses (code, Snakefile). Additional file 8. RMD-file with the code to reproduce the analyses to identify differential methylated predefined regions (code, R script). Additional file 9. R-script with the code to reproduce the clustering and visualizing of the GO enrichment results (code, R script). Supporting files 1. Zip-folder with: i) excel-files listing the genes in DMRs, and ii) PNG-files with the ‘Biological Coefficient of Variation (BCV)’-plots between any of the six pairwise comparisons of Lombardy poplars grouped per ortet and identified with Bioconductor package edgeR. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (processed data). Supporting files 2. Zip-folder with PNG-files representing heatmaps and excel-files with clustered GO terms significant over-represented in promoters and gene regions located in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively. The files were obtained with the Bioconductor package simplifyEnrichment (processed data). --------------------------------------------------------- Version 3: <ul> <li>Renaming of file names according to the publisher's guidelines</li> <li>Additional file 2 includes also bisulfite conversion rates per sample</li> </ul>

Within- and transgenerational stress legacy effects of ocean acidification on red abalone (Haliotis rufescens) growth and survival

Understanding the mechanisms by which individual organisms respond and populations adapt to global climate change is a critical challenge. The role of plasticity and acclimation, within and across generations, may be essential given the pace of change. We investigated plasticity across generations and life stages in response to ocean acidification (OA), which poses a growing threat to both wild populations and the sustainable aquaculture of shellfish. Most studies of OA on shellfish focus on acute effects, and less is known regarding the longer-term carryover effects that may manifest within or across generations. We assessed these longer-term effects in red abalone (Haliotis rufescens) using a multi-generational split-brood experiment. We spawned adults raised in ambient conditions to create offspring that we then exposed to high pCO2 (1,180 μatm; simulating OA) or low pCO2 (450 μatm; control or ambient conditions) during the first three months of life. We then allowed these animals to reach maturity in ambient common garden conditions for four years before returning the adults into high or low pCO2 treatments for 11 months and measuring growth and reproductive potential. Early-life exposure to OA in the F1 generation decreased adult growth rate, even after 5 years, especially when abalone were re-exposed to OA as adults. Adult, but not early-life exposure, to OA negatively impacted fecundity. We then exposed the F2 offspring to high or low pCO2 treatments for the first three months of life in a fully factorial, split-brood design. We found negative transgenerational effects of parental OA exposure on survival and growth of F2 offspring, in addition to significant direct effects of OA on F2 survival. These results show that the negative impacts of OA can last within and across generations, but that buffering against OA conditions at critical life-history windows can mitigate these effects.

Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish

Variation in the composition of skin-associated microbiomes has been attributed to host species, geographic location, and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (Cyprinus carpio) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch, and growth, but not temperature gain while basking, sex, personality, or colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared to the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organisation (richness and composition of fish-associated microbial communities).