Find research datasets worth reusing

opencc-zeroApr 2024View details →

Data from: Dine and dash: How trophic ecology and migration shape functional locomotory traits in Clupeiform fishes

Understanding how interactions between multiple selective forces influence traits at the macroevolutionary scale is key to understanding adaptive landscapes. Diadromy, an extreme form of migration between marine and freshwater environments, is thought to require locomotory traits conducive to long-distance migration. Yet, other selective forces, such as predator avoidance, habitat use, and prey acquisition, are also likely to shape locomotory adaptation in fishes. We examined how diadromy and trophic ecology together influenced locomotory trait diversity across Clupeiformes, a clade of fishes containing high trophic diversity and numerous transitions to diadromy. We found that both diadromy and trophic ecology influenced the pattern and pace of trait evolution. Diadromous taxa rapidly evolved traits characterized by high cruising efficiency, but the extent to which diadromous and non-diadromous taxa differed depended on their trophic ecology. Macropredators showed greater differences in locomotory traits between diadromous and non-diadromous taxa than phytodetritivores and micropredators, suggesting that traits conducive to migration might be most costly to consumers of evasive prey. This work shows that simultaneously characterizing the roles of multiple ecological or life-history factors in phenotypic evolution can bring the topography of adaptive landscapes into sharper focus and provide a more holistic view of the forces driving patterns of trait evolution.

opencc-zeroApr 2024View details →

Data from: Variation in flower size and shape of Impatiens capensis is correlated with urbanization in Montreal, Canada

Urbanization is changing the conditions in which many species live, forcing them to adjust to these novel environments. Floral size and shape are critical traits for the reproduction of plants pollinated by animals as they are involved in the attraction of pollinators and in efficient pollination. Variation in size and shape could be affected by urbanization via its modification of the abiotic environment (habitat fragmentation, water availability, temperature, soil properties), or via its impact on the biotic environment of plants (pollination, herbivory). Although numerous studies have assessed the impact of urbanization on pollinator communities and on many plant traits, few have investigated its impact on floral size and shape while quantifying the proportion of the total urbanization effect that is due to biotic interactions. In this study, we tested if urbanization and pollinator visitation rates affects the flower shape of the spotted jewelweed, Impatiens capensis. We quantified size and shape of flowers in frontal and profile views using geometric morphometrics for 228 individuals from six populations from the region of Montreal, Canada. Pollinator visitation rates were estimated at each site and the main pollinators were found to be bumblebees, honeybees and hummingbirds. We found that floral size and shape are significantly correlated with urbanization as measured by the amount of vegetation in the surrounding environment of the plants (mean normalized vegetation index, NDVI) and by the visitation rates of bumblebees and honey bees. Partitioning of the total flower shape variation suggests that urbanization affects flower shape through abiotic factors and via its impact on pollinator visitation rates. While further studies from other cities are necessary to confirm the role of urbanization in shaping the floral shape of I. capensis, these results support the idea that urbanization could affect flower shapes.

opencc-by-4.0Apr 2024View details →

Data for: Microbiome and metabolic dynamics shape coral post-stress recovery

This is the data underlying the analysis for the coral experiment described in the article: "Microbiome and metabolic dynamics shape coral post-stress recovery" It contains: <ul> <li>The endosymbiotic symbiodiniaceae density calculated to surface area per sample and analytical replicate 4-6.</li> <li>Bactiral taxa identfied and the number of sequence reads assign to that ID (ASV) for each sample.</li> <li>Meta data for the samples collected, linking the sample number to experimental treatments and replicates.</li> <li>Lipid data including the concentration of fatty acids in each sample collected.</li> <li>Protein concentrations in each sample including sample (coral nubin) surface area </li> </ul>

Thalamocortical interactions shape hierarchical neural variability during stimulus perception dataset

Dataset used in the Thalamocortical interactions shape hierarchical neural variability during stimulus perception  article.   Dataset contains neural activity recordings of a vibrotactile detection task recorded in four monkeys in the following areas: somatosensory thalamus (VPL), 3b and area 1 of the somatosensory cortex (S1)

Solvent-triggered shape change in gradient-based 4D printed bilayers: case study on semi-crystalline polymer networks

This dataset comes from the following paper: Lorenzo Bonetti, Aron Cobianchi, Daniele Natali, Stefano Pandini, Massimo Messori, Maurizio Toselli, Giulia Scalet, Solvent-triggered shape change in gradient-based 4D printed bilayers: case study on semi-crystalline polymer networks, Soft Matter, 2024. <a href="https://doi.org/10.1039/D4SM00304G" target="_blank" rel="noopener">https://doi.org/10.1039/D4SM00304G</a> It contains: <ul> <li>"Notes.pdf" describing all the files uploaded</li> <li>.xls files of the experimental data</li> <li>. m of the theoretical computations</li> </ul>

opencc-zeroMay 2024View details →

Out of shape: Ocean acidification simplifies coral reef architecture and reshuffles fish assemblages

Climate change stressors are progressively simplifying biogenic habitats in the terrestrial and marine realms, and consequently altering the structure of associated species communities. Here, we used a volcanic CO2 seep in Papua New Guinea to test in situ if altered reef architecture due to ocean acidification reshuffles associated fish assemblages. We observed replacement of branching corals by massive corals at the seep, with simplified coral architectural complexity driving abundance declines between 60-86% for an assemblage of damselfishes associated with branching corals. An experimental test of habitat preference for a focal species indicated that acidification does not directly affect habitat selection behaviour, with changes in habitat structural complexity consequently appearing to be the stronger driver of assemblage reshuffling. Habitat health affected anti-predator behaviour, with P. moluccensis becoming less bold on dead branching corals relative to live branching corals, irrespective of ocean acidification. We conclude that coral reef fish assemblages are likely to be more sensitive to changes in habitat structure induced by increasing pCO2 than any direct effects on behaviour, indicating that changes in coral architecture and live cover may act as important mediators of reef fish community structures in a future ocean.

opencc-zeroMay 2024View details →

Data from: Skeletal mineralogy of marine organisms shaped by seawater temperature and evolutionary history - a case study of cheilostome bryozoans

The record of CaCO3 biominerals serves as a valuable repository documenting Earth's evolutionary history and environmental changes. An in-depth understanding of the mineralogical diversity within calcifying organisms is essential for interpreting the evolutionary record of CaCO3 and evaluating the adaptability of biomineralizers to past and future environmental change. To offer insights into the relative importance of environment vs. phylogenetic history in determining mineralogy, this study explores the modern-day global distribution of mineralogies in cheilostome bryozoans. Cheilostome bryozoans vary considerably in their mineral composition: in our dataset 65% of the species possess purely calcite skeletons, 15% exclusively employ aragonite, and 20% exhibit mixed (i.e., calcite and aragonite) mineralogies. Temperature is the predominant measured environmental factor influencing bryozoan skeletal mineralogy, accounting for 20% of its variability across species, when phylogenetic relatedness is unaccounted for. Bryozoans in lower latitudes, characterized by higher seawater temperatures, have higher aragonite concentrations. By accounting for phylogenetic structure using a subset of 87 species for which we have topological information, 40% of the observed mineralogical variability could be attributed to present-day temperature. In contrast, depth and salinity played minor roles, explaining less than 1% of the mineralogical variation each. This study emphasizes the influence of evolutionary history on the mineralogical variability of calcifying organisms, even when it can be shown that a single environmental factor (temperature) explains a substantial amount of this variability. When confronted with changing temperature, calcifiers such as bryozoans are likely to respond in diverse ways, depending on the species, given their phylogenetic relatedness and the external conditions they meet.

Statistical learning shapes pain perception and prediction independently of external cues

<h1>Dataset and code for the relevant analysis and results:</h1> <h3>"Statistical learning shapes pain perception and prediction independently of external cues"</h3> Onysk, J., Whitefield, M., Gregory, N., Jain, M., Turner, G., Seymour, B., Mancini, F. (2024). eLife. <a href="https://doi.org/10.7554/eLife.90634.2">https://doi.org/10.7554/eLife.90634.2</a> <h2>1 - data_collection</h2> Contains the code for the psychophysical experiment (PsychToolBox), including the sequence generations scripts. <h2>2 - preprocessing</h2> Contains code that preprocesses behavioural data from PsychToolBox. This includes linear transformation of inputs, exporting data to stan readable format and plotting Supplement figures. - The raw behavioural data can be found in preprocessing/data. Stan ready ready for each condition is found in preprocessing/stan_data <h2>3 - model_fit_analysis</h2> Contains stan models used in the paper ('models/'), model fitting code ('fit_models_cs.R) (inlcuding HPC setup in 'hpc/'), initial analysis script for processing stan samples ('primary_analysis_cs.R'), as well as additional analyis scripts ('extra_analysis_cs.R', 'correlation_beh_model_cs.ipynb') that generate figures from the paper and supplement. - The posterior draws for parameters can be found in model_fit_analysis/output/cs_results  <h2>4 - model_recovery</h2> Contains code that execute model and parameter recovery analysis ('mp_recovery.R'), including HPC setup ('hpc/'). The 'mp_rec_analyse.R' reproduces model and parameter recovery results from the supplement. <h2>5 - Figures</h2> Contains all the figures from the manuscript and the supplement. <h2>6 - RDS_fits</h2> Contains RStan fit objects for each condition for each model

opencc-by-4.0Jul 2023View details →

The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages

This is the datasets and R script for our  manuscript titled "The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages." Study area and sampling of Mecsek_species_Szivaketal.xlsx data The study area is situated in the Mecsek Mountains in Hungary. Stream insects were collected using the kick and sweep sampling technique. A hand net with a frame width of 25 cm and a mesh size of 1000 µm was employed. The collection involved disturbing an area of 0.25 × 0.25 m. We employed a stratified random multihabitat sampling procedure. We collected 20 sample units from the major microhabitats in proportion to their occurrence within the reaches. Each sample unit was individually processed and sorted in the laboratory to ensure thorough and accurate analysis. Disperse_trait_Szivaketal.xlsx data is based on DISPERSE database (Sarremejane et al., 2020) Methods for microhabitat_coverage_reach_transect.xlsx: Prior to sampling, we divided each 100 m long reach into 20 transects of comparable length and created microhabitat coverage maps. Using these maps, we assessed the proportionate coverage of different microhabitat types within each reach References: Sarremejane, R., Cid, N., Stubbington, R., Datry, T., Alp, M., Cañedo-Argüelles, M., Cordero-Rivera, A., Csabai, Z., Gutiérrez-Cánovas, C., Heino, J., Forcellini, M., Millán, A., Paillex, A., Pařil, P., Polá&scaron;ek, M., Tierno de Figueroa, J. M., Usseglio-Polatera, P., Zamora-Muñoz, C., & Bonada, N. (2020). DISPERSE, a trait database to assess the dispersal potential of European aquatic macroinvertebrates. Scientific Data, 7(1), 386. https://doi.org/10.1038/s41597-020-00732-7

opencc-zeroMay 2024View details →

Circular genetic structure of the Abies nephrolepis species complex shaped by the circular landform of Northeast Asia

Aim: Pinaceae have been noted for their tendency towards reticulation as a result of interspecific hybridization. Here, we demonstrated the phylogeographic dynamics of the native Northeast Asian sub-alpine conifer, Abies nephrolepis species complex (ANSC), evolving in circular overlaps along the Northeast Asian landform, which functions as a corridor with the sea, thus acting as a geographic barrier. Location: Northeast Asia: the Korean Peninsula, Japanese Archipelago, Russian Far East, and northeastern China Taxon: Abies nephrolepis species complex (Family Pinaceae, Genus Abies, Section Balsamea, Abies nephrolepis, A. koreana, A. veitchii, and A. sachalinensis) Methods: A total of 728 individuals from 38 ANSC populations were analysed using multiplexed inter-simple sequence repeat genotyping by sequencing to capture variations in bi-parental nuclear genomes. Eight mitochondrial regions and eight chloroplast regions of each individual were sequenced using the MiSeq platform and Sanger sequencing. Species distribution models were generated. Results: Bayesian clustering with 507 nuclear single nucleotide polymorphisms and the discrepancy between cytoplasmic and nuclear genome lineages implied contemporary and ancient connections between neighbouring species in the form of circular overlap. This genetic connectivity was supported by principal component analysis. Strong correlations between genetic distance and geographic distance were observed, suggesting that gene flow occurs through a continuous chain around the sea. We also found that gene flow direction and intensity changed over time, with support from paleodistribution modelling. Conclusion: Past hybridization events were captured in cytoplasmic genomes, generating heterogeneity across maternal ancestries. This intensive phylogeographic study demonstrates speciation with incomplete reproductive isolation (continuous gene flow) among neighbouring species with an alteration of the direction and intensity of gene flow due to climate change. The divergence of ANSC due to repeated isolation and reconnection caused by heterogenous physiological environments and climate fluctuation provides a model to solve evolutionary scenarios for reticulate evolution in Pinaceae and other plants.

Indirect social influence helps shaping the diffusion of innovations

This dataset accompanies the paper "Indirect social influence helps shaping the diffusion of innovations". It contains the participant choices between two colors when shown different information about the choices taken in their social network. The objective of the participants was to arrive to a consensus. One of the colors, which was the minority at the beggining, was given an extra incentive. Further details on the experimental setup are specified in the article. The main file is "Unified_data", which contains all the data from the 21 sessions studied and whose fields are described below. The file "ParticipantsData" contains the gender and age distribution of the participants, while the rest of the files are the individual data for each session, in the format given by oTree. Explanation of "Unified_data.csv" fields: <ul> <li>Experiment: Session number.</li> <li>participant.id_in_session: Identifier for each participant, constant for each session.</li> <li>config_name: Contains the order in which the different Setups were played. Its structure is of the form "egonetwork_1_a_b_c", where a,b,c are the numbers 2,3,4 in different order. These represent: 1-Setup AmAz (first neighbors), 2-Setup VerMag (first+second neighbors), 3-Setup RojNar (first+third neighbors), 4-Setup LilMor (first+fourth neighbors).</li> <li>Setup: Name of the Setup played (AmAz, VerMag, RojNar, LilMor and Instrucctions).</li> <li>node: Node assigned to the participant during that Setup.</li> <li>initialcolor: Initial color prescribed at the beginning of the Setup. Names are in spanish: Azul (blue) = #0072B2, Amarillo (yellow) = #FFC300, Verde (green) = #67E96E, Magenta = #C700AC, Rojo (red) = #E53950, Naranja (orange) = #FFA460, Lila (lilac) = #A792FC, Morado (purple) = #8000FF.</li> <li>InnovationAsInitialcolor: Binary variable showing if participant had the promoted color as initial color.</li> <li>threshold: Best threshold obtained in the model fitting.</li> <li>parameter: Best long-range parameter obtained in the model fitting.</li> <li>Time: Best time simulation obtained in the model fitting.</li> <li>AdoptersConsensus: First round in which all the participants chose the promoted color at least once.</li> <li>SimulationConsensus: Round in which the simulation of the fitted model arrived to consensus.</li> <li>Round: Round number.</li> <li>preg: Only in the Instructions Setup. Answer given to the control question.</li> <li>action: Color chosen by the participant in that round.</li> <li>Adopted_color: Previous varible translated into binary.</li> <li>Adopted_color_bin: Previous variable as logic variable.</li> <li>MajorityColor: Color most seen between the information given to the participant. In case of draw, one was chosen randomly.</li> <li>InnovationAsMajorityColorSeen: Binary variable showing if MajorityColor is equal to Promoted_color.</li> <li>bot: Binary variable showing if the participant was a bot in the current round (did not make a decision on time).</li> <li>color_neighbors_shown: List of the colors of the first neighbors shown to the participant in that round.</li> <li>color_neighbors_shown_color: Previous variable translated from hexadecimal to spanish.</li> <li>perc_color_neighbors: Percentage of neighbors shown with color equal to the promoted color.</li> <li>color_friends_shown: List of the colors of the long-distance friends shown to the participant in that round.</li> <li>color_friends_shown_color: Previous variable translated from hexadecimal to spanish.</li> <li>perc_color_friends: Percentage of long-distance friends shown with color equal to the promoted color.</li> <li>Adopted_innovation: Number of round since the participant first chose the promoted color.</li> <li>Promoted_color: Color with incentive. Setup AmAz - Azul, Setup VerMag - Magenta, Setup RojNar - Naranja, Setup LilMor - Morado.</li> <li>num_adopters: Number of adopters (people that have chosen the promoted color at least once) in the current round.</li> <li>total_participants: Constant showing the size of the network used (31).</li> <li>perc_adopters: Percentage of participants that are adopters in the current round.</li> </ul>

opencc-zeroJun 2024View details →

Data from: Age dominates flight distance and duration, while body size shapes flight speed in Bombus terrestris L. (Hymenoptera: Apidae)

Flight plays crucial role in the fitness of insect pollinators, such as bumble bees. Despite their relatively large body size compared to their wings, bumble bees can fly under difficult ambient conditions, such as cooler temperatures. While their body size is often positively linked to their foraging range and flight ability, the influence of age remains less explored. Here, we studied the flight performance (distance, duration, and speed) of aging bumble bee workers using tethered flight mills. Additionally, we measured their intertegular distance (ITD) and dry mass as proxies for their body size. We found that flight distance and duration was predominantly influenced by age, challenging assumptions that age does not play a key role in foraging and task allocation. From the age of 7 to 14 days, flight distance and duration increased six-fold and five-fold, respectively. Conversely, body size primarily impacted the maximum and average flight speed of workers. Our findings indicate that age substantially influences flight distance and duration in bumble bee workers, affecting foraging performance and potentially altering task allocation strategies. This underscores the importance of considering individual age and physiological changes alongside body size/mass in experiments involving bumble bee workers.

opencc-zeroJun 2024View details →

Data from: Environmental conditions differently shape leaf, seed and seedling trait composition between and within elevations of tropical montane forests

The composition of plant functional traits varies in response to environmental conditions due to processes of community assembly and species sorting. However, there is a lack of understanding of how plant trait composition responds to environmental conditions at different spatial scales and across the plant life cycle. We investigated the trait composition of leaves (specific leaf area), seeds (seed mass) and seedlings (initial seedling height) across elevations and within elevations in relation to soil and light conditions in a tropical montane forest in southern Ecuador. We surveyed traits and communities of adult trees, seeds and seedlings on nine plots at three elevations (1000-3000 m a.s.l.) and calculated community-weighted mean trait values to analyse trait variation across and within elevations. In addition, we measured two environmental factors (soil C/N ratio and canopy openness) to quantify local-scale variation in environmental conditions within elevations. We found that community-weighted means of specific leaf area, seed mass and initial seedling height decreased consistently with increasing elevation. Within elevations, mean trait values of trees, seeds and seedlings responded differently to local-scale environmental conditions. Specific leaf area decreased with increasing soil C/N ratio, and initial seedling height decreased with increasing canopy openness. Seed mass was associated neither with soil nor with light conditions. Our findings show that broad-scale and local-scale processes differently shape the composition of leaf, seed and seedling traits in tropical forests, indicating a scale-dependence in trait-environment associations. Furthermore, plant traits corresponding to different life stages were related differently to environmental conditions within elevations. Community assembly processes may therefore lead to differences in species sorting at early and late plant life stages.

opencc-by-4.0Jun 2024View details →

Characterizing multidimensional cellular physiological states with quantitative three-dimensional shape descriptors for cell membranes

<h3>Supplementary dataset and code for the article "Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes"</h3> CShaper Dataset.zip: The 3D cell regions reused from the previously published article <a href="https://doi.org/10.1038/s41467-020-19863-x">https://doi.org/10.1038/s41467-020-19863-x</a>. Cell Shape Descriptors - Code & Data.zip: The code (exemplifed by embryo Sample04) and data (including embryo Sample04-Sample20) of 12 3D shape descriptors for all 3D cell regions in the CShaper dataset. GUI.zip: The user-friendly software Shape Descriptor Tool is a Graphical User Interface based on Matlab for calculating 12 shape descriptors for a 3D cell region (exemplified by embryo Sample20, time point 14, ABpl cell in the CShaper dataset). The instruction guidebook is included in the Supplementary Material of the article.

opencc-by-4.0Dec 2005View details →

Fig. 2 in Repeatability Analysis Of Egg Shape In A Wild Tree Sparrow (Passer Montanus) Population: A Sensitive Method For Egg Shape Description

Fig. 2. Data collecting method results in 22 co-ordinates of each eggs

opencc-by-4.0Dec 2005View details →

Fig. 1 in Repeatability Analysis Of Egg Shape In A Wild Tree Sparrow (Passer Montanus) Population: A Sensitive Method For Egg Shape Description

Fig. 1. Differently shaped eggs characterised with the same egg shape index (ES = 0.7)

opencc-by-4.0Sep 2023View details →

Fig. 4 in Variation in the colour and shape of capitula in Parkia bicolor (Leguminosae) illustrated by two watercolours from southern Nigeria painted by Dorothy Amaury Talbot (1871-1916)

Fig. 4. – Watercolour of Parkia bicolor A. Chev. by Dorothy Amaury Talbot, mounted upside down,

opencc-by-4.0Sep 2023View details →

Fig. 3 in Variation in the colour and shape of capitula in Parkia bicolor (Leguminosae) illustrated by two watercolours from southern Nigeria painted by Dorothy Amaury Talbot (1871-1916)

Fig. 3. – Map of the Oban District in south-eastern Nigeria prepared by Percy Amaury Talbot.

opencc-by-4.0Feb 2024View details →

Fig. 7. - Humerocyrtis n in New Middle Triassic Bell-Shaped Nassellarian Radiolaria From Alpine And Carpathian Areas

Fig. 7. - Humerocyrtis n. sp., H – shoulder, Rc4.