Find research datasets worth reusing

opencc-zeroFeb 2022View details →

Algal growth, bumblebee colony and individual development, bee behavior and yield of oilseed rape under a trophic cascade and extreme weather

Trophic cascades in the aquatic environment constitute important mechanisms for improving water quality. However, how the presence or non-presence of these trophic cascades may affect interactions across the aquatic-terrestrial interface remains poorly investigated. Pollinators such as bees may be especially vulnerable to changes in water resource quality induced by trophic cascades. Understanding how aquatic trophic cascades affect bees and pollination becomes even more pressing under ongoing climate change due to increased physiological demands for water under extreme weather events.In a novel field experiment combining terrestrial and aquatic mesocosms, we aimed to test how changes in water quality induced by an aquatic trophic cascade affected foraging and growth of bumblebee colonies as well as foraging of solitary bees. While we expected fish predation to reduce top-down control of zooplankton on phytoplankton and thereby, indirectly, induce increased growth of toxic cyanobacteria, we instead found the trophic cascade to induce the formation of algal surface mats that bumblebees used to access water under a severe heat wave and drought. This access to water was associated with higher bumblebee colony reproductive success, growth and weight compared to control colonies with no trophic cascade induced (and hence no algal surface mats). We also found marginal but non-significant effects on oilseed rape yield, but surprisingly with higher yields in the control treatment where bumblebees could not access water.Our results provide new insights on how aquatic trophic cascades can lead to unpredicted ecological interactions across the aquatic-terrestrial interface facilitated by climate change. Our study highlights the importance of water for the fitness of terrestrial ecosystem service providers under altered environmental conditions.

opencc-zeroFeb 2022View details →

Among-individual diet variation within a lake trout ecotype: Lack of stability of niche use

In a polymorphic species, predictable differences in resource use are expected among ecotypes, and homogeneity in resource use is expected within an ecotype. Yet, using a broad resource spectrum has been identified as a strategy for fishes living in unproductive northern environments, where food is patchily distributed and ephemeral. We investigated whether specialization of trophic resources by individuals occurred within the generalist piscivore ecotype of lake trout from Great Bear Lake, Canada, reflective of a form of diversity. Four distinct dietary patterns of resource use within this lake trout ecotype were detected from fatty acid composition, with some variation linked to spatial patterns within Great Bear Lake. Feeding habits of different groups within the ecotype were not associated with detectable morphological or genetic differentiation, suggesting that behavioral plasticity caused the trophic differences. A low level of genetic differentiation was detected between exceptionally large-sized individuals and other piscivore individuals. We demonstrated that individual trophic specialization can occur within an ecotype inhabiting a geologically young system (8,000–10,000 yr BP), a lake that sustains high levels of phenotypic diversity of lake trout overall. The characterization of niche use among individuals, as done in this study, is necessary to understand the role that individual variation can play at the beginning of differentiation processes.

opencc-by-4.0Feb 2022View details →

Data sets for 'Mechanical Compliance of Individual Fractures in a Heterogeneous Rock Mass from Production-type Full-waveform Sonic Data', submitted to JGR: Solid Earth

Synthetic and field FWS data sets are supplied for validation of proposed methods for compliance estimation of individual fractures. Each zip contains ‘ReadMe.txt ‘, which illustrates the files and corresponding parameters. More details about the setup in the submitted paper ‘Mechanical Compliance of Individual Fractures in a Heterogeneous Rock Mass from Production-type Full-waveform Sonic Data’.

opencc-zeroFeb 2022View details →

Street Spectra individual classifications

CSV file containing individual classifications for subjects data and metadata.

Individual glass and secondary standard analyses for tephra described in sediment cores from Skilak Lake, Alaska

This dataset comprises individual glass shard and secondary standard analyses for tephra collected in sediment cores from Skilak Lake, Alaska. These geochemical analyses were used in the research article in Sedimentology titled “Unravelling a 2300 year long sedimentary record of megathrust and intraslab earthquakes in proglacial Skilak Lake, south-central Alaska” by Praet et al. (2022). DOI: <a href="https://doi.org/10.1111/sed.12986">10.1111/sed.12986</a>

Beef Cattle Muzzle/Noseprint database for individual identification

This dataset contains muzzle/noseprint images for beef cattle. A total of 4923 muzzle images for 268 feedyard yearlings in the Midwest US were collected from March to July 2021, using a mirrorless digital camera (26 MP maximum resolution) and a 70-300 mm F4-5.6 focal lens. All images were taken outside of the pen did not create any contact or interference with the animals. These images covered three common US feedyard cattle breeds, including Angus, Angus x Hereford, and Continental x British cross). This database only contains the clean and cropped images showing the cattle muzzle area.  All images are housed in individual folders in the .zip file: “BeefCattle_Muzzle_database.zip”. Each folder contains pictures from the same animal. On average, there were more than 12 images collected for each animal.

Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns (repository for Genome Research paper, 2022)

Simulated ONT and PacBio RNA-Seq data for "Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns" paper (Mikheenko et al., Genome Research, 2022). All details can be found in the Methods section of the paper. PacBio.simulated_uniform_coverage.fasta.gz and ONT.simulated_uniform_coverage.fasta.gz files were used in Supplemental Note “Benchmarking of the read-to-isoform assignment algorithm”. ONT.simulated_real_expression.fasta.gz file and all GTF files were used in the Section "Splice site correction improves transcript discovery precision". mouse.gencode.M26.spatial.15percent.reduced.gtf was used as the annotation file for all tools. mouse.gencode.M26.spatial.15percent.expressed.gtf contains the set of all expressed isoforms. mouse.gencode.M26.spatial.15percent.expressed_kept.gtf contains those of the isoforms that are in presented in the annotation file ("known" transcripts), mouse.gencode.M26.spatial.15percent.reduced.gtf contains expressed isoforms that were removed from the annotation ("novel" transcripts).

openother-openMar 2022View details →

Data from: Individual body mass and length dataset for over 12,000 fish from Iberian streams

Body size data of stream fish in the north-east of the Iberian Peninsula. We provide a unique fish individual body size dataset collected from our own sampling and public sources in north-eastern Spain. The dataset includes individual body size measures (fork length and mass) of 12,288 individuals of 24 fish species within 10 families collected at 118 locations in large rivers and small streams. Fish were caught by one-pass electrofishing following European standard protocols. The fish dataset has information on the local instream conditions including climatic variables (i.e., temperature and precipitation), topography (i.e., altitude), nutrient concentration (i.e., total phosphorus and nitrates), and the IMPRESS values (a measure of cumulative human impacts in lotic ecosystems). The potential uses of this new fish dataset are manifold, including developing size-based indices to further estimate the ecological status of freshwater ecosystems, allometric models, and analysis of variation in body size structure along environmental gradients.

opencc-by-4.0Dec 2021View details →

Data for: Neural correlates of individual odor preference in Drosophila

Data associated with: Neural correlates of individual odor preference in Drosophila Abstract: Behavior varies even among genetically identical animals raised in the same environment1–10. However, little is known about the circuit or anatomical underpinnings of this individuality11,12. Drosophila olfaction is an ideal system for discovering the origins of behavioral individuality among genetically identical individuals. The fly olfactory circuit is well-characterized13–16,17–19 and stereotyped15, yet stable idiosyncrasies in odor preference4, neural coding4, and neural wiring20,21 are present and may be relevant to behavior. Using paired behavior and two-photon imaging measurements, we show that individual odor preferences in odor-vs-air and odor-vs-odor assays are predicted by idiosyncratic calcium dynamics in Olfactory Receptor Neurons (ORNs) and Projection Neurons (PNs), respectively. This suggests that circuit variation at the sensory periphery determines individual odor preferences. Furthermore, paired behavior and immunohistochemistry measurements reveal that variation in ORN presynaptic density also predicts odor-vs-odor preference. This point in the olfactory circuit appears to be a locus of individuality where microscale variation gives rise to idiosyncratic behavior. To unify these results, we constructed a leaky-integrate-and-fire model of 3,062 neurons in the antennal lobe. In these simulations, stochastic fluctuations at the glomerular level, like those observed in our ORN immunohistochemistry, produce variation in PN calcium responses with the same structure as we observed experimentally, the very structure that predicts idiosyncratic behavior. Thus, our results demonstrate how minute physiological and structural variations in a neural circuit may produce individual behavior, even when genetics and environment are held constant.

opencc-zeroMar 2022View details →

Genomics of humic adaptation in Eurasian perch (Perca fluviatilis): SNP genotypes of 32 perch individuals, supplementary figures and tables

Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic environments, including perpetually dark, hypoxic, hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost "nocturnal" environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 SNPs, of which >10,000 were identified as potential candidates under selection (associated with >3,000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole-genome analysis to illuminate multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.

opencc-zeroMar 2022View details →

Data from: Demographic correction – a tool for inference from individuals to populations

Estimation of responses of organisms to their environment using experimental manipulations, and comparison of such responses across sets of species, is one of the primary tools in ecology research. The most common approach is to compare response of a single life stage of species to an environmental factor and use this information to draw conclusions about population dynamics of these species. Such approach ignores the fact that interspecific fitness differences measured at a single life stage are not directly comparable and cannot be extrapolated to lifetime fitness of individuals and thus species' population dynamics. Comparison of one life stage only while omitting demographic information can strongly bias conclusions, both in experimental studies with a few species, and in large comparative studies. We illustrate the effect of this omission using both an exaggerated fictitious example, and biological data on congeneric species differing in their demography. We are showing, taking simple assumptions, that different demography can completely revert conclusions reached by a comparison based on an experiment focusing on a single life stage. We show that a "demographic correction", namely translating observed effects into differences in outcomes of demographic models, is a solution to this problem. It requires turning the detected effects from the experiment into changes of transition probabilities of projection matrix models. Although such solution is limited by the low number of species with demographic data available, we believe that existing data (and data likely to be collected in the near future) permit at least approximate handling of this problem.

DA Diffusion Simulation for: A fluorescent nanosensor paint reveals the heterogeneity of dopamine release from neurons at individual release sites

Code developed for the revision of: Elizarova, S., Chouaib, A., Shaib, A., Mann, F., Brose, N., Kruss, S., & Daniel, J. A. (2021). A fluorescent nanosensor paint reveals the heterogeneity of dopamine release from neurons at individual release sites. BioRxiv, 2021.03.28.437019. https://doi.org/10.1101/2021.03.28.437019

Street Spectra individual classifications

CSV file containing individual classifications for subjects data and metadata.

Individual variability in space use near power lines by a long-lived territorial raptor

Evaluating species responses to anthropogenic infrastructures and other habitat changes is often used to assess environmental impacts and to guide conservation actions. However, such studies are generally carried out at the population-level, disregarding inter-individual variability. Here, we investigate population- and individual-level responses towards power lines of a territorial raptor, the Bonelli's eagle Aquila fasciata. We used GPS-PTT tracking data of seventeen adult eagles to model space use as a function of distance to transmission and distribution lines, while accounting for other habitat features known to affect this species. At population level, eagles increased the intensity of space use in the proximity of power lines (up to 1000 m), suggesting an attraction effect. At individual level, some eagles shared the general population attraction pattern, while others showed reduced intensity of space use in the proximity of power lines. These differential responses were unrelated to the sex of individuals, but were affected by the characteristics of the power grid, with a tendency for apparent attraction to be associated with individuals occupying home ranges with a denser network of transmission lines and transmission pylons. However, the study could not rule out the operation of other potentially influential factors, such as individual idiosyncrasies, the spatial distribution of prey availability, and the availability of natural perches and nesting sites. Overall, these results suggest that power lines may drive different behaviors and have differential impacts across individuals, with those attracted to the proximity of power lines potentially facing increased risk of mortality through electrocution and collision, and those avoiding power lines being potentially subject to exclusion effects. More generally, our results reinforce the need to understand individual variability when assessing and mitigating impacts of anthropogenic infrastructures.

Dataset from 'Klever, L., Mamassian, P., & Billino, J. (2022). Age-related differences in visual confidence are driven by individual differences in cognitive control capacities. Scientific Reports, 12, 1-13. doi: 10.1038/s41598-022-09939-7

We provide two files; one data file contains data on which analyses are based, the other one gives the column labels for the data file. ___________________________________________ For further questions, please contact: lena.klever[at]psychol.uni-giessen.de

Code and data from: Competition among small individuals hinders adaptive radiation despite ecological opportunity

Ontogenetic diet shifts, where individuals change their resource use during development, are the rule rather than the exception in the animal world. Here, we aim to understand how such changes in diet during development affect the conditions for an adaptive radiation in the presence of ecological opportunity. We use a size-structured consumer–resource model and the adaptive dynamics approach to study the ecological conditions for speciation. We assume that small individuals all feed on a shared resource. Large individuals, on the other hand, have access to multiple food sources on which they can specialize. We find that competition among small individuals can hinder an adaptive radiation to unfold, despite plenty of ecological opportunity for large individuals. When small individuals experience strong competition for food, they grow slowly and only a few individuals are recruited to the larger size classes. Hence, competition for food among large individuals is weak and there is therefore no disruptive selection. In addition, initial conditions determine if an adaptive radiation occurs or not. A consumer population initially dominated by small individuals will not radiate. On the other hand, a population initially dominated by large individuals may undergo adaptive radiation and diversify into multiple species.

opencc-by-4.0Apr 2022View details →

Neutralizing immunity induced against the Omicron BA.2 variant in vaccinated and unvaccinated individuals infected by Omicron BA.1

This repository contains the pertinent data files used in the manuscript, Neutralizing immunity induced against the Omicron BA.2 variant in vaccinated and unvaccinated individuals infected by Omicron BA.1.

Data for: Individual differences in song plasticity in response to social stimuli and singing position

Individual animals can react to the changes in their environment by exhibiting behaviours in an individual-specific way leading to individual differences in phenotypic plasticity. However, the effect of multiple environmental factors on multiple traits is rarely tested. Such a complex approach is necessary to assess the generality of plasticity and to understand how among-individual differences in the ability to adapt to changing environments evolve. This study examined whether individuals adjust different song traits to varying environmental conditions in the collared flycatcher (Ficedula albicollis), a passerine with complex song. We also aimed to reveal among-individual differences in behavioural responses by testing whether individual differences in plasticity were repeatable. The presence of general plasticity across traits and/or contexts was also tested. To assess plasticity, we documented 1) short-scale temporal changes in song traits in different social contexts (after exposition to male stimulus, female stimulus or without stimuli), and 2) changes concerning the height from where the bird sang (singing position), used as a proxy of predation risk and acoustic transmission conditions. We found population-level relationships between singing position and both song length and complexity, as well as social context-dependent temporal changes in song length and maximum frequency. We found among-individual differences in plasticity of song length and maximum frequency along both the temporal and positional gradients. These among-individual differences in plasticity were repeatable. Some of the plastic responses correlated across different song traits and environmental gradients. Overall, our results show that the plasticity of bird song 1) depends on the social context, 2) exists along different environmental gradients and 3) there is evidence for trade-offs between the responses of different traits to different environmental variables. Our results highlight the need to consider individual differences and to investigate multiple traits along multiple environmental axes when studying behavioural plasticity.

opencc-by-4.0May 2022View details →

Dataset for the manuscript: Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages.

Dataset for the manuscript: Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages. preprint, bioRxiv, 2022. DOI: 10.1101/2022.05.06.490883 Each zip file contains the raw computational data (as a gzip compressed tarball), YAML input files, as well as Python plotting scripts. The Python plotting scripts have dependencies on the packages: tarfile, multiprocessing, numpy, scipy, and matplotlib. Note that the Python plotting scripts plot directly from the gzip compressed tarballs. The corresponding code can be found on GitHub: https://github.com/Ruth-Bowness-Group/CAModel