Find research datasets worth reusing

opencc-zeroSep 2019View details →

Evidence for individual discrimination and numerical assessment in collective antipredator behaviour in wild jackdaws (Corvus monedula)

Collective responses to threats occur throughout the animal kingdom but little is known about the cognitive processes underpinning them. Antipredator mobbing is one such response. Approaching a predator may be highly risky, but the individual risk declines and the likelihood of repelling the predator increases in larger mobbing groups. The ability to appraise the number of conspecifics involved in a mobbing event could therefore facilitate strategic decisions about whether to join. Mobs are commonly initiated by recruitment calls, which may provide valuable information to guide decision-making. We tested whether the number of wild jackdaws responding to recruitment calls was influenced by the number of callers. As predicted, playbacks simulating three or five callers tended to recruit more individuals than playbacks of one caller. Recruitment also substantially increased if recruits themselves produced calls. These results suggest that jackdaws use individual vocal discrimination to assess the number of conspecifics involved in initiating mobbing events, and use this information to guide their responses. Our results show support for the use of numerical assessment in antipredator mobbing responses and highlight the need for a greater understanding of the cognitive processes involved in collective behaviour.

opencc-zeroNov 2014View details →

Data from: Effect of culling on individual badger (Meles meles) behaviour: potential implications for bovine tuberculosis transmission

1. Culling wildlife as a form of disease management can have unexpected and sometimes counterproductive outcomes. In the UK, badgers (Meles meles) are culled in efforts to reduce badger-to-cattle transmission of Mycobacterium bovis, the causative agent of bovine tuberculosis (TB). However, culling has previously been associated with both increased and decreased incidence of M. bovis infection in cattle. 2. The adverse effects of culling have been linked to cull-induced changes in badger ranging, but such changes are not well documented at the individual level. Using GPS-collars, we characterised individual badger behaviour within an area subjected to widespread industry-led culling, comparing it with the same area before culling and with three unculled areas. 3. Culling was associated with a 61% increase (95% CI 27-103%) in monthly home range size, a 39% increase (95% CI 28-51%) in nightly maximum distance from the sett, and a 17% increase (95% CI 11-24%) in displacement between successive GPS-collar locations recorded at 20-minute intervals. Despite travelling further, we found a 91.2 minute (95% CI 67.1-115.3 minute) reduction in the nightly activity time of individual badgers associated with culling. These changes became apparent while culls were ongoing and persisted after culling ended. 4. Expanded ranging in culled areas was associated with individual badgers visiting 45% (95% CI 15-80%) more fields each month, suggesting that surviving individuals had the opportunity to contact more cattle. Moreover, surviving badgers showed a 19.9-fold increase (95% CI 10.8-36.4 increase) in the odds of trespassing into neighbouring group territories, increasing opportunities for intergroup contact. 5. Synthesis and Applications: Badger culling was associated with behavioural changes among surviving badgers which potentially increased opportunities for both badger-to-badger and badger-to-cattle transmission of M. bovis. Furthermore, by reducing the time badgers spent active, culling may have reduced badgers' accessibility to shooters, potentially undermining subsequent population control efforts. Our results specifically illustrate the challenges posed by badger behaviour to cull-based TB control strategies and furthermore, they highlight the negative impacts culling can have on integrated disease control strategies.

opencc-by-4.0Apr 2019View details →

EpiDiverse individual project introduction videos

Videos of each ESR in the EpiDiverse consortium describing the main aims of their individual research projects

opencc-zeroJan 2016View details →

Common Genetic Variants in FOXP2 are Not Associated with Individual Differences in Language Development

Three data sets used in” Common Genetic Variants in FOXP2 Are Not Associated with Individual Differences in Language Development” are provided.  The discovery data set was comprised of 834 children who were members of a Longitudinal sample and children who were members of a School sample.  Both samples are contained in the Iowa data set.  The Iowa data set contains a quantitative variable LCOMP that represents a composite z-score representing oral language ability.  The data set also identifies which sample the children belonged to and the allele calls for 13 tag SNPs located across FOXP2.  A second data file, ELVS, contains data from a separate sample of children who were used to test for replication of inconsistent evidence of an association between language and the SNP rs1916988.  The ELVS file provides a composite oral language score scaled in standard score units (mean=100, SD=15) and the genotype calls for the  SNP rs1916988.

opencc-by-4.0Feb 2017View details →

Individual work of Bachelor students monitored using a dynamic assessment dashboard

This document explain how data were generated and how to interpret them. LICENSE: CC0 But if you want to combine data with other datasets, feel free to use them as if they were published under CC0 license. Data were published in February 2017. At that time, Zenodo only provided CC BY, CC BY-SA, CC BY-NC, CC BY-ND and CC BY-NC-ND. No CC0 option was available. HOW DATA WERE COLLECTED Data provided in this dataset were collected in Fall 2016 as part of the Bachelor course 'Formation des usagers en bibliothèques' taught at the University of applied sciences Geneva (Information Sciences Department). Data were generated by the interaction of the students with DAD, the Dynamic assessment dashboard, software to be released in 2017 (https://github.com/grolimur/DAD). Only data related to individual activities are published in this set. They were then cleaned and anonymised. The activities.csv file is provided for information purpose. Data are provided in 2 formats: * Comma-spearated values (submissions.csv) * SQLite (submissions.sqlite) CSV is not correctly read by Excel, it's recommended to convert it into an .xslx file before using it. SQLite is provided in order to apply different sorting and filters to the data. It can be read using SQLite manager for Firefox (https://addons.mozilla.org/en-US/firefox/addon/sqlite-manager/). CODEBOOK Here is the name, the meaning and the possible values of the columns (name - description [possible values]). ID - database row ID [(database unique row ID)] ActivityID - unique activity ID [1, 2, 3, 4, 10, 14, 16, 21, 22, 23, 41] StudentID - unique anonymous student ID [#50 to #72] date - recorded by the database [timestamp] year - year extracted from date [2016, 2017] month - month extracted from date [01, 11, 12] day - day extracted from date [1 to 31] weekday - weekday calculated from date [1, 2, 3, 4, 5, 6, 7] hour - hour extracted from date - 00 to 23] minute - minute extracted from date [00 to 59] second - second extracted from date [00 to 59] gr - group activity or not [0] validated - was the submission validated or not [-1 or 1] week - week number [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, H1, H2] ActivityID meaning Activities are described in activities.csv. This file conatins only individual activities description. The 2 activities iwth the bonus particularity are not present in the data because students didn't need to apply for them. A bonus was automatically added when activity 1 AND 2 AND 3 AND 4 (bonus = activity 5) as well as when activities 21 AND 22 AND 23 (activity 24) were completed. Date format The date is formatted like YYYY-MM-DD hh:mm:ss. Weekday meaning 1 stands for Monday, 2 for Tuesday and so on until 7 for Sunday. Group meaning 0 stands for 'individual activity' and 1 would stand for group activity'. Only entries with gr="0" appears in this dataset. Validated meaning -1 stands for 'rejected' and 1 for 'validated'. Week meaning The course lasts 10 weeks. 1 stands for the 1st week and so on until 10 that stands for the 10th week. H1 and H2 stand for the Christmas holiday weeks that took place between week 8 and 9. No submission were sent in weeks 1, 2 and 10.

opencc-by-4.0Jun 2017View details →

Individual-based simulation model of annual movement paths for the Darwin's frog (R code and data)

Desprition of the R code I constructed an individual-based simulation model that describes the movement path of an individual Rhinoderma darwinii through 3-month displacement steps. This model was primarily developed to evaluate the age-specific movement behaviour of Darwin's frogs, however, I also used it to provide better estimates (i.e. alleviating for movement censoring) of age-specific annual displacements in the species. I developed several variations of this model through a combination of different random walk sub-models for juveniles and adults: uncorrelated non-stationary random walks (NRW), correlated non-stationary random walks (CRW), and stationary random walks (SRW). The NRW and CRW were modelled as a first-order Markovian process where the location of an individual i in time t depends on its spatial location in t - 1. The NRW is unbiased, i.e., there is no preferred direction in each movement step. In contrast, the CRW includes persistence in the directionality of movement, so there is a correlation between successive step orientations. Finally, the SRW assumes that individuals have an activity centre to which all their spatial locations are related. Related data are provided (y.txt, x.txt and age.txt)

opencc-by-4.0Jul 2017View details →

Dynamics of individual T cell repertoires: from cord blood to centenarians

The dataset contains processed T-cell receptor repertoire sequencing data from 79 individuals of different sex and age, originally published in [1] and [2]. Note that [1] describes only a subset of samples, while [2] describes the full cohort. The libraries were prepared using a 5'RACE protocol and sequenced on HiSEQ. The libraries incorporate unique molecular identifier (UMI) tags that were mainly used for counting cDNA molecules. Preprocessing was performed using the MIGEC software [3] as follows: all UMI tags represented by a single sequencing read were discarded, the remaining UMI tags were used to assemble cDNA consensus sequences. Note that this procedure eliminates most of cross-sample contamination (batch effect) as described in [2]. VDJ partitioning and CDR3 extraction was performed using MiTCR software [4], sequencing error correction was performed using ETE option in MiTCR. All datasets are converted into VDJtools [5] format, see http://vdjtools-doc.readthedocs.io/en/latest/input.html#vdjtools-format. Sample description: <ul> <li>The A* in sample identifier is the batch ID.</li> <li>Age and sex data is provided in the metadata.txt file.</li> <li>Samples having age "0" are umbilical cord blood samples.</li> </ul> Contributors: <ul> <li>The T-cell repertoire aging study was a project ran in the Genomics of Adaptive Immunity Lab (Prof. Dmitry Chudakov)</li> <li>The samples were acquired, prepared and sequenced by Dr. Olga Britanova</li> <li>The data was analyzed and uploaded by Dr. Mikhail Shugay</li> </ul> Citations: <ul> <li>[1] OV Britanova, EV Putintseva, M Shugay, EM Merzlyak, MA Turchaninova, et al. Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling. The Journal of Immunology 2014; 192 (6), 2689-2698</li> <li>[2] OV Britanova, M Shugay, EM Merzlyak, DB Staroverov, EV Putintseva, et al. Dynamics of individual T cell repertoires: from cord blood to centenarians. The Journal of Immunology 2016; 196 (12), 5005-5013</li> <li>[3] M Shugay, OV Britanova, EM Merzlyak, MA Turchaninova, IZ Mamedov, et al. Towards error-free profiling of immune repertoires. Nature methods 2014; 11 (6), 653-655</li> <li>[4] DA Bolotin, M Shugay, IZ Mamedov, EV Putintseva, MA Turchaninova, et al. MiTCR: software for T-cell receptor sequencing data analysis. Nature methods 2013; 10 (9), 813-814</li> <li>[5] M Shugay, DV Bagaev, MA Turchaninova, DA Bolotin, OV Britanova, et al. VDJtools: unifying post-analysis of T cell receptor repertoires. PLoS computational biology 2015; 11 (11), e1004503</li> </ul>

opencc-by-4.0Jul 2017View details →

Electric field driven switching of individual magnetic skyrmions

Data related to the publication

opencc-by-4.0Aug 2017View details →

Data and script for: A marker of biological age explains individual variation in the strength of the adult stress response

Data and script for: A marker of biological age explains individual variation in the strength of the adult stress response. Comprises 2 CSV data files and one R script.

opencc-by-4.0Oct 2023View details →

Vine Trunk Semantic Segmentation using Individual Vine Trunks

Automatically labeled semantic segmentation dataset of vine trunk thumbnails extracted from VIneSet and other supplementary data. Source paper of this dataset is "Generating vine trunk semantic segmentation dataset via semi-supervised learning and object detection" published in MDPI Robotics https://www.mdpi.com/2218-6581/13/2/20.

opencc-by-4.0Aug 2023View details →

Individual multilocus genotypes from four populations of Helichrysum arenarium (Asteraceae) from Belgium and Germany

Individual multilocus genotypes based on 11 microsatellites loci from four populations of Helichrysum arenarium (Asteraceae) from Belgium and Germany. For more details, see Van Rossum et al. 2024 "Genetic diversity assessment of Helichrysum arenarium (Asteraceae) for the genetic restoration of declining populations" in Ecology and Evolution

Data from: A new mechanistic model for individual growth suggests upregulated maintenance costs when food is scarce in an insect

In order to calibrate and evaluate a recently developed growth model, the Maintenance-Growth Model (MGM), for the case of growth under food restriction, empirical data for house crickets (Acheta domesticus) were collected and analysed. This data set contains data for individually reared crickets growing under two different regimes of controlled food limitation as well as data for food-limited cohorts of growing house crickets. The sets include temporal data for body mass and ingestion as well as age and size at maturation (imago emergence). The data for food-limited cohorts were collected prior to this study and parts of it have previously been analysed and presented in a publication on animal self-thinning.

Evidence for individual vocal recognition in a pair-bonding poison frog, Ranitomeya imitator

Individually distinctive vocalizations are widespread in nature, although the ability of receivers to discriminate these signals has only been explored through limited taxonomic and social lenses. Here, we asked whether anuran advertisement calls, typically studied for their role in territory defense and mate attraction, facilitate recognition and preferential association with partners in a pair-bonding poison frog (Ranitomeya imitator). Combining no- and two-stimulus choice playback experiments, we evaluated behavioral responses of females to male acoustic stimuli. Virgin females oriented to and approached speakers broadcasting male calls independent of caller identity, implying that females are generally attracted to male acoustic stimuli outside the context of a pair bond. When pair-bonded females were presented with calls of a mate and a stranger, they showed significant preference for calls of their mate. Moreover, behavioral responses varied with breeding status: females with eggs were faster to approach stimuli than females that were pair-bonded but did not currently have eggs. Our study suggests a potential role for individual vocal recognition in the formation and maintenance of pair bonds in a poison frog and raises new questions about how acoustic signals are perceived in the context of monogamy and biparental care.

Individual behaviour, growth, survival and vulnerability to hunting in a large mammal

Humans have exploited wild animals for thousands of years. Recent studies indicate that harvest-induced selection on life-history and morphological traits may lead to ecological and evolutionary changes. Less attention has been given to harvest-induced selection on behavioural traits, especially in terrestrial systems. We assessed in a wild population of large terrestrial mammals whether decades of hunting led to harvest-induced selection on trappability, a proxy of risk-taking behaviour. We investigated links between trappability, horn growth and survival across individuals in early life and quantified the correlations between early life trappability and horn growth with availability to hunters and probability of being shot. We found positive among-individual correlations between early life trappability and horn growth, early life trappability and survival, and early life horn growth and survival. Faster growing individuals were more likely to be available to hunters and shot at a young age. We found no correlations between early life trappability and availability to hunters or probability of being shot. Our results show that correlations between behaviour and growth can occur in wild terrestrial population but may be context dependent. This result highlights the difficulty in formulating general predictions about harvest-induced selection on behaviour, which can be affected by species ecology, harvesting regulations, and harvesting methods used. Future studies should investigate mechanisms linking physiological, behavioural, and morphological traits and how this effects harvest vulnerability to evaluate the potential for harvest to drive selection on behaviour in wild animal populations.

Data from: Among-individual behavioural variation in the ornamental red cherry shrimp, Neocaridina heteropoda

Personality variation, defined as among-individual differences in behaviour that are repeatable across time and context, has been reported across animal taxa. From an evolutionary perspective, characterising the amount and structure of this variation is useful since differences among-individuals are the raw material for adaptive behavioural evolution. However, it is becoming apparent that behavioural variation among-individuals also has implications for more applied areas of evolution and ecology – from invasion biology, to ecotoxicology, and selective breeding in captive systems. Here, we investigate the structure of personality variation in the red cherry shrimp, Neocaridina heteropoda, a popular ornamental species that is readily kept and bred under lab conditions and is emerging as a decapod crustacean model across these fields, but for which basic biological, ecological, and behavioural data is limited. Using two assays and a repeated measures approach, we quantify behaviours putatively indicative of shy-bold variation and test for sexual dimorphism and/or size-dependent behaviours (as predicted by some state-dependent models of personality). We find moderate to high behavioural repeatabilities across traits. Although strong individual level correlations across behaviours are consistent with a major personality axis underlying these observed traits, the multivariate structure of personality variation does not fully match a priori expectations of a shy-bold axis. This may reflect our ecological naivety with respect to what really constitutes bolder, more risk prone, behaviour in this species. We find no evidence for sexual dimorphism and only weak support size-dependent behaviour. Our study contributes to the growing literature describing behavioural variation in aquatic invertebrates. Furthermore, it lays a foundation for further studies harnessing the potential of this emerging model system. In particular, this existing behavioural variation could be functionally linked to life-history traits and invasive success, and serve as target of artificial selection or bioassays. It thus holds significant promise in applied research across ecotoxicology, aquaculture, and invasion biology.

opencc-by-4.0Jan 2021View details →

Figure 4 in Individual growth and mortality of Rhithropanopeus harrisii (Decapoda: Panopeidae) in the estuarine region of Patos Lagoon, Southern Brazil

Figure 4. Size-converted catch curve. Significant fit (Fcalc.= 239.81> Fcrit.0.05 1,11 = 4.84; R2 = 0.95).

opencc-zeroMar 2024View details →

Core individual-based model simulation script and landscape data

Habitat loss and isolation caused by landscape fragmentation represent a growing threat to global biodiversity. Existing theory suggests that the process will lead to a decline in metapopulation viability. However, since most metapopulation models are restricted to simple networks of discrete habitat patches, the effects of real landscape fragmentation, particularly in stochastic environments, are not well understood. To close this major gap in ecological theory, we developed a spatially explicit, individual-based model applicable to realistic landscape structures, bridging metapopulation ecology and landscape ecology. This model reproduced classical metapopulation dynamics under conventional model assumptions, but on fragmented landscapes, it uncovered general dynamics that are in stark contradiction to the prevailing views in the ecological and conservation literature. Notably, fragmentation can give rise to a series of dualities: a) positive and negative responses to environmental noise, b) relative slowdown and acceleration in density decline, and c) synchronization and desynchronization of local population dynamics. Furthermore, counter to common intuition, species that interact locally ("residents") were often more resilient to fragmentation than long-ranging "migrants". This set of findings signals a need to fundamentally reconsider our approach to ecosystem management in a noisy and fragmented world.

opencc-by-4.0Feb 2019View details →

Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum

Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet.

opencc-zeroApr 2024View details →

Data from: Variation in nuptial colour in relation to sex, individual quality and mating success in the sex-role reversed red phalarope (Phalaropus fulicarius)

In most bird species, males are more ornamented and compete for females, who contribute more to offspring care. In a minority of species this pattern is reversed, with more colourful females competing for mates and males taking care of parental duties. In such sex-role reversed species, the links between colourful ornamentation, individual quality and mating success are not well established. The red phalarope (Phalaropus fulicarius) is a colourful sex-role reversed migratory shorebird with regular social polyandry, in which both sexes show considerable colour variation. Here, we describe sex differences in colour and quantify associations between colour variation and indicators of quality and mating success in both sexes. Using a large sample of photos collected across three consecutive years on the Arctic breeding grounds, we scored colour variation for four body parts (bill, crown, cheek and breast), and analysed scores separately and combined into an overall colour score. Females were more colourful and larger than males, and individuals could be unambiguously sexed by crown colour. Nevertheless, there was substantial variation within sexes and some overlap between males and females in bill, cheek, breast, and overall colour scores. Assortative mating by colour was only found for the bill. Colour variation did not correlate with plasma testosterone levels, except for male cheek colour. Females in better body condition had yellower bills and higher overall colour scores, while early-arriving birds had higher breast and overall scores. Phalaropes that bred locally were heavier than those that did not, but they did not have higher colour scores. Female colour variation did not predict the probability of local social polyandry nor variation in clutch size, and male coloration did not predict the probability of nest predation. In conclusion, phalarope colour variation showed modest correlations with individual quality and was unrelated to variation in local reproductive success.