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Role of individual and population heterogeneity in shaping dynamics of multi-pathogen shedding in an island endemic bat
<p>Dataset for the manuscript "<strong>Role of individual and population heterogeneity in shaping dynamics of multi-pathogen shedding in an island endemic bat</strong>", including information of the bat samples and infection data.</p>
Behavioral flexibility in solitary foraging ants: how experience, colony size and food distribution shape individual and collective performance
<p>To deal with the unpredictability of available food resources, animals must adjust their behavior to optimize foraging efficiency. Various mechanisms can influence an individual’s food acquisition behaviour, and thus our knowledge of their combined impact on foraging efficiency remains limited. In this study, we conducted laboratory experiments with seven colonies of the solitary foraging ant Dinoponera quadriceps. Foragers were individually observed in semi-controlled experiments where food was offered in aggregated or dispersed distributions. During the experiments, individual participation was voluntary (i.e. ants were free to enter or not the experimental arena), giving us an opportunity to assess internal processes such as motivation. Besides, behavioral traits such as foraging activity, exploration of food patches, and performance were recorded across repeated trials. We found that solitary foragers of D. quadriceps were highly efficient (retrieving food in 77.38% of the trips), especially when exploiting aggregated and abundant food resources. However, individual foraging success declined when more conspecific foragers were present and with longer foraging experience. Foragers increased their exploration levels in environments with larger numbers of dispersed prey items. Individual foraging activity was higher with more experience and in smaller colonies with fewer foragers. Furthermore, foragers and colonies exhibited low but consistent differences in levels of activity, exploration, and success rates. These findings provide a comprehensive view of how different factors combine to give rise to complex behaviors such as foraging. Additionally, they emphasize the importance of individual traits for effective task performance within social groups, an understudied topic.</p>
Supplementary material S30: The trend in times intervals of jolting pulses for four mite individuals on various substrates (petri-dish, brood-comb and honeycomb).
<p>Jolt occurrence time intervals with respect to time. Data are shown here for a second and third mite on petri-dish (a, b and c, d respectively), a second mite on brood-comb (e, f) and the mite that produces audible jolting pulses on the empty honeycomb that is referred to in the main text (g, h). Jolt occurrences and time between consecutive instances of jolting are showcased in both linear (a, c, e, g) and logarithmic (b, d, f, h) forms. A change in the colour of the data points is indicative of the mite moving to a new position on the substrate.</p>
Supplementary material S24: Time course of the loudest Varroa jolting pulse compared to that of a honeybee colony and single bee individual.
<p>Time course of the loudest <em>Varroa </em>jolt on brood-comb with the signal from the full colony and a single bee. The signal seen here in each panel is the integral of the magnitude of acceleration with respect to time. The background vibration that is inherent to the room was calculated and subtracted from this data. The loudest jolt (red) is here compared to the signal of a single bee (black) and the vibrations of the full colony at low and high signal (black). High signal is captured when the frame containing the accelerometer is empty of brood. Low signal is captured when the frame is fully loaded with brood and/or honey. The whooping signal (panel a) was captured during a period of high signal.</p>
Supplementary material S8: Mite jolting behaviour percentages observed in the full collection of individuals.
<p>Pie charts demonstrating the percentage of mite individuals observed jolting (left chart) and their longest jolting time durations (right chart). Percentages have been rounded to the nearest 10.</p>
Selection against individuals from genetic introgression of escaped farmed salmon in a natural population of Atlantic salmon
<p>The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of geneflow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life-stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of two years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort) . This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of geneflow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life-stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of two years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort) . This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.</p>
Data from: Localized neighborhood species mingling is correlated with individual tree size inequality in natural forests in South China
<p>Context: Numerous hypotheses such as Janzen–Connell and herd immunity effects have been proposed to explain the coexistence of diverse species in plant communities. However, these mechanisms for maintaining diversity have been studied primarily through the lens of species diversity, whereas tree size diversity or relationships between size and species diversity resulting from local interactions have rarely been investigated.</p> <p>Aims: We aimed to identify relationships between spatial species mingling and tree size inequality using extensive plot data from species-rich forest ecosystems.</p> <p>Methods: We applied neighborhood-based methods and explored relationships between spatial species mingling and size inequality indices in 22 large forest plots (30 ha in total) in subtropical and tropical China.</p> <p>Results: Forest communities with low species mingling, or segregation of heterospecific trees, exhibited increased segregation of trees with dissimilar sizes. In most plots, large trees (e.g. dbh > 30 cm) were extensively associated with high species mingling, and individual-tree neighborhood species and size diversity were closely correlated.</p> <p>Conclusion: Our findings suggest that both the spatial patterns of conspecific dispersal and neighborhood interactions play an important role in determining the spatial patterns of tree size and species diversity and eventually in shaping the structure of forest communities.</p>
TG 111: Factors Governing the Individual Response of Humans to Ionising Radiation
<p>The current system of radiological protection, that aims to avoid tissue reactions (deterministic effects) and minimize risk of stochastic effects (cancers and hereditary effects), through justification and optimisation of practices and limitation of exposures, is based on estimations of risk to a notional average person. The use of an age- and sex-averaged approach is not a reflection of the reality of population structures, but is a pragmatic approach. However, we know that there are variations in radiosensitivity between individuals within the population. The underlying reasons for this variation can be genetic (for example, the radiation-sensitive syndromes such as ataxia telangiectasia and Gorlin syndrome), epigenetic and also environmental or behavioural (for example, the difference in lung cancer risks in smokers and non-smokers). A better understanding of the factors that underlie inter-individual variation in response to radiation, and the magnitude of the variation could impact on the approaches adopted to radiation protection in the occupational, medical and public sectors. One example where this may impact is in radiotherapy for cancer, where severe normal tissue complications can be observed in a sub-set of the individuals treated. Understanding the subpopulations for which such severe complications occur, and the underlying mechanistic basis could inform radiotherapy treatment decision making, improving tumour cure rates while avoiding the severe complications. In 2018, the International Commission on Radiological Protection established a Task Group, TG111 to consider Factors Governing the Individual Response of Humans to Ionising Radiation. The aim of this presentation is to review the current state of knowledge on variation in individual response to radiation and to provide an update on progress with the work of the ICRP Task Group.</p>
Individual variation in marine larval-fish swimming speed and the emergence of dispersal kernels
<p>Dispersal emerges as a consequence of how an individual's phenotype interacts with the environment. Not all dispersing individuals have the same phenotype, and variation among individuals can generate complex variation in the distribution of dispersal distances and directions. While active locomotion performance is an obvious candidate for a dispersal phenotype, its effects on dispersal are difficult to measure or predict, especially in small organisms dispersing in wind or currents. Therefore, we analyzed the effects of larval swimming on dispersal and settlement of coral-reef fish larvae using a high-resolution biophysical model. The model is, to date, the only biophysical model of marine larval dispersal that has been statistically validated against genetic parentage estimates of larval origin and destination, and incorporates empirically-estimated larval behaviors and their ontogeny. Larval swimming, in combination with depth, orientation, and navigation behaviors, actually reduced dispersal distances compared to those of passive larvae. Swimming had no consistent effects on long distance dispersal, but increased the spread of settlement locations. Swimming speed, in contrast, did not consistently affect median dispersal distances, but faster swimming larvae had greater mean and maximum dispersal distances than slower swimming larvae. Finally, faster larval swimming speeds consistently increased the probability of settlement. Our analysis shows how larval swimming differentially affects multiple properties of dispersal kernels. In doing so, it indicates how selection could favor faster larval swimming to increase settlement, which may actually result in longer dispersal distances as a by-product of larvae trying to locate habitat rather than to disperse greater distances.</p>
The contributions of individual traits to survival among terrestrial juvenile pond-breeding salamanders
<p>Individual survival is influenced by interactions between local environmental conditions and an organism's morphological, behavioral, and physiological traits. Studies examining the effects of individual phenotypes on survival under variable conditions are relatively rare among early transitional life stages, though the vital rates of these life stages can importantly influence population dynamics. We experimentally examined the effects of initial body mass, movement, standard metabolic rate (SMR), and respiratory surface area water loss (RSAWL) on survival in the transitional juvenile life stage of two biphasic amphibian species (Ambystoma maculatum and A. opacum) in a seven-month mark-recapture study under semi-natural conditions. Juveniles with a larger initial body mass, lower initial SMR, and/or a lower tendency to change locations had a higher likelihood of known survival. In contrast, we found no significant effect of RSAWL on juvenile survival. The relationships between individual phenotypes and survival did not differ between species, but equivalent species-specific survival rates may have been attributed to larger initial body sizes in A. maculatum and lower SMR in A. opacum. Our results illuminate the complex ways in which individual traits influence survival during the early transitional life stage of two ambystomatid species under varying abiotic conditions. More generally, our findings illustrate potential advantages of simultaneously examining multiple traits to evaluate survival.</p>
Spatial personalities: a meta-analysis of consistent individual differences in spatial behavior
<p>Individual variation in behavior, particularly consistent among-individual differences (i.e., personality), has important ecological and evolutionary implications for population and community dynamics, trait divergence, and patterns of speciation. Nevertheless, individual variation in spatial behaviors, such as home range behavior, movement characteristics, or habitat use has yet to be incorporated into the concepts or methodologies of ecology and evolutionary biology. To evaluate evidence for the existence of consistent among-individual differences in spatial behavior – which we refer to as "spatial personality" – we performed a meta-analysis of 200 repeatability estimates of home range size, movement metrics, and habitat use. We found that the existence of spatial personality is a general phenomenon, with consistently high repeatability (r) across classes of spatial behavior (r = 0.67 - 0.82), taxa (r = 0.31 - 0.79), and time between repeated measurements (r = 0.54 - 0.74). These results suggest: (1) repeatable spatial behavior may either be a cause or consequence of the environment experienced and lead to spatial personalities that may limit the ability of individuals to behaviorally adapt to changing landscapes; (2) interactions between spatial phenotypes and environmental conditions could result in differential reproduction, survival, and dispersal, suggesting that among-individual variation may facilitate population-level adaptation; (3) spatial patterns of species' distributions and spatial population dynamics may be better understood by shifting from a mean field analytical approach towards methods that account for spatial personalities and their associated fitness and ecological dynamics.</p>
Precise quantification of behavioral individuality from 80 million decisions across 183,000 flies
<p>Data set associated with a study into distributions of individual behavioral measures. </p> <p> </p> <p>Manuscript abstract:<br> <br> Individual animals behave differently from each other. This variability is a component of personality and arises even when genetics and environment are held constant. Discovering the biological mechanisms underlying behavioral variability depends on efficiently measuring individual behavioral bias, a requirement that is facilitated by automated, high-throughput experiments. We compiled a large data set of individual locomotor behavior measures, acquired from over 183,000 fruit flies walking in Y-shaped mazes. With this data set we first conducted a “computational ethology natural history” study to quantify the distribution of individual behavioral biases with unprecedented precision and examine correlations between behavioral measures with high power. We discovered a slight, but highly significant, left-bias in spontaneous locomotor decision-making. We then used the data to evaluate standing hypotheses about biological mechanisms affecting behavioral variability, specifically: the neuromodulator serotonin and its precursor transporter, heterogametic sex, and temperature. We found a variety of significant effects associated with each of these mechanisms that were behavior-dependent. This indicates that the relationship between biological mechanisms and behavioral variability may be highly context dependent. Going forward, automation of behavioral experiments will likely be essential in teasing out the complex causality of individuality. </p>
The individual-based network structure of palm-seed dispersers is explained by a rainforest gradient
<p>How species interactions change in space and time is a major question in ecology. In tropical forests, plant individuals share mutualistic partners (pollinators or seed dispersers), yet we have little understanding of the factors affecting these individual interaction patterns. We used a seed dispersal individual-based network describing interactions between individuals of a palm species with bird species to investigate how intrinsic and extrinsic characteristics of individual plants influence the network structure. In our work we evaluated if average canopy height, number of fruits, distance to forest gap, and habitat type influence the role of palm individuals in the network. From 102 palms, 62 individuals had their seeds dispersed at least once: 17 individual palms in the restinga, 15 in the lowland and 30 in the pre-montane habitat. Twelve bird species were recorded dispersing <em>Euterpe edulis</em> seeds in our study area.</p>
Activity of individual neurons in the Aplysia buccal ganglion before and after in vitro operant conditioning
<p>Dataset for Costa RM, Baxter DA, Byrne JH (2021) Neuronal population activity dynamics reveal a low-dimensional signature of operant learning in Aplysia. Commun Biol. BioRxiv preprint 2021.12.06.471434</p> <p>Data collected by using voltage-sensitive dye imaging to capture population-wide, single neuron resolution activity in the isolated <em>Aplysia</em> buccal ganglion before and after <em>in vitro</em> operant conditioning. Data for 7 contingently trained and 7 yoked control animals includes population spike trains, timing of buccal motor patterns, ganglia images, and pixel coordinates for each neuron (kernels). In addition, the data includes results of the non-negative matrix factorization analyses described in the article.</p> <p>The dataset is organized as a Matlab structure variable.</p>
Deriving population scaling rules from individual-level metabolism and life history traits - Code and Data
<p>Individual metabolism generally scales with body mass with an exponent around 3/4. From dimensional arguments it follows that maximum population growth rate (rmax) scales with a -1/4 exponent. However, the dimensional argument implicitly assumes that offspring size is proportional to adult size. Here we calculate rmax from metabolic scaling at the level of individuals within size-structured populations while explicitly accounting for offspring size. We identify four general patterns of how rmax scales with adult mass based on four empirical life-history patterns employed by groups of species. These life-history patterns are determined by how traits of somatic growth rate and/or offspring mass relate to adult mass. One life-history pattern -- constant adult:offspring mass ratio and somatic growth rate independent of adult mass -- leads to the classic -1/4 scaling of rmax. The other three life-history patterns lead either to non-metabolic population growth scaling with adult mass or do not follow a power-law relationship at all. Using life-history data of five marine taxa and terrestrial mammals, we identify species groups that belong to one of each case. We predict that elasmobranchs, copepods, and mammals follow standard -1/4 power-law scaling, whereas teleost fish and bivalves do not have a pure power-law scaling. Our work highlights how taxa may deviate from the classic -1/4 metabolic scaling pattern of maximum population growth. The approach is generic and can be applied to any taxa.</p>
Individual multilocus genotypes of adults and seed progeny from eight natural populations of Campanula glomerata
<p>Individual multilocus genotypes based on 15 microsatellite loci of adults and seed progeny from eight natural populations of <em>Campanula glomerata</em>. For more details see Van Rossum et al. (2022) in Frontiers in Conservation Science</p>
Individual and species variation in mixed-species aggregations of harvestmen
<p>This dataset is associated with the published paper Escalante, I, M Domínguez, D Gómez-Ruiz, and G Machado. Benefits and costs of multi-specific aggregations in harvestmen (Arachnida: Opiliones). Frontiers in Ecology and Evolution (DOI 10.3389/fevo.2021.766323). Please refer to the paper for the extensive explanations on the collection, analysis, presentation, and analyses of the data. </p> <p>We provide the first description of mixed-species roosting aggregations of seven species of the genus <em>Prionostemma </em>from Costa Rica. We surveyed several plants (trees and palms) for the presence of harvestmen of seven different species across time (14 days). These harvestmen are frequently found in aggregations. Hence, we also counted the number of individuals in each aggregation. Additionally, we counted the number of legs in each harvestmen, as well as the number of parasitic mite larvae found in the harvestmen's bodies. With all of this information, we were able to explore the effects of the roosting status (solitary/aggregated), the aggregation size, and the species composition of the aggregations (single- or multi-species aggregations) with potential benefits (less damage, i.e., individuals with all of their legs) and costs (a higher parasitic infection).</p>
Role of individual dispersal in genetic resilience in fluctuating populations of the gray-sided vole Myodes rufocanus
<p class="a">Population densities of the grey-sided vole <i>Myodes rufocanus</i> fluctuate greatly within and across years in Japan. Here, to investigate the role of individual dispersal in maintaining population genetic diversity, we examined how genetic diversity varied during fluctuations in density by analyzing eight microsatellite loci in voles sampled three times per year for 5 years, using two fixed trapping grids (approximately 0.5 ha each). At each trapping session, all captured voles at each trapping grid were removed. The STRUCTURE program was used to analyze serially collected samples to examine how population crashes were related to temporal variability, based on local-scale genetic compositions in each population. In total, 461 and 527 voles were captured at each trapping grid during this study. The number of voles captured during each trapping session (i.e., vole density) varied considerably at both grids. Although patterns in fluctuations were not synchronized between grids, the peak densities were similar. At both grids, the mean allele number recorded at each trapping session was strongl<span>y</span><span><span>, positively,</span></span><span> a</span>nd non-linearly correlated with density. STRUCTURE analyses revealed that the proportions of cluster compositions among individuals at each grid differed markedly before and after the crash phase, implying the long-distance dispersal of voles from remote areas at periods of low density. The present results suggest that, in grey-sided vole populations, genetic diversity varies with density largely at the local scale; in contrast, genetic variation in a metapopulation is well-preserved at the regional scale due to the density-dependent dispersal behaviors of individuals. By influencing the dispersal patterns of individuals, fluctuations in density affect metapopulation structure spatially and temporally, while the levels of genetic diversity are preserved in a metapopulation.</p>
Linking Problem Landscape Features with the Performance of Individual CMA-ES Modules - Data
<p>This repository contains the performance data used in the paper "Linking Problem Landscape Features with the Performance of Individual CMA-ES Modules".</p> <p>The configurations run are in 'dt_run_confs.csv', and each other csv-file corresponds the the AUC values of one of these configurations.</p> <p>The script used to generate the full performance data is included in 'generate.py', and the processing using IOHanalyzer is shown in 'script.R' </p>
Data repository of Predictors of Social Response to COVID-19 among Health Care Workers Caring for Individuals with Confirmed COVID-19 in Jordan
<p>The outbreak of COVID-19 forced public health authorities around the world to call for national emergency plans. Public responses, in form of social discrimination and stigmatizing behaviors, are increasingly being observed against confirmed individuals with confirmed COVID-19 and healthcare workers (HCWs) caring for those individuals. Hence, this study aimed to investigate the perception of social discrimination and coping strategies, and explore predictors of social discrimination and coping toward COVID-19 among HCWs and individuals with confirmed COVID-19. This study used a cross-sectional descriptive-comparative design to collect data using a convenience sample of 105 individuals with confirmed COVID-19 and 109 HCWs using a web-based survey format. In this study, individuals confirmed with COVID-19 reported a high level of social discrimination compared with HCWs (t = 2.62, <em>p</em> < .01). While HCWs reported high level of coping with COVID-19 compared with individuals with COVID-19 (t = -3.91, <em>p</em> < .001). Educational level, age, monthly income, and taking over-the-counter medication were predictors of social discrimination and coping with COVID-19 among HCWs and individuals confirmed with COVID-19. In conclusion, the findings showed individuals with confirmed COVID-19 were more likely to face social discrimination and HCWs perform better coping with COVID-19 than individuals with confirmed COVID-19.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.