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FIGURE. Euphorbia maculata (Tuscany, Pistoia province, Pistoia city, gravel walkway): A–B) individuals, C) detail of leaf, D) detail of stipules. in Synopsis of Euphorbia section Anisophyllum (Euphorbiaceae) in Italy, with an insight on variation of distribution over time in Tuscany
FIGURE. Euphorbia maculata (Tuscany, Pistoia province, Pistoia city, gravel walkway): A–B) individuals, C) detail of leaf, D) detail of stipules.
FIGURE. Euphorbia humifusa (Lombardia, Pavia province, Romagnese, along pavements): A) individual, B) adaxial view of tip, C) abaxial view of tip, D) detail of capsule. in Synopsis of Euphorbia section Anisophyllum (Euphorbiaceae) in Italy, with an insight on variation of distribution over time in Tuscany
FIGURE. Euphorbia humifusa (Lombardia, Pavia province, Romagnese, along pavements): A) individual, B) adaxial view of tip, C) abaxial view of tip, D) detail of capsule.
FIGURE. Euphorbia prostrata (Tuscany, Pistoia province, Pistoia city, along pavements): A) individual, B) detail of tips, C) detail of capsules, D) detail of leaf. in Synopsis of Euphorbia section Anisophyllum (Euphorbiaceae) in Italy, with an insight on variation of distribution over time in Tuscany
FIGURE. Euphorbia prostrata (Tuscany, Pistoia province, Pistoia city, along pavements): A) individual, B) detail of tips, C) detail of capsules, D) detail of leaf.
FIGURE. Euphorbia ophthalmica (individuals cultivated at Giardino dei Semplici of Florence, Tuscany): A) detail of leaves, B) detail of glomerule, C) detail of cyathia and capsule. in Synopsis of Euphorbia section Anisophyllum (Euphorbiaceae) in Italy, with an insight on variation of distribution over time in Tuscany
FIGURE. Euphorbia ophthalmica (individuals cultivated at Giardino dei Semplici of Florence, Tuscany): A) detail of leaves, B) detail of glomerule, C) detail of cyathia and capsule.
FIGURE. Euphorbia chamaesyce: A) individual (Tuscany, Siena province, Chiusi, arable fields near the lake), B) individual (Tuscany, Arezzo province, Pieve Santo Stefano, gravel road along shores of Montedoglio Lake), C) detail of cyathium and capsule (hairy form), D) detail of tip and capsules (intermediate hairiness form), E) detail of cyathium and capsule (glabrous form). in Synopsis of Euphorbia section Anisophyllum (Euphorbiaceae) in Italy, with an insight on variation of distribution over time in Tuscany
FIGURE. Euphorbia chamaesyce: A) individual (Tuscany, Siena province, Chiusi, arable fields near the lake), B) individual (Tuscany, Arezzo province, Pieve Santo Stefano, gravel road along shores of Montedoglio Lake), C) detail of cyathium and capsule (hairy form), D) detail of tip and capsules (intermediate hairiness form), E) detail of cyathium and capsule (glabrous form).
Figure 4. Individual multilocus genotype clustering analysis for Podarcis carbonelli. A in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers
Figure 4. Individual multilocus genotype clustering analysis for Podarcis carbonelli. A, inferred population structure from the number of clusters (K) = 2 to 5. These plots were obtained from the runs producing the highest values of Ln probability for each value of K, assuming correlated allele frequencies. In these plots, each individual is represented by a column divided into K segments, the size of each corresponding to the individual's estimated membership fraction in each of the K clusters. See Table 1 for locality name abbreviations. B, variation of the value of DK with the number of clusters, following Evanno et al. (2005). C, pie charts representing the mean proportion of membership for K = 4 (chosen by the previous method) for each locality.
Figure 3. Individual multilocus genotype clustering analysis for Podarcis bocagei. A in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers
Figure 3. Individual multilocus genotype clustering analysis for Podarcis bocagei. A, inferred population structure from the number of clusters (K) = 2 to 5. These plots were obtained from the runs producing the highest values of Ln probability for each value of K, assuming correlated allele frequencies. In these plots, each individual is represented by a column divided into K segments, the size of each corresponding to the individual's estimated membership fraction in each of the K clusters. See Table 1 for locality name abbreviations. B, variation of the value of DK with the number of clusters, following Evanno et al. (2005). C, pie charts representing the mean proportion of membership for K = 3 and 5 (chosen by the previous method) for each locality.
Text-fig. 8. Wear stages and height (h) of cheek teeth of Sayimys giganteus from Keseköy. Height in mm of the entoconid (arrow) in lower cheek teeth and paracone (arrow) in upper cheek teeth. Shown are the high value and a low value for each wear stage. Note that h of the different wear stages may show large overlaps, in particular in those of worn teeth. This is due to the often-irregular occlusal surfaces of older individuals. in An Exceptional Large Sample Of The Early Miocene Ctenodactyline Rodent Sayimys Giganteus, Specific Variation And Taxonomic Implications
Text-fig. 8. Wear stages and height (h) of cheek teeth of Sayimys giganteus from Keseköy. Height in mm of the entoconid (arrow) in lower cheek teeth and paracone (arrow) in upper cheek teeth. Shown are the high value and a low value for each wear stage. Note that h of the different wear stages may show large overlaps, in particular in those of worn teeth. This is due to the often-irregular occlusal surfaces of older individuals.
Individual recognition and individual identity signals in Polistes fuscatus wasps vary geographically
<p>Geographic variation in animal phenotypes is common, yet we know surprisingly little about how communication varies across populations. Instead, most communication research focuses on one or a few populations and assumes recognition behavior is consistent across a species' range. Here, we show that individual identity signals and individual recognition vary across the geographic range of <i>Polistes fuscatus</i> wasps. <i>P. fuscatus</i> in MI and NY have variable facial patterns that signal individual identity and are used by receivers for individual recognition. However, <i>P. fuscatus</i> from Rothrock, PA lack individual identity signals, as they have less variable color patterns than <i>P. fuscatus</i> from MI. Further, <i>P. fuscatus</i> from PA are not capable of individual recognition. PA <i>P. fuscatus</i> do not learn and remember individual conspecifics during social interactions or during training. The MI and PA populations are genetically differentiated, but the differentiation is most likely geographic and not driven by differences in recognition. Overall, both signals and receiver responses vary across populations of <i>P. fuscatus</i>. Our results suggest that communication systems may rapidly evolve to produce variation in signals and receiver responses across a species' geographic range.</p>
Predictors of individual performance and evolutionary potential of life-history traits in a hematophagous ectoparasite
<p>Little is known about the intraspecific variation of parasite life-history traits and on how this variation may affect parasite fitness and evolution. We investigated how life-history traits predict success of individual tree-hole ticks <i>Ixodes arboricola</i> and estimated their evolutionary potential, as well as genetic correlations within stages and phenotypic correlations within and across stages. Ticks were followed individually over two generations while allowed to feed on great tits <i>Parus major</i>. After accounting for host and tick maternal effects, we found that short feeding times and high engorgement weights strongly increased moulting success. Also, moulting time was positively correlated with feeding success in adults. In larvae and nymphs we found negative phenotypic correlations between engorgement weight and both feeding and moulting time, the latter supported by a negative genetic correlation. We found sex-related differences in feeding time (longer in male nymphs) and moulting time (longer in male larvae but shorter in male nymphs). Also, time since the last feeding event (set experimentally) reduced larval and nymphal fitness while it increased adult female fitness. Furthermore, we found significant heritability and evolvability, i.e. the potential to respond to selection, for engorgement weight and moulting time across all stages but no significant heritability for feeding time. Our findings suggest that variation in tick fitness is shaped by consistent individual differences in tick quality, for which engorgement weight is a good proxy, rather than by life-history trade-offs.</p>
GVOGs_individual
<p>Individual HMM files for the GVOGs. See preprint for details: https://doi.org/10.1101/2021.05.05.442809</p> <p> </p>
Re-identification of Individuals in Genomic Datasets Using Public Face Images
<p>Image-genome pairs in these synthetic datasets were created by combining a subset of the publicly available face image dataset, CelebA, and genotypes from OpenSNP. The genome in a given pair does not correspond to the individual in the image (taken from CelebA), but comes instead from an individual with the same set of phenotypes (taken from OpenSNP). Artificial genotypes were created for each image (genotype refers only to the small subset of SNPs we are interested in) using all available data from OpenSNP where self-reported phenotypes are present.</p> <p>In the Synthetic-Ideal dataset, to each image, we assigned a genotype from OpenSNP that corresponds to an individual with the same phenotypes, such that the probability of the selected phenotypes is maximized, given the genotype. In other words, we picked the genotype from the OpenSNP data that is most representative of an individual with a given set of phenotypes.</p> <p>In the Synthetic-Realistic dataset, to each image, we assigned a genotype from OpenSNP that corresponds to an individual with the same phenotypes, but at random according to the empirical distribution of phenotypes for particular SNPs in our data.</p> <p>Since CelebA does not have labels for all considered phenotypes, 1000 images from this dataset were manually labeled by one of the authors. After cleaning and removing ambiguous cases, the resulting datasets consist of 456 records.</p>
Individual TE expression detection
<p>This data set was used to study and compare tools with respect to detecting the expression of transposable elements at the level of individual instances.</p>
Data for: Time at risk: Individual spatial behaviour drives effectiveness of marine protected areas and fitness
<p>The effectiveness of Marine Protected Areas (MPAs) depends on the mobility of the populations that are the target of protection, with sedentary species likely to spend more time under protection even within small MPAs. However, little is understood about how individual variation in mobility may influence the risk of crossing an MPA border, as well as the fitness costs associated with being exposed to spillover fisheries. Here we investigated the repeatability of spatial behaviour, its role in determining the probability of being at risk (i.e. exposed to the fishery) and the fitness consequences for the individuals. We acoustically tracked the movements and fate of 282 individuals of three fish species during 8 years in a southern Norwegian fjord. We found that for individuals with a home range centroid inside the MPA, the probability of being at risk outside the MPA increased rapidly with reduced distance from the home range centroid to MPA borders, particularly for individuals having larger and more dispersed home ranges. We also detected that the seasonal expansions of the home range are associated with increased time at risk. Last, we show that individuals spending more time at risk were also more likely to be harvested by the fishery operating outside the MPA. Our study provides clear links between individual fish behaviour, fisheries-induced selection, and the effectiveness of protected areas. These links highlight the importance of intraspecific trait variation for understanding the spatial dynamics of populations and emphasize the need to consider individual behaviour when designing and implementing MPAs.</p>
Focusing on individual plants to understand community scale biodiversity effects: the case of root distribution in grasslands
<p>Spatial resource partitioning between species via differences in rooting depth is one of the main explanations for the positive biodiversity-productivity relationship. However, evidence for the importance of this mechanism is limited. This may be due to the community scale at which these interactions are often investigated. Community measures represent net outcomes of species interactions and may obscure the mechanisms underlying belowground interactions.</p> <p>Here, we assess the performance of ~1700 individual plants and their heterospecific neighbours over three growing seasons in experimental grassland plots containing one, four or 16 different plant species and tested whether their performance in mixtures compared to monocultures was related to their own rooting depth vs. the rooting depth of their heterospecific neighbours.</p> <p>Overall, individuals of deep-rooting species performed better in mixtures and this effect significantly increased when surrounded by more shallow-rooting species. This effect was not apparent for the shallow rooting species. Together, including both deep and shallow rooting species increased mixture performance.</p> <p>Our results show that taking the perspective of the individual rather than the community can elucidate the interactions between species that contribute to positive biodiversity effects, emphasizing the need for studies at different scales to disentangle the myriad interactions that take place in diverse communities.</p>
Resource selection functions based on hierarchical generalized additive models provide new insights into individual animal variation and species distributions
<p>Habitat selection studies are designed to generate predictions of species distributions or inference regarding general habitat associations and individual variation in habitat use. Such studies frequently involve either individually indexed locations gathered across limited spatial extents and analyzed using resource selection functions (RSF), or spatially extensive locational data without individual resolution typically analyzed using species distribution models. Both analytical methodologies have certain desirable features, but analyses that combine individual- and population-level inference with flexible non-linear functions may provide improved predictions while accounting for individual variation. Here, we describe how RSFs can be fit using hierarchical generalized additive models (HGAMs) using widely available software, providing a means to explore individual variation in habitat associations and to generate species distribution maps. We used GPS tracking data from Golden Eagles (Aquila chrysaetos) from across eastern North America with four environmental predictors to generate monthly distribution models. We considered three model structures that assumed different amounts of individual variation in the functional relationship between predictors and habitat use and used k-fold cross-validation to compare model performance. Models accounting for individual variability in shape and smoothness of functional responses performed best. Eagles exhibited the least amount of individual variation in response to land cover variables during winter months, with most individuals more closely adhering to the population-level trend. During summer months, eagles exhibited more substantial individual variation in shape and smoothness of the functional relationships, suggesting some need to account for individual variation in eagle habitat use for both inferential and predictive purposes, during this time of year. Because they allow users to blend flexible functions with random effects structures and are well-supported by a variety of software platforms, we believe that HGAMs provide a useful addition to the suite of analyses used for modeling habitat associations or predicting species distributions.</p>
Seasonal variation of population and individual dietary niche in the avivorous bat, Ia io
<p>The variation in niche breadth can affect how species respond to environmental and resource changes. However, there is still no clear understanding of how seasonal variability in food resources impacts the variation of individual dietary diversity, thereby affecting the dynamics of a population's dietary niche breadth. Optimal foraging theory (OFT) and the niche variation hypothesis (NVH) predict that when food resources are limited, the population niche breadth will widen or narrow due to increased within-individual dietary diversity and individual specialization or reduced within-individual dietary diversity, respectively. Here, we used DNA metabarcoding to examine the composition and seasonality of diets of the avivorous bat <em>Ia</em> <em>io</em>. Furthermore, we investigated how the dietary niches changed among seasons and how the population niche breadth changed when the availability of insect resources was reduced in autumn. We found that there was differentiation in dietary niches among seasons and a low degree of overlap, and the decrease of insect resource availability and the emergence of ecological opportunities of nocturnal migratory birds might drive dietary niche shifts toward birds in <em>I</em>. <em>io</em>. However, the population's dietary niche breadth did not broaden by increasing the within-individual dietary diversity or individual specialization but rather became narrower by reducing dietary diversity via predation on bird resources that served as an ecological opportunity when insect resources were scarce in autumn. Our findings were consistent with the predictions of OFT because birds as prey for bats provided extremely different resources from those of insects in size and nutritional value. Our work highlights the importance of size and quality of prey resources along with other factors (i.e., physiological, behavioral, and life-history traits) in dietary niche variation.</p>
Selection in space and time: individual tree growth is adapted to tropical forest gap dynamics
<p>In the present study, we assessed genotypic diversity within closely-related sympatric tree species belonging to the widespread tropical tree species complex <em>Symphonia globulifera</em>. We addressed the fine-scale spatial and temporal genetic adaptations of individuals through differential growth strategies in response to forest gap dynamics. We finally compared the breadth of successional niches encountered by <em>Symphonia</em> species to other locally abundant species. Combining tree diameter censuses, indirect measures of light environment of the recent past and present, and single nucleotide polymorphisms (SNPs), we used population genomics, environmental association analyses, genome wide association and growth modelling to address the following questions:</p> <ul> <li>Are individual genotypes structured by the mosaic of light and competition environments resulting from forest gap dynamics?</li> <li>Is the growth of individuals determined by genotypes?</li> <li>Is there an association between genotypic adaptations to gap dynamics and to growth?</li> <li>How are genotypic adaptations to gap dynamics and to growth structured in time, i.e., across life stages?</li> <li>Are breadths of successional niches for <em>Symphonia</em> species wider than those of other locally abundant species?</li> </ul> <p>Find the analyses here : https://sylvainschmitt.github.io/GOING/introduction.html</p>
Substrate-Binding Guides Individual Melibiose Permeases MelB to Structurally Soften and to Destabilize Cytoplasmic Middle-Loop C3. Blaimschein et al.: Data sets
<p>Data sets used in the manuscript 'Substrate-Binding Guides Individual Melibiose Permeases MelB to Structurally Soften and to Destabilize Cytoplasmic Middle-Loop C3' by Blaimschein et al.</p> <p>The analysis scripts can be found at https://doi.org/10.5281/zenodo.7268838</p>
Behavior and diet data collected from i) GPS video camera collars and ii) fecal samples collected from individuals from the Fortymile Caribou Herd
<p>Summer diets are crucial for large herbivores in the subarctic and are affected by weather, harassment from insects and a variety of environmental changes linked to climate. Yet understanding foraging behavior and diet of large herbivores is challenging in the subarctic because of their remote ranges. <a name="_Hlk82429015">We used GPS video-camera collars to observe behaviors and summer diets of the migratory Fortymile Caribou Herd (<i>Rangifer tarandus granti</i>) across Alaska, USA and the Yukon, Canada.</a> First, we characterized caribou behavior. Second, we tested if videos could be used to quantify changes in the probability of eating events. Third, we estimated summer diets at the finest taxonomic resolution possible through videos. Finally, we compared summer diet estimates from video collars to microhistological analysis of fecal pellets. We classified 18,134 videos from 30 female caribou over two summers (2018 – 2019). Caribou behaviors included eating (mean = 43.5%), ruminating (25.6%), travelling (14.0%), stationary awake (11.3%) and napping (5.1%). Eating was restricted by insect harassment. We classified forage(s) consumed in 5,549 videos where diet composition (monthly) highlighted a strong tradeoff between lichens and shrubs; shrubs dominated diets in June and July when lichen use declined. We identified 63 species, 70 genus and 33 family groups of summer forages from videos. After adjusting for digestibility, monthly estimates of diet composition were strongly correlated at the scale of the forage functional type (i.e., forage groups comprised of forbs, graminoids, mosses, shrubs, and lichens; <i>r = </i>0.79, <i>p</i> < 0.01). Using video collars, we identified i) a pronounced tradeoff in summer foraging between lichens and shrubs and ii) the costs of insect harassment on eating. Understanding caribou foraging ecology is needed to plan for their long-term conservation across the circumpolar north and video collars can provide a powerful approach across remote regions.</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.