Find research datasets worth reusing

opencc-by-4.0Oct 2017View details →

ED3017 C. elegans Wild Isolate (Ediburgh, Scotland) | 2011-06-14T14:41:00+01:00

<blockquote> This experiment is part of the C.elegans behavioural database. For more information and the complete collection of experiments visit http://movement.openworm.org </blockquote> <ul> <li>preview link : https://www.youtube.com/watch?v=ww4hAwCBj5Y</li> <li>strain : ED3017</li> <li>timestamp : 2011-06-14T14:41:00+01:00</li> <li>gene : -N/A-</li> <li>chromosome : -N/A-</li> <li>allele : -N/A-</li> <li>strain_description : C. elegans Wild Isolate (Ediburgh, Scotland)</li> <li>sex : hermaphrodite</li> <li>stage : adult</li> <li>ventral_side : clockwise</li> <li>media : NGM agar low peptone</li> <li>arena : <ul> <li>style : petri</li> <li>size : 35</li> <li>orientation : away</li> </ul> </li> <li>food : OP50</li> <li>habituation : 30m wait</li> <li>who : Laura Grundy</li> <li>protocol : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li>lab : <ul> <li>name : William R Schafer</li> <li>location : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li>software : <ul> <li>name : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li>version : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li>featureID : @OMG</li> </ul> </li> <li>base_name : 422 ED3017 on food L_2011_06_14__14_41___3___9</li> <li>total time (s) : 898.102</li> <li>frames per second : 24.0385</li> <li>video micrometers per pixel : 4.57016</li> <li>number of segmented skeletons : 21399</li> </ul>

opencc-by-4.0Dec 2018View details →

Simulated in-the-wild Dataset (SWAD)

Simulated in-the-wild dataset, including 44 images, containing a total of 117 Artcodes.

opencc-zeroOct 2022View details →

Broad diversity in monoterpene-sesquiterpene balance across wild sunflowers: implications of leaf and floral volatiles for biotic interactions

• Premise of the study: As plant lineages diversify across environmental gradients, species are predicted to encounter divergent biotic pressures. This study investigates the evolution of volatile secondary metabolism across Helianthus genus. • Methods: Leaves and petals of 40 species of wild Helianthus were analyzed via gas chromatography-mass-spectrometry to describe volatile secondary metabolite profiles. • Key results: Across all species, 500 compounds were identified including 40% sesquiterpenes, 18% monoterpenes, 3% diterpenes, 4% fatty acid derivatives, and 35% other compounds such as phenolics and small organic compounds. Qualitatively, annuals and species from more arid western climates had leaf compositions with a higher proportion of total monoterpenes, while erect perennials and species from more mesic eastern habitats contained a higher proportion of total sesquiterpenes. Among species, mass-based leaf monoterpene and sesquiterpene abundance were identified as largely orthogonal axes of variation by principal components analysis. Leaf and petal profiles were not strongly correlated. • Conclusions: Wide diversity in volatile metabolism was observed among wild Helianthus, indicating value of this genus as a model system, and a rich genetic resource. The independence of leaf and petal volatile profiles indicates a low level of phenotypic integration between vegetative and reproductive structures, implying vegetative defense and reproductive defense or pollinator attraction functions mediated by terpenoid profiles in these two organs can evolve without major tradeoffs. The major biosynthetic pathways manufacturing major terpenoids identified in wild Helianthus have been well described to date, providing a road map to deeper inquiry into the drivers of this diversity.

opencc-by-4.0Nov 2022View details →

RxRx1-Wilds Cell-Level Dataset

Cell-level dataset of RxRx1-Wilds, for the paper "Incorporating Knowledge of Plates in Batch Normalization Improves Generalization of Deep Learning for Microscopy Images" by Alex Lin and Alex Lu. This dataset contains cell crops of the publicly available RxRx1-Wilds, accessed at https://wilds.stanford.edu/datasets/.

opencc-by-4.0Nov 2022View details →

Evaluating noninvasive methods for estimating cestode prevalence in a wild carnivore population

This repository holds the datasets and R code files needed to run the models in: Brandell et al., 2022. Evaluating noninvasive methods for estimating cestode prevalence in a wild carnivore population. PLOS ONE. Excel files have associated KEYs for each data column; CSVs are analyzed with their associated R code.

opencc-zeroNov 2022View details →

Data from: Zoning has little impact on the seasonal diel activity and distribution patterns of wild boar (Sus scrofa) in an UNESCO Biosphere Reserve

Understanding the spatio‐temporal distribution of ungulates is important for effective wildlife management, particularly for economically and ecologically important species such as wild boar (Sus scrofa). Wild boars are generally considered to exhibit substantial behavioral flexibility, but it is unclear how their behavior varies across different conservation management regimes and levels of human pressure. To analyze if and how wild boars adjust their space use or their temporal niche, we surveyed wild boars across the core and buffer zones (collectively referred to as the conservation zone) and the transition zone of a biosphere reserve. These zones represent low and high levels of human pressure, respectively. Specifically, we employed a network of 53 camera traps distributed in the Schaalsee UNESCO Biosphere Reserve over a 14‐month period (19,062 trap nights) and estimated circadian activity patterns, diel activity levels, and occupancy of wild boars in both zones. To account for differences in environmental conditions and day length, we estimated these parameters separately for seven 2‐month periods. Our results showed that the wild boars were primarily nocturnal, with diurnal activity occurring dominantly during the summer months. The diel activity patterns in the two zones were very similar overall, although the wild boars were slightly less active in the transition zone than in the conservation zone. Diel activity levels also varied seasonally, ranging from 7.5 to 11.0 h day−1, and scaled positively with the length of the night (R2 = 0.66–0.67). Seasonal occupancy estimates were exceptionally high (point estimates ranged from 0.65 to 0.99) and similar across zones, suggesting that the wild boars used most of the biosphere reserve. Overall, this result suggests that different conservation management regimes (in this case, the zoning of a biosphere reserve) have little impact on wild boar behavior. This finding is relevant for wildlife management in protected areas where possibly high wild boar densities could interfere with conservation goals within these areas and those of agricultural land use in their vicinity.

opencc-by-4.0Aug 2022View details →

Schematic and adapted figures from IPBES Sustainable Use of Wild Species Assessment - Summary for policymakers

Schematic and adapted figures from the Summary for policymakers of the thematic assessment of the sustainable use of wild species of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES).

opencc-by-4.0Aug 2022View details →

Schematic and adapted figures from IPBES Sustainable Use of Wild Species Assessment - Chapter 1. Setting the Scene

Schematic and adapted figures from Chapter 1 of the thematic assessment of the sustainable use of wild species of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services.

opencc-zeroNov 2022View details →

Genomic characterization of a wild-like tomato accession from Arizona

Tomato domestication history has been revealed to be a highly complex story. A major contributor to this complexity is an evolutionary intermediate group (Solanum lycopersicum var. cerasiforme (Alef.) Voss; SLC) between the cultivated tomato (Solanum lycopersicum var. lycopersicum L.; SLL) and its wild relative (Solanum pimpinellifolium L.; SP). SLC includes accessions with a broad spectrum of genomic and phenotypic characteristics. Some of the SLC accessions were previously hypothesized to be spreading northward from South America into Mesoamerica and that migration probably entailed reversal to wild-like phenotypes such as smaller fruits. Prior to this study, the northernmost confirmed extension of the SLC was limited to northern Mexico. In this study, we employed genomic methods to investigate the origin of a wild-like tomato found in a garden in Scottsdale Arizona, USA. The so-called "Arizona tomato" featured a vigorous growth habit and carried small fruits weighing 2-3 grams. Our phylogenomic analyses revealed the identity of the Arizona tomato as a member of the Mexican SLC population (SLC MEX). To our knowledge, this is the first report of an SLC accession, confirmed using genomics, growing spontaneously in Arizona. This finding could have implications for conservation biology as well as agriculture.

opencc-zeroNov 2022View details →

Data from: Gobbling across landscapes: Eastern wild turkey distribution and occupancy-habitat associations

Extensive restoration and translocation efforts beginning in the mid-20th century helped to reestablish eastern wild turkeys (Meleagris gallopavo silvestris) throughout their ancestral range. The adaptability of wild turkeys resulted in further population expansion in regions that were considered unfavorable during initial reintroductions across the northern United States. Identification and understanding of species distributions and contemporary habitat associations are important for guiding effective conservation and management strategies across different ecological landscapes. To investigate differences in wild turkey distribution across two contrasting regions, heavily forested northern Wisconsin, USA, and predominately agricultural southeast Wisconsin, we conducted 3,050 gobbling call-count surveys from March–May 2014–2018 and used multiseason correlated-replicate occupancy models to evaluate occupancy-habitat associations and distributions of wild turkeys in each study region. Detection probabilities varied widely and were influenced by sampling period, time of day, and wind speed. Spatial autocorrelation between successive stations was prevalent along survey routes but were stronger in our northern study area. In heavily forested northern Wisconsin, turkeys were more likely to occupy areas characterized by moderate availability of open land cover. Conversely, large agricultural fields decreased the likelihood of turkey occupancy in southeast Wisconsin, but occupancy probability increased as upland hardwood forest cover became more aggregated on the landscape. Turkeys in northern Wisconsin were more likely to occupy landscapes with less snow cover and a higher percentage of row crops planted in corn. However, we were unable to find supporting evidence in either study area that abandonment of turkeys from survey routes was associated with snow depth or with the percentage of agricultural cover. Spatially, model-predicted estimates of patch-specific occupancy indicated turkey distribution was nonuniform across northern and southeast Wisconsin. Our findings demonstrate that the environmental constraints of turkey occupancy varied across the latitudinal gradient of the state with open cover, snow, and row crops being influential in the north, and agricultural areas and hardwood forest cover important in the southeast. These forces contribute to non-stationarity in wild turkey-environmental relationships. Key habitat-occupancy associations identified in our results can be used to prioritize and strategically target management efforts and resources in areas that are more likely to harbor sustainable turkey populations.

Wild kangaroos become more social when caring for young and may maintain long-term affiliations with popular individuals

Kangaroos are an iconic group of Australian fauna. Despite considerable research on kangaroo behaviour, key gaps remain in our understanding of their social organization in the wild. In particular, it remains largely unknown whether kangaroos form long-term social bonds and what factors might prompt individuals to associate or dissociate from one another. Over 6 years, we monitored the social affiliations of individually identified eastern grey kangaroos, Macropus giganteus, in a large wild population. We investigated the short-term and long-term relationships of kangaroos and the extent those relationships varied with age, sex and reproductive state. We found evidence that long-term relationships among eastern grey kangaroos are possible, especially between adult females. Those individuals that were more sociable within years were also more likely to establish affiliations across years. Contrary to previous studies, we observed females actively associating with other mothers in the years in which they had young. These data suggest that the fission-fusion dynamics of eastern grey kangaroo social behaviour allow females to modulate their social position with conspecifics according to their current reproductive state. We highlight the adaptive implications of the formation of long-term bonds and the changes in social behaviour observed in females.

Data for: General cognitive performance declines with female age and is negatively related to fledging success in a wild bird

Identifying the causes and fitness consequences of intraspecific variation in cognitive performance is fundamental to understand how cognition evolves. Selection may act on different cognitive traits separately or jointly as part of the general cognitive performance of the individual. To date, few studies have examined simultaneously whether individual cognitive performance covaries across different cognitive tasks, the relative importance of individual and social attributes in determining cognitive variation, and its fitness consequences in the wild. Here, we tested 38 wild southern pied babblers (Turdoides bicolor) on a cognitive test battery targeting associative learning, reversal learning and inhibitory control. We found that a single factor explained 59.5% of the variation in individual cognitive performance across tasks, suggestive of a general cognitive factor. General cognitive performance varied by age and sex; declining with age in females but not males. Older females also tended to produce a higher average number of fledglings per year compared to younger females. Analysing over 10 years of breeding data, we found that individuals with lower general cognitive performance produced more fledglings per year. Collectively, our findings support the existence of a trade-off between cognitive performance and reproductive success in a wild bird.

Data from: Maternal effects and the legacy of extreme environmental events for wild mammals

Nutrition underpins population dynamics of large herbivores. The environmental, physiological, and nutritional state of a mother can have a lifetime effect on her offspring. For ungulates, nutrition of the mother during gestation can have an important and often underappreciated effect on the lifetime phenotype, behavior, and success of her offspring. Research in captive settings has shown even with animals that are closely related (i.e., have similar genetic makeups), maternal condition can have serious lifetime implications for an animal's offspring; mothers in poor condition give birth to sons that exhibit stunted growth compared with sons born to mothers in good condition. Yet, identifying the role of maternal effects in wild animals can be difficult. It requires information on the nutritional legacy of a mother in combination with information on current environmental conditions. We evaluated how nutrition of a mother potentially affected her male offspring's lifetime trajectory using ingesta-free body fat measurements of mule deer (Odocoileus hemionus) in the Wyoming Range of western Wyoming, USA. Following a very harsh winter, one female gave birth to a male who remained small for the entirety of his lifetime, which may be attributed to the nutritional stress his mother experienced during that winter. This dataset includes the means and standard errors of IFBFat for female deer captured in March from 2013–2021 and for male deer captured in December from 2018–2021.

opencc-zeroMar 2023View details →

Divergent water requirements partition exposure risk to parasites in wild equids

For grazing herbivores, dung density in feeding areas is an important determinant of exposure risk to faecal-orally transmitted parasites. When host species share the same parasite species, a non-random distribution of their cumulative dung density and/or non-random ranging and feeding behaviour may skew exposure risk and the relative selection pressure parasites impose on each host. The arid-adapted Grevy's zebra (Equus grevyi) can range more widely than the water-dependent plains zebra (Equus quagga), with which it shares the same species of gastrointestinal nematodes. We studied how the spatial distribution of zebra dung relates to ranging and feeding behaviour to assess parasite exposure risk in Grevy's and plains zebras at a site inhabited by both zebra species. We found that zebra dung density declined with distance from water, Grevy's zebra home ranges (excluding those of territorial males) were farther from water than those of plains zebras, and plains zebra grazing areas had higher dung density than random points while Grevy's zebra grazing areas did not, suggesting a greater exposure risk in plains zebras associated with their water dependence. Faecal egg counts increased with home range proximity to water for both species, but the response was stronger in plains zebras, indicating that this host species may be particularly vulnerable to the elevated exposure risk close to water. We further ran experiments on microclimatic effects on dung infectivity and showed that fewer nematode eggs embryonated in dung in the sun than in the shade. However, only 5% of the zebra dung on the landscape was in shade, indicating that the microclimatic effects of shade on the density of infective larvae is not a major influence on exposure risk dynamics. Ranging constraints based on water requirements appear to be key mediators of nematode parasite exposure in free-ranging equids.

4500 years of morphological diversification in Western Europe wild boars (Sus scrofa) and the consequences of the Neolithic transition

Evolutionary biologists have recently solicited archaeologists to help document and understand the morphological evolution of animals in response to human activities and, more globally, to help reconstruct the history and significance of the anthropogenic impact on worldwide ecosystems. Artificial selection associated with domestication is the best-known example of a major anthropogenic morphological evolution preserved in the archaeological record. However, the impact of the domestication process and dispersal on the morphological evolution of animals has been far less explored. To fill this gap, we focused on 5,000 years of Neolithic transition in Western Europe – a major anthropogenic ecological disturbance involving landscape modification and the translocation of domestic mammals. Using geometric morphometrics on key phenotypic markers preserved in the archaeological record associated with isotopic studies, we explored how and according to which cultural drivers the Neolithic niche construction has influenced the morphological evolution of wild boars (Sus scrofa). The decoupling of size and shape components from bone morphological variation has facilitated the identification of several processes of phenotypic diversification of Sus scrofa in response to human behaviour during the Neolithic transition in Western Europe.

opencc-by-4.0Dec 2022View details →

Supplementary materials. Publication "Three-way relationships between gut microbiota, helminth assemblages and bacterial infections in wild rodent populations" by Bouilloud et al.

Supplementary information Supplementary Figure S1. Maps showing the sampling area (left) and localities (right) in France. Forests are indicated in green and water in blue. The four sampling localities are represented with a colored polygon. The arrow indicates the North.   Supplementary Figure S2. Composition of the gut bacteriota. The relative abundance of six phyla representing 99% of the total composition is represented. Individuals are grouped by sampling localities, which are ordered from North to South. (A) Bar graph shows individual variation in phyla composition (phylum=color). (B) Box and whisker plots represent median and interquartile values for each phylum. Black dots correspond to mean values, and colored dots correspond to individuals.   Supplementary Figure S3. Variations of alpha diversity with individual factors, for the gut bacteriota (family level), pathogenic bacteria and gastro-intestinal helminths of bank voles. Alpha diversity is estimated using the specific richness (A, B and C) and the Shannon index (D, E and F). In graphs C and F, the blue line corresponds to the linear regression line.   Supplementary Figure S4. Relationships between the composition of the gut bacteriota, pathogenic bacteria and gastro-intestinal helminth communities: The db-RDA triplot shows the structure of the gut bacteriota at the phylum level and the correlations with the intra-host parasite communities. The arrows correspond to the significant explanatory variables. Each point corresponds to an individual, and the colors correspond to the different sampling localities.   Supplementary Table S1. Variation of the Firmicutes/Bacteroidetes ratio with localities and individual factors.   Supplementary Table S2. Alpha diversity metrics and statistics for the gut bacteriota, pathogenic bacteria and helminth communities of bank voles.   Supplementary Table S3. Beta diversity metrics and statistics for the gut bacteriota, pathogenic bacteria and helminth communities of bank voles

openDec 2022View details →

100ns REST2 MD Simulation Trajectory of Wild-Type Alpha-Synuclein using the DES-Amber Forcefield

Molecular dynamics simulation trajectory and  for wild-type acylated alpha-Synuclein (Ac-AS) using the REST2 algorithm. The system was parameterised with the DES-Amber force field published by Maxwell et al. The simulation was run for 100 nanoseconds using GROMACS on the Forschungszentrum Jülich JUWELS supercomputer. The reposited trajectory is the lowest temperature replica at 300 K from 32 replicas between 300-500 K. This work was partially performed as part of the Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) and received funding from the Helmholtz Association of German Research Centers. The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS Supercomputer JUWELS at Jülich Supercomputing Centre (JSC).

openDec 2022View details →

25ns REST2 MD Simulation Trajectory of Wild-Type Alpha-Synuclein using the a99SB-disp Forcefield

Molecular dynamics simulation trajectory and  for wild-type acylated alpha-Synuclein (Ac-AS) using the REST2 algorithm. The system was parameterised with the a99SB-disp force field published by Maxwell et al. The simulation was run for 25 nanoseconds using GROMACS on the Forschungszentrum Jülich JUWELS supercomputer. The reposited trajectory is the lowest temperature replica at 300 K from 32 replicas between 300-500 K. This work was partially performed as part of the Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) and received funding from the Helmholtz Association of German Research Centers. The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS Supercomputer JUWELS at Jülich Supercomputing Centre (JSC).

Data from: Savanna resilience to droughts increases with proportion of browsing wild herbivores and plant functional diversity

1. Maintaining the resilience and functionality of savannas is key to sustaining the ecosystem services they provide. This maintenance is largely dependent on the resilience of savannas to stressors, such as prolonged droughts. The resilience to drought is largely determined by the interaction of herbivores and the functional composition of vegetation. So far, our understanding and ability to predict the response of savannas to drought under different types of rangeland use and as a function of vegetation composition are still limited. 2. In this study, we used the ecohydrological, spatially-explicit savanna model EcoHyD to determine if the resilience of a savanna rangeland towards prolonged droughts can be enhanced by the choice of rangeland use type (grazer-dominated, mixed-feeders or browser-dominated) and animal density. We evaluated the ability of a Namibian savanna system to withstand droughts and to recover from droughts based on its perennial grass cover and the overall species composition. 3. Generally, we determined a low resilience under high grazer densities. Most importantly, we found that functional diversification of herbivores and plants acted as resilience insurance against droughts, leading to greater resistance and recovery of perennial grasses. In particular, a higher proportion of herbivores allowed for higher resilience, probably also due to a short-term switch to more drought-resistant or unpalatable species. 4. In this case, herbivore diversification was of high self-regulatory value by reestablishing trophic complexity, reducing the need for additional management interventions. 5. Synthesis and applications. Savanna systems will be more resistant to drought if (i) a dense perennial grass cover is maintained, protecting the topsoil from heat-induced water losses and erosion, encompassing functionally important species that are particularly well adapted to water stress and that are palatable, if (ii) the grazing pressure is adjusted to the productivity of the system, and (iii) the herbivore community includes browsers.

Low-temperature nights delay the timing of breeding in a wild songbird

Global climate change has posed widespread challenges to the ecological process critical to the fitness of many wild organisms, such as reproductive phenology. Many bird species have advanced their reproductive phenology in response to the increases in spring temperatures. However, the mechanism of how climate influences the timing of breeding is still often unclear in many species. We explored the relationship between the timing of breeding and spring temperatures based on 14 years of data on Hair-Crested Drongos (Dicrurus hottentottus) in the wild. By applying a 'sliding window' approach, we aimed to identify the time window and weather variable that best explains the timing of breeding at both population and individual levels. We found that the more nights with a minimum temperature below 17℃, around three weeks earlier than the peak reproduction, delayed the breeding time. Low night temperatures may force females to allocate more energy to thermoregulation and therefore physiologically constrain egg-laying. Although annual minimum and maximum temperatures have increased over the study period, the timing of breeding showed no trend as there was no change in the number of low-temperature nights in the relevant period across years. The repeatability of the laying date for individual females (R = 0.211) and across the years (R = 0.270) were low indicating that Drongos were flexible in adjusting their breeding phenology to environmental variation. These results suggest an effect of low night temperature on avian breeding phenology. This effect may apply commonly across bird species considering shared physiological constraints.