Find research datasets worth reusing

opencc-by-4.0May 2023View details →

Structural variants of 20 wild isolates of Caenorhabditis elegans

20 VCFs of 20 Caenorhabditis elegans wild isolates against VC2010 reference assembly. Reads come Pacific Biosciences sequencing. Alignment was done using ngmlr. Variant calling was done using Sniffles.

opencc-zeroDec 2022View details →

Normalised absorbance ratios of IgG for myxoma and rabbit hemorrhagic disease viruses: Longitudinal dataset wild European rabbits

This study addresses the long-term dynamics of humoral immunity to two viral pathogens of the European rabbit, an endangered keystone species of major ecological relevance. Such studies are particularly challenging in free-ranging species, and a combination of longitudinal capture-mark-recapture and semi-quantitative serology was used to address this question. Over 600 normalised absorbance ratios of indirect ELISA, obtained from 505 individual rabbits in 7 populations over five years were analysed using linear mixed models. The results support a lifelong acquired humoral immunity to myxoma virus and rabbit hemorrhagic disease virus upon natural infection and suggest the presence of maternal immunity to the latter in wild juvenile rabbits. These results contribute to understanding the epidemiology of two viral diseases threatening this keystone species and assist in developing conservation programs.

Data for: Rapid adaptation to a novel pathogen through disease tolerance in a wild songbird

Animal hosts can adapt to emerging infectious disease through both disease resistance, which decreases pathogen numbers, and disease tolerance, which limits damage during infection without limiting pathogen replication. Both resistance and tolerance mechanisms can drive pathogen transmission dynamics. However, it is not well understood how quickly host tolerance evolves in response to novel pathogens or what physiological mechanisms underlie this defense. Using natural populations of house finches (Haemorhous mexicanus) across the temporal invasion gradient of a recently emerged bacterial pathogen (Mycoplasma gallisepticum), we find rapid evolution of tolerance (<25 years). In particular, populations with a longer history of MG endemism have less pathology but similar pathogen loads compared with populations with a shorter history of MG endemism. Further, gene expression data reveal that more targeted immune responses early in infection are associated with tolerance. These results suggest an important role for tolerance in host adaptation to emerging infectious diseases, a phenomenon with broad implications for pathogen spread and evolution.

Data for: Honey bees (Apis mellifera) modify plant-pollinator network structure, but do not alter wild species' interactions

Honey bees (Apis mellifera) are widely used for honey production and crop pollination, raising concern for wild pollinators, as honey bees may compete with wild pollinators for floral resources. The first sign of competition, before changes appear in wild pollinator abundance or diversity, may be changes to wild pollinator interactions with plants. Such changes for a community can be measured by looking at changes to metrics of resource use overlap in plant-pollinator interaction networks. Studies of honey bee effects on plant-pollinator networks have usually not distinguished whether honey bees alter wild pollinator interactions, or if they merely alter total network structure by adding their own interactions. To test this question, we experimentally introduced honey bees to a Canadian grassland and measured plant-pollinator interactions at varying distances from the introduced hives. We found that honey bees increased the network metrics of pollinator and plant functional complementarity and decreased interaction evenness. However, in networks constructed from just wild pollinator interactions, honey bee abundance did not affect any of the metrics calculated. Thus, all network structural changes to the full network (including honey bee interactions) were due only to honey bee-plant interactions, and not to honey bees causing changes in wild pollinator-plant interactions. Given widespread and increasing use of honey bees, it is important to establish whether they affect wild pollinator communities. Our results suggest that honey bees did not alter wild pollinator foraging patterns in this system, even in a year that was drier than the 20-year average.

opencc-by-4.0Jun 2023View details →

GSLW - Greek Sign Language in the Wild Dataset

GSLW: The dataset has been recorded under various background and lighting variations and with different smartphones. The camera position and orientation are gently varied among subsequent recordings to increase video diversity. 15 cases of hearing-impaired people dealing with public services have been recorded. The resulting test dataset has 1,736 videos that were annotated both at individual gloss and sentence level. Instructions:     GSLW.csv file has the paths, gloss and sentence annotations of the videos.     load_gslw.py has a python function to load the GSLW.csv file for training or inference. Citation:      If you use our dataset please cite our work : <pre>@article{gsl, author={N. M. {Adaloglou} and T. {Chatzis} and I. {Papastratis} and A. {Stergioulas} and G. T. {Papadopoulos} and V. {Zacharopoulou} and G. {Xydopoulos} and K. {Antzakas} and D. {Papazachariou} and P. n. {Daras}}, journal={IEEE Transactions on Multimedia}, title={A Comprehensive Study on Deep Learning-based Methods for Sign Language Recognition}, year={2021}, volume={}, number={}, pages={1-1}, doi={10.1109/TMM.2021.3070438}}</pre>

Breastfeeding, carrying, grooming, and playing behaviours in wild Javan gibbons (Hylobates moloch)

In pair-living species, female and male pairs may maintain stable social bonds by adjusting spatial and social associations. Nevertheless, each sex invests differently to maintain the pair bond, and the investment can depend on the presence of paternal care or 'male services.' While most species live in pairs, the sex responsible for pair bond maintenance in gibbons is still controversial. We investigated pair bond maintenance and parental care in three pairs of wild Javan gibbons in Gunung Halimun-Salak National Park, Indonesia, for over 21 months. We found that Javan gibbon fathers groomed their offspring more than adult females, especially as offspring get older. While both parents increased playing time with offspring when offspring became older and more independent, fathers played with offspring 20 times more than mothers on average. Grooming within Javan gibbon pairs was male-biased, suggesting that pair bond maintenance was heavily the job of males. However, offspring age as a proxy for paternal care did not affect the pair bond maintenance. Our study highlights that adult male Javan gibbons may have an important role in pair bond maintenance and the care of juveniles.

Data from: Trait-dependent associations between early- and late-life reproduction in a wild mammal

Early- versus late-life trade-offs are a central prediction of life-history theory that are expected to shape the evolution of ageing. While ageing is widely observed in wild vertebrates, evidence that early–late trade-offs influence ageing rates remains limited. Vertebrate reproduction is a complex, multi-stage process, yet few studies have examined how different aspects of early-life reproductive allocation shape late-life performance and ageing. Here, we use longitudinal data from a 36-year study of wild Soay sheep to show that early-life reproduction predicts late-life reproductive performance in a trait-dependent manner. Females that started breeding earlier showed more rapid declines in annual fecundity with age, consistent with a trade-off. However, age-related declines in offspring first-year survival and birth weight were not associated with early-life reproduction. Selective disappearance was evident in all three late-life reproductive measures, with longer-lived females having higher average performance. Our results provide mixed support for early–late reproductive trade-offs and show that the way early-life reproduction shapes late-life performance and ageing can differ among reproductive traits.

Data from: Multi-locus homozygosity promotes actuarial senescence in a wild mammal

<ol> <li>Genome-wide homozygosity, caused for example by inbreeding, is expected to have deleterious effects on survival and/or reproduction. Evolutionary theory predicts that any fitness costs are likely to be detected in late life because natural selection will filter out negative impacts on younger individuals with greater reproductive value.</li> <li>Here we infer associations between multi-locus homozygosity, sex, disease, and age-dependent mortality risks using Bayesian analysis of the life histories of wild European badgers (Meles meles) in a population naturally infected with Mycobacterium bovis (the causative agent of bovine tuberculosis).</li> <li>We find important effects of multi-locus homozygosity on all parameters of the Gompertz-Makeham mortality hazard function, but particularly in later-life.</li> <li>Our findings confirm the predicted association between genomic homozygosity and actuarial senescence. Increased homozygosity is particularly associated with an earlier onset, and greater rates of actuarial senescence, regardless of sex. The association between homozygosity and actuarial senescence is further amplified among badgers putatively infected with bovine tuberculosis.</li> <li>These results recommend further investigation into the ecological and behavioural processes that result in genome-wide homozygosity, and focused work on whether homozygosity is harmful or beneficial during early life-stages.</li> </ol>

Selection on weapon allometry in the wild

Allometry is the scaling relationship between a trait and body size. This relationship can often explain considerable morphological variation within and among species. Nevertheless, much remains unknown about the factors that underlie allometric patterns. For example, when different allometric relationships are observed amongst closely related species, these differences are regularly considered to be products of selection. However, directional selection on allometry (particularly the slope) has rarely been tested and observed in natural populations. Here, we investigate selection on the scaling relationship between weapon size and body size (i.e., weapon allometry) in a wild population of giant mesquite bugs, Pachylis neocalifornicus (previously Thasus neocalifornicus). Males in this species use their weapons (enlarged femurs) to compete with one another over access to resources and females. We found that large males with relatively large weapons successfully secured access to mates. However, we also found that small males with relatively small weapons could access mates as well. These two patterns together can increase the allometric slope of the sexually selected weapon, suggesting a straightforward process by which the allometric slope can evolve.

Data from: Direct and indirect effects of urbanization, pesticides, and wild insect pollinators on mango yield

<ol> <li>Expanding cities increasingly encroach fertile farmlands, questioning the viability of maintaining agriculture within and around them. Yet, our knowledge on how urbanization influences pollinator communities and the provision of pollination services to crops is limited, especially for the urbanization hotspots of the Global South. </li> <li>Mango (Mangifera indica) is one of the most important fruit crops in tropical countries. To analyze the dependency of mango on its main insect pollinators, and the direct and indirect effects of urbanization and insecticides on pollinator abundance and mango yield, we conducted a pollinator exclusion experiment and sampled flower visitors on 16 mango farms spread across rural-urban landscapes in Bengaluru, a South Indian megacity. </li> <li>We found that allowing flowers access to ants and flying visitors (bees, hoverflies, non-syrphid flies), dramatically increased mango yield by 350%, highlighting the importance of wild insects for mango pollination. We detected a trend between wild bee abundance and the final fruit set, with an increase of 20% when the number of bees increased from 25 to 125. </li> <li>Urbanization did not directly affect pollinator abundance or mango yield. However, the amount of insecticide applications had strong negative effects on wild bee abundance at low and intermediate levels of urbanization, while it had no effect in highly urbanized areas, presumably because of higher availability of flowering resources. Moreover, the amount of insecticides decreased the weight of harvested mango fruits by almost 30%. This may indicate trade-offs between conventional pest control and enhanced crop yields through pollination by wild insects in rural areas. </li> <li> Synthesis and applications. Our results indicate that mango production can be maintained at a profitable level in urbanized landscapes with insect pollinators more than tripling final yield. However, increasing use of insecticides, besides raising farmers' expenses, can have negative effects on wild insect pollinators and mango yield, especially in rural areas. To safeguard crucial pollination services, it is therefore critical to conserve and promote wild insect pollinators by minimizing the negative effects of insecticide applications in these areas. </li> </ol>

opencc-by-4.0Jul 2023View details →

Data from "Optimizing the baiting strategy for oral vaccine delivery to wild boar"

Data from the paper "Optimization of the baiting strategy for the administration of oral vaccines to wild boar". These data are from experiments done in field work based on the baiting preference of different animal species.

Tn-seq wig files for wild-type and ΔrecG library replicates

Maintaining the integrity of the genome is of utmost importance for cell division and propagation. In Escherichia coli, the RecG protein has been implicated in processing branched recombination intermediates during DNA repair processes, but the primary cellular role(s) of RecG and the repair pathways in which it acts have been difficult to define. To gain additional insight into RecG function, we employed transposon sequencing (Tn-seq) to identify recG genetic interactions and reveal complementary or redundant functions. The strongest hits from the screen were the dam, uvrD, rnhA, radA, and rep genes. The conditional importance of these five genes in cells lacking recG was confirmed using a plasmid-based assay, revealing synthetic lethal interactions for most double deletion strains. Several of the synthetic lethal gene combinations (with uvrD, rep, and radA; but not rnhA or dam) were suppressed by deletion of recF or recO, indicating that their genetic relationships involved roles in post-replication gap repair. Additionally, loss of the RecG/SSB interaction phenocopied a recG deletion when combined with dam, uvrD, radA, or rnhA deletions but not with rep. The results reinforce the idea of RecG as a general genome guardian. Its varied genetic interactions reflect critical roles in several different repair contexts, where RecG alleviates toxic DNA intermediates.

GPS and activity data from wild boars tracked in Southern France

Many animals living in anthropized landscapes try to avoid encountering people by being active at night. By doing so, however, they risk being disturbed while at rest during the day. To mitigate this risk, diurnally resting species may be highly selective about where they rest. Here, we used GPS and activity sensors to study how wild boars (Sus scrofa) might adjust their resting site selection and revisitation patterns to the risk of disturbance by people. We evaluated the probability of daytime relocation to assess the efficacy of wild boars' resting strategy in reducing the risk of human encounter while at rest. We attempted to identify the cause of some relocations using audio recordings. Generally, we found that wild boars did not specifically avoid resting near villages or roads, i.e. where the risk of encountering people is higher, if they could find sites with suitable vegetation cover. The risk of disturbance by people was low, even near villages. Resting sites located close to villages were visited more repeatedly than those located further away, suggesting that focusing on a few familiar and quiet resting sites was a successful strategy for resting undisturbed in an anthropized landscape.

Data from: Regional variation in climate change alters the range-wide distribution of colour polymorphism in a wild bird

According to Gloger's rule animal colouration is expected to be darker in wetter and warmer climates. Such environmental clines are predicted to occur in colour polymorphic species and to be shaped by selection if colour morphs represent adaptations to different environments. We studied if the distribution of the colour polymorphic tawny owl (Strix aluco) morphs (a pheomelanic brown and a pale grey) across Europe follow the predictions of Gloger's rule and if there is a temporal change in the geographical patterns corresponding to regional variations in climate change. We used data on tawny owl museum skin specimen collections. First, we investigated long-term spatiotemporal variation in the probability of observing the colour morphs in different climate zones. Second, we studied if the probability of observing the colour morphs was associated with general climatic conditions. Third, we studied if weather fluctuations prior the finding year of an owl explains colour morph in each climate zone. The brown tawny owl morph was historically more common than the grey morph in every studied climate zone. Over time the brown morph has become rarer in the temperate and Mediterranean zone, whereas it has first become rarer but then again more common in the boreal zone. Based on general climatic conditions winter and summer temperature were positively and negatively associated with proportion of brown morph, respectively. Winter precipitation was negatively associated with proportion of brown morph. The effects of five-year means of weather on the probability to observe a brown morph differed between climate zones, indicating region dependent effect of climate change and weather on tawny owl colouration. To conclude, tawny owl colouration does not explicitly follow Gloger's rule, implying a time and space dependent complex system shaped by many factors. We provide novel insights in how the geographic distribution of pheomelanin-based colour polymorphism is changing.

Phenotype images of the developing heart from wild type and Sox7 mutant mouse embryo

The cardiac endothelium influences ventricular chamber development by coordinating trabeculation and compaction. However, the endothelial-specific molecular mechanisms mediating this coordination are not fully understood. Here, we identified the Sox7 transcription factor as a critical cue instructing cardiac endothelium identity during ventricular chamber development. Endothelial-specific loss of Sox7 function in mice results in cardiac ventricular defects similar to non-compaction cardiomyopathy, with a change in the proportions of trabecular and compact cardiomyocytes in the mutant hearts. This phenotype is paralleled by abnormal coronary artery formation. Loss of Sox7 function disrupts the transcriptional regulation of the Notch pathway and connexins 37 and 40, which govern coronary arterial specification. Upon Sox7 endothelial-specific deletion, single-nuclei transcriptomics analysis identified the depletion of a subset of Sox9/Gpc3 positive endocardial progenitor cells and an increase in erythro-myeloid cell lineages. Fate mapping analysis revealed that a subset of Sox7-null endothelial cells transdifferentiate into hematopoietic but not cardiomyocyte lineages. Our findings determine that Sox7 maintains cardiac endothelial cell identity, which is crucial to the cellular cross-talk that drives ventricular compaction and coronary artery development.

opencc-by-4.0Jul 2023View details →

Impressive pan-genomic diversity of E. coli from a wild animal community near urban development reflects human impacts

Data provided here support the findings of this study and code will allow the replication of analyses therein. To do so, first download and unzip the associated data files. For each analysis, the following files are required: PCAs: PCA.R, prokka_annotations.zip (and VirulenceFinder_results.csv for virulence factor PCA) Sankey diagram: Plasmid_AMR_Sankey.R, mlplasmids_results.zip, MOBsuite_results.zip, ResFinder_results.csv Pathotype assignment: VF_data_analysis.R, VirulenceFinder_results.csv TableS1_Ecoli_metadata.csv contains the isolate metadata (n=143) for all above analyses.

Reduced parental brood visit rate in wild zebra finches (Taeniopygia castanotis) is correlated with high maximum daily ambient temperature

As a result of a warming global climate, understanding how organisms adjust their behaviour to environmental thermal conditions has become an increasingly important question in animal biology. Temperature-driven adjustments in parental care are potentially important given the repercussions on offspring size, quality and survival. In 2015 and 2016, we monitored 83 zebra finch (Taeniopygia castanotis) breeding attempts in the wild. We recorded the frequency of parental visits to the nest together with mean maximum ambient temperature experienced between day 7 and 14 of the nestling period. We found that for each increase of 1 °C in the daytime temperature there was a 0.91% reduction in the hourly rate of parental visits, whilst also accounting for other variables such as nestling age, time of season, and wind speed. Our data suggest that nestlings may receive less food under thermally challenging conditions, which is consistent with recent studies that demonstrate offspring are smaller when reared during periods of high temperature. Understanding the behavioural drivers that may contribute to the production of smaller offspring in extreme heat conditions could prove useful to forecast long-term consequences for fitness triggered by climate change.

Sample extraction and SNP sequencing data for: Identification of sex-linked SNP markers in wild populations of monomorphic birds

Single-nucleotide polymorphism (SNP) analyses are a powerful tool for population genetics, pedigree reconstruction and phenotypic trait mapping. However, the untapped potential of SNP markers to discriminate the sex of individuals in species with reduced sexual dimorphism or of individuals during immature stages remains a largely unexplored avenue. Here, we develop a novel protocol for molecular sexing of birds based on the detection of unique Z- and W-linked SNP markers. Our method is based on the identification of two unique loci, one in each sexual chromosome. Individuals are considered males when they show no calls for the W-linked SNP and are heterozygotic or homozygotic for the Z-linked SNP, while females show both Z- and W-linked SNP calls. We validated the method in the Jackdaw (Corvus monedula). The reduced sexual dimorphism in this species makes it difficult to sex individuals in the wild. We assessed the reliability of the method using 36 individuals of known sex and found that their sex was correctly assigned in 100% of cases. The sex-linked markers also proved to be widely applicable to discriminate males and females from a sample of 927 genotyped individuals of different maturity stages with an accuracy of 99.5%. Given that SNP markers are increasingly used in quantitative genetic analyses of wild populations, the approach we propose has a great potential to be integrated into broader genetic research programmes without the need for additional sexing techniques.

Excited state observation of active K-Ras reveals differential structural dynamics of wild-type versus oncogenic G12D and G12C mutants

Despite the prominent role of the K-Ras protein in many different types of human cancer, major gaps in atomic-level information severely limit our understanding of K-Ras function in health and disease. Here, we report the quantitative backbone structural dynamics of K-Ras by solution NMR spectroscopy of the active state of wild-type K-Ras·GTP and two of its oncogenic P-loop mutants, G12D and G12C, using a novel nanoparticle-assisted spin relaxation method, relaxation dispersion and chemical exchange saturation transfer experiments covering the entire range of timescales from picosecond to milliseconds. Our combined experiments allow the detection and analysis of the functionally critical Switch I and Switch II regions that have previously remained largely unobservable by X-ray crystallography and NMR spectroscopy. Our data reveal cooperative transitions of K-Ras·GTP to a highly dynamic excited state that closely resembles the partially disordered K-Ras·GDP state. These results advance our understanding of differential GTPase activities and signaling properties of the WT versus mutants and may thus guide new strategies for the development of therapeutics.

Data from: Early-life behavior, survival and maternal personality in a wild marsupial

Individual behavior varies for many reasons, but how early in life is such variability apparent, and is it under selection? We investigated variation in early-life behavior in a wild eastern grey kangaroo (Macropus giganteus) population, and quantified associations of this behavior with early survival. Behavior of young was measured while still in the pouch and also as subadults, and we also monitored survival to weaning. We found consistent variation between offspring of different mothers in levels of activity at the pouch stage, in flight initiation distance as subadults, and in subadult survival, indicating similarity between siblings. There was no evidence of covariance between the measures of behavior at the pouch young vs subadult stages, nor of the early-life behavioral traits with subadult survival. However, there was a strong covariance between offspring and mothers' flight initiation distance (FID) tested at different times. Further, of the total repeatability of subadult FID (55.3%), more than two-thirds could be attributed to differences between offspring of different mothers. Our results indicate that (i) behavioral variation is apparent at a very early stage of development (still in the pouch in the case of this marsupial); (ii) between-mother differences can make up much of the repeatability of juvenile behavior (or 'personality'); and (iii) mothers and offspring exhibit similar behavioral responses to stimuli, potentially indicating heritability of behavioral responses. However, (iv) we found no evidence of selection via covariance between early-life or maternal behavioral traits and juvenile survival in this wild marsupial. Keywords: animal personality, maternal variance, early-life behaviour and survival, macropods, multivariate Bayesian statistics.