Find research datasets worth reusing

opencc-zeroJun 2022View details →

Do pseudogenes pose a problem for metabarcoding marine animal communities?

Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658 bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. NUMTs were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 309 NUMTs  150 bp were detected, with an average of 1.98 per species (range = 0–33) and a mean length of 391 bp  200 bp. Among this total, 75 (23.4%) lacked indels or stop codons. NUMTs appear to pose the greatest interpretational risk when short (< 313 bp) amplicons are used, such as in eDNA studies, dietary analyses, or processed fish identification. Employing the standard amplicon length (313 bp) for marine metabarcoding, NUMTs could potentially inflate the OTU count by 21% above the true species count while also raising intraspecific variation at COI by 15%. However, when both amplicon length and position are considered, inflation in OTU counts and in barcode variation were just 9% and 10%, respectively, suggesting NUMTs will not seriously distort biodiversity assessments. There was a weak positive correlation between genome size and NUMT count but no variation among phyla or trophic groups. Until bioinformatic advances improve NUMT detection, the best defense involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.

opencc-by-4.0Dec 2021View details →

Comparing conservation and animal welfare professionals' perspectives on domestic cat management (data and scripts)

This repository contains the final datasets and R scripts to run the analyses and create the plots in the main text of this publication.

opencc-by-4.0Jul 2022View details →

Animal Recognition Using Methods Of Fine-Grained Visual Analysis - YOLOv5 Breed Classification Dataset (Tsinghua Dogs)

Tsinghua Dogs Dataset with ground truth labels for breeds in YOLOv5 format.

opencc-by-4.0Jul 2022View details →

Supplementary figure: No evidence of any wild animal samples positive for SARS-CoV-2 RNA or antibodies were found in China.

A compilation of results of wildlife sampling from the Huanan market and from China showing no evidence of positive animal for SARS-CoV-2 in China

opencc-by-4.0Oct 2018View details →

Animation Heverlee Castle

Animation of the Castle at Heverlee (current Arenberg castle), made for the exhibition Noble Living. <a href="https://expo.bib.kuleuven.be/exhibits/show/adellijkwonen/adellijkwonen">The Castle at Heverlee from Croÿ to Arenberg</a>.  Based on:  An idealised view of the castle at Heverlee, after the renovation project of Charles III of Croÿ. Published in: Duvosquel, Jean-Marie (ed.). Les Albums de Croÿ. vol. 1. 26 vols. Brussels: Crédit Communal de Belgique, 1985. Pierre de Bersacques, the castle at Heverlee, c. 1596. University Archives KU Leuven, Archives of the Duchy of Aarschot, 2414.  Technical realisation: De Plannensmederij

opencc-by-4.0Oct 2018View details →

Animation of the Building Phases of the Castle at Heverlee

Animation of the different sixteenth-century construction phases of the Arenberg castle at Heverlee, made for the exhibition <a href="https://bib.kuleuven.be/bijzondere-collecties/tentoonstellingen/adellijk-wonen">Noble Living. The Castle at Heverlee from Croÿ to Arenberg</a>.  Based on: Pierre Lepoivre (attributed to), view of the castle at Heverlee, c. 1596. University Archives KU Leuven, Archives of the Duchy of Aarschot, 2420. Technical realisation: De Plannensmederij

opencc-by-4.0Oct 2018View details →

Animation Itinerary Reconstruction Charles III of Croÿ (1560-1612)

Animation of the itinerary reconstruction of Charles III of Croÿ, over the period 1560-1612, made for the exhibition <a href="https://bib.kuleuven.be/bijzondere-collecties/tentoonstellingen/adellijk-wonen">Noble Living. The Castle at Heverlee from Croÿ to Arenberg</a>. The reconstruction is based on his correspondence (Algemeen Rijksarchief Brussel, Audiences) and his memoirs (published by Reiffenberg: Croÿ, Charles de. Une existence de grand seigneur au seizième siècle. Mémoires autographes de Duc Charles de Croy. Edited by Frédéric Auguste Ferdinand Thomas de Reiffenberg. Bruxelles and Leipzig: C. Muquardt, 1845).  The images used in the animation are views incorporated in the Albums of Croÿ, published by Jean-Marie Duvosquel: Duvosquel, Jean-Marie. Les Albums de Croÿ. 26 vols. Brussels: Crédit Communal de Belgique, 1985. The borders of the Low Countries were drawn by: Jongepier I. Map of the Low Countries around 1600. GIStorical Antwerp: University of Antwerp/Hercules Foundation, 2014.

opencc-zeroAug 2022View details →

Diaspore traits specialized to animal adhesion and sea current dispersal are positively associated with the naturalization of European plants across the World

Understanding what drives non-native species naturalization (the establishment of a self-sustainable population outside its native range) is a central question in invasion science. Plants' capacity for long distance dispersal (LDD) is likely to influence the spread and naturalization of non-native species differently according to their introduction pathways. These pathways include intentional introductions (for economic use, e.g. for agriculture), unintentional introductions (e.g. seed contaminants), plant dispersal via human infrastructures (e.g. roads), and plant spread from an adjacent region where the species was previously introduced. Herein, we tested the relationship between sets of LDD traits (syndromes) of 10,308 European plant species and their global naturalization incidence (i.e. whether a species has become naturalized or not) and extent (i.e. the number of regions where a species has become naturalized) using the most comprehensive database of naturalized plants worldwide (GloNAF). Diaspore traits allowed the identification of four traditional LDD syndromes, namely those with specializations for dispersal by: wind (anemochorous), animal ingestion (endozoochorous), attached to animals (epizoochorous), and sea currents (thalassochorous). These evolutionary specializations have been historically interpreted by biologists even though actual dispersal is not always related to diaspore syndromes. We found that while epizoochorous and thalassochorous traits are positively associated with global plant naturalization incidence, anemochorous and endozoochorous traits show a negative relationship. Species´ residence time outside their native range, their economic use and presence of epizoochorous traits (such as hooks, hairs and adhesive substances) are positively associated with global naturalization extent. Furthermore, we found that plants' economic use reduces the influence of LDD syndromes on the naturalization incidence of intentionally introduced plants. While the success of non-native plants is influenced by a broad array of species- and context-specific factors, LDD syndromes play an important role in this context depending on the economic use of plants.

Discrete element models for understanding the biomechanics of fossorial animals

The morphological features of fossorial animals have continuously evolved in response to the demands of survival. However, existing methods for animal burrowing mechanics are not capable of addressing the large deformation of substrate. The discrete element method (DEM) is able to overcome this limitation. In this study, we used DEM to develop a general model to simulate the motion of an animal body part and its interaction with the substrate. The DEM also allowed us to easily change the forms of animal body parts to examine how those different forms affected the biomechanical functions. These capabilities of the DEM were presented through a case study of modelling the burrowing process of North American Badger. In the case study, the dynamics (forces, work, and soil displacements) of burrowing were predicted for different forms of badger claw and manus, using the model. Results showed that when extra digits are added to a manus, the work required for a badger to dig increases considerably, while the mass of soil dug only increases gradually. According to the proposed efficiency index (ratio of the amount of soil dug to the work required), the modern manus with 5 digits has indeed biomechanical advantage for their fossorial lifestyle, and the current claw curvature (25.3 mm in radius) is indeed optimal. The DEM is able to predict biomechanical relationships between functions and forms for any fossorial animals. Results can provide biomechanical evidences for explaining how the selective pressures for functions influence the morphological evolution in fossorial animals.

A field test of mechanisms underpinning animal diversity in recently burned landscapes

1. Planned burning generates different types of pyrodiversity, however, experimental tests of how alternative spatial patterns of burning influence animal communities remain rare. Field tests are needed to understand the mechanisms through which spatial variation in planned fire affects fauna, and how fire can be applied to benefit biodiversity. 2. We tested five hypotheses of how fire-driven variation in habitat composition and configuration affects fauna at fine scales. Small mammal, reptile and invasive predator activity was monitored at 12 burnt and eight unburnt sites through the year following a large, planned burn in semi-arid 'mallee' woodlands of southern Australia. We explored measures of burnt or unburnt habitat ("habitat status"); amount of unburnt vegetation ("habitat amount"); interspersion of burnt and unburnt patches ("habitat complementation"); distance to external or internal unburnt vegetation ("habitat connectivity"); and unburnt patch size and local vegetation cover ("habitat refuge"). Generalized linear models were used to test the influence of each variable on capture rate of three small mammal and 11 reptile species; activity of the introduced red fox (Vulpes vulpes); and species richness of native animals. 3. We found strong support for the habitat status hypothesis and moderate support for four hypotheses relating to spatial patterns of fire. Reptile assemblages varied between burnt and unburnt sites, and relationships were identified between abundance of one or more reptile species and each measure of spatial variation. Reptile species richness was higher at unburnt sites and at sites with more unburnt vegetation in the surrounding area. Sites that were less connected to unburnt vegetation had fewer reptile species. Mammals did not have clear relationships with fine-scale fire patterns. 4. Synthesis and applications: Application of planned fire to promote biodiversity is globally important. We show that retaining unburnt areas and well-connected habitat refuges is important for reptile diversity. We also found that several species of small mammals and reptiles appear resilient to the fine-scale patterns of planned fire experienced in this study, despite activity of introduced predators. The diversity of animals can remain relatively high in areas subject to planned fire, provided that internal and external habitat refuges are retained.

opencc-by-4.0Dec 2022View details →

Does mechanical loading restore ligament biomechanics after injury? A systematic review of studies using animal models

This RevMan file accompanies our manuscript entitled "Does mechanical loading restore ligament biomechanics after injury? A systematic review of studies using animal models" published in BMC Musculoskeletal Disorders. The file hosts all outcomes (i.e., including tertiary outcomes) under "Data and analyses", as well as more detailed forest plots under "Figures".

Data from: New perspectives on soil animal trophic ecology through the lens of C and N stable isotope ratios of oribatid mites

Knowledge of the trophic ecology of soil animals is important for understanding their high alpha diversity as well as their functional role in soil food webs and systems. In the last 20 years, the analysis of natural variations in stable isotope ratios (15N/14N, 13C/12C) has revolutionized our view on soil animal trophic ecology. Here, we review the state of the art of the trophic ecology of a highly abundant and diverse soil animal taxon, oribatid mites (Oribatida), investigated by stable isotope analyses. The review is based on 25 papers reporting stable isotope data of 292 oribatid mite taxa from 30 different sites. Four main findings emerged. (1) Oribatid mites cluster into six trophic groups, i.e. moss feeders, lichen feeders, primary decomposers, fungal feeders/secondary decomposers, predators/scavengers and marine algal feeders, plus one additional group, which incorporates CaCO3 in their cuticle for defence but still belongs to the fungal feeders/secondary decomposers group. (2) Of the 292 species studied 43.7% were classified as fungal feeders/secondary decomposers, 27.0% as primary decomposers and 15.7% as predators/scavengers, only few species include CaCO3 into their skeleton (6.1%), feed on lichens (4.9%), mosses (2.1%) or marine algae (0.7%). (3) In about one-third of the species studied the trophic niche was constant or varied little between sites or habitats, but in two-thirds of the species, their trophic niche varied between habitats, with some species even shifting trophic levels, indicating trophic plasticity. (4) When aggregated at higher taxonomic level oribatid mite species clustered in only three instead of six trophic groups. This indicates that species within the same high-level taxon often belong to different trophic groups, for example, because feeding habits evolved convergently. Therefore, to accurately reflect the trophic ecology of oribatid mites their stable isotope signatures need to be analysed at the species level. However, stable isotope analyses also have limitations, e.g. feeding on bacteria and fungi cannot be separated, and the same is true for feeding on ectomycorrhizal and arbuscular mycorrhizal fungi. Other methods such as fatty acid, amino acid and molecular gut content analyses as well as microbiome analyses may complement stable isotope studies and resolve oribatid mite trophic niche differentiation at a higher resolution. This will contribute to a better understanding of the local coexistence of large numbers of species in soil. Finally, we provide perspectives on how to integrate microarthropods into soil food webs using stable isotope and other methods allowing deeper insight into their trophic structure.

Environmental drivers of local abundance-mass scaling in soil animal communities

The relationship between species' body masses and densities is strongly conserved around a three-quarter power law when pooling data across communities. However, studies of local within-community relationships have revealed major deviations from this general pattern, which has profound implications for their stability and functioning. Despite multiple contributions of soil communities to people, there is limited knowledge on the drivers of body mass-abundance relationships in these communities. We compiled a dataset comprising 155 soil-animal communities across four countries (Canada, Germany, Indonesia, USA), all sampled using the same methodology. We tested if variation in local climatic and edaphic conditions drives differences in local body mass-abundance scaling relationships. We found substantial variation in the slopes of this power-law relationship across local communities. Structural equation modeling showed that soil temperature and water content have a positive and negative net effect, respectively, on soil communities. These effects are mediated by changes in local edaphic conditions (soil pH and carbon content) and the body-mass range of the communities. These results highlight ways in which alterations of soil climatic and edaphic conditions interactively impact the distribution of abundance between populations of small and large animals. These quantitative mechanistic relationships facilitate our understanding of how global changes in environmental conditions, such as temperature and precipitation, will affect community-abundance distributions and thus the stability and functioning of soil-animal communities.

opencc-by-4.0Jul 2022View details →

Modelling migraine-related features in the nitroglycerin animal model: trigeminal hyperalgesia is associated with affective status and motor behaviour

This dataset comprises the findings obtained in the study aimed at exploring the correlation between trigeminal hyperalgesia and affective status or behavioral components in a migraine-specific animal model based on nitroglycerin administration (see article Modelling migraine-related features in the nitroglycerin animal model: trigeminal hyperalgesia is associated with affective status and motor behaviour). In vivo assessments performed in male Sprague-Dawley rats four hours after treatment with nitroglycerin (10mg/kg, i.p.) or its vehicle: - in the open field test were evaluated: time spent (expressed in seconds) in the center of the apparatus as a measure of anxiety; distance (expressed in meters) travelled in the apparatus as a measure of motor behaviour; number of rearings as a measure of exploratory behaviour; time spent in grooming behavior (expressed in seconds) used as nociception index; - evaluation of trigeminal hyperalgesia in the orofacial formalin test: the face rubbing was measured counting the seconds the animal spent grooming the injected area (upper lip, lateral to the nose) with the ipsilateral forepaw or hindpaw 0–3 min (Phase I) or 12–45 min (Phase II) after formalin injection (50 µl, s.c.). The observation time was divided into 15 blocks of 3 min each. RESULTS The data analysis shows an inverse correlation between trigeminal hyperalgesia and motor or exploratory behavior, and a positive association with anxiety-like behavior of spontaneous grooming. These findings further expand on the translational value of the migraine-specific model based on nitroglycerin administration and prompt additional parameters that can be investigated to explore the complexity of the disease.

Linking animal behaviour and tree recruitment: Caching decisions by a scatter hoarder corvid determine seed fate in a Mediterranean agroforestry system

1. Seed dispersal by scatter-hoarder corvids is key for the establishment of important tree species from the Holarctic region such as the walnut (Juglans regia). However, the factors that drive animal decisions to cache seeds in specific locations and the consequences of these decisions on seed fate are poorly understood. 2. We experimentally created four distinct, replicated habitat types in a Mediterranean agricultural landscape where the Eurasian magpie (Pica pica) is a common scatter-hoarder: soft bare soil; compacted bare soil; compacted soil with a dense herbaceous cover; and soft linear bare soil made up of the irrigation furrows that separated the rest of the treatments. We also experimentally placed visual landmarks (stones, sticks, and bunches of dry plants) to test if magpies use them to place seed caches. Walnut dispersal from feeders to the habitats was monitored by radio-tracking and camera traps. 3. A sowing experiment simulating natural caches tested the effect of caching type on seed germination and seedling emergence. Seed mass was controlled for the dispersal and sowing experiments. 4. Magpies selected the two habitats with soft soil, and avoided the one with compacted soil, to cache nuts. Seed mass did not affect dispersal distance, germination, or emergence; however, heavier seeds were cached more often under litter and in the habitat with herbaceous cover, whereas lighter seeds were more often buried in the soft bare soil habitat. Seed burial under soil or litter determined seed fate, as there was virtually no emergence from unburied nuts. There was no evidence of any effect of the visual landmarks. 5. Synthesis. The consequences of seed caching for seedling early establishment are driven by a fine decision-making process of the disperser. Magpies seemed to ponder the characteristics of the habitat and the seed itself to determine where and how to cache each nut. By doing so, magpies reinforced the quality of seed dispersal effectiveness, as they cached walnuts in locations that enhanced both seed survival and seedling emergence.

opencc-by-4.0Oct 2022View details →

Proteomic Profiling for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)

Proteomic Profiling Dataset for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)

Animal use of fence crossings in Southwestern Rangelands

Net-wire fencing built to confine livestock is common on rangelands in the Southwestern USA, yet the impacts of livestock fencing on wildlife are largely unknown. Many wildlife species cross beneath fences at defined crossing locations because they prefer to crawl underneath rather than jump over fences. Animals occasionally become entangled jumping or climbing over fences, leading to injury or death. More commonly, repeated crossings under net-wire fencing by large animals lead to fence damage, though the damage is often tolerated by landowners until the openings affect the ability to enclose livestock. The usage, placement, characteristics, and passage rates of fence crossings beneath net-wire fencing are poorly understood. We monitored 20 randomly selected fence crossings on net-wire livestock fencing across two study sites on rangelands in South Texas, USA, from April 2018–March 2019. We assessed characteristics of fence-crossing locations (openings beneath the fence created by animals to aid in crossing) and quantified crossing rates and probability of crossing by all species of animals via trail cameras. We documented 10,889 attempted crossing events, with 58% (n = 6,271) successful. Overall, 15 species of medium- and large-size mammals and turkey (Meleagris gallopavo) contributed to crossing events. Crossing locations received 3–4 crossing attempts per day on average, but the number of attempts and probability of successful crossing varied by location and fence condition. Probability of crossing attempts was most consistently influenced by opening size of the crossing and season; as crossing size (opening) increased, the probability of successful crossing significantly increased for all species. Peaks in crossing activity corresponded with species' daily and seasonal movements and activity. Density and size of fence-crossing locations were dependent on fence maintenance and not associated with vegetation communities or habitat variables. However, crossing locations were often re-established in the same locations after fence repairs. This is one of the few studies to monitor how all animal species present interacted with net-wire livestock fencing in rangelands. Our results will help land managers understand the impact of net-wire livestock fencing on animal movement.

Data and code for: Diversity-dependent diversification in the history of marine animals

By comparing detrended estimates of diversity (taxonomic richness) and rates of origination, extinction, and net diversification, I show that, at the global scale over the course of the Phanerozoic Eon, rates of diversification and origination are negatively correlated with diversity. By contrast, extinction rates are only weakly correlated with diversity for the most part. These results hold for both genus- and species-level data and for many alternative analytical protocols. The asymmetry between extinction on the one hand and origination and net diversification, on the other hand, supports a model whereby extinction is largely driven by abiotic perturbations, with subsequent origination filling the void left by depleted diversity. Diversity-dependence is somewhat weaker, but still evident, if the initial Ordovician radiation or rebounds from major mass extinctions are omitted from analysis; thus, diversity-dependence is influenced, but not dominated, by these special intervals of Earth history. In the transition from Paleozoic to post-Paleozoic time, diversity-dependence of origination weakens while that of extinction strengthens; however, diversity-dependence of net diversification barely changes in strength. Despite nuances, individual clades largely yield results consistent with those for the aggregate data on all animals. On the whole, diversity-dependent diversification appears to be a pervasive factor in the macroevolution of marine animal life.

opencc-by-4.0Dec 2022View details →

Fig. 1 in Monitoring Of Animal Dirofilariosis Incidence In Kharkiv Region Of Ukraine

Fig. 1. Infection of dogs with dirofilariae depending on age.

Data from: The viewer doesn't always seem to care - response to fake animal rescues on YouTube and implications for social media self-policing policies

Animal-related content on social media is hugely popular but is not always appropriate in terms of how animals are portrayed or how they are treated. This has potential implications beyond the individual animals involved, for viewers, for wild animal populations, and for societies and their interactions with animals. Whilst social media platforms usually publish guidelines for permitted content, enforcement relies at least in part on viewers reporting inappropriate posts. Currently, there is no external regulation of social media platforms. Based on a set of 241 "fake animal rescue" videos that exhibited clear signs of animal cruelty and strong evidence of being deliberately staged (i.e. fake), we found little evidence that viewers disliked the videos and an overall mixed response in terms of awareness of the fake nature of the videos, and their attitudes towards the welfare of the animals involved. Our findings suggest, firstly, that despite the narrowly defined nature of the videos used in this case study, exposure rates can be extremely high (one of the videos had been viewed over 100 million times), and, secondly, that many YouTube viewers cannot identify (or are not concerned by) animal welfare or conservation issues within a social media context. In terms of the current policy approach of social media platforms, our findings raise questions regarding the value of their current reliance on consumers as watch dogs.