187 Works

SARA module 3: NGS epitope sequencing: Illumina FASTQ files

Thomas Walker, Spyridon Megremis & Janine Lamb
We investigate the accumulated microbial and autoantigen antibody repertoire in adult-onset dermatomyositis patients sero-positive for TIF1γ (TRIM33) autoantibodies. We use an untargeted high-throughput approach which combines immunoglobulin disease-specific epitope-enrichment and identification of microbial and human antigens. We observe antibodies recognizing a wider repertoire of microbial antigens in dermatomyositis. Antibodies recognizing viruses and Poxviridae family species are significantly enriched. The identified autoantibodies recognise a large portion of the human proteome, including interferon regulated proteins; these proteins...

Supporting data for ‘DFENS: Diffusion chronometry using Finite Elements and Nested Sampling’

Euan Mutch, John Maclennan, Oliver Shorttle, John Rudge & David Neave
This is supporting data for the manuscript entitled 'DFENS: Diffusion chronometry using Finite Elements and Nested Sampling' by E. J. F. Mutch, J. Maclennan, O. Shorttle, J. F. Rudge and D. Neave. Preprint here: https://doi.org/10.1002/essoar.10503709.1 Data Set S1. ds01.csv Electron probe microanalysis (EPMA) profile data of olivine crystals used in this study. Standard deviations are averaged values of standard deviations from counting statistics and repeat measurements of secondary standards. Data Set S2. ds02.csv Plagioclase compositional...

Digital 3D models and measurements of avian brain cavity, blood vessel and nerve endocasts

S. A. Walsh, A. N. Iwaniuk, M. A. Knoll, E. Bourdon, P. M. Barrett, A. Milner, R. Nudds, R. L. Abel & P. Dello Sterpaio
This dataset comprises cast reconstructions of brain cavity space in 60 extant avian species, derived from X-ray micro computed-tomography scan image stacks. Each reconstruction was made using Materialise Mimics 14.11 to create volumetric models (brain cavity casts) that were then transformed into the polygon mesh stereolithograph (STL) files archived here. Brain cavity cast models are in most cases accompanied by casts of main vascular features (e.g., carotid arteries) and the olfactory nerves (CN I). A...

Growth, biomass allocation and tissue nutrient concentrations of subtropical and tropical tree seedlings in response to experimental manipulation of soil phosphorus pools

D Burslem, X. Liu, D. Johnson, A. Taylor, J. Taylor, T. Helgason, Y. Chen & M. Liang
This dataset reports metrics of plant growth, including height, total biomass and the biomass of component plant parts, and percentage root colonisation by mycorrhizas, for tree seedlings of eight tropical and seven subtropical growing in pots of soil that had been amended by addition of various sources of phosphorus (inorganic phosphate, adenosine monophosphate, phytic, or a mixture of all three) plus an unfertilized control treatment with no P additions. The aim of the experiment was...

Ecosystem functions and vegetation data for Winklebury Hill, Salisbury Plain, UK 2016

E.L. Fry, A.L. Hall, J. Savage, R.D. Bardgett, N. Ostle, R.F. Pywell, J.M. Bullock, S. Oakley, R. Griffiths, R. McDonald, T. Caruso & M. Ilardi
This dataset contains vegetation survey data, and nitrate and ammonium concentrations, nitrification and mineralisation rates, microbial biomass and carbon and nitrogen stock data from soils taken from an experiment based at Winklebury Hill, UK. The vegetation survey comprises total species percentage cover and species richness data from four 50 cm by 50 cm quadrats. Net ecosystem carbon dioxide exchange, photosynthesis and respiration data were measured with an Infra-red Gas Analyser (IRGA); methane, carbon dioxide and...

Data Collected During Simultaneous Neutron Powder Diffraction and Microwave Characterisation at Elevated Temperatures

Michael Barter, Gemma Smith, Sihai Yang, Martin Schröder, Martin Owen Jones & Adrian Porch
This dataset contains data collected during simultaneous neutron diffraction and microwave characterisation of a metal-organic framework (MOF), MFM-170, at elevated temperatures. The experiment consisted of the desolvation of the as synthesised MOF sample by flowing nitrogen gas heated to 150 °C through the sample, followed by rehydration of the sample by flowing air through the sample, and subsequent desolvation at a higher flow rate. Temperatures throughout the experiment are given (time and temperature) along with...

Data from: Ex situ diet influences the bacterial community associated with the skin of red-eyed tree frogs (Agalychnis callidryas)

Rachael E. Antwis, Rachel L. Haworth, Daniel J. P. Engelmoer, Victoria Ogilvy, Andrea L. Fidgett & Richard F. Preziosi
Amphibians support symbiotic bacterial communities on their skin that protect against a range of infectious pathogens, including the amphibian chytrid fungus. The conditions under which amphibians are maintained in captivity (e.g. diet, substrate, enrichment) in ex situ conservation programmes may affect the composition of the bacterial community. In addition, ex situ amphibian populations may support different bacterial communities in comparison to in situ populations of the same species. This could have implications for the suitability...

Data from: Disentangling plant and soil microbial controls on carbon and nitrogen loss in grassland mesocosms

Franciska T. De Vries, Helene Bracht Jorgensen, Katarina Hedlund & Richard D. Bardgett
1. It is well known that plant–soil interactions play an important role in determining the impact of global change phenomena on biodiversity and ecosystem functioning. Little is known, however, about the individual and relative importance for carbon (C) and nitrogen (N) cycling of non-random changes in plant and soil communities that result from global change phenomena, such as fertilization and agricultural intensification. 2. We set up a field-based mesocosm experiment in which we re-inoculated soil...

Data from: A predation cost to bold fish in the wild

Kaj Hulthén, Ben B. Chapman, P. Anders Nilsson, Lars-Anders Hansson, Christian Skov, Jakob Brodersen, Jerker Vinterstare & Christer Brönmark
Studies of predator-mediated selection on behaviour are critical for our understanding of the evolution and maintenance of behavioural diversity in natural populations. Consistent individual differences in prey behaviour, especially in the propensity to take risks (“boldness”), are widespread in the animal kingdom. Theory predicts that individual behavioural types differ in a cost-benefit trade-off where bolder individuals benefit from greater access to resources while paying higher predation-risk costs. However, explicitly linking predation events to individual behaviour...

Data from: Evolutionary covariation in geometric morphometric data: analyzing integration, modularity, and allometry in a phylogenetic context

Christian Peter Klingenberg & Jesús Marugán-Lobón
Quantifying integration and modularity of evolutionary changes in morphometric traits is crucial for understanding how organismal shapes evolve. For this purpose, comparative studies are necessary, which need to take into account the phylogenetic structure of interspecific data. This study applies several of the standard tools of geometric morphometrics, which mostly have been used in intraspecific studies, in the new context of analyzing integration and modularity based on comparative data. Morphometric methods such as principal component...

Data from: Late-life and intergenerational effects of larval exposure to microbial competitors in the burying beetle Nicrophorus vespilloides

Ailsa H. C. McLean, Andres N. Arce, Per T. Smiseth & Daniel E. Rozen
Intergenerational effects can have either adaptive or nonadaptive impacts on offspring performance. Such effects are likely to be of ecological and evolutionary importance in animals with extended parental care, such as birds, mammals and some insects. Here, we studied the effects of exposure to microbial competition during early development on subsequent reproductive success in the burying beetle Nicrophorus vespilloides, an insect with elaborate parental care. We found that exposure to high levels of microbial competition...

Data from: Bat species comparisons based on external morphology: a test of traditional versus geometric morphometric approaches

Daniela A. Schmieder, Hugo A. Benítez, Ivailo M. Borissov & Carmelo Fruciano
External morphology is commonly used to identify bats as well as to investigate flight and foraging behavior, typically relying on simple length and area measures or ratios. However, geometric morphometrics is increasingly used in the biological sciences to analyse variation in shape and discriminate among species and populations. Here we compare the ability of traditional versus geometric morphometric methods in discriminating between closely related bat species – in this case European horseshoe bats (Rhinolophidae, Chiroptera)...

Data from: The interaction of Saccharomyces paradoxus with its natural competitors on oak bark

Vienna Kowallik, Eric Miller & Duncan Greig
The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high-throughput...

Data from: Testing and quantifying phylogenetic signals and homoplasy in morphometric data

Christian Peter Klingenberg & Nelly A. Gidaszewski
The relationship between morphometrics and phylogenetic analysis has long been controversial. Here we propose an approach that is based on mapping morphometric traits onto phylogenies derived from other data and thus avoids the pitfalls encountered by previous studies. This method treats shape as a single, multidimensional character. We propose a test for the presence of a phylogenetic signal in morphometric data, which simulates the null hypothesis of the complete absence of phylogenetic structure by permutation...

Data from: Two new species of Ichthyosaurus from the lowermost Jurassic (Hettangian) of Somerset, England

Dean R. Lomax & Judy A. Massare
All specimens of Ichthyosaurus from the Lower Jurassic of Somerset were previously identified as I. communis, an abundant and extremely variable species. Here, two new species of Ichthyosaurus are recognized from multiple specimens. The species are assigned to Ichthyosaurus on the basis of the humerus, pectoral girdle and forefin morphologies. I. larkini sp. nov. is distinguished by a broad jugal with a blunt anterior end that extends as far forward as the middle of the...

Data from: Does postcranial palaeoneurology provide insight into pterosaur behaviour and lifestyle? New data from the azhdarchoid Vectidraco and the ornithocheirids Coloborhynchus and Anhanguera

Elizabeth Martin-Silverstone, Daniel Sykes & Darren Naish
The postcranial palaeoneurology of fossil reptiles is understudied, and those studies that exist focus predominantly on crocodyliforms and dinosaurs. The intervertebral foramina of the spine house nerves that exit to innervate surrounding tissues and the extremities. In the heavily fused (and typically distorted or poorly preserved) pterosaurian sacrum, intervertebral foramina can be difficult to observe and are rarely identified. The Early Cretaceous azhdarchoid Vectidraco from the Isle of Wight, UK, exhibits large, paired foramina on...

Data from: Macrophages contribute to the cyclic activation of adult hair follicle stem cells

Donatello Castellana, Ralf Paus & Mirna Perez-Moreno
Skin epithelial stem cells operate within a complex signaling milieu that orchestrates their lifetime regenerative properties. The question of whether and how immune cells impact on these stem cells within their niche is not well understood. Here we show that skin-resident macrophages decrease in number because of apoptosis before the onset of epithelial hair follicle stem cell activation during the murine hair cycle. This process is linked to distinct gene expression, including Wnt transcription. Interestingly,...

Data from: Context-dependent consequences of colour biases in a social fish

Brett Culbert, Sanduni Talagala, Emily Stanbrook, Parker Smale, Sigal Balshine & James Barnett
Colourful visual signals can provide receivers with valuable information about food, danger, and the quality of social partners. However, the value of the information that colour provides varies depending on the situation, and colour may even act as a sensory trap where signals that evolved under one context are exploited in another. Despite some elegant early work on colour as a sensory trap, few empirical studies have examined how colour biases may vary depending on...

Data from: Preserved collagen reveals species identity in archaeological marine turtle bones from Caribbean and Florida sites

Michael Buckley, Virginia L. Harvey, Michelle J. LeFebvre, Susan D. DeFrance, Casper Toftgaard & Andrew C. Kitchener
Advancements in molecular science are continually improving our understanding of marine turtle biology and evolution. However, there are still considerable gaps in our understanding, such as past marine turtle distributions, which can benefit from advanced zooarchaeological analyses. Here we apply collagen fingerprinting to 130 archaeological marine turtle bone samples up to 2500 years old from the Caribbean and Florida’s Gulf Coast for faunal identification, finding the vast majority of samples (88%) to contain preserved collagen...

Competition for resources can promote the divergence of social learning phenotypes

R. Tucker Gilman, Fern Johnson & Marco Smolla
Social learning occurs when animals acquire knowledge or skills by observing or interacting with others, and is the fundamental building block of culture. Within populations, some individuals use social learning more frequently than others, but why social learning phenotypes differ among individuals is poorly understood. We modelled the evolution of social learning frequency in a system where foragers compete for resources and there are many different foraging options to learn about. Social learning phenotypes diverged...

Stoichiometric traits (N:P) of understory plants contribute to reductions in plant diversity following long-term nitrogen addition in subtropical forest

Jianping Wu, Fangfang Shen, Jill Thompson, Wenfei Liu, Honglang Duan & Richard Bardgett
Nitrogen enrichment is pervasive in forest ecosystems, but its influence on understory plant communities and their stoichiometric characteristics is poorly understood. We hypothesize that when forest is enriched with nitrogen (N), the stoichiometric characteristics of plant species explains changes in understory plant diversity. A 13 year field experiment was conducted to explore the effects of N addition on foliar carbon (C): N: phosphorus (P) stoichiometry and understory plant species richness in a subtropical Chinese fir...

Maladaptive migration behaviour in hybrids links to predator-mediated ecological selection

Varpu Pärssinen, Kaj Hulthén, Christer Brönmark, Christian Skov, Jakob Brodersen, Henrik Baktoft, Ben Chapman, Lars-Anders Hansson & Anders Nilsson
1. Different migratory species have evolved distinct migratory characteristics that improve fitness in their particular ecological niches. However, when such species hybridize, migratory traits from parental species can combine maladaptively and cause hybrids to fall between parental fitness peaks, with potential consequences for hybrid viability and species integrity. 2. Here, we take advantage of a natural cross-breeding incident to study migratory behaviour in naturally occurring hybrids as well as in their parental species and explore...

Evolution of ecospace occupancy by Mesozoic marine tetrapods

Jane C. Reeves, Benjamin C. Moon, Michael J. Benton & Thomas L. Stubbs
Ecology and morphology are different, and yet in comparative studies of fossil vertebrates the two are often conflated. The macroevolution of Mesozoic marine tetrapods has been explored in terms of morphological disparity, but less commonly using ecological-functional categories. Here we use ecospace modelling to quantify ecological disparity across all Mesozoic marine tetrapods. We document the explosive radiation of marine tetrapod groups in the Triassic and their rapid attainment of high ecological disparity. Late Triassic extinctions...

Data from: Metamorphosis revealed: time-lapse three-dimensional imaging inside a living chrysalis

Tristan Lowe, Russell J. Garwood, Thomas J. Simonsen, Robert S. Bradley & Philip J. Withers
Studies of model insects have greatly increased our understanding our animal development. Yet they are limited in scope to this small pool of model species: a small number of representatives for a hyperdiverse group with highly varied developmental processes. One factor behind this narrow scope is the challenging nature of traditional methods of study, such as histology and dissection, which can preclude quantitative analysis and do not allow the development of a single individual to...

Data from: Interspecific variation in the structural properties of flight feathers in birds indicates adaptation to flight requirements and habitat

Peter L. Pap, Gergely Osvath, Krisztina Sandor, Orsolya Vincze, Lorinc Barbos, Attila Marton, Robert L. Nudds & Csongor I. Vagasi
1. The functional significance of intra- and interspecific structural variations in the flight feathers of birds is poorly understood. Here, a phylogenetic comparative analysis of four structural features (rachis width, barb and barbule density and porosity) of proximal and distal primary feathers of 137 European bird species was conducted. 2. Flight type (flapping and soaring, flapping and gliding, continuous flapping or passerine type), habitat (terrestrial, riparian or aquatic), wing characteristics (wing area, S and aspect...

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