90 Works

Flow cytometry analysis of water samples for bacterial and Pico-plankton enumeration, samples collected in the Barents Sea during 2017-2018

Elaine Mitchell, Sharon McNeil, Callum Whyte, Finlo Cottier, Joanne Hopkins & Keith Davidson
Collection and preservation of open ocean water samples from stations along a transect in the Barents Sea over the course of a year from July 2017 - July 2018. Four cruises in total to cover seasonal changes, two on board the James Clark Ross (RRS) and two aboard the Helmer Hansen (RV). A standard CTD cast was deployed to collect the samples, the depths were selected to support Primary Production experiments on board the ship,...

Data associated with 'Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region'

Dheeraj Prakaash, Graham Cook, oreste acuto & Antreas Kalli
The T cell receptor (TCR-CD3) initiates T cell activation by binding to peptides of Major Histocompatibility Complexes (pMHC). The TCR-CD3 topology is well understood but the arrangement and dynamics of its cytoplasmic tails remains unknown, limiting our grasp of the signalling mechanism. Here, we use molecular dynamics simulations and modelling to investigate the entire TCR-CD3 embedded in a model membrane. Our study demonstrates conformational changes in the extracellular and transmembrane domains, and the arrangement of...

The first Silurian trilobite with three-dimensionally preserved soft parts reveals novel appendage morphology

Mark Sutton, Derek Siveter, Richard Fortey, Derek Briggs & David Siveter
The first Silurian trilobite known with soft parts preserved, a Dalmanites species, is described from the Herefordshire Lagerstätte. Biramous appendages and much of the alimentary system are evident. High-fidelity three-dimensional preservation reveals a novel, double arrangement of the exopod filaments, interconnected by a presumed membranous sheet. This morphology explains a misinterpretation of the exopod as supporting spiral structures, originally reported nearly 150 years ago. The new exopod morphology is considered primarily respiratory in function and...

Early‐life seasonal, weather and social effects on telomere length in a wild mammal

Sil H.J. Van Lieshout, Elisa P. Badás, Julius G. Bright Ross, Amanda Bretman, Chris Newman, Christina D. Buesching, Terry Burke, David W. Macdonald & Hannah L. Dugdale
Early-life environmental conditions can provide a source of individual variation in life-history strategies and senescence patterns. Conditions experienced in early life can be quantified by measuring telomere length, which can act as a biomarker of survival probability in some species. Here, we investigate whether seasonal changes, weather conditions, and group size are associated with early-life and/or early-adulthood telomere length in a wild population of European badgers (Meles meles). We found substantial intra-annual changes in telomere...

Clinician-researcher’s perspectives on clinical research during the COVID-19 pandemic

Sarah Silverberg, Lisa Puchalski-Ritchie, Nina Gobat, Alistair Nichol & Srinavas Murthy
Objectives: The outcome of well-performed clinical research is essential for evidence-based patient management during pandemics. However, conducting clinical research amidst a pandemic requires researchers to balance clinical and research demands. We seek to understand the values, experiences, and beliefs of physicians working at the onset of the COVID-19 pandemic in order to inform clinical research planning. We aim to understand whether pandemic settings affect physician comfort with research practices, and how physician experiences shape their...

Atmospheric and surface gravity wave data for role of surface gravity waves in aquaplanet ocean climates

Joshua Studholme, Margarita Markina & Sergey Gulev
This data corresponds to the runs analysed in the manscript: Role of Surface Gravity Waves in Aquaplanet Ocean Climates (JAMES, 2021). In this work, we present a set of idealised numerical experiments that demonstrate the thermodynamic and dynamic implications of surface gravity waves for the oceanic climate of an aquaplanet. We study the impact of accounting for modulations by such waves upon air-sea momentum fluxes, Langmuir circulation and the Stokes-Coriolis force. This dataset is made...

Comparison of size-structured and species-level trophic networks reveals antagonistic effects of temperature on vertical trophic diversity at the population and species level

Willem Bonnaffé, Alain Danet, Stephane Legendre & Eric Edeline
It is predicted that warmer conditions should lead to a loss of trophic levels, as larger bodied consumers, which occupy higher trophic levels, experience higher metabolic costs at high temperature. Yet, it is unclear whether this prediction is consistent with the effect of warming on the trophic structure of natural systems. Furthermore, effects of temperature at the species level, which arise through a change in species composition, may differ from those at the population level,...

An island-hopping bird reveals how founder events shape genome-wide divergence

Ashley Sendell-Price, Kristen Ruegg, Bruce Robertson & Sonya Clegg
When populations colonise new areas, both strong selection and strong drift can be experienced due to novel environments and small founding populations, respectively. Empirical studies have predominantly focused on the phenotype when assessing the role of selection, and limited neutral-loci when assessing founder-induced loss of diversity. Consequently, the extent to which processes interact to influence evolutionary trajectories is difficult to assess. Genomic-level approaches provide the opportunity to simultaneously consider these processes. Here, we examine the...

A shift in ontogenetic timing produced the unique sauropod skull

Matteo Fabbri, Guillermo Navalón, Nicolás Mongiardino Koch, Michael Hanson, Holger Petermann & Bhart-Anjan Bhullar
Sauropod dinosaurs include the largest terrestrial vertebrates that have ever lived. Virtually every part of the sauropod body is heavily modified in association with gigantic size and associated physiological alterations. Sauropod skulls are no exception: they feature elongated, telescoped facial regions connected to tilted neurocrania and reoriented jaw adductor muscles. Several of these cranial features have been suggested to be adaptations for feeding on the one hand and the result of paedomorphic transformation near the...

Convex hull estimation of mammalian body segment parameters

Sam Coatham, William Sellers & Thomas Püschel
Obtaining accurate values for body segment parameters (BSPs) is fundamental in many biomechanical studies, particularly for gait analysis. Convex hulling, where the smallest-possible convex object that surrounds a set of points is calculated, has been suggested as an effective and time-efficient method to estimate these parameters in extinct animals, where soft tissues are rarely preserved. We investigated the effectiveness of convex hull BSP estimation in a range of extant mammals, to inform the potential future...

Neisseria cinerea 346T whole genome sequence

Rafael Custodio, Christoph Tang & Rachel Exley
Type VI Secretion Systems (T6SS) are widespread in bacteria and can dictate the development and organisation of polymicrobial ecosystems by mediating contact dependent killing. In Neisseria species, including Neisseria cinerea a commensal of the human respiratory tract, interbacterial contacts are mediated by Type four pili (Tfp) which promote formation of aggregates and govern the spatial dynamics of growing Neisseria microcolonies. Here we show that N. cinerea expresses a plasmid-encoded T6SS that is active and can...

Simulated distribution of the fluid salinity, Cu and temperature in a sub-volcanic region

Jon Blundy, Andrey Afanasyev, Oleg Melnik, Brian Tattitch, Steve Sparks, Alison Rust & Ivan Utkin
The files brinelens.00.vtu, brinelens.01.vtu,... contain the simulated distributions of the fluid bulk salinity (a), the Cu concentration in fluid for the 'no sulfur' case (b), the Cu concenration in fluid for the 'sulfur unlimited' case (c), the Cu deposition for the 'sulfur unlimited' case (d), and the temperature (e) at t=0 yr, 10000 yr, 20000 yr,..., respectively. The distributions shown in Fig. 6a-e are in brinelens.10.vtu. The file brinelens.csv contains the simulated time evolution of...

Data from: Larval density, sex and allocation hierarchy affect life-history trait covariances in a bean beetle

Flavia Barbosa, Samuel Gascoigne & Desire Uwera Nalukwago
Life-history theory aims to understand how different environments result in differential investment in fitness-related traits. While trade-offs between traits are expected, many studies show positive or no correlation between pairs of costly traits. One hypothesis that may explain the inconsistency of trade-offs in the literature is that trait investment may occur in a dichotomous hierarchy (the tree model), that allows for differential trait investment weighted by the traits’ respective positions within the hierarchy. Previous mathematical...

Ecological consequences of large herbivore exclusion in an African savanna: 12 years of data from the UHURU experiment

Jesse Alston, Courtney Reed, Leo Khasoha, Bianca Brown, Gilbert Busienei, Nathaniel Carlson, Tyler Coverdale, Megan Dudenhoeffer, Marissa Dyck, John Ekeno, Abdikadir Hassan, Rhianna Hohbein, Rhiannon Jakopak, Buas Kimiti, Samson Kurukura, Peter Lokeny, Allison Louthan, Simon Musila, Paul Musili, Tosca Tindall, Sarah Weiner, Tyler Kartzinel, Todd Palmer, Robert Pringle & Jacob Goheen
Diverse communities of large mammalian herbivores (LMH), once widespread, are now rare. LMH exert strong direct and indirect effects on community structure and ecosystem functions, and measuring these effects is important for testing ecological theory and for understanding past, current, and future environmental change. This in turn requires long-term experimental manipulations, owing to the slow and often nonlinear responses of populations and assemblages to LMH removal. Moreover, the effects of particular species or body-size classes...

Data from: Substantial intraspecific variation in energy budgets: biology or artefact?

Tomos Potter, David Reznick & Tim Coulson
Data on the growth and reproduction of Trinidadian guppies (Poecilia reticulata) from sixteen different populations, reared under experimental conditions of either high or low food availability. These data were used to fit dynamic energy budgets models for each of the populations. For twelve populations, there are three sets of observations per individual, recorded at each successive parturition event. For four of the populations, data were recorded at each parturition event over the full lifespan of...

Cambrian comb jellies from Utah illuminate the early evolution of nervous and sensory systems in ctenophores - Phylogenetic dataset

Luke Parry, Rudy Lerosey Aubril, James Weaver & Javier Ortega-Hernández
Ctenophores are a group of predatory macroinvertebrates whose controversial phylogenetic position has prompted several competing hypotheses regarding the evolution of animal organ systems. Although ctenophores date back at least to the Cambrian, they have a poor fossil record due to their gelatinous bodies. Here, we describe two ctenophore species from the Cambrian of Utah, which illuminate the early evolution of nervous and sensory features in the phylum. Thalassostaphylos elegans has 16 comb rows, an oral...

Imprinting on time-structured acoustic stimuli in ducklings

Tiago Monteiro, Tom Hart & Alex Kacelnik
Filial imprinting is a dedicated learning process that lacks explicit reinforcement. The phenomenon itself is narrowly heritably canalized, but its content, the representation of the parental object, reflects the circumstances of the newborn. Imprinting has recently been shown to be even more subtle and complex than previously envisaged, since ducklings and chicks are now known to select and represent for later generalization abstract conceptual properties of the objects they perceive as neonates, including movement pattern,...

Data and code for Heterogeneous selection on exploration behavior within and among West European populations of a passerine bird

Alexia Mouchet, Ella Cole, Erik Matthysen, Marion Nicolaus, John Quinn, Allison Roth, Joost Tinbergen, Kees Van Oers, Thijs Van Overveld & Niels Dingemanse
Heterogeneous selection is often proposed as a key mechanism maintaining repeatable behavioral variation (“animal personality”) in wild populations. Previous studies largely focused on temporal variation in selection within single populations. The relative importance of spatial versus temporal variation remains unexplored, despite these processes having distinct effects on local adaptation. Using data from >3500 great tits (Parus major) and 35 nest box plots situated within five West-European populations monitored over 4-18 years, we show that selection...

A habenula-insular circuit encodes the willingness to act

Nima Khalighinejad, Neil Garrett, Luke Priestley, Patricia Lockwood & Matthew FS Rushworth
The decision that it is worth doing something rather than nothing is a core yet understudied feature of voluntary behaviour. Here we study “willingness to act”, the probability of making a response given the context. Human volunteers encountered opportunities to make effortful actions in order to receive rewards, while watching a movie inside a 7T MRI scanner. Reward and other context features determined willingness- to-act. Activity in the habenula tracked trial-by-trial variation in participants’ willingness-to-act....

Data from: Fossils improve phylogenetic analyses of morphological characters

Nicolás Mongiardino Koch, Russell Garwood & Luke Parry
Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here we use simulations to evaluate the performance of inference methods across different levels of fossil...

Geochemical Data for the Olla and Nebo-Hemphill Oil Fields, Louisiana

Rebecca L Tyne, Peter H Barry, Michael Lawson, Hao Xie, Darren J Hillegonds, John M Eiler & Chris J Ballentine
Formation water geochemistry and gas geochemistry from 6 wells in the Olla Oil Field and 7 wells in the Nebo-Hemphill Oil Field Louisiana (Longitude range: -92.2297 to -92.1487, Latitude range: 31.83128 to 31.56586.), sampled in 2015. Formation water geochemistry for cation and anions and in mmol/l and ppm, these were measured at an internal ExxonMobil facility. Casing gases were used to make the remaining measurements. Stable noble gas isotopes (He, Ne, Ar, Kr, Xe) were...

The limits of demographic buffering in coping with environmental variation

Roberto Rodríguez-Caro, Roberto Rodríguez-Caro, Pol Capdevila, Eva Graciá, Jomar Barbosa, Andrés Giménez & Rob Salguero-Gomez
Animal populations have developed multiple strategies to deal with environmental change. Among them, the demographic buffering strategy consists in constraining the temporal variation of the vital rate(s) that most affect(s) the overall performance of the population. Tortoises are known to buffer their temporal variation in adult survival, which typically has the highest contribution to the population growth rate λ, at the expense of a high variability on reproductive rates, which contribute far less to λ....

RepeatModeler and RepeatMasker output files

Reuben Nowell, Christopher Wilson, Pedro Almeida, Philipp Schiffer, Diego Fontaneto, Lutz Becks, Fernando Rodriguez, Irina Arkhipova & Timothy Barraclough
Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates in which males are thus far unknown. Contrary to expectations, we find a variety of active...

Data from: The molecular phylogeny of Chionaster nivalis reveals a novel order of psychrophilic and globally distributed Tremellomycetes (Fungi, Basidiomycota)

Nicholas Irwin, Chantelle Twynstra, Varsha Mathur & Patrick Keeling
Snow and ice present challenging substrates for cellular growth, yet microbial snow communities not only exist, but are diverse and ecologically impactful. These communities are dominated by green algae, but additional organisms, such as fungi, are also abundant and may be important for nutrient cycling, syntrophic interactions, and community structure in general. However, little is known about these non-algal community members, including their taxonomic affiliations. An example of this is Chionaster nivalis, a unicellular fungus...

Data for: Plasmids do not consistently stabilize cooperation across bacteria, but may promote broad pathogen host-range

Anna Dewar
Horizontal gene transfer via plasmids could favour cooperation in bacteria, because transfer of a cooperative gene turns non-cooperative cheats into cooperators. This hypothesis has received support from theoretical, genomic and experimental analyses. In contrast, we show here, with a comparative analysis across 51 diverse species, that genes for extracellular proteins, which are likely to act as cooperative ‘public goods’, were not more likely to be carried on either: (i) plasmids compared to chromosomes; or (ii)...

Registration Year

  • 2021
    90

Resource Types

  • Dataset
    90

Affiliations

  • University of Oxford
    89
  • Yale University
    6
  • University College London
    5
  • Institute of Oceanology. PP Shirshov Russian Academy of Sciences
    4
  • University of Leeds
    4
  • University of Florida
    3
  • University of Georgia
    2
  • University of Groningen
    2
  • University of Cambridge
    2
  • German Center for Integrative Biodiversity Research
    2