98 Works

Data from: Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter

Adelumola Oladeinde, Kimberly Cook, Alex Orlek, Greg Zock, Kyler Herrington, Nelson Cox, Jodie Plumblee Lawrence & Carolina Hall
Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is a clinically-important serovar linked to food-borne illness, and commonly isolated from poultry. Investigations of a large, multistate outbreak in the USA in 2013 identified poultry litter (PL) as an important extra-intestinal environment that may have selected for specific S. Heidelberg strains. Poultry litter is a mixture of bedding materials and chicken excreta that contains chicken gastrointestinal (GI) bacteria, undigested feed, feathers, and other materials of chicken...

Data from: A neural mechanism underlying failure of optimal choice with multiple alternatives

Bolton K H Chau, Nils Kolling, Laurence T Hunt, Mark E Walton & Matthew F S Rushworth
Despite widespread interest in neural mechanisms of decision-making, most investigations focus on decisions between just two options. Here we adapt a biophysically plausible model of decision-making to predict how a key decision variable, the value difference signal—encoding how much better one choice is than another—changes with the value of a third, but unavailable, alternative. The model predicts a surprising failure of optimal decision-making: greater difficulty choosing between two options in the presence of a third...

Data from: Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages

Florentine Riquet, Cathy Liautard-Haag, Lucy Woodall, Carmen Bouza, Patrick Louisy, Bojan Hamer, Francisco Otero-Ferrer, Philippe Aublanc, Vickie Béduneau, Olivier Briard, Tahani El Ayari, Sandra Hochscheid, Khalid Belkhir, Sophie Arnaud-Haond, Pierre-Alexandre Gagnaire & Nicolas Bierne
Diverging semi-isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the latter, although both can contribute to isolation. Rarely these two patterns of spatial distribution are reported in the same study system. Here we report that the long-snouted seahorse Hippocampus guttulatus is subdivided into discrete panmictic entities by both types of hybrid zones....

Data from: The influence of symbiotic bacteria on reproductive strategies and wing polyphenism in pea aphids responding to stress

Miguel L. Reyes, Alice M. Laughton, Benjamin James Parker, Hannah Wichmann, Maretta Fan, Daniel Sok, Jan Hrcek, Tarik Acevedo & Nicole M. Gerardo
1. Environmental stressors can be key drivers of phenotypes, including reproductive strategies and morphological traits. The response to stress may be altered by the presence of microbial associates. For example, in aphids, facultative (secondary) bacterial symbionts can provide protection against natural enemies and stress induced by elevated temperatures. Furthermore, aphids exhibit phenotypic plasticity, producing winged (rather than wingless) progeny that may be better able to escape danger, and the combination of these factors improve the...

Data from: The diversity of population responses to environmental change

Fernando Colchero, Owen R. Jones, Dalia A. Conde, Dave Hodgson, Felix Zajitschek, Benedikt R. Schmidt, Aurelio F. Malo, Susan C. Alberts, Peter H. Becker, Sandra Bouwhuis, Anne M. Bronikowski, Kristel M. De Vleeschouwer, Richard J. Delahay, Stefan Dummermuth, Eduardo Fernández-Duque, John Frisenvænge, Martin Hesselsøe, Sam Larson, Jean-Francois Lemaitre, Jennifer McDonald, David A.W. Miller, Colin O'Donnell, Craig Packer, Becky E. Raboy, Christopher J. Reading … & Chris J. Reading
The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly-explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations, and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and...

Data from: Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)

Laura J. Pollock, Reid Tingley, William K. Morris, Nick Golding, Robert B. O'Hara, Kirsten M. Parris, Peter A. Vesk & Michael A. McCarthy
A primary goal of ecology is to understand the fundamental processes underlying the geographic distributions of species. Two major strands of ecology – habitat modelling and community ecology – approach this problem differently. Habitat modellers often use species distribution models (SDMs) to quantify the relationship between species’ and their environments without considering potential biotic interactions. Community ecologists, on the other hand, tend to focus on biotic interactions and, in observational studies, use co‐occurrence patterns to...

Data from: Glutamate receptor delta2 serum antibodies in paediatric opsoclonus myoclonus ataxia syndrome

Georgina Berridge, David A Menassa, Teresa Moloney, Patrick J Waters, Imogen Welding, Selina Thomsen, Sameer Zuberi, Roman Fischer, A. Radu Aricescu, Michael Pike, Russell C Dale, Benedikt Kessler, Angela Vincent, Ming Lim, Sarosh R Irani & Bethan Lang
Objective: To identify neuronal surface antibodies in opsoclonus myoclonus ataxia syndrome (OMAS) usingcontemporary antigen discovery methodology. Methods: OMAS patient serum IgG immunohistochemistry using age-equivalent rat cerebellar tissue was followed by immunoprecipitation, gel electrophoresis and mass spectrometry. Data are available via ProteomeXchange (identifier PXD009578). This generated a list of potential neuronal surface cerebellar autoantigens. Live cell-based assays (CBA) were used to confirm membrane-surface antigens and adsorb antigen-specific IgGs. The serological results were compared to the clinical...

Data from: Estimating environmental suitability

John M. Drake & Robert L. Richards
Methods for modeling species’ distributions in nature are typically evaluated empirically with respect to data from observations of species occurrence and, occasionally, absence at surveyed locations. Such models are relatively “theory‐free.” In contrast, theories for explaining species’ distributions draw on concepts like fitness, niche, and environmental suitability. This paper proposes that environmental suitability be defined as the conditional probability of occurrence of a species given the state of the environment at a location. Any quantity...

Data from: Hosts do not simply outsource pathogen resistance to protective symbionts

Jan Hrcek, Benjamin J. Parker, Ailsa H.C. McLean, Jean-Christophe Simon, Ciara M. Mann & H. Charles J. Godfray
Microbial symbionts commonly protect their hosts from natural enemies, but it is unclear how protective symbionts influence the evolution of host immunity to pathogens. One possibility is that ‘extrinsic’ protection provided by symbionts allows hosts to reduce investment in ‘intrinsic’ immunological resistance mechanisms. We tested this idea using pea aphids (Acyrthosiphon pisum) and their facultative bacterial symbionts that increase host resistance to the fungal pathogen Pandora neoaphidis. The pea aphid taxon is composed of multiple...

Data from: Rewilding in the English Uplands: policy and practice

Christopher J. Sandom, Benedict Dempsey, David Bullock, Adrian Ely, Paul Jepson, Stefan Jimenez-Wisler, Adrian Newton, Nathalie Pettorelli & Rebecca A. Senior
Rewilding is gaining momentum as a new approach to restore and conserve biodiversity and ecosystem services, despite being imprecisely defined, controversial, and with limited explicit empirical supporting evidence (Lorimer et al., 2015; Pettorelli et al., 2018; Svenning et al., 2016). In a case study region (the English uplands), we discuss what rewilding means to practitioners and policy makers; the risks, opportunities, and barriers to implementation, and potential paths for policy and practice.

Mark-Release-Recapture data showing moth and dung beetle movements in riparian reserves within the SAFE project landscape, Malaysian Borneo, 2016-17

R.E.J. Gray, E.M. Slade, A.Y.C. Chung & O.T. Lewis
This dataset consists of moth and dung beetle recapture, movement, and trait data from a mark-release-recapture experiment conducted within riparian forest reserves, in an oil palm landscape in Sabah, Malaysian Borneo conducted as part of the SAFE project (Stability of Altered Forest Ecosystems). This resource includes information regarding the recapture frequency and movement behaviour of both moths and dung beetles with respect to three habitat types: riparian forest reserve, continuous forest, and oil palm plantation....

Data from: Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of the relationship of angiosperms and Gnetales

Mario Coiro, Guillaume Chomicki & James A. Doyle
The placement of angiosperms and Gnetales in seed plant phylogeny remains one of the most enigmatic problems in plant evolution, with morphological analyses (which have usually included fossils) and molecular analyses pointing to very distinct topologies. Almost all morphology-based phylogenies group angiosperms with Gnetales and certain extinct seed plant lineages, while most molecular phylogenies link Gnetales with conifers. In this study, we investigate the phylogenetic signal present in published seed plant morphological datasets. We use...

Scripts

Dorothy Bishop, Paul Thompson, Zoe Woodhead, Abigail Bradshaw & Adam Parker

CANDICE A2: Assessing reliability of language laterality measures using fTCD

Zoe Woodhead, Abigail Bradshaw, Alexander Wilson, Paul Thompson & Dorothy Bishop

Data from: Neurocranial anatomy of an enigmatic Early Devonian fish sheds light on early osteichthyan evolution

Alice M. Clement, Benedict King, Sam Giles, Brian Choo, Per Ahlberg, Gavin C. Young, John A. Long & Per E Ahlberg
The skull of ‘Ligulalepis’ from the Early Devonian of Australia (AM-F101607) has significantly expanded our knowledge of early osteichthyan anatomy, but its phylogenetic position has remained uncertain. We herein describe a second skull of ‘Ligulalepis’ and present micro-CT data on both specimens to reveal novel anatomical features, including cranial endocasts. Several features previously considered to link ‘Ligulalepis’ with actinopterygians are now considered generalized osteichthyan characters or of uncertain polarity. The presence of a lateral cranial...

Data from: A high density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour

Jun-Mo Kim, Anna W. Santure, Henry J. Barton, John L. Quinn, Eleanor F. Cole, Marcel E. Visser, Ben C. Sheldon, Martien A.M. Groenen, Kees Van Oers, Jon Slate & J.-M. Kim
High density SNP microarrays (‘SNP chips’) are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this paper we describe the development and application of a high density Affymetrix Axiom chip with around 500 000 SNPs, designed to perform genomics studies...

Data from: A redescription of Orovenator mayorum (Sauropsida, Diapsida) using high-resolution μCT and the consequences for early amniote phylogeny

David P. Ford, Roger B.J. Benson & Roger B. J. Benson
The earliest known neodiapsid Orovenator mayorum from the early Permian of Oklahoma is redescribed using high-resolution μCT, revealing remarkable details of the skull anatomy. Our findings are relevant to both palaeoecology (suggesting burrowing and nocturnality) and phylogeny. Orovenator and other sauropsids share at least 16 character states with varanopids, many of which were not recognised by previous studies. These include a rounded subnarial shelf of the premaxilla, a posterodorsal extension of the external naris, the...

Data from: Tropical dung beetle morphological traits predict functional traits and show intra-specific differences across land uses

Elizabeth H. Raine, Claudia L. Gray, Darren J. Mann & Eleanor M. Slade
1. Functional traits and functional diversity measures are increasingly being used to examine land use effects on biodiversity and community assembly rules. 2. Morphological traits are frequently derived from a mean value of many individuals, and used directly as functional traits. However, this approach overlooks the importance of intraspecific differences. 3. We collected morphometric data from over 1700 individuals of 12 species of dung beetle to establish whether morphological measurements can be used as predictors...

Data from: Positive effects of liana cutting on seedlings are reduced during El Niño-induced drought

Michael J. O'Brien, Christopher D. Philipson, Glen Reynolds, Dzaeman Dzulkifli, Jake L. Snaddon, Robert Ong & Andy Hector
1. Liana cutting is a management practice currently applied to encourage seedling regeneration and tree growth in some logged tropical forests. However, there is limited empirical evidence of its effects on forest demographic rates in Southeast Asia. 2. We used 22 four-hectare plots in the Sabah Biodiversity Experiment (a reduced impact logging site) enrichment line planted with 16 dipterocarp species to assess the effects of complete liana cutting on tree growth and survival. We compared...

Data from: Aeroecology of a solar eclipse

Cecilia Nilsson, Kyle G. Horton, Adriaan M. Dokter, Benjamin M. Van Doren & Andrew Farnsworth
Light cues elicit strong responses from nearly all forms of life, perhaps most notably as circadian rhythms entrained by periods of daylight and darkness. Atypical periods of darkness, like solar eclipses, provide rare opportunities to study biological responses to light cues. By using a continental scale radar network, we investigated responses of flying animals to the total solar eclipse of 21 August 2017. We quantified the number of biological targets in the atmosphere at 143...

Data from: Plant controls on Late Quaternary whole ecosystem structure and function

Elizabeth S. Jeffers, Nicki J. Whitehouse, Adrian Lister, Gill Plunkett, Phil Barratt, Emma Smyth, Philip Lamb, Michael W. Dee, Stephen J. Brooks, Katherine J. Willis, Cynthia A. Froyd, Jenny E. Watson & Michael B. Bonsall
Plants and animals influence biomass production and nutrient cycling in terrestrial ecosystems; however their relative importance remains unclear. We assessed the extent to which mega-herbivore species controlled plant community composition and nutrient cycling, relative to other factors during and after the Late Quaternary extinction event in Britain and Ireland, when two-thirds of the region’s mega-herbivore species went extinct. Warmer temperatures, plant-soil and plant-plant interactions, and reduced burning contributed to the expansion of woody plants and...

Data from: Mutual fitness benefits arise during coevolution in a nematode-defensive microbe model

Charlotte Rafaluk-Mohr, Ben Ashby, Dylan A. Dahan & Kayla C. King
Species interactions can shift along the parasitism-mutualism continuum. However, the consequences of these transitions for coevolutionary interactions remain unclear. We experimentally coevolved a novel species interaction between Caenorhabditis elegans hosts and a mildly parasitic bacterium, Enterococcus faecalis, with host-protective properties against virulent Staphylococcus aureus. Coinfections drove the evolutionary transition of the C.elegans-E. faecalis relationship towards a reciprocally beneficial interaction. As E. faecalis evolved to protect nematodes against S. aureus infection, hosts adapted by accommodating greater...

Data from: Warming impacts on early life stages increase the vulnerability and delay the population recovery of a long-lived habitat-forming macroalga

Pol Capdevila, Bernat Hereu, Roberto Salguero-Gómez, Graciel·La Rovira, Alba Medrano, Emma Cebrian, Joaquim Garrabou, Diego K. Kersting & Cristina Linares
1. Understanding the combined effects of global and local stressors is crucial for conservation and management, yet challenging due to the different scales at which these stressors operate. Here we examine the effects of one of the most pervasive threats to marine biodiversity, ocean warming, on the early life stages of the habitat-forming macroalga Cystoseira zosteroides, its long-term consequences for population resilience and its combined effect with physical stressors. 2. First, we performed a controlled...

Data from: Explosive diversification of marine fishes at the Cretaceous-Paleogene boundary

Michael E. Alfaro, Brant C. Faircloth, Richard C. Harrington, Laurie Sorenson, Matt Friedman, Christine E. Thacker, Carl H. Oliveros, David Černý & Thomas J. Near
The Cretaceous–Palaeogene (K–Pg) mass extinction is linked to the rapid emergence of ecologically divergent higher taxa (for example, families and orders) across terrestrial vertebrates, but its impact on the diversification of marine vertebrates is less clear. Spiny-rayed fishes (Acanthomorpha) provide an ideal system for exploring the effects of the K–Pg on fish diversification, yet despite decades of morphological and molecular phylogenetic efforts, resolution of both early diverging lineages and enormously diverse subclades remains problematic. Recent...

Data from: Body ownership and agency altered by an electromyographically-controlled robotic arm

Yuki Sato, Toshihiro Kawase, Kouji Takano, Charles Spence & Kenji Kansaku
Understanding how we consciously experience our bodies is a fundamental issue in cognitive neuroscience. Two fundamental components of this are the sense of body ownership (the experience of the body as one’s own) and the sense of agency (the feeling of control over one’s bodily actions). These constructs have been used to investigate the incorporation of prostheses. To date, however, no evidence has been provided showing whether representations of ownership and agency in amputees are...

Registration Year

  • 2018
    98

Resource Types

  • Dataset
    92
  • Text
    6

Affiliations

  • University of Oxford
    98
  • University of Zurich
    7
  • University of Minnesota
    4
  • Australian National University
    4
  • University of Edinburgh
    4
  • University of Exeter
    4
  • Durham University
    3
  • University of Sheffield
    3
  • National Museum
    2
  • University of Sussex
    2