92 Works

Data from: Genetic diversity and cross-species transmission of kobuviruses in Vietnam

Lu Lu, Nguyen Van Dung, Alisdair Ivens, Carlijn Bogaardt, Aine O'Toole, Juliet E. Bryant, Juan Carrique-Mas, Nguyen Van Cuong, Pham Honh Anh, Maia A. Rabaa, Ngo Tri Tue, Guy E. Thwaites, Stephen Baker, Peter Simmonds & Mark Ej Woolhouse
Cross-species transmission of viruses poses a sustained threat to public health. Due to increased contact between humans and other animal species the possibility exists for cross-species transmissions and ensuing disease outbreaks. By using conventional PCR amplification and next generation sequencing (NGS), we obtained 130 partial or full genome kobuvirus sequences from humans in a sentinel cohort in Vietnam and various mammalian hosts including bats, rodents, pigs, cats, and civets. The evolution of kobuviruses in different...

Data from: Collision and annihilation of nonlinear sound waves and action potentials at interfaces

Shamit Shrivastava, Kevin H. Kang & Matthias F. Schneider
Nerve impulses, previously proposed as manifestations of nonlinear acoustic pulses localized at the plasma membrane, can annihilate upon collision. However, whether annihilation of acoustic waves at interfaces takes place is unclear. We previously showed the propagation of nonlinear sound waves that propagate as solitary waves above a threshold (super-threshold) excitation in a lipid monolayer near a phase transition. Here we investigate the interaction of these waves. Sound waves were excited mechanically via a piezo cantilever...

Data from: In-situ recording of ionic currents in projection neurons and Kenyon cells in the olfactory pathway of the honeybee

Jan Kropf, Wolfgang Roessler & Wolfgang Rössler
The honeybee olfactory pathway comprises an intriguing pattern of convergence and divergence: ~60.000 olfactory sensory neurons (OSN) convey olfactory information on ~900 projection neurons (PN) in the antennal lobe (AL). To transmit this information reliably, PNs employ relatively high spiking frequencies with complex patterns. PNs project via a dual olfactory pathway to the mushroom bodies (MB). This pathway comprises the medial (m-ALT) and the lateral antennal lobe tract (l-ALT). PNs from both tracts transmit information...

Data from: Living on the edge: multiscale habitat selection by cheetahs in a human-wildlife landscape

Britt Klaassen & Femke Broekhuis
Animals select habitats that will ultimately optimise their fitness through access to favourable resources, such as food, mates, and breeding sites. However, access to these resources may be limited by bottom-up effects, such as availability, and top-down effects such as risk avoidance and competition, including that with humans. Competition between wildlife and people over resources, specifically over space, has played a significant role in the worldwide decrease of large carnivores. The goal of this study...

Data from: Ecological correlates of the spatial co-occurrence of sympatric mammalian carnivores worldwide

Courtney L. Davis, Lindsey N. Rich, Zach J. Farris, Marcella J. Kelly, Mario S. Di Bitetti, Yamil Di Blanco, Sebastian Albanesi, Mohammad S. Farhadinia, Navid Gholikhani, Sandra Hamel, Bart J. Harmsen, Claudia Wultsch, Mamadou D. Kane, Quinton Martins, Asia J. Murphy, Robin Steenweg, S. Sunarto, Atieh Taktehrani, Kanchan Thapa, Jody M. Tucker, Jesse Whittington, Febri A. Widodo, Nigel G. Yoccoz & David A.W. Miller
The composition of local mammalian carnivore communities has far-reaching effects on terrestrial ecosystems worldwide. To better understand how carnivore communities are structured, we analyzed camera trap data for 108,087 trap days across 12 countries spanning 5 continents. We estimate local probabilities of co-occurrence among 768 species pairs from the order Carnivora and evaluate how shared ecological traits correlated with probabilities of co-occurrence. Within individual study areas, species pairs co-occurred more frequently than expected at random....

Data from: Internal cranial anatomy of Early Triassic species of †Saurichthys (Actinopterygii: †Saurichthyiformes): implications for the phylogenetic placement of †saurichthyiforms

Thodoris Argyriou, Sam Giles, Matt Friedman, Carlo Romano, Ilja Kogan & Marcelo R. Sanchez-Villagra
Background: †Saurichthyiformes was a successful group of latest Permian-Middle Jurassic predatory actinopterygian fishes and constituted important and widely-distributed components of Triassic marine and freshwater faunas. Their systematic affinities have long been debated, with †saurichthyiforms often being aligned with chondrosteans, a group today comprising sturgeons and paddlefishes. However, their character-rich endocranial anatomy has not been investigated in detail since the first half of the 20th century. Since that time, major advances have occurred in terms of...

Data from: Dogs accompanied humans during the Neolithic expansion into Europe

Morgane Ollivier, Anne Tresset, Laurent A. F. Frantz, Stéphanie Brehard, Adrian Bălășescu, Marjan Mashkour, Adina Boroneant, Maud Pionnier-Capitan, Ophelie Lebrasseur, Rose-Marie Arbogast, László Bartosiewicz, Karyne Debue, Rivka Rabinovich, Mikhail V. Sablin, Greger Larson, Catherine Hänni, Christophe Hitte & Jean-Denis Vigne
Near Eastern Neolithic farmers introduced several species of domestic plants and animals as they dispersed into Europe. Dogs were the only domestic species present in both Europe and the Near East prior to the Neolithic. Here, we assessed whether early Near Eastern dogs possessed a unique mitochondrial lineage that differentiated them from Mesolithic European populations. We then analysed mitochondrial DNA sequences from 99 ancient European and Near-Eastern dogs spanning the Upper Palaeolithic to the Bronze...

Data from: Biophysical models reveal the relative importance of transporter proteins and impermeant anions in chloride homeostasis

Kira Michaela Düsterwald, Christopher Brian Currin, Richard Joseph Burman, Colin J. Akerman, Alan R. Kay & Joseph Valentino Raimondo
Fast synaptic inhibition in the nervous system depends on the transmembrane flux of Cl- ions based on the neuronal Cl- driving force. Established theories regarding the determinants of Cl- driving force have recently been questioned. Here we present biophysical models of Cl- homeostasis using the pump-leak model. Using numerical and novel analytic solutions, we demonstrate that the Na+/K+-ATPase, ion conductances, impermeant anions, electrodiffusion, water fluxes and cation-chloride cotransporters (CCCs) play roles in setting the Cl-...

Data from: Functional heterogeneity within the rodent lateral orbitofrontal cortex dissociates outcome devaluation and reversal learning deficits

Marios C Panayi & Simon Killcross
The orbitofrontal cortex (OFC) is critical for updating reward-directed behaviours flexibly when outcomes are devalued or when task contingencies are reversed. Failure to update behaviour in outcome devaluation and reversal learning procedures are considered canonical deficits following OFC lesions in non-human primates and rodents. We examined the generality of these findings in rodents using lesions of the rodent lateral OFC (LO) in instrumental action-outcome and Pavlovian cue-outcome devaluation procedures. LO lesions disrupted outcome devaluation in...

Data from: Ordinal vs dichotomous analyses of modified Rankin Scale and 5-year outcome and cost of stroke

Aravind Ganesh, Ramon Luengo-Fernandez, Rose M. Wharton & Peter M. Rothwell
Objective – To compare how three common representations (ordinal versus dichotomized as 0-1/2-6 or 0-2/3-6) of the modified Rankin Scale (mRS) – a commonly-used trial outcome measure – relate to long-term outcomes, and quantify trial ineligibility rates based on pre-morbid mRS. Methods – In consecutive ischaemic stroke patients in a population-based, prospective cohort study (Oxford Vascular Study; 2002-2014), we related 3-month mRS to 1-year and 5-year disability and death (logistic regressions), and health/social-care costs (generalized...

Data from: Unravelling the history of hepatitis B virus genotypes A and D infection using a full-genome phylogenetic and phylogeographic approach

Evangelia-Georgia Kostaki, Timokratis Karamitros, Garyfallia Stefanou, Ioannis Mamais, Konstantinos Angelis, Angelos Hatzakis, Anna Kramvis & Dimitrios Paraskevis
Hepatitis B virus (HBV) infection constitutes a global public health problem. In order to establish how HBV was disseminated across different geographic regions, we estimated the levels of regional clustering for genotypes D and A. We used 916 HBV-D and 493 HBV-A full-length sequences to reconstruct their global phylogeny. Phylogeographic analysis was conducted by reconstruction of ancestral states using the criterion of parsimony. The putative origin of genotype D was in North Africa/Middle East. HBV-D...

Data from: Strong responses from weakly interacting species

Sean Tuck, Janielle Porter, Mark Rees, Lindsay A. Turnbull & Sean L. Tuck
The impact of species loss from competitive communities partly depends on how populations of the surviving species respond. Predicting the response should be straightforward using models that describe population growth as a function of competitor densities; but these models require accurate estimates of interaction strengths. Here, we quantified how well we could predict responses to competitor removal in a community of annual plants, using a combination of observation and experiment. It was straightforward to fit...

Data from: A simulation-based approach to statistical alignment

Eli Levy Karin, Haim Ashkenazy, Jotun Hein & Tal Pupko
Classic alignment algorithms utilize scoring functions which maximize similarity or minimize edit distances. These scoring functions account for both insertion-deletion (indel) and substitution events. In contrast, alignments based on stochastic models aim to explicitly describe the evolutionary dynamics of sequences by inferring relevant probabilistic parameters from input sequences. Despite advances in stochastic modeling during the last two decades, scoring-based methods are still dominant, partially due to slow running times of probabilistic approaches. Alignment inference using...

Data from: Competitive asymmetry and local adaptation in Trinidadian guppies

Tomos Potter, Leighton King, Joseph Travis & Ronald D. Bassar
1. The outcome of competition between individuals often depends on body-size. These competitive asymmetries can drive variation in demographic rates, influencing the ecology and evolution of life-histories. The magnitude and direction of such asymmetries differ among taxa, yet little is known empirically about how adaptation to resource limitation alters competitive asymmetries. 2. Here, we investigate the relationship between size-dependent competitive ability and adaptation to resource limitation. 3. We examined size-dependent competition in two ecotypes of...

Data from: A new actinopterygian from the Late Devonian Gogo Formation, Western Australia

Brian Choo, Jing Lu, Sam Giles, Kate Trinajstic & John A. Long
The study of early actinopterygians (ray-finned fishes) from the Devonian has been hampered by imperfect preservation in the majority of taxa. The Late Devonian (early Frasnian) Gogo Formation of north-western Western Australia is notable in producing complete fossil actinopterygians with exceptional three-dimensional preservation of both the dermal and endoskeletal anatomy. Four taxa have been described and have proved invaluable in understanding the anatomy of early representatives of this clade. Here, we present a fifth Gogo...

Data from: The application of self-limiting transgenic insects in managing resistance in experimental metapopulations

Liqin Zhou, Nina Alphey, Adam S. Walker, Laura M. Travers, Neil I. Morrison, Michael B. Bonsall & Ben Raymond
1. The mass release of transgenic insects carrying female lethal self-limiting genes can reduce pest insect populations. Theoretically, substantial releases can be a novel resistance management tool, since wild type alleles conferring susceptibility to pesticides can dilute resistance alleles in target populations. A potential barrier to the deployment of this technology is the need for large-scale area wide releases. Here we address whether localized releases of transgenic insects could provide an alternative, means of population...

Data from: Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

Laurent A. F. Frantz, Anna Rudzinski, Abang Mansyursyah Surya Nugraha, Allowen Evin, James Burton, Ardern Hulme-Beaman, Anna Linderholm, Ross Barnett, Rodrigo Vega, Evan K. Irving-Pease, James Haile, Richard Allen, Kristin Leus, Jill Shephard, Mia Hillyer, Sarah Gillemot, Jeroen Van Den Hurk, Sharron Ogle, Cristina Atofanei, Mark G. Thomas, Friederike Johansson, Abdul Haris Mustari, John Williams, Kusdiantoro Mohamad, Chandramaya Siska Damayanti … & Greger Larson
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions...

Data from: Low siring success of females with an acquired male function illustrates the legacy of sexual dimorphism in constraining the breakdown of dioecy

Luis Santos Del Blanco, Eleri Tudor & John R. Pannell
Evolutionary transitions from dioecy to functional hermaphroditism must overcome the inertia of sexual dimorphism because modified males or females will express the opposite sexual function for which their phenotypes have been optimized. We tested this prediction by assessing the siring success of monoecious individuals of the plant Mercurialis annua with an acquired male function but that are phenotypically still female-like. We found that pollen dispersed by female-like monoecious individuals was ~ 1/3 poorer at siring...

Data from: Variation in defence strategies in the metal hyperaccumulator Noccaea caerulescens is indicative of synergies and trade-offs between forms of defence

Helen N. Fones, Gail M. Preston & J. Andrew C. Smith
The metal hyperaccumulator, N. caerulescens, uses metals as a defence against pathogens. Earlier work has suggested both trade-offs and synergies between metals and inducible defences. Different populations of N. caerulescens vary in metal accumulation. Here, we test the hypothesis that this produces different outcomes in trade-offs between defences. We compare zinc concentrations, glucosinolate concentrations, and inducible stress responses, including ROS and cell death, in four N. caerulescens populations, and relate these to the growth of...

Data from: The insect-focused classification of fruit syndromes in tropical rainforests: an inter-continental comparison

Chris Dahl, Richard Ctvrtecka, Sofia Gripenberg, Owen T. Lewis, Simon T. Segar, Petr Klimes, Katerina Sam, Dominic Rinan, Jonah Filip, Roll Lilip, Pitoon Kongnoo, Montarika Panmeng, Sutipun Putnaul, Manat Reungaew, Marleny Rivera, Hector Barrios, Stuart J. Davies, Sarayudh Bunyavejchewin, Joseph S. Wright, George D. Weiblen, Vojtech Novotny & Yves Basset.
We propose a new classification of rainforest plants into eight fruit syndromes, based on fruit morphology and other traits relevant to fruit-feeding insects. This classification is compared with other systems based on plant morphology or traits relevant to vertebrate fruit dispersers. Our syndromes are based on fruits sampled from 1,192 plant species at three Forest Global Earth Observatory plots: Barro Colorado Island (Panama), Khao Chong (Thailand) and Wanang (Papua New Guinea). The three plots differed...

Data from: Completing the hybridization triangle: the inheritance of genetic incompatibilities during homoploid hybrid speciation in ragworts (Senecio).

Adrian C. Brennan, Simon J. Hiscock & Richard J. Abbott
A new homoploid hybrid lineage needs to establish a degree of reproductive isolation from its parent species if it is to persist as an independent entity, but the role hybridization plays in this process is known in only a handful of cases. The homoploid hybrid ragwort species, Senecio squalidus, (Oxford ragwort) originated following the introduction of hybrid plants to the UK approximately 320 years ago. The source of the hybrid plants was from a naturally...

Data from: No evidence for sibling or parent-offspring coadaptation in a wild population of blue tits, despite high power.

Caroline Thomson, Jarrod D. Hadfield & Caroline E. Thomson
Parent and offspring behaviours are expected to act as both the agents and targets of selection. This may generate parent-offspring coadaptation in which parent and offspring behaviours become genetically correlated in a way that increases inclusive fitness. Cross-fostering has been used to study parent-offspring coadaptation, with the prediction that offspring raised by non-relatives, or parents raising non-relatives, should suffer fitness costs. Using long-term data from more than 400 partially crossed broods of blue tits (Cyanistes...

Microclimate proxy measurements from a logging gradient in Malaysian Borneo

B. Blonder, S. Both, D.A. Coomes, D.M.O. Elias, T. Jucker, J. Kvasnica, N. Majalap, Y.S. Malhi, T. Riutta & M. Svátek
Temperatures recorded 5cm above the forest floor in a gridded design (1 to 13m distance) within three, 1 hectare forest plots in Sabah, Borneo. The dataset also includes air temperature data from a nearby weather station at the same temporal resolution, and spatially-interpolated measurements of topography and canopy structure in each forest plot at a 1m resolution. iButton temperature measurement 5cm above the forest floor in gridded design (1-13m distance) within three 1-ha forest plots...

Strain measurements on 21 trees in Wytham Woods, UK

T. Jackson
This data contains the strain and wind data collected for 21 trees in Wytham Woods, a mature temperate woodland in southern England, from September 2015 to June 2016. This data was collected in order to (a) extract the resonant frequencies of trees, (b) to estimate the critical wind speeds at which the trees would break and (c) to test a finite element model of tree-wind dynamics. The strain data was collected at 4Hz using two...

Avifauna occurrence data from a longitudinal experiment in human-modified Amazonian forests affected by the 2015-16 El Niño drought and associated fires

A. Lees, N. Moura, F.M. Franca, J.N. Ferreira, T. Gardner, E. Berenguer, L. Chesini, C. Andertti & J. Barlow
This data set includes longitudinal occurrence of bird species at 36 forest plots – half of which burned during the 2015-16 El Niño drought – distributed across a gradient of prior human disturbance in the Brazilian Amazon. Data was collected in 2010 and 2016 (around 6 years before, and one year after the 2015-16 El Niño, respectively) as part of the projects ‘Assessing ENSO-induced Fire Impacts in tropical Rainforest Ecosystems’ (AFIRE) and ‘Biodiversity and Ecosystem...

Registration Year

  • 2018
    92

Resource Types

  • Dataset
    92

Affiliations

  • University of Oxford
    92
  • 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