60 Works

High-resolution global topographic index values

T.R. Marthews, S.J. Dadson, B. Lehner, S. Abele & N. Gedney
The topographic index is a hydrological quantity describing the propensity of the soil at landscape points to become saturated with water as a result of topographic position (i.e. not accounting for other factors such as climate that also affect soil moisture but are accounted for separately). Modern land surface models require a characterisation of the land surface hydrological regime and this parameter allows the use of the TOPMODEL hydrological model to achieve this .This Geographic...

High-resolution hydraulic parameter maps for surface soils in tropical South America

T. Marthews, C.A. Quesada, D.R. Galbraith, Y. Malhi, C.E. Mullins, M.G. Hodnett & I. Dharssi
Spatial data files holding gridded parameter maps of surface soil hydraulic parameters derived from a selection of pedotransfer functions. Modern land surface model simulations capture soil profile water movement through the use of soil hydraulics sub-models, but good hydraulic parameterisations are often lacking - especially in the tropics - and it is this lack that we fill here in the context of South America. Optimal hydraulic parameter values are given for the Brooks and Corey,...

Data from: Dispersal and the transition to sympatry in vertebrates

Alex L. Pigot & Joseph A. Tobias
Under allopatric speciation models, a key step in the build-up of species richness is population dispersal leading to the co-occurrence of previously geographically isolated forms. Despite its central importance for community assembly, the extent to which the transition from spatial segregation (allopatry or parapatry) to coexistence (sympatry) is a predictable process, or alternatively one governed by chance and the vagaries of biogeographic history, remains poorly understood. Here, we use estimated divergence times and current patterns...

Data from: strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence

Mark A. Bell & Graeme T. Lloyd
strap (Stratigraphic Tree Analysis for Palaeontology) is a new package for the freely available statistical programming language R designed to perform three main tasks: (1) to time-scale phylogenies of fossil taxa; (2) to plot those time-scaled trees against stratigraphy; and (3) to assess congruence between phylogenies and stratigraphy. Time-scaling is performed with the DatePhylo function, with three approaches offered. Plotting trees against a choice of five different geological time scaless is possible using the geoscalePhylo...

Data from: Establishing macroecological trait datasets: digitalization, extrapolation, and validation of diet preferences in terrestrial mammals worldwide

Wilm Daniel Kissling, Lars Dalby, Camilla Fløjgaard, Jonathan Lenoir, Brody Sandel, Christopher Sandom, Kristian Trøjelsgaard, Jens-Christian Svenning & Jens-Christian Svenning
Ecological trait data are essential for understanding the broad-scale distribution of biodiversity and its response to global change. For animals, diet represents a fundamental aspect of species’ evolutionary adaptations, ecological and functional roles, and trophic interactions. However, the importance of diet for macroevolutionary and macroecological dynamics remains little explored, partly because of the lack of comprehensive trait datasets. We compiled and evaluated a comprehensive global dataset of diet preferences of mammals (“MammalDIET”). Diet information was...

Data from: Impacts of selective logging on inbreeding and gene flow in two Amazonian timber species with contrasting ecological and reproductive characteristics

Christina C. Vinson, Milton Kanashiro, Stephen A. Harris & Dave H. Boshier
Selective logging in Brazil allows for the removal of up to 90% of trees above 50 cm diameter of a given timber species, independent of a species’ life history characteristics or how quickly it will recover. The genetic and demographic effects of selective logging on two Amazonian timber species (Dipteryx odorata Leguminosae, Jacaranda copaia Bignoniaceae) with contrasting ecological and reproductive characteristics were assessed in the same forest. Genetic diversity and gene flow were characterized by...

Data from: Heterozygosity–fitness correlations in a wild mammal population: accounting for parental and environmental effects

Geetha Annavi, Chris Newman, Christina D. Buesching, David W. Macdonald, Terry Burke, Hannah L. Dugdale & Christopher Newman
HFCs (heterozygosity–fitness correlations) measure the direct relationship between an individual's genetic diversity and fitness. The effects of parental heterozygosity and the environment on HFCs are currently under-researched. We investigated these in a high-density U.K. population of European badgers (Meles meles), using a multimodel capture–mark–recapture framework and 35 microsatellite loci. We detected interannual variation in first-year, but not adult, survival probability. Adult females had higher annual survival probabilities than adult males. Cubs with more heterozygous fathers...

Data from: The importance of microhabitat for biodiversity sampling

Zia Mehrabi, Eleanor M. Slade, Angel Solis & Darren J. Mann
Responses to microhabitat are often neglected when ecologists sample animal indicator groups. Microhabitats may be particularly influential in non-passive biodiversity sampling methods, such as baited traps or light traps, and for certain taxonomic groups which respond to fine scale environmental variation, such as insects. Here we test the effects of microhabitat on measures of species diversity, guild structure and biomass of dung beetles, a widely used ecological indicator taxon. We demonstrate that choice of trap...

Data from: Pathogen burden, co-infection and major histocompatibility complex variability in the European badger (Meles meles)

Yung Wa Sin, Geetha Annavi, Hannah L. Dugdale, Chris Newman, Terry Burke & David W. Macdonald
Pathogen-mediated selection is thought to maintain the extreme diversity in the major histocompatibility complex (MHC) genes, operating through the heterozygote advantage, rare-allele advantage and fluctuating selection mechanisms. Heterozygote advantage (i.e., recognizing and binding a wider range of antigens than homozygotes) is expected to be more detectable when multiple pathogens are considered simultaneously. Here, we test if MHC diversity in a wild population of European badgers (Meles meles) is driven by pathogen-mediated selection. We examined individual...

Data from: The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach

Tom Vogwill & R. Craig MacLean
The evolution of antibiotic resistance carries a fitness cost, expressed in terms of reduced competitive ability in the absence of antibiotics. This cost plays a key role in the dynamics of resistance by generating selection against resistance when bacteria encounter an antibiotic-free environment. Previous work has shown that the cost of resistance is highly variable, but the underlying causes remain poorly understood. Here, we use a meta-analysis of the published resistance literature to determine how...

Data from: A Silurian short-great-appendage arthropod

Derek J. Siveter, Derek E. G. Briggs, David J. Siveter, Mark D. Sutton, David J. Legg, Sarah Joomun & D. Legg
A new arthropod, Enalikter aphson gen. et sp. nov., is described from the Silurian (Wenlock Series) Herefordshire Lagerstätte of the UK. It belongs to the Megacheira (=short-great-appendage group), which is recognized here, for the first time, in strata younger than mid-Cambrian age. Discovery of this new Silurian taxon allows us to identify a Devonian megacheiran representative, Bundenbachiellus giganteus from the Hunsrück Slate of Germany. The phylogenetic position of megacheirans is controversial: they have been interpreted...

Data from: Virtual reconstruction of endocast anatomy in early ray-finned fishes (Osteichthyes: Actinopterygii)

Sam Giles & Matt Friedman
Cranial endocasts, infillings of the skeletal void that once contained the brain and associated soft tissues, represent detailed anatomical structures that have long been the focus of paleontological investigation. We applied computed tomographics (CTs) in order to generate endocast models for the Paleozoic actinopterygian fishes Mimipiscis and Kentuckia, which serve as key representatives of anatomically primitive, early ray fins in analyses of early vertebrate relationships. The resultant endocranial models generally corroborate existing accounts of endocranial...

Data from: Linking system-wide impacts of RNA polymerase mutations to the fitness cost of rifampin resistance in Pseudomonas aeruginosa

Qin Qi, Gail M. Preston & R. Craig MacLean
Fitness costs play a key role in the evolutionary dynamics of antibiotic resistance in bacteria by generating selection against resistance in the absence of antibiotics. Although the genetic basis of antibiotic resistance is well understood, the precise molecular mechanisms linking the genetic basis of resistance to its fitness cost remain poorly characterized. Here, we examine how the system-wide impacts of mutations in the RNA polymerase (RNAP) gene rpoB shape the fitness cost of rifampin resistance...

Data from: An experimental study of strong reciprocity in bacteria

R. Fredrik Inglis, Stuart West & Angus Buckling
Strong reciprocity, whereby cooperators punish non-cooperators, may help to explain the evolutionary success of cooperative behaviours. However, theory suggests that selection for strong reciprocity can depend upon tight genetic linkage between cooperation and punishment, to avoid the strategy being outcompeted by non-punishing cooperators. We tested this hypothesis using experimental populations of the bacterium Pseudomonas aeruginosa, which cooperate by producing iron-scavenging siderophores and, in this context, punish non-cooperators with toxins. Consistent with theory, we show that...

Data from: Payoff-based learning explains the decline in cooperation in public goods games

Maxwell N. Burton-Chellew, Heinrich H. Nax & Stuart A. West
Economic games such as the public goods game are increasingly being used to measure social behaviours in humans and non-human primates. The results of such games have been used to argue that people are pro-social, and that humans are uniquely altruistic, willingly sacrificing their own welfare in order to benefit others. However, an alternative explanation for the empirical observations is that individuals are mistaken, but learn, during the game, how to improve their personal payoff....

Data from: Efficient inference of recombination hot regions in bacterial genomes

Koji Yahara, Xavier Didelot, M Azim. Ansari, Samuel K. Sheppard & Daniel Falush
In eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of “hotspots” of highly elevated recombination. In bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. Here we focus in particular on identifying “hot regions” of the genome where DNA is transferred frequently between isolates. We present a...

Data from: Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange, and distinct demographic histories

Mark J. Statham, Zhenghuan Wang, Carl D. Soulsbury, Jan Janecka, Benjamin N. Sacks, Keith B. Aubry, Oliver Berry, Ceiridwen J. Edwards & James Murdoch
Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin...

Data from: Long-term disturbance dynamics and resilience of tropical peat swamp forests

Lydia E. S. Cole, Shonil A. Bhagwat, Kathy J. Willis & Katherine J. Willis
1. The coastal peat swamp forests of Sarawak, Malaysian Borneo, are undergoing rapid conversion, predominantly into oil palm plantations. This wetland ecosystem is assumed to have experienced insignificant disturbance in the past, persisting under a single ecologically-stable regime. However, there is limited knowledge of the past disturbance regime, long-term functioning and fundamentally the resilience of this ecosystem to changing natural and anthropogenic perturbations through time. 2. In this study, long-term ecological data sets from three...

Data from: An experimental test of whether cheating is context dependent

Melanie Ghoul, Stuart A. West, Steve P. Diggle & Ashleigh S. Griffin
Microbial cells rely on cooperative behaviours that can breakdown as a result of exploitation by cheats. Recent work on cheating in microbes, however, has produced examples of populations benefiting from the presence of cheats and/or cooperative behaviours being maintained despite the presence of cheats. These observations have been presented as evidence for selection favouring cheating at the population level. This apparent contradiction arises when cheating is defined simply by the reduced expression of a cooperative...

Data from: Evidence of land-sea transfer of the zoonotic pathogen Campylobacter to a wildlife marine sentinel species

Johanna L. Baily, Guillaume Méric, Sion Bayliss, Geoffrey Foster, Simon E. Moss, Eleanor Watson, Ben Pascoe, Jane Mikhail, Robert J. Goldstone, Romain Pizzi, David G. E. Smith, Kim Willoughby, Alisa J. Hall, Mark P. Dagleish, Samuel K. Sheppard & Ailsa J. Hall
Environmental pollution often accompanies the expansion and urbanization of human populations where sewage and wastewaters commonly have an impact on the marine environments. Here, we explored the potential for faecal bacterial pathogens, of anthropic origin, to spread to marine wildlife in coastal areas. The common zoonotic bacterium Campylobacter was isolated from grey seals (Halichoerus grypus), an important sentinel species for environmental pollution, and compared to isolates from wild birds, agricultural sources and clinical samples to...

Data from: The early spread and epidemic ignition of HIV-1 in human populations

Nuno R. Faria, Andrew Rambaut, Marc A. Suchard, Guy Baele, Trevor Bedford, Melissa J. Ward, Andrew J. Tatem, João D. Sousa, Nimalan Arinaminpathy, Jacques Pépin, David Posada, Martine Peeters, Oliver P. Pybus & Philippe Lemey
Thirty years after the discovery of HIV-1, the early transmission, dissemination and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M...

Data from: Automated stitching of microtubule centerlines across serial electron tomograms

Britta Weber, Erin M. Tranfield, Johanna L. Höög, Daniel Baum, Claude Antony, Tony Hyman, Jean-Marc Verbavatz & Steffen Prohaska
Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed...

Data from: Spiders spinning electrically charged nano-fibres

Katrin Kronenberger & Fritz Vollrath
Most spider threads are on the micrometre and sub-micrometre scale. Yet, there are some spiders that spin true nano-scale fibres such as the cribellate orb spider, Uloborus plumipes. Here, we analyse the highly specialized capture silk-spinning system of this spider and compare it with the silk extrusion systems of the more standard spider dragline threads. The cribellar silk extrusion system consists of tiny, morphologically basic glands each terminating through exceptionally long and narrow ducts in...

Data from: Neuraminidase inhibitors for preventing and treating influenza in healthy adults and children

Tom Jefferson, Mark A. Jones, Peter Doshi, Chris B. Del Mar, Rokuro Hama, Matthew J. Thompson, Elizabeth A. Spencer, Igho Onakpoya, Kamal R. Mahtani, David Nunan, Jeremy Howick, Carl J. Heneghan & Igho J Onakpoya
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN TWO OTHER ARTICLES. PLEASE SEE http://dx.doi.org/10.1136/bmj.g2547 AND http://dx.doi.org/10.1136/bmj.g2545 FOR MORE INFORMATION. Background: Neuraminidase inhibitors (NIs) are stockpiled and recommended by public health agencies for treating and preventing seasonal and pandemic influenza. They are used clinically worldwide. Objectives: To describe the potential benefits and harms of NIs for influenza in all age groups by reviewing all clinical study reports of published and unpublished randomised, placebo-controlled trials and...

Data from: Ecological causes of multi-level covariance between size and first-year survival in a wild bird population

Sandra Bouwhuis, Oscar Vedder, Colin J. Garroway & Ben C. Sheldon
1. Estimates of selection in natural populations are frequent but our understanding of ecological causes of selection, and causes of variation in the direction, strength and form of selection, is limited. 2. Here, we apply a multi-level framework to partition effects of great tit fledging mass on first-year survival to hierarchical levels and quantify their ecological dependence using a data set spanning 51 years. 3. We show that estimates of the effect of fledging mass...

Registration Year

  • 2014
    60

Resource Types

  • Dataset
    60

Affiliations

  • University of Oxford
    60
  • University of Groningen
    4
  • French National Centre for Scientific Research
    3
  • University of St Andrews
    3
  • Yale University
    3
  • Harvard University
    3
  • University of Exeter
    3
  • University of Helsinki
    3
  • Imperial College London
    3
  • Swiss Federal Institute of Technology in Zurich
    3