44 Works

Support for the habitat amount hypothesis from a global synthesis of species density studies

James Watling, Víctor Arroyo-Rodríguez, Marion Pfeifer, Lander Baeten, Cristina Banks-Leite, Laura Cisneros, Rebecca Fang, Caroli Hamel-Leigue, Thibault Lachat, Inara Leal, Luc Lens, Hugh Possingham, Dinarzarde Raheem, Danilo Ribeiro, Eleanor Slade, Nicolas Urbina-Cardona, Eric Wood & Lenore Fahrig
Decades of research suggest that species richness depends on spatial characteristics of habitat patches, especially their size and isolation. In contrast, the habitat amount hypothesis predicts that: 1) species richness in plots of fixed size (species density) is more strongly and positively related to the amount of habitat around the plot than to patch size or isolation; 2) habitat amount better predicts species density than patch size and isolation combined, 3) there is no effect...

High Carbon Stock stratification of the SAFE project site, Sabah, Malaysian Borneo, 2015 [HMTF]

N.J. Deere, G. Guillera-Arroita, E.L. Baking, H. Bernard, M. Pfeifer, G. Reynolds, O.R. Wearn, Z.G. Davies & M.J. Struebig
This data set provides a spatial stratification of forest cover into discrete vegetation classes according to the High Carbon Stock (HCS) Approach. The data set covers the Stability of Altered Forest Ecosystems (SAFE) project site located in Sabah, Malaysian Borneo. Data were collected in 2015 during a project which was included in the NERC Human-modified tropical forest (HMTF) programme.

Community antimicrobial resistance genes and concentrations of polycyclic aromatic hydrocarbons and metals in NE England soils (2016)

C.W. Knapp, D.W. Graham, M. Cooke, C. McCann, Y.-G. Zhu & J. Su
The dataset collates the relative concentration of nearly 300 antimicrobial resistance (AMR) genes, and concentrations of polycyclic aromatic compounds (PAH) and potentially toxic elements (PTE; e.g., “metals”) found in soils across northeastern England during a sampling expedition in June 2016 by researchers at Newcastle University. Top soils (15cm depths; “A” horizon) were obtained from 24 rural and urban locations around Newcastle upon Tyne, representing a spectrum of landscape conditions relative to anticipated PTE contamination. There...

Antibiotic resistance genes found in soils across the entire Scottish landscape (2007-10)

C.W. Knapp, D.W. Graham, T. Freitag, E. Pagaling, R. Hough, L. Avery, Y.-G. Zhu, J. Su & X.Y. Zhou
The dataset collates the relative concentration of nearly 300 antimicrobial resistance (AMR) genes found in soil locations across Scotland. Soils were obtained from the National Soils Inventory of Scotland (NSIS2), from which the total community DNA were extracted and provided to assess AMR gene content. Sampling of the NSIS2 was conducted between 2007-2010 at 183 soil locations representing intersections of a 20km grid across all of Scotland. For each sample, nearly 300 AMR genes were...

Mammal detection data for the SAFE project site, Sabah, Malaysian Borneo, 2015 [HMTF]

N.J. Deere, G. Guillera-Arroita, E.L. Baking, H. Bernard, M. Pfeifer, G. Reynolds, O.R. Wearn, Z.G. Davies & M.J. Struebig
This data set contains stacked detection matrices for 28 recorded mammal species across 115 sampling locations at the Stability of Altered Forest Ecosystems (SAFE) project site located in Sabah, Malaysian Borneo. Information for each camera trap sampling location, including spatial information and sampling effort is included. Data were collected in order to determine the contribution of carbon-based policies to biodiversity conservation in agricultural land-use mosaics. These data are essential to the development of the occupancy...

Soil bacterial cell counts and moisture content from a water stress experiment [NERC Soil Biodiversity Programme]

R.I. Griffiths, A.S. Whiteley, A.G. O'Donnell, M.J. Bailey, D. Mayoux & G. Burt-Smith
These data comprise culturable cell counts in different media from soil microbial analysis within a microcosm experiment investigating moisture perturbations on microbes, set up at the Centre for Ecology & Hydrology, Oxford. The experiment used soil turves from outside the main experimental plots at Sourhope, Scotland, collected in July 2001. Soil moisture data are also included. Data were collected as part of the NERC Soil Biodiversity Thematic Programme, established in 1999 and centred upon the...

Hydrological modelling and simulation data for the River Trent at Colwick under climate change

E.A. Byers, A. Leathard, G.M. O'Donnell, J.W. Hall & J.M. Amezaga
This data contains the time series flow discharge results of hydrological simulation of the River Trent at Colwick using UKCP09 Weather Generator inputs for a variety of time slices and emissions scenarios. The Weather Generator (WG) inputs were run on a hydrological model (Leathard et al., unpublished), calibrated using the observed record 1961-2002. Each simulation is derived from 100 30-year time series of weather at the WG location 4400355 for Control, Low, Medium and High...

Moth abundance and pollen transport from lit and unlit matched pairs of arable field margins in south-east England

C.J. Macgregor, D.M. Evans, R. Fox & M.J.O. Pocock
This dataset contains information about moth abundance and pollen transport at sites lit by high-pressure sodium streetlights and unlit control sites. Moths were sampled at 20 matched pairs of lit and unlit sites within 40 km of Wallingford, Oxfordshire, UK (51°35' N, 1°8' W) during 2014, as part of a study of the effects of street lighting on moths and nocturnal pollen transport. Three sampling methods were used: night-time transects, light-traps and overhead flight activity...

Substrate utilisation profiles and moisture content data from soil sampled in an upland grassland experiment at Sourhope, Scotland [NERC Soil Biodiversity Programme]

R.I. Griffiths, A. S. Whiteley, A. G. O'Donnell, M. J. Bailey & S.M. Buckland
These data comprise substrate utilisation profiles (using the BIOLOG gram-negative method) and moisture content data from soil sampled in an upland grassland experiment at Sourhope, Scotland. BIOLOG-GN (gram-negative) substrate utilisation analyses were used to give an indication of the ability of a subset of the bacterial community to utilise various carbon sources. These data include both temporal and spatial diversity in different depths of semi-natural grassland soil cores collected at different sample dates. Samples were...

Gridded estimates of hourly areal rainfall for Great Britain (1990-2014) [CEH-GEAR1hr]

E. Lewis, N. Quinn, S. Blenkinsop, H.J. Fowler, J. Freer, M. Tanguy, O. Hitt, G. Coxon, P. Bates & R. Woods
The dataset contains 1km gridded estimates of hourly rainfall for Great-Britain for the period 1990-2014. The estimates are derived by applying the nearest neighbour interpolation method to a national database of hourly raingauge observations collated by Newcastle University and the Centre for Ecology & Hydrology (CEH). These interpolated hourly estimates were then used to temporally disaggregate the CEH-GEAR daily rainfall dataset. The estimated rainfall on a given hour refers to the rainfall amount accumulated in...

Bacterial community structure and soil process data from a sewage sludge amended upland grassland soil experiment, 2000 [NERC Soil Biodiversity Programme]

N.D. Gray, R.C. Hastings, S.K. Sheppard, P. Loughnane, D. Lloyd, A.J. McCarthy & I.M. Head
This set of data comprises temporal temperature gradient electrophoresis (TTGE) and soil process measurements, used to analyse the effects of perturbations (sludge and/or lime application) on the structure, community development and activity of bacteria that catalyse fundamental processes in upland soils. These were collected to address the following questions: Do soil improvement treatments select for particular components of bacterial populations and hence drive community development? If so, at what functional and phylogenetic level is this...

Use of sea ice by arctic terns Sterna paradisaea in Antarctica and impacts of climate change

Chris P. F. Redfern & Richard M. Bevan
Arctic Terns spend their breeding and non-breeding seasons in polar environments at opposite ends of the world. The sensitivity of polar regions to climate change makes it essential to understand the ecology of Arctic Terns but the remoteness of the Antarctic presents a considerable challenge. One solution is to use ‘biologgers’ to monitor remotely their behaviour and distribution in the Antarctic. Data from birds tagged with light-level global location sensors (geolocators) in 2015 and 2017...

Data from: Profile of and risk factors for post-stroke cognitive impairment in diverse ethno-regional groups

Jessica W Lo, John D Crawford, David W Desmond, Olivier Godefroy, Hanna Jokinen, Simin Mahinrad, Hee-Joon Bae, Sebastian Köhler, Elles Douven, Julie Staals, Christopher Chen, Xin Xu, Eddie J Chong, Rufus O Akinyemi, Rajesh N Kalaria, Adesola Ogunniyi, Mélanie Barbay, Martine Roussel, Byung-Chul Lee, Velandai K Srikanth, Christopher Moran, Nagaendran Kandiah, Russell J Chander, Behnam Sabayan, J. Wouter Jukema … & Perminder S Sachdev
OBJECTIVE: To address the variability in prevalence estimates and inconsistencies in potential risk factors for post-stroke cognitive impairment (PSCI) using a standardised approach and individual participant data (IPD) from international cohorts in the STROKOG consortium. METHODS: We harmonised data from thirteen studies based in eight countries. Neuropsychological test scores 2 to 6 months after stroke or TIA and appropriate normative data were used to calculate standardised cognitive domain scores. Domain-specific impairment was based on percentile...

Data from: Probabilistic distances between trees

Maryam Garba, Tom M. W. Nye, Richard J. Boys, Maryam K Garba, Tom M W Nye & Richard J Boys
Most existing measures of distance between phylogenetic trees are based on the geometry or topology of the trees. Instead, we consider distance measures which are based on the underlying probability distributions on genetic sequence data induced by trees. Monte Carlo schemes are necessary to calculate these distances approximately, and we describe efficient sampling procedures. Key features of the distances are the ability to include substitution model parameters and to handle trees with different taxon sets...

Data from: A dynamic framework for the study of optimal birth intervals reveals the importance of sibling competition and mortality risks

Matthew G. Thomas, Daryl P. Shanley, Alasdair I. Houston, John M. McNamara, Ruth Mace, Tom B. L. Kirkwood, A. I. Houston, M. G. Thomas, R. Mace, D. P. Shanley & T. B. L. Kirkwood
Human reproductive patterns have been well studied, but the mechanisms by which physiology, ecology and existing kin interact to affect the life history need quantification. Here, we create a model to investigate how age-specific interbirth intervals adapt to environmental and intrinsic mortality, and how birth patterns can be shaped by competition and help between siblings. The model provides a flexible framework for studying the processes underlying human reproductive scheduling. We developed a state-based optimality model...

Data from: A congruent phylogenomic signal places eukaryotes within the Archaea.

Tom A. Williams, Peter G. Foster, Tom M. W. Nye, Cymon J. Cox, T. Martin Embley, T. M. W. Nye, T. A. Williams, P. G. Foster, T. M. Embley & C. J. Cox
Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook 'three domains' tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes within the Archaea, as the nearest relatives of different archaeal lineages. We compared the...

Data from: Drosophila studies support a role for a presynaptic synaptotagmin mutation in a human congenital myasthenic syndrome

Mallory C. Shields, Matthew R. Bowers, McKenzie M. Fulcer, Madelyn K. Bollig, Patrick J. Rock, Bryan R. Sutton, Alysia D. Vrailas-Mortimer, Hanns Lochmüller, Roger G. Whittaker, Rita Horvath & Noreen E. Reist
During chemical transmission, the function of synaptic proteins must be coordinated to efficiently release neurotransmitter. Synaptotagmin 2, the Ca2+ sensor for fast, synchronized neurotransmitter release at the human neuromuscular junction, has recently been implicated in a dominantly inherited congenital myasthenic syndrome associated with a non-progressive motor neuropathy. In one family, a proline residue within the C2B Ca2+-binding pocket of synaptotagmin is replaced by a leucine. The functional significance of this residue has not been investigated...

Data from: Quantitative analysis of the complete larval settlement process confirms Crisp’s model of surface selectivity by barnacles

Nick Aldred, Ahmad Alsaab & Anthony S. Clare
For barnacle cypris larvae at the point of settlement, selection of an appropriate surface is critical. Since post-settlement relocation is usually impossible, barnacles have evolved finely-tuned surface sensing capabilities to identify suitable substrata, and a temporary adhesion system for extensive surface exploration. The pattern of exploratory behaviour appears complex and may last for several hours, imposing significant barriers to quantitative measurement. Here, we employ a novel tracking system that enables simultaneous analysis of the larval...

Data from: Explaining sex differences in lifespan in terms of optimal energy allocation in the baboon

Annette Maria King, Thomas B.L. Kirkwood, Daryl P. Shanley, Annette M. King & Thomas B. L. Kirkwood
We provide a quantitative test of the hypothesis that sex role specialisation may account for sex differences in lifespan in baboons if such specialisation causes the dependency of fitness upon longevity, and consequently the optimal resolution to an energetic trade-off between somatic maintenance and other physiological functions, to differ between males and females. We present a model in which females provide all offspring care and males compete for access to reproductive females and in which...

Data from: Distorted views of biodiversity: spatial and temporal bias in species occurrence data

Elizabeth H. Boakes, Philip J. K. McGowan, Richard A. Fuller, Ding Chang-Qing, Natalie E. Clark, Kim O'Connor & Georgina M. Mace
Historical as well as current data on species distributions are needed to track changes in biodiversity. Species distribution data are found in a variety of sources but is likely that they include different biases towards certain time periods or places. By collating a large historical database of ~170,000 records of species in the avian order Galliformes dating back over two centuries and covering Europe and Asia, we investigate patterns of spatial and temporal bias in...

Data from: The core planar cell polarity gene, Vangl2, directs adult corneal epithelial cell alignment and migration

Amy S. Findlay, D. Alessio Panzica, Petr Walczysko, Amy B. Holt, Deborah J. Henderson, John D. West, Ann M. Rajnicek & J. Martin Collinson
This study shows that the core planar cell polarity (PCP) genes direct the aligned cell migration in the adult corneal epithelium, a stratified squamous epithelium on the outer surface of the vertebrate eye. Expression of multiple core PCP genes was demonstrated in the adult corneal epithelium. PCP components were manipulated genetically and pharmacologically in human and mouse corneal epithelial cells in vivo and in vitro. Knockdown of VANGL2 reduced the directional component of migration of...

Data from: Control of parental investment changes plastically over time with residual reproductive value

Mamoru Takata, Hayato Doi, Cathleen E. Thomas, Satoshi Koyama, M. Takata, H. Doi, S. Koyama & C. E. Thomas
Evolutionary conflict between parents and offspring over parental resource investment is a significant selective force on the traits of both parents and offspring. Empirical studies have shown that for some species, the amount of parental investment is controlled by the parents, whereas in other species, it is controlled by the offspring. The main difference between these two strategies is the residual reproductive value of the parents or opportunities for future reproduction. Therefore, this could explain...

Data from: Cytokine responses in birds challenged with the human food-borne pathogen Campylobacter jejuni implies a Th17 response

William D. K. Reid, Andrew J. Close, Suzanne Humphrey, Gemma Chaloner, Lizeth Lacharme-Lora, Lisa Rothwell, Pete Kaiser, Nicola J. Williams, Thomas J. Humprey, Paul Wigley, Stephen P. Rushton & Tom J. Humphrey
Development of process orientated understanding of cytokine interactions within the gastrointestinal tract during an immune response to pathogens requires experimentation and statistical modelling. The immune response against pathogen challenge depends on the specific threat to the host. Here, we show that broiler chickens mount a breed-dependent immune response to Campylobacter jejuni infection in the caeca by analysing experimental data using frequentist and Bayesian structural equation models (SEM). SEM provides a framework by which cytokine interdependencies,...

Data from: Plant toxin levels in nectar vary spatially across native and introduced populations

Paul A. Egan, Phillip C. Stevenson, Erin Jo Tiedeken, Geraldine A. Wright, Fabio Boylan & Jane C. Stout
Secondary compounds in nectar can function as toxic chemical defences against floral antagonists, but may also mediate plant-pollinator interactions. Despite their ecological importance, few studies have investigated patterns of spatial variation in toxic nectar compounds in plant species, and none outside their native range. Grayanotoxin I (GTX I) occurs in nectar of invasive Rhododendron ponticum where it is toxic to honeybees and some solitary bee species. We examined (i) geographic variation in the composition of...

Data from: Plumage colouration and social context influence male investment in song

Lindsay J. Henderson, Kathleen R. Brazeal, Thomas P. Hahn & L. J. Henderson
Animals use multiple signals to attract mates, including elaborate song, brightly coloured ornaments and physical displays. Female birds often prefer both elaborate male song, and intense carotenoid-based plumage colouration. This could lead less visually ornamented males to increase song production to maximize their attractiveness to females. We tested this possibility in the highly social and non-territorial house finch (Haemorhous mexicanus), in which females discriminate among males based on both song, and on the intensity of...

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  • Newcastle University
  • UK Centre for Ecology & Hydrology
  • University of Queensland
  • University of Edinburgh
  • University of Bristol
  • University of Oxford
  • Bangor University
  • University of Newcastle Australia
  • University of Strathclyde
  • University of Kent
  • Natural History Museum
  • University of Melbourne
  • Leiden University
  • University of Helsinki
  • Universiti of Malaysia Sabah