49 Works

Methane fluxes from peatland plateaus and thawing peatland plateaus and from burnt and unburnt forests from permafrost in subarctic Canada

M.A. Cooper, C. Estop-Aragones, J.P. Fisher, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This dataset contains methane fluxes from peatland plateaus and thawing peatland plateaus and from burnt and unburnt forests from permafrost in subarctic Canada. Methane fluxes were monitored during summer in 2013 and 2014 in Yukon and Northwest Territories. Monitored sites included peatland plateaus and thawing features of peatland plateaus.

Soil dates using 210Pb in profiles from permafrost in subarctic Canada

C. Estop-Aragones, J.P. Fisher, M.A. Cooper, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This dataset consists of soils dated using 210Pb in profiles from permafrost in subarctic Canada. Soil cores were sampled during early summer in 2013 and 2014 from peatland plateaus, thawing peatland plateaus, burnt and unburnt black spruce forests in Yukon and Northwest Territories. The upper part of the soil profile was dated using 210Pb to quantify recent carbon accumulation rates.

Data from: Conserved genetic architecture underlying recombination rate variation in a wild population of Soay sheep (Ovis aries)

Susan E. Johnston, Camillo Bérénos, Jon Slate & Josephine M. Pemberton
Meiotic recombination breaks down linkage disequilibrium and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and for understanding the potential of a population to respond to selection. However, despite attention in model systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here, we used...

Data from: How reliably can we infer diversity-dependent diversification from phylogenies?

Rampal S. Etienne, Alex L. Pigot, Albert Phillimore & Albert B. Phillimore
Slowdowns in lineage accumulation in phylogenies suggest that speciation rates decline as diversity increases. Likelihood methods have been developed to detect such diversity dependence. However, a thorough test of whether such approaches correctly infer diversity dependence is lacking. Here, we simulate phylogenetic branching under linear negative diversity-dependent and diversity-independent models and estimate from the simulated phylogenies the maximum-likelihood parameters for three different conditionings – on survival of the birth–death process given the crown age, on...

Data from: Differential gene expression according to race and host plant in the pea aphid

Isobel Eyres, Julie Jaquiéry, Akiko Sugio, Ludovic Duvaux, Karim Gharbi, Jing-Jiang Zhou, Fabrice Legeai, Michaela Nelson, Jean-Christophe Simon, Carole M. Smadja, Roger Butlin & Julia Ferrari
Host-race formation in phytophagous insects is thought to provide the opportunity for local adaptation and subsequent ecological speciation. Studying gene expression differences amongst host races may help to identify phenotypes under (or resulting from) divergent selection and their genetic, molecular and physiological bases. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on numerous plants in the Fabaceae and provides a unique system for examining the early stages of diversification along a gradient of genetic...

Data from: Recombination changes at the boundaries of fully and partially sex-linked regions between closely related Silene species pairs

Jose L. Campos, Suo Qiu, Sara Guirao-Rico, Roberta Bergero & Deborah Charlesworth
The establishment of a region of suppressed recombination is a critical change during sex chromosome evolution, leading to such properties as Y (and W) chromosome genetic degeneration, accumulation of repetitive sequences and heteromorphism. Although chromosome inversions can cause large regions to have suppressed recombination, and inversions are sometimes involved in sex chromosome evolution, gradual expansion of the non-recombining region could potentially sometimes occur. We here test whether closer linkage has recently evolved between the sex-determining...

Data from: Trait-demography relationships underlying small mammal population fluctuations

Koen J. Van Benthem, Hannah Froy, Tim Coulson, Lowell L. Getz, Madan K. Oli & Arpat Ozgul
Large-scale fluctuations in abundance are a common feature of small mammal populations and have been the subject of extensive research. These demographic fluctuations are often associated with concurrent changes in the average body mass of individuals, sometimes referred to as the ‘Chitty effect’. Despite the long-standing recognition of this phenomenon, an empirical investigation of the underlying coupled dynamics of body mass and population growth has been lacking. Using long-term life-history data combined with a trait-based...

Aquatic carbon and greenhouse gas concentrations in the Auchencorth Moss catchment following drain blocking

K.J. Dinsmore, O. Murphey, F. Leith & J. Carfrae
This dataset contains concentrations of dissolved organic carbon, inorganic carbon, CO2, CH4 and N2O in the Black Burn stream which drains Auchencorth Moss peatland in South East Scotland. Concentrations and fluxes have been measured within the Black Burn on an approximately weekly to fortnightly basis from approximately 2006 to present (see https://doi.org/10.5285/3f0820a7-a8c8-4dd7-a058-8db79ba9c7fe). Concentrations in this dataset are from a series of new sites, upstream of the long-term sampling record, adjacent to an area of drains...

Soil temperature profiles from permafrost in subarctic Canada

C. Estop-Aragones, J.P. Fisher, M.A. Cooper, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This dataset consists of soil temperature profiles from permafrost in subarctic Canada. Soil temperature profiles were monitored during summer in 2013 and 2014 in Yukon and Northwest Territories. Monitored sites included peatland plateaus, thawing features of peatland plateaus, unburnt and burnt black spruce forests, and additional sites.

Soil thaw depth from permafrost in subarctic Canada

C. Estop-Aragones, J.P. Fisher, M.A. Cooper, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This datasets contains measures of soil thaw depth from permafrost in subarctic Canada. Soil thaw depth was measured in 2013 and 2014 in sites from Yukon and Northwest Territories.

Data from: Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

Ignacio Mena, Martha I. Nelson, Francisco Quezada-Monroy, Jayeeta Dutta, Refugio Cortes-Fernández, J. Horacio Lara-Puente, Felipa Castro-Peralta, Luis F. Cunha, Nídia Sequeira-Trovão, Bernardo Lozano-Dubernard, Andrew Rambaut, Harm Van Bakel & Adolfo García-Sastre
Asia is considered an important source of influenza A virus (IAV) pandemics, owing to large, diverse viral reservoirs in poultry and swine. However, the zoonotic origins of the 2009 A/H1N1 influenza pandemic virus (pdmH1N1) remain unclear, due to conflicting evidence from swine and humans. There is strong evidence that the first human outbreak of pdmH1N1 occurred in Mexico in early 2009. However, no related swine viruses have been detected in Mexico or any part of...

Data from: Cohort variation in individual body mass dissipates with age in large herbivores

Sandra Hamel, Jean-Michel Gaillard, Nigel G. Yoccoz, Steve Albon, Steeve D. Côté, Joseph M. Craine, Marco Festa-Bianchet, Mathieu Garel, Phyllis Lee, Cynthia Moss, Daniel H. Nussey, Fanie Pelletier, Audun Stien & Torkild Tveraa
Environmental conditions experienced during early growth and development markedly shape phenotypic traits. Consequently, individuals of the same cohort may show similar life-history tactics throughout life. Conditions experienced later in life, however, could fine-tune these initial differences, either increasing (cumulative effect) or decreasing (compensatory effect) the magnitude of cohort variation with increasing age. Our novel comparative analysis that quantifies cohort variation in individual body size trajectories shows that initial cohort variation dissipates throughout life, and that...

Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus)

Emily E. Puckett, Jane Park, Matthew Combs, Michael J. Blum, Juliet E. Bryant, Adalgisa Caccone, Federico Costa, Eva E. Deinum, Alexandra Esther, Chelsea G. Himsworth, Peter D. Keightley, Albert Ko, Ake Lundkvist, Lorraine M. McElhinney, Serge Morand, Judith Robins, James Russell, Tanja M. Strand, Olga Suarez, Lisa Yon & Jason Munshi-South
Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes....

Data from: The biogeography of kin discrimination across microbial neighbourhoods

Susanne A. Kraemer, Sébastien Wielgoss, Francesca Fiegna & Gregory J. Velicer
The spatial distribution of potential interactants is critical to social evolution in all cooperative organisms. Yet the biogeography of microbial kin discrimination at the scales most relevant to social interactions is poorly understood. Here we resolve the microbiogeography of social identity and genetic relatedness in local populations of the model cooperative bacterium Myxococcus xanthus at small spatial scales, across which the potential for dispersal is high. Using two criteria of relatedness—colony-merger compatibility during cooperative motility...

Data from: Automated single particle detection and tracking for large microscopy datasets

Rhodri S. Wilson, Lei Yang, Alison Dun, Annya M. Smyth, Rory R. Duncan, Colin Rickman & Weiping Lu
Recent advances in optical microscopy have enabled the acquisition of very large datasets from living cells with unprecedented spatial and temporal resolutions. Our ability to process these datasets now plays an essential role in order to understand many biological processes. In this paper, we present an automated particle detection algorithm capable of operating in low signal-to-noise fluorescence microscopy environments and handling large datasets. When combined with our particle linking framework, it can provide hitherto intractable...

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: Spatially coordinated dynamic gene transcription in living pituitary tissue

Karen Featherstone, Kirsty Hey, Hiroshi Momiji, Anne V. McNamara, Amanda L. Patist, Joanna Woodburn, David G. Spiller, Helen C. Christian, Alan S. McNeilly, John J. Mullins, Barbel F. Finkenstadt, David A. Rand, Michael R. H. White & Julian R. E. Davis
Transcription at individual genes in single cells is often pulsatile and stochastic. A key question emerges regarding how this behaviour contributes to tissue phenotype, but it has been a challenge to quantitatively analyse this in living cells over time, as opposed to studying snap-shots of gene expression state. We have used imaging of reporter gene expression to track transcription in living pituitary tissue. We integrated live-cell imaging data with statistical modelling for quantitative real-time estimation...

Data from: Comparative analysis of Begonia plastid genomes and their utility for species-level phylogenetics

Catherine Kidner, Nicola Harrison, Richard Harrison, Richard J. Harrison & Catherine A. Kidner
Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia.

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: Fine with heat, problems with water: microclimate alters water loss in a thermally adapted insular lizard

Anat Belasen, Kinsey Brock, Binbin Li, Dimitra Chremou, Efstratios Valakos, Panayiotis Pafilis, Barry Sinervo & Johannes Foufopoulos
Global change, including habitat isolation and climate change, has both short- and long-term impacts on wildlife populations. For example, genetic drift and inbreeding result in genetic impoverishment in small, isolated populations, while species undergo range shifts or adaptive phenotypic change in response to shifts in environmental temperatures. In this study, we utilize a model system in which Holocene landscape changes have occurred to examine long-term effects of population isolation. To examine how isolation may constrain...

Data from: The global antigenic diversity of swine influenza A viruses

Nicola S. Lewis, Colin A. Russell, Tavis K. Anderson, Kathryn Berger, David F. Burke, Judith M. Fonville, Ronald A.M. Fouchier, Paul Kellam, Bjorn F. Koel, Tung Nguyen, Bundit Nuansrichy, J. S. Malik Peiris, Takehiko Saito, Gaelle Simon, Eugene Skepner, Nobuhiro Takemae, ESNIP3 Consortium, Richard J. Webby, Kristien Van Reeth, Sharon M. Brookes, Lars Larsen, Ian H. Brown, Amy L. Vincent, Pinky Langat, Filip Bielejec … & JS Malik Peiris
Swine influenza presents a substantial disease burden for pig populations worldwide and poses a potential pandemic threat to humans. There is considerable diversity in both H1 and H3 influenza viruses circulating in swine due to the frequent introductions of viruses from humans and birds coupled with geographic segregation of global swine populations. Much of this diversity is characterized genetically but the antigenic diversity of these viruses is poorly understood. Critically, the antigenic diversity shapes the...

Data from: Use of novel psychoactive substances by inpatients on general adult psychiatric wards

Jack L. Stanley, Daniel V. Mogford, Rebecca J. Lawrence & Stephen M. Lawrie
Objectives: Non-illicit alternatives to controlled drugs, known as Novel Psychoactive Substances (NPS) have recently risen to prominence. They are readily available with uncertain pharmacology and no widely available assay. Given that psychiatric patients are at risk of comorbid substance abuse, we hypothesized that NPS use would be present in the psychiatric population, and sought to determine its prevalence and investigate the characteristics of those who use these drugs with a retrospective review of discharge letters....

Data from: Maternal effects alter the severity of inbreeding depression in the offspring

Natalie Pilakouta & Per T. Smiseth
A maternal effect is a causal influence of the maternal phenotype on the offspring phenotype over and above any direct effects of genes. There is abundant evidence that maternal effects can have a major impact on offspring fitness. Yet, no previous study has investigated the potential role of maternal effects in influencing the severity of inbreeding depression in the offspring. Inbreeding depression is a reduction in the fitness of inbred offspring relative to outbred offspring....

Autotrophic and heterotrophic soil respiration fluxes from peatland plateaus and thawing peatland plateaus and from burnt and unburnt forests from permafrost in subarctic Canada

C. Estop-Aragones, J.P. Fisher, M.A. Cooper, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This dataset consists of autotrophic and heterotrophic soil respiration fluxes from peatland plateaus and thawing peatland plateaus and from burnt and unburnt forests from permafrost in subarctic Canada. Autotrophic and heterotrophic soil respiration fluxes (CO2) were monitored during summer in 2013 and 2014 in Yukon and Northwest Territories. Monitored sites included peatland plateaus, unburnt and burnt black spruce forests, and additional sites.

Data from: Selection on parental performance opposes selection for larger body mass in a wild population of blue tits

Caroline Elizabeth Thomson, Florian Bayer, Nicholas Crouch, Samantha Farrell, Elizabeth Heap, Elizabeth Mittell, Mar Zurita-Cassinello & Jarrod D. Hadfield
There is abundant evidence in many taxa for positive directional selection on body size, and yet little evidence for microevolutionary change. In many species, variation in body size is partly determined by the actions of parents, so a proposed explanation for stasis is the presence of a negative genetic correlation between direct and parental effects. Consequently, selecting genes for increased body size would result in a correlated decline in parental effects, reducing body size in...

Registration Year

  • 2016
    49

Resource Types

  • Dataset
    49

Affiliations

  • University of Edinburgh
    49
  • University of Exeter
    13
  • University of Sheffield
    12
  • University of Sussex
    10
  • University of Cambridge
    4
  • University of Oxford
    3
  • Ghent University
    2
  • Centre for Ecology & Hydrology
    2
  • UK Centre for Ecology & Hydrology
    2
  • University of Glasgow
    2