25 Works

Data from: Multilevel and quasi-Monte Carlo methods for uncertainty quantification in particle travel times through random heterogeneous porous media

David Crevillen-Garcia & Henry Power
In this study, we apply four Monte Carlo simulation methods, namely, Monte Carlo, quasi-Monte Carlo, multilevel Monte Carlo and multilevel quasi-Monte Carlo to the problem of uncertainty quantification in the estimation of the average travel time during the transport of particles through random heterogeneous porous media. We apply the four methodologies to a model problem where the only input parameter, the hydraulic conductivity, is modelled as a log-Gaussian random field by using direct Karhunen–Loéve decompositions....

Data from: Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

Faisal Almathen, Pauline Charruau, Elmira Mohandesan, Joram M. Mwacharo, Pablo Orozco-TerWengel, Daniel Pitt, Abdussamad M. Abdussamad, Margarethe Uerpmann, Hans-Peter Uerpmann, Bea De Cupere, Peter Magee, Majed A. Alnaqeeb, Bashir Salim, Abdul Raziq, Tadelle Dessie, Omer M. Abdelhadi, Mohammad H. Banabazi, Marzook Al-Eknah, Chris Walzer, Bernard Faye, Michael Hofreiter, Joris Peters, Olivier Hanotte & Pamela A. Burger
Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and...

Data from: Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells

Minseung Choi, Diane P. Genereux, Jamie Goodson, Haneen Al-Azzawi, Shannon Q. Allain, Noah Simon, Stan Palasek, Carol B. Ware, Chris Cavanaugh, Daniel G. Miller, Winslow C. Johnson, Kevin D. Sinclair, Reinhard Stöger & Charles D. Laird
In storing and transmitting epigenetic information, organisms must balance the need to maintain information about past conditions with the capacity to respond to information in their current and future environments. Some of this information is encoded by DNA methylation, which can be transmitted with variable fidelity from parent to daughter strand. High fidelity confers strong pattern matching between the strands of individual DNA molecules and thus pattern stability over rounds of DNA replication; lower fidelity...

Data from: Species integrity enhanced by a predation cost to hybrids in the wild

P. Anders Nilsson, Kaj Hulthén, Ben B. Chapman, Lars-Anders Hansson, Jakob Brodersen, Henrik Baktoft, Jerker Vinterstare, Christer Brőnmark & Christian Skov
Species integrity can be challenged, and even eroded, if closely related species can hybridize and produce fertile offspring of comparable fitness to that of parental species. The maintenance of newly diverged or closely related species therefore hinges on the establishment and effectiveness of pre- and/or post-zygotic reproductive barriers. Ecological selection, including predation, is often presumed to contribute to reduced hybrid fitness, but field evidence for a predation cost to hybridization remains elusive. Here we provide...

Data from: Deliberation favours social efficiency by making people disregard their relative shares: evidence from USA and India

Valerio Capraro, Brice Corgnet, Antonio M. Espín & Roberto Hernán-González
Groups make decisions on both the production and the distribution of resources. These decisions typically involve a tension between increasing the total level of group resources (i.e. social efficiency) and distributing these resources among group members (i.e. individuals' relative shares). This is the case because the redistribution process may destroy part of the resources, thus resulting in socially inefficient allocations. Here we apply a dual-process approach to understand the cognitive underpinnings of this fundamental tension....

Data from: Waterjet and laser etching: the nonlinear inverse problem

Aitor Bilbao-Guillerna, Dragos A. Axinte, John Billingham, Guillaume B.J. Cadot & G. B. J. Cadot
In waterjet and laser milling, material is removed from a solid surface in a succession of layers to create a new shape, in a depth-controlled manner. The inverse problem consists of defining the control parameters, in particular, the two-dimensional beam path, to arrive at a prescribed freeform surface. Waterjet milling (WJM) and pulsed laser ablation (PLA) are studied in this paper, since a generic nonlinear material removal model is appropriate for both of these processes....

Data from: Climate change may drive cave spiders to extinction

Stefano Mammola, Sara L. Goodacre & Marco Isaia
Subterranean ecosystems present ideal opportunities to study mechanisms underlying responses to changes in climate because species within them are often adapted to a largely constant temperature. We have characterized the thermal conditions of caves in the Western Alps, and related these hypogean climate data to the occurrence of Troglohyphantes spiders (Araneae, Linyphiidae). Our data indicated that present distributions reflect Pleistocene glaciation events and also pointed to specific responses as a consequence of changes in temperature....

Data from: Precipitation drives global variation in natural selection

Adam Siepielski, Michael B. Morrissey, Mathieu Buoro, Stephanie M. Carlson, Christina M. Caruso, Sonya M. Clegg, Tim Coulson, Joseph DiBattista, Kiyoko M. Gotanda, Clinton D. Francis, Joe Hereford, Joel G. Kingsolver, Kate E. Augustine, Loeske E. B. Kruuk, Ryan A. Martin, Ben C. Sheldon, Nina Sletvold, Erik I. Svensson, Michael J. Wade & Andrew D. C. MacColl
Climate change has the potential to affect the ecology and evolution of every species on Earth. Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation—natural selection—are largely unknown. We report that aspects of precipitation and potential evapotranspiration, along with the North Atlantic Oscillation, predicted variation in selection across plant and animal populations throughout many terrestrial biomes, whereas temperature explained little variation. By...

Elemental concentrations in representative species of the ICRP's Reference Animals and Plants and associated soils in terrestrial Mediterranean ecosystems in Spain

J. Guillén, M. Izquierdo, S. Young, C. Wells, C.L. Barnett, N.A. Beresford, A. Baeza, A. Salas, A. Muñóz-Serrano, J.M. Corrales-Vázquez, J.G. Muñoz-Muñoz, E. Tovar & J.S. Chaplow
Data comprise stable element concentrations in terrestrial Reference Animals and Plants (RAPs) and corresponding whole-body concentration ratios determined in two different Mediterranean ecosystems: a Pinewood and a Dehesa (grassland with disperse tree cover). The International Commission on Radiological Protection (ICRP) RAPs considered in the Pinewood ecosystem were Pine Tree and Wild Grass; whereas in the Dehesa ecosystem those considered were Deer, Rat, Earthworm, Bee, Frog, Duck and Wild Grass. The data include: elemental concentrations in...

Data from: Genome-wide SNP data unveils the globalization of domesticated pigs

Bin Yang, Leilei Cui, Miguel Perez-Enciso, Aleksei Traspov, Richard P. M. A. Crooijmans, Natalia Zinovieva, Lawrence B. Schook, Alan Archibald, Kesinee Gatphayak, Christophe Knorr, Alex Triantafyllidis, Panoraia Alexandri, Gono Semiadi, Olivier Hanotte, Deodália Dias, Peter Dovč, Pekka Uimari, Laura Iacolina, Massimo Scandura, Martien A. M. Groenen, Lusheng Huang & Hendrik-Jan Megens
Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global...

Data from: From the animal house to the field: are there consistent individual differences in immunological profile in wild populations of field voles (Microtus agrestis)?

Elena Arriero, Klara M. Wanelik, Richard J. Birtles, Janette E. Bradley, Joseph A. Jackson, Steve Paterson & Mike Begon
Inbred mouse strains, living in simple laboratory environments far removed from nature, have been shown to vary consistently in their immune response. However, wildlife populations are typically outbreeding and face a multiplicity of challenges, parasitological and otherwise. In this study we seek evidence of consistent difference in immunological profile amongst individuals in the wild. We apply a novel method in this context, using longitudinal (repeated capture) data from natural populations of field voles, Microtus agrestis,...

Data from: Strong population structure in a species manipulated by humans since the Neolithic: the European fallow deer (Dama dama dama)

Karis H. Baker, Howard W.I. Gray, Veronica Ramovs, Despoina Mertzanidou, C Akin Peksen, C. Can Bilgin, Naomi Sykes & A.R. Hoelzel
Species that have been translocated and otherwise manipulated by humans may show patterns of population structure that reflect those interactions. At the same time, natural processes shape populations, including behavioural characteristics like dispersal potential and breeding system. In Europe, a key factor is the geography and history of climate change through the Pleistocene. During glacial maxima throughout that period, species in Europe with temperate distributions were forced south, becoming distributed among the isolated peninsulas represented...

Data from: Effects of deer on woodland structure revealed through terrestrial laser scanning

Markus P. Eichhorn, Joseph Ryding, Martin J. Smith, Robin M. A. Gill, Gavin M. Siriwardena & Robert J. Fuller
Terrestrial laser scanning (TLS) captures the three-dimensional structure of habitats. Compared to traditional methods of forest mensuration, it allows quantification of structure at increased resolution, and the derivation of novel metrics with which to inform ecological studies and habitat management. Lowland woodlands in the UK have altered in structure over the last century due to increased abundance of deer and a decline in management. We compared whole-canopy profiles between woodlands with high (>10 deer km−2)...

Data from: Measuring β‐diversity by remote sensing: a challenge for biodiversity monitoring

Duccio Rocchini, Sandra Luque, Nathalie Pettorelli, Lucy Bastin, Daniel Doktor, Nicolò Faedi, Hannes Feilhauer, Jean-Baptiste Féret, Giles M. Foody, Yoni Gavish, Sergio Godinho, William E. Kunin, Angela Lausch, Pedro J. Leitao, Matteo Marcantonio, Markus Neteler, Carlo Ricotta, Sebastian Schmidtlein, Petteri Vihervaara, Martin Wegmann & Harini Nagendra
Biodiversity includes multiscalar and multitemporal structures and processes, with different levels of functional organization, from genetic to ecosystemic levels. One of the mostly used methods to infer bio- diversity is based on taxonomic approaches and community ecology theories. However, gathering extensive data in the field is difficult due to logistic problems, especially when aiming at modelling biodiversity changes in space and time, which assumes statistically sound sampling schemes. In this context, airborne or satellite remote...

Data from: Environmental modification via a quorum sensing molecule influences the social landscape of siderophore production

Roman Popat, Freya Harrison, Ana C. Da Silva, Scott A.S. Easton, Luke McNally, Paul Williams, Stephen P. Diggle & Scott A. S. Easton
Bacteria produce a wide variety of exoproducts that favourably modify their environment and increase their fitness. These are often termed ‘public goods’ because they are costly for individuals to produce and can be exploited by non-producers (cheats). The outcome of conflict over public goods is dependent upon the prevailing environment and the phenotype of the individuals in competition. Many bacterial species use quorum sensing (QS) signalling molecules to regulate the production of public goods. QS,...

Data from: Genetic characterization of dog personality traits

Joanna Ilska, Marie J. Haskell, Sarah C. Blott, Enrique Sanchez-Molano, Zita Polgar, Sarah E. Lofgren, Dylan N. Clements & Pamela Wiener
The genetic architecture of behavioural traits in dogs is of great interest to owners, breeders and professionals involved in animal welfare, as well as to scientists studying the genetics of animal (including human) behaviour. The genetic component of dog behaviour is supported by between-breed differences and some evidence of within-breed variation. However, it is a challenge to gather sufficiently large datasets to dissect the genetic basis of complex traits such as behaviour, which are both...

Data from: Drug delivery in a tumour cord model: a computational simulation

Matthew E. Hubbard, Maria Jove, Paul M. Loadman, Roger M. Phillips, Christopher J. Twelves & Stephen W. Smye
The tumour vasculature and microenvironment is complex and heterogeneous, contributing to reduced delivery of cancer drugs to the tumour. We have developed an in silico model of drug transport in a tumour cord to explore the effect of different drug regimes over a 72 h period and how changes in pharmacokinetic parameters affect tumour exposure to the cytotoxic drug doxorubicin. We used the model to describe the radial and axial distribution of drug in the...

Data from: Abiotic environmental variation drives virulence evolution in a fish host-parasite geographic mosaic

Muayad A. Mahmud, Jannette E. Bradley, Andrew D. C. MacColl & Janette E. Bradley
1.Parasite virulence varies greatly. Theory predicts that this arises from parasites optimising a trade-off between the mortality they inflict on current hosts, and their transmission to future hosts. The effect of the environment on this coevolution is rarely considered. 2.Geographic mosaics are fertile systems for studying coevolution, but again, the diversity of outcomes is often assumed to result from co-evolutionary dynamism, rather than being moulded by the environment. 3.Here we quantify variation in virulence among...

Data from: Signatures of selection for environmental adaptation and zebu x taurine hybrid fitness in East African Shorthorn Zebu

Hussain Bahbahani, Abdulfatai Tijjani, Christopher Mukasa, David Wragg, Faisal Almathen, Oyekanmi Nash, Gerald N. Akpa, Mary Mbole-Kariuki, Sunir Malla, Mark Woolhouse, Tad Sonstegard, Curtis Van Tassell, Martin Blythe, Heather Huson & Olivier Hanotte
The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure...

Data from: Social seeking declines in young adolescents

Indu Dubey, Danielle Ropar & Antonia F. De C. Hamilton
The desire to engage with others is an important motivational force throughout our lifespan. It is known that social behaviour and preferences change from childhood to adulthood, but whether this change is linked with any changes in social motivation is not known. We evaluated 255 typically developing participants from ages 4–20 years on a behavioural paradigm ‘Choose a Movie’ (CAM). On every trial, participants had a choice between viewing social or non-social movies presented with...

Data from: Genomic data illuminates demography, genetic structure and selection of a popular dog breed

Pamela Wiener, Enrique Sánchez-Molano, Dylan N. Clements, John A. Woolliams, Marie J. Haskell & Sarah C. Blott
Background: Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. This study applied genomic methods to investigate population structure and inbreeding in a common UK dog breed, the Labrador Retriever. Results: We found substantial within-breed genetic differentiation, which was associated with the role of the dog (i.e. working, pet, show) and...

Data from: Reciprocity and the tragedies of maintaining and providing the commons

Simon Gächter, Felix Kölle & Simone Quercia
Social cooperation often requires collectively beneficial but individually costly restraint to maintain a public good, or it needs costly generosity to create one. Status quo effects predict that maintaining a public good is easier than providing a new one. Here, we show experimentally and with simulations that even under identical incentives, low levels of cooperation (the ‘tragedy of the commons’) are systematically more likely in maintenance than provision. Across three series of experiments, we find...

Data from: Antisocial punishment across societies

Benedikt Herrmann, Christian Thöni & Simon Gächter
We document the widespread existence of antisocial punishment, that is, the sanctioning of people who behave prosocially. Our evidence comes from public goods experiments that we conducted in 16 comparable participant pools around the world. However, there is a huge cross-societal variation. Some participant pools punished the high contributors as much as they punished the low contributors, whereas in others people only punished low contributors. In some participant pools, antisocial punishment was strong enough to...

Data from: Nutrient limitation or home field advantage: does microbial community adaptation overcome nutrient limitation of litter decomposition in a tropical peatland?

Jorge Hoyos-Santillan, Barry H. Lomax, Benjamin L. Turner & Sofie Sjögersten
Litter decomposition is an important control on carbon accumulation in tropical peatlands. Stoichiometric theory suggests that decomposition is regulated by elemental ratios in litter while the home field advantage (HFA) hypothesis predicts that decomposer communities are adapted to local conditions. To date, the relative importance of these contrasting theories for litter decomposition and therefore the carbon balance of tropical peatlands remain poorly understood. We conducted two in situ litter decomposition experiments in a lowland tropical...

Data from: Signatures of positive selection in African Butana and Kenana dairy zebu cattle

Hussain Bahbahani, Bashir Salim, Faisal Almathen, Fahad Al Enzi, Joram M. Mwacharo, Olivier Hanotte & Fahad Al Enezi
Butana and Kenana are two types of zebu cattle found in Sudan. They are unique amongst African indigenous zebu cattle because of their high milk production. Aiming to understand their genome structure, we genotyped 25 individuals from each breed using the Illumina BovineHD Genotyping BeadChip. Genetic structure analysis shows that both breeds have an admixed genome composed of an even proportion of indicine (0.75 ± 0.03 in Butana, 0.76 ± 0.006 in Kenana) and taurine...

Registration Year

  • 2017
    25

Resource Types

  • Dataset
    25

Affiliations

  • University of Nottingham
    25
  • King Faisal University
    3
  • Roslin Institute
    3
  • International Livestock Research Institute
    3
  • University of Edinburgh
    3
  • Kuwait University
    3
  • Lund University
    2
  • University of Leeds
    2
  • University of Khartoum
    2
  • Scotland's Rural College
    2