74 Works

Data from: Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Maulik R. Upadhyay, Wei Chen, Johannes A. Lenstra, C. R. J. Goderie, David E. MacHugh, Stephen D. E. Park, David A. Magee, Donato Matassino, Ferdinando Ciani, Hendrik-Jan Megens, J. A. M. Van Arendonk, Martien A. M. Groenen, European Cattle Genetic Diversity Consortium & Richard P. M. A. Crooijmans
The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess...

Data from: Leptin regulation of hippocampal synaptic function in health and disease

Andrew J. Irving & Jenni Harvey
The endocrine hormone leptin plays a key role in regulating food intake and body weight via its actions in the hypothalamus. However, leptin receptors are highly expressed in many extra-hypothalamic brain regions and evidence is growing that leptin influences many central processes including cognition. Indeed, recent studies indicate that leptin is a potential cognitive enhancer as it markedly facilitates the cellular events underlying hippocampal-dependent learning and memory, including effects on glutamate receptor trafficking, neuronal morphology...

RNA-sequencing endometrium intact, vasectomized, and control heifers

Sandra Recuero, José María Sánchez, Yentel Mateo-Otero, Sandra Bagés-Arnal, Michael McDonald, Susanta K Behura, Thomas E Spencer, David A Kenny, Marc Yeste, Pat Lonergan & Beatriz Fernandez-Fuertes
An appropriate female reproductive environment is essential for pregnancy success. In several species, including mice, pigs and horses, seminal plasma (SP) components have been shown to modulate this environment, leading to increased embryo viability and implantation. Due to the characteristics of mating in the aforementioned species, SP comes into direct contact with the uterus. However, it is questionable whether any SP reaches the uterus in species that ejaculate inside the vagina, such as humans and...

Data from: Population connectivity and phylogeography of the Mediterranean endemic skate Raja polystigma and evidence of its hybridization with the parapatric sibling R. montagui

Alessia Cariani, ED Farrell, P Carbonara, G Garofalo, M Stagioni, F Tinti, F Fiorentino, N Frodella, A Veloná, R Cannas & MC Follesa
The genetic structure and population connectivity of the Mediterranean endemic speckled skate Raja polystigma were investigated in 10 population samples (N = 232) at 7 exon-primed nuclear microsatellites and at 3 mitochondrial DNA sequence markers. The phylogeographic and population genetic analyses revealed that R. polystigma in the western and central Mediterranean represents a near-panmictic population, with a subtle but significant mitochondrial divergence of the Adriatic deme. Nuclear genotypes revealed that 2.5% of the total individuals...

Data from: Can biosecurity and local network properties predict pathogen species richness in the salmonid industry?

Tadaishi Yatabe, Simon J. More, Fiona Geoghegan, Catherine McManus, Ashley E. Hill & Beatriz Martinez-Lopez
Salmonid farming in Ireland is mostly organic, which implies limited disease treatment options. This highlights the importance of biosecurity for preventing the introduction and spread of infectious agents. Similarly, the effect of local network properties on infection spread processes has rarely been evaluated. In this paper, we characterized the biosecurity of salmonid farms in Ireland using a survey, and then developed a score for benchmarking the disease risk of salmonid farms. The usefulness and validity...

Data from: Fear of the dark? contrasting impacts of humans vs lynx on diel activity of roe deer across Europe

Nadège C. Bonnot, Ophélie Couriot, Anne Berger, Francesca Cagnacci, Simone Ciuti, Johannes De Groeve, Benedikt Gehr, Marco Heurich, Petter Kjellander, Max Kröschel, Nicolas Morellet, Leif Sönnichsen & A.J. Mark Hewison
Humans, as super predators, can have strong effects on wildlife behaviour, including profound modifications of diel activity patterns. Subsequent to the return of large carnivores to human-modified ecosystems, many prey species have adjusted their spatial behaviour to the contrasting landscapes of fear generated by both their natural predators and anthropogenic pressures. The effects of predation risk on temporal shifts in diel activity of prey, however, remain largely unexplored in human-dominated landscapes. We investigated the influence...

Worried, weary and worn out: a mixed methods study of stress and wellbeing in final year medical students

Abbie Lane, McGrath Jack, Cleary Emer, Guerandel Allys & Malone Kevin M.
Objectives: Although there is much focus on burnout and psychological distress amongst doctors, studies about stress and wellbeing in medical students are limited but could inform early intervention and prevention strategies. Design: The primary aim of this mixed methods, cross-sectional survey was to compare objective and subjective levels of stress in Final Year Medical students (2017) and to explore their perspectives on the factors they considered relevant to their wellbeing. Setting: University College Dublin, the...

Appendices interview formats

Una Cunningham, Aoife De Brún, Willgerodt Mayumi, Erin Blakeney & Eilish McAuliffe
Background: Literature on multi-disciplinary healthcare team interventions to improve quality and safety of care in acute hospital contexts tends to focus on evaluating the success of the intervention by assessing patient outcomes. In contrast, there is little focus on the team who delivered the intervention, how the team worked to deliver the intervention or the context in which it was delivered. In practice, there is a poor understanding of why some interventions work and are...

Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria: RNA-seq statistics and results

David MacHugh, Thomas Hall, Michael Mullen, Gillian McHugo, Kate Killick, Donagh Berry, Siobhán Ring, Carolina Correia, John Browne & Stephen Gordon
Background: Bovine TB (bTB), caused by infection with Mycobacterium bovis, is a major endemic disease affecting global cattle production. The key innate immune cell that first encounters the pathogen is the alveolar macrophage, previously shown to be substantially reprogrammed during intracellular infection by the pathogen. Here we use differential expression, and correlation- and interaction-based network approaches to analyse the host response to infection with M. bovis at the transcriptome level to identify core infection response...

Data from: The program STRUCTURE does not reliably recover the correct population structure when sampling is uneven: sub-sampling and new estimators alleviate the problem

Sébastien J. Puechmaille
Inferences of population structure and more precisely the identification of genetically homogeneous groups of individuals are essential to the fields of ecology, evolutionary biology, and conservation biology. Such population structure inferences are routinely investigated via the program STRUCTURE implementing a Bayesian algorithm to identify groups of individuals at Hardy-Weinberg and linkage equilibrium. While the method is performing relatively well under various population models with even sampling between subpopulations, the robustness of the method to uneven...

Data from: Genomic characterisation of the indigenous Irish Kerry cattle breed

Sam Browett, Gillian McHugo, Ian W. Richardson, David A. Magee, Stephen D. E. Park, Alan G. Fahey, John F. Kearney, Carolina N. Correia, Imtiaz A.S. Randhawa, David E. MacHugh & Imtiaz A. S. Randhawa
Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis...

Data from: Mammal madness: is the mammal tree of life not yet resolved?

Nicole M. Foley, Mark S. Springer & Emma C. Teeling
Most molecular phylogenetic studies place all placental mammals into four superordinal groups, Laurasiatheria (e.g. dogs, bats, whales), Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g. armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs), and estimate that these clades last shared a common ancestor 90–110 million years ago. This phylogeny has provided a framework for numerous functional and comparative studies. Despite the high level of congruence among most molecular studies, questions still remain regarding the position...

Data from: Forecasting the response to global warming in a heat-sensitive species

Francesca Brivio, Milena Zurmühl, Stefano Grignolio, Jost Von Hardenberg, Marco Apollonio & Simone Ciuti
Avoiding hyperthermia entails considerable metabolic costs for endotherms. Such costs increase in warm conditions, when endotherms may trade food intake for cooler areas to avoid heat stress and maximize their energy balance. The need to reduce heat stress may involve the adoption of tactics affecting space use and foraging behaviour, which are important to understand and predict the effects of climate change and inform conservation. We used resource selection models to examine the behavioural response...

Data from: Dispositional free riders do not free ride on punishment

Till O. Weber, Ori Weisel & Simon Gächter
Strong reciprocity explains prosocial cooperation by the presence of individuals who incur costs to help those who helped them (‘strong positive reciprocity’) and to punish those who wronged them (‘strong negative reciprocity’). Theories of social preferences predict that in contrast to ‘strong reciprocators’, self-regarding people cooperate and punish only if there are sufficient future benefits. Here, we test this prediction in a two-stage design. First, participants are classified according to their disposition towards strong positive...

Data from: Identifying spawning sites and other critical habitat in lotic systems using eDNA “snapshots”: a case study using the sea lamprey Petromyzon marinus L.

Fiona S.A. Bracken, Sean Rooney, Mary Kelly-Quinn, James J. King, Jens Carlsson & Fiona S. A. Bracken
Many aquatic species of conservation concern exist at low densities and are inherently difficult to detect or monitor using conventional methods. However, the introduction of environmental (e)DNA has recently transformed our ability to detect these species and enables effective deployment of limited conservation resources. Identifying areas for breeding, as well as the ecological distribution of a species are vital to the survival or recovery of a conservation species (i.e. critical habitat). In many species, spawning...

Data from: Machine learning identifies ecological selectivity patterns across the end-Permian mass extinction

William Foster, Georgy Ayzel, Jannes Münchmeyer, Tabea Rettelbach, Niklas Kitzmann, Terry Isson, Maria Mutti & Martin Aberhan
The end-Permian mass extinction occurred alongside a large swathe of environmental changes that are often invoked as extinction mechanisms, even when a direct link is lacking. One way to elucidate the cause(s) of a mass extinction is to investigate extinction selectivity as it can reveal critical information on organismic traits as key determinants of extinction and survival. Here we show that machine learning algorithms, specifically gradient boosted decision trees, can be used to identify determinants...

U-Pb isotope ratios and trace element concentrations of carbonate-fluorapatite from phosphate nodules in Carboniferous sedimentary rocks in northern Co. Clare, Ireland

Gary J O'Sullivan, J Stephen Daly, John Murray, Aodhán Ó'Gogáin, David M Chew, Foteini Drakou, Paul C Guyett & Eszter Badenszki
These data are trace element concentrations and U-Pb isotope ratios from phosphate nodules in Carboniferous-age carbonates, shales and phosphorites in Co. Clare, western Ireland. Sampling locations (both in degrees and as UTM coordinates) are also included. Mineralogically, the analysed material is apatite (species: carbonate-fluorapatite). These data are being used to support a paper which is currently under review. Data were collected by LA-Q-ICPMS in the National Centre for Isotope Geochemistry in University College Dublin, and...

Population asynchrony alone does not explain stability in species rich soil animal assemblages: the stabilising role of forest age on oribatid mite communities

Tancredi Caruso, Viesturs Melecis, Ugis Kagainis & Thomas Bolger
1. The importance of microbial and plant communities in the control of the diversity and structure of soil animal communities has been clarified over the last decade. Previous research focused on abiotic factors, niche separation and spatial patterns. Significant gaps still exist in our knowledge of the factors that control the stability of these communities over time. 2. We analysed a nine-year data set form the national Long-term Ecological Research Network of Latvia. We focused...

Data from: Locomotory abilities and habitat of the Cretaceous bird Gansus yumenensis inferred from limb length proportions

Robert L. Nudds, Jessie Atterholt, Xia Wang, H. L. You, Gareth J. Dyke & H.-L. You
The relative length proportions of the three bony elements of the pelvic (femur, tibiotarsus and tarsometatarsus) and pectoral (humerus, ulna and manus) limbs of the early Cretaceous bird Gansus yumenensis, a well-represented basal ornithuromorph from China are investigated and compared to those of extant taxa. Ternary plots show that the pectoral limb length proportions of Gansus are most similar to Apodiformes (swifts and hummingbirds), which plot away from all other extant birds. In contrast, the...

Data from: Simulating regimes of chemical disturbance and testing impacts in the ecosystem using a novel programmable dosing system

Mark Anthony Browne, Paul R. Brooks, Robert Clough, Andrew S. Fisher, Mariana Mayer Pinto & Tasman P. Crowe
Pollution is a global issue at the frontier between ecology, environmental science, management, engineering and policy. Legislation requires experiments to determine how much contamination an ecosystem can absorb before there are structural or functional changes. Yet, existing methods cannot realistically simulate regimes of chemical disturbance and determine impacts to assemblages in ecosystems. This is because they lack ecologically relevant species and biotic interactions, are logistically difficult to set-up, and lack environmentally relevant regimes of chemical...

Data from: Reproductive biology including evidence for superfetation in the European badger Meles meles (Carnivora: Mustelidae)

Leigh A. L. Corner, Lynsey J. Stuart, David J. Kelly & Nicola M. Marples
The reproductive biology of the European badger (Meles meles) is of wide interest because it is one of the few mammal species that show delayed implantation and one of only five which are suggested to show superfetation as a reproductive strategy. This study aimed to describe the reproductive biology of female Irish badgers with a view to increasing our understanding of the process of delayed implantation and superfetation. We carried out a detailed histological examination...

Data from: An efficient method to exploit LiDAR data in animal ecology

Simone Ciuti, Henriette Tripke, Peter Antkowiak, Ramiro Silveyra Gonzalez, Carsten F. Dormann & Marco Heurich
1. Light detection and ranging (LiDAR) technology provides ecologists with high-resolution data on three-dimensional vegetation structure. Large LiDAR datasets challenge predictive ecologists, who commonly simplify point clouds into structural attributes (namely LiDAR-based metrics such as canopy height), which are used as predictors in ecological models, potentially with loss of relevant information. 2. We illustrate an efficient alternative approach to reduce the dimensionality of LiDAR data that aims at minimal data filtering with no a priori...

Data from: Hysteretic dynamics of active particles in a periodic orienting field

Maksym Romensky, Dimitri Scholz & Vladimir Lobaskin
Active motion of living organisms and artificial self-propelling particles has been an area of intense research at the interface of biology, chemistry and physics. Significant progress in understanding these phenomena has been related to the observation that dynamic self-organization in active systems has much in common with ordering in equilibrium condensed matter such as spontaneous magnetization in ferromagnets. The velocities of active particles may behave similar to magnetic dipoles and develop global alignment, although interactions...

Data from: Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic

Stefano Mariani, Ilaria Coscia, Emmanouella Vogiatzi, Georgios Kotoulas & Costas S. Tsigenopoulos
Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of...

Data from: Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears

Gloria Gonzalez-Fortes, Aurora Grandal-D'Anglade, Ben Kolbe, Daniel Fernandes, Ioana N. Meleg, Ana Garcia-Vazquez, Ana C. Pinto-Llona, Silviu Constantin, Trino J. De Torres, Jose E. Ortiz, Christine Frischauf, Gernot Rabeder, Michael Hofreiter, Axel Barlow & Gloria G. Fortes
Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost...

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