73 Works

Political Agreements in Internal Conflicts (PAIC) Dataset and Codebook

Giuditta Fontana, Argyro Kartsonaki, Natascha Neudorfer, Dawn Walsh, Stefan Wolff & Crystalla Yakinthou

Data from: Higher species richness enhances yield stability in intensively managed grasslands with experimental disturbance

Eamon Haughey, Matthias Suter, Daniel Hofer, Nyncke J. Hoekstra, Jennifer C. McElwain, Andreas Lüscher & John A. Finn
Climate models predict increased frequency and severity of drought events. At an Irish and Swiss site, experimental summer droughts were applied over two successive years to grassland plots sown with one, two or four grassland species with contrasting functional traits. Mean yield and plot-to-plot variance of yield were measured across harvests during drought and after a subsequent post-drought recovery period. At both sites, there was a positive relationship between species richness and yield. Under rainfed...

Data from: Scale-dependent effects of landscape variables on gene flow and population structure in bats

Orly Razgour, Hugo Rebelo, Sébastien J. Puechmaille, Javier Juste, Carlos Ibáñez, Andreas Kiefer, Terry Burke, Deborah A. Dawson & Gareth Jones
Aim: A common pattern in biogeography is the scale-dependent effect of environmental variables on the spatial distribution of species. We tested the role of climatic and land cover variables in structuring the distribution of genetic variation in the grey long-eared bat, Plecotus austriacus, across spatial scales. Although landscape genetics has been widely used to describe spatial patterns of gene flow in a variety of taxa, volant animals have generally been neglected because of their perceived...

Data from: Long-term and trans-generational effects of neonatal experience on sheep behaviour

Michael Mendl, Corinna Clark, Joanna Murrell, Mia Fernyhough & Treasa O'Rourke
Early life experiences can have profound long-term, and sometimes trans-generational, effects on individual phenotypes. However, there is a relative paucity of knowledge about effects on pain sensitivity, even though these may impact on an individual's health and welfare, particularly in farm animals exposed to painful husbandry procedures. Here, we tested in sheep whether neonatal painful and non-painful challenges can alter pain sensitivity in adult life, and also in the next generation. Ewes exposed to tail-docking...

Data from: Density and biotic interactions modify the combined effects of global and local stressors

Paul R. Brooks & Tasman P. Crowe
A key challenge in predicting the effects of global changes is determining how they may modify the influence of localised stressors, such that steps can be taken to minimise combined effects. Combined effects of global and local stressors can be difficult to predict as they are underpinned by influences on individual species and interactions between them, which in turn may be affected by absolute and relative densities. Here we tested experimentally the influence of increased...

Data from: EMMLi: a maximum likelihood approach to the analysis of modularity

Anjali Goswami & John Albert Finarelli
Identification of phenotypic modules, semiautonomous sets of highly correlated traits, can be accomplished through exploratory (e.g., cluster analysis) or confirmatory approaches (e.g., RV coefficient analysis). Although statistically more robust, confirmatory approaches are generally unable to compare across different model structures. For example, RV coefficient analysis finds support for both two- and six-module models for the therian mammalian skull. Here, we present a maximum likelihood approach that takes into account model parameterization. We compare model log-likelihoods...

Data from: Fossilization of melanosomes via sulfurization

Maria E. McNamara, Bart E. Van Dongen, Nick P. Lockyer, Ian D. Bull & Patrick J. Orr
Fossil melanin granules (melanosomes) are an important resource for inferring the evolutionary history of colour and its functions in animals. The taphonomy of melanin and melanosomes, however, is incompletely understood. In particular, the chemical processes responsible for melanosome preservation have not been investigated. As a result, the origins of sulfur-bearing compounds in fossil melanosomes are difficult to resolve. This has implications for interpretations of original colour in fossils based on potential sulfur-rich phaeomelanosomes. Here we...

Data from: Breeding bird species diversity across gradients of land use from forest to agriculture in Europe

Matti J. Koivula, Dan E. Chamberlain, Robert J. Fuller, Stephen C. F. Palmer, Attila Bankovics, Fintan Bracken, Tom Bolger, Eduardo De Juana, Marc Montadert, Renato Neves, Rui Rufino, Angel Sallent, Luís Lopes Da Silva, Pedro J. Leitão, Manfred Steffen & Allan D. Watt
Loss, fragmentation and decreasing quality of habitats have been proposed as major threats to biodiversity world-wide, but relatively little is known about biodiversity responses to multiple pressures, particularly at very large spatial scales. We evaluated the relative contributions of four landscape variables (habitat cover, diversity, fragmentation and productivity) in determining different components of avian diversity across Europe. We sampled breeding birds in multiple 1-km2 landscapes, from high forest cover to intensive agricultural land, in eight...

Data from: Quantifying and modelling decay in forecast proficiency indicates the limits of transferability in land-cover classification

Yoni Gavish, Jerome O’Connell, Tim G. Benton & Jerome O'Connell
1. The ability to provide reliable projections for the current and future distribution patterns of land-covers is fundamental if we wish to protect and manage our diminishing natural resources. Two inter-related revolutions made map productions feasible at unprecedented resolutions- the availability of high-resolution remotely-sensed data and the development of machine-learning algorithms. However, the ground-truth data needed for training models is in most cases spatially and temporally clustered. Therefore, map production requires extrapolation of models from...

High diversity of mites (Acari: Oribatida, Mesostig-mata) supports the high conservation value of a broadleaf forest in Eastern Norway

Anna Seniczak, Stanisław Seniczak, Josef Starý, Sławomir Kaczmarek, Bjarte Jordal, Jarosław Kowalski, Steffen Roth, Per Djursvoll & Thomas Bolger
Broadleaf forests are critical habitats for biodiversity and this biodiversity is in turn essential for their proper functioning. Mites (Acari) are a numerous and functionally essential component of these forests. We report the diversity of two important groups, Oribatida and Mesostigmata, in a broadleaf forest in Eastern Norway which is considered to be a biodiversity hotspot. Eighteen samples, each 500 cm3, were collected from diverse microhabitats (moss on ground, lichens on tree twigs lying on...

Identification and evaluation of serum protein biomarkers which differentiate psoriatic from rheumatoid arthritis

Angela Mc Ardle
Objectives To identify serum protein biomarkers which might separate early inflammatory arthritis (EIA) patients with psoriatic arthritis (PsA) from those with rheumatoid arthritis (RA) and may be used to support appropriate early intervention. Methods The serum proteome of patients with PsA and RA was interrogated using liquid chromatography mass spectrometry (LC-MS/MS) (n=64 patients), a multiplexed antibody assay (Luminex) for 48 proteins (n=64 patients) and an aptamer-based assay (SOMAscan) targeting 1,129 proteins (n=36 patients). Multiple reaction...

Drivers of longitudinal telomere dynamics in the long-lived bat species, Myotis myotis

Nicole Foley, Eric Petit, Thomas Brazier, John Finarelli, Graham Hughes, Frederic Touzalin, Sebastien Puechmaille & Emma Teeling
Age related telomere shortening is considered a hallmark of the ageing process. However, a recent cross-sectional ageing study of relative telomere length (rTL) in bats failed to detect a relationship between rTL and age in the long-lived genus Myotis (M. myotis and M. bechsteinii), suggesting some other factors are responsible for driving telomere dynamics in these species. Here, we test if longitudinal rTL data show signatures of age-associated telomere attrition in M. myotis and differentiate...

European bird declines: do we need to rethink approaches to the management of abundant generalist predators?

Barry John McMahon, Susan Doyle, Aimée Gray, Sean Kelly & Steve M. Redpath
Bird species are declining across Europe. Current European policy, i.e. the Birds and Habitats Directives, focus on habitat management as a way of halting the declines. This paper explores the role of predation in causing bird population declines and asks if we need to reconsider our approach to the management of generalist predators. We analysed bird population trends and distribution changes across Europe, Britain and Ireland, reflecting an increasing gradient of generalist predator abundance (principally...

Data from: The transcriptomics of crushing jaw convergence in cichlid fishes: comparative gene expression in recent sympatric versus older allopatric trophic adaptations

Nidal Karagic, Sarah Weis, Paolo Franchini, Axel Meyer & C. Darrin Hulsey
How gene expression diverges during adaptation might be strongly influenced by the geographic setting and timeframe over which species evolve. To contrast transcriptomic patterns of replicate trophic adaptations that evolved convergently during both allopatric and sympatric contexts, we conducted RNA-seq on the trophically important lower pharyngeal jaws of two sympatrically and four allopatrically diverged species pairs of cichlid fishes. We first show that all of these species pairs have convergently diverged along a crushing trophic...

Microplastics in Eurasian otter (Lutra lutra) spraints and their potential as a biomonitoring tool in freshwater systems

James D. O'Connor, Heather T. Lally, Anne-Marie Mahon, Ian O'Connor, Róisín Nash, John J. O'Sullivan, Michael Bruen, Linda Heerey, Albert A. Koelmans, Ferdia Marnell & Sinéad Murphy
The ubiquitous nature of microplastics in aquatic ecosystems may have serious implications for aquatic biota. While microplastic research in freshwater ecosystems is increasing, very few studies have assessed the physical presence of microplastics among top predators. The Eurasian otter (Lutra lutra), a top predator of aquatic ecosystems, is one of the most widely distributed otter species and has a broad habitat niche. The opportunistic collection of otter spraints (i.e. feces) presents a valuable opportunity to...

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: EFHC1, implicated in juvenile myoclonic epilepsy, functions at the cilium and synapse to modulate dopamine signaling

Catrina M. Loucks, Kwangjin Park, Denise S. Walker, Andrea H. McEwan, Tiffany A. Timbers, Evan L. Ardiel, Laura J. Grundy, Chunmei Li, Jacque-Lynne Johnson, Julie Kennedy, Oliver E. Blacque, William R. Schafer, Catharine H. Rankin & Michel R. Leroux
Neurons throughout the mammalian brain possess non-motile cilia, organelles with varied functions in sensory physiology and cellular signaling, yet their roles in these neurons are poorly understood. To shed light into their functions, we studied EFHC1, an evolutionarily conserved protein required for motile cilia function and linked to a common form of inherited epilepsy in humans, juvenile myoclonic epilepsy (JME). We demonstrate that C. elegans EFHC1 functions within specialized non-motile mechanosensory cilia, where it regulates...

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: The effect of collective dispersal on the genetic structure of a subdivided population

Jonathan M. Yearsley, Frédérique Viard & Thomas Broquet
Correlated dispersal paths between two or more individuals are widespread across many taxa. The population genetic implications of this collective dispersal have received relatively little attention. Here we develop two-sample coalescent theory that incorporates collective dispersal in a finite island model to predict expected coalescence times, genetic diversities and F-statistics. We show that collective dispersal reduces mixing in the system, which decreases expected coalescence times and increases FST. The effects are strongest in systems with...

Data from: A non-lethal sampling method to obtain, generate and assemble whole-blood transcriptomes from small, wild mammals

Zixia Huang, Aurore Gallot, Nga T. Lao, Sébastien J. Puechmaille, Nicole M. Foley, David Jebb, Michaël Bekaert & Emma C. Teeling
The acquisition of tissue samples from wild populations is a constant challenge in conservation biology, especially for endangered species and protected species where nonlethal sampling is the only option. Whole blood has been suggested as a nonlethal sample type that contains a high percentage of bodywide and genomewide transcripts and therefore can be used to assess the transcriptional status of an individual, and to infer a high percentage of the genome. However, only limited quantities...

Data from: Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes

Michelle Sait, Morag Livingstone, Ewan M. Clark, Nick Wheelhouse, Lucy Spalding, Bryan Markey, Simone Magnino, F. Alex Lainson, Garry S. A. Myers & David Longbottom
Background: Chlamydia pecorum is the causative agent of a number of acute diseases, but most often causes persistent, subclinical infection in ruminants, swine and birds. In this study, the genome sequences of three C. pecorum strains isolated from the faeces of a sheep with inapparent enteric infection (strain W73), from the synovial fluid of a sheep with polyarthritis (strain P787) and from a cervical swab taken from a cow with metritis (strain PV3056/3) were determined...

Data from: Diversity dynamics of mammals in relation to tectonic and climatic history: comparison of three Neogene records from North America

Catherine Badgley & John A. Finarelli
In modern ecosystems, regions of topographic heterogeneity, when compared with nearby topographically homogeneous regions, support high species densities of mammals and other groups. This biogeographic pattern could be explained by either greater diversification rates or greater accommodation of species in topographically complex regions. In this context, we assess the hypothesis that changes in landscape history have stimulated diversification in mammals. Landscape history includes tectonic and climatic processes that influence topographic complexity at regional scales. We...

Data from: Spatiotemporal scaling of plant species richness and functional diversity in a temperate semi-natural grassland

Hannah J. White, W. Ian Montgomery, Robin J. Pakeman & Jack J. Lennon
The accumulation of biodiversity in space and time has been modelled extensively using the species-area relationship and the species-time relationship, respectively. Recently, these models have been combined into time-area curves in order to investigate spatiotemporal scaling of species richness. This study expands on previous research by applying these spatiotemporal models to functional diversity. Understanding spatiotemporal dynamics of ecological traits is important due to their crucial role in ecosystem functioning and mediating species responses to environmental...

Data from: Establishment of a coastal fish in the Azores: recent colonisation or sudden expansion of an ancient relict population?

Sergio Stefanni, Rita Castilho, Maria Sala-Bozano, Joana I. Robalo, Sara M. Francisco, Ricardo S. Santos, Nuno Marques, Alberto Brito, Vitor C. Almada & Stefano Mariani
The processes and timescales associated with ocean-wide changes in the distribution of marine species have intrigued biologists since Darwin’s earliest insights into biogeography. The Azores, a mid-Atlantic volcanic archipelago located >1000 km off the European continental shelf, offers ideal opportunities to investigate phylogeographic colonisation scenarios. The benthopelagic sparid fish known as the common two-banded seabream (Diplodus vulgaris) is now relatively common along the coastline of the Azores archipelago, but was virtually absent before the 1990s....

Data from: Genetic population structure of U.S. Atlantic coastal striped bass (Morone saxatilis)

David T. Gauthier, Corinne A. Audemard, Jeanette E. L. Carlsson, Tanya L. Darden, Michael R. Denson, Kimberly S. Reece & Jens Carlsson
Genetic population structure of anadromous striped bass along the US Atlantic coast was analyzed using 14 neutral nuclear DNA microsatellites. Young-of-the-year and adult striped bass (n = 1114) were sampled from Hudson River, Delaware River, Chesapeake Bay, North Carolina, and South Carolina. Analyses indicated clear population structure with significant genetic differentiation between all regions. Global multilocus F ST was estimated at 0.028 (P < 0.001). Population structure followed an isolation-by-distance model and temporal sampling indicated...

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