45 Works

Data from: SIDER: an R package for predicting trophic discrimination factors of consumers based on their ecology and phylogenetic relatedness

Kevin Healy, Thomas Guillerme, Seán B. A. Kelly, Richard Inger, Stuart Bearhop & Andrew L. Jackson
Stable isotope mixing models (SIMMs) are an important tool used to study species’ trophic ecology. These models are dependent on, and sensitive to, the choice of trophic discrimination factors (TDF) representing the offset in stable isotope delta values between a consumer and their food source when they are at equilibrium. Ideally, controlled feeding trials should be conducted to determine the appropriate TDF for each consumer, tissue type, food source, and isotope combination used in a...

First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing

Victoria Elizabeth Mullin, William Stephen, Andres Arce, Will Nash, Calum Raine, David Notton, Ashleigh Whiffin, Vladimir Blagoderov, Karim Gharbi, James Hogan, Tony Hunter, Naomi Irish, Simon Jackson, Steve Judd, Chris Watkins, Wilfried Haerty, Jeff Ollerton, Selina Brace, Richard Gill & Ian Barnes
Insect declines are a global issue with significant ecological and economic ramifications. Yet we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens has the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses, is to understand how molecular preservation varies between specimens. Here,...

Assessing the effects of elephant foraging on the structure and diversity of an Afrotropical forest

Cooper Rosin, Kendall Beals, Michael Belovitch, Ruby Harrison, Megan Pendred, Megan Sullivan, Nicolas Yao & John Poulsen
African forest elephants (Loxodonta cyclotis) are ecosystem engineers that browse and damage large quantities of vegetation during their foraging and movement. Though elephant trail networks and clearings are conspicuous features of many African forests, the consequences of elephant foraging for forest structure and diversity are poorly documented. In this study in northeastern Gabon, we compare stem size, stem density, proportional damage, species diversity, and species relative abundance of seedlings and saplings in the vicinity of...

English WordNet Random Walk Pseudo-Corpora

Filip Klubicka, Alfredo Maldonado, Abhijit Mahalunkar & John D. Kelleher

Data from: Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity

Sanne Boessenkool, Gayle McGlynn, Laura S. Epp, David Taylor, Manuel Pimentel, Abel Gizaw, Sileshi Nemomissa, Christian Brochmann & Magnus Popp
Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in...

Latitudinal influences on bryozoan calcification through the Paleozoic

Catherine Reid, Patrick N Wyse Jackson &
Bryozoans are active non-phototrophic biomineralizers that precipitate their calcareous skeletons in sea-water. Carbonate saturation states vary temporally and spatially in Paleozoic oceans, and we used the Bryozoan Skeletal Index (BSI) to investigate whether bryozoan calcification is controlled by seawater chemistry in Paleozoic trepostome and cryptostome bryozoans. Our results show that cryptostome bryozoan genera are influenced by ocean chemistry throughout the Paleozoic and precipitate the most calcite per autozooid at lower latitudes, where carbonate saturation states...

Data from: Silver nanoparticles as a medical device in healthcare settings: a five-step approach for candidate screening of coating agents

Valentina Marassi, Luisana Di Cristo, Steven G. J. Smith, Simona Ortelli, Magda Blosi, Anna L. Costa, Pierluigi Reschiglian, Yuri Volkov, Adriele Prina-Mello & Stephen G. J. Smith
Silver nanoparticle-based antimicrobials can promote a long lasting bactericidal effect without detrimental toxic side effects. However, there is not a clear and complete protocol to define and relate the properties of the particles (size, shape, surface charge, ionic content) with their specific activity. In this paper, we propose an effective multi-step approach for the identification of a ‘purpose-specific active applicability window’ to maximize the antimicrobial activity of medical devices containing silver nanoparticles (Ag NPs) (such...

The biogeography of community assembly: latitude and predation drive variation in community trait distribution in a guild of epifaunal crustaceans

Collin Gross, Collin Gross, J Duffy, Kevin Hovel, Melissa Kardish, Pamela Reynolds, Christoffer Boström, Katharyn Boyer, Mathiew Cusson, Johan Eklöf, Aschwin Engelen, Klemens Eriksson, Joel Fodrie, John Griffin, Clara Hereu, Masakazu Hori, A Randall Hughes, Mikhail Ivanov, Pablo Jorgensen, Claudia Kruschel, Kun-Seop Lee, Jonathan Lefcheck, Karen McGlathery, Per-Olav Moksnes, Masahiro Nakaoka … & Jay Stachowicz
While considerable evidence exists of biogeographic patterns in the intensity of species interactions, the influence of these patterns on variation in community structure is less clear. Using a model selection approach on measures of trait dispersion in crustaceans associated with eelgrass (Zostera marina) spanning 30º of latitude in two oceans, we found that dispersion strongly increased with increasing predation and decreasing latitude. Ocean and epiphyte load appeared as secondary predictors; Pacific communities were more overdispersed...

Date From: The myriad of complex demographic responses of terrestrial mammals to climate change and gaps of knowledge: A global analysis

Maria Paniw, Tamora James, C. Ruth Archer, Gesa Römer, Sam Levin, Aldo Compagnoni, Judy Che-Castaldo, Joanne Bennett, Andrew Mooney, Dylan Childs, Arpat Ozgul, Owen Jones, Jean Burns, Andrew Beckerman, Abir Patwari, Nora Sanchez-Gassen, Tiffany Knight & Roberto Salguero-Gómez
Approximately 25% of mammals are currently threatened with extinction, a risk that is amplified under climate change. Species persistence under climate change is determined by the combined effects of climatic factors on multiple demographic rates (survival, development, reproduction), and hence, population dynamics. Thus, to quantify which species and regions on Earth are most vulnerable to climate-driven extinction, a global understanding of how different demographic rates respond to climate is urgently needed. Here, we perform a...

Data for: Freeze tolerance influenced forest cover and hydrology during the Pennsylvanian

William Matthaeus, Sophia I. Macarewich, Jon D. Richey, Jonathan P. Wilson, Jennifer C. McElwin, Isabel P. Montañez, William A. DiMichele, Michael T. Hren, Christopher J. Poulsen & Joseph D. White
Global forest cover affects the Earth system by altering surface mass and energy exchange. Physiology determines plant environmental limits and influences geographical vegetation distribution. Ancient plant physiology, therefore, likely affected vegetation-climate feedbacks. We combine climate modeling and ecosystem-process modeling to simulate arboreal vegetation in the late Paleozoic ice age. Using GENESIS V3 GCM simulations, varying pCO2, pO2, and ice extent for the Pennsylvanian, and fossil-derived leaf C:N, maximum stomatal conductance, and specific conductivity for several...

Endothermy makes fishes faster but does not expand their thermal niche

Lucy Harding, Andrew Jackson, Adam Barnett, Ian Donohue, Lewis Halsey, Charlie Huveneers, Carl Meyer, Yannis Papastamatiou, Jayson Semmens, Erin Spencer, Yuuki Watanabe & Nicholas Payne
1. Regional endothermy has evolved several times in marine fishes, and two competing hypotheses are generally proposed to explain the evolutionary drivers behind this trait: thermal niche expansion and elevated cruising speeds. Evidence to support either hypothesis is equivocal, and the ecological advantages conferred by endothermy in fishes remain debated. 2. By compiling published biologging data and collecting precise speed measurements from free-swimming fishes in the wild, we directly test whether endothermic fishes encounter broader...

Experimental evidence of warming-induced disease emergence and its prediction by a trait-based mechanistic model

Devin Kirk, Pepijn Luijckx, Natalie Jones, Leila Krichel, Clara Pencer, Peter Molnar & Martin Krkosek
Predicting the effects of seasonality and climate change on the emergence and spread of infectious disease remains difficult, in part because of poorly understood connections between warming and the mechanisms driving disease. Trait-based mechanistic models combined with thermal performance curves arising from the Metabolic Theory of Ecology (MTE) have been highlighted as a promising approach going forward; however, this framework has not been tested under controlled experimental conditions that isolate the role of gradual temporal...

Data from: Systems and complexity thinking in the general practice literature: an integrative, historical narrative review

Joachim P. Sturmberg, Carmel M. Martin & David A. Katerndahl
PURPOSE: Over the past 7 decades, theories in the systems and complexity sciences have had a major influence on academic thinking and research. We assessed the impact of complexity science on general practice/family medicine. METHODS: We performed a historical integrative review using the following systematic search strategy: medical subject heading [humans] combined in turn with the terms complex adaptive systems, nonlinear dynamics, systems biology, and systems theory, limited to general practice/family medicine and published before...

Worldwide evidence of a unimodal relationship between productivity and plant species richness

Lauchlan H. Fraser, Jason Pither, Anke Jentsch, Marcelo Sternberg, Martin Zobel, Diana Askarizadeh, Sandor Bartha, Carl Beierkuhnlein, Jonathan A. Bennett, Alex Bittel, Bazartseren Boldgiv, Ilsi I. Boldrini, Edward Bork, Leslie Brown, Marcelo Cabido, James Cahill, Cameron N. Carlyle, Giandiego Campetella, Stefano Chelli, Ofer Cohen, Anna-Maria Csergo, Sandra Diaz, Lucas Enrico, David Ensing, Alessandra Fidelis … & Szilárd Szentes
The search for predictions of species diversity across environmental gradients has challenged ecologists for decades. The humped-back model (HBM) suggests that plant diversity peaks at intermediate productivity; at low productivity few species can tolerate the environmental stresses, and at high productivity a few highly competitive species dominate. Over time the HBM has become increasingly controversial, and recent studies claim to have refuted it. Here, by using data from coordinated surveys conducted throughout grasslands worldwide and...

Data from: A critical analysis of the potential for EU Common Agricultural Policy measures to support wild pollinators on farmland

Lorna Cole, David Kleijn, Lynn Dicks, Jane Stout, Simon Potts, Matthias Albrecht, Mario Balzan, Ignasi Bartomeus, Penelope Bebeli, Danilo Bevk, Jacobus Biesmeijer, Róbert Chlebo, Anželika Dautartė, Nikolaos Emmanouil, Chris Hartfield, John Holland, Andrea Holzschuh, Nieke Knoben, Anikó Kovács-Hostyánszki, Yael Mandelik, Heleni Panou, Robert Paxton, Theodora Petanidou, Miguel Pinheiro De Carvalho, … & Jeroen Scheper
1. Agricultural intensification and associated loss of high-quality habitats are key drivers of insect pollinator declines. With the aim of decreasing the environmental impact of agriculture, the 2014 EU Common Agricultural Policy (CAP) defined a set of habitat and landscape features (Ecological Focus Areas: EFAs) farmers could select from as a requirement to receive basic farm payments. To inform the post-2020 CAP, we performed a European-scale evaluation to determine how different EFA options vary in...

Homeless persons use of unscheduled care in St James's Hospital August 2015-July 2017

Clíona Ní Cheallaigh
The data contains all ED presentations and unscheduled admissions to St James's Hospital, Dublin, from August 2015 to July 2017. Data has been anonymised. Individuals are coded as homeless (1) or non-homeless (2) based on the address recorded on their patient record.

Data from: Allopolyploidy, diversification, and the Miocene grassland expansion

Matt C. Estep, Michael R. McKain, Dilys Vela Diaz, Jinshun Zhong, John G. Hodge, Trevor R. Hodkinson, Daniel J. Layton, Simon T. Malcomber, Rémy Pasquet & Elizabeth A. Kellogg
The role of polyploidy, particularly allopolyploidy, in plant diversification is a subject of debate. Whole-genome duplications precede the origins of many major clades (e.g., angiosperms, Brassicaceae, Poaceae), suggesting that polyploidy drives diversification. However, theoretical arguments and empirical studies suggest that polyploid lineages may actually have lower speciation rates and higher extinction rates than diploid lineages. We focus here on the grass tribe Andropogoneae, an economically and ecologically important group of C4 species with a high...

Micro-computed tomography of the holotype of the early tetrapod Ichthyerpeton bradleyae (Huxley in Wright and Huxley, 1866) from the Pennsylvanian of Ireland

Aodhán Ó Gogáin & Patrick N. Wyse Jackson
Ichthyerpeton bradleyae is one of the seven tetrapods originally described by Huxley from the Jarrow Coal (Pennsylvanian; Langsettian Regional Substage equated with the Bashkirian International Stage) in south-eastern Ireland. The holotype, one of only two specimens considered to represent the taxon, consists of the post-cranial skeleton, which has been highly compressed and has undergone extensive replacement of bone by carbonaceous material. The holotype is studied using microcomputed tomography, which reveals that the vertebral column has...

Plant diversity enhanced yield and mitigated drought impacts in intensively managed grassland communities

Guylain Grange, John Finn & Caroline Brophy
There is a global requirement to improve the environmental sustainability of intensively managed grassland monocultures that rely on high rates of nitrogen fertiliser, which is associated with negative environmental impacts. Multi-species grass-legume mixtures are a promising tool for stimulating both productivity and sustainability in intensively managed grasslands, but questions remain about the benefit of increasing the diversity of plant functional groups. We established a plot-scale experiment that manipulated the diversity of plant communities from a...

Cryptic sexual dimorphism reveals differing selection pressures on continental islands - Sulawesi Babbler (Pellorneum celebense) Morphometric Dataset

Fionn Ó Marcaigh
Birds are well known for their sexual dimorphism. But not all forms of dimorphism are the same, and differences in morphology can be so subtle that they aren’t detected by casual observation. We report that this is the case with the Sulawesi Babbler (Pellorneum celebense), the first reported instance of sexual dimorphism in this species or any of the ground babblers of the Southeast Asian islands. Our finding is based on a combination of morphometric...

Data from: Dietary niche constriction when invaders meet natives: evidence from freshwater decapods

Michelle C. Jackson, Jonathan Grey, Katie Miller, J. Robert Britton & Ian Donohue
1. Invasive species are a key driver of global environmental change, with frequently strong negative consequences for native biodiversity and ecosystem processes. Understanding competitive interactions between invaders and functionally similar native species provides an important benchmark for predicting the consequences of invasion. However, even though having a broad dietary niche is widely considered a key factor determining invasion success, little is known about the effects of competition with functionally similar native competitors on the dietary...

Data from: Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT)

Charles L. Nunn & Natalie Cooper
For traits showing correlated evolution, one trait may evolve more slowly than the other, producing evolutionary lag. The species-pairs evolutionary lag test (SPELT) uses an independent contrasts based approach to detect evolutionary lag on a phylogeny. We investigated the statistical performance of SPELT in relation to degree of lag, sample size (species pairs), and strength of association between traits. We simulated trait evolution under two models: one in which trait X changes during speciation and...

Influence of polydimethylsiloxane substrate stiffness on corneal epithelial cells

Mark Ahearne & Sophia Masterton
Many cell types are known to modulate their behavior in response to changes in material stiffness, however little is known about how stiffness effects corneal epithelial cells. This study aims to investigate the response of a corneal epithelial cell line to polydimethylsiloxane (PDMS) substrates with a range of Young’s moduli from 10 kPa to 1500 kPa. Cellular morphology, proliferation, differentiation and mechanobiology were examined. Cells grown on PDMS adopted the typical cobblestone morphology exhibited by...

Data from: Dynamic transmission, host quality and population structure in a multi-host parasite of bumble bees

Mario Xavier Ruiz-González, John Bryden, Yannick Moret, Christine Reber-Funk, Paul Schmid-Hempel & Mark J. F. Brown
The evolutionary ecology of multi-host parasites is predicted to depend upon patterns of host quality and the dynamics of transmission networks. Depending upon the differences in host quality and transmission asymmetries, as well as the balance between intra- and inter-specific transmission, the evolution of specialist or generalist strategies is predicted. Using a trypanosome parasite of bumble bees we ask how host quality and transmission networks relate to parasite population structure across host species, and thus...

Data from: Effects of land use on lake nutrients: the importance of scale, hydrologic connectivity, and region

Patricia A. Soranno, Kendra Spence Cheruvelil, Tyler Wagner, Katherine E. Webster & Mary Tate Bremigan
Catchment land uses, particularly agriculture and urban uses, have long been recognized as major drivers of nutrient concentrations in surface waters. However, few simple models have been developed that relate the amount of catchment land use to downstream freshwater nutrients. Nor are existing models applicable to large numbers of freshwaters across broad spatial extents such as regions or continents. This research aims to increase model performance by exploring three factors that affect the relationship between...

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