158 Works

Ancient geological dynamics impact neutral biodiversity accumulation and are detectable in phylogenetic reconstructions

Leonel Herrera-Alsina, Adam Algar, Greta Bocedi, Cecile Gubry-Rangin, Lesley Lancaster, Poppy Mynard, Owen Osborne, Alexander Papadopulos, Simon Creer, Meis Nangoy, Fahri Fahri, Pungki Lupiyaningdyah, I Made Sudiana, Berry Juliandi & Justin Travis
Aim Landmasses have been continuously modified by tectonic activity, the breakup and collision of landmasses is thought to have generated or suppressed ecological opportunities, altering the rates of speciation, dispersal and extinction. However, the extent to which the signatures of past geologic events are retained in modern biodiversity patterns - or obliterated by recent ecological dynamics - remains unresolved. We aim to identify the fingerprint of different scenarios of geological activity on phylogenetic trees and...

Data from: Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae).

Andrew G. Briscoe, Sarah Goodacre, Susan E. Masta, Martin I. Taylor, Miquel A. Arnedo, David Penney, John Kenny, Simon Creer & Sara Goodacre
The development of second generation sequencing technology has resulted in the rapid production of large volumes of sequence data for relatively little cost, thereby substantially increasing the quantity of data available for phylogenetic studies. Despite these technological advances, assembling longer sequences, such as that of entire mitochondrial genomes, has not been straightforward. Existing studies have been limited to using only incomplete or nominally intra-specific datasets resulting in a bottleneck between mitogenome amplification and downstream high-throughput...

Data from: When one phenotype is not enough - divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species

Giulia Zancolli, Juan J. Calvete, Michael D. Cardwell, Harry W. Greene, William K. Hayes, Matthew J. Hegarty, Hans-Werner Herrmann, Andrew T. Holycross, Dominic I. Lannutti, John F. Mulley, Libia Sanz, Zachary D. Travis, Joshua R. Whorley, Catharine E. Wüster & Wolfgang Wuster
Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus,...

Data from: Medically important differences in snake venom composition are dictated by distinct postgenomic mechanisms

Nicholas R. Casewell, Simon C. Wagstaff, Wolfgang Wüster, Darren A. N. Cook, Fiona M. S. Bolton, Sarah I. King, Davinia Pla, Libia Sanz, Juan J. Calvete & Robert A. Harrison
Variation in venom composition is a ubiquitous phenomenon in snakes and occurs both interspecifically and intraspecifically. Venom variation can have severe outcomes for snakebite victims by rendering the specific antibodies found in antivenoms ineffective against heterologous toxins found in different venoms. The rapid evolutionary expansion of different toxin-encoding gene families in different snake lineages is widely perceived as the main cause of venom variation. However, this view is simplistic and disregards the understudied influence that...

Data from: Contrasting patterns of leaf trait variation among and within species during tropical dry forest succession in Costa Rica

Geraldine Derroire, Jennifer S. Powers, Catherine M. Hulshof, Luis E. Cárdenas Varela & John R. Healey
A coordinated response to environmental drivers amongst individual functional traits is central to the plant strategy concept. However, whether the trait co-ordination observed at the global scale occurs at other ecological scales (especially within species) remains an open question. Here, for sapling communities of two tropical dry forest types in Costa Rica, we show large differences amongst traits in the relative contribution of species turnover and intraspecific variation to their directional changes in response to...

Data from: Colonisation history and genetic diversity: adaptive potential in early stage invasions

Roger S. Thorpe, Jacqualyn Eales & Anita Malhotra
The introduction of Anolis cristatellus from the multiple species anole community of Puerto Rico in the Greater Antilles to the island of Dominica in the Lesser Antilles, with its solitary endemic anole, provides an example of a very recent, timed, single introduction. We investigate the geographic origin and adaptive potential of the Dominican population using a range of methods including mtDNA phylogeography, nuclear microsatellite variation and multiple paternity studies, as well as heritability estimates, common...

Data from: Predicting function from sequence in a large multifunctional toxin family

Anita Malhotra, Simon Creer, John B. Harris, Reto Stöcklin, Philippe Favreau & Roger S. Thorpe
Venoms contain active substances with highly specific physiological effects and are increasingly being used as sources of novel diagnostic, research and treatment tools for human disease. Experimental characterisation of individual toxin activities is a severe rate-limiting step in the discovery process, and in-silico tools which allow function to be predicted from sequence information are essential. Toxins are typically members of large multifunctional families of structurally similar proteins that can have different biological activities, and minor...

Data from: Incorporating the geometry of dispersal and migration to understand spatial patterns of species distributions

Luis Gimenez
Dispersal and migration can be important drivers of species distributions. Because the paths followed by individuals of many species are curvilinear, spatial statistical models based on rectilinear coordinates systems would fail to predict population connectivity or the ecological consequences of migration or species invasions. I propose that we view migration/dispersal as if organisms were moving along curvilinear geometrical objects called smooth manifolds. In that view, the curvilinear pathways become the “shortest realised paths” arising from...

Data from: Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod

Robert Fairweather, Ian R. Bradbury, Sarah J. Heylar, Mark De Bruyn, Nina O. Therkildsen, Paul Bentzen, Jakob Hemmer-Hansen & Gary R. Carvalho
Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range‐wide examinations suggest significant transatlantic divergence, although the fine‐scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data‐synthesis approach, integrating multiple genome‐wide single‐nucleotide polymorphism (SNP)...

Data from: How quantitative is metabarcoding: a meta-analytical approach

Philip D. Lamb, Ewan Hunter, John K. Pinnegar, Simon Creer, Richard G. Davies & Martin I. Taylor
Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis, and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding we conducted a structured review and meta-analysis. The analysis suggests that a weak quantitative relationship may...

Data from: Immanent conditions determine imminent collapses: nutrient regimes define the resilience of macroalgal communities

Jordi Boada, Rohan Arthur, David Alonso, Jordi F. Pagès, Albert Pessarrodona, Silvia Oliva, Giulia Ceccherelli, Luigi Piazzi, Javier Romero & Teresa Alcoverro
Predicting where state-changing thresholds lie can be inherently complex in ecosystems characterized by nonlinear dynamics. Unpacking the mechanisms underlying these transitions can help considerably reduce this unpredictability. We used empirical observations, field and laboratory experiments, and mathematical models to examine how differences in nutrient regimes mediate the capacity of macrophyte communities to sustain sea urchin grazing. In relatively nutrient-rich conditions, macrophyte systems were more resilient to grazing, shifting to barrens beyond 1 800 g m−2...

Data from: Negative effects of vertebrate on invertebrate herbivores mediated by enhanced plant nitrogen content

Yu Zhu, Zhiwei Zhong, Jordi Pagès, Deborah Finke, Deli Wang, Quanhui Ma, Nazim Hassan, Zhu Hui, Ling Wang & Hui Zhu
1. Classic theory holds that the main interaction within the herbivore guild is competition, based on research focused on co-occurring, similarly-sized species that reduce the quantity of shared plant resources. However, plant quality may also be crucial in mediating herbivore interspecific interactions. This is especially true when competition occurs between distantly-related herbivore species, given that small terrestrial herbivores (e.g. insect herbivores) appear to be more sensitive to alterations of plant quality than plant quantity. 2....

Data from: Gynaecological cancer follow-up: national survey of current practice in the UK

Simon Leeson, Nick Stuart, Yvonne Sylvestre, Liz Hall & Rhiannon Whitaker
Objective: To establish a baseline of national practice for follow-up after treatment for gynaecological cancer. Design: Questionnaire survey. Setting: Gynaecological cancer centres and units. Geographical location: UK Participants: Members of the British Gynaecological Cancer Society and the National Forum of Gynaecological Oncology Nurses. Interventions: A questionnaire survey. Outcome measures: To determine schedules of follow-up, who provides it and what routine testing is used for patients who have had previous gynaecological cancer. Results: A total of...

Data from: A spatially integrated framework for assessing socioecological drivers of carnivore decline

Nicolás Gálvez, Gurutzeta Guillera-Arroita, Freya A. V. St. John, Elke Schüttler, David W. Macdonald & Zoe G. Davies
Habitat loss, fragmentation and degradation are key threats to the long-term persistence of carnivores, which are also susceptible to direct persecution by people. Integrating natural and social science methods to examine how habitat configuration/quality and human–predator relations may interact in space and time to effect carnivore populations within human-dominated landscapes will help prioritise conservation investment and action effectively. We propose a socioecological modelling framework to evaluate drivers of carnivore decline in landscapes where predators and...

Data from: Plasticity in growth of farmed and wild Atlantic salmon: is the increased growth rate of farmed salmon caused by evolutionary adaptations to the commercial diet?

Alison C. Harvey, Monica F. Solberg, Eva Troianou, Gary R. Carvalho, Martin I. Taylor, Simon Creer, Lise Dyrhovden, Ivar Helge Matre & Kevin A. Glover
Background: Domestication of Atlantic salmon for commercial aquaculture has resulted in farmed salmon displaying substantially higher growth rates than wild salmon under farming conditions. In contrast, growth differences between farmed and wild salmon are much smaller when compared in the wild. The mechanisms underlying this contrast between environments remain largely unknown. It is possible that farmed salmon have adapted to the high-energy pellets developed specifically for aquaculture, contributing to inflated growth differences when fed on...

Data from: Impacts of logging roads on tropical forests

Fritz Kleinschroth & John R. Healey
Road networks are expanding in tropical countries, increasing human access to remote forests that act as refuges for biodiversity and provide globally important ecosystem services. Logging is one of the main drivers of road construction in tropical forests. We evaluated forest fragmentation and impacts of logging roads on forest resilience and wildlife, considering the full life cycle of logging roads. Through an extensive evidence review we found that for logging road construction, corridors between 3...

Data from: Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus

Sonia Pascoal, Gary Carvalho, Olga Vasieva, Roger Hughes, Andrew Cossins, Yongxiang Fang, Kevin Ashelford, Lisa Olohan, Carlos Barroso, Sonia Mendo & Simon Creer
Anthropogenic endocrine disruptors now contaminate all environments globally, with concomitant deleterious effects across diverse taxa. While most studies on endocrine disruption (ED) have focused on vertebrates, the superimposition of male sexual characteristics in the female dogwhelk, Nucella lapillus (imposex), caused by organotins, provides one of the most clearcut ecological examples of anthropogenically induced ED in aquatic ecosystems. To identify the underpinning mechanisms of imposex for this ‘nonmodel’ species, we combined Roche 454 pyrosequencing with custom...

Data from: A genomic island linked to ecotype divergence in Atlantic cod

Jakob Hemmer-Hansen, Einar E. Nielsen, Nina O. Therkildsen, Martin I. Taylor, Rob Ogden, Audrey J. Geffen, Dorte Bekkevold, Sarah Helyar, Christophe Pampoulie, Torild Johansen & Gary R. Carvalho
The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome-wide or localized in “genomic mosaics” during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate...

Microbial enzyme activities under experimental drought and warming at Clocaenog forest and Peaknaze Moor (2012)

M. Dominguez, S. Reinsch, E. Holthof, A.R. Smith, E. Koller & B.A. Emmett
This data consist of measurements on soil microbial enzyme activity of six hydrolytic enzymes and related soil measurements from the experimental field sites at Clocaenog forest and Peaknaze. Samples were collected in 2012 from plots subjected to experimental drought and warming as well as untreated control plots. Soil cores were taken for the topsoil 0 to10 centimetres. Enzymes were measured at the climate change field site Climoor that is located in Clocaenog forest, North East...

Enteric virus concentrations, pH and turbidity in wastewater discharged to the Conwy River and estuary, North Wales (2016-2017)

K. Farkas, M.R. Marshall, D.M. Cooper, J.E. McDonald, S.K. Malham & D.L. Jones
This dataset contains pH, turbidity and viral concentration information in untreated and treated wastewater samples at wastewater discharge points and wastewater treatment plants along the Conwy River. The aim of the data collection was to investigate diurnal changes in enteric virus concentrations in wastewater and to investigate any correlation with wastewater pH and turbidity. Untreated wastewater samples were collected at one wastewater treatment plant for two events. Treated wastewater samples were collected at two wastewater...

Coastal Biodiversity and Ecosystem Service Sustainability (CBESS) spider and beetle abundance on salt marsh sites at Morecambe Bay and Essex

H. Ford, A. Garbutt & M. Skov
The dataset comprises the spider and beetle abundance sampled by suction sampling in each 1metre (m) x 1m quadrat. Sampling was conducted at six salt marsh sites at four spatial scales: 1 m (the minimal sampling unit) nested within a hierarchy of increasing scales of 1-10 m, 10-100 m and 100-1000 m. Three of the sites were in Morecambe Bay, North West England and three of the sites were in Essex, South East England. All...

Coastal Biodiversity and Ecosystem Service Sustainability (CBESS) soil pH on salt marsh sites at Morecambe Bay and Essex

H. Ford, A. Garbutt & M. Skov
The dataset comprises the pH of a 10 gram soil sample from the top 5 centimetre of soil taken within each 1metre (m) x 1m quadrat. Sampling was conducted at six salt marsh sites at four spatial scales: 1 m (the minimal sampling unit) nested within a hierarchy of increasing scales of 1-10 m, 10-100 m and 100-1000 m. Three of the sites were in Morecambe Bay, North West England and three of the sites...

Time series of microbial carbon release from soil as carbon dioxide under different nitrogen and phosphorus treatments with a high molecular weight substrate added as a carbon source, Conwy catchment, North Wales, UK (2016)

H.C. Glanville, L.L. De Sosa, M.R. Marshall, D.M. Cooper & D.L. Jones
Time series data of carbon release in disintegrations per minute are presented for different nitrogen and phosphorus treatments with a high molecular weight substrate added as a carbon source to soil samples from six depths (0-15, 15-30, 50-100, 100-150, 150-200 and 250-300 centimetres). Soil cores were collected from a field experiment in the Conwy catchment in July 2016 and returned the laboratories of the School of Environment, Natural Resources and Geography, Bangor University. A high...

Perception of environmental and other risks - data from a 2018 social science questionnaire in the UK

K. Farkas, E. Green, P. Cross & D.L. Jones
This dataset contains the answers gathered from the 806 participants who successfully finished an on-line survey on risk perception of environment-associated risks. The survey was launched on the 15th of February 2018 and ran for five days. The survey contained best worst scaling (BWS) to understand people’s perceptions to certain risks. In this study 16 risks were included in the BWS including four air-, food- and waterborne illnesses and 12 other hazards. The BWS was...

Topsoil physico-chemical properties from the Glastir Monitoring and Evaluation Programme, Wales 2013-2016

D.A. Robinson, S. Astbury, G. Barrett, A. Burden, H. Carter, B.A. Emmett, A. Garbutt, C. Giampieri, J. Hall, P. Henrys, S. Hughes, A. Hunt, S. Jarvis, D.L. Jones, P. Keenan, I. Lebron, D. Nunez, A. Owen, M. Patel, M.G. Pereira, F. Seaton, K. Sharps, B. Tanna, N. Thompson, B. Williams … & C.M. Wood
This data set includes a range of physico-chemical properties measured from topsoil within a wide range of land use types across Wales, collected as part of the Glastir Monitoring and Evaluation Programme (GMEP). The properties included are: soil organic matter (loss on ignition (LOI)), derived carbon concentration, total soil organic carbon (SOC), nitrogen, total soil phosphorous, Olsen-phosphorous (within improved land only), pH, electrical conductivity, soil bulk density of fine earth, fine earth volumetric water content...

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