66 Works

Robustness and Prediction Accuracy of Machine Learning for Objective Visual Quality Assessment

Andrew Hines, Paul Kendrick, Adriaan Barri, Manish Narwaria & Judith Redi

Fine-scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multi-modelling approach

Ilaria Coscia, Sophie Wilmes, Joseph Ironside, Goward-Brown Alice, Enda O'Dea, Shelagh Malham, Allan McDevitt & Peter Robins
Population dynamics of marine species that are sessile as adults are driven by oceanographic dispersal of larvae from spawning to nursery grounds. This is mediated by life-history traits such as the timing and frequency of spawning, larval behaviour and duration, and settlement success. Here, we use 1725 single nucleotide polymorphisms (SNPs) to study the fine scale spatial genetic structure in the commercially important cockle species Cerastoderma edule and compare it to environmental variables and current-mediated...

Parallel evolution of Varroa resistance in honey bees; a common mechanism across continents?

Isobel Grindrod & Stephen Martin
The near-globally distributed ecto-parasitic mite of the Apis mellifera honey bee, Varroa destructor, has formed a lethal association with Deformed wing virus, a once rare and benign RNA virus. In concert the two have killed millions of wild and managed colonies, particularly across the northern hemisphere, forcing the need for regular acaricide application to ensure colony survival. However, despite the short association (in evolutionary terms), A. mellifera populations across the globe have been surviving many...

Primer biases in the molecular assessment of diet in multiple insectivorous mammals

Samuel Browett, Thomas Curran, Denise O'Meara, Andrew Harrington, Naiara Guimarães Sales, Rachael Antwis, David O'Neill & Allan McDevitt
Our understanding of trophic interactions of small insectivorous mammals has been drastically improved with the advent of DNA metabarcoding. The technique has continued to be optimised over the years, with primer choice repeatedly being a vital factor for dietary inferences. However, the majority of dietary studies examining the effect of primer choice often rely on in silico analyses or comparing between species that occupy an identical niche type. Here we apply DNA metabarcoding to empirically...

Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

Allan McDevitt, Holly Broadhurst, Luke Gregory, Emma Bleakley, Joseph Perkins, Jenna Lavin, Polly Bolton, Samuel Browett, Claire Howe, Natalie Singleton, Darren Tansley & Naiara Sales
Finding more efficient ways to monitor, and estimate the diversity of, mammalian communities is a major step towards their management and conservation. Environmental DNA (eDNA) from river water has recently been shown to be a viable method for biomonitoring mammalian communities. Yet, most of the studies to date have focused on the potential for eDNA to detect individual species, with little focus on describing patterns of community diversity and structure. In this study, we focus...

The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest

Anthony Ferreira, Albertina Lima, Robert Jehle, Miquéias Ferrão & Adam Stow
Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism loci. A population tree and clustering analyses revealed...

A database of radionuclide biological half-life values for wildlife

N.A. Beresford, K. Beaugelin-Seiller, C. Wells, S. Vives-Lynch, J. Vives I Batlle, M.D. Wood, K. Tagami, A. Real, J. Burgos, S. Fesenko, M. Cujic, A. Kryshev, N. Pachal, B.S. Su, C.L. Barnett, S. Uchida, T. Hinton, J. Mihalík, K. Stark, C. Willrodt & J.S. Chaplow
Data comprise biological and ecological half-life values for marine, freshwater, terrestrial and riparian organisms. The database includes 1908 biological half-life values for 52 elements across a range of wildlife groups (marine, freshwater, terrestrial and riparian). The compilation of values from a range of sources was conducted by an international working group under the auspices of an International Atomic Energy Agency programme.

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 on immunological expression and phenotypes in a natural population of field voles in Kielder Forest, UK 2015-2017

S. Paterson, J. Jackson, I. Jackson, J. Bradley, M. Begon, K. Wanelik & C. Taylor
Data comprise morphometric measurements, sex determination, maturity and immunological analysis of blood pathogens from wild field voles (Microtus agrestis) in Kielder Forest, Northumberland, UK in 2015-17.

Soil and vegetation radionuclide activity concentrations and calculated dose rates from the Red Forest, Chernobyl, Ukraine, 2016-2017

C.L. Barnett, S. Gashchak, A. Maksimenko, J.S. Chaplow, M.D. Wood & N.A. Beresford
Data comprise plot details and radionuclide activity concentrations for Sr-90, Cs-137, Am-241, Pu-238, Pu-239 and Pu-240 in ‘grassy’ vegetation and soil. These radionuclide activity concentrations have been used to make estimations of total weighted absorbed doses to grassy vegetation, deciduous trees and bacteria; no dose rate estimates for grassy vegetation have been made for those sites where grassy vegetation was absent. Radiation from the 1986 Chernobyl nuclear power plant accident killed coniferous trees in a...

Data from: Effects of land-use change on functional and taxonomic diversity of Neotropical bats

Fábio Z. Farneda, Christoph F. J. Meyer & Carlos E. V. Grelle
Human land-use changes are particularly extensive in tropical regions, representing one of the greatest threats to terrestrial biodiversity and a key research topic in conservation. However, studies considering the effects of different types of anthropogenic disturbance on the functional dimension of biodiversity in human-modified landscapes are rare. Here, we obtained data through an extensive review of peer-reviewed articles and compared 30 Neotropical bat assemblages in well-preserved primary forest and four different human-disturbed habitats in terms...

Data from: All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment

Lorenzo Talarico, Tommaso Russo, Giulia Maiello, Charles Baillie, Giuliano Colosimo, Lorenzo D'Andrea, Federico Di Maio, Fabio Fiorentino, Simone Franceschini, Germana Garofalo, Dario Scannella, Stefano Cataudella & Stefano Mariani
AbstractMonitoring marine resource exploitation is a key activity in fisheries science and biodiversity conservation. Since research surveys are time-consuming and costly, fishery-dependent data (i.e. derived directly from fishing vessels) are increasingly credited with a key role in expanding the reach of ocean monitoring. Fishing vessels may be seen as widely ranging data-collecting platforms, which could act as a fleet of sentinels for monitoring marine life, in particular exploited stocks. Here, we investigate the possibility of...

Optimising bat bioacoustic surveys in human-modified neotropical landscapes

Adrià López-Baucells, Natalie Yoh, Ricardo Rocha, Paulo Bobrowiec, Jorge Palmeirim & Christoph Meyer
During the last decades, the use of bioacoustics as a non-invasive and cost-effective sampling method has greatly increased worldwide. For bats, acoustic surveys have long been known to complement traditional mist-netting, however, appropriate protocol guidelines are still lacking for tropical regions. Establishing the minimum sampling effort needed to detect ecological changes in bat assemblages (e.g., activity, composition and richness) is crucial in view of workload and project cost constraints, and because detecting such changes must...

Data from: Widespread loss of mammalian lineage and dietary diversity in the early Oligocene of Afro-Arabia

Dorien De Vries, Steven Heritage, Matthew Borths, Hesham Sallam & Erik Seiffert
Diverse lines of geological and geochemical evidence indicate that the Eocene-Oligocene transition (EOT) marked the onset of a global cooling phase, rapid growth of the Antarctic ice sheet, and a worldwide drop in sea level. Paleontologists have established that shifts in mammalian community structure in Europe and Asia were broadly coincident with these events, but the potential impact of early Oligocene climate change on the mammalian communities of Afro-Arabia has long been unclear. Here we...

Data from: An advanced shape-fitting algorithm applied to quadrupedal mammals: improving volumetric mass estimates

Charlotte A. Brassey & James D. Gardiner
Body mass is a fundamental physical property of an individual and has enormous bearing upon ecology and physiology. Generating reliable estimates for body mass is therefore a necessary step in many palaeontological studies. Whilst early reconstructions of mass in extinct species relied upon isolated skeletal elements, volumetric techniques are increasingly applied to fossils when skeletal completeness allows. We apply a new ‘alpha shapes’ (α-shapes) algorithm to volumetric mass estimation in quadrupedal mammals. α-shapes are defined...

Data from: Ecogeographical patterns of morphological variation in pygmy shrews Sorex minutus (Soricomorpha: Soricinae) within a phylogeographic and continental-and-island framework

Rodrigo Vega, Allan D. Mcdevitt, Boris Kryštufek & Jeremy B. Searle
Ecogeographical patterns of morphological variation were studied in the Eurasian pygmy shrew Sorex minutus aiming to understand the species’ morphological diversity in a continental and island setting, and within the context of previous detailed phylogeographical studies. In total, 568 mandibles and 377 skulls of S. minutus from continental and island populations from Europe and Atlantic islands were examined using a geometric morphometrics approach, and the general relationships of mandible and skull size and shape with...

Data from: Human commercial models’ eye colour shows negative frequency-dependent selection

Isabela Rodrigues Nogueira Forti & Robert John Young
In this study we investigated the eye colour of human commercial models registered in the UK (400 female and 400 male) and Brazil (400 female and 400 male) to test the hypothesis that model eye colour frequency was the result of negative frequency-dependent selection. The eye colours of the models were classified as: blue, brown or intermediate. Chi-square analyses of data for countries separated by sex showed that in the United Kingdom brown eyes and...

Data from: Does sex matter? Gender-specific responses to forest fragmentation in Neotropical bats

Ricardo Rocha, Diogo F. Ferreira, Adrià López-Baucells, Fabio Z. Farneda, Joao M.B. Carreiras, Jorge M. Palmeirim & Christoph F. J. Meyer
Understanding the consequences of habitat modification on wildlife communities is central to the development of conservation strategies. However, albeit male and female individuals of numerous species are known to exhibit differences in habitat use, sex-specific responses to habitat modification remain little explored. Here, we used a landscape-scale fragmentation experiment to assess, separately for males and females, the effects of fragmentation on the abundance of Carollia perspicillata and Rhinophylla pumilio, two widespread Neotropical frugivorous bats. We...

Data from: Metabarcoding of shrimp stomach content: harnessing a natural sampler for fish biodiversity monitoring

Andjin Siegenthaler, Owen S. Wangensteen, Ana Z. Soto, Chiara Benvenuto, Laura Corrigan & Stefano Mariani
Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services, and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time are one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on...

Data from: Dispersal and group formation dynamics in a rare and endangered temperate forest bat (Nyctalus lasiopterus, Chiroptera: Vespertilionidae)

João D. Santos & Christoph F. J. Meyer
For elusive mammals like bats, colonization of new areas and colony formation are poorly understood, as is their relationship with the genetic structure of populations. Understanding dispersal and group formation behaviors is critical not only for a better comprehension of mammalian social dynamics, but also for guiding conservation efforts of rare and endangered species. Using nuclear and mitochondrial markers, we studied patterns of genetic diversity and differentiation among and within breeding colonies of giant noctule...

Craniodental morphology and phylogeny of marsupials

Robin M. D. Beck, Robert S. Voss & Sharon A. Jansa
The current literature on marsupial phylogenetics includes numerous studies based on analyses of morphological data with limited sampling of Recent and fossil taxa and many studies based on analyses of molecular data with dense sampling of Recent taxa, but few studies have combined both data types. Another dichotomy in the marsupial phylogenetic literature is between studies focused on New World taxa, and those focused on Sahulian taxa. To date, there has been no attempt to...

Establishing an evidence-base for erect pelvis radiography : positioning, radiation dose and image quality

Kholoud Alzyoud
Purpose: Pelvic radiography using X-ray imaging has traditionally been used for the identification of hip joint changes, including the identification of pathologies such as osteoarthritis. For patients suffering from hip pain, the supine pelvis X-ray examination is one of the initial diagnostic steps. Despite this, many recent studies have recommended that the position should now be undertaken erect and not supine to reflect the functional appearances of the hip joint. This thesis aims to establish...

Embedding Life Cycle Costing in 5D BIM

Dermot Kehily & Jason Underwood
Life Cycle Costing (LCC) is the consideration of all ‘relevant’ costs and revenues associated with the acquisition and ownership of an asset. LCC has a number of relevant applications, these include project appraisal; facilities management; procurement and tendering and as a means to evaluate sustainable construction. Although these advantages are well recognised, the process is underutilised due to a number of documented barriers to adoption. Notably these include lack of accurate historical databases; the perceived...

Environmental DNA effectively captures functional diversity of coastal fish communities

Giorgio Aglieri, Charles Baillie, Stefano Mariani, Carlo Cattano, Antonio Calò, Gabriele Turco, Davide Spatafora, Antonio Di Franco, Manfredi Di Lorenzo, Paolo Guidetti & Marco Milazzo
Robust assessments of taxonomic and functional diversity are essential components of research programs aimed at understanding current biodiversity patterns and forecasting trajectories of ecological changes. Yet, evaluating marine biodiversity along its dimensions is challenging and dependent on the power and accuracy of the available data collection methods. Here we combine three traditional survey methodologies [Underwater Visual Census strip transects (UVCt), Baited Underwater Videos (BUVs) and Small Scale Fishery catches (SSFc)], and one novel molecular technique...

Data from: Sexual selection impacts brain anatomy in frogs and toads

Yu Zeng, Shang Ling Lou, Wen Bo Liao, Robert Jehle & Alexander Kotrschal
Natural selection is a major force in the evolution of vertebrate brain size, but the role of sexual selection in brain size evolution remains enigmatic. At least two opposing schools of thought predict a relationship between sexual selection and brain size. Sexual selection should facilitate the evolution of larger brains because better cognitive abilities may aid the competition for mates. However, it may also restrict brain size evolution due to energetic trade-offs between brain tissue...

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