57 Works

Data from: DNA metabarcoding unveils multi‐scale trophic variation in a widespread coastal opportunist

Andjin Siegenthaler, Owen S. Wangensteen, Chiara Benvenuto, Joana Campos & Stefano Mariani
A thorough understanding of ecological networks relies on comprehensive information on trophic relationships among species. Since unpicking the diet of many organisms is unattainable using traditional morphology‐based approaches, the application of high‐throughput sequencing methods represents a rapid and powerful way forward. Here, we assessed the application of DNA‐metabarcoding with nearly universal primers for the mitochondrial marker cytochrome c oxidase I (COI) in defining the trophic ecology of adult brown shrimp, Crangon crangon, in six European...

Acoustic and temporal birdsong measurements

Tristan Kleyn, Mariane Da Cruz Kaizer & Luiza Figueiredo Passos
In tropical birds, survival is dependent on the ability to effectively communicate with others against a background of high ambient noise. The Acoustic Niche Hypothesis proposes that the deterrent selective force of signal masking has caused animals sharing a habitat to partition their calling behaviour amongst the acoustic bandwidths available, so as to minimise interference between one another. Whether and why species share the so-called ‘acoustic space’ remains a gap in our understanding of animal...

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...

Influence of preservation methods, sample medium and sampling time on eDNA recovery in a neotropical river

Naiara Sales, Owen S. Wangensteen, Daniel Carvalho & Stefano Mariani
Environmental DNA (eDNA) has rapidly emerged as a promising biodiversity monitoring technique, proving to be a sensitive and cost‐effective method for species detection. Despite the increasing popularity of eDNA, several questions regarding its limitations remain to be addressed. We investigated the effect of sampling me‐ dium and time, and preservation methods, on fish detection performance based on eDNA metabarcoding of neotropical freshwater samples. Water and sediment sam‐ ples were collected from 11 sites along the...

Data from: The cost of infection: Argulus foliaceus and its impact on the swimming performance of the three-spined stickleback (Gasterosteus aculeatus)

Alexander Stewart, Rhiannon Hunt, Valantine Muhawenimana, Catherine A.M.E. Wilson, Joseph A. Jackson & Joanne Cable
For fish, there can be multiple consequences of parasitic infections, including the physical impacts on swimming and the pathological costs of infection. This study utilised the three-spined stickleback (Gasterosteus aculeatus) and the ectoparasitic fish louse, Argulus foliaceus, to assess both physical (including form drag and mass) and pathological effects of infection. Both sustained (prolonged swimming within an open channel flume) and burst (C-start) swimming performance were measured on individual fish before (Trials 1-2) and after...

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: 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: 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: 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: 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...

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: 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...

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: 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...

Datasets from: 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...

Natural radionuclide concentrations in soil, water, sediment and biota in England and Wales

N.A. Beresford, C.L. Barnett, D.G. Jones, M.D. Wood, J.D. Appleton, N. Breward & D. Copplestone
Data comprise estimates of activity concentrations of naturally occurring radionuclides (40K, 238U and 232Th series radionuclides) in environmental media (soil and stream sediments and waters) and non-human biota (focusing on the ICRP Reference Animals and Plants). For soil, stream sediments and stream waters data were derived from total K, U and Th concentrations mainly from the ongoing geochemical survey of the United Kingdom (G-BASE), conducted by the British Geological Survey. The geochemical survey data are...

Growth, biomass allocation and tissue nutrient concentrations of subtropical and tropical tree seedlings in response to experimental manipulation of soil phosphorus pools

D Burslem, X. Liu, D. Johnson, A. Taylor, J. Taylor, T. Helgason, Y. Chen & M. Liang
This dataset reports metrics of plant growth, including height, total biomass and the biomass of component plant parts, and percentage root colonisation by mycorrhizas, for tree seedlings of eight tropical and seven subtropical growing in pots of soil that had been amended by addition of various sources of phosphorus (inorganic phosphate, adenosine monophosphate, phytic, or a mixture of all three) plus an unfertilized control treatment with no P additions. The aim of the experiment was...

Soil biological activity in the Chernobyl Exclusion Zone, Ukraine, September 2005 and spring 2016

C.L. Barnett, S. Gashchak, C. Wells, A. Maksimenko, J. Chaplow, M.D. Wood, N.R. Parekh & N.A. Beresford
Data comprise site location, soil chemistry (pH, soil moisture), soil radionuclide activity concentrations (the isotopes measured were: Americium-241, Caesium-137, Plutonium-238, -239 and -240, Strontium-90 (K-40 and U-238 activity concentrations were estimated from stable element data) and soil biological activity (derived from application of bait lamina sticks) at 18 sites in the Chernobyl Exclusion Zone (CEZ), Ukraine in 2016; data for four sites in 2005 are also presented. Estimate absorbed radionuclide dose rates to soil invertebrates...

Data from: Vanishing refuge? Testing the forest refuge hypothesis in coastal East Africa using genome-wide sequence data for seven amphibians

Christopher D. Barratt, Beryl A. Bwong, Robert Jehle, H. Christoph Liedtke, Peter Nagel, Renske E. Onstein, Daniel M. Portik, Jeffrey W. Streicher & Simon P. Loader
High-throughput sequencing data have greatly improved our ability to understand the processes that contribute to current biodiversity patterns. The “vanishing refuge” diversification model is speculated for the coastal forests of eastern Africa, whereby some taxa have persisted and diversified between forest refugia, while others have switched to becoming generalists also present in non-forest habitats. Complex arrangements of geographical barriers (hydrology and topography) and ecological gradients between forest and non-forest habitats may have further influenced the...

Data from: Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Magdalena Guardiola, Owen S. Wangensteen, Pierre Taberlet, Eric Coissac, María Jesús Uriz & Xavier Turon
We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda,...

Fishing for mammals: landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from lotic ecosystems

Naiara Sales, Maisie B. McKenzie, Joseph Drake, Lynsey R. Harper, Samuel S. Browett, Ilaria Coscia, Owen S. Wangensteen, Charles Baillie, Emma Bryce, Deborah A. Dawson, Erinma Ochu, Bernd Hänfling, Lori Lawson Handley, Stefano Mariani, Xavier Lambin, Christopher Sutherland & Allan McDevitt
1. Environmental DNA (eDNA) metabarcoding has revolutionised biomonitoring in both marine and freshwater ecosystems. However, for semi-aquatic and terrestrial animals, the application of this technique remains relatively untested. 2. We first assess the efficiency of eDNA metabarcoding in detecting semi-aquatic and terrestrial mammals in natural lotic ecosystems in the UK by comparing sequence data recovered from water and sediment samples to the mammalian communities expected from historical data. Secondly, using occupancy modelling we compared the...

Stable species boundaries despite ten million years of hybridization in tropical eels

Julia Barth, Chrysoula Gubili, Michael Matschiner, Ole Tørresen, Shun Watanabe, Bernd Egger, Yu-San Han, Eric Feunteun, Ruben Sommaruga, Robert Jehle & Robert Schabetsberger
Genomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genus Anguilla), and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past gene flow across a time-calibrated phylogeny. We show that the seven...

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