100 Works

Large‐scale genome sampling reveals unique immunity and metabolic adaptations in bats

Diana Daniela Moreno Santillan, Tanya Lama, Yocelyn T Gutierrez Guerrero, Zixia Huang, Graham Hughes, Alexis Brown, Paul Donat, Huabin Zhao, Stephen Rossiter, Laurel Yohe, Joshua Potter, Emma Teeling, Sonja Vernes, Kalina Davies, Eugene Myers, Federico Hoffmann, Angelique Corthals, David Ray & Liliana Davalos
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large...

Plagioclase and clinopyroxene mineral chemical and Sr isotope data from Unit 10, Rum Layered Suite, NW Scotland

Brian O'Driscoll, Luke Hepworth & Stephen Daly
These plagioclase and clinopyroxene mineral chemical and Sr isotope data come from Unit 10, Rum Layered Suite, NW Scotland. They underpin a publication entitled 'Rapid crystallisation of precious metal-mineralised layers in mafic magmatic systems', to be published in Nature Geoscience in 2020.

Rural Landscape Case Study from ICOMOS/IUCN Connecting Practice Project: Learning about resilience and sustainability from practical experience

Kristal Buckley, Gwenaelle Bourdin & Leanna Wigboldus
This paper will contribute a case study from the ICOMOS/IUCN Connecting Practice project that aims to develop new approaches to the recognition of interconnected character of natural and cultural values in heritage designation and management frameworks. Reflections on a case study from Phase III of this project (2018-2020) will focus on the natural and cultural systems that can support the resilience of agricultural and biocultural landscapes. Conducted in cooperation with the FAO (Food and Agriculture...

Why Do We Keep Resurrecting the Dead

Siobhan Doyle

A Model of Organic Matter Accumulation in a Developing Fen/Raised Bog Complex

Alan Gilmer, Nicholas Holden, Shane Ward, Anthony Brereton & Edward Farrell

Reformulation Strategies of Repeated References in the Context of Robot Perception Errors in Situated Dialogue

Niels Schütte, John Kelleher & Brian Mac Namee

VISQOL: The Virtual Speech Quality Objective Listener

Andrew Hines, Jan Skoglund, Anil Kokaram & Naomi Harte

Data from: Reconstruction of caribou evolutionary history in Western North America and its implications for conservation

Byron V. Weckworth, Marco Musiani, Allan D. McDevitt, Mark Hebblewhite & Stefano Mariani
The role of Beringia as a refugium and route for trans-continental exchange of fauna during glacial cycles of the past 2 million years are well documented; less apparent is its contribution as a significant reservoir of genetic diversity. Using mitochondrial DNA sequences and 14 microsatellite loci, we investigate the phylogeographic history of caribou (Rangifer tarandus) in western North America. Patterns of genetic diversity reveal two distinct groups of caribou. Caribou classified as a Northern group,...

Data from: Partial genomic survival of cave bears in living brown bears

Axel Barlow, James A. Cahill, Stefanie Hartmann, Christoph Theunert, Georgios Xenikoudakis, Gloria G. Fortes, Johanna L. A. Paijmans, Gernot Rabeder, Christine Frischauf, Aurora Grandal-D'Anglade, Ana García-Vázquez, Marine Murtskhvaladze, Urmas Saarma, Peeter Anijalg, Tomaž Skrbinšek, Giorgio Bertorelle, Boris Gasparian, Guy Bar-Oz, Ron Pinhasi, Montgomery Slatkin, Love Dalén, Beth Shapiro & Michael Hofreiter
Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the...

Data from: Using Illumina Next Generation Sequencing Technologies to sequence multigene families in de novo species

Graham M. Hughes, Li Gang, William J. Murphy, Desmond G. Higgins & Emma C. Teeling
The advent of Next Generation Sequencing Technology (NGST) has revolutionized molecular biology research, allowing for rapid gene/genome sequencing from a multitude of diverse species. As high throughput sequencing becomes more accessible, more efficient workflows must be developed to deal with the amounts of data produced and better assemble the genomes of de novo lineages. We combine traditional laboratory methods with Illumina NGST to amplify and sequence the largest mammalian multigene family, the Olfactory Receptor gene...

Data from: Low fossilization potential of keratin protein revealed by experimental taphonomy

Evan T. Saitta, Chris Rogers, Richard A. Brooker, Geoffrey D. Abbott, Sumit Kumar, Shane S. O'Reilly, Paul Donohoe, Suryendu Dutta, Roger E. Summons & Jakob Vinther
Recent studies have suggested the presence of keratin in fossils dating back to the Mesozoic. However, ultrastructural studies revealing exposed melanosomes in many fossil keratinous tissues suggest that keratin should rarely, if ever, be preserved. In this study, keratin's stability through diagenesis was tested using microbial decay and maturation experiments on various keratinous structures. The residues were analysed using pyrolysis-gas chromatography-mass spectrometry and compared to unpublished feather and hair fossils and published fresh and fossil...

Data from: An early chondrichthyan and the evolutionary assembly of a shark body plan

Michael I. Coates, John A. Finarelli, Ivan J. Sansom, Plamen S. Andreev, Katharine E. Criswell, Kristen Tietjen, Mark L. Rivers & Patrick J. La Riviere
Although relationships among the major groups of living gnathostomes are well established, the relatedness of early jawed vertebrates to modern clades is intensely debated. Here, we provide a new description of Gladbachus, a Middle Devonian (Givetian ~385-million-year-old) stem chondrichthyan from Germany, and one of the very few early chondrichthyans in which substantial portions of the endoskeleton are preserved. Tomographic and histological techniques reveal new details of the gill skeleton, hyoid arch and jaws, neurocranium, cartilage,...

Data from: Re-visiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations

Alain C. Frantz, Allan D. McDevitt, Lisa C. Pope, Joanna Kochan, John Davison, Chris F. Clements, Morten Elmeros, Guillem Molina-Vacas, Aritz Ruiz-Gonzalez, Alessandro Balestrieri, Koen Van Den Berge, Peter Breyne, Emmanuel Do Linh San, Erik O. Ågren, Franz Suchentrunk, Laurent Schley, Rafał Kowalczyk, Berit I. Kostka, Dusko Ćirović, Nikica Šprem, Marc Colyn, Marco Ghirardi, Venislava Racheva, Christophe Braun, Rita Oliveira … & Terry Burke
Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples...

Data from: Enhancing the diversity of breeding invertebrates within field margins of intensively managed grassland: effects of alternative management practices

Rochelle A. Fritch, Helen Sheridan, John A. Finn, Stephen McCormack & Daire Ó HUallacháin
Severe declines in biodiversity have been well documented for many taxonomic groups due to intensification of agricultural practices. Establishment and appropriate management of arable field margins can improve the diversity and abundance of invertebrate groups; however, there is much less research on field margins within grassland systems. Three grassland field margin treatments (fencing off the existing vegetation “fenced”; fencing with rotavation and natural regeneration “rotavated” and; fencing with rotavation and seeding “seeded”) were compared to...

Data from: Peptides derived from cadherin juxtamembrane region inhibit platelet function

Kalyan Golla, Ilias Stavropoulos, Denis Shields, Nimah Moran, Denis C. Shields & Niamh Moran
The juxtamembrane domains (JMD) of transmembrane proteins are rich in critical peptide sequences that participate in dynamic cell signaling events. Synthetic JMD peptides derived from cadherin cell adhesion proteins have previously been shown to modulate platelet function. In this study, we aimed to develop functional bioactive agents from bioinformatically-identified critical peptide sequences. We synthesized overlapping 12-15 amino acids peptides from E- and N-cadherin JMD and assessed their effect on platelet aggregation and platelet ATP secretion....

Data from: Olfactory receptor repertoire size in dinosaurs

Graham M. Hughes & John A. Finarelli
The olfactory bulb (OB) ratio is the size of the olfactory bulb relative to the cerebral hemisphere, and is used to estimate the proportion of the forebrain devoted to smell. In birds, OB ratio correlates with the number of olfactory receptor (OR) genes and therefore has been used as a proxy for olfactory acuity. By coupling OB ratios with known OR gene repertoires in birds, we infer minimum repertoire sizes for extinct taxa, including non-avian...

Data from: Large birds travel farther in homogeneous environments

Marlee A. Tucker, Olga Alexandrou, , Keith L. Bildstein, Katrin Böhning-Gaese, Chloe Bracis, John N. Brzorad, Evan R. Buechley, David Cabot, Justin M. Calabrese, Carlos Carrapato, André Chiaradia, Lisa C. Davenport, Sarah C. Davidson, Mark Desholm, Christopher R. DeSorbo, Robert Domenech, Peter Enggist, William F. Fagan, Nina Farwig, Wolfgang Fiedler, Christen H. Fleming, Alastair Franke, John M. Fryxell, Clara García-Ripollés … & João Paulo Silva
Aim: Animal movement is an important determinant of individual survival, population dynamics, and ecosystem structure and function. Yet it is still unclear how local movements are related to resource availability and the spatial arrangement of resources. Using resident bird species and migratory bird species outside of the migratory period, we examined how the distribution of resources affect the movement patterns of both large terrestrial birds (e.g., raptors, bustards, hornbills) and waterbirds (e.g., cranes, storks, ducks,...

Data from: Genetic drift and collective dispersal can result in chaotic genetic patchiness

Thomas Broquet, Frédérique Viard & Jonathan M. Yearsley
Chaotic genetic patchiness denotes unexpected patterns of genetic differentiation that are observed at a fine scale and are not stable in time. These patterns have been described in marine species with free-living larvae, but are unexpected because they occur at a scale below the dispersal range of pelagic larvae. At the scale where most larvae are immigrants, theory predicts spatially homogeneous, temporally stable genetic variation. Empirical studies have suggested that genetic drift interacts with complex...

Data from: Sex change and effective population size: implications for population genetic studies in marine fish

Ilaria Coscia, Julien Chopelet, Robin S. Waples, Bruce Mann & Stefano Mariani
Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (sex-changing) fish, the sex ratio is typically skewed and biased towards the 'first' sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected...

Data from: Idiosyncratic species effects confound size-based predictions of responses to climate change

Marion Twomey, Eva Brodte, Ute Jacob, Ulrich Brose, Tasman P. Crowe & Mark C. Emmerson
Understanding and predicting the consequences of warming for complex ecosystems and indeed individual species remains a major ecological challenge. Here, we investigated the effect of increased seawater temperatures on the metabolic and consumption rates of five distinct marine species. The experimental species reflected different trophic positions within a typical benthic East Atlantic food web, and included a herbivorous gastropod, a scavenging decapod, a predatory echinoderm, a decapod and a benthic-feeding fish. We examined the metabolism–body...

Data from: Acoustic identification of Mexican bats based on taxonomic and ecological constraints on call design

Veronica Zamora-Gutierrez, Celia Lopez-Gonzalez, M. Cristina MacSwiney Gonzalez, Brock Fenton, Gareth Jones, Elisabeth K. V. Kalko, Sebastien J. Puechmaille, Vassilios Stathopoulos & Kate E. Jones
Monitoring global biodiversity is critical for understanding responses to anthropogenic change, but biodiversity monitoring is often biased away from tropical, megadiverse areas that are experiencing more rapid environmental change. Acoustic surveys are increasingly used to monitor biodiversity change, especially for bats as they are important indicator species and most use sound to detect, localise and classify objects. However, using bat acoustic surveys for monitoring poses several challenges, particularly in megadiverse regions. Many species lack reference...

Supplementary data from: Decoupling of morphological disparity and taxonomic diversity during the end-Permian mass extinction

Junyu Wan, William Foster, Li Tian, Thomas Stubbs, Michael Benton, Xincheng Qiu & Aihua Yuan
An increasing number of unexpectedly diverse benthic communities are being reported from microbially-precipitated carbonate facies in shallow-marine platform settings after the end-Permian mass extinction. Ostracoda, which was one of the most diverse and abundant metazoan groups during this interval, recorded their greatest diversity and abundance associated with these facies. Previous studies, however, focused mainly on their taxonomic diversity and, therefore, left room for discussion of paleoecological significance. Here, we apply a morphometric method (semi-landmarks) to...

In utero accumulated steroids predict neonate anti-predator response in a wild mammal

Bawan Amin, Dómhnall Jennings, Adam Smith, Matthew Quinn, Srivats Chari, Amy Haigh, Devorah Matas, Lee Koren & Simone Ciuti
This file contains the raw data and R-scripts used for the analysis published in the research article: "In utero accumulated steroids predict neonate anti‐predator response in a wild mammal" (https://doi.org/10.1111/1365-2435.13790). A full and detailed description of the methods can be found in the manuscript, or at request from the author (BA). The R-scripts can be used to follow all the steps taken in the analysis and fully reproduce the effects reported. The file contains data...

Use of Deep Learning for structural analysis of CT-images of soil samples

Ralf Wieland, Chinatsu Ukawa, Monika Joschko, Adrian Krolczyk, Guido Fritsch, Thomas Hildebrandt, Juliane Filser, Olaf Schmidt & Juan J. Jimenez
Soil samples from several European countries were scanned using medical computer tomography (CT) device and are now available as CT images. The analysis of these samples was carried out using deep learning methods. For this purpose, a VGG16 network was trained with the CT-images (X). For the annotation (y) a new method for automated annotation, "surrogate'' learning, was introduced. The generated neural networks (NN) were subjected to a detailed analysis. Among other things, transfer learning...

A forest pool as a habitat island for mites in a limestone forest in Southern Norway

Anna Seniczak, Stanislaw Seniczak, Radomir Graczyk, Sławomir Kaczmarek, Bjarte H. Jordal, Jarosław Kowalski, Per Djursvoll, Steffen Roth & Thomas Bolger
Forest water bodies, e.g., pools, constitute ‘environmental islands’ within forests, with specific flora and fauna thus contributing considerably to the landscape biodiversity. The mite communities of Oribatida and Mesostigmata in two distinctive microhabitats, water-soaked Sphagnum mosses at the edge of a pool and other mosses growing on the medium-wet forest floor nearby, were compared in a limestone forest in Southern Norway. In total, 16,189 specimens of Oribatida representing 98 species, and 499 specimens of Mesostigmata,...

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