166 Works

Pervasive admixture and the spread of a large-lipped form in a cichlid fish radiation

Will Sowersby, José Cerca, Bob Wong, Topi Lehtonen, David Chapple, Mariana Leal-Cardin, Marta Barluenga & Mark Ravinet
Adaptive radiations have proven important for understanding the mechanisms and processes underlying biological diversity. The convergence of form and function, as well as admixture and adaptive introgression, are common in adaptive radiations. However, distinguishing between these two scenarios remains a challenge for evolutionary research. The Midas cichlid species complex (Amphilophus spp.) is a prime example of adaptive radiation, with phenotypic diversification occurring at various stages of genetic differentiation. One species, A. labiatus, has large fleshy...

Abundance of Anolis bicaorum, and niche measurements of plots on the island Utila, Honduras

Emma Higgins, Doreen Boyd, Tom Brown, Sarah Owen & Adam Algar
The question of what controls animal abundance has always been fundamental to ecology, but given rapid environmental change, understanding the drivers and mechanisms governing abundance is more important than ever. Here, we determine how multidimensional environments and niches interact to determine population abundance along a tropical habitat gradient. Focusing on the endemic lizard Anolis bicaorum on the island of Utila (Honduras), we evaluate direct and indirect effects of three interacting niche axes on abundance: thermal...

Data for: Mapping the evolution of accurate Batesian mimicry of social wasps in hoverflies

Alice Leavey, Christopher Taylor, Matthew Symonds, Francis Gilbert & Tom Reader
Hoverflies (Diptera: Syrphidae) provide an excellent opportunity to study the evolution of Batesian mimicry, where defenceless prey avoid predation by evolving to resemble defended ‘model’ species. While some hoverflies beautifully resemble their hymenopteran models, others seem to be poor mimics or are apparently non-mimetic. The reasons for this variation are still enigmatic despite decades of research. Here, we address this issue by mapping social-wasp mimicry across the phylogeny of Holarctic hoverflies. Using the ‘distance transform’...

Corine land cover changes between 2012 and 2018 for the UK, Isle of Man, Jersey and Guernsey

B. Cole, B. De La Barreda, A. Hamer, T. Codd, M. Payne, L. Chan, G. Smith & H. Balzter
This dataset is the Corine Land Cover (CLC) change map between 2012 and 2018, consisting of 44 classes in the hierarchical three level Corine nomenclature. The Corine land cover changes between 2012 and 2018 for the UK, Isle of Man, Jersey and Guernsey dataset forms part of the Corine Land Cover Maps collection and is produced within the frame of the Copernicus programme on land monitoring. Corine Land Cover (CLC) provides consistent information on land...

Dataset for ‘Serial Small- and Wide-Angle X-ray Scattering with Laboratory Sources’

Mark Levenstein, Karen Robertson, Thomas Turner, Liam Hunter, Cate O’Brien, Cedrick O'Shaughnessy, Alexander Kulak, Pierre Le Magueres, Jakub Wojciechowski, Oleksandr Mykhaylyk, Nikil Kapur & Fiona Meldrum
This dataset contains measurements used in the paper, ‘Serial Small- and Wide-Angle X-ray Scattering with Laboratory Sources' from the journal, IUCrJ (doi: 10.1107/S2052252522007631). Included are the raw SAXS, WAXS, and XRD patterns used in the evaluation of different samples, sample environments, and X-ray scattering instruments. From these data, the authors determined that it is feasible to perform serial SAXS/WAXS analysis of materials using laboratory X-ray sources with the aid of micro- and milli-fluidic sample environments.

Additional file 4 of Design decisions and data completeness for experience sampling methods used in psychosis: systematic review

Emilia Deakin, Fiona Ng, Emma Young, Naomi Thorpe, Christopher Newby, Carol Coupland, Michael Craven & Mike Slade
Additional file 4. Quality assessment.

Additional file 4 of Design decisions and data completeness for experience sampling methods used in psychosis: systematic review

Emilia Deakin, Fiona Ng, Emma Young, Naomi Thorpe, Christopher Newby, Carol Coupland, Michael Craven & Mike Slade
Additional file 4. Quality assessment.

Additional file 1 of Venetoclax combined with low dose cytarabine compared to standard of care intensive chemotherapy for the treatment of favourable risk adult acute myeloid leukaemia (VICTOR): Study protocol for an international, open-label, multicentre, molecularly-guided randomised, phase II trial

Richard Dillon, Shanna Maycock, Aimee Jackson, Sonia Fox, Sylvie Freeman, Charles Craddock, Catherine Thomas, Emma Homer, Jane Leahy, Anna Mamwell, Nicola Potter, Nigel Russell, Andrew Wei, Hans Beier Ommen, Claire Hemmaway, Steve Knapper & Lucinda Billingham
Additional file 1: Supplementary Appendix 1. SPIRIT checklist for the VICTOR protocol A completed Standard Protocol Items: Recommendations for Intervention Trials (SPIRIT) checklist for the VICTOR protocol. Supplementary Appendix 2. WHO trial registration data set for the VICTOR trial The World Health Organization (WHO) trial registration data set for the VICTOR trial. Supplementary Appendix 3. VICTOR informed consent forms Exemplar informed consent and blood sample analysis consent form for the VICTOR trial. Supplementary Appendix 4....

Prior exposure to long day photoperiods alters immune responses and increases susceptibility to parasitic infection in stickleback

James Whiting, Muayad Mahmud, Janette Bradley & Andrew MacColl
Seasonal disease and parasitic infection are common across organisms, including humans, and there is increasing evidence for intrinsic seasonal variation in immune systems. Changes are orchestrated through organisms’ physiological clocks using cues such as day length. Ample research in diverse taxa has demonstrated multiple immune responses are modulated by photoperiod, but to date, there have been few experimental demonstrations that photoperiod cues alter susceptibility to infection. We investigated the interactions among photoperiod history, immunity, and...

miR-342-5p inhibits osteosarcoma cell growth, migration, invasion, and sensitivity to Doxorubicin through targeting Wnt7b

Qing Liu, Zhenting Wang, Xiaohua Zhou, Mingying Tang, Wei Tan, Tianshi Sun & Youwen Deng
Osteosarcoma (OS) accounts for 9 percent of cancer-related deaths in young people. The PI3K/Akt signaling, a well-known carcinogenic signaling pathway in human cancer, cooperates with other signaling pathways such as Wnt signaling to promote cancer progression. Wnt7b, as a transforming member of the Wnt family, could activate mTORC1 through PI3K-AKT signaling and is upregulated in OS. In the present study, we found that miR-342-5p inhibits Wnt7b expression via direct binding to Wnt7b 3′-UTR. miR-342-5p overexpression...

miR-342-5p inhibits osteosarcoma cell growth, migration, invasion, and sensitivity to Doxorubicin through targeting Wnt7b

Qing Liu, Zhenting Wang, Xiaohua Zhou, Mingying Tang, Wei Tan, Tianshi Sun & Youwen Deng
Osteosarcoma (OS) accounts for 9 percent of cancer-related deaths in young people. The PI3K/Akt signaling, a well-known carcinogenic signaling pathway in human cancer, cooperates with other signaling pathways such as Wnt signaling to promote cancer progression. Wnt7b, as a transforming member of the Wnt family, could activate mTORC1 through PI3K-AKT signaling and is upregulated in OS. In the present study, we found that miR-342-5p inhibits Wnt7b expression via direct binding to Wnt7b 3′-UTR. miR-342-5p overexpression...

Ammonium Complexes of Orthoester Cryptands Are Inherently Dynamic and Adaptive

Oleksandr Shyshov, Max von Delius, Xiang Wang, Christof Jäger & Marko Hanževački
Fluxional chemical species such as bullvalene have been a valuable source of inspiration and fundamental insight into the nature of chemical bonds. A supramolecular analogue of bullvalene, i.e., a “fluxional host–guest system”, in which the ensemble of a well-defined host and guest is engaged in continuous, degenerate constitutional rearrangements, is still elusive, however. Here, we report experimental and computational evidence for guest-induced dynamic covalent rearrangements in the ammonium complexes of self-assembled orthoester cryptands. This unique...

Data from: Multiple aspects of plasticity in clutch size vary among populations of a globally distributed songbird

David F. Westneat, Veronika Bókony, Terry Burke, Olivier Chastel, Henrik Jensen, Thomas Kvalnes, Ádám Z. Lendvai, András Liker, Douglas Mock, Julia Schroeder, P. L. Schwagmeyer, Gabriele Sorci & Ian R. K. Stewart
1. Plasticity in life-history characteristics can influence many ecological and evolutionary phenomena, including how invading organisms cope with novel conditions in new locations or how environmental change affects organisms in native locations. Variation in reaction norm attributes is a critical element to understanding plasticity in life history, yet we know relatively little about the ways in which reaction norms vary within and among populations. 2. We amassed data on clutch size from marked females in...

Data from: The emergence of the lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (Decapoda: Achelata, Astacidea, Glypheidea, Polychelida)

Heather D. Bracken-Grissom, Shane T. Ahyong, Richard D. Wilkinson, Rodney M. Felmann, Carrie E. Schweitzer, Jesse W. Breinholt, Matthew Bendall, Ferran Palero, Tin-Yam Chan, Darryl L. Felder, Rafael Robles, Ka-Hou Chu, Ling-Ming Tsang, Dohyup Kim, Joel W. Martin, Keith A. Crandall & Rodney M. Feldmann
Lobsters are a ubiquitous and economically important group of decapod crustaceans that includes the infraorders Polychelida, Glypheidea, Astacidea and Achelata. They include familiar forms such as the spiny, slipper, clawed lobsters and crayfish and unfamiliar forms such as the deep-sea and “living fossil” species. The high degree of morphological diversity among these infraorders has led to a dynamic classification and conflicting hypotheses of evolutionary relationships. In this study, we estimated phylogenetic relationships amongst the major...

Data from: Increased survival of experimentally evolved antimicrobial peptide-resistant Staphylococcus aureus in an animal host

Adam J. Dobson, Joanne Purves & Jens Rolff
Antimicrobial peptides (AMPs) have been proposed as new class of antimicrobial drugs, following the increasing prevalence of bacteria resistant to antibiotics. Synthetic AMPs are functional analogues of highly evolutionarily conserved immune effectors in animals and plants, produced in response to microbial infection. Therefore, the proposed therapeutic use of AMPs bears the risk of ‘arming the enemy’: bacteria that evolve resistance to AMPs may be cross-resistant to immune effectors (AMPs) in their hosts. We used a...

Data from: Macroparasites at peripheral sites of infection are major and dynamic modifiers of systemic anti-microbial pattern recognition responses

Ida M. Friberg, Susan Little, Catriona Ralli, Ann Lowe, Amy Hall, Joseph A. Jackson & Jan E. Bradley
Immune defences and the maintenance of immunological homeostasis in the face of pathogenic and commensal microbial exposures are channelled by innate anti-microbial pattern recognition receptors (PRRs) such as toll-like receptors (TLRs). Whilst PRR-mediated response programmes are the result of long-term host-pathogen or host-commensal co-evolutionary dynamics involving microbes, an additional possibility is that macroparasitic co-infections may be a significant modifier of such interactions. We demonstrate experimentally that macroparasites (the model gastrointestinal nematode, Heligmosomoides) at peripheral sites...

Data from: RAD-Seq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene

Paul M. Richards, M. Maureen Liu, Natalie Lowe, John W. Davey, Mark L. Blaxter & Angus Davison
Studies on the classic shell colour and banding polymorphism of the land snail Cepaea played a crucial role in establishing the importance of natural selection in maintaining morphological variation. Cepaea is also a pre-eminent model for ecological genetics because the outward colour and banding phenotype is entirely genetically determined, primarily by a ‘supergene’ of at least five loci. Unfortunately, progress in understanding the evolution and maintenance of the Cepaea polymorphism stalled, partly because of a...

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: Cost-effectiveness of a specialist geriatric medical intervention for frail older people discharged from acute medical units: economic evaluation in a two-centre randomised controlled trial (AMIGOS)

Lukasz Tanajewski, Matthew Franklin, Georgios Gkountouras, Vladislav Berdunov, Judi Edmans, Simon Conroy, Lucy E. Bradshaw, John R. F. Gladman & Rachel A. Elliott
Background: Poor outcomes and high resource-use are observed for frail older people discharged from acute medical units. A specialist geriatric medical intervention, to facilitate Comprehensive Geriatric Assessment, was developed to reduce the incidence of adverse outcomes and associated high resource-use in this group in the post-discharge period. Objective: To examine the costs and cost-effectiveness of a specialist geriatric medical intervention for frail older people in the 90 days following discharge from an acute medical unit,...

Data from: Geographic variation and trade-offs in parasitoid virulence

Lisa Fors, Robert Markus, Ulrich Theopold, Lars Ericson & Peter A. Hambäck
Host–parasitoid systems are characterized by a continuous development of new defence strategies in hosts and counter-defence mechanisms in parasitoids. This co-evolutionary arms race makes host–parasitoid systems excellent for understanding trade-offs in host use caused by evolutionary changes in host immune responses and parasitoid virulence. However, knowledge obtained from natural host–parasitoid systems on such trade-offs is still limited. In this study, the aim was to examine trade-offs in parasitoid virulence in Asecodes parviclava (Hymenoptera: Eulophidae) when...

Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus)

Emily E. Puckett, Jane Park, Matthew Combs, Michael J. Blum, Juliet E. Bryant, Adalgisa Caccone, Federico Costa, Eva E. Deinum, Alexandra Esther, Chelsea G. Himsworth, Peter D. Keightley, Albert Ko, Ake Lundkvist, Lorraine M. McElhinney, Serge Morand, Judith Robins, James Russell, Tanja M. Strand, Olga Suarez, Lisa Yon & Jason Munshi-South
Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes....

Data from: Do perceptual biases emerge early or late in visual processing? Decision-biases in motion perception

Elisa Zamboni, Timothy Ledgeway, Paul V. McGraw & Denis Schluppeck
Visual perception is strongly influenced by contextual information. A good example is reference repulsion, where subjective reports about the direction of motion of a stimulus are significantly biased by the presence of an explicit reference. These perceptual biases could arise early, during sensory encoding, or alternatively, they may reflect decision-related processes occurring relatively late in the task sequence. To separate these two competing possibilities, we asked (human) subjects to perform a fine motion-discrimination task and...

Data from: The ecology of wildlife disease surveillance: demographic and prevalence fluctuations undermine surveillance

Laura Walton, Glenn Marion, Ross S. Davidson, Piran C. L. White, Lesley A. Smith, Dolores Gavier-Widen, Lisa Yon, Duncan Hannant, Michael R. Hutchings & Piran C.L. White
Wildlife disease surveillance is the first line of defence against infectious disease. Fluctuations in host populations and disease prevalence are a known feature of wildlife disease systems. However, the impact of such heterogeneities on the performance of surveillance is currently poorly understood. We present the first systematic exploration of the effects of fluctuations' prevalence and host population size on the efficacy of wildlife disease surveillance systems. In this study, efficacy is measured in terms of...

Data from: A 1,000-year-old antimicrobial remedy with antistaphylococcal activity

Freya Harrison, Aled E. L. Roberts, Rebecca Gabrilska, Kendra P. Rumbaugh, Christina Lee & Stephen P. Diggle
Plant-derived compounds and other natural substances are a rich potential source of compounds that kill or attenuate pathogens that are resistant to current antibiotics. Medieval societies used a range of these natural substances to treat conditions clearly recognizable to the modern eye as microbial infections, and there has been much debate over the likely efficacy of these treatments. Our interdisciplinary team, comprising researchers from both sciences and humanities, identified and reconstructed a potential remedy for...

Data from: Environmental modification via a quorum sensing molecule influences the social landscape of siderophore production

Roman Popat, Freya Harrison, Ana C. Da Silva, Scott A.S. Easton, Luke McNally, Paul Williams, Stephen P. Diggle & Scott A. S. Easton
Bacteria produce a wide variety of exoproducts that favourably modify their environment and increase their fitness. These are often termed ‘public goods’ because they are costly for individuals to produce and can be exploited by non-producers (cheats). The outcome of conflict over public goods is dependent upon the prevailing environment and the phenotype of the individuals in competition. Many bacterial species use quorum sensing (QS) signalling molecules to regulate the production of public goods. QS,...

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