166 Works

Deep structure, long-distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis

Angus Davison, Daniel Ramos Gonzalez & Suzanne Saenko
While snails of the genus Cepaea have historically been important in studying colour polymorphism an ongoing issue is that there is a lack of knowledge of the underlying genetics of the polymorphism, as well as an absence of genomic data to put findings in context. We therefore used phylogenomic methods to begin to investigate the post-glacial history of Cepaea nemoralis, with a long-term aim to understand the roles that selection and drift have in determining...

Data from: Epigenetic potential and DNA methylation in an ongoing House Sparrow (Passer domesticus) range expansion

Haley E Hanson, Chengqi Wang, Aaron W Schrey, Andrea L Liebl, Mark Ravinet, Rays H Y Jiang & Lynn B Martin
During range expansions, organisms can use epigenetic mechanisms to adjust to conditions in novel areas by altering gene expression and enabling phenotypic plasticity. Here, we predicted that the number of CpG sites within the genome, one form of epigenetic potential, would be important for successful range expansions because DNA methylation can modulate gene expression, and consequently plasticity. We asked how the number of CpG sites and DNA methylation varied across five locations in the ~70...

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.

Additional file 2 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 2. Data abstraction table.

Additional file 2 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 2. Data abstraction table.

Large scale eDNA monitoring of multiple aquatic pathogens as a tool to provide risk maps for wildlife diseases

Natalie Sieber, Alex King, Raphael Krieg, Armin Zenker, Christoph Vorburger & Hanna Hartikainen
Multiple parasites and pathogens cause disease in aquatic wildlife and in aquaculture species, generating a need for monitoring and management. Conventional disease monitoring methods involve laborious, costly and invasive capture and examination of host species, and require specialised expertise for every host and pathogen of interest. These restrictions could be alleviated by using pathogen detection techniques based on environmental DNA that provide simultaneous surveys of multiple aquatic pathogens across different host taxa. This would also...

Data from: Acquisition of germ plasm accelerates vertebrate evolution.

Teri Evans, Christopher M. Wade, Frank A. Chapman, Andrew D. Johnson & Matthew Loose
Primordial germ cell (PGC) specification occurs either by induction from pluripotent cells (epigenesis) or by a cell-autonomous mechanism mediated by germ plasm (preformation). Among vertebrates, epigenesis is basal, whereas germ plasm has evolved convergently across lineages and is associated with greater speciation. We compared protein-coding sequences of vertebrate species that employ preformation with their sister taxa that use epigenesis and demonstrate that genes evolve more rapidly in species containing germ plasm. Furthermore, differences in rates...

Data from: Speciation despite globally overlapping distributions in Penicillium chrysogenum: the population genetics of Alexander Fleming's lucky fungus

Daniel A. Henk, Carly E. Eagle, Kevin Brown, Marco A. Van Den Berg, Paul S. Dyer, Stephen W. Peterson & Matt C. Fisher
Eighty years ago, Alexander Fleming described the antibiotic effects of a fungus that had contaminated his bacterial culture, kick starting the antimicrobial revolution. The fungus was later ascribed to a putatively globally distributed asexual species, Penicillium chrysogenum. Recently, the species has been shown to be genetically diverse, and possess mating-type genes. Here, phylogenetic and population genetic analyses show that this apparently ubiquitous fungus is actually composed of at least two genetically distinct species with only...

Data from: Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

David Wragg, Joram M. Mwacharo, Paul M. Hocking, Olivier Hanotte & Jose A. Alcalde
Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide single-nucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional...

Data from: Quorum sensing and cheating in bacterial biofilms

Roman Popat, Shanika A. Crusz, Marco Messina, Paul Williams, Stuart A. West & Stephen P. Diggle
The idea from human societies that self-interest can lead to a breakdown of cooperation at the group level is sometimes termed the public goods dilemma. We tested this idea in the opportunistic bacterial pathogen, Pseudomonas aeruginosa, by examining the influence of putative cheats that do not cooperate via cell-to-cell signalling (quorum-sensing, QS). We found that: (i) QS cheating occurs in biofilm populations owing to exploitation of QS-regulated public goods; (ii) the thickness and density of...

Data from: Intrinsic honesty and the prevalence of rule violations across societies

Simon Gächter & Jonathan F. Schulz
Deception is common in nature and humans are no exception. Modern societies have created institutions to control cheating, but many situations remain where only intrinsic honesty keeps people from cheating and violating rules. Psychological, sociological and economic theories suggest causal pathways to explain how the prevalence of rule violations in people’s social environment, such as corruption, tax evasion or political fraud, can compromise individual intrinsic honesty. Here we present cross-societal experiments from 23 countries around...

Data from: High throughput method for analysis of repeat number for 28 phase variable loci of Campylobacter jejuni strain NCTC11168

Lea Lango-Scholey, Jack Aidley, Alexandra Woodacre, Michael A. Jones & Christopher D. Bayliss
Mutations in simple sequence repeat tracts are a major mechanism of phase variation in several bacterial species including Campylobacter jejuni. Changes in repeat number of tracts located within the reading frame can produce a high frequency of reversible switches in gene expression between ON and OFF states. The genome of C. jejuni strain NCTC11168 contains 29 loci with polyG/polyC tracts of seven or more repeats. This protocol outlines a method—the 28-locus-CJ11168 PV-analysis assay—for rapidly determining...

Data from: Phenological shifts in hoverflies (Diptera: Syrphidae): linking measurement and mechanism

Christopher Hassall, Jennifer Owen, Francis S. Gilbert & Francis Gilbert
An understanding of ecological and evolutionary responses to global environmental change requires both a robust measurement of the change that is occurring and a mechanistic framework for understanding the drivers of that change. Such a requirement provides a challenge because biological monitoring is often ad hoc, and mechanistic experiments are often performed under highly simplified conditions. This study integrates multiple datasets to evaluate our current knowledge of the measurement and mechanism of phenological shifts in...

Data from: Fixational eye movements predict visual sensitivity

Chris Scholes, Paul V. McGraw, Marcus Nyström & Neil W. Roach
During steady fixation, observers make small fixational saccades at a rate of around 1-2 per second. Presentation of a visual stimulus triggers a biphasic modulation in fixational saccade rate – an initial inhibition followed by a period of elevated rate and a subsequent return to baseline. Here we show that, during passive viewing, this rate signature is highly sensitive to small changes in stimulus contrast. By training a linear support vector machine to classify trials...

Data from: Parasites contribute to ecologically dependent postmating isolation in the adaptive radiation of three spined stickleback

Aliya El Nagar & Andrew D. C. MacColl
Spatial variation in parasitic infections is common, and has the potential to drive population divergence and the reproductive isolation of hosts. However, despite support from theory and model laboratory systems, little strong evidence has been forthcoming from the wild. Here, we show that parasites are likely to cause reproductive isolation in the adaptive radiation of three-spined stickleback. Adjacent wild populations on the Scottish island of North Uist differ greatly and consistently in the occurrence of...

Data from: GlobTherm, a global database on thermal tolerances for aquatic and terrestrial organisms

Joanne M. Bennett, Piero Calosi, Susana Clusella-Trullas, Brezo Martínez, Jennifer Sunday, Adam C. Algar, Miguel B. Araújo, Bradford A. Hawkins, Sally Keith, Ingolf Kühn, Carsten Rahbek, Laura Rodríguez, Alexander Singer, Fabricio Villalobos, Miguel Ángel Olalla-Tárraga & Ignacio Morales-Castilla
How climate affects species distributions is a longstanding question receiving renewed interest owing to the need to predict the impacts of global warming on biodiversity. Is climate change forcing species to live near their critical thermal limits? Are these limits likely to change through natural selection? These and other important questions can be addressed with models relating geographical distributions of species with climate data, but inferences made with these models are highly contingent on non-climatic...

Data from: Co-foundress confinement elicits kinship effects in a naturally sub-social parasitoid

Ian C. W. Hardy, Daniela Lupi & Mohamed K. Abdi
Kinship among interacting individuals is often associated with sociality and also with sex ratio effects. Parasitoids in the bethylid genus Goniozus are sub-social, with single foundress females exhibiting post-ovipositional maternal care via short-term aggressive host and brood defence against conspecific females. Due to local mate competition (LMC) and broods normally being produced by a single foundress, sex ratios are female biased. Contests between adult females are, however, not normally fatal and aggression is reduced when...

Diversification in evolutionary arenas – assessment and synthesis

Nicolai M. Nürk, H. Peter Linder, Renske E. Onstein, Matthew J. Larcombe, Colin E. Hughes, Laura Piñeiro Fernández, Philipp M. Schlüter, Luis Valente, Carl Beierkuhnlein, Vanessa Cutts, Michael J. Donoghue, Erika J. Edwards, Richard Field, Suzette G.A. Flantua, Steven I. Higgins, Anke Jentsch, Sigrid Liede-Schumann & Michael D. Pirie
Understanding how and why rates of evolutionary diversification vary is a central issue in evolutionary biology, ecology and biogeography. The concept of adaptive radiation has attracted much interest, but is metaphorical and verbal in nature, making it difficult to quantitatively compare different evolutionary lineages or geographic regions. In addition, the causes of evolutionary stasis are relatively neglected. Here we review the central concepts in the evolutionary diversification literature and bring these together by proposing a...

Automated detection of lameness in sheep using machine learning approaches: novel insights into behavioural differences among lame and non-lame sheep

Jasmeet Kaler, Jurgen Mitsch, Jorge Vazquez Diosdado, Nicola Bollard, Tania Dottorini & Keith Ellis
Lameness in sheep is the biggest cause of concern regarding poor health and welfare among sheep producing countries. Best practice for lameness relies on rapid treatment, yet there are no objective measures of lameness detection. Use of accelerometers and gyroscopes have been widely used in human activity studies and their use is becoming increasingly common in livestock. In this study, we used 23 datasets (10 non-lame and 13 lame sheep) from an accelerometer and gyroscope-based...

Nucleotide alignments of eight meiosis genes under extreme selection following whole genome duplication in Arabidopsis lyrata/A.arenosa.

Paul Seear, Martin France, Catherine Gregory, Darren Heavens, Roswitha Schmickl, Levi Yant & James Higgins
In this study we performed a genotype-phenotype association analysis of meiotic stability in ten autotetraploid Arabidopsis lyrata and A. lyrata/A. arenosa hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (ASY1, ASY3, PDS5b, PRD3, REC8, SMC3, ZYP1a/b) implicated in synaptonemal complex...

Elemental concentrations in representative species of the ICRP's Reference Animals and Plants and associated soils in terrestrial Mediterranean ecosystems in Spain

J. Guillén, M. Izquierdo, S. Young, C. Wells, C.L. Barnett, N.A. Beresford, A. Baeza, A. Salas, A. Muñóz-Serrano, J.M. Corrales-Vázquez, J.G. Muñoz-Muñoz, E. Tovar & J.S. Chaplow
Data comprise stable element concentrations in terrestrial Reference Animals and Plants (RAPs) and corresponding whole-body concentration ratios determined in two different Mediterranean ecosystems: a Pinewood and a Dehesa (grassland with disperse tree cover). The International Commission on Radiological Protection (ICRP) RAPs considered in the Pinewood ecosystem were Pine Tree and Wild Grass; whereas in the Dehesa ecosystem those considered were Deer, Rat, Earthworm, Bee, Frog, Duck and Wild Grass. The data include: elemental concentrations in...

Data from: Genome-wide SNP data unveils the globalization of domesticated pigs

Bin Yang, Leilei Cui, Miguel Perez-Enciso, Aleksei Traspov, Richard P. M. A. Crooijmans, Natalia Zinovieva, Lawrence B. Schook, Alan Archibald, Kesinee Gatphayak, Christophe Knorr, Alex Triantafyllidis, Panoraia Alexandri, Gono Semiadi, Olivier Hanotte, Deodália Dias, Peter Dovč, Pekka Uimari, Laura Iacolina, Massimo Scandura, Martien A. M. Groenen, Lusheng Huang & Hendrik-Jan Megens
Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global...

Data from: From the animal house to the field: are there consistent individual differences in immunological profile in wild populations of field voles (Microtus agrestis)?

Elena Arriero, Klara M. Wanelik, Richard J. Birtles, Janette E. Bradley, Joseph A. Jackson, Steve Paterson & Mike Begon
Inbred mouse strains, living in simple laboratory environments far removed from nature, have been shown to vary consistently in their immune response. However, wildlife populations are typically outbreeding and face a multiplicity of challenges, parasitological and otherwise. In this study we seek evidence of consistent difference in immunological profile amongst individuals in the wild. We apply a novel method in this context, using longitudinal (repeated capture) data from natural populations of field voles, Microtus agrestis,...

Data from: Strong population structure in a species manipulated by humans since the Neolithic: the European fallow deer (Dama dama dama)

Karis H. Baker, Howard W.I. Gray, Veronica Ramovs, Despoina Mertzanidou, C Akin Peksen, C. Can Bilgin, Naomi Sykes & A.R. Hoelzel
Species that have been translocated and otherwise manipulated by humans may show patterns of population structure that reflect those interactions. At the same time, natural processes shape populations, including behavioural characteristics like dispersal potential and breeding system. In Europe, a key factor is the geography and history of climate change through the Pleistocene. During glacial maxima throughout that period, species in Europe with temperate distributions were forced south, becoming distributed among the isolated peninsulas represented...

Data from: Effects of deer on woodland structure revealed through terrestrial laser scanning

Markus P. Eichhorn, Joseph Ryding, Martin J. Smith, Robin M. A. Gill, Gavin M. Siriwardena & Robert J. Fuller
Terrestrial laser scanning (TLS) captures the three-dimensional structure of habitats. Compared to traditional methods of forest mensuration, it allows quantification of structure at increased resolution, and the derivation of novel metrics with which to inform ecological studies and habitat management. Lowland woodlands in the UK have altered in structure over the last century due to increased abundance of deer and a decline in management. We compared whole-canopy profiles between woodlands with high (>10 deer km−2)...

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