46 Works

Data from: Crowdsourcing the identification of organisms: a case-study of iSpot

Jonathan Silvertown, Martin Harvey, Richard Greenwood, Mike Dodd, Jon Rosewell, Tony Rebelo, Janice Ansine & Kevin McConway
Accurate species identification is fundamental to biodiversity science, but the natural history skills required for this are neglected in formal education at all levels. In this paper we describe how the web application ispotnature.org and its sister site ispot.org.za (collectively, "iSpot") are helping to solve this problem by combining learning technology with crowdsourcing to connect beginners with experts. Over 94% of observations submitted to iSpot receive a determination. To date (2014), iSpot has crowdsourced the...

Data from: Hybridisation in closely related Rhododendron species: half of all species differentiating markers experience serious transmission ratio distortion

Tobias Marczewski, David F. Chamberlain & Richard I. Milne
An increasing number of studies of hybridization in recent years have revealed that complete reproductive isolation between species is frequently not finalized in more or less closely related organisms. Most of these species do, however, seem to retain their phenotypical characteristics despite the implication of gene flow, highlighting the remaining gap in our knowledge of how much of an organism's genome is permeable to gene flow, and which factors promote or prevent hybridization. We used...

Data from: The influence of nonrandom extra-pair paternity on heritability estimates derived from wild pedigrees

Josh A. Firth, Jarrod D. Hadfield, Anna W. Santure, Jon Slate & Ben C. Sheldon
Quantitative genetic analysis is often fundamental for understanding evolutionary processes in wild populations. Avian populations provide a model system due to the relative ease of inferring relatedness amongst individuals through observation. However, extra-pair paternity (EPP) creates erroneous links within the social pedigree. Previous work has suggested this causes minor underestimation of heritability if paternal misassignment is random and hence not influenced by the trait being studied. Nevertheless, much literature suggests numerous traits are associated with...

Data from: Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

James A. Nicholls, R. Toby Pennington, Erik J. Koenen, Colin E. Hughes, Jack Hearn, Lynsey Bunnefeld, Kyle G. Dexter, Graham N. Stone, Catherine A. Kidner & Erik J. M. Koenen
Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown...

Data from: Risk of bias in reports of in vivo research: a focus for improvement

Malcolm Robert Macleod, Aaron Lawson McLean, Aikaterini Kyriakopoulou, Styllianos Serghiou, Arno De Wilde, Nicki Sherratt, Theo Hirst, Rachel Hemblade, Zsanett Bahor, Cristina Nunes-Fonseca, Aparna Potluru, Andrew Thomson, Julija Baginskaite, Kieren Egan, Hanna Vesterinen, Gillian L. Currie, Leonid Churilov, David W. Howwels, Emily S. Sena, Stylianos Serghiou, Julija Baginskitae & David W. Howells
The reliability of experimental findings depends on the rigour of experimental design. Here we show limited reporting of measures to reduce the risk of bias in a random sample of life sciences publications, significantly lower reporting of randomisation in work published in journals of high impact, and very limited reporting of measures to reduce the risk of bias in publications from leading United Kingdom institutions. Ascertainment of differences between institutions might serve both as a...

Data from: Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

Nicola J. Barson, Tuku Aykanat, Kjetil Hindar, Matthew Baranski, Geir H. Bolstad, Peder Fiske, Céleste Jacq, Arne J. Jensen, Susan E. Johnston, Sten Karlsson, Matthew Kent, Thomas Moen, Eero Niemelä, Torfinn Nome, Tor F. Næsje, Panu Orell, Atso Romakkaniemi, Harald Sægrov, Kurt Urdal, Jaakko Erkinaro, Sigbjørn Lien & Craig R. Primmer
Males and females share many traits that have a common genetic basis; however, selection on these traits often differs between the sexes, leading to sexual conflict. Under such sexual antagonism, theory predicts the evolution of genetic architectures that resolve this sexual conflict. Yet, despite intense theoretical and empirical interest, the specific loci underlying sexually antagonistic phenotypes have rarely been identified, limiting our understanding of how sexual conflict impacts genome evolution and the maintenance of genetic...

Data from: Determinants of flammability in savanna grass species

Kimberley J. Simpson, Brad S. Ripley, Pascal-Antione Christin, Claire M. Belcher, Caroline E. R. Lehmann, Gavin H. Thomas, Colin P. Osborne & Pascal-Antoine Christin
1. Tropical grasses fuel the majority of fires on Earth. In fire-prone landscapes, enhanced flammability may be adaptive for grasses via the maintenance of an open canopy and an increase in spatiotemporal opportunities for recruitment and regeneration. In addition, by burning intensely but briefly, high flammability may protect resprouting buds from lethal temperatures. Despite these potential benefits of high flammability to fire-prone grasses, variation in flammability among grass species, and how trait differences underpin this...

Data from: Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion

Alex Twyford, Jannice Friedman & Alex D. Twyford
Organisms exhibit an incredible diversity of life history strategies as adaptive responses to environmental variation. The establishment of novel life history strategies involves multilocus polymorphisms, which will be challenging to establish in the face of gene flow and recombination. Theory predicts that adaptive allelic combinations may be maintained and spread if they occur in genomic regions of reduced recombination, such as chromosomal inversion polymorphisms, yet empirical support for this prediction is lacking. Here, we use...

Data from: Dissecting the hydrological niche: soil moisture, space and lifespan

Gonzalo García-Baquero, Jonathan Silvertown, David J. Gowing & Cipriano J. Valle
Questions: Are communities structured on a hydrological (soil moisture) gradient? Is there spatial segregation into hydrological niches? What is the shape of the hydrological niches of individual species? Controlling for spatial autocorrelation, how much of the spatial structure in the community is due to variation in hydrology? Do annuals and perennials behave alike with respect to the above questions? Locations: La Mina in Moscosa Farm, Salamanca, western Spain (dehesa community) and Laguna Larga in the...

Data from: Are molecular markers useful predictors of adaptive potential?

Elizabeth A. Mittell, Shinichi Nakagawa & Jarrod D. Hadfield
Estimates of molecular genetic variation are often used as a cheap and simple surrogate for a population's adaptive potential, yet empirical evidence suggests they are unlikely to be a valid proxy. However, this evidence is based on molecular genetic variation poorly predicting estimates of adaptive potential rather than how well it predicts true values. As a consequence, the relationship has been systematically underestimated and the precision with which it could be measured severely overstated. By...

Data from: Expression of parasite genetic variation changes over the course of infection: implications of within-host dynamics for the evolution of virulence

Melanie Clerc, D. Ebert & M. D. Hall
How infectious disease agents interact with their host changes during the course of infection and can alter the expression of disease-related traits. Yet by measuring parasite life-history traits at one or few moments during infection, studies have overlooked the impact of variable parasite growth trajectories on disease evolution. Here we show that infection-age-specific estimates of host and parasite fitness components can reveal new insight into the evolution of parasites. We do so by characterizing the...

Data from: How integrated are behavioural and endocrine stress response traits? A repeated measures approach to testing the stress coping style model

Kay Boulton, Elsa Couto, Andrew J. Grimmer, Ryan L. Earley, Adelino V.M. Canario, Alastair J. Wilson, Craig A. Walling & Adelino V. M. Canario
It is widely expected that physiological and behavioral stress responses will be integrated within divergent stress-coping styles (SCS) and that these may represent opposite ends of a continuously varying reactive–proactive axis. If such a model is valid, then stress response traits should be repeatable and physiological and behavioral responses should also change in an integrated manner along a major axis of among-individual variation. While there is some evidence of association between endocrine and behavioral stress...

Data from: State-dependent cooperation in burying beetles: parents adjust their contribution towards care based on both their own and their partner’s size

Natalia Pilakouta, Jon Richardson & Per T. Smiseth
Handicapping experiments on species with biparental care show that a focal parent increases its contribution when its partner is handicapped. Such results are interpreted as evidence for negotiation, whereby each parent adjusts its amount of care to that of its partner. However, it is currently unclear whether the focal parent responds to a change in its handicapped partner's behaviour or state. To address this gap, we conducted an experiment on the burying beetle Nicrophorus vespilloides...

Data from: RAD-mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region

Suo Qiu, Roberta Bergero, Sara Guirao-Rico, Jose L. Campos, Timothée Cezard, Karim Gharbi & Deborah Charlesworth
How loss of genetic exchanges (recombination) evolves between sex chromosomes is a long-standing question. Suppressed recombination may evolve when a sexually antagonistic (SA) polymorphism occurs in a partially sex-linked, “pseudo-autosomal’ region (or “PAR”), maintaining allele frequency differences between the two sexes, and creating selection for closer linkage with the fully sex-linked region of the Y chromosome in XY systems, or the W in ZW sex chromosome systems. Most evidence consistent with the SA polymorphism hypothesis...

Data from: Regional heritability mapping method helps explain missing heritability of blood lipid traits in isolated populations

Masoud Shirali, Ricardo Pong-Wong, Pau Navarro, Sara Knott, Caroline Hayward, Veronique Vitart, Igor Rudan, Harry Campbell, Nicholas Hastie, Alan Wright & Christopher Haley
Single single-nucleotide polymorphism (SNP) genome-wide association studies (SSGWAS) may fail to identify loci with modest effects on a trait. The recently developed regional heritability mapping (RHM) method can potentially identify such loci. In this study, RHM was compared with the SSGWAS for blood lipid traits (high-density lipoprotein (HDL), low-density lipoprotein (LDL), plasma concentrations of total cholesterol (TC) and triglycerides (TG)). Data comprised 2246 adults from isolated populations genotyped using ~300 000 SNP arrays. The results...

Data from: Integrated radar and lidar analysis reveals extensive loss of remaining intact forest on Sumatra 2007–2010

Murray B. Collins & Edward T. A. Mitchard
Forests with high above ground biomass (AGB), including those growing on peat swamps, have historically not been thought suitable for biomass mapping and change detection using Synthetic Aperture Radar (SAR). However, by integrating L-band (λ = 0.23 m) SAR with lidar data from the ALOS and ICESat earth-observing satellites respectively, and 56 forest plots, we were able to create a forest biomass and change map for a 10.7 Mha section of eastern Sumatra that still...

Data from: Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population

Tutku Aykanat, Susan E. Johnston, Eero Niemelä, Panu Orell, Jaakko Erkinaro & Craig R. Primmer
Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high-resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined...

Data from: Growth responses of a green alga to multiple environmental drivers

Georgina L. Brennan & Sinead Collins
One feature of global change is that biota must respond not to single, but to multiple environmental drivers. By growing a model photosynthetic microbe in environments containing between one and eight different drivers, including changes in CO2, temperature, and pH, in different combinations, we show that the number as well as the identities of drivers explain shifts in population growth rates. This is because the biotic response to multiple environmental drivers depends on the response...

Data from: High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment

Antonia G. P. Ford, Kanchon K. Dasmahapatra, Lukas Rüber, Karim Gharbi, Timothée Cezard & Julia J. Day
Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found...

Data from: Concordance of bacterial communities of two tick species and blood of their shared rodent host

Evelyn C. Rynkiewicz, Chris Hemmerich, Clay Fuqua, Keith Clay & Douglas B. Rusch
High-throughput sequencing is revealing that most macro-organisms house diverse microbial communities. Of particular interest are disease vectors whose microbiome could potentially affect pathogen transmission and vector competence. We investigated bacterial community composition and diversity of the ticks Dermacentor variabilis (n = 68) and Ixodes scapularis (n = 15) and blood of their shared rodent host, Peromyscus leucopus (n = 45) to quantify bacterial diversity and concordance. The 16S rRNA gene was amplified from genomic DNA...

Data from: Drug repurposing: a systematic approach to evaluate candidate oral neuroprotective interventions for secondary progressive multiple sclerosis

Hanna M. Vesterinen, Peter Connick, Cadi M. J. Irvine, Emily S. Sena, Kieren J. Egan, Gary G. Carmichael, Afiyah Tariq, Sue Pavitt, Jeremy Chattaway, Malcolm Robert Macleod, Siddharthan Chandran & Jeremy Chataway
Objective: To develop and implement an evidence based framework to select, from drugs already licenced, candidate oral neuroprotective drugs to be tested in secondary progressive multiple sclerosis. Design: Systematic review of clinical studies of oral putative neuroprotective therapies in MS and four other neurodegenerative diseases with shared pathological features, followed by systematic review and meta-analyses of the in vivo experimental data for those interventions. We presented summary data to an international multi-disciplinary committee, which assessed...

Data from: The relative efficiency of modular and non-modular networks of different size

Colin R. Tosh & Luke McNally
Most biological networks are modular but previous work with small model networks has indicated that modularity does not necessarily lead to increased functional efficiency. Most biological networks are large, however, and here we examine the relative functional efficiency of modular and non-modular neural networks at a range of sizes. We conduct a detailed analysis of efficiency in networks of two size classes: ‘small’ and ‘large’, and a less detailed analysis across a range of network...

Data from: The kinetochore prevents centromere-proximal crossover recombination during meiosis

Nadine Vincenten, Lisa-Marie Kuhl, Isabel Lam, Ashwini Oke, Alastair R. W. Kerr, Andreas Hochwagen, Jennifer C. Fung, Scott Keeney, Gerben Vader & Adèle L. Marston
During meiosis, crossover recombination is essential to link homologous chromosomes and drive 22 faithful chromosome segregation. Crossover recombination is non-random across the genome, 23 and centromere-proximal crossovers are associated with an increased risk of aneuploidy, 24 including Trisomy 21 in humans. Here, we identify the conserved Ctf19/CCAN kinetochore sub- 25 complex as a major factor that minimizes potentially deleterious centromere-proximal crossovers 26 in budding yeast. We uncover multi-layered suppression of pericentromeric recombination by the 27...

Data from: Unified pre- and postsynaptic long-term plasticity enables reliable and flexible learning

Rui Ponte Costa, Robert C. Froemke, Per Jesper Sjöström & Mark C. W. Van Rossum
Although it is well known that long-term synaptic plasticity can be expressed both pre- and postsynaptically, the functional consequences of this arrangement have remained elusive. We show that spike-timing-dependent plasticity with both pre- and postsynaptic expression develops receptive fields with reduced variability and improved discriminability compared to postsynaptic plasticity alone. These long-term modifications in receptive field statistics match recent sensory perception experiments. Moreover, learning with this form of plasticity leaves a hidden postsynaptic memory trace...

Data from: Maintenance of species boundaries in a Neotropical radiation of Begonia

Alex D. Twyford, Catherine A. Kidner & Richard A. Ennos
A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by-product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by...

Registration Year

  • 2015
    46

Resource Types

  • Dataset
    46

Affiliations

  • University of Edinburgh
    46
  • University of Glasgow
    5
  • Centre for Ecology and Hydrology
    4
  • University of St Andrews
    3
  • University of Exeter
    3
  • University of Oxford
    3
  • New York University
    2
  • McGill University
    2
  • University of Leeds
    2
  • Natural Resources Institute Finland
    2