31 Works

Data from: Visual and non-visual navigation in blind patients with a retinal prosthesis

Sara Garcia, Karin Petrini, Gary S. Rubin, Lyndon Da Cruz & Marko Nardini
Human adults with normal vision can combine visual landmark and non-visual self-motion cues to improve their navigational precision. Here we asked whether blind individuals treated with a retinal prosthesis could also benefit from using the resultant new visual signal together with non-visual information when navigating. Four patients (blind for 15-52 years) implanted with the Argus II retinal prosthesis (Second Sight Medical Products Inc. Sylmar, CA), and five age-matched and six younger controls, participated. Participants completed...

Data from: Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution

Alison E. Wright, Peter W. Harrison, Fabian Zimmer, Stephen H. Montgomery, Marie A. Pointer & Judith E. Mank
Higher rates of coding sequence evolution have been observed on the Z chromosome relative to the autosomes across a wide range of species. However, despite a considerable body of theory, we lack empirical evidence explaining variation in the strength of the Faster-Z Effect. To assess the magnitude and drivers of Faster-Z Evolution, we assembled six de novo transcriptomes, spanning 90 million years of avian evolution. Our analysis combines expression, sequence and polymorphism data with measures...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: The evolution of sexually dimorphic tail feathers is not associated with tail skeleton dimorphism

Ryan N. Felice & Patrick M. O'Connor
Sexual selection can influence the evolution of sexually dimorphic exaggerated display structures. Herein, we explore whether such costly ornamental integumentary structures evolve independently or if they are correlated with phenotypic change in the associated skeletal system. In birds, elongate tail feathers have frequently evolved in males and are beneficial as intraspecific display structures but impart a locomotor/energetic cost. Using the sexually dimorphic tail feathers of several passeriform species as a model system, we test the...

Data from: Genetics of plasminogen activator inhibitor-1 (PAI-1) in a Ghanaian population

Marquitta J. White, Nuri M. Kodaman, Reed H. Harder, Folkert W. Asselbergs, Douglas E. Vaughan, Nancy J. Brown, Jason H. Moore & Scott M. Williams
Plasminogen activator inhibitor 1 (PAI-1), a major modulator of the fibrinolytic system, is an important factor in cardiovascular disease (CVD) susceptibility and severity. PAI-1 is highly heritable, but the few genes associated with it explain only a small portion of its variation. Studies of PAI-1 typically employ linear regression to estimate the effects of genetic variants on PAI-1 levels, but PAI-1 is not normally distributed, even after transformation. Therefore, alternative statistical methods may provide greater...

Nitrogen and Carbon isotope data from 210Pb dated lake sediment cores in the United Kingdom

S.D. Turner & N.L. Rose
A dataset of historical sediment Carbon and Nitrogen isotope measurements from lake cores (n=95) spanning the range of lake types and catchments found across the UK. These data have been obtained from the Environmental Change Research Centre (ECRC) lake sediment core archive with well-resolved time intervals (1850, 1900, 1980 and present) determined by radiometric dating (210Pb; 137Cs). This data has been collated to investigate historical sources and accumulation of C and N in lakes. This...

Data from: An overrepresentation of high frequencies in the mouse inferior colliculus supports the processing of ultrasonic vocalizations

Jose A. Garcia-Lazaro, Kathryn N. Shepard, Jason A. Miranda, Robert C. Liu & Nicholas A. Lesica
Mice are of paramount importance in biomedical research and their vocalizations are a subject of interest for researchers across a wide range of health-related disciplines due to their increasingly important value as a phenotyping tool in models of neural, speech and language disorders. However, the mechanisms underlying the auditory processing of vocalizations in mice are not well understood. The mouse audiogram shows a peak in sensitivity at frequencies between 15-25 kHz, but weaker sensitivity for...

Data from: Anthropogenic and ecological drivers of amphibian disease (Ranavirosis)

Alexandra C. North, David J. Hodgson, Stephen J. Price & Amber G. F. Griffiths
Ranaviruses are causing mass amphibian die-offs in North America, Europe and Asia, and have been implicated in the decline of common frog (Rana temporaria) populations in the UK. Despite this, we have very little understanding of the environmental drivers of disease occurrence and prevalence. Using a long term (1992-2000) dataset of public reports of amphibian mortalities, we assess a set of potential predictors of the occurrence and prevalence of Ranavirus-consistent common frog mortality events in...

Data from: Paleo-islands as refugia and sources of genetic diversity within volcanic archipelagos: The case of the widespread endemic Canarina canariensis (Campanulaceae)

Mario Mairal, Isabel Sanmartín, Juan José Aldasoro, Victoria Culshaw, Ioanna Manolopoulou & Marisa Alarcón
Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within-island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the...

Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

Carmelo Andújar, Paula Arribas, Filip Ruzicka, Alexandra Crampton Platt, Martijn J. T. N. Timmermans, Alfried P. Vogler & Alex Crampton-Platt
High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum...

Data from: The interaction of Saccharomyces paradoxus with its natural competitors on oak bark

Vienna Kowallik, Eric Miller & Duncan Greig
The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high-throughput...

Data from: Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values and small sample sizes

Aristides Moustakas & Matthew R. Evans
Background: Plant survival is a key factor in forest dynamics and survival probabilities often vary across life stages. Studies specifically aimed at assessing tree survival are unusual and so data initially designed for other purposes often need to be used; such data are more likely to contain errors than data collected for this specific purpose. Results: We investigate the survival rates of ten tree species in a dataset designed to monitor growth rates. As some...

Data from: Polygyny without wealth: popularity in gift games predicts polygyny in BaYaka Pygmies

Nikhil Chaudhary, Gul Deniz Salali, James Thompson, Mark Dyble, Abigail Page, Daniel Smith, Ruth Mace & Andrea Bamberg Migliano
The occurrence of polygynous marriage in hunter–gatherer societies, which do not accumulate wealth, remains largely unexplored since resource availability is dependent on male hunting capacity and limited by the lack of storage. Hunter–gatherer societies offer the greatest insight in to human evolution since they represent the majority of our species' evolutionary history. In order to elucidate the evolution of hunter–gatherer polygyny, we study marriage patterns of BaYaka Pygmies. We investigate (i) rates of polygyny among...

Data from: The REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) statement: methods for arriving at consensus and developing reporting guidelines

Stuart G. Nicholls, Pauline Quach, Erik Von Elm, Astrid Guttmann, David Moher, Irene Petersen, Henrik T. Sørensen, Liam Smeeth, Sinéad M. Langan & Eric I. Benchimol
Objective: Routinely collected health data, collected for administrative and clinical purposes, without specific a priori research questions, are increasingly used for observational, comparative effectiveness, health services research, and clinical trials. The rapid evolution and availability of routinely collected data for research has brought to light specific issues not addressed by existing reporting guidelines. The aim of the present project was to determine the priorities of stakeholders in order to guide the development of the REporting...

Data from: A life-cycle model of human social groups produces a u-shaped distribution in group size

Gul Deniz Salali, Harvey Whitehouse & Michael E. Hochberg
One of the central puzzles in the study of sociocultural evolution is how and why transitions from small-scale human groups to large-scale, hierarchically more complex ones occurred. Here we develop a spatially explicit agent-based model as a first step towards understanding the ecological dynamics of small and large-scale human groups. By analogy with the interactions between single-celled and multicellular organisms, we build a theory of group lifecycles as an emergent property of single cell demographic...

Data from: How to calculate the non­-synonymous to synonymous rate ratio of protein-coding genes under the Fisher­-Wright mutation­-selection framework

Mario Dos Reis
First principles of population genetics are used to obtain formulae relating the non-synonymous to synonymous substitution rate ratio to the selection coefficients acting at codon sites in protein-coding genes. Two theoretical cases are discussed and two examples from real data (a chloroplast gene and a virus polymerase) are given. The formulae give much insight into the dynamics of non-synonymous substitutions and may inform the development of methods to detect adaptive evolution.

Data from: Analysis of iris surface features in populations of diverse ancestry

Melissa Edwards, David Cha, S. Krithika, Monique Johnson & Esteban J. Parra
There are many textural elements that can be found in the human eye, including Fuchs’ crypts, Wolfflin nodules, pigment spots, contraction furrows and conjunctival melanosis. Although iris surface features have been well-studied in populations of European ancestry, the worldwide distribution of these traits is poorly understood. In this paper, we develop a new method of characterizing iris features from photographs of the iris. We then apply this method to a diverse sample of East Asian,...

Data from: Redesigning the ‘choice architecture’ of hospital prescription charts: a mixed methods study incorporating in-situ simulation

Dominic King, Ali Jabbar, Esmita Charani, Colin Bicknell, Zhe Wu, Gavin Miller, Mark Gilchrist, Ivo Vlaev, Bryony Dean Franklin & Ara Darzi
Objectives: To incorporate behavioural insights into the user-centred design of an inpatient prescription chart (Imperial Drug Chart Evaluation and Adoption Study, IDEAS chart) and to determine whether changes in the content and design of prescription charts could influence prescribing behaviour and reduce prescribing errors. Design: A mixed-methods approach was taken in the development phase of the project; in situ simulation was used to evaluate the effectiveness of the newly developed IDEAS prescription chart. Setting: A...

Data from: New record of Egertonia (Elopiformes, Phyllodontidae) from the Late Cretaceous of South India

Thomas J. D. Halliday, Andrew R. Cuff, Guntupalli V. R. Prasad, Mechek S. Thanglemmoi & Anjali Goswami
We report a new occurrence of the phyllodontid teleost fish Egertonia from the Late Cretaceous Kallamedu Formation of the Cauvery Basin, South India. This is the oldest occurrence of Phyllodontidae in India, and only the second Cretaceous Gondwanan occurrence of this genus, following a toothplate previously described from the Late Cretaceous Maevarano Formation, Madagascar. The presence of phyllodontid fish supports a fluvial–deltaic or brackish environment for the lower part of the Kallamedu Formation, a rich...

Data from: Anxiety-like behavioural inhibition is normative under environmental threat-reward correlations

Dominik R. Bach
Behavioural inhibition is a key anxiety-like behaviour in rodents and humans, distinct from avoidance of danger, and reduced by anxiolytic drugs. In some situations, it is not clear how behavioural inhibition minimises harm or maximises benefit for the agent, and can even appear counterproductive. Extant explanations of this phenomenon make use of descriptive models but do not provide a formal assessment of its adaptive value. This hampers a better understanding of the neural computations underlying...

Data from: Resilience of self-organised and top-down planned cities—a case study on London and Beijing street networks

Jiaqiu Wang
The success or failure of the street network depends on its reliability. In this article, using resilience analysis, the author studies how the shape and appearance of street networks in self-organised and top-down planned cities influences urban transport. Considering London and Beijing as proxies for self-organised and top-down planned cities, the structural properties of London and Beijing networks first are investigated based on their primal and dual representations of planar graphs. The robustness of street...

Data from: Binding space and time through action

Nicola Binetti, Nobuhiro Hagura, Charles Fadipe, Alessandro Tomassini, Vincent Walsh & Sven Bestmann
Space and time are intimately coupled dimensions in the human brain. Several lines of evidence suggest that space and time are processed by a shared analogue magnitude system. It has been proposed that actions are instrumental in establishing this shared magnitude system. Here we provide evidence in support of this hypothesis, by showing that the interaction between space and time is enhanced when magnitude information is acquired through action. Participants observed increases or decreases in...

Data from: Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages

Carola Gómez-Rodríguez, Alex Crampton-Platt, Martijn J. T. N. Timmermans, Andrés Baselga & Alfried P. Vogler
1. The biodiversity of mixed-species samples of arthropods can be characterized by shotgun sequencing of bulk genomic DNA and subsequent bioinformatics assembly of mitochondrial genomes. Here, we tested the power of mitochondrial metagenomics by conducting Illumina sequencing on mixtures of >2600 individuals of leaf beetles (Chrysomelidae) from 10 communities. 2. Patterns of species richness, community dissimilarity and biomass were assessed from matches of reads against three reference databases, including (i) a custom set of mitogenomes...

Nutrient chemistry of Arctic Lakes in Greenland, Norway, Russia and Alaska

E. J. Whiteford, M. Van Hardenbroek, S. McGowan, V. J. Jones, M.E. Edwards, P. G. Langdon & N. J. Anderson
This dataset contains nutrient chemistry data from 14 lakes in the Arctic region: 4 in Russia and Alaska and 3 in Greenland and Norway. Nutrient chemistry was measured on one occasion only at each lake, with date of collection ranging from 01/04/2011 to 14/03/2014. The following nutrients were measured: total phosphorus, soluble reactive phosphorus, total nitrogen, nitrate, ammonium, chlorophyll a, silicate, sodium, magnesium, potassium, calcium, sulphate, chloride and dissolved organic carbon. All nutrients were measured...

Data from: High levels of genetic structure and striking phenotypic variability in a sexually dimorphic suckermouth catfish from the African Highveld

Jake Morris, Antonia G. P. Ford, Jarome R. Ali, Claire R. Peart, Roger Bills & Julia J. Day
Uncovering biological diversity to more accurately understand diversity patterns, and ultimately the processes driving diversification, is important not only from an evolutionary perspective but also a conservation perspective. This is particularly pertinent in Africa's rivers in which overall diversity, as well as how it arose, is poorly understood in comparison with lacustrine environments. Here we investigate population divergence in the sexually dimorphic suckermouth catfish species Chiloglanis anoterus (Crass, 1960) from the African Highveld, in which...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University College London
  • University of Southampton
  • Natural History Museum
  • University of Toronto
  • University of Bath
  • Federal Institute of São Paulo
  • Sao Paulo State University
  • Western General Hospital
  • London School of Hygiene & Tropical Medicine
  • University of Hohenheim