355 Works

Data from: Direct evidence for encoding of motion streaks in human visual cortex

Deborah Apthorp, D. Samuel Schwarzkopf, Christian Kaul, Bahador Bahrami, David Alais & Geraint Rees
Temporal integration in the visual system causes fast-moving objects to generate static, oriented traces (‘motion streaks’), which could be used to help judge direction of motion. While human psychophysics and single-unit studies in non-human primates are consistent with this hypothesis, direct neural evidence from the human cortex is still lacking. First, we provide psychophysical evidence that faster and slower motions are processed by distinct neural mechanisms: faster motion raised human perceptual thresholds for static orientations...

Data from: Genetic drift in antagonistic genes leads to divergence in sex-specific fitness between experimental populations of Drosophila melanogaster

Jack Hesketh, Kevin Fowler & Max Reuter
Males and females differ in their reproductive roles and as a consequence are often under diverging selection pressures on shared phenotypic traits. Theory predicts that divergent selection can favor the invasion of sexually antagonistic alleles, which increase the fitness of one sex at the detriment of the other. Sexual antagonism can be subsequently resolved through the evolution of sex-specific gene expression, allowing the sexes to diverge phenotypically. While sexual dimorphism is very common, recent evidence...

Data from: Continental diversification of an African catfish radiation (Mochokidae: Synodontis)

Julia J. Day, Claire R. Peart, Katherine J. Brown, Roger Bills, John P. Friel & Timo Moritz
Despite African rivers containing high species diversity, continental-scale studies investigating the mechanisms generating biological diversity of African riverine faunas are limited compared to lacustrine systems.To investigate the build up of diversity in a tropical aquatic continental radiation, we test different models of lineage diversification and reconstruct the biogeographic history in a species-rich siluriform genus, Synodontis (~130 species), with a broad distribution across all major tropical African drainage basins. The resulting robust species-level phylogeny (~60% complete,...

Data from: Best practices for justifying fossil calibrations

James F. Parham, Philip C. J. Donoghue, Christopher J. Bell, Tyler D. Calway, Jason J. Head, Patricia A. Holroyd, Jun G. Inoue, Randall B. Irmis, Walter G. Joyce, Daniel T. Ksepka, José S. L. Patané, Nathan D. Smith, James E. Tarver, Marcel Van Tuinen, Ziheng Yang, Kenneth D. Angielczyk, Jenny M. Greenwood, Christy A. Hipsley, Jacobs Louis, Peter J. Makovicky, Johannes Müller, Krister T. Smith, Jessica M. Theodor, Rachel C. M. Warnock, Michael J. Benton … & Louis Jacobs
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule; with replacement rates established (calibrated) using inaccurate paleontological age estimates...

Data from: The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome

Hooman K. Moghadam, Peter W. Harrison, Gergely Zachar, Tamás Székely & Judith E. Mank
We assembled a de novo transcriptome of short-read Illumina RNA-Seq data generated from telencephalon and diencephalon tissue samples from the Kentish plover, Charadrius alexandrinus. This is a species of considerable interest in behavioural ecology for its highly variable mating system and parental behaviour, but it lacks genomic resources and is evolutionarily distant from the few available avian draft genome sequences. We assembled and identified over 21 000 transcript contigs with significant expression in our samples,...

Data from: Dating phylogenies with sequentially sampled tips

Tanja Stadler & Ziheng Yang
We develop a Bayesian Markov chain Monte Carlo (MCMC) algorithm for estimating divergence times using sequentially sampled molecular sequences. This type of data is commonly collected during viral epidemics and is sometimes available from different species in ancient DNA studies. We derive the distribution of ages of nodes in the tree under a birth–death-sequential-sampling (BDSS) model and use it as the prior for divergence times in the dating analysis. We implement the prior in 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: 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: 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: 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: Diet quality determines interspecific parasite interactions in host populations

Benjamin Lange, Max Reuter, Dieter Ebert, Koenraad Muylaert & Ellen Decaestecker
The widespread occurrence of multiple infections and the often vast range of nutritional resources for their hosts allow that interspecific parasite interactions in natural host populations might be determined by host diet quality. Nevertheless, the role of diet quality with respect to multispecies parasite interactions on host population level is not clear. We here tested the effect of host population diet quality on the parasite community in an experimental study using Daphnia populations. We studied...

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: Estimation of the dispersal of a major pest of maize by cline analysis of a temporary contact zone between two invasive outbreaks

Gérald Bermond, Aurélie Blin, Elodie Vercken, Virginie Ravigné, Adrien Rieux, Sophie Mallez, Thibaut Morel-Journel, Thomas Guilllemaud & Thomas Guillemaud
Dispersal is a key factor in invasion, and in the persistence and evolution of species. Despite the importance of estimates of dispersal distance, dispersal measurement remains a real methodological challenge. In this study, we characterized dispersal by exploiting a specific case of biological invasion, in which multiple introductions in disconnected areas lead to secondary contact between two differentiated expanding outbreaks. By applying cline theory to this ecological setting, we estimated σ, the standard deviation of...

Palaeolimnological data from 5 Arctic lakes in Greenland, Alaska and Norway [Lakes and Arctic Carbon]

E.J. Whiteford, E. Hopla, N. Solovieva, J. Swales, S. Turner, M. Van Hardenbroek, E. Wiik, M.E. Edwards, V.J. Jones, P.G. Langdon, S. McGowan & N.J. Anderson
This dataset contains palaeolimnological data from sediment cores taken from five Arctic lakes. Two lakes located in Alaska were cored in July 2013, one lake located in Greenland was cored in April 2013, and two lakes located in Norway were cored in March 2014. The data includes macrofossil, chironomids and Cladocera analysis at 2 cm resolution; and loss on ignition, diatoms, biogenic silica, nitrogen and carbon isotopes, algal photosynthetic pigments and pollen analyses at 1...

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: 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: Rates of dinosaur body mass evolution indicate 170 million years of sustained ecological innovation on the avian stem lineage

Roger B. J. Benson, Nicolás E. Campione, Matthew T. Carrano, Philip D. Mannion, Corwin Sullivan, Paul Upchurch & David C. Evans
Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation,...

Data from: Niche divergence promotes rapid diversification of East African sky island white-eyes (Aves: Zosteropidae)

Siobhan C. Cox, Robert P. Prys-Jones, Jan C. Habel, Bernard A. Amakobe & Julia J. Day
The Eastern Afromontane biodiversity hotspot composed of highly fragmented forested highlands (sky islands) harbours exceptional diversity and endemicity, particularly within birds. To explain their elevated diversity within this region, models founded on niche conservatism have been offered, although detailed phylogeographic studies are limited to a few avian lineages. Here we focus on the recent songbird genus Zosterops, represented by montane and lowland members, to test the roles of niche conservatism versus niche divergence in the...

Data from: Variation in male reproductive longevity across traditional societies

Lucio Vinicius, Ruth Mace, Andrea B. Migliano & Andrea Migliano
Most accounts of human life history propose that women have short reproductive spans relative to their adult lifespans, while men not only remain fertile but carry on reproducing until late life. Here we argue that studies have overlooked evidence for variation in male reproductive ageing across human populations. We apply a Bayesian approach to census data from Agta hunter-gatherers and Gambian farmers to show that long post-reproductive lifespans characterise not only women but also males...

Data from: The impact of phylogenetic dating method on interpreting trait evolution: a case study of Cretaceous–Palaeogene eutherian body-size evolution

Thomas J.D. Halliday, Anjali Goswami & T. J. D. Halliday
The fossil record of the earliest Cenozoic contains the first large-bodied placental mammals. Several evolutionary models have been invoked to explain the transition from small to large body sizes, but methods for determining evolutionary mode of trait change depend on input from tree topology and divergence dates. Different dating methods may therefore affect inference of evolutionary model. Here, we fit models of body mass evolution onto dated phylogenies of Cretaceous and Palaeogene mammals, comparing the...

Data from: Impact of person-centred care training and person-centred activities on quality of life, agitation, and antipsychotic use in people with dementia living in nursing homes: a cluster-randomised controlled trial

Clive Ballard, Anne Corbett, Martin Orrell, Gareth Williams, Esme Moniz-Cook, Renee Romeo, Bob Woods, Lucy Garrod, Ingelin Testad, Barbara Woodward-Carlton, Jennifer Wenborn, Martin Knapp & Jane Fossey
Background: Agitation is a common, challenging symptom affecting large numbers of people with dementia and impacting on quality of life (QoL). There is an urgent need for evidence-based, cost-effective psychosocial interventions to improve these outcomes, particularly in the absence of safe, effective pharmacological therapies. This study aimed evaluate the efficacy of a person-centered care and psychosocial intervention (WHELD) on QoL, agitation and antipsychotic use in people with dementia living in nursing homes, and to determine...

Data from: Approach-induced biases in human information sampling

Laurence T. Hunt, Robb B. Rutledge, W. M. Nishantha Malalasekera, Steven W. Kennerley & Raymond J. Dolan
IInformation sampling is often biased towards seeking evidence that confirms one’s prior beliefs. Despite such biases being a pervasive feature of human behavior, their underlying causes remain unclear. Many accounts of these biases appeal to limitations of human hypothesis testing and cognition, de facto evoking notions of bounded rationality, but neglect more basic aspects of behavioral control. Here, we investigated a potential role for Pavlovian approach in biasing which information humans will choose to sample....

Data from: Community water improvement, household water insecurity, and women’s psychological distress: an intervention and control study in Ethiopia

Edward G. J. Stevenson, Argaw Ambelu, Bethany A. Caruso, Yihenew Tesfaye & Matthew C. Freeman
Background: Over 650 million people worldwide lack access to safe water supplies, and even among those who have gained access to ‘improved’ sources, water may be seasonally unreliable, far from homes, expensive, and provide insufficient quantity. Measurement of water access at the level of communities and households remains crude, and better measures of household water insecurity are urgently needed to inform needs assessments and monitoring and evaluation. We set out to assess the validity of...

Data from: Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

Rachel C. M. Warnock, Ziheng Yang & Philip C. J. Donoghue
Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and...

Data from: Predicting animal behaviour using deep learning: GPS data alone accurately predict diving in seabirds

Ella Browning, Mark Bolton, Ellie Owen, Akiko Shoji, Tim Guilford & Robin Freeman
1.In order to prevent further global declines in biodiversity, identifying and understanding key habitats is crucial for successful conservation strategies. For example, globally, seabird populations are under threat and animal movement data can identify key at-sea areas and provide valuable information on the state of marine ecosystems. To date, in order to locate these areas, studies have used Global Positioning System (GPS) to record position and are sometimes combined with Time Depth Recorder (TDR) devices...

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