271 Works

Data from: Reproduction has different costs for immunity and parasitism in a wild mammal

Gregory Albery, Kathryn Watt, Rosie Keith, Sean Morris, Alison Morris, Fiona Kenyon, Daniel Nussey & Josephine Pemberton
Life history theory predicts that reproductive allocation draws resources away from immunity, resulting in increased parasitism. However, studies of reproductive tradeoffs rarely examine multiple measures of reproduction, immunity, and parasitism. It is therefore unclear whether the immune costs of reproductive traits correlate with their resource costs, and whether increased parasitism emerges from weaker immunity. We examined these relationships in wild female red deer (Cervus elaphus) with variable reproductive allocation and longitudinal data on mucosal antibody...

Data from: The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries)

Alexandra Sparks, Kathryn Watt, Rona Sinclair, Jill Pilkington, Josephine Pemberton, Tom McNeilly, Daniel Nussey & Susan Johnston
Much of our knowledge of the drivers of immune variation, and how these responses vary over time, comes from humans, domesticated livestock or laboratory organisms. While the genetic basis of variation in immune responses have been investigated in these systems, there is a poor understanding of how genetic variation influences immunity in natural, untreated populations living in complex environments. Here, we examine the genetic architecture of variation in immune traits in the Soay sheep of...

Explaining illness with evil: Pathogen prevalence fosters moral vitalism

Brock Bastian, Christin-Melanie Vauclair, Steve Loughnan, Paul Bain, Ashwini Ashokkumar, Maja Becker, Michal Bilewicz, Emma Collier-Baker, Carla Crespo, Paul W. Eastwick, Ronald Fischer, Malte Friese, Ángel Gómez, Valeschka M. Guerra, Jose Luis Castellanos Guevara, Katja Hanke, Nic Hooper, Li-Li Huang, Shi Junqi, Minoru Karasawa, Peter Kuppens, Siri Leknes, Müjde Peker, Cesar Pelay, Afoditi Pina … & William B. Swann
Pathogens represent a significant threat to human health leading to the emergence of strategies designed to help manage their negative impact. We examined how spiritual beliefs developed to explain and predict the devastating effects of pathogens and spread of infectious disease. Analysis of existing data in Studies 1 and 2 suggests that moral vitalism (beliefs about spiritual forces of evil) is higher in geographical regions characterized by historical higher levels of pathogens. Furthermore, drawing on...

Data from: Temporal, spatial and household dynamics of typhoid fever in Kasese district, Uganda

Bernadette Basuta Mirembe, Stella Mazeri, Rebecca Callaby, Luke Nyakarahuka, Clovice Kankya & Adrian Muwonge
Typhoid fever affects 21 million people globally, 1% of whom succumb to the disease. The social, economic and public health consequences of this disease disproportionately affect people in Africa and Asia. In order to design context specific prevention strategies, we need to holistically characterise outbreaks in these settings. Here we used retrospective data (2013-2016) at national and district level to characterize temporal and spatial dynamics of typhoid fever outbreaks using time series and spatial analysis....

Data from: Consistent within‐individual plasticity is sufficient to explain temperature responses in red deer reproductive traits

Hannah Froy, Julien Martin, Katie Stopher, Alison Morris, Sean Morris, Tim Clutton-Brock, Josephine Pemberton & Loeske Kruuk
Warming global temperatures are affecting a range of aspects of wild populations, but the exact mechanisms driving associations between temperature and phenotypic traits may be difficult to identify. Here, we use a 36‐year data set on a wild population of red deer to investigate the causes of associations between temperature and two important components of female reproduction: timing of breeding and offspring size. By separating within‐ versus between‐individual associations with temperature for each trait, we...

Data from: Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches

Camillo Bérénos, Philip A. Ellis, Jill G. Pilkington & Josephine M. Pemberton
The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genome-wide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness:...

Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

(LPWG), Legume Phylogeny Working Group, Anne Bruneau, Nasim Azani, Marielle Babineau, Edeline Gagnon, Carole Sinou, Royce Steeves, Erin Zimmerman, C. Donovan Bailey, Lynsey Kovar, Madhugiri Nageswara-Rao, Hannah Banks, RuthP. Clark, Manuel De La Estrella, Peter Gasson, GeoffreyC. Kite, BenteB. Klitgaard, GwilymP. Lewis, Danilo Neves, Gerhard Prenner, María De Lourdes Rico-Arce, ArianeR. Barbosa, Maria Cristina López-Roberts, Luciano Paganucci De Queiroz, PétalaG. Ribeiro … & Tingshuang Yi
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most...

Data from: Re-mating across years and intra-lineage polygyny are associated with greater than expected levels of inbreeding in wild red deer

Katie V. Stopher, Daniel H. Nussey, Tim H. Clutton-Brock, Fiona Guinness, Alison Morris, Josephine M. Pemberton, T. H. Clutton-Brock, F. Guinness, A. Morris & J. M. Pemberton
The interaction between philopatry and non-random mating has important consequences for the genetic structure of populations, influencing co-ancestry within social groups but also inbreeding. Here, using genetic paternity data, we describe mating patterns in a wild population of red deer (Cervus elaphus) which are associated with marked consequences for co-ancestry and inbreeding in the population. Around a fifth of females mate with a male with whom they have mated previously, and further, females frequently mate...

Data from: Increasing temperature, not mean temperature, is a cue for avian timing of reproduction

Sonja Verena Schaper, Alistair S. Dawson, Peter J. Sharp, Phillip Gienapp, Samuel P. Caro, Marcel E. Visser, Sonja V. Schaper & Alistair Dawson
Timing of reproduction in temperate zone birds is strongly correlated with spring temperature, with an earlier onset of breeding in warmer years. Females adjust their laying between years to be synchronized with local food sources and thereby optimize reproductive output. However, climate change currently disrupts the link between predictive environmental cues and spring phenology. To investigate direct effects of temperature on the decision to lay, and its genetic basis, we used pairs of Great Tits...

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: 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: Spatially coordinated dynamic gene transcription in living pituitary tissue

Karen Featherstone, Kirsty Hey, Hiroshi Momiji, Anne V. McNamara, Amanda L. Patist, Joanna Woodburn, David G. Spiller, Helen C. Christian, Alan S. McNeilly, John J. Mullins, Barbel F. Finkenstadt, David A. Rand, Michael R. H. White & Julian R. E. Davis
Transcription at individual genes in single cells is often pulsatile and stochastic. A key question emerges regarding how this behaviour contributes to tissue phenotype, but it has been a challenge to quantitatively analyse this in living cells over time, as opposed to studying snap-shots of gene expression state. We have used imaging of reporter gene expression to track transcription in living pituitary tissue. We integrated live-cell imaging data with statistical modelling for quantitative real-time estimation...

Data from: Contrasting responses of male and female foraging effort to year-round wind conditions

Sue Lewis, Richard A. Phillips, Sarah J. Burthe, Sarah Wanless & Francis Daunt
1. There is growing interest in the effects of wind on wild animals, given evidence that wind speeds are increasing and becoming more variable in some regions, particularly at temperate latitudes. Wind may alter movement patterns or foraging ability, with consequences for energy budgets and, ultimately, demographic rates. 2. These effects are expected to vary among individuals due to intrinsic factors such as sex, age or feeding proficiency. Furthermore, this variation is predicted to become...

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: 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: Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

Konrad Lohse, Magnus Clarke, Michael G. Ritchie & William J. Etges
Models of speciation-with-gene-flow have shown that the reduction in recombination between alternative chromosome arrangements can facilitate the fixation of locally adaptive genes in the face of gene flow and contribute to speciation. However, it has proven frustratingly difficult to show empirically that inversions have reduced gene flow and arose during or shortly after the onset of species divergence rather than represent ancestral polymorphisms. Here we present an analysis of whole genome data from a pair...

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: 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: Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations

Laurent A. F. Frantz, Ole Madsen, Hendrik-Jan Megens, Martien A. M. Groenen & Konrad Lohse
In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island Southeast Asia (ISEA). A previous study revealed...

Data from: Gradual assembly of avian body plan culminated in rapid rates of evolution across dinosaur-bird transition

Stephen L. Brusatte, Graeme T. Lloyd, Steve C. Wang & Mark A. Norell
Brusatte et al. 2014 Current Biology Dryad File1Supplementary appendices: list of phylogenetic characters, phylogenetic character-taxon matrix, list of taxon ages, list of supplementary figure captions (relevant to Dryad File 2)BrusatteetalRevisionDryadFile1.docxBrusatte et al. 2014 Current Biology Dryad File2Supplementary figuresBrusatteetalRevisionDryadFile2.pdfBrusatte et al. 2014 Current Biology Dryad File3R code (Graeme T. Lloyd)BrusatteetalRevisionDryadFile3.zip

Data from: Cultural evolution of systematically structured behaviour in a non-human primate

Nicolas Claidière, Kenny Smith, Simon Kirby, Joël Fagot, S. Kirby & K. Smith
Culture pervades human life and is at the origin of the success of our species. A wide range of other animals have culture too, but often in a limited form that does not complexify through the gradual accumulation of innovations. We developed a new paradigm to study cultural evolution in primates in order to better evaluate our closest relatives' cultural capacities. Previous studies using transmission chain experimental paradigms, in which the behavioural output of one...

Data from: Additive genetic variance and developmental plasticity in growth trajectories in a wild cooperative mammal

Elise Huchard, Anne Charmantier, Sinead English, Andrew Bateman, Johanna F. Nielsen, Tim Clutton-Brock, J. F. Nielsen, S. English, A. Charmantier, E. Huchard, A. Bateman & T. Clutton-Brock
Individual variation in growth is high in cooperative breeders and may reflect plastic divergence in developmental trajectories leading to breeding vs. helping phenotypes. However, the relative importance of additive genetic variance and developmental plasticity in shaping growth trajectories is largely unknown in cooperative vertebrates. This study exploits weekly sequences of body mass from birth to adulthood to investigate sources of variance in, and covariance between, early and later growth in wild meerkats (Suricata suricatta), a...

Data from: The translational landscape of the splicing factor SRSF1 and its role in mitosis

Magdalena M. Maslon, Sara R. Heras, Nicolas Bellora, Eduardo Eyras & Javier F. Cáceres
The shuttling Serine/Arginine rich (SR) protein SRSF1 (previously known as SF2/ASF) is a splicing regulator that also activates translation in the cytoplasm. In order to dissect the gene network that is translationally regulated by SRSF1, we performed a high-throughput deep sequencing analysis of polysomal fractions in cells overexpressing SRSF1. We identified approximately 1,500 mRNAs that are translational targets of SRSF1. These include mRNAs encoding proteins involved in cell cycle regulation, such as spindle, kinetochore and...

Data from: Basal dinosauriform and theropod dinosaurs from the middle-late Norian (Late Triassic) of Poland: implications for Triassic dinosaur evolution and distribution

Grzegorz Niedźwiedzki, Stephen L. Brusatte, Tomasz Sulej & Richard J. Butler
The rise of dinosaurs during the Triassic is a widely studied evolutionary radiation, but there are still many unanswered questions about early dinosaur evolution and biogeography that are hampered by an unevenly sampled Late Triassic fossil record. Although very common in western North America and parts of South America, dinosaur (and more basal dinosauriform) remains are relatively rare in the Upper Triassic deposits of Europe, making any new discoveries critically important. One of the most...

Data from: Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography

Filip Bielejec, Philippe Lemey, Guy Baele, Andrew Rambaut & Marc A. Suchard
Molecular phylogenetic and phylogeographic reconstructions generally assume time-homogeneous substitution processes. Motivated by computational convenience, this assumption sacrifices biological realism and offers little opportunity to uncover the temporal dynamics in evolutionary histories. Here, we propose an evolutionary approach that explicitly relaxes the time-homogeneity assumption by allowing the specification of different infinitesimal substitution rate matrices across different time intervals, called epochs, along the evolutionary history. We focus on an epoch model implementation in a Bayesian inference framework...

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