34 Works

Data from: The evolutionary dynamics of sexually antagonistic mutations in pseudoautosomal regions of sex chromosomes

Brian Charlesworth, Crispin Y. Jordan & Deborah Charlesworth
Sex chromosomes can evolve gene contents that differ from the rest of the genome, as well as larger sex differences in gene expression compared with autosomes. This probably occurs because fully sex-linked beneficial mutations substitute at different rates from autosomal ones, especially when fitness effects are sexually antagonistic (SA). The evolutionary properties of genes located in the recombining pseudo-autosomal region (PAR) of a sex chromosome have not previously been modelled in detail. Such PAR genes...

Data from: The action of stabilizing selection, mutation and drift on epistatic quantitative traits

Victoria Ávila, Andrés Pérez-Figueroa, Armando Caballero, William G. Hill, Aurora García-Dorado & Carlos López-Fanjul
For a quantitative trait under stabilizing selection, the effect of epistasis on its genetic architecture and on the changes of genetic variance caused by bottlenecking were investigated using theory and simulation. Assuming empirical estimates of the rate and effects of mutations and the intensity of selection, we assessed the impact of two-locus epistasis (synergistic/antagonistic) among linked or unlinked loci on the distribution of effects and frequencies of segregating loci in populations at the mutation-selection-drift balance....

Data from: Understanding genetic variation in in vivo tolerance to artesunate: implications for treatment efficacy and resistance monitoring

Laura C. Pollitt, Derek Sim, Rahel Salathé & Andrew F. Read
Artemisinin-based drugs are the front-line weapon in the treatment of human malaria cases, but there is concern that recent reports of slow clearing infections may signal developing resistance to treatment. In the absence of molecular markers for resistance, current efforts to monitor drug efficacy are based on the rate at which parasites are cleared from infections. However, some knowledge of the standing variation in parasite susceptibility is needed to identify a meaningful increase in infection...

Data from: Faster-X Effects in two Drosophila lineages

Victoria Ávila, Sophie Marion De Procé, José L. Campos, Helen Borthwick, Brian Charlesworth & Andrea J. Betancourt
Under certain circumstances, X-linked loci are expected to experience more adaptive substitutions than similar autosomal loci. To look for evidence of faster-X evolution, we analyzed the evolutionary rates of coding sequences in two sets of Drosophila species, the melanogaster and pseudoobscura clades, using whole-genome sequences. One of these, the pseudoobscura clade, contains a centric 15 fusion between the ancestral X chromosome and the autosomal arm homologous to 3L in D.melanogaster. This offers an opportunity to...

Measurements of respiration and microbial assimilation of carbon substrates and priming of soil organic matter mineralisation in tropical lowland and montane forest soils

J. Whitaker, N. Ostle, N. McNamara, A.T. Nottingham, A.W. Stott, R.D. Bardgett, N. Salinas, A.J.Q. Ccahuana & P. Meir
This dataset includes measurements of microbial community composition by phospholipid fatty acid (PLFA) analysis, soil respiration (Carbon dioxide (CO2)), soil physico-chemical properties and 13C enrichment in CO2 samples and microbial Phospholipid Fatty Acids (PLFAs). Data were produced for an investigation of the effects of carbon (C) substrate addition on soil carbon cycling processes in ten tropical soils from the Peruvian Andes. Soils were amended with 13C labelled substrates (xylose, glycine, vanillin and hemicellulose) and incubated...

Data from: Plasticity predicts evolution in a marine alga

C. Elisa Schaum & Sinéad Collins
Under global change, populations have four possible responses: ‘migrate, acclimate, adapt or die’ (Gienapp et al. 2008 Climate change and evolution: disentangling environmental and genetic response. Mol. Ecol. 17, 167–178. (doi:10.1111/j.1365-294X.2007.03413.x)). The challenge is to predict how much migration, acclimatization or adaptation populations are capable of. We have previously shown that populations from more variable environments are more plastic (Schaum et al. 2013 Variation in plastic responses of a globally distributed picoplankton species to ocean...

Data from: The effect of funding sources on donepezil randomised controlled trial outcome: a meta-analysis

Lewis O. J. Killin, Tom C. Russ, John M. Starr, Sharon Abrahams & Sergio Della Sala
Objective: To investigate whether there is a difference in the treatment effect of donepezil on cognition in Alzheimer disease between industry-funded and independent randomised controlled trials. Design: Fixed effects meta-analysis of standardised effects of donepezil on cognition as measured by the Mini Mental State Examination and the Alzheimer’s Disease Assessment Scale-cognitive subscale. Data sources: Studies included in the meta-analyses reported in the National Institute for Health and Care Excellence (NICE) technical appraisal 217 updated with...

Data from: Detecting slow introgression of invasive alleles in an extensively restocked game bird

Ines Sanchez-Donoso, Jisca Huisman, Jorge Echegaray, Manel Puigcerver, José Domingo Rodríguez-Teijeiro, Frank Hailer & Carles Vilà
Interbreeding of two species in the wild implies introgression of alleles from one species into the other only when admixed individuals survive and successfully backcross with the parental species. Consequently, estimating the proportion of first generation hybrids in a population may not inform about the evolutionary impact of hybridization. Samples obtained over a long time span may offer a more accurate view of the spreading of introgressed alleles in a species’ gene pool. Common quail...

Data from: Genotypic variation in a foundation tree (Populus tremula L.) explains community structure of associated epiphytes

Chantel Davies, Christopher J. Ellis, Glenn R. Iason & Richard A. Ennos
Community genetics hypothesizes that within a foundation species the genotype of an individual significantly influences the assemblage of dependent organisms. To assess whether these intra-specific genetic effects are ecologically important, it is required to compare their impact on dependent organisms with that attributable to environmental variation experienced over relevant spatial scales. We assessed bark epiphytes on 27 aspen (Populus tremula L.) genotypes grown in a randomized experimental array at two contrasting sites spanning the environmental...

Data from: Late-life and intergenerational effects of larval exposure to microbial competitors in the burying beetle Nicrophorus vespilloides

Ailsa H. C. McLean, Andres N. Arce, Per T. Smiseth & Daniel E. Rozen
Intergenerational effects can have either adaptive or nonadaptive impacts on offspring performance. Such effects are likely to be of ecological and evolutionary importance in animals with extended parental care, such as birds, mammals and some insects. Here, we studied the effects of exposure to microbial competition during early development on subsequent reproductive success in the burying beetle Nicrophorus vespilloides, an insect with elaborate parental care. We found that exposure to high levels of microbial competition...

Data from: Role of sex and migration in adaptation to sink environments

Mato Lagator, Andrew Morgan, Paul Neve & Nick Colegrave
Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a...

Data from: The early spread and epidemic ignition of HIV-1 in human populations

Nuno R. Faria, Andrew Rambaut, Marc A. Suchard, Guy Baele, Trevor Bedford, Melissa J. Ward, Andrew J. Tatem, João D. Sousa, Nimalan Arinaminpathy, Jacques Pépin, David Posada, Martine Peeters, Oliver P. Pybus & Philippe Lemey
Thirty years after the discovery of HIV-1, the early transmission, dissemination and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M...

Data from: Why do frog and toad forelimbs suddenly (but asynchronously) appear every time metamorphosis is near?

Luigi Zechini, Alison Lilley, J. Roger Downie & Patrick T. Walsh
1. The internal development and the emergence of the forelimbs at metamorphosis is a defining feature of anuran amphibians (frogs and toads). However, although forelimb emergence is considered sudden, it is rarely synchronous. Any asynchrony may or may not exacerbate the increased drag that is predicted to occur with the emergence of the forelimbs at metamorphic climax. 2. Despite the impact forelimb emergence is hypothesized to have on individual survival and life-history evolution, the degree...

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: Population clustering and clonal structure evidence the relict state of Ulmus minor Mill. in the Balearic Islands

Luis Gil, Pablo Fuentes-Utrilla, María Valbuena-Carabaña & Richard Ennos
Field elm (Ulmus minor) is a riparian tree that grows in rare, small populations scattered along temporary watercourses in the Balearic Islands, nowadays mostly covered with Mediterranean vegetation. Agriculture and farming on the fertile land along the periodically flooded plains have reduced the elm populations to sparse tree lines along the creek beds. The presence of field elm in this very anthropic landscape has led some authors to consider it as an introduced species in...

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...

Data from: ABC inference of multi-population divergence with admixture from unphased population genomic data

John D. Robinson, Lynsey Bunnefeld, Jack Hearn, Graham N. Stone & Michael J. Hickerson
Rapidly developing sequencing technologies and declining costs have made it possible to collect genome-scale data from population-level samples in non-model systems. Inferential tools for historical demography given these datasets are, at present, underdeveloped. In particular, approximate Bayesian computation (ABC) has yet to be widely embraced by researchers generating these data. Here, we demonstrate the promise of ABC for analysis of the large datasets that are now attainable from non-model taxa through current genomic sequencing technologies....

Data from: Parasitism in early life: environmental conditions shape intra-brood variation in responses to infection

Hanna M. V. Granroth-Wilding, Sarah J. Burthe, Sue Lewis, Thomas E. Reed, Katherine A. Herborn, Mark A. Newell, Emi A. Takahashi, Francis Daunt & Emma J. A. Cunningham
Parasites play key ecological and evolutionary roles through the costs they impose on their host. In wild populations, the effect of parasitism is likely to vary considerably with environmental conditions, which may affect the availability of resources to hosts for defense. However, the interaction between parasitism and prevailing conditions is rarely quantified. In addition to environmental variation acting on hosts, individuals are likely to vary in their response to parasitism, and the combined effect of...

Data from: Fitness decline in spontaneous mutation accumulation lines of Caenorhabditis elegans with varying effective population sizes

Vaishali Katju, Lucille B. Packard, Lijing Bu, Peter David Keightley & Ulfar Bergthorsson
The rate and fitness effects of new mutations have been investigated by mutation accumulation (MA) experiments in which organisms are maintained at a constant minimal population size to facilitate the accumulation of mutations with minimal efficacy of selection. We evolved 35 MA lines of Caenorhabditis elegans in parallel for 409 generations at three population sizes (N = 1, 10, and 100), representing the first spontaneous long-term MA experiment at varying population sizes with corresponding differences...

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: Early life expenditure in sexual competition is associated with increased reproductive senescence in male red deer

Jean-François Lemaître, Jean-Michel Gaillard, Josephine M. Pemberton, Tim H. Clutton-Brock, Daniel H. Nussey, J.-F. Lemaitre & J.-M. Gaillard
The evolutionary theories of senescence predict that investment in reproduction in early life should come at the cost of reduced somatic maintenance, and thus earlier or more rapid senescence. There is now growing support for such trade-offs in wild vertebrates, but these exclusively come from females. Here, we test this prediction in male red deer (Cervus elaphus) using detailed longitudinal data collected over a 40-year field study. We show that males which had larger harems...

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: Integrating influenza antigenic dynamics with molecular evolution

Trevor Bedford, Marc A. Suchard, Philippe Lemey, Gytis Dudas, Victoria Gregory, Alan J. Hay, John W. McCauley, Colin A. Russell, Derek J. Smith & Andrew Rambaut
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata,...

Data from: Variation in early life testosterone in a wild population of red deer

Alyson T. Pavitt, Craig A. Walling, Alan S. McNeilly, Josephine M. Pemberton & Loeske E. B. Kruuk
1. Individual differences in circulating hormone concentrations can affect life history traits throughout an animal’s life. Despite this, relatively little is known about the potential drivers or consequences of individual variation in hormone levels, particularly in early life. In animals showing maternal care, early development is often dependent on maternal characteristics and condition. It is therefore possible that individual hormone profiles early in life are dependent on condition-linked characteristics of the mother. 2. Using data...

Data from: Multivariate immune defences and fitness in the wild: complex but ecologically important associations among plasma antibodies, health and survival

Daniel H. Nussey, Kathryn A. Watt, Abigail Clark, Jill G. Pilkington, Josephine M. Pemberton, Andrea L. Graham & Tom N. McNeilly
Despite our rapidly advancing mechanistic understanding of vertebrate immunity under controlled laboratory conditions, the links between immunity, infection and fitness under natural conditions remain poorly understood. Antibodies are central to acquired immune responses, and antibody levels circulating in vivo reflect a composite of constitutive and induced functional variants of diverse specificities (e.g. binding antigens from prevalent parasites, self tissues or novel non-self sources). Here, we measured plasma concentrations of 11 different antibody types in adult...

Registration Year

  • 2014

Resource Types

  • Dataset


  • University of Edinburgh
  • University of Glasgow
  • National Institutes of Health
  • David Geffen School of Medicine at UCLA
  • University of Cambridge
  • University of Warwick
  • University of Manchester
  • French National Centre for Scientific Research
  • American Museum of Natural History
  • University of California Los Angeles