29 Works

Data from: Genome-wide evidence for speciation with gene flow in Heliconius butterflies

Simon H. Martin, Kanchon K. Dasmahapatra, Nicola J. Nadeau, Camilo Salazar, James R. Walters, Fraser Simpson, Mark Blaxter, Andrea Manica, James Mallet & Chris D. Jiggins
Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting the extent and timing of admixture between diverging species can clarify the role of geographic isolation in speciation. Here we use new methodology to quantify admixture at different stages of divergence in Heliconius butterflies, based on whole genome sequences of 31 individuals. Comparisons between...

Data from: Substantial contribution of submicroscopical Plasmodium falciparum gametocyte carriage to the infectious reservoir in an area of seasonal transmission.

André Lin Ouédraogo, Teun Bousema, Petra Schneider, Sake J. De Vlas, Edith Ilboudo-Sanogo, Nadine Cuzin-Ouattara, Issa Nébié, Will Roeffen, Jan Peter Verhave, Adrian J.F. Luty & Robert Sauerwein
Background: Man to mosquito transmission of malaria depends on the presence of the sexual stage parasites, gametocytes, that often circulate at low densities. Gametocyte densities below the microscopical threshold of detection may be sufficient to infect mosquitoes but the importance of submicroscopical gametocyte carriage in different transmission settings is unknown. Methodology/Principal Findings: Membrane feeding experiments were carried out on 80 children below 14 years of age at the end of the wet season in an...

Data from: Genetic differentiation and species cohesion in two widespread Central American Begonia species

Alex D. Twyford, Catherine A. Kidner & Richard A. Ennos
Begonia is one of the ten largest plant genera, with over 1500 species. This high species richness may in part be explained by weak species cohesion, which has allowed speciation by divergence in allopatry. In this study, we investigate species cohesion in the widespread Central American Begonia heracleifolia and Begonia nelumbiifolia, by genotyping populations at microsatellite loci. We then test for post-zygotic reproductive barriers using experimental crosses, and assess whether sterility barriers are related to...

Data from: Introgression and the fate of domesticated genes in a wild mammal population

Philine G. D. Feulner, Jacob Gratten, James W. Kijas, Peter M. Visscher, Josephine M. Pemberton, Jon Slate & Jon. Slate
When domesticated species are not reproductively isolated from their wild relatives, the opportunity arises for artificially selected variants to be re-introduced into the wild. However, the evolutionary consequences of introgression of domesticated genes back into the wild are poorly understood. By combining high-throughput genotyping with 25 years of long-term ecological field data, we describe the occurrence and consequences of admixture between a primitive sheep breed, the free-living Soay sheep of St Kilda, and more modern...

Data from: Patterns of mating and generation of diversity in a Geum hybrid swarm

Markus Ruhsam, Peter M. Hollingsworth & Richard A. Ennos
To understand the evolutionary consequences of hybridization between the outcrossing plant Geum rivale and the selfer G. urbanum we tested the predictions of two simple models which assume either A). low or B). high pollen fitness in hybrids. Model A predicts only four genotypic classes (G. rivale, G. rivale backcross (BCR), F1 and G. urbanum) and asymmetric introgression from inbreeding to outbreeding species. Model B predicts additional genotypic classes and potential generation of novel inbreeding...

Data from: Why we are not dead 100 times over

Brian Charlesworth
The possibility of pervasive weak selection at tens or hundreds of millions of sites across the genome, suggested by recent studies of silent site DNA sequence variation and divergence, raises the problem of the survival of the population in the face of the large genetic load that may result. Two alternative resolutions of this problem are presented for populations where recombination is sufficiently frequent that different sites under selection evolve independently. One invokes weak stabilizing...

Data from: Asymmetry in pay-off predicts how familiar individuals respond to one another

Hanna M. V. Granroth-Wilding & Anne E. Magurran
Familiarity influences individual decision-making in many vertebrate species. Here, we propose that familiarity modulates behaviour to different extents depending on the social context of the interaction. Specifically, the more that one player stands to gain relative to the other, the less important familiarity will be in influencing their responses to one another. We test this prediction using pairs of male guppies (Poecilia reticulata) in three competitive scenarios of increasing asymmetry in outcome to the two...

Data from: Host nutrition alters the variance in parasite transmission potential

Pedro F. Vale, Marc Choisy & Tom J. Little
The environmental conditions experienced by hosts are known to affect their mean parasite transmission potential. How different conditions may affect the variance of transmission potential has received less attention but is an important question for disease management, especially if specific ecological contexts are more likely to foster a few extremely infectious hosts. Using the obligate-killing bacterium Pasteuria ramosa and its crustacean host Daphnia magna, we analysed how host nutrition affected the variance of individual parasite...

Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing

Rob Ogden, Karim Gharbi, Nikolai Mugue, Jann Martinsohn, Helen Senn, John Davey, Mohammad Pourkazemi, Ross McEwing, Cathlene Eland, Michele Vidotto, Alexander Sergeev, Leonardo Congiu & J. W. Davey
Caviar-producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a...

Data from: A synchronized global sweep of the internal genes of modern avian influenza virus

Michael Worobey, Guan-Zhu Han & Andrew Rambaut
Zoonotic infectious diseases such as influenza continue to pose a grave threat to human health. However, the factors that mediate the emergence of RNA viruses such as influenza A virus (IAV) are still incompletely understood. Phylogenetic inference is crucial to reconstructing the origins and tracing the flow of IAV within and between hosts. Here we show that explicitly allowing IAV host lineages to have independent rates of molecular evolution is necessary for reliable phylogenetic inference...

Data from: Fold or hold: experimental evolution in vitro

Sinead Collins, Andrew Rambaut & Stephen J. Bridgett
We introduce a system for experimental evolution consisting of populations of short oligonucleotides (Oli populations) evolving in a modified quantitative polymerase chain reaction (qPCR). It is tractable at the genetic, genomic, phenotypic and fitness levels. The Oli system uses DNA hairpins designed to form structures that self-prime under defined conditions. Selection acts on the phenotype of self-priming, after which differences in fitness are amplified and quantified using qPCR. We outline the methodological and bioinformatics tools...

Data from: Perched at the mito-nuclear crossroads: divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flow in an Australian bird

Alexandra Pavlova, J. Nevil Amos, Leo Joseph, Kate Loynes, Jeremy J. Austin, J. Scott Keogh, Graham N. Stone, James Allan Nicholls & Paul Sunnucks
Relationships among multi-locus genetic variation, geography and environment can reveal how evolutionary processes affect genomes. We examined the evolution of an Australian bird, the eastern yellow robin Eopsaltria australis, using mitochondrial (mtDNA) and nuclear (nDNA) genetic markers, and bioclimatic variables. In southeastern Australia, two divergent mtDNA lineages occur east and west of the Great Dividing Range, perpendicular to latitudinal nDNA structure. We evaluated alternative scenarios to explain this striking discordance in landscape genetic patterning. Stochastic...

Data from: Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome

Yann X. C. Bourgeois, Emeline Lhuillier, Timothée Cézard, Joris A. M. Bertrand, Boris Delahaie, Josselin Cornuault, Thomas Duval, Olivier Bouchez, Borja Milá & Christophe Thébaud
Here, we present an adaptation of restriction-site-associated DNA sequencing (RAD-seq) to the Illumina HiSeq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the Réunion grey white-eye (Zosterops borbonicus), a nonmodel passerine bird species with no reference genome. We sequenced a set of six pools of 18–25 individuals using a single sequencing lane. This allowed us to build around 600 000 contigs, among which at least...

Data from: Variation in plastic responses of a globally distributed picoplankton species to ocean acidification

Elisa Schaum, Rost Björn, J. Millar Andrew & Collins Sinéad
Phytoplankton are the basis of marine food webs, and affect biogeochemical cycles. As CO2 levels increase, shifts in the frequencies and physiology of ecotypes within phytoplankton groups will affect their nutritional value and biogeochemical function. However, studies so far are based on a few representative genotypes from key species. Here, we measure changes in cellular function and growth rate at atmospheric CO2 concentrations predicted for the year 2100 in 16 ecotypes of the marine picoplankton...

Data from: RAD-Seq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene

Paul M. Richards, M. Maureen Liu, Natalie Lowe, John W. Davey, Mark L. Blaxter & Angus Davison
Studies on the classic shell colour and banding polymorphism of the land snail Cepaea played a crucial role in establishing the importance of natural selection in maintaining morphological variation. Cepaea is also a pre-eminent model for ecological genetics because the outward colour and banding phenotype is entirely genetically determined, primarily by a ‘supergene’ of at least five loci. Unfortunately, progress in understanding the evolution and maintenance of the Cepaea polymorphism stalled, partly because of a...

Data from: Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions

Pablo Fuentes-Utrilla, Martin Venturas, Peter M. Hollingsworth, Jane Squirrell, Carmen Collada, Graham N. Stone & Luis Gil
Conservation policies usually focus on in situ protection of native populations, a priority that requires accurate assessment of population status. Distinction between native and introduced status can be particularly difficult (and at the same time, is most important) for species whose natural habitat has become both rare and highly fragmented. Here we address the status of the white elm (Ulmus laevis Pallas), a European riparian tree species whose populations have been fragmented by human activity...

Data from: Disentangling genetic and prenatal sources of familial resemblance across ontogeny in a wild passerine.

Jarrod D. Hadfield, Elizabeth A. Heap, Florian Bayer, Elizabeth A. Mittell & Nicholas M. A. Crouch
Cross-fostering experiments are widely used by quantitative geneticists to study genetics and by behavioral ecologists to study the effects of prenatal in- vestment. Generally, the effects of genes and prenatal investment are confounded and the interpretation given to such experiments is largely dependent on the in- terests of the researcher. Using a large-scale well controlled experiment on a wild population of blue tits (Cyanistes caeruleus) we are able to partition variation in body mass across...

Data from: Recommendations for using msBayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al.

Michael James Hickerson, Graham N. Stone, Konrad Lohse, Terrence C. Demos, Xiaoou Xie, Cedric Landerer & Naoki Takebayashi
Prior specification is an essential component of parameter estimation and model comparison in Approximate Bayesian computation (ABC). Oaks et al. present a simulation-based power analysis of msBayes and conclude that msBayes has low power to detect genuinely random divergence times across taxa, and suggest the cause is Lindley's paradox. Although the predictions are similar, we show that their findings are more fundamentally explained by insufficient prior sampling that arises with poorly chosen wide priors that...

Data from: Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes

Francesco Commandatore, Davide Sassera, Matteo Montagna, Sujai Kumar, Georgios Koutsovoulos, Graham Thomas, Charlotte Repton, Simon A. Babayan, Nick Gray, Richard Cordaux, Alistair Darby, Benjamin Makepeace & Mark Blaxter
Wolbachia, endosymbiotic bacteria of the order Rickettsiales, are widespread in arthropods but also present in nematodes. In arthropods, A and B supergroup Wolbachia are generally associated with distortion of host reproduction. In filarial nematodes, including some human parasites, multiple lines of experimental evidence indicate that C and D supergroup Wolbachia are essential for the survival of the host, and here the symbiotic relationship is considered mutualistic. The origin of this mutualistic endosymbiosis is of interest...

Data from: Chemotherapy, within-host ecology and the fitness of drug-resistant malaria parasites

Silvie Huijben, William A. Nelson, Andrew R. Wargo, Derek G. Sim, Damien R. Drew & Andrew F. Read
A major determinant of the rate at which drug-resistant malaria parasites spread through a population is the ecology of resistant and sensitive parasites sharing the same host. Drug treatment can significantly alter this ecology by removing the drug-sensitive parasites, leading to competitive release of resistant parasites. Here, we test the hypothesis that the spread of resistance can be slowed by reducing drug treatment and hence restricting competitive release. Using the rodent malaria model Plasmodium chabaudi,...

Data from: Real-time characterization of the molecular epidemiology of an influenza pandemic

Jessica Hedge, Andrew Rambaut & Samantha J. Lycett
Early characterization of the epidemiology and evolution of a pandemic is essential for determining the most appropriate interventions. During the 2009 H1N1 influenza A pandemic, public databases facilitated widespread sharing of genetic sequence data from the outset. We employ Bayesian phylogenetics to simulate real-time estimation of the evolutionary rate, date of emergence and intrinsic growth rate (r0) of the pandemic from whole-genome sequences. We investigate the effects of temporal range of sampling and dataset size...

Data from: Disentangling the effects of mating systems and mutation rates on cytoplamic diversity in gynodioecious Silene nutans and dioecious Silene otites

Pascal Touzet, Emna Lahiani, Mathilde Dufay, Vincent Castric, Solenn Le Cadre, Deborah Charlesworth & Fabienne Van Rossum
Many flowering plant species exhibit a variety of distinct sexual morphs, the two most common cases being the co- occurrence of females and males (dioecy) or the co-occurrence of hermaphrodites and females (gynodioecy). In this study we compared DNA sequence variability of the three genomes (nuclear, mitochondrial and chloroplastic) of a gynodioecious species, Silene nutans, with that of a closely related dioecious species, Silene otites. In the light of theoretical models, we expect cytoplasmic diversity...

Data from: Endocrine phenotype, reproductive success and survival in the great tit, Parus major

Jenny Q. Ouyang, Peter Sharp, Michael Quetting & Michaela Hau
A central goal in evolutionary ecology is to characterize and identify selection patterns on the optimal phenotype in different environments. Physiological traits, such as hormonal responses, provide important mechanisms by which individuals can adapt to fluctuating environmental conditions. It is therefore expected that selection shapes hormonal traits, but the strength and the direction of selection on plastic hormonal signals are still under investigation. Here, we determined whether, and in which way, selection is acting on...

Data from: Rapid change in parasite infection traits over the course of an epidemic in a wild host–parasite population

Stuart K. J. R. Auld, Philip J. Wilson & Tom J. Little
By combining a field study with controlled laboratory experimentation, we examined how infection traits of the sterilizing bacterium, Pasteuria ramosa, changed over the course of a growing season in a natural population of its crustacean host Daphnia magna. The number of parasite transmission spores per infected host increased ten-fold over the course of the season, concomitant with a decline in the density of infected hosts. Plausible explanations for this variation include changes in environmental conditions,...

Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies

Jack Hearn, Graham N. Stone, James A. Nicholls, Nick H. Barton, Konrad Lohse & Lynsey Bunnefeld
Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage...

Registration Year

  • 2013
    29

Resource Types

  • Dataset
    29

Affiliations

  • University of Edinburgh
    29
  • French National Centre for Scientific Research
    4
  • Royal Botanic Garden Edinburgh
    3
  • University of Illinois at Chicago
    2
  • Royal Zoological Society of Scotland
    2
  • University of Padua
    1
  • Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle
    1
  • City University of New York
    1
  • University of Adelaide
    1
  • London School of Hygiene & Tropical Medicine
    1