19 Works

Data from: Intra-clutch differences in egg characteristics mitigate the consequences of age-related hierarchies in a wild passerine.

Jarrod D. Hadfield, Elizabeth A. Heap, Florian Bayer, Elizabeth A. Mittell & Nicholas M. A. Crouch
The relative age of an individual's siblings is a major cause of fitness variation in many species. In Blue tits (Cyanistes caeruleus) we show that age hierarchies are predominantly caused by incubation pre-clutch completion, such that last laid eggs hatch later than early laid eggs. However, after statistically controlling for incubation behavior late laid eggs are shown to hatch more quickly than early laid eggs reducing the amount of asynchrony. By experimentally switching early and...

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: 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, M. Vidotto, L. Congiu, H. Senn, J. W. Davey, J. Martinsohn, K. Gharbi & C. Eland
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: Costs of crowding for the transmission potential in malaria parasites

Laura C. Pollitt, Thomas S. Churcher, Emma J. Dawes, Shahid M. Khan, Mohammed Sajid, Maria-Gloria Basáñez, Nick Colegrave & Sarah E. Reece
The utility of using evolutionary and ecological frameworks to understand the dynamics of infectious diseases is gaining increasing recognition. However, integrating evolutionary ecology and infectious disease epidemiology is challenging because within-host dynamics can have counterintuitive consequences for between-host transmission, especially for vector-borne parasites. A major obstacle to linking within- and between-host processes is that the drivers of the relationships between the density, virulence, and fitness of parasites are poorly understood. By experimentally manipulating the intensity...

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: Host nutrition alters the variance in parasite transmission potential

Pedro F. Vale, Marc Choisy, Tom J. Little, T. J. Little & P. F. Vale
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: 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...

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

Hanna M. V. Granroth-Wilding, Anne E. Magurran, A. E. Magurran & H. M. V. Granroth-Wilding
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: 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: 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: Endocrine phenotype, reproductive success and survival in the great tit, Parus major

Jenny Q. Ouyang, Peter Sharp, Michael Quetting, Michaela Hau, M. Quetting, M. Hau, J. Q. Ouyang & P. Sharp
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: Real-time characterization of the molecular epidemiology of an influenza pandemic

Jessica Hedge, Andrew Rambaut, Samantha J. Lycett, J. Hedge, S. J. Lycett & A. Rambaut
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: Does nasal echolocation influence the modularity of the mammal skull?

Sharlene E. Santana, Sarah E. Lofgren, S. E. Santana & S. E. Lofgren
In vertebrates, changes in cranial modularity can evolve rapidly in response to selection. However, mammals have apparently maintained their pattern of cranial integration throughout their evolutionary history and across tremendous morphological and ecological diversity. Here, we use phylogenetic, geometric morphometric and comparative analyses to test the hypothesis that the modularity of the mammalian skull has been remodelled in rhinolophid bats due to the novel and critical function of the nasal cavity in echolocation. We predicted...

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: 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 & James A. Nicholls
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: Signatures of diversifying selection in European pig breeds

Samantha Wilkinson, Zen H. Lu, Hendrik-Jan Megens, Alan L. Archibald, Chris Haley, Ian J. Jackson, Martien A. M. Groenen, Richard P. M. A. Crooijmans, Rob Ogden & Pamela Wiener
Porcine_60K_Data_Wilkinsonetal2013.tarMapping and variant calling data on SSC5:98000000-99000000This file shares the same REAME as SSC11_53500000-55500000.tarSSC5_98000000-99000000.tarMapping and variant calling data on SSC5:3100000-34000000This file shares the same REAME as SSC11_53500000-55500000.tarSSC5_3100000-34000000.tarMapping and variant calling data on SSC11:53500000-55500000SSC11_53500000-55500000.tar

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: 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: Fold or hold: experimental evolution in vitro

Sinead Collins, Andrew Rambaut, Stephen J. Bridgett, S. Collins, A. Rambaut & S. 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...

Registration Year

  • 2013
    19

Resource Types

  • Dataset
    19

Affiliations

  • University of Edinburgh
    19
  • French National Centre for Scientific Research
    2
  • University of Illinois at Chicago
    2
  • Royal Zoological Society of Scotland
    2
  • Max Planck Institute for Ornithology
    1
  • University of Padua
    1
  • University of Adelaide
    1
  • University of Washington
    1
  • Princeton University
    1
  • European Commission
    1
  • University of Queensland
    1
  • Australian National University
    1
  • University of Nottingham
    1
  • Monash University
    1
  • Museo Nacional de Ciencias Naturales
    1