21 Works

Data from: Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers

Nian Wang, Marian Thomson, William J. A. Bodles, Robert M. M. Crawford, Harriet V. Hunt, Alan Watson Featherstone, Jaume Pellicer & Richard J. A. Buggs
New sequencing technologies allow development of genome-wide markers for any genus of ecological interest, including plant genera such as Betula (birch) that have previously proved difficult to study due to widespread polyploidy and hybridisation. We present a de novo reference genome sequence assembly, from 67X short read coverage, of Betula nana (dwarf birch) – a diploid that is the keystone woody species of sub-arctic scrub communities but of conservation concern in Britain. We also present...

Data from: Special features of RAD Sequencing data: implications for genotyping

John W. Davey, Timothée Cezard, Pablo Fuentes-Utrilla, Cathlene Eland, Karim Gharbi & Mark L. Blaxter
RAD Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools...

Data from: A framework for estimating the fixation time of an advantageous allele in stepping-stone models

Matthew Hartfield
Determining how population subdivision increases the fixation time of an advantageous allele is an important problem in evolutionary genetics as this influences many processes. Here, I lay out a framework for calculating the fixation time of a positively selected allele in a subdivided population, as a function of the number of demes present, the migration rate between them, and the manner in which they are connected. Using this framework it becomes clear that a beneficial...

Data from: The experimental evolution of herbicide-resistance in Chlamydomonas reinhardtii results in a positive correlation between fitness in the presence and absence of herbicides

Tom Vogwill, Nick Colegrave, Paul Neve & Mato Lagator
Pleiotropic fitness trade-offs will be key determinants of the evolutionary dynamics of selection for pesticide resistance. However, for herbicide resistance, empirical support for a fitness cost of resistance is mixed, and it is therefore also questionable what further ecological trade-offs can be assumed to apply to herbicide resistance. Here, we test the existence of trade-offs by experimentally evolving herbicide resistance in Chlamydomonas reinhardtii. Although fitness costs are detected for all herbicides, we find that, counterintuitively,...

Data from: The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness

Andrea J. Betancourt, Bernardo Blanco-Martin & Brian Charlesworth
We explore factors affecting patterns of polymorphism and divergence (as captured by the neutrality index) at mammalian mitochondrial loci. To do this, we develop a population genetic model that incorporates a fraction of neutral amino acid sites, mutational bias, and a probability distribution of selection coefficients against new nonsynonymous mutations. We confirm, by reanalyzing publicly available data sets, that the mitochondrial cyt-b gene shows a broad range of neutrality indices across mammalian taxa, and explore...

Data from: The maintenance of obligate sex in finite, structured populations subject to recurrent beneficial and deleterious mutation

Matthew Hartfield, Sarah P. Otto & Peter David Keightley
Although there is no known general explanation as to why sexual populations resist asexual invasion, previous work has shown that sexuals can outcompete asexuals in structured populations. However, it is currently unknown whether costly sex can be maintained with the weak structure that is commonly observed in nature. We investigate the conditions under which obligate sexuals resist asexual invasion in structured populations subject to recurrent mutation. We determine the level of population structure needed to...

Data from: Detecting genes for variation in parasite burden and immunological traits in a wild population: testing the candidate gene approach

Emily A. Brown, Jill G. Pilkington, Dan H. Nussey, Kathryn A. Watt, Adam D. Hayward, Rachel Tucker, Andrea L. Graham, Steve Paterson, Dario Beraldi, Josephine M. Pemberton & Jon Slate
Identifying the genes underlying phenotypic variation in natural populations can provide novel insight into the evolutionary process. Here we test the candidate gene approach to identifying loci involved in variation in gastrointestinal parasite burden, in a wild population of Soay sheep. A comprehensive literature review, Gene Ontology databases, and comparative genomics resources were used to generate a list of candidate genes. In a pilot study these candidates, along with 50 random genes, were then sequenced...

Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates

Simon Aeschbacher, Andreas Futschik & Mark A. Beaumont
We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland....

Data from: Selection and microevolution of coat pattern are cryptic in a wild population of sheep

Jacob Gratten, Jill G. Pilkington, Emily A. Brown, Timothy H. Clutton-Brock, Josephine M. Pemberton & Jon Slate
Understanding the maintenance of genetic variation in natural populations is a core aim of evolutionary genetics. Insight can be gained by quantifying selection at the level of the genotype, as opposed to the phenotype. Here, we show that in a natural population of Soay sheep which is polymorphic for coat pattern, recessive genetic variants at the causal gene, agouti signalling protein (ASIP), are associated with reduced lifetime fitness. This was due primarily to a reduction...

Data from: Intergenerational effects of inbreeding in Nicrophorus vespilloides: offspring suffer fitness costs when either they or their parents are inbred

Sarah N. Mattey, Luke Strutt & Per T. Smiseth
Inbreeding depression is the reduction in fitness caused by mating between related individuals. Inbreeding is expected to cause a reduction in offspring fitness when the offspring themselves are inbred, but outbred individuals may also suffer a reduction in fitness when they depend on care from inbred parents. At present, little is known about the significance of such intergenerational effects of inbreeding. Here, we report two experiments on the burying beetle Nicrophorus vespilloides, an insect with...

Data from: Post-hatching parental care masks the effects of egg size on offspring fitness: a removal experiment on burying beetles

Katy M. Monteith, Clare Andrews & Per T. Smiseth
Parents can increase the fitness of their offspring by allocating nutrients to eggs and/or providing care for eggs and offspring. Although we have a good understanding of the adaptive significance of both egg size and parental care, remarkably little is known about the co-evolution of these two mechanisms for increasing offspring fitness. Here, we report a parental removal experiment on the burying beetle Nicrophorus vespilloides in which we test whether post-hatching parental care masks the...

Data from: Inbreeding and inbreeding depression of early life traits in a cooperative mammal

Johanna F. Nielsen, Sinead English, William P. Goodall-Copestake, Jinliang Wang, Craig A. Walling, Andrew W. Bateman, Loeske E. B. Kruuk, Tim H. Clutton-Brock & Josephine M. Pemberton
Mating between relatives often results in negative fitness consequences or inbreeding depression. However, the expression of inbreeding in populations of wild cooperative mammals and the effects of environmental, maternal and social factors on inbreeding depression in these systems are currently not well understood. This study uses pedigree-based inbreeding coefficients from a long-term study of meerkats (Suricata suricatta) in South Africa to reveal that 44% of the population have detectably non-zero (F>0) inbreeding coefficients. 15% of...

Data from: Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

David Wragg, Joram M. Mwacharo, Paul M. Hocking, Olivier Hanotte & Jose A. Alcalde
Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide single-nucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional...

Data from: Fisher's geometrical model of fitness landscape and variance in fitness within a changing environment

Xu-Sheng Zhang
The fitness of an individual can be simply defined as the number of its offspring in the next generation. However, it is not well understood how selection on the phenotype determines fitness. In accordance with Fisher’s fundamental theorem, fitness should have no or very little genetic variance, whereas empirical data suggest that is not the case. To bridge these knowledge gaps, we follow Fisher’s geometrical model and assume that fitness is determined by multivariate stabilizing...

Data from: Model-based comparisons of phylogeographic scenarios resolve the intraspecific divergence of cactophilic Drosophila mojavensis

Gilbert Smith, Konrad Lohse, William J. Etges & Michael G. Ritchie
The cactophilic fly Drosophila mojavensis exhibits considerable intraspecific genetic structure across allopatric geographic regions and shows associations with different host cactus species across its range. The divergence between these populations has been studied for more than 60 years, yet their exact historical relationships have not been resolved. We analysed sequence data from 15 intronic X-linked loci across populations from Baja California, mainland Sonora-Arizona and Mojave Desert regions under an isolation-with-migration model to assess multiple scenarios...

Data from: A likelihood-based comparison of population histories in a parasitoid guild

Konrad Lohse, Nick Barton, Graham Stone & George Melika
Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models...

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
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: The phylogenetics of Anguillicolidae (Nematoda: Anguillicolidea), swimbladder parasites of eels

Dominik R. Laetsch, Emanuel G. Heitlinger, Horst Taraschewski, Steven A. Nadler & Mark L. Blaxter
BACKGROUND: Anguillicolidae Yamaguti, 1935 is a family of nematode parasites infecting fresh-water eels of the genus Anguilla, with five species in the genera Anguillicola and Anguillicoloides. Anguillicolidae is part of Spirurina, a diverse clade made up of only animal parasites. Anguillicoloides crassus is of particular importance, as it has recently spread from its endemic range in the Eastern Pacific to Europe and North America, where it poses a significant threat to new, naïve hosts such...

Data from: Genome-wide patterns of divergence and gene flow across a butterfly radiation

Nicola J. Nadeau, Simon H. Martin, Krzysztof M. Kozak, Camilo Salazar, Kanchon K. Dasmahapatra, John W. Davey, Simon W. Baxter, Mark L. Blaxter, James Mallet & Chris D. Jiggins
The Heliconius butterflies are a diverse recent radiation comprising multiple levels of divergence with on-going gene flow between species. The recently sequenced genome of Heliconius melpomene allowed us to investigate the genomic evolution of this group using dense RAD marker sequencing. Phylogenetic analysis of 54 individuals robustly supported reciprocal monophyly of H. melpomene and H. cydno and refuted previous phylogenetic hypotheses that H. melpomene may be paraphylectic with respect to H. cydno. H. timareta also...

Data from: Shared spatial effects on quantitative genetic parameters: accounting for spatial autocorrelation and home range overlap reduces estimates of heritability in wild red deer

Katie V. Stopher, Craig A. Walling, Alison Morris, Fiona E. Guinness, Tim H. Clutton-Brock, Josephine M. Pemberton & Daniel H. Nussey
Social structure, limited dispersal and spatial heterogeneity in resources are ubiquitous in wild vertebrate populations. As a result, relatives share environments as well as genes, and environmental and genetic sources of similarity between individuals are potentially confounded. Quantitative genetic studies in the wild therefore typically account for easily captured shared environmental effects (e.g. parent, nest or region). Fine-scale spatial effects are likely to be just as important in wild vertebrates, but have been largely ignored....

Data from: Mechanisms and fitness effects of antibacterial defenses in a carrion beetle

Andres N. Arce, Paul R. Johnston, Per T. Smiseth & Daniel E. Rozen
Parents of many species care for their offspring by protecting them from a wide range of environmental hazards, including desiccation, food shortages, predators, competitors, and parasites and pathogens. Currently, little is known about the mechanisms and fitness consequences of parental defenses against bacterial pathogens and competitors. Here we combine approaches from microbiology and behavioural ecology to investigate the role and mechanistic basis of antibacterial secretions applied to carcasses by parents of the burying beetle Nicrophorus...

Registration Year

  • 2012

Resource Types

  • Dataset


  • University of Edinburgh
  • University of Cambridge
  • University of St Andrews
  • University of Sheffield
  • Princeton University
  • Royal Botanic Gardens
  • University of Warwick
  • University of Nottingham
  • University of Veterinary Medicine Vienna
  • Queen Mary University of London