Peter D Keightley

Summary

Publications

  1. pmc Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
    Peter D Keightley
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genome Res 19:1195-201. 2009
  2. pmc Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents
    Daniel L Halligan
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Genet 9:e1003995. 2013
  3. doi Positive and negative selection in murine ultraconserved noncoding elements
    Daniel L Halligan
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    Mol Biol Evol 28:2651-60. 2011
  4. pmc Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation
    Peter D Keightley
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
    Genetics 187:1153-61. 2011
  5. pmc A comparison of models to infer the distribution of fitness effects of new mutations
    Athanasios Kousathanas
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genetics 193:1197-208. 2013
  6. doi Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura
    Sophie Marion de Procé
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK
    J Mol Evol 69:601-11. 2009
  7. doi Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice
    Athanasios Kousathanas
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    Mol Biol Evol 28:1183-91. 2011
  8. doi Estimating the rate of adaptive molecular evolution when the evolutionary divergence between species is small
    Peter D Keightley
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
    J Mol Evol 74:61-8. 2012
  9. pmc A method for inferring the rate of occurrence and fitness effects of advantageous mutations
    Adrian Schneider
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    Genetics 189:1427-37. 2011
  10. pmc Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans
    Peter D Keightley
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    Genetics 188:931-40. 2011

Detail Information

Publications19

  1. pmc Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
    Peter D Keightley
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genome Res 19:1195-201. 2009
    ..Of seven short indel mutations confirmed, six were deletions, consistent with the deletion bias that is thought to exist in Drosophila...
  2. pmc Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents
    Daniel L Halligan
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Genet 9:e1003995. 2013
    ..We conclude that although there appear to be many more adaptive noncoding changes, substitutions in proteins may dominate phenotypic evolution...
  3. doi Positive and negative selection in murine ultraconserved noncoding elements
    Daniel L Halligan
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    Mol Biol Evol 28:2651-60. 2011
    ..This result suggests that there is widespread adaptation in mammalian conserved noncoding DNA elements, some of which have been implicated in the regulation of crucially important processes, including development...
  4. pmc Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation
    Peter D Keightley
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
    Genetics 187:1153-61. 2011
    ..Synonymous site selective constraint is weakest in murids, a surprising result, considering that murid effective population sizes are likely to be considerably higher than the other two taxa...
  5. pmc A comparison of models to infer the distribution of fitness effects of new mutations
    Athanasios Kousathanas
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genetics 193:1197-208. 2013
    ..A lognormal DFE best explains the data for D. melanogaster, whereas we find evidence for a bimodal DFE in M. m. castaneus...
  6. doi Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura
    Sophie Marion de Procé
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK
    J Mol Evol 69:601-11. 2009
    ....
  7. doi Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice
    Athanasios Kousathanas
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    Mol Biol Evol 28:1183-91. 2011
    ....
  8. doi Estimating the rate of adaptive molecular evolution when the evolutionary divergence between species is small
    Peter D Keightley
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
    J Mol Evol 74:61-8. 2012
    ..This bias may be substantial if branch lengths are less than 10N (e) generations...
  9. pmc A method for inferring the rate of occurrence and fitness effects of advantageous mutations
    Adrian Schneider
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    Genetics 189:1427-37. 2011
    ..melanogaster are positively selected, with a scaled selection coefficient representing the product of the effective population size, N(e), and the strength of selection on heterozygous carriers of ∼2.5...
  10. pmc Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans
    Peter D Keightley
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    Genetics 188:931-40. 2011
    ..Under the variable effects model, we infer that 11% of synonymous mutations are subject to strong purifying selection...
  11. ncbi Faster-X adaptive protein evolution in house mice
    Athanasios Kousathanas
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genetics 196:1131-43. 2014
    ..We discuss how our results help to explain the large effect of the X chromosome in speciation. ..
  12. pmc Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family
    Peter D Keightley
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genetics 196:313-20. 2014
    ..We also detected three short deletion mutations and no insertions, giving a deletion mutation rate of 1.2 × 10(-9) (95% confidence interval = 0.7 × 10(-9) - 11 × 10(-9)). ..
  13. doi The maintenance of obligate sex in finite, structured populations subject to recurrent beneficial and deleterious mutation
    Matthew Hartfield
    Laboratoire MIVEGEC UMR CNRS 5290, UR IRD 224, UM1, UM2, 911 Avenue Agropolis, B P 64501, 34394 Montpellier Cedex 5, France
    Evolution 66:3658-69. 2012
    ..g., when arrayed along one dimension), although this effect is often modest, especially if some long-distance dispersal is present...
  14. pmc The role of advantageous mutations in enhancing the evolution of a recombination modifier
    Matthew Hartfield
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    Genetics 184:1153-64. 2010
    ..However, the strength of selection on a modifier is less than the summed strengths had there been deleterious mutations only and advantageous mutations only...
  15. pmc Evidence for pervasive adaptive protein evolution in wild mice
    Daniel L Halligan
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Genet 6:e1000825. 2010
    ..Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans...
  16. doi Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes
    Lél Eöry
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    Mol Biol Evol 27:177-92. 2010
    ..Including coding and noncoding sites, we estimate that the genomic deleterious mutation rate U = 4.2. The mutational load predicted under a multiplicative model is therefore about 99% in hominids...
  17. pmc Nuclear gene variation in wild brown rats
    Rob W Ness
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
    G3 (Bethesda) 2:1661-4. 2012
    ....
  18. doi Current hypotheses for the evolution of sex and recombination
    Matthew Hartfield
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
    Integr Zool 7:192-209. 2012
    ..However, there is still a need to collect more data from natural populations and experimental studies, which can be used to test different hypotheses...
  19. pmc Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster
    Cathy Haag-Liautard
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Biol 6:e204. 2008
    ..Strand-asymmetric mutation bias, coupled with selection to maintain specific nonsynonymous bases, therefore provides an explanation for the extreme base composition of the mitochondrial genome of Drosophila...