Adam Eyre-Walker

Summary

Affiliation: University of Sussex
Country: UK

Publications

  1. pmc Fluctuating selection models and McDonald-Kreitman type analyses
    Toni I Gossmann
    School of Life Sciences, University of Sussex, Brighton, United Kingdom Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
    PLoS ONE 9:e84540. 2014
  2. pmc Evidence of selection upon genomic GC-content in bacteria
    Falk Hildebrand
    Centre for the Study of Evolution and School of Life Sciences, University of Sussex, Brighton, United Kingdom
    PLoS Genet 6:e1001107. 2010
  3. pmc The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes
    Toni I Gossmann
    School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Genome Biol Evol 4:658-67. 2012
  4. ncbi request reprint The role of mutation rate variation and genetic diversity in the architecture of human disease
    Ying Chen Eyre-Walker
    School of Life Sciences, University of Sussex, Brighton, United Kingdom
    PLoS ONE 9:e90166. 2014
  5. ncbi request reprint The genomic rate of adaptive evolution
    Adam Eyre-Walker
    National Evolutionary Synthesis Center, Durham, NC 27705, USA
    Trends Ecol Evol 21:569-75. 2006
  6. pmc Evolution in health and medicine Sackler colloquium: Genetic architecture of a complex trait and its implications for fitness and genome-wide association studies
    Adam Eyre-Walker
    School of Life Sciences, University of Sussex, Brighton BN1 7FR, United Kingdom
    Proc Natl Acad Sci U S A 107:1752-6. 2010
  7. pmc The distribution of fitness effects of new deleterious amino acid mutations in humans
    Adam Eyre-Walker
    School of Life Sciences, University of Sussex, Brighton, UK
    Genetics 173:891-900. 2006
  8. ncbi request reprint Problems with parsimony in sequences of biased base composition
    A Eyre-Walker
    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, UK
    J Mol Evol 47:686-90. 1998
  9. ncbi request reprint The distribution of fitness effects of new mutations
    Adam Eyre-Walker
    Centre for the Study of Evolution, University of Sussex, Brighton, BN1 9QG, UK
    Nat Rev Genet 8:610-8. 2007
  10. pmc Changing effective population size and the McDonald-Kreitman test
    Adam Eyre-Walker
    Centre for the Study of Evolution, University of Sussex, Brighton BN1 9QG, United Kingdom
    Genetics 162:2017-24. 2002

Detail Information

Publications60

  1. pmc Fluctuating selection models and McDonald-Kreitman type analyses
    Toni I Gossmann
    School of Life Sciences, University of Sussex, Brighton, United Kingdom Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
    PLoS ONE 9:e84540. 2014
    ..Never-the-less we show that methods tend to underestimate the rate of adaptive evolution when selection fluctuates. ..
  2. pmc Evidence of selection upon genomic GC-content in bacteria
    Falk Hildebrand
    Centre for the Study of Evolution and School of Life Sciences, University of Sussex, Brighton, United Kingdom
    PLoS Genet 6:e1001107. 2010
    ..Since synonymous GC-content is highly correlated to genomic GC-content, we further conclude that there is selection on genomic base composition in many bacteria...
  3. pmc The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes
    Toni I Gossmann
    School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Genome Biol Evol 4:658-67. 2012
    ..The low rate of adaptive evolution and the high proportion of effectively neutral substitution in species with small N(e) are expected to combine to make it difficult to detect adaptive molecular evolution in species with small N(e)...
  4. ncbi request reprint The role of mutation rate variation and genetic diversity in the architecture of human disease
    Ying Chen Eyre-Walker
    School of Life Sciences, University of Sussex, Brighton, United Kingdom
    PLoS ONE 9:e90166. 2014
    ..We predict that the mutation rate and its genetic diversity should be higher in genes associated with disease, unless all genes that could cause disease have already been identified...
  5. ncbi request reprint The genomic rate of adaptive evolution
    Adam Eyre-Walker
    National Evolutionary Synthesis Center, Durham, NC 27705, USA
    Trends Ecol Evol 21:569-75. 2006
    ..Estimates in microorganisms are even higher. By contrast, there is little evidence of widespread adaptive evolution in our own species...
  6. pmc Evolution in health and medicine Sackler colloquium: Genetic architecture of a complex trait and its implications for fitness and genome-wide association studies
    Adam Eyre-Walker
    School of Life Sciences, University of Sussex, Brighton BN1 7FR, United Kingdom
    Proc Natl Acad Sci U S A 107:1752-6. 2010
    ..g., coding or regulatory) depends largely upon the mean strength of selection; this has implications for understanding which types of mutations are likely to be responsible for the variance in fitness and inherited disease...
  7. pmc The distribution of fitness effects of new deleterious amino acid mutations in humans
    Adam Eyre-Walker
    School of Life Sciences, University of Sussex, Brighton, UK
    Genetics 173:891-900. 2006
    ....
  8. ncbi request reprint Problems with parsimony in sequences of biased base composition
    A Eyre-Walker
    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, UK
    J Mol Evol 47:686-90. 1998
    ..Caution must therefore be excercised in the use of parsimony...
  9. ncbi request reprint The distribution of fitness effects of new mutations
    Adam Eyre-Walker
    Centre for the Study of Evolution, University of Sussex, Brighton, BN1 9QG, UK
    Nat Rev Genet 8:610-8. 2007
    ....
  10. pmc Changing effective population size and the McDonald-Kreitman test
    Adam Eyre-Walker
    Centre for the Study of Evolution, University of Sussex, Brighton BN1 9QG, United Kingdom
    Genetics 162:2017-24. 2002
    ..This problem is exacerbated by the removal of low-frequency polymorphisms. However, selection on synonymous codon use restricts the conditions under which artifactual evidence of adaptive evolution is produced...
  11. pmc How clonal are human mitochondria?
    A Eyre-Walker
    Centre for the Study of Evolution, University of Sussex, Brighton, UK
    Proc Biol Sci 266:477-83. 1999
    ..We present evidence which suggests that hypervariable sites do not exist in our data. It therefore seems likely that recombination has occurred between mitochondrial lineages in humans...
  12. ncbi request reprint Quantifying the slightly deleterious mutation model of molecular evolution
    Adam Eyre-Walker
    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, UK
    Mol Biol Evol 19:2142-9. 2002
    ..Only approximately 10% or fewer of mutations seem to behave as SDMs, but SDMs could comprise a substantial fraction of mutations in protein-coding genes that have a chance of becoming fixed between species...
  13. pmc Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA
    A Eyre-Walker
    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton, BN1 9QG, United Kingdom
    Genetics 152:675-83. 1999
    ..The results therefore suggest that selection may be acting upon the base composition of isochores and large sections of junk DNA...
  14. ncbi request reprint The evolution of isochores
    A Eyre-Walker
    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, UK
    Nat Rev Genet 2:549-55. 2001
    ..However, although we have known about isochores for over 25 years, we still have a poor understanding of why they exist. In this article, we review the current evidence for the three main hypotheses...
  15. pmc Do mitochondria recombine in humans?
    A Eyre-Walker
    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton, UK
    Philos Trans R Soc Lond B Biol Sci 355:1573-80. 2000
    ..However, the population-genetic evidence, although not conclusive, is strongly suggestive of recombination in mitochondrial DNA. The implications of non-clonality for our understanding of human and mitochondrial evolution are discussed...
  16. ncbi request reprint A broad survey of recombination in animal mitochondria
    Gwenael Piganeau
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, UK
    Mol Biol Evol 21:2319-25. 2004
    ..For others, it cannot be determined whether the recombinants are real or produced by laboratory error. Either way, the results have important implications for how mtDNA is sequenced and used...
  17. ncbi request reprint The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny
    Elise M S Belle
    Centre for the Study of Evolution School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
    J Mol Evol 58:653-60. 2004
    ..These results are of interest because they confirm the recently suggested disappearance of GC-rich isochores in some mammalian genomes, and more importantly, they suggest that this disappearance started very early in mammalian evolution...
  18. doi request reprint Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change
    Adam Eyre-Walker
    Centre for the Study of Evolution and School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Mol Biol Evol 26:2097-108. 2009
    ....
  19. ncbi request reprint Evolution. Size does not matter for mitochondrial DNA
    Adam Eyre-Walker
    National Evolutionary Synthesis Center, Durham, NC 27705, USA, and Centre for the Study of Evolution, University of Sussex, Brighton BN1 9QG, UK
    Science 312:537-8. 2006
  20. pmc Hundreds of putatively functional small open reading frames in Drosophila
    Emmanuel Ladoukakis
    School of Life Sciences, University of Sussex, Falmer, Brighton, UK
    Genome Biol 12:R118. 2011
    ..However, coding sequence detection methods are biased against detecting such very short open reading frames. Thus, a substantial number of non-canonical coding regions encoding short peptides might await characterization...
  21. pmc Human triallelic sites: evidence for a new mutational mechanism?
    Alan Hodgkinson
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, United Kingdom
    Genetics 184:233-41. 2010
    ..Approximately half of these seem to be generated simultaneously since they have identical minor allele frequencies. We estimate that the mutation of adjacent nucleotides accounts for a little less than 1% of all SNPs...
  22. ncbi request reprint The genomic rate of adaptive amino acid substitution in Drosophila
    Nicolas Bierne
    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton, UK
    Mol Biol Evol 21:1350-60. 2004
    ..The analysis of several Drosophila data sets suggests that approximately 25% +/- 20% of amino acid substitutions were driven by positive selection in the divergence between D. simulans and D. yakuba...
  23. pmc The genomic distribution and local context of coincident SNPs in human and chimpanzee
    Alan Hodgkinson
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Genome Biol Evol 2:547-57. 2010
    ..Furthermore, we identify regions that contain high numbers of coincident SNPs and suggest that one in particular, a region containing the gene PRIM2, may be under balancing selection...
  24. ncbi request reprint An investigation of the variation in the transition bias among various animal mitochondrial DNA
    Elise M S Belle
    Centre for the Study of Evolution, School of Biological Sciences, University of Sussex, BN1 9QG Brighton, United Kingdom
    Gene 355:58-66. 2005
    ..We find no evidence in support of the hypothesis that this variation could be due to different metabolic rates...
  25. pmc Quantifying the variation in the effective population size within a genome
    Toni I Gossmann
    School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
    Genetics 189:1389-402. 2011
    ....
  26. pmc Cryptic variation in the human mutation rate
    Alan Hodgkinson
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
    PLoS Biol 7:e1000027. 2009
    ..We conclude that there is substantial variation in the mutation that has, until now, been hidden from view...
  27. doi request reprint The McDonald-Kreitman test and slightly deleterious mutations
    Jane Charlesworth
    Centre for the Study of Evolution, University of Sussex, Brighton, United Kingdom
    Mol Biol Evol 25:1007-15. 2008
    ..Our analysis also suggests that the level of adaptive evolution has probably been underestimated, possibly substantially, in both bacteria and Drosophila...
  28. pmc Genome wide analyses reveal little evidence for adaptive evolution in many plant species
    Toni I Gossmann
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Mol Biol Evol 27:1822-32. 2010
    ..We observe very similar results in all species; we find little evidence of adaptive amino acid substitution in any comparison except sunflowers. This may be because many plant species have modest effective population sizes...
  29. ncbi request reprint Searching for sequence directed mutagenesis in eukaryotes
    Emmanuel D Ladoukakis
    Centre for Study of Evolution and School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
    J Mol Evol 64:1-3. 2007
    ..We conclude that sequence directed mutagenesis is not prevalent in eukaryotes and that the examples of human diseases, apparently caused by sequence directed mutagenesis, are probably coincidental...
  30. ncbi request reprint Transposable elements: insertion pattern and impact on gene expression evolution in hominids
    Maria Warnefors
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Mol Biol Evol 27:1955-62. 2010
    ..This provides an alternative neutral explanation for the accumulation of TEs in upstream sequences...
  31. ncbi request reprint The rate of adaptive evolution in enteric bacteria
    Jane Charlesworth
    Centre for Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Mol Biol Evol 23:1348-56. 2006
    ..coli and S. enterica lineages. We also show that the proportion of adaptive substitutions is uncorrelated with the rate of amino acid substitution or gene function but that it may be correlated with levels of synonymous codon usage bias...
  32. pmc A selection index for gene expression evolution and its application to the divergence between humans and chimpanzees
    Maria Warnefors
    School of Life Sciences, University of Sussex, Brighton, United Kingdom
    PLoS ONE 7:e34935. 2012
    ..We also demonstrate how the same framework can be used to estimate the proportion of adaptive gene expression evolution...
  33. doi request reprint The large-scale distribution of somatic mutations in cancer genomes
    Alan Hodgkinson
    School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Hum Mutat 33:136-43. 2012
    ..Finally, we show that the density of mutations varies at a 10-Mb and a chromosomal scale, but that the variation at these scales is weak...
  34. ncbi request reprint Adaptive protein evolution in Drosophila
    Nick G C Smith
    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, UK
    Nature 415:1022-4. 2002
    ..yakuba. We estimate that 45% of all amino-acid substitutions have been fixed by natural selection, and that on average one adaptive substitution occurs every 45 years in these species...
  35. ncbi request reprint Why are young and old repetitive elements distributed differently in the human genome?
    Elise M S Belle
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, UK
    J Mol Evol 60:290-6. 2005
    ..We propose that the differential distribution of Alu elements is likely to be due to a change in their pattern of insertion or their probability of fixation through evolutionary time...
  36. doi request reprint The positive correlation between dN/dS and dS in mammals is due to runs of adjacent substitutions
    Nina Stoletzki
    Centre for Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Mol Biol Evol 28:1371-80. 2011
    ..Genuine adjacent substitutions may be due to mutation or selection...
  37. pmc A problem with the correlation coefficient as a measure of gene expression divergence
    Vini Pereira
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
    Genetics 183:1597-600. 2009
    ..We also show that the Euclidean distance yields low estimates of expression divergence for genes with a conserved uniform pattern of expression...
  38. pmc The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations
    Jane Charlesworth
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Proc Natl Acad Sci U S A 104:16992-7. 2007
    ..We show that the predicted pattern of evolution is observed...
  39. pmc A resolution of the mutation load paradox in humans
    Yann Lesecque
    School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom
    Genetics 191:1321-30. 2012
    ..Under the relative fitness model, we show that depends jointly on U and the selective effects of new deleterious mutations and that a species could tolerate 10's or even 100's of new deleterious mutations per genome each generation...
  40. pmc The accumulation of gene regulation through time
    Maria Warnefors
    School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Genome Biol Evol 3:667-73. 2011
    ....
  41. ncbi request reprint Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis
    Elise M S Belle
    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, BN1 9QG Brighton, United Kingdom e m s belle sussex ac uk
    J Mol Evol 55:356-63. 2002
    ..However, we find no correlation between either the mean GC3 or the standard deviation in GC3 and body temperature...
  42. doi request reprint Variation in the mutation rate across mammalian genomes
    Alan Hodgkinson
    School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK com
    Nat Rev Genet 12:756-66. 2011
    ..Variation in the mutation rate has important implications in evolutionary biology and underexplored implications for our understanding of hereditary disease and cancer...
  43. doi request reprint Estimation of the neutrality index
    Nina Stoletzki
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
    Mol Biol Evol 28:63-70. 2011
    ..We therefore suggest that a new statistic be used to study patterns of selection when data are sparse, the direction of selection: DoS = D(n)/(D(n) + D(s)) - P(n)/(P(n) + P(s))...
  44. doi request reprint The excess of small inverted repeats in prokaryotes
    Emmanuel D Ladoukakis
    Centre for the Study of Evolution and School of Life Sciences, University of Sussex, Brighton, UK
    J Mol Evol 67:291-300. 2008
    ..We show by simulation that even very low levels of SDM, relative to the rate of point mutation, can generate a substantial excess of inverted repeats...
  45. pmc The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias
    Nicolas Bierne
    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom
    Genetics 165:1587-97. 2003
    ..We argue that the Goldman-Yang method is misleading in this context and conclude that methods that rely on a mutational-opportunity definition of a site should be used with caution...
  46. pmc The assessment of science: the relative merits of post-publication review, the impact factor, and the number of citations
    Adam Eyre-Walker
    School of Life Sciences, University of Sussex, Brighton, United Kingdom
    PLoS Biol 11:e1001675. 2013
    ..However, we emphasise that it is likely to be a very error-prone measure of merit that is qualitative, not quantitative. ..
  47. pmc Estimating the distribution of fitness effects from DNA sequence data: implications for the molecular clock
    Gwenael Piganeau
    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom
    Proc Natl Acad Sci U S A 100:10335-40. 2003
    ..Our results provide an estimate of the distribution of fitness effects of weakly selected mutations and provide a possible explanation for why the molecular clock is fairly constant across taxa and time...
  48. pmc The effect of transposable element insertions on gene expression evolution in rodents
    Vini Pereira
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
    PLoS ONE 4:e4321. 2009
    ..However, recent observations suggest that TEs may have played a very important role in the evolution of gene expression because many conserved non-genic sequences, some of which are know to be involved in gene regulation, resemble TEs...
  49. ncbi request reprint Partitioning the variation in mammalian substitution rates
    Nick G C Smith
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
    Mol Biol Evol 20:10-7. 2003
    ..The variance in the ratio of amino acid and synonymous substitution rates is dominated by gene effects, but there is also a significant gene-by-lineage interaction...
  50. pmc Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies
    Peter D Keightley
    Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
    Genetics 177:2251-61. 2007
    ....
  51. pmc The evolution of isochores: evidence from SNP frequency distributions
    Martin J Lercher
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
    Genetics 162:1805-10. 2002
    ..The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions...
  52. ncbi request reprint Human disease genes: patterns and predictions
    Nick G C Smith
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, 752 36 Uppsala, Sweden
    Gene 318:169-75. 2003
    ..We also investigated other factors affecting the mode of evolution in the disease genes: Ka/Ks is significantly affected by protein function, mode of inheritance, and the reduction of life expectancy caused by disease...
  53. ncbi request reprint A new perspective on isochore evolution
    Laurent Duret
    CNRS UMR 5558, BBE, Université C Bernard Lyon 1, France
    Gene 385:71-4. 2006
    ..In this article we review the existing support for these two hypotheses, and discuss how they can be combined to provide a new perspective on isochore evolution...
  54. ncbi request reprint The compositional evolution of the murid genome
    Nick G C Smith
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE 752 36 Uppsala, Sweden
    J Mol Evol 55:197-201. 2002
    ..However, the patterns of compositional change suggested by the polymorphism and divergence data differ, suggesting the possibility of two murid shifts...
  55. pmc Understanding the degradation of hominid gene control
    Peter D Keightley
    PLoS Comput Biol 2:e19; author reply e26. 2006
  56. pmc The evolution of courtship behaviors through the origination of a new gene in Drosophila
    Hongzheng Dai
    Committee on Genetics, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 105:7478-83. 2008
    ..melanogaster. D. melanogaster therefore seems to have evolved in its courtship behaviors by the recruitment of a new chimeric gene...
  57. pmc Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila
    Daniel L Halligan
    University of Edinburgh, School of Biological Sciences, Edinburgh EH9 3JT, UK
    Genome Res 14:273-9. 2004
    ....
  58. ncbi request reprint A dissection of volatility in yeast
    Nina Stoletzki
    Section of Evolutionary Biology, Department Biology II, Ludwig Maximilians University Munich, Planegg Martinsried, Germany
    Mol Biol Evol 22:2022-6. 2005
    ....
  59. pmc Evidence for widespread degradation of gene control regions in hominid genomes
    Peter D Keightley
    School of Biological Sciences, University of Edinburgh, United Kingdom
    PLoS Biol 3:e42. 2005
    ..This has resulted in the accumulation of a large number of deleterious mutations in sequences containing gene control elements and hence a widespread degradation of the genome during the evolution of humans and chimpanzees...
  60. ncbi request reprint Synonymous codon usage in Escherichia coli: selection for translational accuracy
    Nina Stoletzki
    Ludwig Maximilan Universität, Biocenter, Planegg Martinsried, Germany
    Mol Biol Evol 24:374-81. 2007
    ..Considering each amino acid by itself confirms our results. We conclude that selection on synonymous codon use in E. coli is largely due to selection for translational accuracy, to reduce the costs of both missense and nonsense errors...