P D Keightley

Summary

Affiliation: University of Edinburgh
Country: UK

Publications

  1. pmc MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution
    Peter D Keightley
    University of Edinburgh, School of Biological Sciences, Ashworth Laboratories, Edinburgh EH9 3JT, UK Peter Keightley_at_ed ac uk
    Genome Res 14:442-50. 2004
  2. ncbi request reprint Deleterious mutations and the evolution of sex
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Science 290:331-3. 2000
  3. ncbi request reprint Response to Kondrashov
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, EH9 3JT, Edinburgh, UK
    Trends Genet 17:77-8. 2001
  4. pmc Properties of ethylmethane sulfonate-induced mutations affecting life-history traits in Caenorhabditis elegans and inferences about bivariate distributions of mutation effects
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland
    Genetics 156:143-54. 2000
  5. pmc Multigeneration maximum-likelihood analysis applied to mutation-accumulation experiments in Caenorhabditis elegans
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland
    Genetics 154:1193-201. 2000
  6. ncbi request reprint Testing the correspondence between map positions of quantitative trait loci
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, UK
    Genet Res 74:323-8. 1999
  7. pmc Inference of genome-wide mutation rates and distributions of mutation effects for fitness traits: a simulation study
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK
    Genetics 150:1283-93. 1998
  8. ncbi request reprint Toward a realistic model of mutations affecting fitness
    Peter D Keightley
    University of Edinburgh, Institute of Cell, Animal and Population Biology, West Mains Road, Edinburgh EH9 3JT, United Kingdom
    Evolution 57:683-5; discussion 686-9. 2003
  9. ncbi request reprint Mapping quantitative trait loci for body weight on the X chromosome in mice. II. Analysis of congenic backcrosses
    K A Rance
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Scotland, UK
    Genet Res 70:125-33. 1997
  10. pmc A genetic map of quantitative trait loci for body weight in the mouse
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Scotland
    Genetics 142:227-35. 1996

Collaborators

Detail Information

Publications69

  1. pmc MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution
    Peter D Keightley
    University of Edinburgh, School of Biological Sciences, Ashworth Laboratories, Edinburgh EH9 3JT, UK Peter Keightley_at_ed ac uk
    Genome Res 14:442-50. 2004
    ..We show that there is excellent agreement between true and estimated alignments over a wide range of sequence divergences, and that the method outperforms other available alignment methods...
  2. ncbi request reprint Deleterious mutations and the evolution of sex
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Science 290:331-3. 2000
    ..In species with short generation times, U is predicted to be far below 1, suggesting that sex is not maintained by its capacity to purge the genome of deleterious mutations...
  3. ncbi request reprint Response to Kondrashov
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, EH9 3JT, Edinburgh, UK
    Trends Genet 17:77-8. 2001
    ..Following criticism by Kondrashov, here we defend our methods for estimating U and challenge the mutational deterministic hypothesis...
  4. pmc Properties of ethylmethane sulfonate-induced mutations affecting life-history traits in Caenorhabditis elegans and inferences about bivariate distributions of mutation effects
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland
    Genetics 156:143-54. 2000
    ..We show that strong mutation-induced genetic correlations do not necessarily imply strong directional correlations between mutational effects, since correlation is also generated by lines carrying different numbers of mutations...
  5. pmc Multigeneration maximum-likelihood analysis applied to mutation-accumulation experiments in Caenorhabditis elegans
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland
    Genetics 154:1193-201. 2000
    ..elegans experiments are dominated by mutations with large effects, but the analysis does not rule out the presence of a large class of deleterious mutations with very small effects...
  6. ncbi request reprint Testing the correspondence between map positions of quantitative trait loci
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, UK
    Genet Res 74:323-8. 1999
    ..We apply the test to data from three recent mouse body weight QTL mapping experiments. The results from the test are non-significant, and imply a lack of overall concordance between the QTLs that were segregating in these experiments...
  7. pmc Inference of genome-wide mutation rates and distributions of mutation effects for fitness traits: a simulation study
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK
    Genetics 150:1283-93. 1998
    ..It is argued that such lower (upper) limits are appropriate minima (maxima). Estimates of the mean mutational effect are unbiased but may convey little about the properties of the distribution if it is leptokurtic...
  8. ncbi request reprint Toward a realistic model of mutations affecting fitness
    Peter D Keightley
    University of Edinburgh, Institute of Cell, Animal and Population Biology, West Mains Road, Edinburgh EH9 3JT, United Kingdom
    Evolution 57:683-5; discussion 686-9. 2003
    ..We evaluate this in the light of data from other MA experiments, along with molecular evidence, that suggest the vast majority of new mutations are deleterious...
  9. ncbi request reprint Mapping quantitative trait loci for body weight on the X chromosome in mice. II. Analysis of congenic backcrosses
    K A Rance
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Scotland, UK
    Genet Res 70:125-33. 1997
    ..4 +/- 1.2 cM on the X chromosome, which increases body weight by approximately 18% at 10 weeks. A strategy to positionally clone the QTL is discussed...
  10. pmc A genetic map of quantitative trait loci for body weight in the mouse
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Scotland
    Genetics 142:227-35. 1996
    ..Tests for the presence of more than one QTL in regions where there were large changes of marker allele frequency were mostly inconclusive...
  11. ncbi request reprint Mapping quantitative trait loci for body weight on the X chromosome in mice. I. Analysis of a reciprocal F2 population
    K A Rance
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Scotland, UK
    Genet Res 70:117-24. 1997
    ..Dominance effects in the females were found to be non-significant. No significant X-linked effect on carcass fat percentage was detected, but a single X-linked QTL appears to explain almost the entire X-linked body weight effect...
  12. ncbi request reprint Quantitative trait loci for growth traits in C57BL/6J x DBA/2J mice
    K H Morris
    Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Mamm Genome 10:225-8. 1999
    ....
  13. ncbi request reprint High-resolution quantitative trait locus mapping for body weight in mice by recombinant progeny testing
    X Liu
    Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Genet Res 77:191-7. 2001
    ....
  14. 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
    ....
  15. pmc A test for epistasis among induced mutations in Caenorhabditis elegans
    A D Peters
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genetics 156:1635-47. 2000
    ..We also suggest a new mechanism by which deleterious mutations may provide an advantage to sexual reproduction under low selection coefficients...
  16. ncbi request reprint Mapping of obesity QTLs in a cross between mouse lines divergently selected on fat content
    S Horvat
    Roslin Institute Edinburgh, Division of Molecular Biology, Roslin EH25 9PS, Scotland, UK
    Mamm Genome 11:2-7. 2000
    ..3% of the F2 phenotypic variance for fat%, respectively. This study identified four loci that contributed to the response to divergent selection and control a significant proportion of the difference in obesity between the F and L lines...
  17. 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...
  18. pmc Genomic selective constraints in murid noncoding DNA
    Daniel J Gaffney
    Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Genet 2:e204. 2006
    ..91 per diploid genome, per generation. This estimated rate is over twice as large as a previous estimate in murids...
  19. pmc EMS-induced polygenic mutation rates for nine quantitative characters in Drosophila melanogaster
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Scotland
    Genetics 148:753-66. 1998
    ..Predicted mutational coefficients of variation were in good agreement with published estimates. Predicted changes in means were up to 0.14% or 0.6% for life history traits, depending on the model of scaling assumed...
  20. ncbi request reprint Characterization of a major X-linked quantitative trait locus influencing body weight of mice
    X Liu
    Institute of Cell, Animal, and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, Scotland, UK
    J Hered 92:355-7. 2001
    ..Body weight at late ages appears to allow the most efficient detection of allelic differences at the QTL, although assignment of genotypic state based on phenotype is never unambiguous...
  21. pmc Dominance and overdominance of mildly deleterious induced mutations for fitness traits in Caenorhabditis elegans
    A D Peters
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genetics 165:589-99. 2003
    ..Further investigation of two of these lines partially confirmed this finding...
  22. pmc Genomic mutation rates for lifetime reproductive output and lifespan in Caenorhabditis elegans
    P D Keightley
    Institute of Cell, Animal, and Population Biology, University of Edinburgh, United Kingdom
    Proc Natl Acad Sci U S A 94:3823-7. 1997
    ..The estimated deleterious mutation rate per haploid genome for fitness, U, was 0.0026, a figure two orders of magnitude smaller than previously measured for viability in Drosophila...
  23. ncbi request reprint Interference among deleterious mutations favours sex and recombination in finite populations
    Peter D Keightley
    Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Nature 443:89-92. 2006
    ..The mechanism supported by our results offers a robust and broadly applicable explanation for the evolutionary advantage of recombination and can explain the spread of costly sex...
  24. pmc Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
    Daniel L Halligan
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genome Res 16:875-84. 2006
    ..Most deleterious mutations therefore occur in non-coding DNA, and these may make an important contribution to a wide variety of evolutionary processes...
  25. pmc The scale of mutational variation in the murid genome
    Daniel J Gaffney
    Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genome Res 15:1086-94. 2005
    ..This raises questions about the biological mechanism(s) that produce new mutations and has implications for the study of male-driven evolution...
  26. ncbi request reprint Unexpected conserved non-coding DNA blocks in mammals
    Daniel J Gaffney
    Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, Scotland, United Kingdom
    Trends Genet 20:332-7. 2004
    ..If functional, it could mark a turning point in the way we think about the evolution of the genome...
  27. pmc Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents
    Peter D Keightley
    Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom
    Proc Natl Acad Sci U S A 100:13402-6. 2003
    ..Deleterious mutations in noncoding DNA have predominantly quantitative effects and could be an important source of the burden of complex genetic disease variation in human populations...
  28. ncbi request reprint Fine mapping of a murine growth locus to a 1.4-cM region and resolution of linked QTL
    Julian K Christians
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Ashworth Laboratories, King s Buildings, West Mains Road, Edinburgh, EH9 3JT, UK
    Mamm Genome 15:482-91. 2004
    ..4-cM region, approximately the region from D1Mit451 to D1Mit219. The central QTL also affected tail length and body mass at 3 and 6 weeks of age, but to a lesser degree than 10-week tail length...
  29. pmc MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution
    Jun Wang
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    BMC Bioinformatics 7:292. 2006
    ..Unraveling the functional significance of non-coding DNA depends on how well we are able to align non-coding DNA sequences. However, the alignment of non-coding DNA sequences is more difficult than aligning protein-coding sequences...
  30. ncbi request reprint Characterization of a QTL affecting skeletal size in mice
    Julian K Christians
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Ashworth Laboratories, King s Buildings, West Mains Road, UK
    Mamm Genome 14:175-83. 2003
    ..No significant effect was found on the number of bones in the tail or on the dimensions of the ulna, skull, or first vertebra...
  31. ncbi request reprint Genetic instability of C. elegans comes naturally
    Peter D Keightley
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, Scotland, UK
    Trends Genet 21:67-70. 2005
    ..Phenotypic assays of the same lines detected only a small proportion of mutations that were predicted to have evolutionarily significant fitness effects...
  32. 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...
  33. ncbi request reprint Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sites
    Jun Wang
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    J Mol Evol 65:627-39. 2007
    ..Finally, we show that GC content for each site within INE-1 sequences has evolved toward an equilibrium value (approximately 33%) since insertion...
  34. doi request reprint 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...
  35. doi request reprint 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
    ....
  36. ncbi request reprint Test of candidate gene--quantitative trait locus association applied to fatness in mice
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, U K
    Heredity (Edinb) 81:630-7. 1998
    ..The test is significant for gonadal fat pad weight in males, and gives weak support for an association with the diabetes gene...
  37. ncbi request reprint Understanding quantitative genetic variation
    N H Barton
    Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Nat Rev Genet 3:11-21. 2002
    ....
  38. ncbi request reprint Genetic complexity of an obesity QTL ( Fob3) revealed by detailed genetic mapping
    Ioannis M Stylianou
    Roslin Institute Edinburgh, Roslin, EH25 9PS, Scotland, UK
    Mamm Genome 15:472-81. 2004
    ....
  39. ncbi request reprint Microarray gene expression analysis of the Fob3b obesity QTL identifies positional candidate gene Sqle and perturbed cholesterol and glycolysis pathways
    Ioannis M Stylianou
    Department of Gene Expression, Roslin Institute, Edinburgh, Scotland
    Physiol Genomics 20:224-32. 2005
    ....
  40. ncbi request reprint Rates of molecular evolution in nuclear genes of east Mediterranean scorpions
    Benjamin Gantenbein
    School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom
    Evolution 58:2486-97. 2004
    ....
  41. ncbi request reprint Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila
    Cathy Haag-Liautard
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Nature 445:82-5. 2007
    ..2 per diploid genome. This high rate suggests that selection against deleterious mutations may have a key role in explaining patterns of genetic variation in the genome, and help to maintain recombination and sexual reproduction...
  42. pmc Regulatory variation at glypican-3 underlies a major growth QTL in mice
    Fiona Oliver
    University of Edinburgh, Institute of Evolutionary Biology, School of Biological Sciences, Edinburgh, United Kingdom
    PLoS Biol 3:e135. 2005
    ..Furthermore, these findings show that small changes in gene expression can have substantial phenotypic effects...
  43. pmc Intron size and exon evolution in Drosophila
    Gabriel Marais
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, UK
    Genetics 170:481-5. 2005
    ....
  44. pmc Genetic basis of response to 50 generations of selection on body weight in inbred mice
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Scotland
    Genetics 148:1931-9. 1998
    ..The results of the analysis of data from a cross between the selected high line and an unselected control line indicated that two major factors were involved, with the suggestion of an additional minor factor...
  45. pmc Nature of deleterious mutation load in Drosophila
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Scotland
    Genetics 144:1993-9. 1996
    ..This explanation accords well with the data and implies a spontaneous mutation rate for viability two orders of magnitude lower than previously assumed, with most mutation load attributable to major effects...
  46. ncbi request reprint Behavioural genetics: finding genes that cause complex trait variation
    Julian K Christians
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, Scotland, UK
    Curr Biol 15:R19-21. 2005
    ..Identifying genes that influence phenotypic variation is extremely difficult, especially when the allelic variants only have a small effect. A recent study has used a novel approach to identify a gene that affects the behaviour of mice...
  47. pmc What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?
    Peter D Keightley
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Philos Trans R Soc Lond B Biol Sci 365:1187-93. 2010
    ..Finally, we examine models involving slightly advantageous mutations. We show that the distribution of the absolute strength of selection is well estimated if mutations are assumed to be unconditionally deleterious...
  48. ncbi request reprint How many lethal alleles?
    Daniel L Halligan
    Institute of Cell, Animal and Population Biology, University of Edinburgh, EH9 3JT, Edinburgh, UK
    Trends Genet 19:57-9. 2003
    ..A new study has revealed unexpectedly low numbers of segregating lethal alleles in two species of fish. More experiments are needed, however, to know whether this result is general...
  49. pmc Bottleneck effect on genetic variance. A theoretical investigation of the role of dominance
    J Wang
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland
    Genetics 150:435-47. 1998
    ..This article suggests that dominance is the main cause for increased genetic variances for fitness components and fitness-related traits after bottlenecks observed in various experiments...
  50. pmc Evolutionary constraints in conserved nongenic sequences of mammals
    Peter D Keightley
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genome Res 15:1373-8. 2005
    ....
  51. 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...
  52. ncbi request reprint Quantitative genetics. Loci with large effects
    P D Keightley
    Institute of Cell, Animal and Population Biology, University of Edinburgh, UK
    Curr Biol 5:485-7. 1995
    ..Recent studies with the fruitfly Drosophila suggest that alleles of loci known from classical genetics can make major contributions to continuous-trait variation...
  53. doi request reprint Analysis and implications of mutational variation
    Peter D Keightley
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
    Genetica 136:359-69. 2009
    ....
  54. 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...
  55. ncbi request reprint Genetic architecture: dissecting the genetic basis of phenotypic variation
    Julian K Christians
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Ashworth Laboratories, King s Buildings, West Mains Road, UK
    Curr Biol 12:R415-6. 2002
    ..Identifying genes that influence phenotypic variation within species has proven to be more difficult than expected. A recent study has achieved exceptional success in yeast, and demonstrates how complex genetic architecture can be...
  56. ncbi request reprint Estimating numbers of EMS-induced mutations affecting life history traits in Caenorhabditis elegans in crosses between inbred sublines
    Daniel L Halligan
    Institute of Cell, Animal and Population Biology, University of Edinburgh, UK
    Genet Res 82:191-205. 2003
    ..Nonetheless, given that we expect there to be many mutations induced per line, our results support the hypothesis that mutations vary widely in their effects...
  57. ncbi request reprint DNA sequence error rates in Genbank records estimated using the mouse genome as a reference
    Philipp L Wesche
    University of Edinburgh, School of Biological Sciences, Ashworth Laboratories, UK
    DNA Seq 15:362-4. 2004
    ..The frequency of insertion-deletion (indel) errors in non-coding DNA approaches that of single nucleotide errors in non-coding DNA, whereas indel errors are uncommon in coding sequences...
  58. 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...
  59. 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
    ....
  60. pmc Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals
    Daniel J Gaffney
    McGill University and Genome Quebec Innovation Centre, 740 ave Dr Penfield Rm 7208, Montreal, Quebec, H3A 1A4, Canada
    BMC Evol Biol 8:265. 2008
    ..Although it likely that this procedure is biased, it is generally assumed that the bias is negligible if species are very closely related...
  61. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  62. pmc Patterns of selective constraints in noncoding DNA of rice
    Xingyi Guo
    Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, China
    BMC Evol Biol 7:208. 2007
    ..Here, we investigate selective constraints in a recent segmental duplication that includes 605 paralogous intron pairs that occurred about 7 million years ago in rice (O. sativa)...
  63. 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
    ....
  64. pmc Understanding the degradation of hominid gene control
    Peter D Keightley
    PLoS Comput Biol 2:e19; author reply e26. 2006
  65. pmc Comparing analysis methods for mutation-accumulation data
    Peter D Keightley
    Genetics 167:551-3. 2004
  66. ncbi request reprint Enhanced CpG mutability and tumorigenesis in MBD4-deficient mice
    Catherine B Millar
    Wellcome Trust Centre for Cell Biology, The King s Buildings, Edinburgh University, Edinburgh EH9 3JR, UK
    Science 297:403-5. 2002
    ..On a cancer-susceptible Apc(Min/+) background, Mbd4-/- mice showed accelerated tumor formation with CpG --> TpG mutations in the Apc gene. Thus MBD4 suppresses CpG mutability and tumorigenesis in vivo...
  67. pmc Spontaneous mutational variation for body size in Caenorhabditis elegans
    Ricardo B R Azevedo
    Department of Biology, Imperial College, Berks SL5 7PY, United Kingdom
    Genetics 162:755-65. 2002
    ..We observed a strongly asymmetrical response to selection of a magnitude consistent with the input of mutational variance observed in the MA experiment...
  68. 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...
  69. pmc PAPPA2, an enzyme that cleaves an insulin-like growth-factor-binding protein, is a candidate gene for a quantitative trait locus affecting body size in mice
    Julian K Christians
    University of Edinburgh Institute of Evolutionary Biology, School of Biological Sciences, United Kingdom
    Genetics 173:1547-53. 2006
    ....