Daniel L Halligan

Summary

Affiliation: University of Edinburgh
Country: UK

Publications

  1. 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
  2. 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
  3. 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
  4. pmc Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over
    Penelope R Haddrill
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK
    Genome Biol 8:R18. 2007
  5. doi request reprint 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
  6. 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
  7. 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
  8. pmc Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content
    Penelope R Haddrill
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    Genome Biol 6:R67. 2005
  9. 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
  10. 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

Collaborators

Detail Information

Publications22

  1. 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...
  2. 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...
  3. 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
    ....
  4. pmc Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over
    Penelope R Haddrill
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK
    Genome Biol 8:R18. 2007
    ..In freely recombining regions of the genome, selection should more effectively incorporate new beneficial mutations, and eliminate deleterious ones, than in regions with low rates of genetic recombination...
  5. doi request reprint 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...
  6. 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...
  7. 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...
  8. pmc Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content
    Penelope R Haddrill
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    Genome Biol 6:R67. 2005
    ..No consistent patterns have emerged from studies that have investigated general levels of evolutionary constraint in introns...
  9. 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...
  10. 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
    ....
  11. doi request reprint 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
    ....
  12. 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...
  13. 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. ..
  14. doi request reprint Effects of spontaneous mutation accumulation on sex ratio traits in a parasitoid wasp
    Bart A Pannebakker
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
    Evolution 62:1921-35. 2008
    ..e., pleiotropy), as has been argued to be the case more generally...
  15. ncbi request reprint Natural selection drives extremely rapid evolution in antiviral RNAi genes
    Darren J Obbard
    Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, United Kingdom
    Curr Biol 16:580-5. 2006
    ..This is a signature of host-pathogen arms races and implies that the ancient battle between RNA viruses and host antiviral RNAi genes is active and significant in shaping RNAi function...
  16. 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
    ....
  17. 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)). ..
  18. 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...
  19. 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...
  20. 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
    ....
  21. 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...
  22. 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...