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Genomes and Genes | Daniel L HalliganSummaryAffiliation: University of Edinburgh Country: UK Publications
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Publications
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...
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparisonDaniel 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...
Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscuraSophie 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....- Reduced efficacy of selection in regions of the Drosophila genome that lack crossing overPenelope 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... - Positive and negative selection in murine ultraconserved noncoding elementsDaniel 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... - Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomesLél 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... - Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sitesJun 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... - Patterns of intron sequence evolution in Drosophila are dependent upon length and GC contentPenelope 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... - Analysis and implications of mutational variationPeter 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.... - Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computationPeter 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... - Positive and negative selection on noncoding DNA close to protein-coding genes in wild house miceAthanasios Kousathanas
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
Mol Biol Evol 28:1183-91. 2011.... - Direct estimation of per nucleotide and genomic deleterious mutation rates in DrosophilaCathy 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... - Effects of spontaneous mutation accumulation on sex ratio traits in a parasitoid waspBart 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... - Natural selection drives extremely rapid evolution in antiviral RNAi genesDarren 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... - Patterns of evolutionary constraints in intronic and intergenic DNA of DrosophilaDaniel L Halligan
University of Edinburgh, School of Biological Sciences, Edinburgh EH9 3JT, UK
Genome Res 14:273-9. 2004.... - Evidence for pervasive adaptive protein evolution in wild miceDaniel 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... - Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humansPeter 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... - Evolutionary constraints in conserved nongenic sequences of mammalsPeter D Keightley
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
Genome Res 15:1373-8. 2005.... - Evolution of genes and genomes on the Drosophila phylogenyAndrew 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... - Estimating numbers of EMS-induced mutations affecting life history traits in Caenorhabditis elegans in crosses between inbred sublinesDaniel 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...