Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation linesPeter 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...
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...
- 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...
- 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
....
- 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
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- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
