Selected Publications

Gossmann, T. I., Keightley, P. D. and Eyre-Walker, A. (2012).
The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes.
Genome Biology and Evolution 4: 658-667. [PDF]

Keightley, P. D. and Eyre-Walker, A. (2012).
Estimating the rate of adaptive molecular evolution when the evolutionary divergence between species is small.
Journal of Molecular Evolution 74: 61-68. [PDF]

Keightley, P. D. (2012).
Rates and fitness consequences of new mutations in humans.
Genetics 190: 295-304. [PDF]

Schneider, A., Charlesworth, B., Eyre-Walker, A. and Keightley, P. D. (2011).
A method for inferring the rate of occurrence and fitness effects of advantageous mutations.
Genetics 189: 1427-1437. [PDF]

Halligan, D. L., Oliver, F., Guthrie, J., Stemshorn, K. C., Harr, B. and Keightley, P. D. (2011).
Positive and negative selection in murine ultra-conserved noncoding elements.
Molecular Biology and Evolution 28: 2651-2660. [PDF]

Keightley, P. D., and Halligan, D. L. (2011).
Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans.
Genetics 188: 931-940. [PDF]

Keightley, P. D., Eöry, L., Halligan, D. L. and Kirkpatrick, M. (2011).
Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation.
Genetics 187: 1153-1161. [PDF]

Kousathanas, A., Oliver, F., Halligan, D. L. and Keightley, P. D. (2011).
Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice.
Molecular Biology and Evolution 28: 1183-1191. [PDF]

Hartfield, M., Otto, S. P. and Keightley, P. D. (2010).
The role of advantageous mutations in enhancing the evolution of a recombination modifier.
Genetics 184: 1153-1164. [PDF]

Keightley, P. D. and Eyre-Walker, A. (2010).
What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?
Phil. Trans. R. Soc. B 365: 1187-1193. [PDF]

Halligan, D. L., Oliver, F., Eyre-Walker, A., Harr, B. and Keightley, P. D. (2010).
Evidence for pervasive adaptive protein evolution in wild mice.
PLoS Genetics 6: e1000825. [Article]

Eöry, L., Halligan, D. L. and Keightley, P. D. (2010).
Distribution of selectively constrained sites and the deleterious mutation rate in the hominid and murid genomes.
Molecular Biology and Evolution 27: 177-192. [PDF]

Marion de Procé, S., Halligan, D. L., Keightley, P. D. and Charlesworth, B. (2009).
Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura.
Journal of Molecular Evolution 69: 601-611. [PDF]

Halligan, D. L. and Keightley, P. D. (2009).
Spontaneous mutation accumulation studies in evolutionary genetics.
Annual Review of Ecology, Evolution and Systematics 40: 151-172. [PDF]

Eyre-Walker, A. and Keightley, P. D. (2009).
Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change.
Molecular Biology and Evolution 26: 2097-2108. [PDF]

Keightley, P. D., Trivedi, U., Thomson, M., Oliver, F., Kumar S. and Blaxter, M. L. (2009).
Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines.
Genome Research 19: 1195-1201. [PDF]

Keightley, P. D. and Halligan, D. L. (2009).
Analysis and implications of mutational variation.
Genetica 136: 359-369. [PDF]

Gaffney, D. J. and Keightley, P. D. (2008).
Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.
BMC Evolutionary Biology 8: 265. [Article]

Haag-Liautard, C., Coffey, N., Houle, D., Lynch, M., Charlesworth, B. and Keightley, P. D. (2008).
Direct estimation of the mitochondrial DNA mutation rate in D. melanogaster.
PLoS Biology 6: e204. [Article]

Guo, X., Wang, Y., Keightley, P. D. and Fan, L. (2007).
Patterns of selective constraints in noncoding DNA of rice.
BMC Evolutionary Biology 7: 208. [Article]

Wang, J., Keightley, P. D. and Halligan, D. L. (2007).
Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sites.
Journal of Molecular Evolution 65: 627-639. [PDF]

Keightley, P. D. and Eyre-Walker, A. (2007).
Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies.
Genetics 177: 2251-2261. [PDF]

Drosophila 12 Genomes Consortium (2007).
Evolution of genes and genomes on the Drosophila phylogeny.
Nature 450: 203-218. [Pubmed]

Eyre-Walker, A. and Keightley, P. D. (2007).
The distribution of fitness effects of new mutations.
Nature Reviews Genetics 8: 610-618. [PDF]

Haag-Liautard, C., Dorris, M., Maside, X., Macaskill, S., Halligan, D. L., Houle, D., Charlesworth, B. and Keightley, P. D. (2007).
Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila.
Nature 445: 82-85. [PDF]

Gaffney, D. J. and Keightley, P. D. (2006).
Genomic selective constraints in murid noncoding DNA.
PLoS Genetics 2: e204. [Article]

Keightley, P. D. and Otto, S. P. (2006).
Interference among deleterious mutations favours sex and recombination in finite populations.
Nature 443: 89-92. [PDF]

Wang, J., Keightley, P. D. and Johnson, T. (2006).
MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution.
BMC Bioinformatics 7: 292. [Article]

Christians, J. K., Hoeflich, A. and Keightley, P. D. (2006).
PAPPA2, an enzyme that cleaves an insulin-like growth factor binding protein, is a candidate gene for a QTL affecting body size in mice.
Genetics 173: 1547-1553. [PDF]

Halligan, D. L. and Keightley, P. D. (2006).
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison.
Genome Res. 16: 875-884. [PDF]

Keightley, P. D., Lercher, M. J. and Eyre-Walker, A. (2006).
Understanding the degradation of hominid gene control.
PLoS Comput. Biol. 2: e19. [Article]

Keightley, P. D., Kryukov, G. V., Sunyaev, S., Halligan, D. L. and Gaffney, D. J. (2005).
Evolutionary constraints in conserved nongenic sequences of mammals.
Genome Res. 15: 1373-1378. [PDF]

Gaffney, D. J. and Keightley, P. D. (2005).
The scale of mutational variability in the murid genome.
Genome Res. 15: 1086-1094. [PDF]

Marais G., Nouvellet P., Keightley P. D. and Charlesworth, B. (2005).
Intron size and exon evolution in Drosophila.
Genetics 170: 481-485. [PDF]

Oliver, F., Christians, J. K., Liu, X., Rhind, S., Verma, V., Davison, C., Brown, S. D. M., Denny, P. and Keightley, P. D. (2005).
Regulatory variation at glypican-3 underlies a major growth QTL in mice.
PLoS Biology 3: 872-877. [Article]

Keightley, P. D., Lercher, M. J. and Eyre-Walker, A. (2005).
Evidence for widespread degradation of gene control regions in hominid genomes.
PLoS Biology 3: 282-288. [Article]

Stylianou, I. M., Clinton, M. I., Keightley, P. D., Pritchard, C., Lallane, Z., Bünger, L. and Horvat, S. (2005).
Microarray gene expression analysis of the Fob3b obesity QTL identifies positional candidate gene Sqle and perturbed cholesterol and glycolysis pathways.
Physiological Genomics 20: 224-232. [PDF]

Keightley, P. D. and Charlesworth, B. (2005).
Genetic instability of C. elegans comes naturally.
Trends in Genetics 21: 67-70. [PDF]

Christians, J. K. and Keightley, P. D. (2005).
Finding genes that cause complex trait variation.
Current Biology 15: R19-R21. [PDF]

Wesche, P. L., Gaffney, D. J. and Keightley, P. D. (2004).
DNA sequence error rates in Genbank records estimated using the mouse genome as a reference.
DNA Sequence 15: 362-364. [PDF]

Gantenbein, B. and Keightley, P. D. (2004).
Rates of molecular evolution in nuclear genes of East Mediterranean scorpions.
Evolution 58: 2486-2497. [PDF]

Christians, J. K. and Keightley, P. D. (2004).
Fine mapping of a murine growth locus to a 1.4cM region and resolution of linked QTL.
Mamm. Genome 15: 482-491. [PDF]

Gaffney, D. J. and Keightley, P. D. (2004).
Unexpected conserved non-coding DNA blocks in mammals.
Trends. Genet. 20: 332-337. [PDF]

Stylianou, I. M., Christians, J. K., Keightley, P. D., Bünger, L., Clinton, M., Bulfield, G. and Horvat, S. (2004).
Genetic complexity of an obesity QTL (Fob3) revealed by detailed genetic mapping.
Mamm. Genome 15: 472-481. [PDF]

Keightley, P. D. (2004).
Comparing analysis methods for mutation-accumulation data.
Genetics 167: 551-553. [PDF]

Keightley, P. D. and Johnson, T. (2004).
MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution.
Genome Res. 14: 442-450. [PDF]

Keightley, P. D. (2004).
Mutational variation and long-term selection response.
Plant Breeding Reviews 24: part 1 227-247. [PDF]

Halligan, D. L., Eyre-Walker, A. Andolfatto, P. and Keightley, P. D. (2004).
Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.
Genome Res. 14: 273-279. [PDF] [Publication support]

Halligan, D. L., Peters, A. D., & Keightley, P. D. (2003).
Estimating numbers of EMS-induced mutations affecting life history traits in Caenorhabditis elegans in crosses between inbred sublines.
Genet. Res. 82: 191-205. [PDF]

Keightley, P. D. and Gaffney, D. J. (2003).
Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents.
Proc. Natl. Acad. Sci. USA 100: 13402-13406. [PDF]

Peters, A. D., Halligan, D. L., Whitlock, M. C. and Keightley, P. D. (2003).
Dominance and overdominance of mildly deleterious induced mutations for fitness traits in Caenorhabditis elegans.
Genetics 165: 589-599. [PDF]

Keightley, P. D. and Lynch, M. (2003).
Towards a realistic model of mutations affecting fitness.
Evolution 57: 683-685. [PDF]

Christians, J. K., Bingham, V., Oliver, F., Heath, T. and Keightley, P. D. (2003).
Characterisation of a QTL affecting skeletal size in mice.
Mammalian Genome, 14: 175-183. [PDF]

Halligan , D. L. and Keightley, P. D. (2003).
How many lethal alleles?
Trends in Genetics 19: 57-59. [PDF]

Eyre-Walker, A., Keightley,  P. D.,  Smith, N. G. C. and Gaffney, D. (2002).
Quantifying the slightly deleterious model of molecular evolution.
Molecular Biology and Evolution 19: 2142-2149. [PDF]

Barton, N. H. and Keightley, P. D. (2002).
Understanding quantitative genetic variation.
Nature Reviews Genetics 3: 11-21. [PDF]

Millar, C. B., Guy, J., Sansom, O. J., Selfridge, J., MacDougall, E., Hendrich, B., Keightley, P. D., Bishop, S. M., Clarke, A. R. and Bird. A. (2002).
Enhanced CpG mutability and tumorigenesis in MBD4-deficient mice.
Science 297: 403-405.

Azevedo, R. B. R., Keightley, P. D. Laurén-Määttä, C., Vassilieva, L. L., Lynch, M. and Leroi, A. M. (2002).
Spontaneous mutational variation for body size in Caenorhabditis elegans.
Genetics, 162: 755-765. [PDF] .

Christians, J. K. and Keightley, P. D. (2002).
Dissecting the genetic basis of phenotypic variation.
Current Biology 12: R415-R416.

Keightley, P. D. and Eyre-Walker, A. (2001).
Sex and U - Response to Kondrashov.
Trends in Genetics 17: 77-78.

Liu, X., Oliver, F., Brown, S. D. M., Denny, P., and Keightley, P. D. (2001).
High resolution quantitative trait locus mapping for body weight in mice by recombinant progeny testing.
Genetical Research 77: 191-197. [PDF]

Liu, X., Bünger, L. and Keightley, P. D. (2001).
Characterisation of a major X-linked QTL influencing body weight in mice.
Journal of Heredity 92: 355-357. [PDF]

Horvat, S., Bünger, L., Falconer, V. M., Mackay, P., Law, A., Bulfield, G. and Keightley, P. D. (2000).
Mapping of obesity QTLs in a cross between mouse lines divergently selected on fat content.
Mammalian Genome 11: 2-7. [PDF]

Keightley, P. D. and Bataillon, T. A. (2000).
Multi-generation maximum likelihood analysis applied to mutation accumulation experiments in Caenorhabditis elegans.
Genetics 154: 1193-1201. [PDF]

Keightley, P. D., Davies, E. K., Peters, A. D. and Shaw. R. G. (2000).
Properties of EMS-induced mutations affecting life history traits in Caenorhabditis elegans and inferences about bivariate distributions of mutation effects.
Genetics 156: 143-154. [PDF]

Keightley, P. D. and Eyre-Walker, A. (2000).
Deleterious mutations and the evolution of sex.
Science 290 : 331-333.[PDF]

Peters, A. D. and Keightley, P. D. (2000).
A test for epistasis among induced mutations in Caenorhabditis elegans.
Genetics 156: 1635-1647. [PDF]

Johnson, T. and Keightley, P. D. (2000).
Quantitative genetics: Resolving wing shape genes.
Current Biology 10: R113-R115.

Fry, J. D., Keightley, P. D., Heinsohn, S. L. and Nuzhdin, S. V. (1999).
New estimates of rates and effects of mildly deleterious mutation in Drosophila melanogaster.
Proc. Natl. Acad. Sci. USA 96: 574-579.

Eyre-Walker, A. and Keightley, P. D. (1999).
High genomic deleterious mutation rates in hominids.
Nature 397: 344-347. [PDF]

Morris, K. H., Ishikawa, A. and Keightley, P. D. (1999).
Quantitative trait loci for growth traits in C57BL/6J x DBA/2J mice.
Mammalian Genome 10: 225-228. [PDF]

Keightley, P. D. (1999).
Analysis of mutation accumulation experiments - response to Deng, Li and Li.
Genetical Research 74: 87-91.

Davies, E. K., Peters, A. D. and Keightley, P. D. (1999).
High frequency of cryptic deleterious mutations in Caenorhabditis elegans.
Science 285: 1745-1747. [PDF]

Keightley, P. D. and Knott, S. A. (1999).
Testing the correspondence between map positions of quantitative trait loci.
Genetical Research 74: 323-328.

Keightley, P. D. and Eyre-Walker, A. (1999).
Terumi Mukai and the riddle of deleterious mutation rates.
Genetics 153: 515-523. [PDF]

Keightley, P. D. (1998).
Genetic basis of response to 50 generations of selection on body weight in inbred mice.
Genetics 148: 1931-1939. [PDF]

Caballero, A. and Keightley, P. D. (1998).
Inferences on genome-wide deleterious mutation rates in inbred populations of Drosophila and mice.
Genetica 102/103: 229-239.

Wang, J., Caballero, A., Keightley, P. D. and Hill, W. G. (1998).
Bottleneck effect on genetic variance: a theoretical investigation of the role of dominance.
Genetics 150 : 435-447.

Keightley, P. D. (1998).
Inference of genome wide mutation rates and distributions of mutation effects for fitness traits: a simulation study.
Genetics 150: 1283-1293. [PDF]

Keightley, P. D., Morris, K. H., Ishikawa, A., Falconer, V. M. and Oliver, F. (1998).
Test of candidate gene-quantitative trait locus association applied to fatness in mice.
Heredity 81 : 630-637. [Article]

Nuzhdin, S. V., Keightley, P. D., Pasyukova, E. G. and Morozova, E. A. (1998).
Mapping quantitative trait loci affecting Drosophila melanogaster sternopleural bristle number using changes of marker allele frequencies in divergently selected lines.
Genetical Research 72: 79-91.

Keightley, P. D. and Ohnishi, O. (1998).
EMS-induced polygenic mutation rates for nine quantitative characters in Drosophila melanogaster.
Genetics 148: 753-766. [PDF]

Keightley, P. D., Caballero, A. and Garcia-Dorado, A. (1998).
Surviving under mutation pressure.
Current Biology 8: R235-237.

Keightley, P. D. and Caballero, A. (1997).
Genomic mutation rates for lifetime reproductive output and lifespan in Caenorhabditis elegans.
Proc. Natl. Acad. Sci. USA 94: 3823-3827. [PDF]

Keightley, P. D. and Bulfield, G. (1993).
Detection of quantitative trait loci from frequency changes at marker loci under selection.
Genetical Research 62: 195-203. [PDF]

Keightley, P. D. and Hill, W. G. (1990).
Variation maintained in quantitative traits with mutation selection balance: pleiotropic side-effects on fitness traits.
Proceedings of the Royal Society B 242: 95-100. [PDF]

Keightley, P. D. and Hill, W. G. (1989).
Quantitative variability maintained by mutation-stabilizing selection balance: sampling variation and response to subsequent directional selection.
Genetical Research 54: 45-57. [PDF]

Keightley, P. D. (1989).
Models of quantitative variation of flux in metabolic pathways.
Genetics 121: 869-876. [PDF]

Keightley, P. D. and Hill, W. G. (1988).
Quantitative genetic variability maintained by mutation-stabilizing selection balance in finite populations.
Genetical Research 52: 33-42. [PDF]

Keightley, P. D. and Hill, W. G. (1983).
Effects of linkage on response to directional selection from new mutations.
Genetical Research 42 :193-206. [PDF]