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Peter D Keightley

Publications and source records attributed to Peter D Keightley.

At least 19 recordsLinked to original sources
PubMed2005

The scale of mutational variation in the murid genome.

Mutation rates vary across mammalian genomes, but little is known about the scale over which this variation occurs. Knowledge of the magnitude and scale of mutational variation is required to understand the processes that drive mutation, and is essential in formulating a robust null hypothesis for comparative genomics studies. Here we estimate the scale of mutational variation in the murid genome by calculating the spatial autocorrelation of nucleotide substitution rates in ancestral repeats. Such transposable elements are good candidates for neutrally evolving sequence and therefore well suited for the study of mutation rate variation. We find that the autocorrelation coefficient decays to a value close to zero by approximately 15 Mb, with little apparent variation in mutation rate under 100 kb. We conclude that the primary scale over which mutation rates vary is subchromosomal. Furthermore, our analysis shows that within-chromosome mutational variability exceeds variation among chromosomes by approximately one order of magnitude. Thus, differences in mutation rate between different regions of the same chromosome frequently exceed differences both between whole autosomes and between autosomes and the X-chromosome. Our results indicate that factors other than the time spent in the male germ line are important in driving mutation rates. This raises questions about the biological mechanism(s) that produce new mutations and has implications for the study of male-driven evolution.

Animals↗
PubMed2005

Regulatory variation at glypican-3 underlies a major growth QTL in mice.

The genetic basis of variation in complex traits remains poorly understood, and few genes underlying variation have been identified. Previous work identified a quantitative trait locus (QTL) responsible for much of the response to selection on growth in mice, effecting a change in body mass of approximately 20%. By fine-mapping, we have resolved the location of this QTL to a 660-kb region containing only two genes of known function, Gpc3 and Gpc4, and two other putative genes of unknown function. There are no non-synonymous polymorphisms in any of these genes, indicating that the QTL affects gene regulation. Mice carrying the high-growth QTL allele have approximately 15% lower Gpc3 mRNA expression in kidney and liver, whereas expression differences at Gpc4 are non-significant. Expression profiles of the two other genes within the region are inconsistent with a factor responsible for a general effect on growth. Polymorphisms in the 3' untranslated region of Gpc3 are strong candidates for the causal sequence variation. Gpc3 loss-of-function mutations in humans and mice cause overgrowth and developmental abnormalities. However, no deleterious side-effects were detected in our mice, indicating that genes involved in Mendelian diseases also contribute to complex trait variation. Furthermore, these findings show that small changes in gene expression can have substantial phenotypic effects.

Aging↗
PubMed2005

Intron size and exon evolution in Drosophila.

We have found a negative correlation between evolutionary rate at the protein level (as measured by d(N)) and intron size in Drosophila. Although such a relation is expected if introns reduce Hill-Robertson interference within genes, it seems more likely to be explained by the higher abundance of cis-regulatory elements in introns (especially first introns) in genes under strong selective constraints.

Animals↗
PubMed2005

Evidence for widespread degradation of gene control regions in hominid genomes.

Although sequences containing regulatory elements located close to protein-coding genes are often only weakly conserved during evolution, comparisons of rodent genomes have implied that these sequences are subject to some selective constraints. Evolutionary conservation is particularly apparent upstream of coding sequences and in first introns, regions that are enriched for regulatory elements. By comparing the human and chimpanzee genomes, we show here that there is almost no evidence for conservation in these regions in hominids. Furthermore, we show that gene expression is diverging more rapidly in hominids than in murids per unit of neutral sequence divergence. By combining data on polymorphism levels in human noncoding DNA and the corresponding human-chimpanzee divergence, we show that the proportion of adaptive substitutions in these regions in hominids is very low. It therefore seems likely that the lack of conservation and increased rate of gene expression divergence are caused by a reduction in the effectiveness of natural selection against deleterious mutations because of the low effective population sizes of hominids. 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.

Animals↗
PubMed2005

Genetic instability of C. elegans comes naturally.

There have been many attempts to measure the genome-wide mutation rate for spontaneous mutations, using measurements of traits in inbred lines in which mutations have accumulated. However, these are likely to miss many small-effect mutations that are important for evolutionary processes. Recently, the genome-wide spontaneous mutation rate in inbred lines of Caenorhabditis elegans was estimated, using DNA sequencing. The results imply that the mutation rate is surprisingly high, and that insertion-deletion mutations are unexpectedly common. Phenotypic assays of the same lines detected only a small proportion of mutations that were predicted to have evolutionarily significant fitness effects.

Animals↗
PubMed2005

Evolutionary constraints in conserved nongenic sequences of mammals.

Mammalian genomes contain many highly conserved nongenic sequences (CNGs) whose functional significance is poorly understood. Sets of CNGs have previously been identified by selecting the most conserved elements from a chromosome or genome, but in these highly selected samples, conservation may be unrelated to purifying selection. Furthermore, conservation of CNGs may be caused by mutation rate variation rather than selective constraints. To account for the effect of selective sampling, we have examined conservation of CNGs in taxa whose evolution is largely independent of the taxa from which the CNGs were initially identified, and we have controlled for mutation rate variation in the genome. We show that selective constraints in CNGs and their flanks are about one-half as strong in hominids as in murids, implying that hominids have accumulated many slightly deleterious mutations in functionally important nongenic regions. This is likely to be a consequence of the low effective population size of hominids leading to a reduced effectiveness of selection. We estimate that there are one and two times as many conserved nucleotides in CNGs as in known protein-coding genes of hominids and murids, respectively. Polymorphism frequencies in CNGs indicate that purifying selection operates in these sequences. During hominid evolution, we estimate that a total of about three deleterious mutations in CNGs and protein-coding genes have been selectively eliminated per diploid genome each generation, implying that deleterious mutations are eliminated from populations non-independently and that sex is necessary for long-term population persistence.

Animals↗
PubMed2004

Microarray gene expression analysis of the Fob3b obesity QTL identifies positional candidate gene Sqle and perturbed cholesterol and glycolysis pathways.

Obesity-related diseases are poised to become the primary cause of death in developed nations. While a number of monogenic causes of obesity have recently been identified, these are responsible for only a small proportion of human cases of obesity. Quantitative trait locus (QTL) studies using animal models have revealed hundreds of potential loci that affect obesity; however, few have been further analyzed beyond the original QTL scan. We previously mapped four QTL in an F(2) between divergently selected Fat (F) and Lean (L) lines. A QTL of large effect on chromosome 15 (Fob3) was subsequently mapped to a higher resolution into two smaller-effect QTL (Fob3a and Fob3b) using crosses between the F-line and a congenic line containing L-line alleles at the Fob3 QTL region. Here we report the gene expression characterization of Fob3b. Microarray expression analysis using the NIA-NIH 15K cDNA array set containing 14,938 mouse ESTs was employed to identify candidate genes and pathways that are differentially expressed between the F-line and a congenic line containing only the Fob3b QTL (Fob3b-line). Our study suggests squalene epoxidase (Sqle), a cholesterol biosynthesis enzyme, as a strong positional candidate gene for Fob3b. Several other cholesterol biosynthesis pathway genes unlinked to Fob3b were found to be differentially expressed, suggesting that a perturbation of this pathway could be in part responsible for the phenotypic difference between the F-line and Fob3b-line mice.

Animals↗
PubMed2004

Genetic complexity of an obesity QTL ( Fob3) revealed by detailed genetic mapping.

Obesity is proving to be a serious health concern in the developed world as well as an unwanted component of growth in livestock production. While recent advances in genetics have identified a number of monogenic causes of obesity, these are responsible for only a small proportion of human cases of obesity. By divergent selection for high and low fat content over 60 generations, we have created Fat (F) and Lean (L) lines of mice that represent a model of polygenic obesity similar to the situation in human populations. From previous crosses of these lines, four body fat quantitative trait loci (QTL) were identified. We have created congenic lines (F(chr15L)), by recurrent marker-assisted backcrossing, to introgress the QTL region with the highest LOD score, Fob3 on Chr 15, from the L-Iine into the F-line background. We have further mapped this QTL by progeny testing of recombinants, produced from crosses between the F-line and congenic F(chrl5L) mice, showing that the Fob3 QTL region is a composite of at least two smaller effect QTL-the proximal QTL Fob3a is a late-onset obesity QTL, whereas the distal Fob3b is an early-onset obesity QTL.

Analysis of Variance↗
PubMed2004

Fine mapping of a murine growth locus to a 1.4-cM region and resolution of linked QTL.

Previous work identified a QTL affecting murine size (particularly tail length) in a cross between C57BL/6J and DBA/2J mice and refined its location to an 8-cM region between D1Mit30 and D1Mit57. The present study used recombinant progeny testing to fine map this QTL. Individuals from a partially congenic strain carrying chromosomes recombinant between D1Mit30 and D1Mit57 were mated to DBA/2J, generating 942 progeny. Two QTL affecting 10-week tail length were identified in this population: one at 9.7 cM distal to D1Mit30 (the position estimated in previous work), and another of smaller effect near D1Mit30. A second population ( n = 787) was generated by mating siblings from the progeny test population that were heterozygous for the same segment of chromosome, including only recombinants between D1Mit265 and D1Mit57. In the latter population, two QTL were also identified: one at 10.2 cM distal to D1Mit30, and another of smaller effect at the distal end of the mapped region (at D1Mit150). When the two populations were analyzed together, the estimated location of the central QTL was 10.2 cM distal to D1Mit30 and there was marginally significant evidence of the distal QTL. The central QTL explained approximately 7% of the phenotypic variance, and the 95% confidence interval for its position (determined by bootstrapping) was a 1.4-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.

Animals↗
PubMed2004

Unexpected conserved non-coding DNA blocks in mammals.

The significance of non-coding DNA is a longstanding riddle in the study of molecular evolution. Using a comparative genomics approach, Dermitzakis and colleagues have recently shown that at least some non-coding sequence, frequently ignored as meaningless noise, might bear the signature of natural selection. If functional, it could mark a turning point in the way we think about the evolution of the genome.

Animals↗
PubMed2004

Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.

We develop methods to infer levels of evolutionary constraints in the genome by comparing rates of nucleotide substitution in noncoding DNA with rates predicted from rates of synonymous site evolution in adjacent genes or other putatively neutrally evolving sites, while accounting for differences in base composition. We apply the methods to estimate levels of constraint in noncoding DNA of Drosophila. In introns, constraint (the estimated fraction of mutations that are selectively eliminated) is absolute at the 5' and 3' splice junction dinucleotides, and averages 72% in base pairs 3-6 at the 5'-end. Constraint at the 5' base pairs 3-6 is significantly lower in the lineage leading to Drosophila melanogaster than in Drosophila simulans, a finding that agrees with other features of genome evolution in Drosophila and indicates that the effect of selection on intron function has been weaker in the melanogaster lineage. Elsewhere in intron sequences, the rate of nucleotide substitution is significantly higher than at synonymous sites. By using intronic sites outside splice control regions as a putative neutrally evolving standard, constraint in the 500 bp of intergenic DNA upstream and downstream regions of protein-coding genes averages approximately 44%. Although the estimated level of constraint in intergenic regions close to genes is only about one-half of that of amino acid sites, selection against single-nucleotide mutations in intergenic DNA makes a substantial contribution to the mutation load in Drosophila.

Animals↗
PubMed2004

MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution.

A method is described for performing global alignment of noncoding DNA sequences based on an evolutionary model parameterized by the frequency distribution of lengths of insertion/deletion events (indels) and their rate relative to nucleotide substitutions. A stochastic hill-climbing algorithm is used to search for the most probable alignment between a pair of sequences or three sequences of known phylogenetic relationship. The performance of the procedure, parameterized according to the empirical distribution of indel lengths in noncoding DNA of Drosophila species, is investigated by simulation. 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.

Algorithms↗
PubMed2004

Rates of molecular evolution in nuclear genes of east Mediterranean scorpions.

Scorpions of the genus Mesobuthus represent a useful terrestrial model system for studying molecular evolution. They are distributed on several Aegean islands and the adjacent mainland, they are believed to have low rates of dispersal, and evolutionary divergence dates of taxa are available based on biogeographic events that separated islands from each other and the mainland. Here, we present data on polymorphism and synonymous (Ks) and non-synonymous (Ka) substitution rates for nine nuclear protein-coding genes of two east Mediterranean scorpion species, Mesobuthus gibbosus and M. cyprius (Buthidae). Levels of polymorphism tend to be lower in populations from islands (mean nucleotide diversity pi = 0.0071 +/- 0.0028) than in mainland populations (mean pi = 0.0201 +/- 0.0085). By using linear regression of genetic divergence versus isolation time, we estimate Ks to be 3.17 +/- 1.54 per (site x 10(9) years), and Ka to be 0.39 +/- 0.94 per (site x 10(9) years). These estimates for both Ks and Ka are considerably lower than for many other invertebrates, such as Drosophila, and may be attributed to scorpions' mammal-like generation times (approximately 2 years) and low metabolic rates. Phylogenetic analysis using maximum likelihood revealed a phylogeny that is congruent with that expected based on biogeographic events and in which divergences at synonymous sites are proportional to the dates that the taxa are believed to have split. Tests of equality of branch lengths for the Cyprus and Crete lineages revealed that Ks-estimates are about the same in both lineages, as expected from the biogeographic events that separated the islands, but Ka was increased in the Cyprus lineage compared to the Cretan lineage.

Animals↗
PubMed2003

Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents.

Selection against deleterious mutations imposes a mutation load on populations because individuals die or fail to reproduce. In vertebrates, estimates of genomic rates of deleterious mutations in protein-coding genes imply the existence of a substantial mutation load, but many functionally important regions of the genome are thought to reside in noncoding DNA, and the contribution of noncoding DNA to the mutation load has been unresolved. Here, we infer the frequency of deleterious mutations in noncoding DNA of rodents by comparing rates of substitution at noncoding nucleotides with rates of substitution at the fastest evolving intronic sites of adjacent genes sampled from the whole genome sequences of mouse and rat. We show that the major elements of selectively constrained noncoding DNA are within 2,500 bp upstream and downstream of coding sequences and in first introns. Our estimate of the genomic deleterious point mutation rate for noncoding DNA (0.22 per diploid per generation) is similar to that for coding DNA. Mammalian populations therefore experience a substantial genetic load associated with selection against deleterious mutations in noncoding DNA. 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.

Animals↗
PubMed2003

Characterization of a QTL affecting skeletal size in mice.

Previous work identified a tail length QTL on Chromosome (Chr) 1 in an F(2) population of C57BL/6J x DBA/2J mice. The goals of the present study were to (1) refine the position of this QTL by additional genotyping of samples from the original study; (2) confirm the effect of this QTL by producing a partially congenic strain carrying the C57BL/6J allele against the DBA/2J background; and (3) examine the effect of the QTL on skeletal dimensions. The presence of the QTL was confirmed in a new F(2) population (N = 431) derived from the partially congenic strain, and estimates of its additive effects were similar to those from the original F(2) population (N = 901) in both sexes, i.e., the C57BL/6J chromosomal segment increased tail length, the additive effect (half the difference between homozygotes) being 0.5-0.8 standard deviations. The QTL region was more than halved, relative to that in the previous study, to an 8-cM region between D1Mit30 and D1Mit57. Among a subsample of individuals (N = 30) from the new F(2) population that were not recombinant within the QTL region, there was a significant additive effect of the QTL on the length of the humerus, femur, tibia, mandible, scapula, pelvic girdle, and a tail bone; the direction of the effect was the same as for tail length. No significant effect was found on the number of bones in the tail or on the dimensions of the ulna, skull, or first vertebra.

Animals↗
PubMed2003

How many lethal alleles?

Knowledge of the frequency of lethal mutant alleles in a population is important for our understanding of population genetics and evolution, and yet there have been few attempts to measure their number in wild populations. 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.

Alleles↗