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Peter D Keightley

Publications and source records attributed to Peter D Keightley.

32 records · Page 2Linked to original sources
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↗
PubMed2003

Estimating numbers of EMS-induced mutations affecting life history traits in Caenorhabditis elegans in crosses between inbred sublines.

Inbred lines of the nematode Caenorhabditis elegans containing independent EMS-induced mutations were crossed to the ancestral wild-type strain (N2). Replicated inbred sublines were generated from the F1 offspring under conditions of minimal selection and, along with the N2 and mutant progenitor lines, were assayed for several fitness correlates including relative fitness (w). A modification of the Castle-Wright estimator and a maximum-likelihood (ML) method were used to estimate the numbers and effects of detectable mutations affecting these characters. The ML method allows for variation in mutational effects by fitting either one or two classes of mutational effect, and uses a Box-Cox power transformation of residual values to account for a skewed distribution of residuals. Both the Castle-Wright and the ML analyses suggest that most of the variation among sublines was due to a few (approximately 1.5-2.5 on average) large-effect mutations. Under ML, a model with two classes of mutational effects, including a class with small effects, fitted better than a single mutation class model, although not significantly better. 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.

Animals↗
PubMed2003

Toward a realistic model of mutations affecting fitness.

Analysis of a recent mutation accumulation (MA) experiment has led to the suggestion that as many as one-half of spontaneous mutations in Arabidopsis are advantageous for fitness. We evaluate this in the light of data from other MA experiments, along with molecular evidence, that suggest the vast majority of new mutations are deleterious.

Animals↗
PubMed2002

Enhanced CpG mutability and tumorigenesis in MBD4-deficient mice.

The mammalian protein MBD4 contains a methyl-CpG binding domain and can enzymatically remove thymine (T) or uracil (U) from a mismatched CpG site in vitro. These properties suggest that MBD4 might function in vivo to minimize the mutability of 5-methylcytosine by removing its deamination product from DNA. We tested this hypothesis by analyzing Mbd4-/- mice and found that the frequency of of C --> T transitions at CpG sites was increased by a factor of three. On a cancer-susceptible Apc(Min/+) background, Mbd4-/- mice showed accelerated tumor formation with CpG --> TpG mutations in the Apc gene. Thus MBD4 suppresses CpG mutability and tumorigenesis in vivo.

5-Methylcytosine↗
PubMed2002

Spontaneous mutational variation for body size in Caenorhabditis elegans.

We measured the impact of new mutations on genetic variation for body size in two independent sets of C. elegans spontaneous mutation-accumulation (MA) lines, derived from the N2 strain, that had been maintained by selfing for 60 or 152 generations. The two sets of lines gave broadly consistent results. The change of among-line genetic variation between cryopreserved controls and the MA lines implied that broad sense heritability increased by 0.4% per generation. Overall, MA reduced mean body size by approximately 0.1% per generation. The genome-wide rate for mutations with detectable effects on size was estimated to be approximately 0.0025 per haploid genome per generation, and their mean effects were approximately 20%. The proportion of mutations that increase body size was estimated by maximum likelihood to be no more than 20%, suggesting that the amount of mutational variation available for selection for increased size could be quite small. This hypothesis was supported by an artificial selection experiment on adult body size, started from a single highly inbred N2 individual. We observed a strongly asymmetrical response to selection of a magnitude consistent with the input of mutational variance observed in the MA experiment.

Animals↗
PubMed2002

Quantifying the slightly deleterious mutation model of molecular evolution.

We have attempted to quantify the frequency and effects of slightly deleterious mutations (SDMs), those that have selective effects close to the reciprocal of the effective population size of a species, by comparing the level of selective constraint in protein-coding genes of related species that have different present-day effective population sizes. In our two comparisons, the species with the smaller effective population size showed lower constraint, implying that SDMs had become fixed. The fixation of SDMs was supported by the observation of a higher fraction of radical to conservative amino acid substitutions in species with smaller effective population sizes. The fraction of strongly deleterious mutations (which rarely become fixed) is >70% in most species. Only approximately 10% or fewer of mutations seem to behave as SDMs, but SDMs could comprise a substantial fraction of mutations in protein-coding genes that have a chance of becoming fixed between species.

Amino Acid Substitution↗
PubMedDate not supplied

DNA sequence error rates in Genbank records estimated using the mouse genome as a reference.

We estimate DNA sequence error rates in Genbank records containing protein-coding and non-coding DNA sequences by comparing sequences of the inbred mouse strain C57BL/6J, sequenced as part of the mouse genome project and independently by other laboratories. C57BL/6J was produced by more than 100 generations of brother-sister mating, and can be assumed to be virtually free of residual polymorphism and mutational variation, so differences between independent sequences can be attributed to error. The estimated single nucleotide error rate for coding DNA is 0.10% (SE 0.012%), which is substantially lower than previous estimates for error rates in Genbank accessions. The estimated single nucleotide error rate for intronic DNA sequences (0.22%; SE 0.051%) is significantly higher than the rate for coding DNA. Since error rates for the mouse genome sequence are very low, the vast majority of the errors we detected are likely to be in individual Genbank accessions. The frequency of insertion-deletion (indel) errors in non-coding DNA approaches that of single nucleotide errors in non-coding DNA, whereas indel errors are uncommon in coding sequences.

Animals↗