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A Eyre-Walker

Publications and source records attributed to A Eyre-Walker.

At least 37 records · Page 2Linked to original sources
PubMed1998

Investigation of the bottleneck leading to the domestication of maize.

Maize (Zea mays ssp. mays) is genetically diverse, yet it is also morphologically distinct from its wild relatives. These two observations are somewhat contradictory: the first observation is consistent with a large historical population size for maize, but the latter observation is consistent with strong, diversity-limiting selection during maize domestication. In this study, we sampled sequence diversity, coupled with simulations of the coalescent process, to study the dynamics of a population bottleneck during the domestication of maize. To do this, we determined the DNA sequence of a 1,400-bp region of the Adh1 locus from 19 individuals representing maize, its presumed progenitor (Z. mays ssp. parviglumis), and a more distant relative (Zea luxurians). The sequence data were used to guide coalescent simulations of population bottlenecks associated with domestication. Our study confirms high genetic diversity in maize-maize contains 75% of the variation found in its progenitor and is more diverse than its wild relative, Z. luxurians-but it also suggests that sequence diversity in maize can be explained by a bottleneck of short duration and very small size. For example, the breadth of genetic diversity in maize is consistent with a founding population of only 20 individuals when the domestication event is 10 generations in length.

Agriculture↗
PubMed1998

Patterns of base composition within the genes of Drosophila melanogaster.

Base composition is not uniform across the genome of Drosophila melanogaster. Earlier analyses have suggested that there is variation in composition in D. melanogaster on both a large scale and a much smaller, within-gene, scale. Here we present analyses on 117 genes which have reliable intron/exon boundaries and no known alternative splicing. We detect significant heterogeneity in G+C content among intron segments from the same gene, as well as a significant positive correlation between the intron and the third codon position G+C content within genes. Both of these observations appear to be due, in part, to an overall decline in intron and third codon position G+C content along Drosophila genes with introns. However, there is also evidence of an increase in third codon position G+C content at the start of genes; this is particularly evident in genes without introns. This is consistent with selection acting against preferred codons at the start of genes.

Animals↗
PubMed1998

Problems with parsimony in sequences of biased base composition.

Parsimony is commonly used to infer the direction of substitution and mutation. However, it is known that parsimony is biased when the base composition of the DNA sequence is skewed. Here I quantify this effect for several simple cases. The analysis demonstrates that parsimony can be misleading even when levels of sequence divergence are as low as 10%; parsimony incorrectly infers an excess of common to rare changes. Caution must therefore be excercised in the use of parsimony.

Base Composition↗
PubMed1998

Translational selection and molecular evolution.

An interplay among experimental studies of protein synthesis, evolutionary theory, and comparisons of DNA sequence data has shed light on the roles of natural selection and genetic drift in 'silent' DNA evolution.

Animals↗
PubMed1998

Mutation pressure, natural selection, and the evolution of base composition in Drosophila.

Genome sequencing in a number of taxa has revealed variation in nucleotide composition both among regions of the genome and among functional classes of sites in DNA. Mutational biases, biased gene conversion, and natural selection have been proposed as causes of this variation. Here, we review patterns of base composition in Drosophila DNA. Nucleotide composition in Drosophila melanogaster varys regionally, and base composition is correlated between introns and exons. Drosophila species also show striking patterns of non-random codon usage. Patterns of synonymous codon usage and the biochemistry of translation suggest that natural selection may act at 'silent' sites. A relationship between recombination rates and codon usage and comparisons of the evolutionary dynamics of silent mutations within and between species support natural selection discriminating among synonymous codons. The causes of regional base composition variation are less clear. Progress in functional studies of non-coding DNA, further investigations of genome patterns, and statistical tests based on evolutionary theory will lead to a greater understanding of the contributions of mutational processes and natural selection in patterning genome-wide nucleotide composition.

Animals↗
PubMed1997

Correlated rates of synonymous site evolution across plant genomes.

Synonymous substitution rates have been shown to vary among evolutionary lineages of both nuclear and organellar genes across a broad range of taxonomic groups. In animals, rate heterogeneity does not appear to be correlated across nuclear and mitochondrial genes. In this paper, we contrast substitution rates in two plant groups and show that grasses evolve more rapidly than palms at synonymous sites in a mitochondrial, a nuclear, and a plastid gene. Furthermore, we show that the relative rates of synonymous substitution between grasses and palms are similar at the three loci. The correlation in synonymous substitution rates across genes is particularly striking because the three genes evolve at very different absolute rates. In contrast, relative rates of nonsynonymous substitution are not conserved among the three genes.

Alcohol Dehydrogenase↗
PubMed1996

The close proximity of Escherichia coli genes: consequences for stop codon and synonymous codon use.

It is shown that synonymous codon usage is less biased in favor of those codons preferred by highly expressed genes at the end of Escherichia coli genes than in the middle. This appears to be due to the close proximity of many E. coli genes. It is shown that a substantial number of genes overlap either the Shine-Dalgarno sequence or the coding sequence of the next gene on the chromosome and that the codons that overlap have lower synonymous codon bias than those which do not. It is also shown that there is an increase in the frequency of A-ending codons, and a decrease in the frequency of G-ending codons at the end of E. coli genes that lie close to another gene. It is suggested that these trends in composition could be associated with selection against the formation of mRNA secondary structure near the start of the next gene on the chromosome. Stop codon use is also affected by the close proximity of genes; many genes are forced to use TGA and TAG stop codons because they terminate either within the Shine-Dalgarno or coding sequence of the next gene on the chromosome. The implications these results have for the evolution of synonymous codon use are discussed.

Base Sequence↗
PubMed1996

Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?

The levels of synonymous codon bias is shown to be positively correlated to gene length in Escherichia coli genes which are thought to be expressed at similar levels; these are genes whose products are present in multimeric proteins in equimolar amounts. It is argued that the positive correlation could be caused by selection to avoid missense errors during translation. Since the cost of producing a protein is proportional to its length, selection in favor of codons which increase accuracy should be greater in longer genes, and long genes should therefore have higher synonymous codon bias. It is also shown that there is variation in synonymous codon use which is independent of either expression level, gene length, amino acid composition, or chromosomal location. This variation is consistent with selection for translational accuracy but may have other origins.

Codon↗
PubMed1995

Synonymous substitution rates in enterobacteria.

It has been shown previously that the synonymous substitution rate between Escherichia coli and Salmonella typhimurium is lower in highly than in weakly expressed genes, and it has been suggested that this is due to stronger selection for translational efficiency in highly expressed genes as reflected in their greater codon usage bias. This hypothesis is tested here by comparing the substitution rate in codon families with different patterns of synonymous codon use. It is shown that the decline in the substitution rate across expression levels is as great for codon families that do not appear to be subject to selection for translational efficiency as for those that are. This implies that selection on translational efficiency is not responsible for the decline in the substitution rate across genes. It is argued that the most likely explanation for this decline is a decrease in the mutation rate. It is also shown that a simple evolutionary model in which synonymous codon use is determined by a balance between mutation, selection for an optimal codon, and genetic drift predicts that selection should have little effect on the substitution rate in the present case.

Codon↗
PubMed1994

Synonymous substitutions are clustered in enterobacterial genes.

The spatial distribution of synonymous substitutions in enterobacterial genes is investigated. It is shown that synonymous substitutions are significantly clustered in such a way that a synonymous substitution in one codon elevates the rate of synonymous substitution in an adjacent codon by about 10%. The level of clustering does not appear to be related to the level of gene expression, and it is restricted to a range of two or three codons. There are at least three possible explanations: (1) sequence-directed mutagenesis, (2) recombination, and (3) selection.

Base Sequence↗
PubMed1994

DNA mismatch repair and synonymous codon evolution in mammals.

It has been suggested that the differences in synonymous codon use between mammalian genes within a genome are due to differences in the efficiency of DNA mismatch repair. This hypothesis was tested by developing a model of mismatch repair, which was used to predict the expected relationship between the rate of substitution and G+C content at silent sites. It was found that the silent-substitution rate should decline with increasing G+C content over most of the G+C-content range, if it is assumed that mismatch repair is G+C biased, an assumption which is supported by data. This prediction was then tested on a set of 58 primate and artiodactyl genes. There was no evidence of a direct decline in substitution rate with increasing G+C content, for either twofold- or fourfold-degenerate sites. It was therefore concluded that variation in the efficiency of mismatch repair is not responsible for the differences in synonymous codon use between mammalian genes. In support of this conclusion, analysis of the model also showed that the parameter range over which mismatch repair can explain the differences in synonymous codon use between genes is very small.

Animals↗
PubMed1993

Reduced synonymous substitution rate at the start of enterobacterial genes.

Synonymous codon usage is less biased at the start of Escherichia coli genes than elsewhere. The rate of synonymous substitution between E.coli and Salmonella typhimurium is substantially reduced near the start of the gene, which suggests the presence of an additional selection pressure which competes with the selection for codons which are most rapidly translated. Possible competing sources of selection are the presence of secondary ribosome binding sites downstream from the start codon, the avoidance of mRNA secondary structure near the start of the gene and the use of sub-optimal codons to regulate gene expression. We provide evidence against the last of these possibilities. We also show that there is a decrease in the frequency of A, and an increase in the frequency of G along the E.coli genes at all three codon positions. We argue that these results are most consistent with selection to avoid mRNA secondary structure.

Base Composition↗
PubMed1993

Recombination and mammalian genome evolution.

Several lines of evidence are presented which suggest that sequence G + C content and recombination frequency are related in mammals: (i) chromosome G + C content is positively correlated to chiasmata density; (ii) the non-pairing region of the Y chromosome has one of the lowest G + C contents of any chromosomal segment; (iii) a reduction in the rate of recombination at several loci is mirrored by a decrease in G + C content; and (iv) when compared with humans, mice have a lower variance in chiasmata density which is reflected in a lower variance in G + C content. The observed relation between recombination frequency and sequence G + C content provides an elegant explanation of why gene density is higher in G + C rich isochores than in other parts of the genome, and why long interspersed elements (LINES) are exclusive to G + C poor isochores. However, the cause of the relation is as yet unknown. Several possibilities are considered, including gene conversion.

Animals↗
PubMed1992

Evidence that both G + C rich and G + C poor isochores are replicated early and late in the cell cycle.

Since the G + C content of a gene is correlated to that of the isochore in which it resides, and early replicating isochores are thought to be relatively G + C rich, early replicating genes should also be rich in G + C. This hypothesis is tested on a sample of 44 mammalian genes for which replication time data and sequence information are available. Early replicating genes do not appear to be more G + C rich than late replicating genes, instead there is considerable variation in the G + C content of genes replicated during both halves of S phase. These results show that both G + C rich and poor fractions of the genome are replicated early and late in the cell cycle, and suggest that isochores are not maintained by the replication of DNA sequences in compositionally biased free nucleotide pools.

Animals↗