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REVIEWS 'I t has been proved remarkably difficult to get compelling evidence for changes in enzymes brought about by selection, not to speak of adaptive changes' 1. Although Darwin's theory of evolution by natural selection is generally accepted by biologists for morphological traits (including behavioural and physiological), the importance of natural(More)
The selective pressure at the protein level is usually measured by the nonsynonymous/synonymous rate ratio (omega = dN/dS), with omega < 1, omega = 1, and omega > 1 indicating purifying (or negative) selection, neutral evolution, and diversifying (or positive) selection, respectively. The omega ratio is commonly calculated as an average over sites. As every(More)
Bayes prediction quantifies uncertainty by assigning posterior probabilities. It was used to identify amino acids in a protein under recurrent diversifying selection indicated by higher nonsynonymous (d(N)) than synonymous (d(S)) substitution rates or by omega = d(N)/d(S) > 1. Parameters were estimated by maximum likelihood under a codon substitution model(More)
The tailoring of existing genetic systems to new uses is called genetic co-option. Mechanisms of genetic co-option have been difficult to study because of difficulties in identifying functionally important changes. One way to study genetic co-option in protein-coding genes is to identify those amino acid sites that have experienced changes in selective(More)
The rapid accumulation of genomic sequences in public databases will finally allow large scale studies of gene family evolution, including evaluation of the role of positive Darwinian selection following a duplication event. This will be possible because recent statistical methods of comparing synonymous and nonsynonymous substitution rates permit reliable(More)
The relationships between synonymous and nonsynonymous substitution rates and between synonymous rate and codon usage bias are important to our understanding of the roles of mutation and selection in the evolution of Drosophila genes. Previous studies used approximate estimation methods that ignore codon bias. In this study we reexamine those relationships(More)
Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express host-like photosynthesis genes, presumably to augment the host photosynthetic machinery during infection. To study the prevalence and(More)
Because a microdeletion containing the DAZ gene is the most frequently observed deletion in infertile men, the DAZ gene was considered a strong candidate for the azoospermia factor. A recent evolutionary analysis, however, suggested that DAZ was free from functional constraints and consequently played little or no role in human spermatogenesis. The major(More)
Models of codon evolution are useful for investigating the strength and direction of natural selection via a parameter for the nonsynonymous/synonymous rate ratio (omega = d(N)/d(S)). Different codon models are available to account for diversity of the evolutionary patterns among sites. Codon models that specify data partitions as fixed effects allow the(More)
Genes encoded by mitochondrial DNA display considerable heterogeneity of sequence change. Among protein-coding genes, rates and patterns of nonsynony-mous nucleotide substitutions are influenced by differential selective constraints relative to amino acid composition and function of the gene product. Synonymous substitutions are presumably free of(More)