From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins

Abstract

Accumulation of complete genome sequences of diverse organisms creates new possibilities for evolutionary inferences from whole-genome comparisons. In the present study, we analyze the distributions of substitution rates among proteins encoded in 19 complete genomes (the interprotein rate distribution). To estimate these rates, it is necessary to employ another fundamental distribution, that of the substitution rates among sites in proteins (the intraprotein distribution). Using two independent approaches, we show that intraprotein substitution rate variability appears to be significantly greater than generally accepted. This yields more realistic estimates of evolutionary distances from amino-acid sequences, which is critical for evolutionary-tree construction. We demonstrate that the interprotein rate distributions inferred from the genome-to-genome comparisons are similar to each other and can be approximated by a single distribution with a long exponential shoulder. This suggests that a generalized version of the molecular clock hypothesis may be valid on genome scale. We also use the scaling parameter of the obtained interprotein rate distribution to construct a rooted whole-genome phylogeny. The topology of the resulting tree is largely compatible with those of global rRNA-based trees and trees produced by other approaches to genome-wide comparison.Multiple, complete genome sequences from taxonomically diverse species create unprecedented opportunities for new phylogenetic approaches (Huynen and Bork 1998). Comparative genome analysis shows a striking complexity of evolutionary scenarios that involve, in addition to vertical descent, a number of horizontal gene transfer and lineage-specific gene loss events Doolittle 1999). With these "illicit" events being so prominent in the history of life (at least as far as prokaryotes are concerned), the question arises as to whether whole-genome comparisons are still capable of detecting a sufficiently strong signal to produce a coherent, large-scale phylogeny. One way to approach this problem is based on the presence or absence of representatives of different genomes in orthologous protein families (Fitz-Gibbon and House 1999;Snel et al. 1999;Tekaia et al. 1999). Another strategy involves the analysis of multiple protein families, with a subsequent attempt to derive a consensus that could reflect the "organismal" phylogeny (Teichmann and Mitchison 1999).In the present study, we apply an alternative approach that, to our knowledge, has not been systematically explored before. The methodology is based on the analysis of the distributions of evolutionary rates among orthologous proteins (Fitch 1970), or the interprotein rate distribution. We hypothesized that the distribution of relative evolutionary rates does not change significantly in the course of evolution because all organisms possess similar repertoires of core protein functions that are primarily represented among orthologs (Tatusov et al. 1997). Below we describe a statistical test for this hypothesis. Under...

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