A Nonstationary Model of DNA Sequence Evolution: Evidence for a
Nonhyperthermophilic  Common Ancestor
Nicolas Galtier
Laboratoire "Genome, Populations, Interactions" 
Universite Montpellier 2, F-34095 Montpellier 
  galtier@crit1.univ-montp2.fr

        Genomic sequences are a valuable source of information about the evolutionary history of species. Significant advances in our understanding of, say, microbial diversity has been achieved by comparing homologous DNA sequences sampled in many species. Correct reconstruction of the past, however, requires knowledge or realistic assumptions about the evolutionary process driving sequence evolution, especially when highly divergent sequences are to be compared. This is because the phylogenetic signal tends to saturate when too many changes per site occur. During the last 30 years, markovian models of DNA sequence evolution became more and more realistic, making phylogenetic reconstructions more reliable. 
        All these models, however, assume homogeneity and stationarity of the evolutionary process, implying an equal expected nucleotide composition between
species. This assumption is clearly violated by many data sets, including the highly used ribosomal RNA in which G+C% can vary from less than 30% to more than 70%. We proposed a nonhomogeneous, nonstationary model of DNA sequence evolution that accounts for G+C% variation in time and between lineages, and designed a maximum-likelihood implementation for phylogenetic purposes. A remarkable property of this method is that ancestral G+C-contents can be estimated with high accuracy, in contrast with intuition, as shown from computer simulations. This method was applied to ribosomal RNA from species distributed throughout the universal tree of life, allowing estimation of the G+C-content of the common ancestor to extant life forms. Ribosomal G+C-content is highly correlated with a physiologic trait in present-day prokaryotes, namely optimal growth temperature. Our estimate of the ribosomal G+C-content of the common ancestor to extant life forms is not compatible with life at very high temperature, in contrast with standard conjectures about the first steps of life on earth.

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