Journal of Molecular Evolution

, Volume 29, Issue 5, pp 407–411 | Cite as

DNA microenvironments and the molecular clock

  • C. Saccone
  • G. Pesole
  • G. Preparata


A few years ago we presented a stationary Markov model of gene evolution according to which only homologous genes from not too divergent species obeying the condition of being stationary may behave as reliable molecular clocks. A compartmentalized model of the nuclear genome in which the genes are distributed in compartments, the isochores, defined by their G+C content has been proposed recently. We have found that only homologous gene pairs that are stationary, and belong to the same isochore, can be used consistently for the determination of phylogeny and base substitution rate. In particular, for the rodent-human couple, only about half of the homologous gene pairs are stationary. Stationary genes evolve at the third silent codon position with the same velocity independent of the genes and base composition. By contrast, nonstationary genes display apparent rate values (pseudovelocities) that are significantly higher. Our results cast doubt upon recent claims of a large acceleration in the rate of molecular evolution in rodents.

Key words

Stationary Markov process Silent substitution rates Pseudovelocities Base composition Isochore Nuclear genes Rodents Human Artiodactyls 


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Copyright information

© Springer-Verlag New York Inc 1989

Authors and Affiliations

  • C. Saccone
    • 1
  • G. Pesole
    • 1
  • G. Preparata
    • 2
  1. 1.Centro Studi sui Mitocondri e Metabolismo Energetico, CNR, presso Dipartimento di Biochimica e Biologia MolecolareUniversità di BariItaly
  2. 2.Dipartimento di FisicaUniversità di MilanoItaly

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