Molecular Biology and Evolution 17:835-838 (2000)
© 2000 Society for Molecular Biology and Evolution
Letter to the Editor |
How Molecules Evolve in Eubacteria
,*
*Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand;
Program in Applied and Computational Mathematics, Princeton University;
Fachbereich Biologie, Zellbiologie und Angewandte Botanik, Philipps-Universität Marburg, Marburg, Germany;
§Fakultät Biologie, Evolutionsbiologie, Universität Konstanz, Konstanz, Germany;
||Department of Biochemistry and Cambridge Centre for Molecular Recognition, University of Cambridge, Cambridge, England;
¶Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand.
A fundamental assumption in building evolutionary trees is that processes of change are constant across the tree of life (Li and Gu 1996;
Swofford et al. 1996
). Despite this universal view, it is now clear that nucleotide compositions, amino acid compositions (e.g., Lanave et al. 1984;
Sueoka 1988;
Hasegawa and Hashimoto 1993
; Barbrook, Lockhart, and Howe 1998
; Forster and Hickey 1999
; Lockhart et al. 1999
), and, as we demonstrate here for eubacterial sequences, the distribution of sites in sequences that can accept substitutions may change over time.
We investigated anciently diverged eubacterial sequences using a simple linear dissimilarity measure (dlcov) that was sensitive to the type of variable sequence evolution predicted by a covarion/covariotide model (a model of evolution in which the same sequence positions are free to substitute in some taxa but not in others). Since tree-building properties of dlcov differ under
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