How molecules evolve on the eubacterial tree.

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 covarion/covariotide and rates-across-sites models, dlcov allowed us to test for evidence of covarion/covariotide evolution in eubacterial sequences. Our analyses demonstrated that evolving distributions of variable sites in molecules provide support for deep-branching patterns in phylogenies reconstructed for eubacterial trees of life. This finding joins growing evidence supporting the covarion/covariotide evolution of sequences (Fitch and Markowitz 1970 ; Lockhart et al. 1996, 1998; Phillippe and Laurent 1998; Germot and Philippe 1999 ; Lopez, Forterre, and Philippe 1999 ; Moreira, Guyader, and Philippe 1999 ; Philippe et al. 2000; Steel, Huson, and Lockhart 2000 ).

Lockhart, P.J., Huson, D., Maier, U.-G., Fraunholz, M.J., Van de Peer, Y., Barbrook, A.C., Howe, C.J., Steel, M.A. (2000) How molecules evolve on the eubacterial tree. Mol. Biol. Evol. 17(5):835-838.

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