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Fig. 3. Numbering of sites in selected sequences from our proteorhodopsins (PR) alignment are compared with the numbering of sites according to Man et al. (1). The gray bars indicate those sites present in the 3D structure model of Béjà et al. (2). The spectral tuning switch at position 105 is highlighted in yellow. The conserved lysine residue to which the retinal is covalently attached is highlighted in green. The conserved residues that act as the primary proton acceptor and donor are highlighted in blue and purple, respectively.

1. Man, D., Wang, W., Sabehi, G., Aravind, L., Post, A. F., Massana, R., Spudich, E. N., Spudich, J. L. & Béjà, O. (2003) EMBO J. 22, 1725-1731.

2. Béjà, O., Aravind, L., Koonin, E. V., Suzuki, M. T., Hadd, A., Nguyen, J. P., Jovanovich, S. B., Gates, C. M., Feldman, R. A., Spudich, J. L., et al. (2000) Science 289, 1902-1906.

Fig. 4. Phylogenetic tree inferred from amino acid variation contained within the 80-PR data set. Maximum likelihood was used to estimate pairwise distances under the Whelan and Goldman (WAG) substitution matrix (1), combined with empirical estimates of amino acid frequencies and a gamma model of among-sites rate variation (2). Phylogenetic trees were inferred from the matrix of pairwise distances by using the minimum evolution (ME) criterion.

1. Whelan, S. & Goldman, N. (2001) Mol. Biol. Evol. 18, 691-699.

2. Yang, Z. (1994) J. Mol. Evol. 39, 306-314.

Fig. 5. Exchange of genetic information by means of recombination could lead to changes in phylogenetic relationships among different regions of the PR alignment. We tested for such a mosaic structure in the phylogenetic signal of these data by using the difference in the sum of squares (DSS) statistic as implemented in the program TOPAL 2.0 (1). The PR alignment was analyzed by using a window size of 400 (A), 300 (B), and 200 (C) bp. In each case, the window was incremented by 2 bp. The horizontal line is the 95% significance point of DSS, obtained by parametric bootstrapping.

1. McGuire, G. & Wright, F. (2000) Bioinformatics 16, 130-134.