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Notes added in proof

The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa, by T. Cavalier-Smith

International Journal of Systematic and Evolutionary Microbiology vol. 52, part 2, pp. 297-354

Note 1. The great superiority of protein trees based on large numbers of different genes over single-gene trees is again strikingly demonstrated by the eukaryote phylogeny of Bapteste et al. (2002) using 123 different genes. Their gamma-corrected maximum-likelihood analysis shows the monophyly of Archamoebae with 98% support and of the amoebozoan subphylum Conosa with 97% support, even though neither clade is even shown on most uncorrected rRNA trees. This impressive congruence between multigene trees and groups established on the basis of complex ultrastructural features of the cytoskeleton, such as the centriolar cone of Amoebozoa, or membrane topology should not come as a surprise, since such features are necessarily determined multigenically. Although the rooting of their trees is suspect, as they explicitly say, because the long-branch archaebacterial outgroup is probably placed artefactually among the long-branch excavates, if treated as unrooted they are almost identical to the trees of Figs 2–5 in the present paper. In particular, on the gamma-corrected tree, the bipartition between bikonts and Amoebozoa/opisthokonts has 93% support, strongly supporting the monophyly of bikonts; excavates (represented only by diplomonads and kinetoplastids) have 96% support and chromalveolates have 62% support. In a preliminary analysis of only 56 genes, the monophyly of opisthokonts, alveolates, plants (represented only by Viridaeplantae and Rhodophyta), animals and fungi was strongly supported (all groups originally established by microscopic/ultrastructural criteria). The only difference from my interpretation of Fig. 4 is that their gamma-corrected tree, if rooted like mine, would have chromalveolates as sisters to excavates (but with only 68% support) rather than to Plantae; however, on the non-gamma-corrected tree, the sole chromist was instead a sister to plants, not alveolates/excavates. A more comprehensive testing of the topology of Fig. 4 requires comparable multigene data for Rhizaria, currently not included in the tree at all, and much broader sampling within all included groups, especially among chromists, excavates and Amoebozoa, and the exclusion of the possibly perturbing archaebacterial outgroup.

Note 2. As the only bacteria known to make melatonin, which couples eukaryotic circadian oscillators to downstream rhythms, are photosynthetic alpha-proteobacteria (Tilden et al., 1997), this biosynthetic pathway probably entered eukaryotes via the possibly photosynthetic mitochondrial ancestor. Whether the central oscillators are homologous throughout eukaryotes is unclear, but circadian rhythms using cryptochrome as the light receptor were probably present in the cenancestor; phylogenetic evidence for separate origins from DNA photolyase of animals and plant cryptochromes (Cashmore et al., 1999) is unconvincing – we cannot rule out a common origin in a stem eukaryote or actinobacterial ancestor. Shared domains between cyanobacterial and plant clock proteins (Harmer et al., 2001) suggest that some components may have been substituted from the cyanobacterial ancestor of plastids.

References

Bapteste, E., Brinkmann, H., Moore, D. V., Sensen, C. W., Gordon, P., Duruflé, L., Gaasterland, T., Lopez, P., Müller, M. & Philippe, H. (2002). The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci U S A (in press).

Cashmore, A. R., Jarillo, J. A., Wu, Y. J. & Liu, D. (1999). Cryptochromes: blue light receptors for plants and animals. Science 284, 760–765.

Harmer, S. L., Panda, S. & Kay, S. A. (2001). Molecular basis of circadian rhythms. Annu Rev Cell Dev Biol 17, 215–253.

Tilden, A. R., Becker, M. A., Amma, L. L., Arciniega, J. & McGaw, A. K. (1997). Melatonin production in an aerobic photosynthetic bacterium: an evolutionarily early association with darkness. J Pineal Res 22, 102–106.

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