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the result of constructive neutrality similar to that described above for the kinetoplastid mitochondrion.

CONCLUSIONS

The deeper we look at protist biology, the greater the variety we discover in how cells can accomplish fundamental processes. Not only do protists represent the majority of the phylogenetic tree of eukaryotes, and therefore the greatest evolutionary diversity, but they also have pushed the limits of many biological systems and bending the “rules” of biology (such as the central dogma) far beyond what we see in the better studied multicellular eukaryotes. The alveolates and the euglenozoans may be “hotspots” for the generation of diverse solutions to fundamental processes, but it is also possible that they only appear this way because they are among the best studied protist groups. Other odd protists abound, but we know next to nothing about many of them, particularly at the molecular and genomics levels. All this is presently changing, and to interpret genomic diversity in eukaryotes we will have to set aside many of our preconceptions.

Comparing the alveolates and the euglenozoans is also appealing because they have broken many of the same rules in the same general way. Because they are so distant on the phylogenetic tree of eukaryotes (Keeling et al., 2005; Hampl et al., 2009), convergence between the 2 groups would ultimately be influenced only by intrinsic factors of a very basic nature (i.e., that are likely common to most or all eukaryotes) (Leander, 2008). In contrast, where multiple aspects of a system have all converged similarly, it is likely that the convergent appearance of one new characteristic can be a strong factor in the convergent evolution of others. Even if these characteristics are not obligatorily functionally linked, their evolution may be tightly linked. For example, polycistronic mRNAs can exist without an SL, but they are evolutionarily linked because adding the SL allows the polycistronic mRNA to function. Conversely, one can imagine other ways to get a polycistronic mRNA to function without SL processing (e.g., changes to translation initiation), but because no such system is known, these are evidently less likely than the advent of SL processing. In other words, within the limited universe of acceptable changes, one change closes some possibilities, but opens new ones as well.

So why have protists in general and alveolates and euglenozoans in particular engaged in so much evolutionary experimentation? Many characteristics discussed here have been considered individually and concluded to be ancient relicts, going back even so far as the RNA world, or to



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