The vast majority of eukaryotes on the planet, in terms of both abundance and diversity, are microbial. Generalities about fundamental biological processes are based on knowledge of a few model organisms, yet many microeukaryotes have deviated well beyond these generalities over the course of evolutionary history, which is a reflection of the deep phylogenetic distances between eukaryotic lineages that are neither plants nor animals nor fungi. It is also clear that some groups of protists have broken more rules than others, and 2 diverse lineages that particularly stand out in this regard are the Euglenozoa and the Alveolata (Fig. 4.1). In members of both of these groups, fundamental structures and processes have substantially deviated from those of other eukaryotes; however, perhaps even more interestingly, both groups have frequently departed in the same general fashion, resulting in surprising levels of convergence that suggest limits to the ways these features can be altered.

The Euglenozoa is a monophyletic group within the Excavata consisting of single-celled flagellates composed of 2 major subgroups (kinetoplastids and euglenids), and 1 smaller subgroup (diplonemids) (Fig. 4.1). Members of Euglenozoa have diverse modes of nutrition, including predation, parasitism, and photoautotrophy. Predatory euglenozoans are phylogenetically widespread within the group and tend to have diverse feeding apparatuses, feeding strategies, and prey preferences (Leander et al., 2007). For instance, some predatory species are limited to small prey such as bacteria, whereas other species frequently consume larger prey, such as other eukaryotic cells. Photoautotrophy is restricted to a specific subclade of euglenids and originated via secondary endosymbiosis between a predatory euglenid and a green algal prey (Leander et al., 2007). Parasitic and commensalic euglenozoans appear to have evolved independently several times within kinetoplastids (Simpson et al., 2006), and some species (e.g., Trypanosoma and Leishmania) cause important human illnesses such as African sleeping sickness, Chagas’s disease, and leishmaniases.

The Alveolata, another monophyletic group of primarily single-celled eukaryotes that have adopted similarly diverse modes of life, is composed of 3 major subgroups: ciliates, apicomplexans, and dinoflagellates (Fig. 4.1). All 3 subgroups contain predatory and parasitic species, and only dinoflagellates and an unusual lineage called Chromera are known