Protists: A convenient informal term of traditional origin used by biologists to describe a diverse group of predominantly unicellular eukaryotic organisms, not classifiable as animals, plants, or fungi — the three familiar kingdoms of the domain, Eukarya, viz., Animalia, Plantae, and Fungi — formerly classified as a fourth kingdom of Eukarya, viz., Protista, but now, through the study of their molecular phylogenetic [evolutionary] relationships, for classified into multiple high-level taxa, possibly 'kingdoms', 5-7 in number, but possibly more (or less) as the evolutionary relationships remain under study. 
Classification of protists
Adl et al. "recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional ‘‘kingdoms.’’ The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles", summarized below.
Adapted from Adl et al. and references cited:
Molecular phylogenies group eukaryotes into six clusters:
- the Opisthokonta, including the animal and fungi, and choanoflagellates (a diverse group of unicellular aquatic organisms containing a single flagellum with encircling microvilli at its base, all members of the group having descended from a common ancestor), and Mesomycetozoa, also Mesomycetozoea;
- the Amoebozoa, grouping most traditional amoebae, slime moulds, many testate amoebae, some amoebo-flagellates, and several species without mitochondria;
- the Excavata, grouping oxymonads, parabasalids, diplomonads, jakobids, and several other genera of heterotrophic flagellates, and possibly including the Euglenozoa and Heterolobosea;
- the Rhizaria, grouping the Foraminifera, most of the traditional Radiolaria, and the Cercozoa with filose pseudopodia, such as many amoebo-flagellates and some testate amoebae;
- the Archaeplastida, grouping the Glaucophyta, red algae, green algae, and Plantae;
- the Chromalveolata, grouping the Alveolata (ciliates, dinoflagellates, Apicomplexa), the Stramenopiles (brown algae, diatoms, many zoosporic fungi, and the opalinids amongst others), with the Haptophyta and Cryptophyceae.
It is argued that chromalveolates are derived from a single symbiosis of a phagotrophic heterotrophic eukaryote with a photosynthetic red alga eukaryote (Keeling 2003). The plastid was secondarily lost in several lineages (Delwiche et al. 2004). Whereas each of these lineages is monophyletic, the grouping of Alveolata and Stramenopiles with Haptophyta and Cryptophyceae may not be monophyletic. It remains contentious whether the Ciliophora had an ancestral Archaeplastida endosymbiont.
—Sina M. Adl et al., for the Int. Soc. Protistologists
- Note: In addition to genetic relationships, biologists also look at ultrastructural (e.g., electron microscopical) and metabolic pathway similarities to infer relationship.
- Dawson SC, Pace NR. (2002) Novel kingdom-level eukaryotic diversity in anoxic environments. Proc Natl Acad Sci USA. 99(12): 8324–8329.
- Sina M. Adl. (2005) The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists. J. Eukaryot. Microbiol. 52(5):399–451.
- ABSTRACT: This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional ‘‘kingdoms.’’ The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.
- Carr M, Leadbeater BS, Hassan R, Nelson M, Baldauf SL. (2008) Molecular phylogeny of choanoflagellates, the sister group to Metazoa. Proc Natl Acad Sci U S A’’. 105(43):16641-6. Free Full Text.
- Mendoza L, Taylor J, Ajello L. (2002) "The Class Mesomycetozoea: A Heterogeneous Group of Microorganisms at the Animal-Fungal Boundary". ‘’Annual Review of Microbiology’’ 56: 315-344.