A protist is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor, the last eukaryotic common ancestor, the exclusion of other eukaryotes means that protists do not form a natural group, or clade. Therefore, some protists may be more closely related to animals, plants, or fungi than they are to other protists. However, like algae, invertebrates and protozoans, the grouping is used for convenience.

Many protists have neither hard parts nor resistant spores, and their fossils are extremely rare or unknown. Examples of such groups include the apicomplexans,Introduction to the Apicomplexa. Ucmp.berkeley.edu. Retrieved 2014-03-20. most ciliates,Fossil Record of the Ciliata. Ucmp.berkeley.edu. Retrieved 2014-03-20. some green algae (the Klebsormidiales),Klebsormidiales. Ucmp.berkeley.edu. Retrieved 2014-03-20. choanoflagellates,Introduction to the Choanoflagellata. Ucmp.berkeley.edu. Retrieved 2014-03-20. oomycetes,Introduction to the Oomycota. Ucmp.berkeley.edu. Retrieved 2014-03-20. brown algae,Introduction to the Phaeophyta . Ucmp.berkeley.edu. Retrieved 2014-03-20. yellow-green algae,Introduction to the Xanthophyta. Ucmp.berkeley.edu. Retrieved 2014-03-20. Excavata (e.g., euglenids).Introduction to the Basal Eukaryotes. Ucmp.berkeley.edu. Retrieved 2014-03-20. Some of these have been found preserved in amber (fossilized tree resin) or under unusual conditions (e.g., Paleoleishmania, a kinetoplastid).

Others are relatively common in the fossil record,Why Is The Museum On The Web?. Ucmp.berkeley.edu. Retrieved 2014-03-20. as the diatoms,Fossil Record of Diatoms. Ucmp.berkeley.edu. Retrieved 2014-03-20. golden algae,Introduction to the Chrysophyta. Ucmp.berkeley.edu. Retrieved 2014-03-20. haptophytes (coccoliths),Introduction to the Prymnesiophyta. Ucmp.berkeley.edu. Retrieved 2014-03-20. silicoflagellates, tintinnids (ciliates), dinoflagellates,Fossil Record of the Dinoflagellata. Ucmp.berkeley.edu. Retrieved 2014-03-20. green algae,Systematics of the "Green Algae", Part 1. Ucmp.berkeley.edu. Retrieved 2014-03-20. red algae,Fossil Record of the Rhodophyta. Ucmp.berkeley.edu. Retrieved 2014-03-20. heliozoans, radiolarians,Fossil Record of the Radiolaria. Ucmp.berkeley.edu. Retrieved 2014-03-20. foraminiferans,Fossil Record of Foraminifera. Ucmp.berkeley.edu. Retrieved 2014-03-20. ebriids and testate amoebae (euglyphids, arcellaceans).Introduction to the Testaceafilosea. Ucmp.berkeley.edu. Retrieved 2014-03-20. Some are used as paleoecological indicators to reconstruct ancient environments.

More probable eukaryote fossils begin to appear at about 1.8 billion years ago, the acritarchs, spherical fossils of likely algal protists.Fossil Record of the Eukaryota. Ucmp.berkeley.edu. Retrieved 2014-03-20. Another possible representative of early fossil eukaryotes are the Gabonionta.

Modern classifications

Systematists today do not treat Protista as a formal taxon, but the term "protist" is still commonly used for convenience in two ways. The most popular contemporary definition is a phylogenetic one, that identifies a paraphyletic group: a protist is any eukaryote that is not an animal, (land) plant, or (true) fungus; this definition excludes many unicellular groups, like the Microsporidia (fungi), many Chytridiomycetes (fungi), and yeasts (fungi), and also a non-unicellular group included in Protista in the past, the Myxozoa (animal).

The other definition describes protists primarily by functional or biological criteria: protists are essentially those eukaryotes that are never multicellular, that either exist as independent cells, or if they occur in colonies, do not show differentiation into tissues (but vegetative cell differentiation may occur restricted to sexual reproduction, alternate vegetative morphology, and quiescent or resistant stages, such as cysts); this definition excludes many brown, multicellular red and green algae, which may have tissues.

The taxonomy of protists is still changing. Newer classifications attempt to present monophyletic groups based on morphological (especially ultrastructural),Pitelka, D. R. (1963). Electron-Microscopic Structure of Protozoa. Pergamon Press, Oxford.Berner, T. (1993). Ultrastructure of Microalgae. Boca Raton: CRC Press. Beckett, A., Heath, I. B., and Mclaughlin, D. J. (1974). An Atlas of Fungal Ultrastructure. Longman, Green, New York. biochemical (chemotaxonomy)Ragan M.A. & Chapman D.J. (1978). A Biochemical Phylogeny of the Protists. London, New York: Academic Press. Lewin R. A. (1974). "Biochemical taxonomy", pp. 1–39 in Algal Physiology and Biochemistry, Stewart W. D. P. (ed.). Blackwell Scientific Publications, Oxford. and DNA sequence (molecular research) information.Oren, A., & Papke, R. T. (2010). Molecular phylogeny of microorganisms. Norfolk, UK: Caister Academic Press. Horner, D. S., & Hirt, R. P. (2004). "An overview on eukaryote origins and evolution: the beauty of the cell and the fabulous gene phylogenies", pp. 1–26 in Hirt, R.P. & D.S. Horner. Organelles, Genomes and Eukaryote Phylogeny, An Evolutionary Synthesis in the Age of Genomics. New York: CRC Press. However, there are sometimes discordances between molecular and morphological investigations; these can be categorized as two types: (i) one morphology, multiple lineages (e.g. morphological convergence, cryptic species) and (ii) one lineage, multiple morphologies (e.g. phenotypic plasticity, multiple life-cycle stages).

Because the protists as a whole are paraphyletic, new systems often split up or abandon the kingdom, instead treating the protist groups as separate lines of eukaryotes. The recent scheme by Adl et al. (2005) does not recognize formal ranks (phylum, class, etc.) and instead treats groups as clades of phylogenetically related organisms. This is intended to make the classification more stable in the long term and easier to update. Some of the main groups of protists, which may be treated as phyla, are listed in the taxobox, upper right. Many are thought to be monophyletic, though there is still uncertainty. For instance, the Excavata are probably not monophyletic and the chromalveolates are probably only monophyletic if the haptophytes and cryptomonads are excluded.

Archaeplastida (in part)

Red algae One of the oldest fossils identified as a red alga is also the oldest fossil eukaryote that belongs to a specific modern taxon. Bangiomorpha pubescens, a multicellular fossil from arctic Canada, strongly resembles the modern red alga Bangia and occurs in rocks dating to 1.05 billion years ago.

Two kinds of fossils resembling red algae were found sometime between 2006 and 2011 in well-preserved sedimentary rocks in Chitrakoot, central India. The presumed red algae lie embedded in fossil mats of cyanobacteria, called stromatolites, in 1.6 billion-year-old Indian phosphorite – making them the oldest plant-like fossils ever found by about 400 million years.

Red algae are important builders of limestone reefs. The earliest such coralline algae, the solenopores, are known from the Cambrian period. Other algae of different origins filled a similar role in the late Paleozoic, and in more recent reefs.

Calcite crusts that have been interpreted as the remains of coralline red algae, date to the Ediacaran Period. Thallophytes resembling coralline red algae are known from the late Proterozoic Doushantuo formation.

Glaucophyta

SAR supergroup

Stramenopiles

Brown algae The occurrence of Phaeophyceae as fossils is rare due to their generally soft-bodied nature, and scientists continue to debate the identification of some finds. Part of the problem with identification lies in the convergent evolution of morphologies between many brown and red algae. Most fossils of soft-tissue algae preserve only a flattened outline, without the microscopic features that permit the major groups of multicellular algae to be reliably distinguished. Among the brown algae, only species of the genus Padina deposit significant quantities of minerals in or around their cell walls. Other algal groups, such as the red algae and green algae, have a number of calcareous members. Because of this, they are more likely to leave evidence in the fossil record than the soft bodies of most brown algae and more often can be precisely classified.

Fossils comparable in morphology to brown algae are known from strata as old as the Upper Ordovician, but the taxonomic affinity of these impression fossils is far from certain. Claims that earlier Ediacaran fossils are brown algae have since been dismissed. While many carbonaceous fossils have been described from the Precambrian, they are typically preserved as flattened outlines or fragments measuring only millimeters long. Because these fossils lack features diagnostic for identification at even the highest level, they are assigned to fossil form taxa according to their shape and other gross morphological features. A number of Devonian fossils termed fucoids, from their resemblance in outline to species in the genus Fucus, have proven to be inorganic rather than true fossils. The Devonian megafossil Prototaxites, which consists of masses of filaments grouped into trunk-like axes, has been considered a possible brown alga. However, modern research favors reinterpretation of this fossil as a terrestrial fungus or fungal-like organism. Likewise, the fossil Protosalvinia was once considered a possible brown alga, but is now thought to be an early land plant.

A number of Paleozoic fossils have been tentatively classified with the brown algae, although most have also been compared to known red algae species. Phascolophyllaphycus possesses numerous elongate, inflated blades attached to a stipe. It is the most abundant of algal fossils found in a collection made from Carboniferous strata in Illinois. Each hollow blade bears up to eight pneumatocysts at its base, and the stipes appear to have been hollow and inflated as well. This combination of characteristics is similar to certain modern genera in the order Laminariales (kelps). Several fossils of Drydenia and a single specimen of Hungerfordia from the Upper Devonian of New York have also been compared to both brown and red algae. Fossils of Drydenia consist of an elliptical blade attached to a branching filamentous holdfast, not unlike some species of Laminaria, Porphyra, or Gigartina. The single known specimen of Hungerfordia branches dichotomously into lobes and resembles genera like Chondrus and Fucus or Dictyota.

The earliest known fossils that can be assigned reliably to the Phaeophyceae come from Miocene diatomite deposits of the Monterey Formation in California. Several soft-bodied brown macroalgae, such as Julescraneia, have been found.

Diatoms Heterokont chloroplasts appear to derive from those of red algae, rather than directly from prokaryotes as occurred in plants. This suggests they had a more recent origin than many other algae. However, fossil evidence is scant, and only with the evolution of the diatoms themselves do the heterokonts make a serious impression on the fossil record.

The earliest known fossil diatoms date from the early Jurassic (~185 Ma ago), although the molecular clock and sedimentary evidence suggests an earlier origin. It has been suggested that their origin may be related to the end-Permian mass extinction (~250 Ma), after which many marine niches were opened. The gap between this event and the time that fossil diatoms first appear may indicate a period when diatoms were unsilicified and their evolution was cryptic. Since the advent of silicification, diatoms have made a significant impression on the fossil record, with major fossil deposits found as far back as the early Cretaceous, and with some rocks such as diatomaceous earth, being composed almost entirely of them.