Protist

Phylogenomic tree of eukaryotes, as regarded in 2020. Supergroups are in color.

The evolutionary relationships of protists have been explained through molecular phylogenetics, the sequencing of entire genomes and transcriptomes, and electron microscopy studies of the flagellar apparatus and cytoskeleton. New major lineages of protists and novel biodiversity continue to be discovered, resulting in dramatic changes to the eukaryotic tree of life. The newest classification systems of eukaryotes, revised in 2019, do not recognize the formal taxonomic ranks (phylum, class, order...) and instead only recognize the group that are clades of related organisms, making the classification more stable in the long term and easier to update. In this new cladistic scheme, the protists are divided into wide branches informally named supergroups:[7][1]

• Archaeplastida[lower-alpha 1] — consists of groups that have evolved from a photosynthetic common ancestor that obtained chloroplasts directly through a single event of endosymbiosis with a cyanobacterium:
  • Picozoa (1 species), non-photosynthetic predators.[15]
  • Glaucophyta (26 species), unicellular algae found in freshwater and terrestrial environments.[16]
  • Rhodophyta (5,000–6,000 species), mostly multicellular marine algae that lost chlorophyll and only harvest light energy through phycobiliproteins.[16]
  • Rhodelphidia (2 species), predators with non-photosynthetic plastid.[17]
  • Viridiplantae or Chloroplastida, containing both green algae and land plants which are not protists. The green algae comprise many lineages of varying diversity, such as Chlorophyta (7,000), Prasinodermophyta (10), Zygnematophyceae (4,000), Charophyceae (877), Klebsormidiophyceae (48) or Coleochaetophyceae (36).[7]

• Sar, SAR or Harosa – a clade of three highly diverse lineages exclusively containing protists.
  • Stramenopiles is a wide clade of photosynthetic and heterotrophic organisms that evolved from a common ancestor with hairs in one of their two flagella. The photosynthetic stramenopiles, called Ochrophyta, are a monophyletic group that acquired chloroplasts from secondary endosymbiosis with a red alga. Among these, the best known are: the unicellular or colonial Bacillariophyta (>60,000 species),[18] known as diatoms; the filamentous or genuinely multicellular Phaeophyta (2,000 species),[19] known as brown algae; and the Chrysomonadea (>1,200 species). The heterotrophic stramenopiles are more diverse in forms, ranging from fungi-like organisms such as the Hyphochytrea, Oomycota and Labyrinthulea, to various kinds of protozoa such as the flagellates Opalinata and Bicosoecida.[7]
  • Alveolata contains three of the most well-known groups of protists: Apicomplexa, a parasitic group with species harmful to humans and animals; Dinoflagellata, an ecologically important group as a main component of the marine microplankton and a main cause of algal blooms; and Ciliophora (4,500 species),[20] the extremely diverse and well-studied group of mostly free-living heterotrophs known as ciliates.[7]
  • Rhizaria is a morphologically diverse lineage mostly comprised of heterotrophic amoebae, flagellates and amoeboflagellates, and some unusual algae (Chlorarachniophyta) and spore-forming parasites. The most familiar rhizarians are Foraminifera and Radiolaria, groups of large and abundant marine amoebae, many of them macroscopic. Much of the rhizarian diversity lies within the phylum Cercozoa, filled with free-living flagellates which usually have pseudopodia, as well as Phaeodaria, a group previously considered radiolarian. Other groups are comprised of various amoebae like Vampyrellida or are important parasites like Phytomyxea, Paramyxida or Haplosporida.[7]

• Haptista — includes the Haptophyta algae and the heterotrophic Centrohelida, which are "heliozoan"-type amoebae.[7]

• Cryptista — closely related to Archaeplastida, it includes the Cryptophyta algae, with a plastid of red algal origin, and two obscure relatives with two flagella, katablepharids and Palpitomonas.[7]

• Discoba — includes many lineages previously grouped under the paraphyletic "Excavata": the Jakobida, flagellates with bacterial-like mitochondrial genomes; Tsukubamonas, a free-living flagellate; and the Discicristata clade, which unites well-known phyla Heterolobosea and Euglenozoa. Heterolobosea includes amoebae, flagellates and amoeboflagellates with complex life cycles, and the unusual Acrasida, a group of slime molds. Euglenozoa encompasses a clade of algae with chloroplasts of green algal origin and many groups of anaerobic, parasitic or free-living heterotrophs.[7]

• Metamonada — a clade of completely anaerobic protozoa, primarily flagellates. Some are gut symbionts of animals, others are free-living, and others are well-known parasites (for example, Giardia lamblia).[7]

• Amorphea — unites two huge clades:
  • Amoebozoa (2,400 species) is a large group of heterotrophic protists, mostly amoebae. Many lineages are slime molds that produce spore-releasing fruiting bodies, such as Myxogastria, Dictyostelia and Protosporangiida, and are often studied by mycologists. Within the non-fruiting amoebae, the Tubulinea contain many naked amoebae (such as Amoeba itself) and a well-studied order of testate amoebae known as Arcellinida. Other non-fruiting amoebozoans are Variosea, Discosea and Archamoebae.[7]
  • Obazoa includes the two kingdoms Metazoa (animals) and Fungi,[lower-alpha 2] and their closest protist relatives inside a clade known as Opisthokonta. The opisthokont protists are Nucleariida, Ichthyosporea, Pluriformea, Filasterea, Choanoflagellata and the elusive Tunicaraptor (1 species).[24] They are flagellated or amoeboid heterotrophs of vital importance in the search for the genes that allow animal multicellularity. Sister groups to Opisthokonta are Apusomonadida (28 species)[25] and Breviatea (4 species).[7]

Many lineages do not belong to any of these supergroups, and are usually poorly known groups with limited data. Some, such as the CRuMs clade, Malawimonadida and Ancyromonadida, appear to be related to Amorphea.[7] Others, like Hemimastigophora (10 species)[26] and Provora (7 species), appear to be related to or within Diaphoretickes, a clade that unites SAR, Archaeplastida, Haptista and Cryptista.[2]

Although the root of the tree is still unresolved, one possible topology of the eukaryotic tree of life is:[27][2]

Goldfuss' system of life, introducing the Protozoa within animals.

From the start of the 18th century, the popular term "infusion animals" (later infusoria) referred to protists, bacteria and small invertebrate animals. In the mid-18th century, while Swedish scientist Carl von Linnaeus largely ignored the protists,[lower-alpha 3] his Danish contemporary Otto Friedrich Müller was the first to introduce protists to the binomial nomenclature system.[28][29]

In the early 19th century, German naturalist Georg August Goldfuss introduced Protozoa (meaning 'early animals') as a class within Kingdom Animalia,[30] to refer to four very different groups: infusoria (ciliates), corals, phytozoa (such as Cryptomonas) and jellyfish. Later, in 1845, Carl Theodor von Siebold was the first to establish Protozoa as a phylum of exclusively unicellular animals consisting of two classes: Infusoria (ciliates) and Rhizopoda (amoebae, foraminifera).[31] Other scientists did not consider all of them part of the animal kingdom, and by the middle of the century they were regarded within the groupings of Protozoa (early animals), Protophyta (early plants), Phytozoa (animal-like plants) and Bacteria (mostly considered plants). Microscopic organisms were increasingly constrained in the plant/animal dichotomy. In 1858, the palaeontolgist Richard Owen was the first to define Protozoa as a separate kingdom of eukaryotic organisms, with "nucleated cells" and the "common organic characters" of plants and animals, although he also included sponges within protozoa.[8]

John Hogg's illustration of the Four Kingdoms of Nature, showing "Regnum Primigenum" (Protoctista) as a greenish haze at the base of the Animals and Plants, 1860

In 1860, British naturalist John Hogg proposed Protoctista (meaning 'first-created beings') as the name for a fourth kingdom of nature (the other kingdoms being Linnaeus' plant, animal and mineral) which comprised all the lower, primitive organisms, including protophyta, protozoa and sponges, at the merging bases of the plant and animal kingdoms.[32][8]

Haeckel's 1866 tree of life, with the third kingdom Protista.

In 1866 the 'father of protistology', German scientist Ernst Haeckel, addressed the problem of classifying all these organisms as a mixture of animal and vegetable characters, and proposed Protistenreich[33] (Kingdom Protista) as the third kingdom of life, comprising primitive forms that were "neither animals nor plants". He grouped both bacteria[34] and eukaryotes, both unicellular and multicellular organisms, as Protista. He retained the Infusoria in the animal kingdom, until German zoologist Otto Butschli demonstrated that they were unicellular.[35][36] At first, he included sponges and fungi, but in later publications he explicitly restricted Protista to predominantly unicellular organisms or colonies incapable of forming tissues. He clearly separated Protista from true animals on the basis that the defining character of protists was the absence of sexual reproduction, while the defining character of animals was the blastula stage of animal development. He also returned the terms protozoa and protophyta as subkingdoms of Protista.[8]

Butschli considered the kingdom to be too polyphyletic and rejected the inclusion of bacteria. He fragmented the kingdom into protozoa (only nucleated, unicellular animal-like organisms), while bacteria and the protophyta were a separate grouping. This strengthened the old dichotomy of protozoa/protophyta from German scientist Carl Theodor von Siebold, and the German naturalists asserted this view over the worldwide scientific community by the turn of the century. However, British biologist C. Clifford Dobell in 1911 brought attention to the fact that protists functioned very differently compared to the animal and vegetable cellular organization, and gave importance to Protista as a group with a different organization that he called "acellularity", shifting away from the dogma of German cell theory. He coined the term protistology and solidified it as a branch of study independent from zoology and botany.[8]

In 1938, American biologist Herbert Copeland resurrected Hogg's label, arguing that Haeckel's term Protista included anucleated microbes such as bacteria, which the term Protoctista (meaning "first established beings") did not. Under his four-kingdom classification (Monera, Protoctista, Plantae, Animalia), the protists and bacteria were finally split apart, recognizing the difference between anucleate (prokaryotic) and nucleate (eukaryotic) organisms. To firmly separate protists from plants, he followed Haeckel's blastular definition of true animals, and proposed defining true plants as those with chlorophyll a and b, carotene, xanthophyll and production of starch. He also was the first to recognize that the unicellular/multicellular dichotomy was invalid. Still, he kept fungi within Protoctista, together with red algae, brown algae and protozoans.[8][37] This classification was the basis for Whittaker's later definition of Fungi, Animalia, Plantae and Protista as the four kingdoms of life.[38]

In the popular five-kingdom scheme published by American plant ecologist Robert Whittaker in 1969, Protista was defined as eukaryotic "organisms which are unicellular or unicellular-colonial and which form no tissues". Just as the prokaryotic/eukaryotic division was becoming mainstream, Whittaker, after a decade from Copeland's system,[38] recognized the fundamental division of life between the prokaryotic Monera and the eukaryotic kingdoms: Animalia (ingestion), Plantae (photosynthesis), Fungi (absorption) and the remaining Protista.[39][40][8]

In the five-kingdom system of American evolutionary biologist Lynn Margulis, the term "protist" was reserved for microscopic organisms, while the more inclusive kingdom Protoctista (or protoctists) included certain large multicellular eukaryotes, such as kelp, red algae, and slime molds.[41] Some use the term protist interchangeably with Margulis' protoctist, to encompass both single-celled and multicellular eukaryotes, including those that form specialized tissues but do not fit into any of the other traditional kingdoms.[42]

Phylogenetic and symbiogenetic tree of living organisms, showing the origins of eukaryotes

The five-kingdom model remained the accepted classification until the development of molecular phylogenetics in the late 20th century, when it became apparent that protists are a paraphyletic group from which animals, fungi and plants evolved from, and the three-domain system (Bacteria, Archaea, Eukarya) became prevalent.[43] Today, protists are not treated as a formal taxon, but the term is commonly used for convenience in two ways:[44]

• Phylogenetic definition: protists are a paraphyletic group.[45] A protist is any eukaryote that is not an animal, land plant or fungus,[46] thus excluding many unicellular groups like the fungal Microsporidia, Chytridiomycetes and yeasts, and the non-unicellular Myxozoan animals included in Protista in the past.[47]
• Functional definition: protists are essentially those eukaryotes that are never multicellular,[44] that either exist as independent cells, or if they occur in colonies, do not show differentiation into tissues.[48] While in popular usage, this definition excludes the variety of non-colonial multicellularity types that protists exhibit, such as aggregative (e.g. choanoflagellates) or complex multicellularity (e.g. brown algae).[49]

There is, however, one classification of protists based on traditional ranks that lasted until the 21st century. The British protozoologist Thomas Cavalier-Smith, since 1998, developed a six-kingdom model:[lower-alpha 4] Bacteria, Animalia, Plantae, Fungi, Protozoa and Chromista.[14][50] In his context, paraphyletic groups take preference over clades:[14] both protist kingdoms Protozoa and Chromista contain paraphyletic phyla such as Apusozoa, Eolouka or Opisthosporidia. Additionally, red and green algae are considered true plants, while the fungal groups Microsporidia, Rozellida and Aphelida are considered protozoans under the phylum Opisthosporidia. This scheme endured until 2021, the year of his last publication.[21]

Difference between morphological (A) and genetic (B) view of total eukaryotic diversity. Protists dominate DNA barcoding analyses, but comprise a minority of catalogued species.[51]

According to molecular data, protists dominate eukaryotic diversity, accounting for a vast majority of environmental DNA sequences or operational taxonomic units (OTUs). However, their species diversity is severely underestimated by traditional methods that differentiate species based on morphological characteristics. The number of described protistan species is very low (ranging from 26,000[52] to 74,400[51] as of 2012) in comparison to the diversity of plants, animals and fungi, which are historically and biologically well-known and studied. The predicted number of species also varies greatly, ranging from 1.4×10⁵ to 1.6×10⁶, and in several groups the number of predicted species is arbitrarily doubled. Most of these predictions are highly subjective.[51]

Molecular techniques such as DNA barcoding are being used to compensate for the lack of morphological diagnoses, but this has revealed an unknown vast diversity of protists that is difficult to accurately process because of the exceedingly large genetic divergence between the different protistan groups. Several different molecular markers need to be used to survey the vast protistan diversity, because there is no universal marker that can be applied to all lineages.[51]

Protists make up a large portion of the biomass in both marine and terrestrial ecosystems. It has been estimated that protists account for 4 gigatons (Gt) of biomass in the entire planet Earth. This amount is smaller than 1% of all biomass, but is still double the amount estimated for all animals (2 Gt). Together, protists, animals, archaea (7 Gt) and fungi (12 Gt) account for less than 10% of the total biomass of the planet, because plants (450 Gt) and bacteria (70 Gt) are the remaining 80% and 15% respectively.[53]

Marine diatoms are important oxygen producers.

Marine protists are highly diverse, have a fundamental impact on biogeochemical cycles (particularly, the carbon cycle)[55] and are at the base of the marine trophic networks as part of the plankton.[56]

Phototrophic marine protists located in the photic zone as phytoplankton are vital primary producers in the oceanic systems. They fix as much carbon as all terrestrial plants together.[54] The smallest fractions, the picoplankton (<2 μm) and nanoplankton (2–20 μm), are dominated by several different algae (prymnesiophytes, pelagophytes, prasinophytes); fractions larger than 5 μm are instead dominated by diatoms and dinoflagellates. The heterotrophic fraction of marine picoplankton encompasses primarily early-branching stramenopiles (e.g. bicosoecids and labyrinthulomycetes), as well as alveolates, ciliates and radiolarians; protists of lower frequency include cercozoans and cryptophytes.[57]

Prymnesium, a constitutive mixotroph that participates in toxic algal blooms.

Mixotrophic marine protists, while not very researched, are present abundantly and ubiquitously in the global oceans, on a wide range of marine habitats. In metabarcoding analyses, they constitute more than 12% of the environmental sequences. They are an important and underestimated source of carbon in eutrophic and oligotrophic habitats.[56] Their abundance varies seasonally.[58] Planktonic protists are classified into various functional groups or 'mixotypes' that present different biogeographies:

• Constitutive mixotrophs, also called 'phytoplankton that eat', have the innate ability to photosynthesize. They have diverse feeding behaviors: some require phototrophy, others phagotrophy, and others are obligate mixotrophs.[56] They are responsible for harmful algal blooms. They dominate the eukaryotic microbial biomass in the photic zone, in eutrophic and oligotrophic waters across all climate zones, even in non-bloom conditions. They account for significant, often dominant predation of bacteria.[59]

Noctiluca, a specialist non-constitutive mixotroph that photosynthesizes through endosymbionts.

• Non-constitutive mixotrophs acquire the ability to photosynthesize by stealing chloroplasts from their prey. They can be divided into two: generalists, which can use chloroplasts stolen from a variety of prey (e.g. oligotrich ciliates), or specialists, which have developed the need to only acquire chloroplasts from a few specific prey. The specialists are further divided into two: plastidic, those which contain differentiated plastids (e.g. Mesodinium, Dinophysis), and endosymbiotic, those which contain endosymbionts (e.g. mixotrophic Rhizaria such as Foraminifera and Radiolaria, dinoflagellates like Noctiluca).[59] Both plastidic and generalist non-constitutive mixotrophs have similar biogeographies and low abundance, mostly found in eutrophic coastal waters. Generalist ciliates can account for up to 50% of ciliate communities in the photic zone. The endosymbiotic mixotrophs are the most abundant non-constitutive type.[56]

Freshwater planktonic protist communities are characterized by a higher "beta diversity" (i.e. highly heterogeneous between samples) than soil and marine plankton. The high diversity can be a result of the hydrological dynamic of recruiting organisms from different habitats through extreme floods.[60] The main freshwater producers (chrysophytes, cryptophytes and dinophytes) behave alternatively as consumers (mixotrophs). At the same time, strict consumers (non-photosynthetic) are less abundant in freshwater, implying that the consumer role is partly taken by these mixotrophs.[54]

Soil protist communities are ecologically the richest. This may be due to the complex and highly dynamic distribution of water in the sediment, which creates extremely heterogenous environmental conditions. The constantly changing environment promotes the activity of only one part of the community at a time, while the rest remains inactive; this phenomenon promotes high microbial diversity in prokaryotes as well as protists. Only a small fraction of the detected diversity of soil-dwelling protists has been described (8.1% as of 2017).[54] Soil protists are also morphologically and functionally diverse, with four major categories:[61]

Dictyostelids are fungus-like protists present in soil.

Cercomonads (Rhizaria) are important phagotrophic protists in soil.

• Photoautotrophic soil protists, or algae, are as abundant as their marine counterparts. Given the importance of marine algae, soil algae may provide a larger contribution to the global carbon cycle than previously thought, but the magnitude of their carbon fixation has yet to be quantified.[54] Most soil algae belong to the supergroups Stramenopiles (diatoms, Xanthophyceae and Eustigmatophyceae) and Archaeplastida (Chlorophyceae and Trebouxiophyceae). There is also the presence of environmental DNA from dinoflagellates and haptophytes in soil, but no living forms have been seen.[61]

• Fungus-like protists are present abundantly in soil. Most environmental sequences belong to the Oomycetes (Stramenopiles), an osmotrophic and saprotrophic group that contains free-living and parasitic species of other protists, fungi, plants and animals. Another important group in soil are slime molds (found in Amoebozoa, Opisthokonta, Rhizaria and Heterolobosea), which reproduce by forming fruiting bodies known as sporocarps (originated from a single cell) and sorocarps (from aggregations of cells).[61]

• Phagotrophic protists are abundant and essential in soil ecosystems. As bacterial grazers, they have a significant role in the foodweb: they excrete nitrogen in the form of NH₃, making it available to plants and other microbes.[62] Many soil protists are also mycophagous, and facultative (i.e. non-obligate) mycophagy is a widespread evolutionary feeding mode among soil protozoa.[63] Amoeboflagellates like the glissomonads and cercomonads (in Rhizaria) are among the most abundant soil protists: they possess both flagella and pseudopodia, a morphological variability well suited for foraging between soil particles. Testate amoebae (e.g. arcellinids and euglyphids) have shells that protect against desiccation and predation, and their contribution to the silica cycle through the biomineralization of shells is as important as that of forest trees.[61]

• Parasitic soil protists (in Apicomplexa) are diverse, ubiquitous and have an important role as parasites of soil-dwelling invertebrate animals. In Neotropical forests, environmental DNA from the apicomplexan gregarines dominates protist diversity.[61]

Blastocystis (Stramenopiles) is a prevalent intestinal parasite in humans.

Parasitic protists represent around 15–20% of all environmental DNA in marine and soil systems, but only around 5% in freshwater systems, where chytrid fungi likely fill that ecological niche. In oceanic systems, parasitoids (i.e. those which kill their hosts, e.g. Syndiniales) are more abundant. In soil ecosystems, true parasites (i.e. those which do not kill their hosts) are primarily animal-hosted Apicomplexa (Alveolata) and plant-hosted oomycetes (Stramenopiles) and plasmodiophorids (Rhizaria). In freshwater ecosystems, parasitoids are mainly Perkinsea and Syndiniales (Alveolata), as well as the fungal Chytridiomycota. True parasites in freshwater are mostly oomycetes, Apicomplexa and Ichthyosporea.[54]

Some protists are significant parasites of animals (e.g.; five species of the parasitic genus Plasmodium cause malaria in humans and many others cause similar diseases in other vertebrates), plants[64][65] (the oomycete Phytophthora infestans causes late blight in potatoes)[66] or even of other protists.[67][68]

Around 100 protist species can infect humans.[61] Two papers from 2013 have proposed the use of viruses to treat infections caused by protozoa.[69][70]

Researchers from the Agricultural Research Service are taking advantage of protists as pathogens to control red imported fire ant (Solenopsis invicta) populations in Argentina. Spore-producing protists such as Kneallhazia solenopsae (recognized as a sister clade or the closest relative to the fungus kingdom now)[71] can reduce red fire ant populations by 53–100%.[72] Researchers have also been able to infect phorid fly parasitoids of the ant with the protist without harming the flies. This turns the flies into a vector that can spread the pathogenic protist between red fire ant colonies.[73]

Paramecium aurelia with contractile vacuoles

While, in general, protists are typical eukaryotic cells and follow the same principles of physiology and biochemistry described for those cells within the "higher" eukaryotes (animals, fungi or plants),[74] they have evolved a variety of unique physiological adaptations that do not appear in those eukaryotes.[75]

• Osmoregulation. Freshwater protists without cell walls are able to regulate their osmosis through contractile vacuoles, specialized organelles that periodically excrete fluid high in potassium and sodium through a cycle of diastole and systole. The cycle stops when the cells are placed in a medium with different salinity, until the cell adapts.[75]

Light micrograph of an ocelloid-containing dinoflagellate. n: nucleus, double arrowhead: ocelloid, scale bar: 10 µm.[76]

• Energetic adaptations. The last eukaryotic common ancestor was aerobic, bearing mitochondria for oxidative metabolism. Many lineages of free-living and parasitic protists have independently evolved and adapted to inhabit anaerobic or microaerophilic habitats, by modifying the early mitochondria into hydrogenosomes, organelles that generate ATP anaerobically through fermentation of pyruvate. In a parallel manner, in the microaerophilic trypanosomatid protists, the fermentative glycosome evolved from the peroxisome.[75]

• Sensory adaptations. Many flagellates and probably all motile algae exhibit a positive phototaxis (i.e. they swim or glide toward a source of light). For this purpose, they exhibit three kinds of photoreceptors or "eyespots": (1) receptors with light antennae, found in many green algae, dinoflagellates and cryptophytes; (2) receptors with opaque screens; and (3) complex ocelloids with intracellular lenses, found in one group of predatory dinoflagellates, the Warnowiaceae. Additionally, some ciliates orient themselves in relation to the Earth's gravitational field while moving (geotaxis), and others swim in relation to the concentration of dissolved oxygen in the water.[75]

• Endosymbiosis. Protists have an accentuated tendency to include endosymbionts in their cells, and these have produced new physiological opportunities. Some associations are more permanent, such as Paramecium bursaria and its endosymbiont Chlorella; others more transient. Many protists contain captured chloroplasts, chloroplast-mitochondrial complexes, and even eyespots from algae. The xenosomes are bacterial endosymbionts found in ciliates, sometimes with a methanogenic role inside anaerobic ciliates.[75]

Two similar-looking but sexually distinct Coleps partners connected at their front ends exchange genetic material via a plasma bridge.

Protists generally reproduce asexually under favorable environmental conditions, but tend to reproduce sexually under stressful conditions, such as starvation or heat shock. Oxidative stress, which leads to DNA damage, also appears to be an important factor in the induction of sex in protists.[77]

Eukaryotes emerged in evolution more than 1.5 billion years ago.[78] The earliest eukaryotes were protists. Although sexual reproduction is widespread among multicellular eukaryotes, it seemed unlikely until recently, that sex could be a primordial and fundamental characteristic of eukaryotes. The main reason for this view was that sex appeared to be lacking in certain pathogenic protists whose ancestors branched off early from the eukaryotic family tree. However, several of these "early-branching" protists that were thought to predate the emergence of meiosis and sex (such as Giardia lamblia and Trichomonas vaginalis) are now known to descend from ancestors capable of meiosis and meiotic recombination, because they have a set core of meiotic genes that are present in sexual eukaryotes.[79][80] Most of these meiotic genes were likely present in the common ancestor of all eukaryotes,[81] which was likely capable of facultative (non-obligate) sexual reproduction.[82]

This view was further supported by a 2011 study on amoebae. Amoebae have been regarded as asexual organisms, but the study describes evidence that most amoeboid lineages are ancestrally sexual, and that the majority of asexual groups likely arose recently and independently.[83] Even in the early 20th century, some researchers interpreted phenomena related to chromidia (chromatin granules free in the cytoplasm) in amoebae as sexual reproduction.[84]

Some commonly found protist pathogens such as Toxoplasma gondii are capable of infecting and undergoing asexual reproduction in a wide variety of animals – which act as secondary or intermediate host – but can undergo sexual reproduction only in the primary or definitive host (for example: felids such as domestic cats in this case).[85][86][87]

Some species, for example Plasmodium falciparum, have extremely complex life cycles that involve multiple forms of the organism, some of which reproduce sexually and others asexually.[88] However, it is unclear how frequently sexual reproduction causes genetic exchange between different strains of Plasmodium in nature and most populations of parasitic protists may be clonal lines that rarely exchange genes with other members of their species.[89]

The pathogenic parasitic protists of the genus Leishmania have been shown to be capable of a sexual cycle in the invertebrate vector, likened to the meiosis undertaken in the trypanosomes.[90]

By definition, all eukaryotes before the existence of plants, animals and fungi are considered protists. For that reason, this section contains information about the deep ancestry of all eukaryotes.

All living eukaryotes, including protists, evolved from the last eukaryotic common ancestor (LECA). Descendants of this ancestor are known as "crown-group" or "modern" eukaryotes. Molecular clocks suggest that LECA originated between 1200 and more than 1800 million years ago (Ma). Based on all molecular predictions, modern eukaryotes reached morphological and ecological diversity before 1000 Ma in the form of multicellular algae capable of sexual reproduction, and unicellular protists capable of phagocytosis and locomotion. However, the fossil record of modern eukaryotes is very scarce around this period, which contradicts the predicted diversity.[91]

Instead, the fossil record of this period contains "stem-group eukaryotes". These fossils cannot be assigned to any known crown group, so they probably belong to extinct lineages that originated before LECA. They appear continuously throughout the Mesoproterozoic fossil record (1650–1000 Ma). They present defining eukaryote characteristics such as complex cell wall ornamentation and cell membrane protrusions, which require a flexible endomembrane system. However, they had a major distinction from crown eukaryores: the composition of their cell membrane. Unlike crown eukaryotes, which produce "crown sterols" for their cell membranes (e.g. cholesterol and ergosterol), stem eukaryotes produced "protosterols", which appear earlier in the biosynthetic pathway.[91]

Crown sterols, while metabolically more expensive, may have granted several evolutionary advantages for LECA's descendants. Specific unsaturation patterns in crown sterols protect against osmotic shock during desiccation and rehydration cycles. Crown sterols can also receive ethyl groups, thus enhancing cohesion between lipids and adapting cells against extreme cold and heat. Moreover, the additional steps in the biosynthetic pathway allow cells to regulate the proportion of different sterols in their membranes, in turn allowing for a wider habitable temperature range and unique mechanisms such as asymmetric cell division or membrane repair under exposure to UV light. A more speculative role of these sterols is their protection against the Proterozoic changing oxygen levels. It is theorized that all of these sterol-based mechanisms allowed LECA's descendants to live as extremophiles of their time, diversifying into ecological niches that experienced cycles of desiccation and rehydration, daily extremes of high and low temperatures, and elevated UV radiation (such as mudflats, rivers, agitated shorelines and subaerial soil).[91]

In contrast, the named mechanisms were absent in stem-group eukaryotes, as they were only capable of producing protosterols. Instead, these protosterol-based life forms occupied open marine waters. They were facultative anaerobes that thrived in Mesoproterozoic waters, which at the time were low on oxygen. Eventually, during the Tonian period (Neoproterozoic era), oxygen levels increased and the crown eukaryotes were able to expand to open marine environments thanks to their preference for more oxygenated habitats. Stem eukaryotes may have been driven to extinction as a result of this competition. Additionally, their protosterol membranes may have posed a disadvantage during the cold of the Cryogenian "Snowball Earth" glaciations and the extreme global heat that came afterwards.[91]

Modern eukaryotes began to appear abundantly in the Tonian period (1000–720 Ma), fueled by the proliferation of red algae. The oldest fossils assigned to modern eukaryotes belong to two photosynthetic protists: the multicellular red alga Bangiomorpha (from 1050 Ma), and the chlorophyte green alga Proterocladus (from 1000 Ma).[91] Abundant fossils of heterotrophic protists appear later, around 900 Ma, with the emergence of fungi.[91] For example, the oldest fossils of Amoebozoa are vase-shaped microfossils resembling modern testate amoebae, found in 800 million-year-old rocks.[92][93] Radiolarian shells are found abundantly in the fossil record after the Cambrian period (~500 Ma), but more recent paleontological studies are beginning to interpret some Precambrian fossils as the earliest evidence of radiolarians.[94][95][96]

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