By | July 25, 2021


Excavata is a large and diverse grouping that has been proposed based on a synthesis of morphological and molecular data. Many excavates share a similar feeding groove structure (from which the name is derived) (Simpson and Patterson, 2001; Simpson and Patterson, 1999). Many others lack this structure, but are demonstrably related to lineages that possess it in molecular phylogenies (Simpson, 2003; Simpson et al., 2006; Simpson et al., 2002). Putting this evidence together led to the suggestion of shared ancestry, and some recent multi-gene phylogenies in fact provide tentative support for the monophyly of the whole group (Burki et al., 2008; Rodriguez-Ezpeleta et al., 2007).  Many excavates are anaerobes/microaerophiles and contain mitosomes or hydrogenosomes (e.g. diplomonads and parabasalids).  Some are important parasites of animals (e.g. trypanosomes, Giardia).  One lineage, the euglenids, includes photosynthetic species that have plastids derived from a green alga by secondary endosymbiosis (Breglia et al., 2007; Leander et al., 2007).


Chromalveolates comprises six major groups of primarily single celled eukaryotes: apicomplexans, dinoflagellates and ciliates are members of the alveolates, they are hypothesised to be related to stramenopiles, cryptomonads, and haptophytes (Cavalier-Smith, 2004; Keeling, 2009). The basis for this hypothesis is the widespread presence of plastids in these groups that are all derived from secondary endosymbiosis with a red alga. It was therefore proposed that all chromalveolates share a common ancestor where this endosymbiosis took place (Cavalier-Smith, 1999). The monophyly of the plastids has been demonstrated with limited sampling (Hagopian et al., 2004; Rogers et al., 2007; Yoon et al., 2002), and some phylogenies inferred from many different nuclear genes show that the Chromalveolata are monophyletic with the Rhizaria nested within (see below) (Hackett et al., 2007). Additional support comes from two genes with unusual evolutionary histories involving lateral gene transfer and/or re-targeting to the plastid that are most consistent with a common origin of chromalveolate plastids


Rhizaria comprises several very large and diverse groups of amoebae, flagellates and amoeboflagellates (Cavalier-Smith and Chao, 2003). Many of these will not be familiar to many readers, but they are ubiquitous in nature and important predators in many environments. Major lineages include Cercozoa, Foraminifera, and Radiolaria. Rhizaria is the most recently recognized supergroup, having been identified exclusively from molecular phylogenetic reconstruction (Cavalier-Smith, 2002; Cavalier-Smith, 2003; Nikolaev et al., 2004). Prior to this, there was little reason to anticipate this grouping, because there is no major structural character that unites them. (Although the amoeboid members of the group tend to produce fine pseudopodia, rather than the broad pseudopodia seen in many Amoebozoa – see below.) However, analyses of molecular phylogenies based on nearly all genes examined, as well as rare molecular markers such as insertions and deletions, initially identified the Cercozoa as a group that has then expanded to include the Foraminifera and eventually the Radiolaria (Archibald et al., 2002; Bass et al., 2005; Burki et al., 2007; Burki et al., 2008; Keeling, 2001; Longet et al., 2003; Moreira et al., 2007; Nikolaev et al., 2004; Polet et al., 2004). Analyses of multiple protein coding genes have further supported the monophyly of Rhizaria, and suggested a relationship to chromalveolates.


Opisthokonta is a grouping consisting of Animals (Metazoa), the true Fungi and their close protistan relatives.  The closest relatives of animals include choanoflagellates, which are free-living unicellular or colonial flagellates, and the parasitic Ichthyosporea (also known as Mesomycetozoea).  Fungi are most closely related to a group of amoebae called nucleariids.  Opisthokonts share two conspicuous features that are uncommon in other eukaryotes: Almost all cells in this group have flat mitochondrial cristae, while flagellated cells typically have a single emergent flagellum that inserts at the posterior end of the cell (Cavalier-Smith, 1987).   The monophyly of this group has been shown convincingly by molecular phylogenies (Baldauf and Palmer, 1993; Lang et al., 1999; Ragan et al., 1996; Ruiz-Trillo et al., 2006; Steenkamp et al., 2006; Wainright et al., 1993), and also by a large, conserved insertion within the protein Elongation Factor 1-alpha (Baldauf and Palmer, 1993; Steenkamp et al., 2006).  Recently a possible shared lateral gene transfer has been reported


The Amoebozoa are a diverse collection of protozoan eukaryotes, almost all of which are amoebae (i.e. cells that produce pseudopodia, but lack flagella) for some or all of their life cycle.  Many produce lobose or fan-shaped pseudopodia (in contrast to the elongate, fine pseudopodia typical of Rhizaria), although short, fine sub-pseudopodia are also common.  Amoebozoa includes lineages of ‘lobose amoebae’ (e.g the well known Amoeba and Chaos), the lobose testate amoebae (with the cell enclosed in a shell), most of the lineages of ‘slime molds’, the pelobionts and Entamoebae, which lack classical mitochondria, and a few mitochondriate flagellates.  Amoebozoa were only recently united as group.  Detailed microscopy studies had shown that amoebae as a whole were polyphyletic, and thus when early molecular phylogenetic studies based especially on ribosomal RNA sequences placed slime molds, lobose amoebae, pelobionts and entamoebae as multiple independent lineages (Hinkle et al., 1994; Sogin, 1989), this result seemed plausible.  In the last few years, increasingly sophisticated molecular phylogenies incorporating many more taxa and/or genes have tended to unite these previously disparate groups (Bapteste et al., 2002; Fahrni et al., 2003), though not always with strong statistical support.  A recent study suggests that the pseudopodia-producing flagellate Breviata represents the deepest branch within a monophyletic amoebozoa clade.

‘Unikonts’: A Clade Consisting of Opisthokonts & Amoebozoans

There is now considerable evidence from molecular phylogenies that the opisthokonts and amoebozoans are closely related (Baldauf et al., 2000; Bapteste et al., 2002), and they also share a handful of other molecular characteristics in common (Richards and Cavalier-Smith, 2005). They have been proposed to be a clade called ‘unikonts’ because many of these organisms have a single flagellum (Cavalier-Smith, 2002), but biflagellated lineages are also known in this group. The root of the tree of eukaryotes has been proposed to be somewhere near this lineage, so it is possible the ‘unikonts’ are paraphyletic (Stechmann and Cavalier-Smith, 2002; Stechmann and Cavalier-Smith, 2003).

Do rhizarians branch within the chromalveolates?

There has long been very strong evidence from several kinds of data for the monophyly of alveolates. Multi-gene trees have also consistently and strongly supported a relationship between alveolates and stramenopiles (Burki et al., 2007; Burki et al., 2008; Hackett et al., 2007; Patron et al., 2007; Rodriguez-Ezpeleta et al., 2005; Rodriguez-Ezpeleta et al., 2007; Simpson et al., 2006). There is now also very strong evidence from molecular phylogenies and a shared lateral gene transfer for the monophyly of cryptomonads, haptophytes, and their relatives (Burki et al., 2008; Hackett et al., 2007; Patron et al., 2007; Rice and Palmer, 2006). In addition there is evidence from the plastid genome and plastid targeted proteins for the monophyly of chromalveolates and their plastids (Fast et al., 2001; Hagopian et al., 2004; Harper and Keeling, 2003; Patron et al., 2004; Rogers et al., 2007; Yoon et al., 2002). However, multi-gene trees also consistently show that the entire rhizarian supergroup is closely related to alveolates and stramenopiles (Burki et al., 2007; Burki et al., 2008; Hackett et al., 2007; Rodriguez-Ezpeleta et al., 2007), and some support the monophyly of chromalveolates as a whole with the Rhizaria nested within the group. These relationships will doubtless be refined with further data, but for now we follow the consensus of the available evidence and place the Rhizaria within the Chromalveolata.

Five supergroups:

A global tree of eukaryotes from a consensus of phylogenetic evidence (in particular, phylogenomics), rare genomic signatures, and morphological characteristics is presented in Adl et al. 2012 and Burki 2014/2016 with the Cryptophyta and picozoa having emerged within the Archaeplastida. A similar inclusion of Glaucophyta, Cryptista (and also, unusually, Haptista) has also been made.

he division of the eukaryotes into two primary clades, bikonts (Archaeplastida + SAR + Excavata) and unikonts (Amoebozoa + Opisthokonta), derived from an ancestral biflagellar organism and an ancestral uniflagellar organism, respectively, had been suggested earlier. A 2012 study produced a somewhat similar division, although noting that the terms “unikonts” and “bikonts” were not used in the original sense.In some analyses, the Hacrobia group (Haptophyta + Cryptophyta) is placed next to Archaeplastida, but in other ones it is nested inside the Archaeplastida. However, several recent studies have concluded that Haptophyta and Cryptophyta do not form a monophyletic group. The former could be a sister group to the SAR group, the latter cluster with the Archaeplastida (plants in the broad sense).

A highly converged and congruent set of trees appears in Derelle et al. (2015), Ren et al. (2016), Yang et al. (2017) and Cavalier-Smith (2015) including the supplementary information, resulting in a more conservative and consolidated tree. It is combined with some results from Cavalier-Smith for the basal Opimoda. The main remaining controversies are the root, and the exact positioning of the Rhodophyta and the bikonts Rhizaria, Haptista, Cryptista, Picozoa and Telonemia, many of which may be endosymbyotic eukaryote-eukaryote hybrids. Archaeplastida acquired chloroplasts probably by endosymbiosis of a prokaryotic ancestor related to a currently extant cyanobacterium, Gloeomargarita lithophora.

Thomas Cavalier-Smith 2010, 2013, 2014, 2017 and 2018 places the eukaryotic tree’s root between Excavata (with ventral feeding groove supported by a microtubular root) and the grooveless Euglenozoa, and monophyletic Chromista, correlated to a single endosymbyotic event of capturing a red-algae. He et al. specifically supports rooting eukaryotic tree between a monophyletic Discoba (Discicristata + Jakobida) and a Amorphea-Diaphoretickes clade.

Cavalier-Smith’s tree:

Origin of eukaryotes

The three-domains tree and the Eocyte hypothesis

Phylogenetic tree showing a possible relationship between the eukaryotes and other forms of life;eukaryotes are colored red, archaea green and bacteria blue

Eocyte tree.


The origin of the eukaryotic cell is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The timing of this series of events is hard to determine; Knoll (2006) suggests they developed approximately 1.6–2.1 billion years ago. Some acritarchs are known from at least 1.65 billion years ago, and the possible alga Grypania has been found as far back as 2.1 billion years ago. The Geosiphon-like fossil fungus Diskagma has been found in paleosols 2.2 billion years old.

Organized living structures have been found in the black shales of the Palaeoproterozoic Francevillian B Formation in Gabon, dated at 2.1 billion years old. Eukaryotic life could have evolved at that time. Fossils that are clearly related to modern groups start appearing an estimated 1.2 billion years ago, in the form of a red algae, though recent work suggests the existence of fossilized filamentous algae in the Vindhya basin dating back perhaps to 1.6 to 1.7 billion years ago.

Biomarkers suggest that at least stem eukaryotes arose even earlier. The presence of steranes in Australian shales indicates that eukaryotes were present in these rocks dated at 2.7 billion years old, although it was suggested they could originate from samples contamination.

Whenever their origins, eukaryotes may not have become ecologically dominant until much later; a massive uptick in the zinc composition of marine sediments 800 million years ago has been attributed to the rise of substantial populations of eukaryotes, which preferentially consume and incorporate zinc relative to prokaryotes.

In April 2019, biologists reported that the very large medusavirus, or a relative, may have been responsible, at least in part, for the evolutionary emergence of complex eukaryotic cells from simpler prokaryotic cells.

Relationship to Archaea:

The nuclear DNA and genetic machinery of eukaryotes is more similar to Archaea than Bacteria, leading to a controversial suggestion that eukaryotes should be grouped with Archaea in the clade Neomura. In other respects, such as membrane composition, eukaryotes are similar to Bacteria. Three main explanations for this have been proposed:

  • Eukaryotes resulted from the complete fusion of two or more cells, wherein the cytoplasm formed from a eubacterium, and the nucleus from an archaeon, from a virus, or from a pre-cell.
  • Eukaryotes developed from Archaea, and acquired their eubacterial characteristics through the endosymbiosis of a proto-mitochondrion of eubacterial origin.
  • Eukaryotes and Archaea developed separately from a modified eubacterium.

Diagram of the origin of life with the Eukaryotes appearing early, not derived from Prokaryotes, as proposed by Richard Egel in 2012. This view implies that the UCA was relatively large and complex.

Alternative proposals include:

  • The chronocyte hypothesis postulates that a primitive eukaryotic cell was formed by the endosymbiosis of both archaea and bacteria by a third type of cell, termed a chronocyte.
  • The universal common ancestor (UCA) of the current tree of life was a complex organism that survived a mass extinction event rather than an early stage in the evolution of life. Eukaryotes and in particular akaryotes (Bacteria and Archaea) evolved through reductive loss, so that similarities result from differential retention of original features.

Assuming no other group is involved, there are three possible phylogenies for the Bacteria, Archaea and Eukaryota in which each is monophyletic. These are labelled 1 to 3 in the table below. The eocyte hypothesis is a modification of hypothesis 2 in which the Archaea are paraphyletic. (The table and the names for the hypotheses are based on Harish and Kurland, 2017.)

  • The universal common ancestor (UCA) of the current tree of life was a complex organism that survived a mass extinction event rather than an early stage in the evolution of life. Eukaryotes and in particular akaryotes (Bacteria and Archaea) evolved through reductive loss, so that similarities result from differential retention of original features.

Assuming no other group is involved, there are three possible phylogenies for the Bacteria, Archaea and Eukaryota in which each is monophyletic. These are labelled 1 to 3 in the table below. The eocyte hypothesis is a modification of hypothesis 2 in which the Archaea are paraphyletic. (The table and the names for the hypotheses are based on Harish and Kurland, 2017.)

In recent years, most researchers have favoured either the three domains (3D) or the eocyte hypotheses. An rRNA analyses supports the eocyte scenario, apparently with the Eukaryote root in Excavata. A cladogram supporting the eocyte hypothesis, positioning eukaryotes within Archaea, based on phylogenomic analyses of the Asgard archaea, is:

In this scenario, the Asgard group is seen as a sister taxon of the TACK group, which comprises Crenarchaeota (formerly named eocytes), Thaumarchaeota, and others.

In 2017, there has been significant pushback against this scenario, arguing that the eukaryotes did not emerge within the Archaea. Cunha et al. produced analyses supporting the three domains (3D) or Woese hypothesis (2 in the table above) and rejecting the eocyte hypothesis (4 above). Harish and Kurland found strong support for the earlier two empires (2D) or Mayr hypothesis (1 in the table above), based on analyses of the coding sequences of protein domains. They rejected the eocyte hypothesis as the least likely. A possible interpretation of their analysis is that the universal common ancestor (UCA) of the current tree of life was a complex organism that survived an evolutionary bottleneck, rather than a simpler organism arising early in the history of life.

Endomembrane system and mitochondria:

The origins of the endomembrane system and mitochondria are also unclear. The phagotrophic hypothesis proposes that eukaryotic-type membranes lacking a cell wall originated first, with the development of endocytosis, whereas mitochondria were acquired by ingestion as endosymbionts. The syntrophic hypothesis proposes that the proto-eukaryote relied on the proto-mitochondrion for food, and so ultimately grew to surround it. Here the membranes originated after the engulfment of the mitochondrion, in part thanks to mitochondrial genes (the hydrogen hypothesis is one particular version).

In a study using genomes to construct supertrees, Pisani et al. (2007) suggest that, along with evidence that there was never a mitochondrion-less eukaryote, eukaryotes evolved from a syntrophy between an archaea closely related to Thermoplasmatales and an α-proteobacterium, likely a symbiosis driven by sulfur or hydrogen. The mitochondrion and its genome is a remnant of the α-proteobacterial endosymbiont.



Different hypotheses have been proposed as to how eukaryotic cells came into existence. These hypotheses can be classified into two distinct classes – autogenous models and chimeric models.

Autogenous models:

An autogenous model for the origin of eukaryotes.

Autogenous models propose that a proto-eukaryotic cell containing a nucleus existed first, and later acquired mitochondria. According to this model, a large prokaryote developed invaginations in its plasma membrane in order to obtain enough surface area to service its cytoplasmic volume. As the invaginations differentiated in function, some became separate compartments – giving rise to the endomembrane system, including the endoplasmic reticulum, golgi apparatus, nuclear membrane, and single membrane structures such as lysosomes. Mitochondria are proposed to come from the endosymbiosis of an aerobic proteobacterium, and it is assumed that all the eukaryotic lineages that did not acquire mitochondria became extinct. Chloroplasts came about from another endosymbiotic event involving cyanobacteria. Since all eukaryotes have mitochondria, but not all have chloroplasts, the serial endosymbiosis theory proposes that mitochondria came first.

Chimeric models:

Chimeric models claim that two prokaryotic cells existed initially – an archaeon and a bacterium. The closest living relatives of these appears to be Asgardarchaeota and (distantly related) the alphaproteobacteria. These cells underwent a merging process, either by a physical fusion or by endosymbiosis, thereby leading to the formation of a eukaryotic cell. Within these chimeric models, some studies further claim that mitochondria originated from a bacterial ancestor while others emphasize the role of endosymbiotic processes behind the origin of mitochondria.

The inside-out hypothesis:

The inside-out hypothesis, developed by cousins David and Buzz Baum, suggest the fusion between a free-living mitochondria-like bacteria and an archaea into an eykaryotic cell happened gradually over a long period of time, instead of phagocytosis in a single gulp. In this scenario an archaea would trap aerobic bacteria with cell protrusions, and then keeping them alive to draw energy from them instead of digesting them. During the early stages the bacteria would still be partly in direct contact with the environment, and the archaea would not have to provide them with all the required nutrients. But eventually the archaea would engulf the bacteria completely, creating the internal membrane structures and nucleus membrane in the process.

It is assumed the archaean group called halophiles went through a similar procedure, where they acquired as much as a thousand genes from a bacterium, way more than through the conventional horizontal gene transfer that often occurs in the microbial world, but that the two microbes separated again before they had fused into a single eukaryote-like cell.

Based on the process of mutualistic symbiosis, the hypotheses can be categorized as – the serial endosymbiotic hypothesis or theory (SET), the hydrogen hypothesis (mostly a process of symbiosis where hydrogen transfer takes place among different species), and the syntrophy hypothesis. These hypotheses are discussed separately in the following sections.

An expanded version of the inside-out hypothesis proposes that the eukaryotic cell was created by physical interactions between two prokarytic organisms and that the last common ancestor of eukaryotes got its genome from a whole population or community of microbes participating in cooperative relationships to thrive and survive in their environment. The genome from the various types of microbes would complement each other, and occasional horizontal gene transfer between them would be largely to their own benefit. This accumulation of beneficial genes gave rise to the genome of the eukaryotic cell, which contained all the genes required for independence.

The serial endosymbiotic hypothesis:

According to serial endosymbiotic theory (championed by Lynn Margulis), a union between a motile anaerobic bacterium (like Spirochaeta) and a thermoacidophilic crenarchaeon (like Thermoplasma which is sulfidogenic in nature) gave rise to the present day eukaryotes. This union established a motile organism capable of living in the already existing acidic and sulfurous waters. Oxygen is known to cause toxicity to organisms that lack the required metabolic machinery. Thus, the archaeon provided the bacterium with a highly beneficial reduced environment (sulfur and sulfate were reduced to sulfide). In microaerophilic conditions, oxygen was reduced to water thereby creating a mutual benefit platform. The bacterium on the other hand, contributed the necessary fermentation products and electron acceptors along with its motility feature to the archaeon thereby gaining a swimming motility for the organism.

From a consortium of bacterial and archaeal DNA originated the nuclear genome of eukaryotic cells. Spirochetes gave rise to the motile features of eukaryotic cells. Endosymbiotic unifications of the ancestors of alpha-proteobacteria and cyanobacteria, led to the origin of mitochondria and plastids respectively. For example, Thiodendron has been known to have originated via an ectosymbiotic process based on a similar syntrophy of sulfur existing between the two types of bacteria – Desulphobacter and Spirochaeta.

However, such an association based on motile symbiosis have never been observed practically. Also there is no evidence of archaeans and spirochetes adapting to intense acid-based environments.

The hydrogen hypothesis:

In the hydrogen hypothesis, the symbiotic linkage of an anaerobic and autotrophic methanogenic archaeon (host) with an alpha-proteobacterium (the symbiont) gave rise to the eukaryotes. The host utilized hydrogen (H2) and carbon dioxide (CO
2) to produce methane while the symbiont, capable of aerobic respiration, expelled H2 and CO
2 as byproducts of anaerobic fermentation process. The host’s methanogenic environment worked as a sink for H2, which resulted in heightened bacterial fermentation.

Endosymbiotic gene transfer (EGT) acted as a catalyst for the host to acquire the symbionts’ carbohydrate metabolism and turn heterotrophic in nature. Subsequently, the host’s methane forming capability was lost. Thus, the origins of the heterotrophic organelle (symbiont) are identical to the origins of the eukaryotic lineage. In this hypothesis, the presence of H2 represents the selective force that forged eukaryotes out of prokaryotes.

The syntrophy hypothesis:

The syntrophy hypothesis was developed in contrast to the hydrogen hypothesis and proposes the existence of two symbiotic events. According to this theory, the origin of eukaryotic cells was based on metabolic symbiosis (syntrophy) between a methanogenic archaeon and a delta-proteobacterium. This syntrophic symbiosis was initially facilitated by H2 transfer between different species under anaerobic environments. In earlier stages, an alpha-proteobacterium became a member of this integration, and later developed into the mitochondrion. Gene transfer from a delta-proteobacterium to an archaeon led to the methanogenic archaeon developing into a nucleus. The archaeon constituted the genetic apparatus, while the delta-proteobacterium contributed towards the cytoplasmic features.

This theory incorporates two selective forces at the time of nucleus evolution

  • presence of metabolic partitioning to avoid the harmful effects of the co-existence of anabolic and catabolic cellular pathways, and
  • prevention of abnormal protein biosynthesis due to a vast spread of introns in the archaeal genes after acquiring the mitochondrion and losing methanogenesis.

6+ serial endosymbiosis scenario:

Pitts and Galbanón propose a complex scenario of 6+ serial endosymbiotic events of Archaea and bacteria in which mitochondria and an asgard related archaeota were acquired at a late stage of eukaryogenesis, possibly in combination, as a secondary endosymbiote. The findings have been rebuked as an artefact.

List of sequenced eukaryotic genomes:

This list of “sequenced” eukaryotic genomes contains all the eukaryotes known to have publicly available complete nuclear and organelle genome sequences that have been sequenced, assembled, annotated and published; draft genomes are not included, nor are organelle-only sequences.

DNA was first sequenced in 1977. The first free-living organism to have its genome completely sequenced was the bacterium Haemophilus influenzae, in 1995. In 1996 Saccharomyces cerevisiae (baker’s yeast) was the first eukaryote genome sequence to be released and in 1998 the first genome sequence for a multicellular eukaryote, Caenorhabditis elegans, was released.

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