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8.16A: Phylogeny of the Eukarya

Eukaryotes are very diverse in phylogenic terms, the common feature being a membrane bound nucleus.




Assess the phylogeny of Eukarya



Key Points


  • Eukaryotes are broadly determined by the prescence of a membrane bound nucleus, though many eukaryotes have other membrane bound structures.
  • The domain of eukarya are broadly grouped into six kingdoms: Excavata, Amoebozoa, Opisthokonta, Rhizaria, Chromalveolata, and Archaeplastida.
  • The exact nature of the relationships (i.e. common ancestors) of the the eukarya domain are still debated.


Key Terms


  • crown group: In phylogenetics, the crown group of a collection of species consists of the living representatives of the collection together with their ancestors back to their last common ancestor as well as all of that ancestor’s descendants. It is thus a clade, a group consisting of a species and all its descendents.
  • cristae: Cristae (singular crista) are the internal compartments formed by the inner membrane of a mitochondrion. They are studded with proteins, including ATP synthase and a variety of cytochromes.

Phylogeny of the Eukarya

A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is carried. Most eukaryotic cells also contain other membrane-bound organelles such as mitochondria, chloroplasts, and the Golgi apparatus. All large complex organisms are eukaryotes, including animals, plants, and fungi. The group also includes many unicellular organisms.

rRNA trees constructed during the 1980s and 1990s left most eukaryotes in an unresolved crown group, which was usually divided by the form of the mitochondrial cristae. The few groups that lack mitochondria branched separately, and so the absence was believed to be primitive. But this is now considered an artifact of a divergent evolutionary line, and they are known to have lost them secondarily.

Eukaryotes are split into 6, subdivisions, referred to as kingdoms. They include:


The Six Kingdoms: This is one hypothesis of eukaryotic relationships. The Opisthokonta group includes both animals (Metazoa) and fungi. Plants (Plantae) are placed in Archaeplastida.

1. Excavata – Various flagellate protozoa

2. Amoebozoa – Most lobose amoeboids and slime moulds

3. Opisthokonta – Animals, fungi, choanoflagellates

4. RhizariaForaminifera – Radiolaria, and various other amoeboid protozoa

5. ChromalveolataStramenopiles (or Heterokonta) – Haptophyta, Cryptophyta (or cryptomonads), and Alveolata

6. Archaeplastida (or Primoplantae) – Land plants, green algae, red algae, and glaucophytes

There is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup, so that Rhizara is not one of the main eukaryote groups. The Amoeboza and Opisthokonta are each monophyletic and form a clade, often called the unikonts. There is debate about the true constituents of the animal kingdoms.

Beyond this, there does not appear to be a consensus. It has been estimated that there may be 75 distinct lineages of eukaryotes. Most of these lineages are protists. The known eukaryote genome sizes vary from 8.2 megabases (Mb) in Babesia bovis to 112,000 to 220,050 Mb in the dinoflagellate Prorocentrum micans. This suggests that the genome of the ancestral eukaryote has undergone considerable variation during its evolution. The last common ancestor of all eukaryotes is believed to have been a phagotrophic protist with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex (meiosis), a dormant cyst with a cell wall of chitin, cellulose, and peroxisomes. Later endosymbiosis led to the spread of plastids in some lineages.