Forms of Life part 2: Overview of the Phylogenetic Tree of Life and Endosymbiosis

In the first part of this series, I discussed taxonomic terminology such as clades and kingdoms, but didn't go into the actual groups and the lifeforms within them. This article will provide a top-down phylogenetic overview of all lifeforms on Earth, as well as a discussion of how endosymbiosis has provided an alternate path for genetic material and evolution.

Phylogenetic tree of all known Earth Lifeforms

The graph above is my attempt to show the entire tree of life in a cladistic/phylogenetic way (i.e. by their genetic ancestry), keeping it as simple as possible while still showing all the important steps and how the traditional "kingdoms" of biological classification fit in.

Blue Squares: Clades which are the three "Domains" in modern taxonomy.
Green Diamonds: Clades which correspond to the "Kingdoms" of Animals, Fungi and Plants in traditional taxonomy.
Red Hexagons: Clades which contain only Protists.
Black Ellipses: All other clades (i.e. which contain at least some non-protists but are not a Domain or Kingdom).
Solid arrows: Genetic descent.
Dotted arrows: Endosymbiontic descent (Cyanobacteria to Archaeplastida, and Rhodophyta to Heterokonta).

The graph does not include every clade of Protists, as there are far too many. Only clades containing significant groups of Algae and Amoebae are shown.

Note that viruses, viroids and prions are not included anywhere as they not considered "true" lifeforms (see part 1).

The rest of this article will explain these relationships in more detail.

From Kingdoms to Domains

Traditional Kingdoms

In traditional taxonomy - before we knew about DNA/RNA and how to decode it - life was divided into a number of subjectively defined "Kingdoms". Originally just plants and animals, as more lifeforms were discovered and existing ones were studied in more detail, more Kingdoms were defined:

  • Animals
  • Plants
  • Protists
  • Bacteria (originally part of Protists)
  • Archea (originally part of Bacteria)
  • Fungi (originally part of Plants or Protists, now known to be more closely related to Animals than Plants)
  • Chromista (Algae, many formerly considered Plants, now known to be polyphyletic)
  • Protozoa (now known to be highly polyphyletic and classified Protists)
  • Archezoa (now known to be highly polyphyletic and classified Protists)

Instead of subjective categories, modern taxonomy is based around Clades (see the first part of this series for details), groupings determined by their genetic ancestors as shown in the tree above.

Fortunately most Kingdoms correspond exactly to a clade - Bacteria, Archea, Plants, Fungi and Animals are all each descended from an exclusive ancestor and can be also categorized as clades. Only Protists, including Algae, Amoebae and Protozoa do not fit within a single monophyletic group.

In the Beginning: The First Lifeform and The LUCA

Advances in biochemistry and genetics have allowed us to more accurately determine the nature of historical lifeforms and age them using the "molecular clock" - known rates of mutation.

The "last universal common ancestor" (or "last universal ancestor", as the word universal implies commonality anyway) is the most recent lifeform from which all known life is descended. The LUCA is not the oldest lifeform that ever existed - it evolved from earlier lifeforms around 4.5 billion years ago.

All life forms from bacteria to humans share many biochemical features inherited from LUCA and the earlier lifeforms, such as the Citric Acid Cycle and use of DNA/RNA to encode proteins and mechanisms to transcribe and construct proteins from that genetic code. A 2016 study in Nature identified 355 genes as likely to be within LUCA's genetic code, concluding that it likely thrived in high temperature deep sea areas.

The Three Domains: Bacteria, Archea and Eukaryota

Modern taxonomy divides life primarily into three "Domains" which originate from the LUCA and have distinct characteristics:

Bacteria: Simple prokyarotic cells (without a true membrane-bound nucleus or organelles within the cell) and simple DNA/RNA transcription.
Archea: Prokaryotes similar to Bacteria but with different cell structural compounds, and DNA/RNA transcription processes more similar to Eukarya.
Eukarya or Eukaryota:
  Eukaryotic cells containing a nucleus with chromosomal DNA, and organelles within the cell which perform specialised functions.

Prokaryotes (Bacteria and Archea) are always unicellular; Eukaryotes can be single-celled or multicellular. Although Eukarya thus includes the more "advanced" life forms such as plants and animals, there are far more Bacteria and Archea on Earth both in terms of number of species and number of organisms.

Prokaryotes (Bacteria and Archea)

Prokaryotes are the simplest forms of life. They are the smallest, are always unicellular, and can only reproduce asexually, usually by binary fission.

Prokaryote cells have a radically different structure to Eukaryote cells, although many processes are similar. Eukaryote cells store DNA in "double helix" chromosomes; Prokaryote cellss store DNA in a single circular molecule and sometimes in separate structures called Plasmids. Prokaryote cells also lack many of the specialised organelles and membrand structures characteristic of Eukaryotes such as mitochondria, chloroplasts, plastids and the Golgi apparatus.

More details about prokaryotes will wait for a a future article; for the purposes of this article about the overall phylogenetic tree of life the most important prokaryotes are the Cyanobacteria.

Cyanobacteria ("blue-green algae") - the origin of Photosynthetic Plants and Algae

Cyanobacteria (often incorrectly called "blue-green algae") used to be considered a form of algae; it is now known that they are a form of (prokaryotic) bacteria and are different to "true" algae, which are Eukaryotic and have an utterly different cell structure and biochemistry.

However, the Plastid organelles within plants and (eukaryotic) algae which allow them to perform photosynthesis are strikingly similar to individual cyanobacteria cells, including a circular DNA molecule. Genetic analysis of Plastid DNA across all Archaeplastida indicates that it is most likely that the Plastid organelle was originally a cyanobacterium consumed by an early Archaeplastida, with both continuing to live on and reproduce in a symbiotic relationship.

This "Endosymbiotic Event" is estimated to have occurred about 1400 million years ago, and Gloeomargarita lithophora is the most likely cyanobacterium - without this snack, plants and algae would not exist.

The mitochondria organelles within most eukaryotic cells are also believed to have formed in a similar way (by a eukaryotic consuming a prokyarotic one and the prokyarote turning onto an organelle), which is why mitochondria have their own DNA. Mitochondria have many features in common with Rickettsiales proteobacteria, but the event is likely to have occurred further ago and so the relationship is less clear.

Other Endosymbiotic Events

In addition to the one which led to modern Plants and Algae, other endosymbiotic events have occured in other lifeforms:

  • Paulinella is a genus of photosynthetic amoebae which contains plastids derived from consumption of a cyanobacterium about 90-140 million years ago.
  • Some clades within Heterokonta, including "brown algae" (such as kelp and most seaweeds) contain chloroplasts which appear to be derived from a consumed red algae cell.

In contrast to "primary endosymbiosis", where a eukaryotic organism consumes and converts a prokyarotic one into a symboyant, "secondary endosymbiosis" involves consumption of another eukaryote, as in the example of Heterokonts above.

Secondary endosymbiosis has been witnessed in natural or laboratory environments, with many protists and marine organisms observed consuming smaller algae cells for use as symbionts. The host can use the sugars produced by the algae's photosynthesis as food, while the algae can use some waste products of the host organism as it's own food.

  • Many species of Ciliates can hunt down and consume algae which live on inside the larger cell.
  • The protist Hatena Arenicola has a predatory stage of its life cycle, where it hunts down a green alga. After consuming one it loses its feeding apparatus and hunts light to power the algae. Hatena only divides and reproduces in the latter stage, and one of the daughter cells will retain the algae, the other will revert to the predatory stage.
  • Elysia is a genus of sea slugs which graze on algae; in some species the chloroplasts within the algae are consumed slowly in such a way that they form a lining on Elysia's digestive tract. Elysia manufactures many of the proteins necessary for the chloroplasts to survive inside it, and can live off the photosynthesis of its intestinal lining for months.
  • Most corals consume algae of the family Symbiodiniaceae; the Symbiodiniaceae typically reproduce and thrive within the host coral, providing the coral with energy and nutrients. During "bleaching" events the corals expel the algae, usually in response to abnormally high temperatures. The coral will starve after bleaching unless it can recover more algae.

Major Clades within Eukarya

Archaeplastida - Plants and (some) Algae

Archeplastidia is a clade of Eukaryotes containing Plants, most "True" Algae (not Cyanobacteria or Heterokont algae) and some other protists.

Archeplastidia are characterized by the presence of choloroplasts, probably derived from symbiotic cyanobacteria, which allows them to use energy from light to produce food.

Viridiplantae and Embryophyta

Viridiplantae ("Green plants"), is a clade within Archeplastidia which includes all true Plants as well as many sub-clades of green algae, but not red algae.

Embryophyta (land plants) is a clade within Viridiplantae characterized by their relatively complex multicellular forms, including having distinct tissues, organs and systems like animals. Embryophyta are in the strictest sense true Plants, rather than Algae.


Algae are polyphyletic group (not a clade; does not have an exclusive genetic ancestor that is not shared with species outside the group) of Eukaryotes which is capable of photosynthesis but not within the Plantae clade.

Algae were once considered to form the kingdom Chromista; they are now considered part of the miscellaneous "Protist" group of Eukaryotes.

More details about Algae will be discussed in a future article on Protists.

Opisthokonta - Animals and Fungi

Opisthokonts are a clade of Eukaryotes notable for containing all Animals and Fungi, as well as many Protists including many groups previously considered Protozoa.

Along with their genetic lineage, Opisthokonts notably share many metabolic enzymes not present in Archeplastidia, such as carbamoyl phosphate synthetase, dihydroorotase, and aspartate carbamoyltransferase

Animalia (Animals/Metazoa)

Eukaryotes characterized by their formation of a blastula during embryonic development - which allows them to to develop highly specialised cells and organs - and their consequent highly varied anatomy and caabilities.

All animals are also strict heterotrophs, breaking down complex molecules produced by other lifeforms for food.

Fungi (Eumycota)

Eukaryotes originally considered Plants due to their sessile nature; some fungi such as yeasts/molds were also at times considered a form of bacteria or protist.

Modern genetic analysis shows Fungi are are more closely related to animals than to plants. Notably, Fungi do not posess plastids or chlorophyll and cannot photosynthesize as plants do; they are are always heterotrophs, like animals. Fungi also produce chitin for their cell walls (the same substance used by some animals for their exoskeleton) wheras plants and oomycetes (water molds) have cell walls made of cellulose.

Most Fungi grow as cooperative colonies of "Hyphae", long branching filaments. Cells within hyphae are joined by internal walls called "septa" which have pores allowing transfer of nutrients and hormones, sometimes large enough that entire organelles can be transferred.

Other Fungi may be unicellular (e.g. yeasts) or form multicellular structures with distinct tissues (e.g. the cap, underside and stalk of mushrooms). Some fungi such as Candida can change from a single-celled yeast into a Hyphae form and back, depending on the environment.

Note that Fungi as a clade are distinct from the morphologically similar myxomycetes (slime molds), which are Amoeboid protists, and oomycetes (water molds), which are Heterokont protists.

Protists - the Miscellaneous Kingdom

"Protist" is the term for all Eukaryotes which are not Animals, Plants or Fungi.

Therefore, as the only Prokyarotes are Bacteria and Archea, it follows that any organism which is not a Bacteria, Archea, Animal, Plant or Fungus is categorized as a Protist.

Due to their "miscellaneous" categorization, Protists are a highly polyphyletic group (no exclusive genetic ancestor that is not shared with species not in the group). Some Protists are more closely related to plants, animals or fungi than to most other protists.

They consequently have widely varying anatomy and capabilities. Some protists are capable of photosynthesis, some are sessile, some are mobile, some hunt down and prey on other organisms, including animals and other protists.

More details will be in a future article on Protists (hopefully).