Major lessons of the “Big Tree” of Life.

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What is the point?

  1. To be able to describe the "Universal" 5-Domain molcular phylogenetic tree in general terms.
  2. To be able to describe how the Archaea as a group emerge as a coherent Domain from this tree.
  3. To be able to describe how macroscopic organisms (plants, animals and fungi) fit into the 3-Domain tree.
  4. To be able to describe how "Gram-positive Bacteria" fit into the bacterial part of the 3-Domain tree.
  5. To be able to describe the endosymbiont theory, and how the 3-Domain tree verifies this theory.

1. The discovery of the Archaea

The Big 3-Domain Tree
Representative "Universal" 3-Domain tree, redrawn to Norman Pace

To peoples great surprise when these molecular phylogenetic trees first began to come out in 1977 (I was taking General Microbiology at the time), and to many peoples continuing great consternation, it turns out that there are three major, distinct evolutionary groups of known living things:

  • Bacteria : a.k.a. eubacteria
  • Archaea : a.k.a. archaebacteria
  • Eukarya : the nuclear/cytoplasmic component of eukaryotes (does not include the mitochondria or chloroplasts, see below)

These major groups are sometimes referred to as “Kingdoms”, and so this tree is sometimes known as the “3 Kingdom Tree”. In order to allow at least some of the classically-defined Kingdoms to remain unscathed (let’s be specific: Plants, Animals and Fungi), these three major phylogenetic groups are more often referred to as “Domain”s, a level added to the Linnaean taxonomy higher than Kingdoms. And so this tree is also sometimes referred to as the “3 Domain Tree”, and this is how this tree will be referred to in this book.

The species that turned out to be members of the previously unrecognized group “Archaea” had previously been scattered haphazardly amongst the bacterial taxomony. For example, Halobacteria were considered to be odd Pseudomonads, and Sulfolobus was thought to be a weird relative of Corynebacteria. Phenotypically, these organisms are grossly similar to Bacteria, but it turns out that in many ways they are more similar to Eukarya, especially in their central information systems (think Central Dogma). They are generally primitive, having apparently changed less since their common ancestry than either the Bacteria or Eukarya, and so more closely resemble our common ancestry than do other known organisms. This makes them an ideal system to study the early evolution of organisms, and especially that of eukaryotes.

2. Big Eukaryotes represent a small portion of biological diversity

Notice that the so-called "prokaryotes" (Archaea plus Bacteria) represent 2/3rds of the tree; two of the three Domains. But it turns out that these two entirely separate groups of “prokaryotes” are very different, and the tree shows that they are, in fact, not really “of a kind”. This is why we argued earlier that the term “prokaryotes” is invalid, meaning nothing more than “not a eukaryote”.

Even within the Eukarya, multicellular eukaryotes are delegated to a very small portion of evolutionary diversity - just the tips of some branches, not 3/5ths of evolutionary diversity that the 5-Kingdom scheme implies. And again let me point out that even most fungi, plants and animals are microscopic, and so “microbial”.

It also turns out that the Eukarya are as ancient a group as are the Bacteria and Archaea, and they did not evolve from within either of the other groups. This is counter to the usually unspoken view of the traditional “5-kingdom tree”. Interestingly, all of the known branches of eukaryotes are 'late' (there is a long bare branch connecting eukaryotes to the other Domains). There are no known primitive eukaryotes or early branches in the eukaryotic group, unless you count the Archaea (see below). It isn't clear how many main eukaryotic groups there might be, as there are huge numbers of visually described protists that have not been analyzed genetically. In fact, the eukaryotes are probably the least well-studied (or at least the least well-understood) of the Domains in terms of molecular phylogeny.

3. Gram-positive vs Gram-negative is not the major division in Bacteria

Gram-positive Bacteria

Phylogenetic tree of the Bacteria showing the major lineages ("Phyla"). Gram-positive phyla are highlighted, all others are Gram-negative.

The Bacteria turn out to be composed of a handful of major groups and an ever-growing list of minor groups. All of these groups have Gram-negative type cell envelopes except two related groups: the Firmicutes and Actinobacteria. Most of the other (Gram-negative) Bacteria we're familiar with are members of the Proteobacteria, just a single one of the major branches. Cyanobacteria (blue-green algae) also represent a single bacterial lineage.

4. Mitochondria and Chloroplasts are bacterial endosymbionts

Mitochondria
Thin-section electron micrograph of mammalian lung mitochondia
TEM from Louisa Howard, available in the Wikimedia Commons

The 3-Domain tree provided final verification of the endosymbiont theory for the origin of mitochondria and chloroplasts. These organelles contains their own DNA, distinct from that of the nucleus, they replicate by fission, and in many other ways look like Bacteria living inside of eukaryal hosts. Mitochondrial and chloroplast DNAs contain, amongst other things, genes encoding ssu-rRNA, and so they can be analyzed separately from nuclear ssu-rRNA sequences. The mitochondria turn out to be proteobacteria, and more specifically the alpha-proteobacteria that are commonly symbionts of eukaryotes, such as Wolbachia and Rickettsia. Chloroplasts (and plastids generally) are cyanobacteria, and specifically related to prochlorals that, like chloroplasts, contain chlorophyl a and b.