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Taxonomy and phylogeny

Taxonomies are classification schemes for species. There are three related parts to taxonomy:

1. Grouping : The organization of organisms into groups based on similarity
2. Naming : Labeling organisms & groups of organisms with names
3. Identifying : The identification of organisms when they're found

Taxonomies are artificial constructions, methods for structuring & organizing species. Any self-consistent taxonomy is valid, whether it reflects the natural history of the organisms or not.

For example, many wildflower field guides organize species by features that are readily observed in the field. The first division might be by flower color, a trivial feature of the plants in evolutionary terms, but perfectly reasonable for a taxonomy. There is no implication that plants with the same color flower are actually related genetically, nor that plants with different colored flowers are not related. The field guide taxonomy is designed for groupng, naming, and identifying species, and are good taxonomies.

Phylogenies are evolutionary pathways, i.e. geneologies. Phylogenies represent our understanding of the natural relationships between organisms.

Unfortunately, their aren't natural delineations between groups in these phylogenies. However, taxonomists can start with a phylogenetic tree and try to divide the tree into reasonable groups based on the branches of the tree. In doing so, they attempt to devise a taxonomy that reflects the phylogenetic relationships between the species as closely as possible.

The classical taxonomies of plants and animals are fairly close to their phylogenetic relationships because the complex morphology of these organisms reveals their ancestry. This is not true for microbes. There was no way to determine evolutionary relationships between Bacteria, Archaea, or even protists, algae or fungi until the development of molecular phylogenetics, which is based on the analysis of gene sequences.

Why is an understanding of phylogeny important?

1. To predict the properties of organisms based on the properties of their relatives. Think about how much insight you can get into a person by knowing their family! Understanding an organisms relationships to other species is the key to understanding its properties.
   
2. To prevent inappropriate comparisons based on nonexistant relationships. For example, Euglena was used for years as a unicellular model system to study photosynthesis in plants. However, Euglena isn't related to plants, but to the trypanosomes! It's 'chloroplast' is not homologous to plant chloroplasts. Chlamydomonas is a better system - it really is a unicellular plant.

The Evolution of Evolutionary Thought

The Ladder of Life - a pre-evolutionary organization of living (and non-living) things.

All species & substances are placed onto individual rungs of a ladder or links of a chain, ascending from inferior to superior. Great thought & energy was put into deciding exactly how to order the major catagories, species, and races (and even individuals) onto separate rungs of the ladder.

The earliest forms of evolutionary thought had each specie (up to but not including humans) moving up the "Evolutionary" ladder. Although the notion of an evolutionary ladder is pre-Darwinian and hopelessly incorrect, this scheme is firmly imbedded in modern biological unconcious thought. You even hear the term 'evolutionary ladder' fairly often by research scientists that actually know better. The terms 'higher' and 'lower' eukaryotes and 'missing link', which are in common use, are holdovers of this view.

By the time of Charles Darwin, it was clear that this was not a reasonable view of evolution. Darwin describes a much better view, which has proven to be correct, in which species originate by divergence, as shown below:

In this diagram, species A and I at the beginning (bottom) split many times and diverge constantly. Most of these divergences don't go anywhere (i.e. become extinct), but some do make it, at least for a while, resulting in this case in species A splitting into 3 separate species and species I into 2 species at time X. Species A and I no longer exist at the end - or at least they are seen to have changed from the original type. Note that most of the original species, B-H, K and L, are in stasis, remaining unchanged through the time shown here - this is consistant with the 'punctuated equilibrium' view of evolutionary change.

So, species actually evolve by diversification, not by progression (i.e. advancement up the ladder). Eukaryotes did not evolve from Bacteria, animals did not evolve from cilates, plants did not evolve from fungi, humans did not evolve from chimps. Each of these pairs of organisms share a common ancestor, from which each diverged.

Haeckel's Tree - a big step forward, based on Darwinian evolutionary thought.

One of the best developed of these divergent evolutionary trees was that of Ernst Haeckel, shown above. In this tree, there are 3 major, equivalent divisions of life - plants, animals, & protists

This tree is an improvement over the ladder in many ways. It's a tree - species are not ranked, and modern species are not considered to be the ancestors of other modern organisms. Plants & animals are not thought of as having evolved from modern prokaryotes (monerans), but are separate groups.

The 5-Kingdom tree being taught in most classes is a refined version of this tree:

In some ways, the 5-Kingdom tree is actually a step backwards toward the 'ladder of life'. In most versions of this scheme, eukaryotes are descended from modern Bacteria, and specifically, eukaryotic algae are descendants of cyanobacteria (not true), fungi are descendants of filamentous Gram-positive Bacteria (not true), and protists are descendants of wall-less Gram-positive Bacteria (also not true). Also notice the implications of the vertical axis: it implies time and superiority (usually expressed as 'complexity'). However, Bacteria did not evolve before eukaryotes, and once again, all of these are modern organisms, alive today!

Molecular phylogenetic trees

This type of molecular phylogenetic tree is a rooted dendrogram (the root is marked in red - we'll talk later about how these trees are constructed). The length of the branches quantitatively represents the evolutionary distance separating organisms.

Some features of these molecular phylogenetic trees:

• All previous trees were subjective & qualitative. This tree is quantitative and objective, based on statistical analysis of gene sequences, in this case small subunit ribosomal RNA.
  
• The tips of all the branches are modern organisms. Each node within the tree represents a common ancestor.
  
• There is no ranking of above (superior) or below (inferior) in the tree. Evolutionary distance (divergence) is measured along the lengths of the branches connecting species.
  
• There are 3 major evolutionary groups
  1. Bacteria = eubacteria
  2. Archaea = archaebacteria
  3. Eukarya = eukaryotic nuclear/cytoplasmic lineage

  One of the most exciting outcomes of this method early on was the discovery of a new type of organism - the Archaea, These species had previously been scattered haphazardly amongst the bacteria. Phenotypically, these organisms are generally similar to Bacteria, but biochemically they are generally similar to Eukarya. They have changed less since their common ancestry than the other groups, and so more closely resemble our common ancestry.
  

• Non-eukaryotes fill 2/3rds of the tree (2 of the 3 Domains). There are 2 separate groups of non-eukaryotes: Bacteria and Archaea.
  
• Multicellular eukaryotes are a very small portion of evolutionary diversity - just the tip of one branch of the eukaryotes, not 3/5ths of evolutionary diversity as the 5-Kingdom scheme implies.
  
• Eukaryotes are as ancient a group as are the prokaryotic Domains, they did not evolve from them.
  
• Bacteria are every bit as highly evolved as eukaryotes.
  
• The tree also offers final proof of the endosymbiont theory for the origin of mitochondria and chloroplasts. These organelles have their own DNA & genes, including ssu-rDNA, & so can be analyzed separately from the nucleus by molecular phylogenetics. The mitochondria turn out to be related by ancestry to (i.e. members of) the purple Bacteria, and the chloroplasts are cyanoabacteria.

The false eukaryote / prokaryote dichotomy.

So, how different are "eukaryotic" and "prokaryotic" cells, the classic deepest division of life? Most texts have a chart indicating how 'different' they are....

The problem with the prokaryote/eukaryote dichotomy is that it is exclusionary - a lot like the vertebrate/invertebrate dichotomy of animals. The problem is that the terms "prokaryote" or "invertebrate" tells what an organism is not but it doesn't tell you what it is. All "prokaryote" means is "not a eukaryote"! Therefore, the term "prokaryote" as a label for a group of organisms is scientifically invalid! Over the years, for no real reason other than default, it became an assumption the all non-eukaryotes were of a single kind, but this is not the case - any more than all invertebrates are of a kind. There are in fact two fundamentally different kinds of "prokaryotes" (Bacteria and Archaea), as different or more from each other as either are from eukaryotes.

Many of the stark contrasts between Bacteria (prokaryotes, in the case of this table) and eukaryotes come from falsely assuming that plants & animals are typical eukaryotes, and E. coli is the typical prokaryote, and from an active striving to identify differences, no matter how trivial, in order to glorify eukaryotes. But what's true in E. coli is not necessarily true in other Bacteria, & what's true in plants & animals is not necessarily true in other eukaryotes. Bacteria are not primative - they are modern organisms, the result of over 3.6 billion years of evolution, just like eukaryotes.

Lastly, as a matter of fact, eukaryotes & bacteria aren't at all as different as these tables suggest. All of the apparent differences listed above are bogus in one way or another - at best over-generalizations and at worse just plain wrong.

Questions for thought...

• Can you think of a positive trait (i.e. something that's present or has a positive characteristic) that is typical of Bacteria but not eukaryotes?
• Can you think of a positive trait that is characteristic of protists but not higher eukaryotes? What is a 'higher' eukaryote? Why? Would you still think this if you were ae egocentric trypanosome?
• What's the difference between a multicellular organism and just a lump of cells of the same species?
• How many of the groups shown in the 3-Kingdom molecular phylogenetic tree can you name species from?
• In the molecular phylogenetic tree shown above, where would a novel organism fit that shared only an earlier common ancestor that the last common ancestor of the Bacteria, Archaea, and Eukarya?
• Where is the last common ancestor of all known Bacteria?
• What modern organism(s) are closest in evolutionary distance in this tree to the last common ancestor?