Principles of Microbial Diversity. James W. Brown
File it in your mind alongside the term “phlogiston.”
Table 2.1 Sample “eukaryotes versus prokaryotes” table common to biology and even microbiology textbooks
| Eukaryotes | “Prokaryotes” |
| Large (20–100 μm) | Small (1–5 μm) |
| Contain nucleus | No nucleus |
| Contain many large linear chromosomes | Contain one small circular DNA chromosome |
| Contain organelles | No organelles |
| Diploid | Haploid |
| Cell cycle includes mitosis | No mitosis |
| Reproduce sexually or by budding | Reproduce by binary fission |
| Cells contain a cytoskeleton | No internal skeleton |
| Ingestive or photosynthetic | Absorptive |
| Multicellular | Unicellular |
| Complex life cycles and cellular differentiation | Simple division cycle, no differentiation |
| mRNAs are polyadenylated | No polyadenylation |
| Genes transcribed separately | Genes transcribed together in operons |
| Genes contain introns | No introns |
| DNA packaged with histones | DNA not packaged |
In addition, many of the stark contrasts between bacteria (“prokaryotes” in the case of this table) and eukaryotes come from falsely assuming that plants and animals are typical eukaryotes and that E. coli and Bacillus subtilis are typical prokaryotes, and from an active striving to identify differences, no matter how trivial, in order to make eukaryotes “higher” and prokaryotes “lower.” But something that is true for E. coli and B. subtilis is not necessarily true for other bacteria, and something that is true for plants and animals is not necessarily true for other eukaryotes. Bacteria are not primitive—they are modern organisms, the result of over 3.6 billion years of evolution, just like eukaryotes. As a matter of fact, Eukarya, Bacteria, and Archaea are not at all as different as these tables suggest. All of the apparent differences listed above are bogus in one way or another: at best overgeneralizations and at worse simply false.
Questions for thought
1 1. Can you think of a positive trait (i.e., something that is present or has a positive characteristic) that is typical of bacteria but not eukaryotes?
2 2. 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 an egocentric trypanosome?
3 3. What is the difference between a multicellular organism and just a lump of cells of the same species?
4 4. For how many of the groups shown in the three-kingdom molecular phylogenetic tree can you name species?
5 5. In the molecular phylogenetic tree shown above, how would you add a novel organism whose ancestors diverged from other living things before the last common ancestor of the Bacteria, Archaea, and Eukarya?
6 6. Where is the last common ancestor of all known bacteria?
7 7. Which modern organism(s) is closest in evolutionary distance in this tree to the last common ancestor?
3
Phylogenetic Information
Molecular phylogenetic analysis is the use of macromolecular structure (usually nucleotide or amino acid sequences) to reconstruct the phylogenetic relationships between organisms. The extent of difference between homologous DNA, RNA, or protein sequences in different organisms is used as a measure of how much these organisms have diverged from one another in evolutionary history.
The typical scenario where a phylogenetic analysis is needed is the characterization of a novel organism: for example, determining the phylogenetic placement (phylotype) of a novel organism, in order to make predictions about its unknown properties. This might be a clinical isolate of a potential pathogen, an organism that carries out useful biochemistry, an organism that seems to be abundant in an interesting environment, or anything else of interest.
The process of molecular phylogenetic analysis can be divided into four critical parts, each of which, of course, also has various subparts:
1 1. Decide which organisms and sequences to use in the analysis
2 2. Obtain the required sequence experimentally or from databases
3 3. Assemble these sequences in a multiple-sequence alignment
4 4. Use this alignment to generate phylogenetic trees
In this chapter, we walk through the first three steps of this process.
Deciding which organisms and sequences to use in the analysis
The sequences of genes, RNAs, or proteins contain two very different kinds of information: structural/functional information and historical information. Think of it this way: any particular amino acid in a specific protein is what it is (say, for example, an alanine) in part because it facilitates the formation of the correct structure and function of the protein. But usually there are a number of alternatives that might function just as well. The reason it is what it is, and not any of these alternatives, is that it was inherited from a successful ancestor. This is historical information. Comparisons among an aligned collection of homologous sequences can be used to sort out both the structure of the functional molecule (especially for RNAs) and their historical relationships: a phylogenetic tree.
Phylogenetic trees are usually generated by using alignments of single genes, RNAs, or proteins, but no such sequence is either ideal or universally useful for the generation of informative phylogenetic trees. This being said, some sequences do carry more phylogenetic information than others; these sequences can be called “molecular clocks.”
Features required of a good molecular clock
Clock-like behavior
The sequences of genes, RNAs, and proteins change over time. If this change is entirely random (within the constraint of the structure and function of the molecule; i.e., by genetic drift), the amount of divergence between any particular sequence in two organisms should be a measure of how long ago these organisms diverged from their common ancestor. If this is true, these sequences can be said to exhibit clock-like behavior (Fig. 3.1).
Clock-like behavior depends mostly on functional constancy of the sequence; a change in the function (or functional properties) leads to large, selected (and therefore nonrandom) sequence change,