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A Natural System
Difficulties in
Classifying Microbes

Molecular Phylogeny
Molecular Ecology

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©2000 Gary Olsen, University of Illinois

1 To discover that the longest word in King Lear is flibbertigibbet, we classify the words by length.

2 For simplicity, further splitting of the various levels (e.g., subfamily) are not shown. The need for a level, now called Domain, that is higher than Kingdom is a consequence of the discovery in 1977 that there are distinctions among organisms that are more fundamental than the distinctions between plants and animals, which had served as the prototype for a Kingdom level separation.

3 Technically, Drosophila melanogasteris the species binomial (two-part name), and melanogaster is the species epithet.

4 A few of these biologists (or more correctly,natural scientists) were Jean Batiste de Lamarck, Charles Lyell, T. H.Huxley, and Charles Darwin. From their points of view, it was not a question of whether species change with time, it was only a question of how and why. One of Darwin's great insights was that there was no need for organisms to know how to make changes for the better (i.e., the source of variation need not anticipate the consequences of the changes, whether a change will be good or bad); it is only necessary to make random changes, and let the bad ones fail "in the struggle for existence."

5 The failure to find smooth progressions from ancient forms to present-day forms was a cause of concern (the "missing links"). Darwin was convinced that most of this was due to the limited sampling provided by the fossils that had been found. This remains a lively debate over 130 years later.

6 The 19th century estimates were tens to hundreds of millions of years, rather than the thousands that had been previously assumed - an increase of about 10,000-fold. The current estimate of 4550 million years is a product of 20th century science.

7 Darwin, C. 1859. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London: John Murray. 490 pp. If you have not read it, give it a try - just for fun; it is an enjoyable and insightful book, and it is easy reading.

8 Because the number of possible changes is so great, the chance of making exactly the same changes at random is very small.

9 Darwin was not completely comfortable with a single origin for all of life. He saw, and lucidly described, this progression,but he could not see the similarities between trees and rats; he could not know (as we do now) about the molecular similarities that so clearly unite even the most diverse forms of life.

10 Which is used in assigning precedence to proposed names.

11 In contrast, in the case of chairs, there is no underlying history to be reflected in the classification. There is no reason to expect that other properties, such as color, can be inferred simply by knowing that something is a chair. More detailed characterization - itis a rocking chair - does not provide more information about the color. In the case of organisms, the more resolved the phylogenetic placement, the more properties that we can project (extrapolate) from related organisms.

12 The alternative would be that the features were independently invented in the two species, which is called convergence or parallelism.

13 There is now also a Bergey's Manual of Systematic Bacteriology, reflecting the desire to move to a natural classification.

14 But, if the specific organism was not previously characterized, then the physician learns little or nothing.

15 One can view this as looking at the structure of a molecule, not just its presence or absence as assayed by a physiological test (or by its effect on pigmentation, cell shape, developmental program,etc.). The former data characterize the molecule itself, while the latter only characterize its activity. The full potential of molecular phylogeny was spelled out in a beautiful paper by Zuckerkandl and Pauling (Zuckerkandl,E., and Pauling, L. 1965. Molecules as documents of evolutionary history.J. The or. Biol. 8: 357-366).

16 The primary reason for this is that very different gene sequences are capable of producing similar or identical proteins.

17 Generally this is the case for genes that perform complex functions that are important to the cell.

18 If I asked you to describe an organism that I had never seen, you could provide a much more precise description if you were allowed to use 1000 letters (150-200 words) than if you were restricted to 100 letters (15-20 words).

19 Pace, B., and Campbell, L. L. 1971. Homology of ribosomal ribonucleic acid of diverse bacterial species with Escherichia coli and Bacillus stearothermophilus. J. Bacteriol. 107:543-547.

20 Protein sequence determination had been possible since 1951 (Sanger, F., and Tuppy, H. 1951. The amino acid sequence in the phenylananyl chain of insulin. Biochem. J. 49: 463-490),and the sequences were used explicitly to examine evolutionary relationships by 1967 (Fitch, W. M., and Margoliash, E. 1967. Construction of phylogenetic trees: A method based on mutational distances as estimated from cytochromec sequences is of general applicability. Science 155: 279-284).

21 Woese, C. R., Kandler, O., and Wheelis,M. L. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579. There question of names for the domains is awkward. When they were recognized, the Archaea were called "archaebacteria" - a name that seems to connote a specific relationship to the Bacteria (which were called "eubacteria").The switch to the name Archaea clarifies the distinctiveness of these organisms.However, the name Bacteria (which Woese et al. have defined phylogenetically)is sometimes taken by others as synonymous with prokaryote (which is defined in terms of cell structure, that is, not a eukaryote).

22 A group that includes an ancestor and all of its descendants is called a monophyletic group. Plants, animals and fungi are monophyletic groups. Protists are not monophyletic. Knowing that something is a eukaryotic protist only tells you that it is not a plant, an animal, or a fungus; it tells you what properties the organism does not have, not which ones it does have (beyond those associated with being a eukaryote).

23 Neither are many other "groups" that are defined by exclusion, such as eukaryotic protists.

24 Prior to 2.4 billion years ago there was little oxygen in the Earth's atmosphere. In the interval between 2.4and 1.8 billion years ago there was a substantial rise in the level, leading to the deposition of large quantities of oxidized minerals, especially iron. (These deposits now provide some of the richest sources of iron ore,including the Lake Superior formation.)

25 This view is being called into question by recent sequencing of genes from these lineages. However, at present there are only one or two genes that suggest that all known eukaryotes might have had mitochondria at some point in their past. With so few examples,it is necessary to consider that there might have been earlier (limited)lateral gene transfer, before the endosymbiosis that gave rise to the modern mitochondrion.

26 Though, as noted above, there are other species that have lost their walls separately from the major mycoplasma group.

27 This logic actually goes back earlier,but the molecules examined (e.g., lipids) generally did not provide precise phylogenetic identifications.

28 The total change is found simply by adding the lengths of the branches connecting the two species of interest.

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