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A Natural System
Difficulties in
Classifying Microbes

Molecular Phylogeny
Molecular Ecology

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Molecular Microbial Ecology

©2000 Gary Olsen, University of Illinois

One of the most dramatic contributions of molecular phylogeny to our understanding of microorganisms is its application to the area of microbial ecology.

The Difficulty of Growth for Characterization

Traditional methods of microbial ecology require that organisms from an environment be cultivated in the laboratory so that they can be characterized and identified. However, if the number of cells visible in an environmental sample are directly counted and compared with the number of cells successfully cultivated from the sample, it is found that anywhere from 90% to 99.9% of the cells defy cultivation, and therefore evade identification. Thus, most characterizations by cultivation methods have contained a large bias in an unknown direction.

Using Molecular Sequences to Represent the Organisms in an Environment

Starting about 15 years ago it was realized that the genes and other molecules present in an environment are completely defined by the organisms living there, so that an inventory of appropriately chosen molecules (such as the small subunit rRNA) is equivalent to an inventory of the organisms.27

The advances in molecular phylogenetic methods provide the necessary technologies for isolating RNA or DNA from an environment, and inferring the sequences of individual molecules. The large collection of sequence data from well-characterized (cultured) organisms provides a framework into which these sequence data can be placed phylogenetically. In this way, a molecular census can be performed on natural populations.

In addition, if a new sequence is related to those from organisms with particular physiological properties, then those properties can be extrapolated onto the organism in the environment that was the source of the particular new sequence. Thus, it is even possible to learn something about the biochemical processes that might be going on in an environment, even without the ability to grow the organisms and make the measurements in the laboratory.

The same methodologies are being applied to human and animal pathogens. These techniques have permitted the phylogenetic identification of organisms that have defied cultivation and have provided the basis for rapid detection of specific organisms or groups of organisms in clinical samples.


It is very important to understand what phylogenetic trees do, and do not, mean. The trees that I have shown provide two kinds of information: Branching order and branch length.

Branching Order in a Phylogenetic Tree

The branching pattern (often called branching order) shows the genealogy of the organisms. That is, it shows which species share more common ancestry than which others.

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In the tree above, A and B share the most recent common ancestry. Thus, of the species in the tree, A and B are the most closely related.

The next most recent common ancestry is C with the group composed of A and B. Notice that the relationship of C is with the group containing A and B. In particular, C is not more closely related to B than to A. This can be emphasized by the following two trees, which are equivalent to each other:

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It is only a matter of taste which way it is drawn. In essence, in both versions A and B share a more recent common ancestor than do either of them with C. Thus it does not make sense for either A or B to be closer to C than is the other, since the alternative drawing would seem to imply the opposite.

Going back to the first drawing:

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the most ancient common ancestry in this tree is that of D with the group composed of A, B and C.

Branch Lengths in a Phylogenetic Tree

In the above drawing, the length of the line leading from the A+B common ancestry to A is shorter than the line leading from the A+B common ancestry to B. This is intended to represent the accumulation of a different amount of change. Note that the both A and B represent present-day species, and their most recent common ancestor lived some specific period of time ago. That is, the time represented by the branches is the same, even though a different amount of change has accumulated.

To get unequal amounts of change in equal time periods, the rate of change must differ. There is no reason why rates of molecular change have to be either constant or equal in all lineages. When we examine molecular sequence data, we often find that some lineages have changed a different average rates.

A seemingly paradoxical result of unequal rates of change is that for the drawing above, the total amount of change that has accumulated between A and B is greater than between A and C.28 This does not alter the fact that A and B are more closely related to one another than either is to C, since A and B share a more recent common ancestor.

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