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Classification
A Natural System
Difficulties in
Classifying Microbes

Molecular Phylogeny
Eucarya
Archaea
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History of Descent: A Natural System of Classification

©2000 Gary Olsen, University of Illinois

Although there are no right and wrong ways to classify things, when the natures of objects are defined by a common history then there is a "natural" way to classify them. For most objects, their natures are largely independent of their histories; but organisms are products of their genetic history.

Organisms are Similar because of their Common Ancestry

For millennia it has been appreciated that organisms give rise to new individuals of the same kind (i.e., same species). Thus, humans give rise to more humans, dandelions give rise to more dandelions, Escherichia coli gives rise to more E. coli, and so forth. In essence,

like begets like begets like begets like etc. ad nauseam.

The continuity of a species is a consequence of the genes passed from each generation to the next. This is a static view of the biological world; without other processes, life could not change.

Species are Dynamic - They Change (albeit slowly)

In the 19th century, biologists began to recognize that species are dynamic, not static; that is, species change over time.4 Several discoveries necessitated this view and overcame seemingly conflicting observations. For example, the "like begets like" view does not accommodate the variation evident among individuals of a species. Also, the discovery of fossils indicated that ancient life forms were not the same as those alive today. Some of the fossils could even be organized into progressions, with later forms being similar, but not identical, to earlier forms.5 The simplest modification to the static view would be to suggest that

like begets similar.

At the same time, work in geology was revealing that the Earth was old - very much older than had been previously believed.6 This meant that even if changes between successive generations were small, there had been time for changes to accumulate into the large divergences that distinguish species. These observations (and others) led to the view that

like begets similar begets less similar begets still less similar etc.

The impact of this new perspective is profound. In the earlier static view, if we followed members of a species (call it A0) over time, their descendants and their descendants' descendants, and so on, would belong to the same species, forever, regardless of the duration of the intervening interval:

A0-->A0-->A0-->A0-->...-->A0-->A0

In contrast, the dynamic view of species implies that, given sufficient time, naturally occurring changes would accumulate, ultimately changing the lineage to such an extent that a descendent would be a member of a new species, A1, that is distinct from that of its distant ancestors:

A0-->A0'-->A0''-->A0'''-->...-->A1'-->A1

This realization was the motivation for Darwin's title: On the Origin of Species7. This could be represented diagrammatically as:

page4-1 picture

A Consequence of Common Ancestry Is Residual Similarity of Species

Consider the consequences of species A0 giving rise to two lineages that are prevented from further interbreeding. With sufficient time, the first lineage would change enough to be called a new species, A1 (as above), while in the same interval of time, the second group would also have changed enough to be a new species. Because the two lineages have accumulated changes independently (there was no interbreeding), most of the changes in the groups will be different.8 Thus the second group will have become a species that is not the same as either A0 or A1, so it needs a name of its own, A2:

page4-2 picture

Species A1 and A2 must each bear residual similarity to A0 (their most recent common ancestor), so they must also be similar to each other. Most similarities between present-day species are due to their common ancestry. To first approximation, the more recent their common ancestry, the more similar two species will be (the more properties they will share).

Turning this around, the most similar species today tend to be those that share the most recent common ancestry. More distinct species tend to have more remote common ancestry. Darwin (and others) saw that once we accept this perspective, then we inevitably continue until we have accepted the common ancestry of all life.9

A Natural System of Classification for Organisms

As noted above, there is no absolute rule for designing a classification; we can classify things by any criterion we choose. This is true in classifying organisms, as well. We can classify by size, shape, color, alphabetical order (in any language), or even chronology of published descriptions.l0 There is however a practical question: what do we learn from our classification? How useful is it? Is there a preferred classification of organisms from which we can learn more than we can from alternative classifications?

If we classify by an arbitrary criterion, then knowing an organism's placement within the classification can be remarkably uninformative. For example, if we classify bacteria on the basis of shape (i.e., rod, coccus, spiral, etc.), then knowing an organism's classification tells us little more than its shape. We cannot begin to guess whether it is pathogenic, whether it makes food taste good, or whether it enhances the growth of our lawn.

In the case of organisms, we can do much better than an arbitrary classification. Ideally, we wish to base our classification on the relationships of the organisms, that is, on their genealogy or phylogeny. This is uniquely useful because knowing that two organisms are closely related tells us that they will have many properties in common. Knowing historical relationships has more predictive potential (more applicability to properties that have not yet been measured) than does an arbitrary classification.

Darwin referred to a classification based on evolutionary history as a natural system. In recognizing the parallel between phylogenetic closeness and species similarity, Darwin explained why the Linnaean system had been so successful for macroscopic plants and animals: they had been placed into the hierarchical groups of the Linnaean classification on the basis of similarities, and because these similarities reflected the evolutionary closeness of the respective species, the classification tended to reflect their historical relationships. In general, when similarities due to common ancestry are easy to recognize and measure, a classification of the organisms tends to approximate a natural system.11

The original successes of the Linnaean system were largely limited to complex plants and animals. In these cases there are numerous features that can be seen and compared between organisms. In addition, many of the features are sufficiently complex that it is safe to assume that they were only invented once, so that similarities really are the result of inheritance from a common ancestor that also possessed the shared feature.12


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