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Phylogeny is the inferred evolutionary history of a group of organisms. Paleontologists are interested in understanding life through time—not just at one time in the past or present, but over long periods of past time. Before they can attempt to reconstruct the forms, functions, and lives of once-living organisms, paleontologists have to place these organisms in context. The relationships of those organisms to each other are based on the ways they have branched out, or diverged, from a common ancestor. A phylogeny is usually represented as a phylogenetic tree or cladogram, which are like genealogies of species.

Phylogenetics, the science of phylogeny, is one part of the larger field of systematics, which also includes taxonomy. Taxonomy is the science of naming and classifying the diversity of organisms. Not only is phylogeny important for understanding paleontology (study of fossils), but paleontology in turn contributes to phylogeny. Many groups of organisms are now extinct, and without their fossils we would not have as clear a picture of how modern life is interrelated.

There is an amazing diversity of life, both living and extinct. For biologists to communicate with each other about these many organisms, there must also be a classification of these organisms into groups. Ideally, the classification should be based on the evolutionary history of life, such that it predicts properties of newly discovered or poorly known organisms.

Phylogenetic systematics is an attempt to understand the evolutionary interrelationships of living things, trying to interpret the way in which life has diversified and changed over time. While classification is primarily the creation of names for groups, systematics goes beyond this to elucidate new theories of the mechanisms of evolution.

Cladistics is a particular method of hypothesizing relationships among organisms. Like other methods, it has its own set of assumptions, procedures, and limitations. Cladistics is now accepted as the best method available for phylogenetic analysis, for it provides an explicit and testable hypothesis of organismal relationships.

The basic idea behind cladistics is that members of a group share a common evolutionary history, and are "closely related," more so to members of the same group than to other organisms. These groups are recognized by sharing unique features which were not present in distant ancestors. These shared derived characteristics are called synapomorphies. Synapomorphies are the basis for cladistics.

In a cladistic analysis, one attempts to identify which organisms belong together in groups, or clades, by examining specific derived features or characters that those organisms share. For example, if a genus of plants has both red flowered and white flowered species, then flower color might be a useful character for determining the evolutionary relationships of those plants. If it were known that the white flowered form arose from the previously existing red flowered form (i.e., through a mutation that prevents formation of the red pigment), then it could be inferred that all of the white colored species arose from a single red-colored ancestor. Characters that define a clade (e.g., white flower color in the example above) are called synapomorphies. Characters that do not unite a clade because they are primitive (e.g., red flower color) are called plesiomorphies.

In a cladistic analysis, it is important to know which character states are primitive and which are derived (that is, evolved from the primitive state). A technique called outgroup comparison is commonly used to make this determination. In outgroup comparison, the individuals of interest (the ingroup) are compared with a close relative. If some of the individuals of the ingroup possess the same character state as the outgroup, then that character state is assumed to be primitive. In the example discussed above, the outgroup has red flowers, so white is the derived state for flower color.

There are three basic assumptions in cladistics:

  • any group of organisms are related by descent from a common ancestor.
  • there is a bifurcating pattern of cladogenesis.
  • change in characteristics occurs in lineages over time.

The first assumption is a general assumption made for all evolutionary biology. It essentially means that life arose on Earth only once, and therefore all organisms are related in one way or another. Because of this, we can take any collection of organisms and determine a meaningful pattern of relationships, provided we have the right kind of information.

The second assumption is that new kinds of organisms may arise when existing species or populations divide into exactly two groups. The final assumption, that characteristics of organisms change over time, is the most important assumption in cladistics. It is only when characteristics change that we are able to recognize different lineages or groups. The convention is to call the "original" state of the characteristic plesiomorphic and the "changed" state apomorphic. The terms primitive and derived have also been used for these states, but they are often avoided by cladists, since those terms have been abused in the past.

Cladistics is useful for creating systems of classification. It is now the most commonly used method to classify organisms because it recognizes and employs evolutionary theory. Cladistics predicts the properties of organisms. It produces hypotheses about the relationships of organisms in a way that makes it possible to predict properties of the organisms. This can be especially important in cases when particular genes or biological compounds are being sought. Such genes and compounds are being sought all the time by companies interested in improving crop yield or disease resistance, and in the search for medicines. Only an hypothesis based on evolutionary theory, such as cladistic hypotheses, can be used for these endeavors.

As an example, consider the plant species Taxus brevifolia. This species produces a compound, taxol, which is useful for treating cancer. Unfortunately, large quantities of bark from this rare tree are required to produce enough taxol for a single patient. Through cladistic analysis, a phylogeny for the genus Taxus has been produced that shows Taxus cuspidata, a common ornamental shrub, to be a very close relative of T. brevifolia. Taxus cuspidata, then, may also produce large enough quantities of taxol to be useful. Having a classification based on evolutionary descent will allow scientists to select the species most likely to produce taxol.

Cladistics helps to elucidate mechanisms of evolution. Unlike previous systems of analyzing relationships, cladistics is explicitly evolutionary. Because of this, it is possible to examine the way characters change within groups over time—the direction in which characters change, and the relative frequency with which they change. It is also possible to compare the descendants of a single ancestor and observe patterns of origin and extinction in these groups, or to look at relative size and diversity of the groups. Perhaps the most important feature of cladistics is its use in testing long-standing hypotheses about adaptation.

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Science EncyclopediaScience & Philosophy: Philosophy of Mind - Early Ideas to Planck length