(Continued from the previous page)
As we have seen, when different traits are used to construct phylogenetic trees for the same set of organisms, different trees are implied. There is very often a lack of concordance in the results based on different datasets. Some traits may suggest the relationships of the organisms should be described by one tree, while other traits may suggest the nature of their relationships are quite different. Under such circumstances, the tree that "best" fits the data is selected. But this procedure presupposes that some "real" tree of descent actually exists. If the production of new forms of life via stabilization processes is common over evolutionary time, then there will be no real tree, let alone a best one. The reason: such processes so often involve hybridization that they would give rise to a weblike network of descent, not a tree. Under such circumstances, "best" would merely mean "best, given a particular set of assumptions about how the data should be weighted." But the supposition that "best" means "real," the usual assumption under orthodox theory, causes discordant data to be treated as statistical noise and ignored.
It is important to realize that the results of this categorization process depend on initial assumptions that are arbitrary and subject to bias. Any given organism has an essentially infinite number of traits. From this infinite set, the investigator must choose some particular, finite subset of traits if the classification process is to be carried out. A geneticist might consider genetic traits more significant and limit her attention to genes. A paleontologist has no genetic information and instead bases classifications on morphological traits, as do many naturalists. If a different set of traits, whether genetic, morphological, or a combination thereof, is chosen to serve as the basis for categorizing a given set of organisms, a different taxonomic classification often results. Nevertheless, there is no proven, objective criterion that allows one category of traits to be excluded in favor of another.
Even after a subset of traits has been chosen, subjective decisions remain. Rules for evaluating the selected set of traits must also be chosen. Certain traits might be considered more significant or reliable and be given greater weight in the analysis. Sometimes, this weighting is done almost unconsciously. For example, existing opinion concerning the way taxa are related to one another can limit the mental scope of the investigator. Thus, if two taxa have traditionally been considered distantly related, then traits they hold in common (and that therefore would seem to contradict tradition) are likely to be discounted. For example, although pterosaurs (winged creatures, formerly known as pterodactyls, that lived concurrently with dinosaurs) are now known to have been furry and are generally believed to have been warm-blooded (read more about this topic >>), they remain classified as reptiles. In other words, there is a conservative tendency to dismiss what seems to undermine accepted ideas concerning the natural order. The result of this circular mode of reasoning is that ideas of the natural order become bogged in dogma.
This logic is reflected in the wide acceptance of the concepts of homology and analogy. Biologists call the existence of similar features in organisms they consider to be unrelated "analogy." They say analogy is found when organisms live under similar conditions or have similar habits. The same needs in each case are supposed to cause structures serving similar functions to evolve over time. When a given situation is viewed in this light, it is said that the organisms in question have undergone "convergent" evolution. Here, use of the word convergent indicates the speaker believes the organisms are actually distantly related, but have approached each other in form. The nature of the correspondence between the two organs or structures is presumed to be one of mere similarity, not genetic relationship. Therefore, when attempting to arrange a set of organisms into a phylogenetic tree reflecting their mutual relationships, anyone holding such views can justify omitting traits from analysis by claiming they are analogous. By definition, if a trait is analogous, it has no bearing on questions of genetic kinship. For example, it could be claimed that the fur seen in fossil pterosaurs, mentioned in the previous paragraph, does not indicate a relationship between these animals and mammals. Indeed, one could argue that pterosaurs were reptiles, entirely unrelated to mammals, and that fur arose in these creatures independently of the evolution of fur in mammals. To justify this claim, one might assert flight placed on pterosaurs metabolic constraints requiring the evolution of a more efficient form of insulation than ordinary reptilian scales. Such is the typical line of reasoning of those who think habitually in terms of analogy and convergence.
In contrast, when biologists believe two organisms are related, they often claim dissimilar structures are essentially the same, in the sense that both are descended with modification from a corresponding structure in a common ancestor. In this case, the word homology is employed. Thus, if a researcher believed a theory asserting the swim bladder of fishes evolved into the lung of land animals, she would say lungs and swim bladders are homologous. Claims of homology allow a researcher to make claims of relationship even when organisms have dissimilar traits.
Rarely, then, is a scientist stating a known fact when he makes an assertion about whether two structures are analogous or homologous. Rather, he is indicating something about his own beliefs concerning the nature of the relationship between the two organisms in question (i.e., whether their relationship is close or distant). He is also saying something about whether he believes the trait to be useful from the standpoint of constructing phylogenetic trees (i.e., whether it is "phylogenetically informative"). The concepts of homology and analogy therefore have a potentially insidious effect. Once a widely accepted hierarchy of relationships has been established by tradition, claims of analogy allow a researcher to discount the presence of similar traits in organisms that have traditionally been considered unrelated, and to ignore dissimilarities in those considered related. This approach to evolutionary analysis gives carte blanche to those who wish to ignore new data and maintain the status quo. Also, to those who wish to claim conflicting gene trees are rare, it provides a simple means of homogenizing the data. Faced with such inconsistencies, they can simply say similar genes are the result of convergence in organisms they consider unrelated.
Biologists are apparently motivated to unwittingly shape their experiments and, under the influence of the concepts of analogy and homology, inadvertently even to selectively winnow their data to obtain concordant results. For example, the writer has seen cases where professors encouraged their graduate students to limit the number of taxa and traits in phylogenetic studies in order to obtain "clean" results (i.e., results where all the data implied the same tree of relationships). The object of this approach seems to be to eliminate unnecessary complications that stand in the way of presenting clearly resolved trees. But its effect is to prevent evidence of nonconcordance from emerging. Those who engage in such practices clearly believe the true history of evolution has been a matter of branching divergence. "Clean" results consistent with this view are therefore seen as correct. However, as we saw in Section 5, phylogenetic trees are often, even typically, non-concordant despite such biases that tend to tidy the results. Naturalists have long believed that a supposedly treelike pattern of evolutionary history was reflected in the treelike configuration of their chosen system of classification. But this notion may be entirely illusory. The two patterns may well be—indeed much evidence suggests they are—entirely distinct. Perhaps, then, we should look for another evolutionary topology. NEXT PAGE >>
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8.1: Dubious Assumptions - © Macroevolution.net