Reconstruction of phylogenetic trees

Regardless of whether morphological or molecular data are analyzed, reconstruction of phylogenetic relationships between species depends on interpretation of shared similarities. In principle, it is relatively easy to survey similarities between species for individual characters. This task is particularly straightforward with molecular data because the individual components at defined positions in sequences of DNA (nucleotide bases) or proteins (amino acids) are relatively simple and directly comparable. Furthermore, because the primary process underlying evolutionary change is point mutation (random replacement of one nucleotide base by another in a DNA sequence), comparison of DNA sequences directly reveals basic evolutionary steps. Most changes in DNA sequences lead to changes in corresponding protein sequences, but there is some degree of redundancy in the genetic code, because up to six different triplet sequences of nucleotides can correspond to a single amino acid. For this reason, about 25% of point mutations in DNA are "silent" and do not lead to a change in protein sequences. Such redundancy applies particularly to the third base position in DNA triplets.

Analysis of similarities between species to construct phy-logenetic trees is more difficult than it seems at first sight. In the first place, similarities can arise independently through convergent evolution at any time after the separation between two lineages. For instance, rodent-like incisor teeth have developed several times independently during the evolution of mammals. But reconstruction of the relationships between species depends on exclusion of convergent similarities and identification of homologous similarities that have been inherited through descent from a common ancestor. In the case of morphological characters, it is often possible to identify convergent similarities directly because development of similar characters is typically driven by similar functional requirements. For example, rodent-like incisors develop in response to selection pressure for gnawing behavior. For complex morphological characters, convergent similarity is typically only superficial because it merely needs to meet a particular functional requirement. Hence, detailed examination of such characters commonly reveals fundamental differences. With incisors, for instance, a rodent-like pattern can develop without altering the structure of enamel that characterizes a particular group of mammals. With molecular characters, by contrast, each type of nucleotide base or amino acid shows complete chemical identity, so it is impossible to determine from direct examination whether convergent evolution has occurred. Instead, convergence in molecular

Dna Proof Evolution
Due to DNA evidence, cetaceans like the bottlenosed dolphin (Tur-siops truncatus) have been linked to hippopotamuses (Hippopotamus amphibius). (Photo by © Tom Brakefield/Corbis. Reproduced by permission.)

evolution is recognizable only from the phylogenetic tree after it has been generated on the assumption that the tree requiring the smallest total amount of change (the most parsimonious solution) is the correct one. Because there are so few possibilities for evolutionary change at the molecular level (4 nucleotide bases; 20 amino acids), convergent evolution is very common. As a rule, about half of the similarities between species recorded in any tree that is generated must have arisen independently through convergent evolution. Convergence is therefore a major problem with any tree derived from molecular data, particularly because functional aspects of changes in nucleotide bases and amino acids are rarely considered (thus excluding any possibility of identifying functional convergence). Moreover, precisely because there are so few possibilities for change in DNA base sequences, repeated point mutation at a given site will mask previous changes and can easily lead to chance return to the original condition. Although it is now standard practice to make a global correction for repeated mutation at a given site in molecular trees, it is virtually impossible to reconstruct the mutational history of individual sites if repeated change has occurred.

In fact, there is a further problem in interpreting similarities for the reconstruction of phylogenetic trees. Even if it is possible to exclude certain cases of convergent evolution, as is often true with complex morphological similarities, an important distinction remains with respect to inherited homologous similarities. For any group of species considered, a particular set of features will be present in the initial common ancestor. If such a primitive feature is retained as a homologous similarity in any descendants, it reveals nothing about

Phylogenetic Tree Red Panda

The red panda (Ailurus fulgens) is very hard to classify, but was placed with the other Ursidae species due to similar DNA. (Photo by Tim Davis/Photo Researchers, Inc. Reproduced by permission.)

branching relationships within the tree. The only homologous features that provide information about branching within a tree are novel features that arise at some point and are subsequently retained by descendants as shared derived similarities. This crucial distinction between primitive and derived homologous similarities is particularly relevant if there are marked differences between lineages in the rate of evolutionary change. For instance, members of two slowly evolving lineages can retain many primitive similarities and would thus be grouped together on grounds of overall homologous similarity if no special attempt were made to identify derived similarities. It was once believed that rates of change are reasonably constant at the molecular level, thus reducing the need to distinguish between primitive and derived homologous similarities, but the availability of large molecular data sets has revealed that there can be major differences in rates between lineages.

In conclusion, the increasing availability of molecular data has provided a major benefit for the reconstruction of phylo-genetic trees. The large numbers of directly comparable characters included in molecular data sets provide a highly informative basis for quantitative comparisons. On the other hand, because the methods used do not explicitly tackle the crucial distinction between convergent, primitive, and derived similarities, the results are subject to error. Accordingly, if there is a conflict between a tree based on molecular data and one based on morphological data, it should not be automatically assumed that the latter is necessarily incorrect. After all, there is quite often a similar conflict between trees based on two different molecular data sets. The safest procedure is therefore to take a balanced approach that gives due consideration to both morphological and molecular evidence. Combined studies that do precisely this with comprehensive data sets are becoming increasingly common.

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