Chapter 2: Taxonomy and Phylogeny
While it is uncommon, people sometimes give names to individual plants. For example, in Sequoia National park stands ‘General Sherman’, considered to be the largest organism living on earth. Because organisms are discrete packages (i.e., with boundaries in space and time) it certainly possible to name them. But there are an awful lot of them and it is simply impractical to name them all. However, if one observes organisms, it is quickly apparent that they occur in groups, i.e. there are groups of them that look similar and thus the group can be considered an entity itself. Moreover, additional study will usually reveal that identified (i.e., defined) groups of organisms can often be: (1) subdivided into smaller groups and (2) lumped together into bigger groups; that is, that the diversity of organisms is organized into clusters of similarity and there are clusters of the clusters. These biological patterns seek an explanation: why do organisms come in groups and why are there groups of groups?
Even if organisms did not ‘naturally’ occur in groups it would be important for biologist to define groups; there is simply so much biological diversity that some sort of ‘filing system’ is required to organize it all. Thus, there are two aspects to organizing organisms into groups: (1) a practical aspect, producing a way to manage all the variety of organismal life, to arrange its vast diversity, (2) a mechanistic (process) aspect, producing a system that will allow biologists to understand mechanisms that result in the patterns of diversity, e.g., why there are groups. To a large extent these two aspects can be satisfied simultaneously, i.e., there are systems that categorize life easily and also allow users to study the processes (evolutionary mechanisms) that lead to the categories. However, the biological landscape is vast; clusters range from groups (species, or perhaps subspecies) that might have less than 1000 organisms that all ‘look’ very similar to groups (families, orders) that are comprised of millions of individuals, with members that do not ‘look’ very similar yet do possess some ‘fundamental similarities.’ With such a span in scale one should appreciate that there may be situations where a system that is useful to consider the evolutionary relationships (i.e., the phylogeny) between groups of organisms may not very handy as a filing system. Or, looking at it from a different perspective, classification schemes that easily organize life’s diversity may not do so in a way that reflects the phylogeny of different groups. An example familiar to most biology students would be ‘reptiles’, a handy group in terms of classification (reptiles are vertebrates that aren’t amphibians, birds or mammals), but a group that does not represent phylogeny. This book is primarily about organisms. And while in general it will use a phylogenetically based classification scheme, occasionally it will consider groups that are ‘artifi