Phylogeny and Classification
For most of the past 250 years, the classification of organisms has followed the Linnean system, which uses ranks to designate levels of organization of the organisms being classified.
Most readers will be familiar with the main formal Linnean ranks, ordered hierarchically from most to least inclusive: Kingdom, Phylum, Class, Order, Family, Genus, and Species. Researchers have differed in assigning rank to the vertebrates and their relatives. For example, some authors have recognized three phyla: Phylum Echinodermata, Phylum Hemichordata, and Phylum Chordata. Others consider the Urochordata and Cephalochordata as phyla on their own, separate from the Chordata. Still others have viewed the Urochordata as a separate phylum, but the Cephalochordata as a subphylum of the Phylum Chordata. If you find this confusing, you’re not alone! The different designations did—or at any rate were meant to—have some grounding in biological reality. They reflected a particular researcher’s perception of the magnitude of the difference in the levels of organization (a quality that may be referred to as a grade) among the taxa under consideration. Thus, if a taxon was considered a phylum, it mainly implied that its members made their living in a very different way than if they were considered only a subphylum of a larger taxon. As you have probably already realized, researchers’ perceptions along these lines are subjective.In recent years, however, the formal Linnean ranking system has fallen increasingly into disuse as systematists have become aware that there is no intrinsic or “special” value of any particular taxon that would justify its recognition as a higher or lower rank, compared to other taxa. In other words, there is no special reason for “elevating” birds or Aves to the rank of Class, equal and thereby excluded from, the Class Reptilia.
In fact, it is improper to do so, because the birds are properly part of the taxon named Reptilia. Here, formal ranks are not used, and taxa are referred to simply by their name.Formal names are applied to natural or monophyletic groups. A monophyletic group includes an ancestor and all of its descendants (provided that the phylogeny has been carefully reconstructed). Such groups are termed clades. Clades are recognized based on common ancestry. If two taxa are in a clade, it is because they are linked by a common ancestor. Biologists infer such ancestral relationships through the presence of shared derived characters or synapomorphies (see below). If two (or more) taxa share a character that is exclusive to them, then we assume that they share this feature because they have inherited it from a common ancestor, rather than each having evolved the character independently, and so infer that the taxa are descendants of the same ancestor (which we are not able to actually recognize, and thus refer to as hypothetical). This, of
| deuterostomata | Pharyngotremata | chordata |
| • first embryonic opening becomes anus; second opening becomes mouth • basally, mesoderm forms bilaterally as out-pocketing of embryonic gut; ceolom, which develops within mesoderm, thus originally has connection with gut • basally, a ciliated looped band is present on surface of larva | • pharyngeal skeleton • pharyngeal slits • blood vascular system | • pharyngeal slits • endostyle • dorsal, hollow nerve cord • notochord • postanal tail |
FIGURE 1.1 Cladogram showing phylogeny of the Deuterostomata. Some Synapomorphies of the main groups are provided in the boxes below the cladogram.
course, is the idealized situation.
In reality, biologists use many characters in trying to reconstruct phylogeny. The practice is complicated by the fact that organisms can and do evolve very similar characters independently of each other, an occurrence referred to as homoplasy. In reconstructing phylogeny, a researcher considers the totality of evidence. It is rare that only a single character can be used to reconstruct phylogeny.The pattern of relationships among taxa is depicted visually by a cladogram, which is essentially a diagram of nodes and branches, with the nodes representing ancestors and the branches that diverge from a node representing the descendant taxa of the ancestor. The node, then, may be thought of as representing the hypothetical ancestor of the two taxa that diverge from it. The pattern of branching represents the pattern of relationship. Examine the cladogram in Figure 1.1. Note the node from which the Hemichordata and Chordata diverge. This node represents the ancestor species that split to produce two lineages, one that evolved into the Chordata and the other into the Hemichordata. The two branches that diverge from this ancestor represent the evolutionary paths to the divergent taxa.
Only the branching pattern is of concern. The length of the branches is immaterial in terms of absolute time, but relative time is implied by branching sequence. Clearly, the divergence of the Cephalochordata and Craniata occurred after the divergence of the Hemichordata and Somitichordata.
Informal names, set between quotation marks, are used to designate a group of organisms that do not descend from the same common ancestor but that do possess (or lack) some of the features of the taxon in which we are interested. Many of these terms were considered formal names in earlier classifications. For example, the term “protochordates” is commonly used to refer to the hemichordates, urochordates, and cephalochordates. Grouping them together is a shorthand way of referring to them as close relatives of chordates (no quotation marks here, so this is the vernacular form of the formal name Chordata), and that they lack various characters that chordates possess.
We must be clear that informal groups, though convenient, do not reflect phylogeny; they are not monophyletic.In discussing how biologists reconstruct phylogeny, the nature of the similarity among organisms must be considered, because it is necessary to differentiate between those similarities that are useful in reconstructing phylogeny and those that are not. One kind, termed ple- siomorphic, refers to similarity based on the presence of primitive or ancestral conditions or states. Consider the Vertebrata, in which the presence of vertebrae is an ancestral feature—in other words, it was present in the common ancestor of all vertebrates. These structures may inform us that all vertebrates share a common ancestor, but their presence per se cannot be used to decipher the relationships among vertebrates. As a practical example, let us consider a turtle, a bird, and a mammal. All possess vertebrae, and are therefore vertebrates, but the presence of these structures does not allow us to say which two of these forms are more closely related to each other than either would be to the third. This similarity, therefore, is due to the retention of a trait that is ancestral for vertebrates. When an ancestral character it shared by various forms, it is described as symplesiomorphic.
A second kind of similarity is due to the inheritance of a modified character state. Such modification is considered derived or apomorphic. When organisms share a derived trait, it is described as synapomorphic. Synapomorphies do indicate phylogenetic relationship. In the most basic sense, sharing a derived trait is a shorthand way of saying that the organisms under consideration possess a modified trait because it was inherited from an ancestor that first acquired or evolved the modification. An assortment of organisms united by synapomorphies forms a natural group or clade; that is, the clade is a real entity in evolutionary terms. It means that all the organisms included within the clade were ultimately derived from the same ancestor.
All vertebrates that possess jaws do so because this character was inherited from an ancestor that had evolved jaws as a modification of the mandibular arch (see below). If we wish to understand the relationships among a lamprey, a fish, and a dog, the presence of jaws is a character state that indicates that the dog and fish are more closely related to each other than either is to a lamprey. When two groups are each other’s closest relatives, they are said to be sister groups.A natural or monophyletic group may be recognized formally by a name. The only restriction imposed is that a monophyletic group include the ancestor and all descendants of the ancestor, even though the latter cannot be identified. A monophyletic group may also be termed a clade, from which is derived the alternate term cladistics for phylogenetic systematics. Cladistics is the methodology that recognizes shared derived traits as the only valid indicators for inferring phylogenetic relationships.
The third type of similarity is termed homoplasic and results from morphologically similar solutions to particular selection pressures. For example, the fusiform body shape of fishes and of dolphins, which are mammals, is not due to inheritance from a common ancestor, but to selection pressure to adopt a form suitable for moving efficiently through water. Such similarity does not indicate phylogenetic relationship, although in some cases the similarity may be so profound that it may lead us inaccurately to attribute its cause to phylogenetic proximity. The reliable method of recognizing homoplasy is to identify it as similarity in different monophyletic groups, following, of course, a phylogenetic analysis.
In addition to clades or monophyletic groups, we may speak of grades, which are not natural groups. A grade recognizes a group of organisms based on a shared level of organization or complexity. A new grade may be achieved through the accumulation of a number of derived characters so that a new “mode of living” is made possible.
In the past, some groups were formally recognized, but they were united essentially because their members shared a particular grade of evolution. We now recognize such groups as artificial rather than natural.Probably the most familiar example is the case of the Reptilia. Formerly the Reptilia included living and fossil crocodiles, turtles, snakes, and lizards, as well as their extinct relatives, such as dinosaurs, pterosaurs, and plesiosaurs. The Class Reptilia was given a rank equivalent to that of the Aves (birds) and Mammalia (mammals), even though the ancestors (and early relatives) of these two groups were considered reptiles. As so defined, however, the Reptilia is not a natural group because it does not include all of its descendants, as the birds and mammals are excluded and each belong to a group of equal rank. Current usage of Reptilia varies. As its traditional concept is so embedded in our thinking, some authors have preferred to abandon it entirely for formal purposes but retain it in its colloquial sense. In this latter meaning, reptile represents a grade that includes coldblooded amniote tetrapods or land-dwelling vertebrates, with scales (lacking hair or feathers); that is, the features we usually associate with living reptiles such as crocodiles, snakes, and lizards. Other authors redefine Reptilia as a formal group that includes the typical reptiles and birds. The more primitive fossil allies of the mammals, termed mammal-like reptiles, are excluded from the Reptilia and properly united with their mammalian descendants in the Synapsida.
The discussion given here provides the basic background information required to interpret cladograms and how they are constructed. For more detailed discussions on cladistics and classification, consult a text in comparative anatomy that provides more detailed explanations of these concepts. Liem et al. (2002) provide a particularly thorough discussion.