2.1. Introduction: Systematics—What Is It and Why Do It?

Systematics is the study of biological diversity that has as its emphasis on the reconstruction of phylogeny, the evolutionary history of a particular group of organisms (e.g., species). Systematic knowledge provides a framework for interpreting biological diversity. Because it does this in an evolutionary context it is possible to examine the ways in which attributes of organisms change over time, the direction in which attributes change, the relative frequency with which they change, and whether change in one attribute is correlated with change in another. It also is possible to compare the descendants of a single ancestor to look for patterns of origin and extinction or relative size and diversity of these groups. Systematics also can be used to test hypotheses of adaptation. For example, consider the evolution of the ability to hear high frequency sounds, or echolocation, in toothed whales. One hypothesis for how toothed whales developed echolocation suggests that the lower jaw evolved as a unique pathway for the transmission of high frequency sounds under water. However, based on a study of the hearing apparatus of archaic whales, Thewissen et al. (1996) proposed that the lower jaw of toothed whales may have arisen for a different function, that of transmitting low frequency sounds from the ground, as do several vertebrates including the mole rat. According to this hypothesis, the lower jaw became specialized later for hearing high frequency sound. In this way the lower jaw of toothed whales may be an exaptation for hearing high frequency sounds. An exaptation is defined as any adaptation that performs a function different from the function that it originally held. A more complete understanding of the evolution of echolocation requires examination of other characters involved such as the presence of a melon and the morphology of the middle ear and jaw as well as the bony connections between the ear and skull (see Chapter 11).

An understanding of the evolutionary relationships among species can also assist in identifying priorities for conservation (Brooks et al., 1992). For example, the argument for the conservation priority of sperm whales is strengthened by knowing that this lineage occupies a key phylogenetic position as basal relative to the other species of toothed whales. These pivotal species are of particular importance in providing baseline comparative data for understanding the evolutionary history of the other species of toothed whales. Sperm whales provide information on the origin of various morphological characters that permit suction feeding and the adaptive role of these features in the early evolution of toothed whales.

Perhaps most importantly, systematics predicts properties of organisms. For example, as discussed by Promislow (1996), it has been noted that some toothed whales (e.g., pilot whales and killer whales) that have extended parental care also show signs of reproductive aging (i.e., pregnancy rates decline with increasing age of females), whereas baleen whales (e.g., fin whales) demonstrate neither extended parental care nor reproductive aging (Marsh and Kasuya, 1986). Systematics predicts that these patterns would hold more generally among other whales and that we should expect other toothed whales to show reproductive aging.

Finally, systematics also provides a useful foundation from which to study other biological patterns and processes. Examples of such studies include the coevolution of pinniped parasites and their hosts (Hoberg, 1992, 1995), evolution of locomotion and feeding in pinnipeds (Berta and Adam, 2001; Adam and Berta, 2002), evolution of body size in phocids (Wyss, 1994), evolution of phocid breeding patterns (Perry et al., 1995) and pinniped recognition behavior (Insley et al., 2003), and the evolution of hearing in whales (Nummela et al., 2004). Male social behavior among cetaceans was studied using a phylogenetic approach (Lusseau, 2003), and Kaliszewska et al. (2005) explored the population structure of right whales, based on genetic studies of lice that live in association with these whales.

2.2. Some Basic Terminology and Concepts

The discovery and description of species and the recognition of patterns of relationships among them is founded on the concept of evolution. Patterns of relationships among species are based on changes in the features or characters of an organism. Characters are diverse, heritable attributes of organisms that include DNA base pairs, anatomical and physiological features, and behavioral traits. Two or more forms of a given character are termed the character states. For example, the character “locomotor pattern” might consist of the states “alternate paddling of the four limbs (quadrupedal paddling),” “paddling by the hind limbs only (pelvic paddling),” “lateral undulations of the vertebral column and hind limb (caudal undulation),” and “vertical movements of the tail (caudal oscillation).” Evolution of a character may be recognized as a change from a preexisting, or ancestral (also referred to as plesiomorphic or primitive), character state to a new derived (also referred to as apomorphic) character state. For example, in the evolution of locomotor patterns in cetaceans, the pattern hypothesized for the earliest whales is one in which they swam by paddling with the hind limbs. Later diverging whales modified this feature and show two derived conditions: (1) lateral undulations of the vertebral column and hind limbs and (2) vertical movements of the tail.

The basic tenet of phylogenetic systematics, or cladistics (from the Greek word meaning “branch”), is that shared derived character states constitute evidence that the species possessing these features share a common ancestry. In other words, the shared derived features or synapomorphies represent unique evolutionary events that may be used to link two or more species together in a common evolutionary history. Thus, by sequentially linking species together based on their common possession of synapomorphies, the evolutionary history of those taxa (named groups of organisms) can be inferred.

Relationships among taxonomic groups (e.g., species) are commonly represented in the form of a cladogram, or phylogenetic tree, a branching diagram that conceptually represents the best estimate of phylogeny (Figure 2.1). The lines or branches of the cladogram are known as lineages or clades. Lineages represent the sequence of ancestor-descendant populations through time. Branching of the lineages at nodes on the cladogram represents speciation events, a splitting of a lineage resulting in the formation of two species from one common ancestor. Trees can be drawn to display the branching pattern only or in the case of molecular phylogenetic trees drawn with proportional branch lengths that correspond to the amount of evolution (approximate percentage sequence divergence) between the two nodes they connect.

The task in inferring a phylogeny for a group of organisms is to determine which characters are derived and which are ancestral. If the ancestral condition of a character or character state is established, then the direction of evolution, from ancestral to derived, can be inferred, and synapomorphies can be recognized. The methodology for inferring direction of character evolution is critical to cladistic analysis. Outgroup comparison is the most widely used procedure. It relies on the argument that a character state found in close relatives of a group (the outgroup) is likely also to be the ancestral or primitive state for the group of organisms in question (the ingroup). Usually more than one outgroup is used in an analysis, the most important being the first or genealogically closest outgroup to the ingroup, called the sister group. In many cases, the primitive state for a taxon can be ambiguous. The primitive state can only be determined if the primitive states for the nearest outgroup are easy to identify and those states are the same for at least the two nearest outgroups (Maddison et al., 1984).

Using the previous example, determination of the primitive cetacean locomotor pattern is based on its similarity to that of an extinct relative to the cetaceans, a group of four legged mammals known as the mesonychids (i.e., an outgroup), which are thought to have swam by quadrupedal paddling. Locomotion in whales went through several stages. Ancestral whales (i.e., Ambulocetus) swam by pelvic paddling propelled by the hind limbs only. Later diverging whales (i.e., Kutchicetus) went through a caudal undulation stage propelled by the feet and tail. Finally, extinct dorudontid cetaceans and modern whales adopted caudal oscillation using vertical movements of the tail as their swimming mode (Figure 2.2; Fish, 1993).

Derived characters are used to link monophyletic groups, groups of taxa that consist of a common...