Chapter 2
Phylogeny, Taxonomy, and Classification
Abstract
Introduction is provided to the basic terminology and concepts involved in systematics and reconstruction of the evolutionary history of marine mammals. The construction of phylogenetic trees is reviewed as are methods for testing phylogenetic hypotheses. Also explored is the application of phylogenetic trees to elucidate evolutionary and ecological patterns using various marine mammal examples. The chapter concludes with presentation of the principles of taxonomy and classification as they relate to marine mammals.
Keywords
Classification; Systematics; Taxonomy
2.1. Introduction: Investigating Evolutionary Histories
The study of biological diversity has at its roots the reconstruction of
phylogeny, the evolutionary history of a particular group of organisms (e.g., species). Knowledge of evolutionary history provides a framework for interpreting biological diversity. This context makes it 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 is also possible to compare the descendants of a single ancestor to look for patterns of origin and extinction or relative size and diversity of these descendant groups. Phylogenies can also be used to test hypotheses of adaptation. For example, consider the evolution of large heads in some of the baleen whales. One hypothesis for how baleen whales evolved such big heads suggests that they facilitated lunge feeding. However, based on a study of allometry, which is the change in the proportion of various body parts as a consequence of growth in whales,
Goldbogen et al. (2010) proposed that the big heads of some baleen whales (e.g., in particular, balaenopterids such as blue and fin whales,
Balaenoptera musculus and
B. physalus) may have evolved for a different function. In this case, large heads may have evolved simply because of an overall expansion of body size, which in turn facilitated the deposition of fat stores required for fasting and long-distance migration. According to this hypothesis, the large heads of these baleen whales may be an
exaptation associated with large body size. 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 large heads in baleen whales requires examination of other characters involved in large body size (see
Chapter 12).
An understanding of the evolutionary relationships among species can also assist in identifying priorities for conservation (
May-Collado and Agnarsson, 2011). For example, the argument for the conservation priority of sperm whales is strengthened by knowing that this major lineage consisting of this single species occupies a key phylogenetic position relative to the other species of toothed whales. This pivotal branch is 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, phylogenies predict current properties of organisms. For example, as discussed by
Promislow (1996), it has been noted that some toothed whales (e.g., pilot whales,
Globicephala spp. and killer whales,
Orcinus orca) 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). Phylogenetic inference predicts that these patterns would hold more generally among other whales and that we should expect other toothed whales to show reproductive aging. We look forward to readers exploring the large-scale patterns of diversification seen in marine mammals as well as hypotheses about processes underlying these patterns.
Finally, the reconstruction of phylogenies provides a useful foundation from which to study other biological patterns and processes. Numerous examples of the use of a phylogenetic tree to consider the evolution of characters among marine mammals exist including the evolution of feeding in pinnipeds (
Adam and Berta, 2002); body size in phocids (
Wyss, 1994); diving capacity in pinnipeds, cetaceans, and sirenians (
Mirceta et al. 2013); large eyes and deep diving in pinnipeds (
Debey and Pyenson, 2013); pinniped recognition behavior (
Insley et al. 2003); pelage coloration in pinnipeds (
Caro et al. 2012); hearing in whales (
Nummela et al. 2004); hindlimb loss in cetaceans (
Thewissen et al. 2006); and suction feeding in cetaceans (
Johnston and Berta, 2011). Male social behavior among cetaceans has also been studied using a phylogenetic approach (
Lusseau, 2003), and
Kaliszewska et al. (2005) explored the population structure of right whales (
Eubalaena spp.) 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 that code for anatomical and physiological features and behavioral traits. Two or more forms of a given character are termed the character states. For example, the character “locomotory pattern” might consist of the states “alternate paddling of the four limbs (quadrupedal paddling),” “paddling using the hindlimbs only (pelvic paddling),” “lateral undulations of the vertebral column and hindlimb (caudal undulation),” or “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 hindlimbs. Later diverging whales modified this feature and show two derived conditions: (1) lateral undulations of the vertebral column and hindlimbs 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, as in the case of molecular phylogenetic trees, patterns 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, called the
sister group. However, 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....