Craniata and Vertebrata

The vertebrates or Vertebrata form an ancient group with a history spanning some 545 million years. On the one hand, they include the organisms most familiar to us, such as fish, birds, cats and dogs, as well as humans; on the other, few people are aware of the great diversity in their form, structure, and habits. Indeed, they include some of the largest and more complex organisms ever evolved. But vertebrates are part of a larger grouping of animals, and to understand their history and the development of their structure, they must be placed in phylogenetic context.

In discussing vertebrates, several other groups of organisms are usually considered. A monophyletic or natural group (see later) of organisms is referred to as a taxon (plur., taxa). The taxa related (in terms of recent common ancestry) to vertebrates include Echinodermata (sand dollars, sea lilies, star fish, sea cucumbers, urchins), Hemichordata (acorn worms and pterobranchs), Urochordata (tunicates or sea squirts), and Cephalochordata (amphioxus). These are the typical nonvertebrate (or “invertebrate”) relatives of the group in which we are mainly interested. The vertebrates themselves, or Vertebrata, are included in a larger taxon termed Craniata. Within Craniata and Vertebrata are many taxa. These taxa and the evolutionary relationships among them (see Figure 1.1) are briefly outlined here to provide an organizational framework for undertaking the dissection of the vertebrates discussed in this manual. Before this, however, it is necessary to present an explanation of several important terms used in discussions of phylogeny. Phylogeny refers to the pattern of descent among taxa. It describes, in other words, the evolutionary or genealogical relationships among them. Evolution is a historical (and on-going) process. Therefore, the evolution of organisms occurred in only one way—for example, humans and chimpanzees are, among living creatures, either each other’s closest relatives (they share a common ancestor not shared by other organisms) or they are not. Only one of these possibilities is correct. Evolutionary biologists try to recover the pattern of descent based on the data they have available to them. Phylogenies are therefore hypotheses that approximate the true pattern of descent. As hypotheses, they are testable and thus open to falsification when new data become available. If a hypothesis is falsified, then another one may be proposed—for example, new evidence might show that humans share a recent common ancestor with a different great ape than chimpanzees, such as orangutans.

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 Urochordata and Cephalochordata as phyla on their own, separate from Chordata. Still others have viewed Urochordata as a separate phylum, but 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 had a fundamentally different basic body plan than if it was 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 (except for the preceding paragraph, in which ranks were used to reflect the historical understanding of the groups).

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 later). 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). 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.1 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 ancestor species that split to produce two lineages, one that evolved into Chordata and the other into 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 Cephalochordata and Craniata occurred after the divergence of 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 plesiomorphic, refers to similarity based on presence of ancestral conditions or states. Consider the Vertebrata, in which the presence of vertebrae is an ancestral feature—in...