To illustrate how a phylogenetic tree is constructed, consider the eight vertebrate animals listed in Table 21.1: lamprey, perch, salamander, lizard, crocodile, pigeon, mouse, and chimpanzee. We will initially assume that any given derived trait arose only once during the evolution of these animals (that is, there has been no convergent evolution), and that no derived traits were lost from any of the descendant groups (there has been no evolutionary reversal). For simplicity, we have selected traits that are either present (+) or absent (–).

In a phylogenetic study, the group of organisms of primary interest is called the ingroup. As a point of reference, an ingroup is compared with an outgroup: a species or group that is closely related to the ingroup but is known to be phylogenetically outside it. In other words, the root of the tree is located between the ingroup and the outgroup. Any trait that is present in both the ingroup and the outgroup must have evolved before the origin of the ingroup and thus must be ancestral for the ingroup. In contrast, traits that are present in only some members of the ingroup must be derived traits within that ingroup. As we will see in Chapter 32, a group of jawless fish called the lampreys is thought to have separated from the lineage leading to the other vertebrates before the jaw arose. Therefore we have included the lamprey as the outgroup for our analysis. Because derived traits are traits acquired by other members of the vertebrate lineage after they diverged from the outgroup, any trait that is present in both the lamprey and the other vertebrates is judged to be ancestral.

We begin by noting that the chimpanzee and mouse share two traits—mammary glands and fur—that are absent in both the outgroup and in the other species of the ingroup. Therefore we infer that mammary glands and fur are derived traits that evolved in a common ancestor of chimpanzees and mice after that lineage separated from the lineages leading to the other vertebrates. These characters are synapomorphies that unite chimpanzees and mice (as well as all other mammals, although we have not included other mammalian species in this example). By the same reasoning, we can infer that the other shared derived traits are synapomorphies for the various groups in which they are expressed. For instance, keratinous scales are a synapomorphy of the lizard, crocodile, and pigeon.

Table 21.1 also tells us that, among the animals in our ingroup, the pigeon has a unique trait: feathers. Feathers are a synapomorphy of birds and their extinct relatives. However, because we only have one bird in this example, the presence of feathers provides no clues concerning relationships among these eight species of vertebrates. However, gizzards are found in both birds and crocodiles, so this trait is evidence of a close relationship between birds and crocodilians.

By combining information about the various synapomorphies, we can construct a phylogenetic tree. We infer from our information that mice and chimpanzees—the only two animals that share fur and mammary glands—share a more recent common ancestor with each other than they do with pigeons and crocodiles. Otherwise we would need to assume that the ancestors of pigeons and crocodiles also had fur and mammary glands but subsequently lost them. There is no need to make these additional assumptions.

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Figure 21.5 shows a phylogenetic tree for the vertebrates in Table 21.1, based on the shared derived traits we examined. This particular tree was easy to construct because it is based on a very small sample of traits, and the derived traits we examined evolved only once and were never lost after they appeared. Had we included a snake in the group, our analysis would not have been as straightforward. We would have needed to examine additional characters to determine that snakes evolved from a group of lizards that had limbs. In fact, the analysis of many characters shows that snakes evolved from burrowing lizards that became adapted to a subterranean existence.