Phylogenetics is one of two related disciplines within systematics, the study of evolutionary relationships among organisms. The other is taxonomy, the classification of organisms.

The aim of taxonomy is to recognize and name groups of individuals as species, and, subsequently, to group closely related species into the more inclusive taxonomic group of the genus, and so on up through the taxonomic ranks—species, genus, family, order, class, phylum, kingdom, domain. Taxonomy, then, provides us with a hierarchical classification of species in groups that are more and more inclusive, giving us a convenient way to communicate information about the features each group possesses. So, if we want to tell someone about a small animal we have seen with fur, mammary glands, and extended finger bones that permit it to fly, we can give them this long description, or we can just say we saw a bat, or a member of Order Chiroptera. All the rest is understood (or can be looked up in a reference).

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Phylogenetics, on the other hand, aims to discover the pattern of evolutionary relatedness among groups of species or other groups by comparing their anatomical or molecular features, and to depict these relationships as a phylogenetic tree. A phylogenetic tree is a hypothesis about the evolutionary history, or phylogeny, of the species. Phylogenetic trees are hypotheses because they represent the best model, or explanation, of the relatedness of organisms on the basis of all the existing data. As with any model or hypothesis, new data may provide evidence for alternative relationships, leading to changes in the hypothesized pattern of branching on the tree.

Many phylogenetic trees explore the relatedness of particular groups of individuals, populations, or species. We may, for example, want to understand how wheat is related to other, non-commercial grasses, or how disease-causing populations of Escherichia coli relate to more benign strains of the bacterium. At a much larger scale, universal similarities of molecular biology indicate that all living organisms are descended from a single common ancestor. This insight inspires the goal of reconstructing phylogenetic relationships for all species in order to understand how biological diversity has evolved since life originated. This universal tree is commonly referred to as the tree of life (Chapter 1). In Part 2 of this book, we will make use of the tree of life and many smaller-scale phylogenetic trees to understand our planet’s biological diversity.

Fig. 23.2 shows a phylogenetic tree for vertebrate animals. The informal name at the end of each branch represents a group of organisms, many of them familiar. We sometimes find it useful to refer to groups of species this way (for example, “frogs,” or “Class Anura”) rather than name all the individual species or list the characteristics they have in common. It is important, however, to remember that such named groups represent a number of member species. If, for example, we were able to zoom in on the branch labeled “Frogs,” we would see that it consists of many smaller branches, each representing a distinct species of frog, either living or extinct.

This tree provides information about evolutionary relationships among vertebrates. For example, it proposes that the closest living relatives of birds are crocodiles and alligators. The tree also proposes that the closest relatives of all tetrapod (four-legged) vertebrates are lungfish, which are fish with lobed limbs and the ability to breathe air. Phylogenetic trees are built from careful analyses of the morphological and molecular attributes of the species or other groups under study. A tree is therefore a hypothesis about the order of branching events in evolution, and it can be tested by gathering more information about anatomical and molecular traits.

A phylogenetic tree does not in any way imply that more recently evolved groups are more advanced than groups that arose earlier. A modern lungfish, for example, is not more primitive or “less evolved” than an alligator, even though its group branches off the trunk of the vertebrate tree earlier than the alligator group does. After all, both species are the end products of the same interval of evolution since their divergence from a common ancestor more than 370 million years ago.