For over two hundred years the subject of vertebrate paleontology—the study of ancient vertebrates (animals with backbones) and their nearest relatives—has been popular among the lay public. Everyone seems to have a certain fascination with gigantic bones of extinct animals, be they mastodons or dinosaurs. The discovery of a “new” early hominid skull that bears on the evolution of humans can still make front-page headlines around the globe. In a very real sense, the field of vertebrate paleontology has helped shape the way that modern humans think about themselves and the world around them. Vertebrate paleontology, in a literal sense, has helped elucidate humankind's place in nature, especially within the larger context of life on planet Earth through the last four billion years.

The origin of the Craniata (hagfish + Vertebrata [Vertebrata = lamprey + Gnathostoma]—Janvier, 1981), one of the three subphyla of the Phylum Chordata, has generated more controversy in terms of numbers of likely ancestors than the origin of any other metazoan group. The primary difficulty with the origin of craniates, as opposed to the origin of birds, for example, is the bauplan dichotomy that separates craniates from all other “invertebrates.” This dichotomy results in the almost equal plausibility of deriving craniates from any “invertebrate” ancestor. The first attempt at trying to understand the bauplan differences between “invertebrates” and craniates was by Geoffroy St. Hilaire in 1822, who envisioned craniates as arthropods lying on their backs. Since then, many bilaterian phyla have been hypothesized as either direct ancestors or sister groups to the craniates with some recent notable examples being: arthropods (Raw, 1960); nemertines (Willmer, 1975); molluscs (Sillman, 1960; Løvtrup, 1977); urochordates (Jefferies, 1986); and cephalochordates (Gans and Northcutt, 1983).

All living organisms possess mechanisms for obtaining nutrition. Many invertebrates also possess movable mouthparts capable of capturing prey or particulate food (e.g., polychaetes, cephalopods, arthropods and echinoderms). All living vertebrates have specialized mouthparts, and as far as we know all fossil agnathans had them also, but movable jaws supported by an internal skeleton are absent in living and fossil agnathans.

Bony fishes or osteichthyans comprise two main monophyletic groups: the actinopterygians (rayfins, including the staples of the fish market and aquarium) and sarcopterygians (lobefins, fringefins or tasselfins, including lungfishes, coelacanths, and, perhaps unexpectedly or inconveniently, all land vertebrates or tetrapods). In the broadest terms, the two groups have similar histories, each with beginnings in the late Silurian or earliest Devonian, each with a primary radiation in the late Devonian and Mississippian, a secondary radiation in the Mesozoic, and a major Tertiary radiation, and each with an extant diversity of roughly 25,000 species (Nelson, 1994, p. 2). The remainder of this course (eight topics) is devoted to sarcopterygians, so I shall give almost all my space to the other half of bony fish diversity, the actinopterygians.

The origin of tetrapods is one of the longest standing (and still not fully resolved) fields in vertebrate evolution (Thomson, 1993). The discovery of living lungfishes in the nineteenth century sparked interest because of their apparent intermediate position between other kinds of fishes and amphibians. (As is well known, the South American lungfish Lepidosiren was actually first described as a degenerate amphibian.) The discovery of the Australian lungfish provided a direct link between a living form (a “living fossil” to use Darwin's term) and well-known Triassic fossils. The lungfishes therefore accorded well with Darwinian theory, just as did Archaeopteryx. The discovery of the living coelacanth Latimeria in 1938 continues to spark public interest (Thomson, 1991a).

Fossils conventionally classified as amphibians comprise a diverse, paraphyletic assemblage of roughly 15 distinctive lineages (=clades; Figure 1) of non–amniote tetrapods whose phylogenetic interrelationships continue to defy resolution (Carroll, 1992; Figure 2). The historical accumulation of morphological data, new paleontological discoveries, better understanding of characters and transformation series, and refinement of rigorous cladistic analytical methodology have stimulated a resurgence of interest in the phylogenetics of early tetrapods (Bolt, 1991; Bolt and Lombard, 1991; Clack, 1988, 1991; Duellman, 1988; Gauthier et al., 1988b; Lombard and Bolt, 1988; Milner, 1988, 1990, 1993; Panchen, 1991; Panchen and Smithson, 1987, 1988; Smithson, 1985; Trueb and Cloutier, 1991a, 1991b). However, most investigations have done little more than substantiate the distinctiveness of the major non–amniote tetrapod clades and clarify within–clade relationships. Differences in parsimony between alternative phylogenies proposed for the early lineages are generally too minor to consider any as strongly corroborated (Carroll, 1990, 1992; e.g. Panchen and Smithson, 1988).

Publication of the English-language version of Hennig's (1966) Phylogenetic Systematics marked a turning point in the history of inquiry into the genealogy of life. Hennig catalyzed a long overdue reevaluation of systematic theory and method that should have followed immediately upon publication of Darwin's revolutionary ideas (de Queiroz, 1988). Hennig revitalized the field by taking the Theory of Descent to the core of systematics (de Queiroz, 1988, 1992)—the methods for investigating life's genealogy—and taxonomy—the methods for communicating the results of those investigations (de Queiroz and Gauthier, 1992). Unfortunately, the Darwinian revolution has yet to sweep aside all vestiges of nonevolutionary thinking in this field. To further that goal, and to provide an update of Gauthier et al. (1989), this contribution summarizes current progress in the phylogeny and taxonomy of the major clades of land-egg-laying, or amniote, vertebrates.

In recent years, one of the most exciting and important revelations in all of paleontology has been clarification of many of the details surrounding the question of the origin of birds. This has been a persistant enigma for centuries. Today, it is perhaps the hottest topic among challenges before us and it appears closer to a near unanimous opinion than ever before.

No area of paleontology has changed more in recent years than the history of birds, both during the Mesozoic Era and the Tertiary Period. The most controversial issue in the study of birds for several decades has been their origin, and the origin of avian flight and feathers, and clearly too much emphasis has been placed on the earliest known bird, the late Jurassic Archaeopteyx, an arboreal form that was already well on its way to becoming a modern bird (Feduccia, 1993a). Over the past two decades this urvögel has mistakenly been characterized as an earth-bound, feathered theropod, and a number of rather bizarre scenarios have been envisioned to account for the origin of flight and feathers in birds. However, the debate has centered on two main themes. Were birds derived directly from small, bipedal theropod dinosaurs (Ostrom, 1991), and therefore evolved via the scenario of the cursorial (ground-up) theory (Ostrom, 1986); or were they derived earlier in time from small, arboreal “thecodonts” or basal archosaurs, and therefore evolved via the scenario of the arboreal (trees-down) theory (Bock, 1986; Martin, 1991; Feduccia and Wild, 1993).

The Synapsida is the mammal-like ramus of the Amniota, the sister group of the Sauropsida (or Reptilia of Gauthier et al., 1988). Synapsids are characterized by the possession of a lateral temporal fenestra (Fig. 1A), among other features (see Gauthier, this volume). Of all the great transitions between major structural grades within vertebrates, the transition from basal amniotes to basal mammals is represented by the most complete and continuous fossil record, extending from the Middle Pennsylvanian to the Late Triassic and spanning some 75 to 100 million years. Structural evolution of particular functional systems has been well investigated, notably the feeding mechanism (Barghusen, 1968; Crompton, 1972; Crompton and Parker, 1978; Crompton and Hylander, 1986) and the middle ear (Hopson, 1966; Allin, 1975, 1986; Allin and Hopson, 1992), and these studies have demonstrated the gradual nature of these major adaptive modifications.

The placental or eutherian mammals comprise about twenty living orders and several extinct ones. The morphological and adaptive range of this group is extraordinary; diversification has produced lineages as varied as humans and their primate relatives, flying bats, swimming whales, ant-eating anteaters, pangolins and aardvarks, a baroque extravagance of horned, antlered, and trunk-nosed herbivores (ungulates), as well as the supremely diverse rats, mice, beavers and porcupines of the order Rodentia. Such adaptive diversity, and the emergence of thousands of living and fossil species, apparently resulted from a radiation beginning in the late Mesozoic between 65 and 80 million years ago (Novacek, 1990). This explosive radiation (Figure 1) is one of the more intriguing chapters of vertebrate history, and the problem has attracted interest from unusually varied perspectives. As a result, eutherian mammals are known from a rapidly growing molecular database, as well as a wealth of morphological characters and a comparatively enriched fossil record. The interplay of molecular and morphological investigation is more apparent in the case of placental mammals that in any other vertebrates, perhaps more than in any other group of organisms.

The evolution of certain mammalian lineages has become the favorite examples of nearly every introductory textbook in historical geology, paleontology, and evolutionary biology. The evolution of the horse is the most frequently used, since it emerged in 1851 and has been reproduced many times in nearly 150 years (see Gould, 1987, and MacFadden, 1992). Occasionally, one sees a revival of one of Osborn's (1929) evolutionary sequences of brontotheres, and some books may show a sequence of mammoths and mastodonts. In most historical geology books, the discussion of fossil mammals usually consists of just these selected examples, since the authors seem to think that a fuller account of Cenozoic mammal evolution is beyond the level of their readers. Children's books, trade books, and museum displays typically show little more than the evolution of the horse and few selected pictures of spectacular beasts such as saber-toothed cats, ground sloths, mammoths, and the gigantic hornless rhinoceros Paraceratherium (called by the obsolete names Baluchitherium or Indricotherium in virtually every caption). Given these conditions, one cannot fault students or the general public for thinking that only horses have a good fossil record, or that there are no other well-studied groups of fossil mammals.