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Summary of the known vertebrate fossil record

(We start off with primitive jawless fish)

Transition from primitive jawless fish to sharks, skates, and rays Late Silurian -- first little simple shark-like denticles.
Early Devonian -- first recognizable shark teeth, clearly derived from scales.
Cladoselache (late Devonian) -- Magnificent early shark fossils, found in Cleveland roadcuts during the construction of the U.S. interstate highways. Probably not directly ancestral to sharks, but gives a remarkable picture of general early shark anatomy, down to the muscle fibers!
Tristychius & similar hybodonts (early Mississippian) -- Primitive proto-sharks with broad-based but otherwise shark-like fins.
Ctenacanthus & similar ctenacanthids (late Devonian) -- Primitive, slow sharks with broad-based shark-like fins & fin spines. Probably ancestral to all modern sharks, skates, and rays. Fragmentary fin spines (Triassic) -- from more advanced sharks.
Paleospinax (early Jurassic) -- More advanced features such as detached upper jaw, but retains primitive ctenacanthid features such as two dorsal spines, primitive teeth, etc.
Spathobatis (late Jurassic) -- First proto-ray.
Protospinax (late Jurassic) -- A very early shark/skate. After this, first heterodonts, hexanchids, & nurse sharks appear (late Jurassic). Other shark groups date from the Cretaceous or Eocene. First true skates known from Upper Cretaceous.
A separate lineage leads from the ctenacanthids through Echinochimaera (late Mississippian) and Similihari (late Pennsylvanian) to the modern ratfish.

Transition from from primitive jawless fish to bony fish
Upper Silurian -- first little scales found.
Acanthodians(?) (Silurian) -- A puzzling group of spiny fish with similarities to early bony fish.
Palaeoniscoids (e.g. Cheirolepis, Mimia; early Devonian) -- Primitive bony ray-finned fishes that gave rise to the vast majority of living fish. Heavy acanthodian-type scales, acanthodian-like skull, and big notochord.
Canobius, Aeduella (Carboniferous) -- Later paleoniscoids with smaller, more advanced jaws.
Parasemionotus (early Triassic) -- "Holostean" fish with modified cheeks but still many primitive features. Almost exactly intermediate between the late paleoniscoids & first teleosts. Note: most of these fish lived in seasonal rivers and had lungs. Repeat: lungs first evolved in fish.
Oreochima & similar pholidophorids (late Triassic) -- The most primitive teleosts, with lighter scales (almost cycloid), partially ossified vertebrae, more advanced cheeks & jaws.
Leptolepis & similar leptolepids (Jurassic) -- More advanced with fully ossified vertebrae & cycloid scales. The Jurassic leptolepids radiated into the modern teleosts (the massive, successful group of fishes that are almost totally dominant today). Lung transformed into swim bladder.
Eels & sardines date from the late Jurassic, salmonids from the Paleocene & Eocene, carp from the Cretaceous, and the great group of spiny teleosts from the Eocene. The first members of many of these families are known and are in the leptolepid family (note the inherent classification problem!).

Transition from primitive bony fish to amphibians
Few people realize that the fish-amphibian transition was not a transition from water to land. It was a transition from fins to feet that took place in the water. The very first amphibians seem to have developed legs and feet to scud around on the bottom in the water, as some modern fish do, not to walk on land (see Edwards, 1989). This aquatic-feet stage meant the fins didn't have to change very quickly, the weight-bearing limb musculature didn't have to be very well developed, and the axial musculature didn't have to change at all. Recently found fragmented fossils from the middle Upper Devonian, and new discoveries of late Upper Devonian feet (see below), support this idea of an "aquatic feet" stage. Eventually, of course, amphibians did move onto the land. This involved attaching the pelvis more firmly to the spine, and separating the shoulder from the skull. Lungs were not a problem, since lungs are an ancient fish trait and were present already.

Paleoniscoids again (e.g. Cheirolepis) -- These ancient bony fish probably gave rise both to modern ray-finned fish (mentioned above), and also to the lobe-finned fish.
Osteolepis (mid-Devonian) -- One of the earliest crossopterygian lobe-finned fishes, still sharing some characters with the lungfish (the other lobe-finned fishes). Had paired fins with a leg-like arrangement of major limb bones, capable of flexing at the "elbow", and had an early-amphibian-like skull and teeth.
Eusthenopteron, Sterropterygion (mid-late Devonian) -- Early rhipidistian lobe-finned fish roughly intermediate between early crossopterygian fish and the earliest amphibians. Eusthenopteron is best known, from an unusually complete fossil first found in 1881. Skull very amphibian-like. Strong amphibian- like backbone. Fins very like early amphibian feet in the overall layout of the major bones, muscle attachments, and bone processes, with tetrapod-like tetrahedral humerus, and tetrapod-like elbow and knee joints. But there are no perceptible "toes", just a set of identical fin rays. Body & skull proportions rather fishlike.
Panderichthys, Elpistostege (mid-late Devonian, about 370 Ma) -- These "panderichthyids" are very tetrapod-like lobe-finned fish. Unlike Eusthenopteron, these fish actually look like tetrapods in overall proportions (flattened bodies, dorsally placed orbits, frontal bones! in the skull, straight tails, etc.) and have remarkably foot-like fins.
Fragmented limbs and teeth from the middle Late Devonian (about 370 Ma), possibly belonging to Obruchevichthys -- Discovered in 1991 in Scotland, these are the earliest known tetrapod remains. The humerus is mostly tetrapod-like but retains some fish features. The discoverer, Ahlberg (1991), said: "It [the humerus] is more tetrapod-like than any fish humerus, but lacks the characteristic early tetrapod 'L-shape'...this seems to be a primitive, fish-like character....although the tibia clearly belongs to a leg, the humerus differs enough from the early tetrapod pattern to make it uncertain whether the appendage carried digits or a fin. At first sight the combination of two such extremities in the same animal seems highly unlikely on functional grounds. If, however, tetrapod limbs evolved for aquatic rather than terrestrial locomotion, as recently suggested, such a morphology might be perfectly workable."
Hynerpeton, Acanthostega, and Ichthyostega (late Devonian) -- A little later, the fin-to-foot transition was almost complete, and we have a set of early tetrapod fossils that clearly did have feet. The most complete are Ichthyostega, Acanthostega gunnari, and the newly described Hynerpeton bassetti (Daeschler et al., 1994). (There are also other genera known from more fragmentary fossils.) Hynerpeton is the earliest of these three genera (365 Ma), but is more advanced in some ways; the other two genera retained more fish- like characters longer than the Hynerpeton lineage did.
Labyrinthodonts (eg Pholidogaster, Pteroplax) (late Dev./early Miss.) -- These larger amphibians still have some icthyostegid fish features, such as skull bone patterns, labyrinthine tooth dentine, presence & pattern of large palatal tusks, the fish skull hinge, pieces of gill structure between cheek & shoulder, and the vertebral structure. But they have lost several other fish features: the fin rays in the tail are gone, the vertebrae are stronger and interlocking, the nasal passage for air intake is well defined, etc.
Coates & Clack (1990) also recently found the first really well- preserved feet, from Acanthostega (front foot found) and Ichthyostega (hind foot found). (Hynerpeton's feet are unknown.) The feet were much more fin-like than anyone expected. It had been assumed that they had five toes on each foot, as do all modern tetrapods. This was a puzzle since the fins of lobe-finned fishes don't seem to be built on a five-toed plan. It turns out that Acanthostega's front foot had eight toes, and Ichthyostega's hind foot had seven toes, giving both feet the look of a short, stout flipper with many "toe rays" similar to fin rays. All you have to do to a lobe- fin to make it into a many-toed foot like this is curl it, wrapping the fin rays forward around the end of the limb. In fact, this is exactly how feet develop in larval amphibians, from a curled limb bud. (Also see Gould's essay on this subject, "Eight Little Piggies".) Said the discoverers (Coates & Clack, 1990): "The morphology of the limbs of Acanthostega and Ichthyostega suggest an aquatic mode of life, compatible with a recent assessment of the fish-tetrapod transition. The dorsoventrally compressed lower leg bones of Ichthyostega strongly resemble those of a cetacean [whale] pectoral flipper. A peculiar, poorly ossified mass lies anteriorly adjacent to the digits, and appears to be reinforcement for the leading edge of this paddle-like limb." Coates & Clack also found that Acanthostega's front foot couldn't bend forward at the elbow, and thus couldn't be brought into a weight-bearing position. In other words this "foot" still functioned as a horizontal fin. Ichthyostega's hind foot may have functioned this way too, though its front feet could take weight. Functionally, these two animals were not fully amphibian; they lived in an in-between fish/amphibian niche, with their feet still partly functioning as fins. Though they are probably not ancestral to later tetrapods, Acanthostega & Ichthyostega certainly show that the transition from fish to amphibian is feasible!

Hynerpeton, in contrast, probably did not have internal gills and already had a well-developed shoulder girdle; it could elevate and retract its forelimb strongly, and it had strong muscles that attached the shoulder to the rest of the body (Daeschler et al., 1994). Hynerpeton's discoverers think that since it had the strongest limbs earliest on, it may be the actual ancestor of all subsequent terrestrial tetrapods, while Acanthostega and Ichthyostega may have been a side branch that stayed happily in a mostly-aquatic niche.

In summary, the very first amphibians (presently known only from fragments) were probably almost totally aquatic, had both lungs and internal gills throughout life, and scudded around underwater with flipper-like, many-toed feet that didn't carry much weight. Different lineages of amphibians began to bend either the hind feet or front feet forward so that the feet carried weight. One line (Hynerpeton) bore weight on all four feet, developed strong limb girdles and muscles, and quickly became more terrestrial.

Transitions among amphibians
Temnospondyls, e.g Pholidogaster (Mississippian, about 330 Ma) -- A group of large labrinthodont amphibians, transitional between the early amphibians (the ichthyostegids, described above) and later amphibians such as rhachitomes and anthracosaurs. Probably also gave rise to modern amphibians (the Lissamphibia) via this chain of six temnospondyl genera , showing progressive modification of the palate, dentition, ear, and pectoral girdle, with steady reduction in body size (Milner, in Benton 1988). Notice, though, that the times are out of order, though they are all from the Pennsylvanian and early Permian. Either some of the "Permian" genera arose earlier, in the Pennsylvanian (quite likely), and/or some of these genera are "cousins", not direct ancestors (also quite likely).
Dendrerpeton acadianum (early Penn.) -- 4-toed hand, ribs straight, etc.
Archegosaurus decheni (early Permian) -- Intertemporals lost, etc.
Eryops megacephalus (late Penn.) -- Occipital condyle splitting in 2, etc.
Trematops spp. (late Permian) -- Eardrum like modern amphibians, etc.
Amphibamus lyelli (mid-Penn.) -- Double occipital condyles, ribs very small, etc.
Doleserpeton annectens or perhaps Schoenfelderpeton (both early Permian) -- First pedicellate teeth! (a classic trait of modern amphibians) etc.

From there we jump to the Mesozoic:

Triadobatrachus (early Triassic) -- a proto-frog, with a longer trunk and much less specialized hipbone, and a tail still present (but very short).
Vieraella (early Jurassic) -- first known true frog.
Karaurus (early Jurassic) -- first known salamander.

Transition from amphibians to amniotes (first reptiles)
The major functional difference between the ancient, large amphibians and the first little reptiles is the amniotic egg. Additional differences include stronger legs and girdles, different vertebrae, and stronger jaw muscles. For more info, see Carroll (1988) and Gauthier et al. (in Benton, 1988)
Proterogyrinus or another early anthracosaur (late Mississippian) -- Classic labyrinthodont-amphibian skull and teeth, but with reptilian vertebrae, pelvis, humerus, and digits. Still has fish skull hinge. Amphibian ankle. 5-toed hand and a 2-3-4-5-3 (almost reptilian) phalangeal count.
Limnoscelis, Tseajaia (late Carboniferous) -- Amphibians apparently derived from the early anthracosaurs, but with additional reptilian features: structure of braincase, reptilian jaw muscle, expanded neural arches.
Solenodonsaurus (mid-Pennsylvanian) -- An incomplete fossil, apparently between the anthracosaurs and the cotylosaurs. Loss of palatal fangs, loss of lateral line on head, etc. Still just a single sacral vertebra, though.
Hylonomus, Paleothyris (early Pennsylvanian) -- These are protorothyrids, very early cotylosaurs (primitive reptiles). They were quite little, lizard-sized animals with amphibian-like skulls (amphibian pineal opening, dermal bone, etc.), shoulder, pelvis, & limbs, and intermediate teeth and vertebrae. Rest of skeleton reptilian, with reptilian jaw muscle, no palatal fangs, and spool-shaped vertebral centra. Probably no eardrum yet. Many of these new "reptilian" features are also seen in little amphibians (which also sometimes have direct-developing eggs laid on land), so perhaps these features just came along with the small body size of the first reptiles.
The ancestral amphibians had a rather weak skull and paired "aortas" (systemic arches). The first reptiles immediately split into two major lines which modified these traits in different ways. One line developed an aorta on the right side and strengthened the skull by swinging the quadrate bone down and forward, resulting in an enormous otic notch (and allowed the later development of good hearing without much further modification). This group further split into three major groups, easily recognizable by the number of holes or "fenestrae" in the side of the skull: the anapsids (no fenestrae), which produced the turtles; the diapsids (two fenestrae), which produced the dinosaurs and birds; and an offshoot group, the eurapsids (two fenestrae fused into one), which produced the ichthyosaurs.

The other major line of reptiles developed an aorta on left side only, and strengthened the skull by moving the quadrate bone up and back, obliterating the otic notch (making involvement of the jaw essential in the later development of good hearing). They developed a single fenestra per side. This group was the synapsid reptiles. They took a radically different path than the other reptiles, involving homeothermy, a larger brain, better hearing and more efficient teeth. One group of synapsids called the "therapsids" took these changes particularly far, and apparently produced the mammals.

Some transitions among reptiles
I will review just a couple of the reptile phylogenies, since there are so many.... Early reptiles to turtles: (Also see Gaffney & Meylan, in Benton 1988)
Captorhinus (early-mid Permain) -- Immediate descendent of the protorothryids.
Here we come to a controversy; there are two related groups of early anapsids, both descended from the captorhinids, that could have been ancestral to turtles. Reisz & Laurin (1991, 1993) believe the turtles descended from procolophonids, late Permian anapsids that had various turtle-like skull features. Others, particularly Lee (1993) think the turtle ancestors are pareiasaurs:

Scutosaurus and other pareiasaurs (mid-Permian) -- Large bulky herbivorous reptiles with turtle-like skull features. Several genera had bony plates in the skin, possibly the first signs of a turtle shell.
Deltavjatia vjatkensis (Permian) -- A recently discovered pareiasaur with numerous turtle-like skull features (e.g., a very high palate), limbs, and girdles, and lateral projections flaring out some of the vertebrae in a very shell-like way. (Lee, 1993)
Proganochelys (late Triassic) -- a primitive turtle, with a fully turtle-like skull, beak, and shell, but with some primitive traits such as rows of little palatal teeth, a still-recognizable clavicle, a simple captorhinid-type jaw musculature, a primitive captorhinid- type ear, a non-retractable neck, etc..
Recently discovered turtles from the early Jurassic, not yet described.
Mid-Jurassic turtles had already divided into the two main groups of modern turtles, the side-necked turtles and the arch-necked turtles. Obviously these two groups developed neck retraction separately, and came up with totally different solutions. In fact the first known arch-necked turtles, from the Late Jurassic, could not retract their necks, and only later did their descendents develop the archable neck. Early reptiles to diapsids: (see Evans, in Benton 1988, for more info)
Hylonomus, Paleothyris (early Penn.) -- The primitive amniotes described above
Petrolacosaurus, Araeoscelis (late Pennsylvanian) -- First known diapsids. Both temporal fenestra now present. No significant change in jaw muscles. Have Hylonomus-style teeth, with many small marginal teeth & two slightly larger canines. Still no eardrum.
Apsisaurus (early Permian) -- A more typical diapsid. Lost canines. (Laurin, 1991)
Claudiosaurus (late Permian) -- An early diapsid with several neodiapsid traits, but still had primitive cervical vertebrae & unossified sternum. probably close to the ancestry of all diapsides (the lizards & snakes & crocs & birds).
Planocephalosaurus(early Triassic) -- Further along the line that produced the lizards and snakes. Loss of some skull bones, teeth, toe bones.
Protorosaurus, Prolacerta (early Triassic) -- Possibly among the very first archosaurs, the line that produced dinos, crocs, and birds. May be "cousins" to the archosaurs, though.
Proterosuchus (early Triassic) -- First known archosaur.
Hyperodapedon, Trilophosaurus (late Triassic) -- Early archosaurs.

Some species-to-species transitions:
De Ricqles (in Chaline, 1983) documents several possible cases of gradual evolution (also well as some lineages that showed abrupt appearance or stasis) among the early Permian reptile genera Captorhinus, Protocaptorhinus, Eocaptorhinus, and Romeria.
Horner et al. (1992) recently found many excellent transitional dinosaur fossils from a site in Montana that was a coastal plain in the late Cretaceous. They include:
-Many transitional ceratopsids between Styracosaurus and Pachyrhinosaurus
-Many transitional lambeosaurids (50! specimens) between Lambeosaurus and Hypacrosaurus.
-A transitional pachycephalosaurid between Stegoceras and Pachycephalosaurus
-A transitional tyrannosaurid between Tyrannosaurus and Daspletosaurus.
All of these transitional animals lived during the same brief 500,000 years. Before this site was studied, these dinosaur groups were known from the much larger Judith River Formation, where the fossils showed 5 million years of evolutionary stasis, following by the apparently abrupt appearance of the new forms. It turns out that the sea level rose during that 500,000 years, temporarily burying the Judith River Formation under water, and forcing the dinosaur populations into smaller areas such as the site in Montana. While the populations were isolated in this smaller area, they underwent rapid evolution. When sea level fell again, the new forms spread out to the re-exposed Judith River landscape, thus appearing "suddenly" in the Judith River fossils, with the transitional fossils only existing in the Montana site. This is an excellent example of punctuated equilibrium (yes, 500,000 years is very brief and counts as a "punctuation"), and is a good example of why transitional fossils may only exist in a small area, with the new species appearing "suddenly" in other areas. (Horner et al., 1992) Also note the discovery of Ianthosaurus, a genus that links the two synapsid families Ophiacodontidae and Edaphosauridae. (see Carroll, 1988, p. 367)