Critics of Charles Darwin's theory of evolution often cited the fossil record's lack of creatures "caught in the act" of evolution. And though fossils had been important to the development of Darwin’s evolutionary thoughts, these absences frustrated him. Read more on strange, inspiring dinosaur fossils in an excerpt from the new book by Brian Switek, Written in Stone. Fossils had been important to the development of Darwin’s evolutionary thoughts. He had collected the bones of many strange fossil mammals from South America during his days voyaging on the Beagle and wondered if there was a connection between animals like the giant ground sloths of prehistory and the continent's modern, arboreal sloths. If sloths, armadillos and other mammals were so different in the ancient past, then obviously life was not static and could change over time. But by 1859 when On the Origin of Species was published, Darwin had largely left paleontology behind. It was up to other researchers to find the fossil proofs of evolutionary change. Many paleontologists agreed with Darwin that some sort of natural laws were behind the succession of different organisms through time discovered in the earth's layers. But many — if not most — were not convinced that natural selection was the driving force behind these changes. Even so, Darwin brought the subject of evolution to the forefront of Victorian science. And with an eye toward evolution, his colleagues began to pick through the traces of ancient life for clues about how organisms changed. This is a gallery of some of the key fossil species that have both confounded and inspired scientists in their efforts to understand the history of life and, placed in context of what we know today, have confirmed Darwin's vision of a branching tree of life produced by natural selection. Image: During his 1876 American lecture tour, T.H. Huxley used this diagram to illustrate how the limbs of dinosaurs (middle) were more similar to those of birds (left) than crocodiles (right)./Written in Stone

Archaeopteryx On the surface, it would seem that Archaeopteryx showed up at just the right time to confirm the gradual evolution of species. The early bird was heralded by some as the sort of creature that proved evolution by tiny tweaks over vast expanses of time. In 1863 the British paleontologist Hugh Falconer wrote to Charles Darwin: "Had the Solenhofen quarries been commissioned — by august command — to turn out a strange being à la Darwin — it could not have executed the behest more handsomely — than in the Archaeopteryx." Apparently half-reptile, half-bird, this creature seemed to be just what Darwin was hoping for, yet he was cautious in his assessment of it. Rather than direct evidence for his theory, Darwin cast Archaeopteryx as an example that there were still mysteries remaining to be uncovered in the fossil record. T.H. Huxley was similarly reserved about the fossil. Though Huxley prominently espoused the hypothesis that birds had evolved from small, dinosaur-like creatures, he considered Archaeopteryx to be a relatively irrelevant side-branch that only showed that the reptile/bird division could be breached without actually playing a direct role in the transition. Darwin and Huxley’s qualms aside, Archaeopteryx became widely regarded as the first bird and played a major role in hypotheses about bird origins since the time of its discovery. Some naturalists connected it to dinosaurs, others to pterosaurs and others to generalized, bipedal cousins of early crocodiles called pseudosuchians. But it was not until 1996 that the discovery of the feathered dinosaur Sinosauropteryx — combined with an increased understanding of dinosaur biology and evolution — confirmed that birds had evolved from a stock of small, feathered dinosaurs. Within the past 10 years, dozens of feathered dinosaurs have been found, and numerous characteristics thought to be unique to birds — from nesting behavior to air sacs which leaves tell-tale marks on skeletons — have been found among dinosaurs. In fact, within this wider context, Archaeopteryx may be better classified as a feathered dinosaur near the ancestry of birds rather than the first bird itself. But even if this turns out to be true it has been a traditionally important part of debates about bird origins for a century and a half. Image: Heilmann, Gerhard. 1926. The Origin of Birds. New York: D. Appleton and Company

Dicynodon During the 1830's a young Scottish man named Andrew Geddes Bain began poking around the rocks in South Africa. There he began finding the skulls of animals which seemed to defy classification, especially a "bidental" animal that had a turtle-like beak between two large tusks. In 1844, Bain sent the skull and other bones back to England where they were described by the eminent anatomist Richard Owen, who identified them as belonging to exceptionally mammal-like reptiles. Soon Owen had seemingly everyone — even Prince Alfred — sending him fossils from the Cape Colony, and he amassed a wide array of reptiles that appeared to be cracking the boundaries of nature in approaching mammals in form. Discoveries of more archaic, but still vaguely mammal-like creatures such as the sail-backed Dimetrodon and Edaphosaurus from the southwestern United States supplemented these finds and were eventually cast as the transitional types between mammals and their reptilian ancestors. Yet these creatures were not truly "mammal-like reptiles." Creatures such as Dimetrodon were certainly reptile-like, but they had already split from the last common ancestor of all reptiles and were more closely related to early mammals than any reptile. Bain's bidental animal, named Dicynodon by Owen, was also one of these reptilian creatures that actually had more in common with early mammals than reptiles. Most of these animals, called synapsids, went extinct by the end of that period in the worst mass extinction of all time. Only a few lineages survived, and it was from one of these, called the cynodonts, that the first mammals eventually originated. For almost 150 million years mammals would not get bigger than a housecat, but after the non-avian dinosaurs became extinct, mammals underwent a massive evolutionary radiation of their own. Image: Owen, R. 1861. Palaeontology. Edinburgh: Adam and Charles Black.

Basilosaurus The discovery of Basilosaurus preceded the publication of Darwin’s famous book by 25 years, yet it would become central to the long-running debate over the origins of whales. First, however, scientists had to recognize that it was actually a whale. In 1834, the Philadelphia naturalist Richard Harlan described a set of bone fragments which had been exhumed from an Alabama judge's plantation. They most closely resembled the bones of the recently described plesiosaurs and ichthyosaurs, and so Harlan tentatively proposed that this animal was the largest marine reptile of all time. He called it Basilosaurus — "king reptile" — in honor of its size. Within a few years, new specimens and a thorough examination of Harlan's fossils by Richard Owen confirmed that the animal was truly a whale, although the name Basilosaurus stuck. It was unlike any whale previously known, especially since it had a formidable set of piercing and shearing teeth in its jaws, and naturalists such as T.H. Huxley used this fact to suggest that whales had evolved from land-dwelling, carnivorous mammals. Frustratingly, though, Basilosaurus was already fully aquatic and provided few clues as to how this transition occurred. The origin of whales remained a mystery until paleontologists began finding the skeletons of the earliest whales in rocks around 40 million years old in Pakistan and India starting in the 1980's. These were not marine mammals, but amphibious whales that walked on land. As more and more fossils have been found, whales have gone from one of the biggest evolutionary mysteries to one of the best examples of large-scale evolutionary change. Thanks to additional finds such as Indohyus, Pakicetus, and Maiacetus we now know that whales are highly specialized hoofed mammals whose closest living relatives are hippos. Basilosaurus was one of the first fully aquatic forms, living between 40 and 34 million years ago, and it ranged from ancient seas preserved today in the rocks of Egypt and Pakistan to the southern United States. Despite living its entire life at sea, though, Basilosaurus still had vestigial hindlimbs that stuck out from its underbelly, and even today many whales have remnants of their hips and legs inside their bodies. Image: Gidley, J.W. 1913. A recently mounted Zeuglodon skeleton in the United States National Museum. Proceedings of the United States National Museum 44: 649-654

Hipparion Shortly after the publication of On the Origin of Species, the French paleontologist Albert Gaudry searched the fauna that lived in Pikermi Greece between 5 and 23 million years ago for mammal fossils. There he found primates, archaic giraffes, saber-toothed cats and other bizarre creatures, but among the most significant fossils were those of a three-toed horse called Hipparion. While Gaudry did not himself agree with natural selection, he used the fossils to draw a branching evolutionary tree of horse evolution, with Hipparion representing an intermediate stage between more ancient ancestors and modern, one-toed horses. Other scientists followed Gaudry's lead in constructing step-by-step sequences of European horse evolution from ancient, tapir-like ancestors through Hipparion to modern Equus. These sequences would later be supplanted by much more complete fossil evidence that showed that horses had evolved in North America. But the trouble was that paleontologists kept finding more horses. A straight-line sequence of horse evolution from tiny Eohippus to modern-day Equus was popularized, but this "missing link" type imagery had to leave out many collateral relatives. While scientific studies of fossil horses are not quite as lively as they used to be, recent work has debunked this straight-line imagery. The story of fossil horse evolution is best understood as a wildly branching bush in which three-toed forms proliferated for tens of millions of years and there were even a few reversals along the way, such as the evolution of dwarf lineages. As is now understood, Hipparion was not a stepping stone to modern horses, but instead was part of a successful and widespread radiation of three-toed horses which were entirely wiped out in the not-too-distant prehistoric past. Image: Matthew, W.D. and Chubb, S.H. 1913. Evolution of the Horse. New York: American Museum of Natural History

Woolly Mammoth Above anything else, the woolly mammoth is an evolutionary icon for its role in proving the truth of extinction. It was interpreted as an underground monster by some of the native people of Siberia and as the remains of wayward elephants from a time when the earth was warmer by European naturalists. In 1796, the French naturalist Georges Cuvier compared their bones to those of living elephants and a bizarre fossil type from America. He showed that the bones of the mammoth were distinct and came from a unique, extinct form of elephant. Combined with the following discoveries of the giant ground sloth Megatherium and the immense seagoing reptile Mosasaurus, the mammoth testified to a very different prehistoric world. Only recently have paleontologists been able to discern the pattern of their evolution. Traditionally, mammoths have been cast as following a straight-line progression with relatively few splits. In a 2005 study, however, woolly mammoths were placed in context of a stop-and-go pattern of evolutionary divergences. The story goes something like this. Around 2.5 million years ago one of the earliest mammoths, Mammuthus meridionalis, began to spread through Asia, but about a million years later a population of these mammoths split off into a new species popularly known as the steppe mammoth (M. trogontherii). The two species coexisted until about 600,000 years ago, by which time the steppe mammoth had largely replaced its ancestor. Like its predecessor, the steppe mammoth traveled widely and was in turn ancestral to two species: the wide-ranging woolly mammoth (M. primigenius) and the Columbian mammoth of North America (M. columbi). These speciation events were abrupt, with the new species occurring rapidly and coexisting alongside other populations of the ancestral species before eventually replacing them on the landscape. (And the splitting didn't stop here. A population of Columbian mammoths which became trapped on California's Santa Rosa island became a unique, dwarf species called M. exilis.) This follows the model of punctuated equilibrium proposed by Stephen Jay Gould and Niles Eldredge in the 1970s, and is one of the best examples of evolutionary patterns in the fossil record. Image: Wikipedia