The geological time scale is based on the evolutionary succession of animal life found as fossils in superposed strata of sedimentary rocks covering large areas of the earth's surface. The Paleo-zoic, Meso-zoic, and Ceno-zoic eras are separated by mass extinctions and associated profound faunal change. Periods, epochs, ages, and biochrons are progressively finer subdivisions of the time scale distinguished by faunal differences and by extinction-origination turnovers of lesser magnitudes. The history of life through geological time is not a smooth and seamless history, but rather an episodic history. Times of turnover, whatever their scale, are critical events, often coming at a juncture of unusual extrinsic-environmental and intrinsic-biotic change, that challenges the survival of species. Those that survive may do so by moving or by changing at evolutionary rates that appear rapid in the context of geological time.
Dinosaurs and other reptiles dominated Mesozoic terrestrial and marine faunas. On land, dinosaurs were replaced by mammals that evolved to dominate succeeding terrestrial Cenozoic faunas. Condylartha or 'archaic ungulates' are common in terrestrial mammalian faunas of the Paleocene epoch, but were largely replaced by modern mammalian orders in the Eocene. In the sea, plesiosaurs, ichthyosaurs, and mosasaurs were replaced by mammals too, but marine mammals are not known from the Paleocene. The reign of dinosaurs, plesiosaurs, ichthyosaurs, and mosasaurs ended with the Mesozoic; mammals crossed the Cretaceous-Tertiary boundary and seemingly took advantage of new opportunities, diversifying broadly on land and eventually invading the sea. Most modern orders of mammals appeared at or near the Paleocene-Eocene boundary, replacing archaic orders from which they probably evolved, and the initial appearance of many orders closely spaced in time may reflect rapid evolution associated with a Paleocene-Eocene turnover event of some kind.
The geological time scale or evolutionary succession of life is calibrated in two ways that yield very different results. The conventional way in geology is to calibrate the evolutionary succession of animal life by finding interbedded crystaline rocks (principally basalts) that can be dated radiometrically (Dalrymple 1991). This assumes that the ejection or capture of energetic electrons in radioactive elements of rock-forming minerals happens randomly and independently of biotic evolution. A new and as yet unproven approach promoted by some biologists is to calibrate the evolutionary succession using molecular genetic differences between pairs of living plants or animals as clocks of divergence time (Zuckerkandl and Pauling 1962, 1965). This assumes that the genetic code changes randomly and independently of biotic evolution, which seems unlikely when development of each new generation depends so directly on the code it inherited.
Calibration of the evolutionary succession of life with molecular clocks is selective, meaning that divergences of animals like mammals that live today can be calibrated independently of faunal context, while divergences of and from animals like dinosaurs that are extinct cannot. This leads to faunal inconsistencies like wholesale overlap of otherwise Cenozoic mammalian orders with Mesozoic dinosaurs (Hedges et al. 1996, Kumar and Hedges 1998). Here we consistently use the geological radiometric time scale rather than molecular clocks to calibrate evolutionary succession. The numbers we use are drawn from the Haq et al. (1987) time scale because sea level change is sometimes important for interpreting shallow marine habitats of whales, but taking numbers from more recent timescales (e.g., Berggren et al. 1995, Gradstein and Ogg 1996, or Hardenbol et al. 1998) would not change our conclusions significantly.
Our focus is on Cetacea. Looking backward from the present, whales, like other mammalian orders, undoubtedly have a pedigree extending back to the earliest mammals known from the Triassic period, and before that to the earliest vertebrates of the Cambrian or Ordovician. The continuity of the cetacean germ line, whether followed backward in time or forward in time, is not in question because individuals propagate new individuals and new species necessarily evolve from old ones. Evolution is first and foremost a history of ancestors and their sometimes-divergent descendants. What in the complex genealogy of mammals makes a whale a whale? What are the characteristics by which whales are recognized? And when did whales first appear in the evolution of mammals?