Skeletal remains of Eocene Archaeoceti provide the only direct and unequivocal evidence of the evolutionary transition of whales from land to sea. Archaeocete skeletons complete enough to be informative about locomotion are rare (principally Rodhocetus and Dorudon), and these deserve to be studied in comparison to the full spectrum of semiaquatic mammals. A principal components analysis of 14 trunk and limb measurements for 50 species of living semiaquatic mammals reduces the observed variation to three informative axes. The first principal axis (PC-I) represents overall size (water mice and shrews have the lowest scores on this axis and the hippopotamus has the highest); the second axis (PC-II) represents a spectrum of aquatic adaptation (seals have the lowest scores and tapirs have the highest); and the third principal axis (PC-III) represents a spectrum ranging from hindlimb- to forelimb-dominated locomotion (sea otters have the lowest scores and the platypus the highest).

Dorudon fits poorly into a morphospace defined solely by living semiaquatic mammals; thus a second 53-species set was analyzed, adding an anthracothere to represent an artiodactyl ancestral morphology and two species of archaeocetes to represent successive stages of early whale evolution. This addition has little effect on the first two principal axes but changes the third substantially. PC-III now represents a contrast of lumbus- (and presumably tail-) dominated versus hindlimb-dominated locomotion (Dorudon has the lowest score and Rodhocetus the highest, whereas the otter shrew has the lowest score among living mammals and the desman the highest). Mammals that are more aquatic have a shorter ilium and femur combined with longer manual and pedal phalanges, whereas the reverse is true for more terrestrial taxa. Lumbus- and tail-dominated swimmers tend to have a longer lumbus combined with shorter pedal elements, whereas the reverse is true for hindlimb-dominated swimmers. Trunk and limb proportions of early middle Eocene Rodhocetus are most similar to those of the living, highly aquatic, foot-powered desmans. Trunk and limb proportions of late middle Eocene Dorudon indicate that it was a lumbus-and-tail-powered swimmer specialized in the direction of modern whales. Thus it appears that the land-to-sea transition in whale evolution involved at least two distinct phases of locomotor specialization: (1) hindlimb domination for drag-based pelvic paddling in protocetids (Rodhocetus), with tail elongation for stability, followed by (2) lumbus domination for lift-based caudal undulation and oscillation in basilosaurids (Dorudon). Rates of evolution in both phases of this change of adaptive zone are about an order of magnitude higher than background rates for the timescale involved.