ABSTRACT
Phylogenetic analysis of 14 cetacean species, including members from two baleen whale families and three toothed whale families, was undertaken using restriction site mapping of mitochondrial DNA and using cladistic and distance measures to infer phylogenies. The amount of between-taxa sequence divergence inferred from the data was lower than expected from the standard interpretation of the fossil record, but more consistent with some recent estimates of sequence divergence in cetacean mitochondrial DNA or nuclear DNA. This implies either that the rate of molecular evolution of cetacean DNA is much lower than that of other mammalian orders or that the fossil record of cetaceans requires reinterpretation. The incompleteness of the cetacean fossil record precludes resolution of the paradox at the present time. However, this discrepancy could in part be attributed to the sampling error inherent in the restriction site mapping technique, as comparative studies using the complete mtDNA genome and restriction site data of the blue and fin whales (genus Balaenoptera) indicate that the restriction site maps underestimate sequence divergence by about 40%. In contrast to a recent study suggesting that toothed whales were paraphyletic, with the sperm whales being more closely related to the rorquals than to the other toothed whales, the restriction data tend to support the monophyly of the baleen and the toothed whales, a finding which is consistent with a recent molecular-based study and with morphological and paleontological data. Topologies of the subfamily and generic levels are generally consistent with morphologically based schemes.
