Unrooted molecular phylogeny of cetaceans based on nuDNA and mtDNA sequences. The left and right sides show the NJ (under LogDet distances) and MP (under Goloboff fit criterion with k = 2) trees, respectively. Bootstrap values are indicated at the nodes (1,000 and 400 replicates for NJ and MP, respectively). Values between parentheses correspond to bootstrap values (400 replicates) for ML analyses (see Fig. 2 for tree topology). Topology of the MP tree is stable to Goloboff weighting (with k = 0–8). Unweighted MP analysis yielded a tree in which the positions of the sperm whale and [beaked whales + susu] clades are exchanged; these two alternative topologies have tree lengths differing by two evolutionary events and are not significantly different under the Kishino-Hasegawa test. The large and small shaded boxes indicate the radiation of delphinids and the four river dolphin species, respectively. Note that the exact placement of the susu differs between the NJ and MP/ML trees.

ML tree topology (−lnL = 19019.05697) combined with calculated dates of divergences as well as estimates of generic diversity of relevant fossil taxa (gray-shaded boxes). Generic diversity estimates are from ref. 32. Only genera considered stable enough and based on diagnostic material are considered. Numbers of extant species are given between parentheses for each group. Vertical colored boxes indicate habitat: green, specialization in filter feeding (baleen whales); dark blue, specialization for deep feeding on squids (beaked and sperm whales); orange, coastal waters; light blue, oceanic waters; and red, fluvial environment (whereas the boto, baiji, and susu are exclusively riverine, some delphinoid species consist of distinct coastal and fluvial populations). Each horizontal yellow bar indicates twice the value of the standard deviation for the age of the corresponding node. Hence, standard deviations are not referring to the topology of the tree. Dotted triangles indicate the radiation of Delphinidae and concurrent gradual extinction of Waipitiidae, Squalodelphidae, and Squalodontidae. The black arrow at the base of the tree indicates the position of the root when all nu and mt data are used in a simultaneous ML analysis and by using hippopotamus as an outgroup. This result is, however, unstable because several gene fragments support an alternative root, indicated by the white arrow. Whichever of these two rooting hypotheses is correct is irrelevant to the issues discussed and conclusions reached in the present paper. P, Pliocene and p, Pleistocene.