The Phylogenetic Position of Cetaceans: Further Combined Data Analyses, Comparisons with the Stratigraphic Record and a Discussion of Character Optimization

A recent total evidence analysis of the position of cetaceans(whales, dolphins and porpoises and extinct relatives) amongmammals indicated that the phylogeny of these taxa remains poorlyresolved. Molecular data show that 1) the order Artiodactyla(even-toed ungulates) is paraphyletic unless whales are includedwithin it and 2) that the traditional relationships of cladeswithin Artiodactyla are not supported. This controversy alsoaffects the position of a wholly extinct clade, Mesonychia,which has been argued to be the group of terrestrial mammalsmost closely related to whales. Here I update a previous totalevidence analysis by adding several hundred new informativemolecular characters from the literature. Even with the additionof these characters the phylogeny remains unresolved. All mostparsimonious trees, however, indicate a paraphyletic Artiodactylawith conflict existing over the exact sister taxon of Cetacea.Congruence between different equally parsimonious cladogramsand the stratigraphic record as measured using the modifiedManhattan Stratigraphic Measure shows that all of the competingtopologies, including those with a paraphyletic Artiodactyla,are significantly congruent with the stratigraphic record. Infossil taxa cladistic optimization can be used as an alternativeto "argument from design" (Lauder, 1996) to reconstruct behaviorand soft tissues that do not fossilize or osteological charactersthat have not preserved. In certain scenarios of cetacean phylogeny,optimization indicates that taxa such as the archaic whalesAmbulocetus and Pakicetus, and possibly mesonychians, are morecorrectly reconstructed without hair.