Abstract

The phylogenetic position of Cetacea (whales, dolphins and porpoises) is an important exemplar problem for combined data parsimony analyses because the clade is ancient and includes many well-known and relatively complete fossil species. We combined molecular and morphological data for 71 terminal taxa (43 extinct/28 extant) to test where Cetacea fits within Cetartiodactyla, and where various fossil hoofed mammals (e.g., entelodonts, anthracotheriids, and mesonychians) are positioned. The taxon sample included representatives of most living families of cetaceans, artiodactylans, and perissodactylans, and almost 50% of wholly extinct families of artiodactylans. We scored 635 phenotypic characters (osteology, dentition, soft tissue, behavior), approximately three times the number of characters in the last major analysis of this clade, and combined these with >40,000 molecular characters, including new data from ten genes. The combined analysis supported a topology consistent with the majority of recently published molecular studies. In all most parsimonious trees: Cetacea was the extant sister taxon of Hippopotamidae, followed successively by Ruminantia, Suina and Camelidae. Several extinct taxa were phylogenetically unstable, upsetting resolution of the strict consensus and limiting branch support, but the positions of several key fossils were consistently resolved. The wholly extinct Mesonychia was more closely related to Cetacea than was any artiodactylan. Anthracotheriids were paraphyletic, and, with the exception of one species, were more closely related to Hippopotamidae than to any other living taxon. Taxa classified as triisodontids, entelodonts and helohyids also clustered on the stem lineage of Hippopotamidae. The character partition that could be scored for the fossil taxa (osteological and dental characters) included more informative characters than most molecular partitions in our analysis, and had the fewest missing data by a large margin. The osteological-dental data alone, however, did not support inclusion of cetaceans within crown Artiodactyla. In the context of our combined analysis, recently discovered ankle bones from early fossil whales broadly reinforced the monophyly of Cetartiodactyla but provided no particular evidence of derived similarities between hippopotamids and fossil cetaceans that were not shared with other artiodactylans.