Molecular phylogeny of the Arctoidea (Carnivora): Effect of missing data on supertree and supermatrix analyses of multiple gene data sets

Phylogenetic relationships of 79 caniform carnivores were addressed based on four nuclear sequence-tagged sites (STS) and one nuclear exon, IRBP, using both supertree and supermatrix analyses. We recovered the three major arctoid lineages, Ursidae, Pinnipedia, and Musteloidea, as monophyletic, with Ursidae (bears) strongly supported as the basal arctoid lineage. Within Pinnipedia, Phocidae (true seals) were sister to the Otaroidea [Otariidae (fur seals and sea lions) and Odobenidae (walrus)]. Phocid subfamily and tribal designations were supported, but the otariid subfamily split between fur seals and sea lions was not. All family designations within Musteloidea were strongly supported: Mephitidae (skunks), Ailuridae (monotypic red panda), Mustelidae (weasels, badgers, otters), and Procyonidae (raccoons). A novel hypothesis for the position of the red panda was recovered, placing it as branching after Mephitidae and before Mustelidae + Procyonidae. Within Mustelidae, subfamily taxonomic changes are considered. This study represents the most comprehensive sampling to date of the Caniformia in a molecular study and contains the most complete molecular phylogeny for the Procyonidae. Our data set was also used in an empirical examination of the effect of missing data on both supertree and supermatrix analyses. Sequence for all genes in all taxa could not be obtained, so two variants of the data set with differing amounts of missing data were examined. The amount of missing data did not have a strong effect; instead, phylogenetic resolution was more dependent on the presence of sufficient informative characters. Supertree and supermatrix methods performed equivalently with incomplete data and were highly congruent; conflicts arose only in weakly supported areas, indicating that more informative characters are required to confidently resolve close species relationships.