Therefore, the tree supported by Bayesian and ML analyses of the molecular partition was used as a topological scaffold in an additional analysis of the morphological partition to determine how this underlying topology influences phylogenetic interpretations of extinct taxa.
These additional analyses of the morphological partition support monophyly of Mysticeti, Balaenoidea, Odontoceti, Physeteroidea, Ziphiidae, Inioidea, Delphinoidea, and Inioidea + Delphinoidea.
JHG collected all new morphological data, analyzed the morphological partition, executed most of the parsimony analyses of the supermatrix including all branch support calculations and character optimizations, conducted all analyses that tested temporal implications, and took the lead in writing the manuscript.
As in an analysis of an earlier version of the morphological partition [ 2], monophyly of Mysticeti, Odontoceti, Inioidea, and Physteridae + Kogiidae (Physeteroidea) was supported.
The supermatrix is characterized by extensive missing data, especially for fossils that can only be coded for a subset of the morphological partition and for none of the molecular characters.
For the present dataset, the addition of the morphological partition improves branch support for the majority of nodes present in both the optimal MP and Bayesian topologies of the combined dataset (Fig. 2; Table 1).
Regarding a minimum age for Synrhina, placement of Notocetus within Platanistoidea is supported by our analysis of the morphological partition with the Bayesian/ML constraint but not our parsimony analysis of the supermatrix.
A Bayesian analysis of the morphological partition also was executed using MrBayes 3.1.2 [ 126].
Bayesian and maximum likelihood (ML) searches were conducted on the molecular partition, and a molecular scaffold obtained from these searches was used to constrain a parsimony search of the morphological partition.
For eight of these, the morphological partition conflicted with all the molecular partitions that contributed clade support.
