Use of spectral analysis to test hypotheses on the origin of pinnipeds

The evolutionary origin of the pinnipeds (seals, sea lions, and walruses)is still uncertain. Most authors support a hypothesis of a monophyleticorigin of the pinnipeds from a caniform carnivore. A minority view suggestsa diphyletic origin with true seals being related to the mustelids (ottersand ferrets). The phylogenetic relationships of the walrus to otherpinniped and carnivore families are also still particularly problematic.Here we examined the relative support for mono- and diphyletic hypothesesusing DNA sequence data from the mitochondrial small subunit (12S) rRNA andcytochrome b genes. We first analyzed a small group of taxa representingthe three pinniped families (Phocidae, Otariidae, and Odobenidae) andcaniform carnivore families thought to be related to them. We inferredphylogenetic reconstructions from DNA sequence data using standardparsimony and neighbor-joining algorithms for phylogenetic inference aswell as a new method called spectral analysis (Hendy and Penny) in whichphylogenetic information is displayed independently of any selected tree.We identified and compensated for potential sources of error known to leadto selection of incorrect phylogenetic trees. These include sampling error,unequal evolutionary rates on lineages, unequal nucleotide compositionamong lineages, unequal rates of change at different sites, andinappropriate tree selection criteria. To correct for these errors, weperformed additional transformations of the observed substitution patternsin the sequence data, applied more stringent structural constraints to theanalyses, and included several additional taxa to help resolve long,unbranched lineages in the tree. We find that there is strong support for amonophyletic origin of the pinnipeds from within the caniform carnivores,close to the bear/raccoon/panda radiation. Evidence for a diphyletic originwas very weak and can be partially attributed to unequal nucleotidecompositions among the taxa analyzed. Subsequently, there is slightly moreevidence for grouping the walrus with the eared seals versus the trueseals. A more conservative interpretation, however, is that the walrus isan early, but not the first, independent divergence from the commonpinniped ancestor.