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Abstract
Cetaceans are remarkable among mammals for their numerous adaptations to an entirely
aquatic existence, yet many aspects of their phylogeny remain unresolved. Here we
merged 37 new sequences from the nuclear genes RAG1 and PRM1 with most published molecular
data for the group (45 nuclear loci, transposons, mitochondrial genomes), and generated
a supermatrix consisting of 42,335 characters. The great majority of these data have
never been combined. Model-based analyses of the supermatrix produced a solid, consistent
phylogenetic hypothesis for 87 cetacean species. Bayesian analyses corroborated odontocete
(toothed whale) monophyly, stabilized basal odontocete relationships, and completely
resolved branching events within Mysticeti (baleen whales) as well as the problematic
speciose clade Delphinidae (oceanic dolphins). Only limited conflicts relative to
maximum likelihood results were recorded, and discrepancies found in parsimony trees
were very weakly supported. We utilized the Bayesian supermatrix tree to estimate
divergence dates among lineages using relaxed-clock methods. Divergence estimates
revealed rapid branching of basal odontocete lineages near the Eocene-Oligocene boundary,
the antiquity of river dolphin lineages, a Late Miocene radiation of balaenopteroid
mysticetes, and a recent rapid radiation of Delphinidae beginning approximately 10
million years ago. Our comprehensive, time-calibrated tree provides a powerful evolutionary
tool for broad-scale comparative studies of Cetacea.