Cytochrome b and Bayesian inference of whale phylogenyIntroductionMaterials and methodsResultsBayesian analysisPruned Bayesian analysesParsimony analysesDiscussionRecovery of benchmark cladesMonophyly and placement of Mysticeti (baleen whales)Monophyly of Odontoceti (toothed whales)DelphinoidsRiver DolphinsBeaked and sperm whalesConcluding remarksAcknowledgmentsReferencesMolecular Phylogenetics and Evolution 38 (2006) 344–354www.elsevier.com/locate/ympev1055-7903/$ - see front matter  2005 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2005.09.019Cytochrome b and Bayesian inference of whale phylogenyLaura May-Colladoa,b,¤, Ingi Agnarssonc,da Department of Biological Sciences, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USAb Esuela de Biologia, Universidad de Costa Rica, Apto. 2060, San Jose, Costa Ricac The University of British Columbia, Departments of Zoology and Botany, 3529-6270 University Blvd., Vancouver, BC., Canada V6T 1Z4d Systematic Biology-Entomology, E-530, Smithsonian Institution, NHB-105, P.O. Box 37012, Washington, DC 20013-7012, USAReceived 31 March 2005; revised 30 August 2005; accepted 20 September 2005Available online 1 December 2005AbstractIn the mid 1990s cytochrome b and other mitochondrial DNA data reinvigorated cetacean phylogenetics by proposing many noveland provocative hypotheses of cetacean relationships. These results sparked a revision and reanalysis of morphological datasets, and thecollection of new nuclear DNA data from numerous loci. Some of the most controversial mitochondrial hypotheses have now becomebenchmark clades, corroborated with nuclear DNA and morphological data; others have been resolved in favor of more traditionalviews. That major conXicts in cetacean phylogeny are disappearing is encouraging. However, most recent papers aim speciWcally toresolve higher-level conXicts by adding characters, at the cost of densely sampling taxa to resolve lower-level relationships. No molecularstudy to date has included more than 33 cetaceans. More detailed molecular phylogenies will provide better tools for evolutionary studies.Until more genes are available for a high number of taxa, can we rely on readily available single gene mitochondrial data? Here, we esti-mate the phylogeny of 66 cetacean taxa and 24 outgroups based on Cytb sequences. We judge the reliability of our phylogeny based onthe recovery of several deep-level benchmark clades. A Bayesian phylogenetic analysis recovered all benchmark clades and for the Wrsttime supported Odontoceti monophyly based exclusively on analysis of a single mitochondrial gene. The results recover the monophyly ofall but one family level taxa within Cetacea, and most recently proposed super- and subfamilies. In contrast, parsimony never recoveredall benchmark clades and was sensitive to a priori weighting decisions. These results provide the most detailed phylogeny of Cetacea todate and highlight the utility of both Bayesian methodology in general, and of Cytb in cetacean phylogenetics. They furthermore suggestthat dense taxon sampling, like dense character sampling, can overcome problems in phylogenetic reconstruction. 2005 Elsevier Inc. All rights reserved. Keywords: Balaneidae; Cetancodonta; Cetartiodactyla; Delphinidae; Delphinoidea; Euungulata; Iniidae; Missing data; Mitochondrial DNA; Monodenti-dae; Mysticeti; Odontoceti; Monophyly; Perissodactyla; Phocenidae; Platanistidae; Phylogeny; Taxon sampling; Ziphiidae1. IntroductionSeveral issues of Cetacean phylogenetics have beenintensely debated, as a result of independent datasets(morphology, nuclear DNA, and mitochondrial DNA)suggesting conXicting hypotheses. These debates includethe phylogenetic placement of Cetacea as sister to Artio-dactyla (e.g., Luckett and Hong, 1998; O’Leary and Geis-ler, 1999; see also Gingerich et al., 1990) or embeddedwithin Artiodactyla, a clade called Cetartiodactyla (e.g.,Arnason et al., 2004; Gatesy, 1997; Gatesy et al., 1996,1999; Graur and Higgins, 1994; Hasegawa and Adachi,1996; Lum et al., 2000; Matthee et al., 2001; Montgelardet al., 1997; Murphy et al., 2001; Nikaido et al., 1999;Reyes et al., 2004; Shimamura et al., 1999; Thewissen andMadar, 1999; Thewissen et al., 2001), the relationshipbetween toothed whales and baleen whales (e.g., Cerchioand Tucker, 1998; Douzery, 1993; Geisler and Sanders,2003; Luckett and Hong, 1998; Messenger and McGuire,1998; Milinkovitch, 1995, 1997; Milinkovitch et al., 1993,1994, 1995, 1996; Nikaido et al., 2001; Nishida et al.,2003), the relationships among delphinoids (e.g.,*Corresponding author. Fax: +1 305 348 1986.E-mail addresses: [email protected] (L. May-Collado), [email protected] (I. Agnarsson).L. May-Collado, I. Agnarsson / Molecular Phylogenetics and Evolution 38 (2006) 344–354 345Milinkovitch et al., 1993; Nishida et al., 2003; Waddellet al., 2000), dolphins (e.g., Barnes et al., 1985; deMuizon,1988; Fordyce et al., 1994; Kasuya, 1973; LeDuc et al.,1999; Mead, 1975; Perrin, 1989; Pichler et al., 2001), riverdolphins (e.g., Cassens et al., 2000; Cozzuol, 1985;Flower, 1867; Hamilton et al., 2001; Nikaido et al., 2001;Simpson, 1945; Slijper, 1936; Winge, 1921; Yan et al.,2005), and porpoises (Rosel et al., 1995).Since the mid 1990s mitochondrial DNA data have beenat the forefront of advancing understanding of cetacean phy-logenetics (e.g., Arnason et al., 1992, 1993, 2004; Arnason andGullberg, 1993, 1994, 1996; Gatesy et al., 1996; Irwin andArnason, 1994; Graur and Higgins, 1994; Milinkovitch,1995, 1997; Milinkovitch et al., 1993, 1994; Montgelard et al.,1997; Sasaki et al., 2005), for several reasons. MitochondrialDNA is relatively easy to amplify and sequence, it is mostlyfree of problems with paralogy, and it has a relatively highsubstitution rate and thus oVers information at various phy-logenetic levels (Irwin et al., 1991; Milinkovitch, 1997).Results based on mitochondrial DNA oVered novel, oftencontroversial hypotheses (e.g., Arnason and Gullberg, 1994;Irwin and Arnason, 1994; Milinkovitch, 1995; Milinkovitchet al., 1993, 1994) and sparked renewed interest in the recon-struction of the evolutionary history of whales. Some of thesehypothesis such as the placement of Cetacea within Artio-dactyla (Cetartiodactyla sensu Montgelard et al., 1997) (e.g.,Graur and Higgins, 1994; Irwin and Arnason, 1994), and theunexpected hypothesis of the sister relationship of Cetaceaand Hippopotamidae (Cetancodonta sensu Arnason et al.,2000) (see