Cytochrome b and Bayesian inference of whale phylogeny

Laura May-Collado*, Ingi Agnarsson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

117 Citations (Scopus)


In the mid 1990s cytochrome b and other mitochondrial DNA data reinvigorated cetacean phylogenetics by proposing many novel and provocative hypotheses of cetacean relationships. These results sparked a revision and reanalysis of morphological datasets, and the collection of new nuclear DNA data from numerous loci. Some of the most controversial mitochondrial hypotheses have now become benchmark clades, corroborated with nuclear DNA and morphological data; others have been resolved in favor of more traditional views. That major conflicts in cetacean phylogeny are disappearing is encouraging. However, most recent papers aim specifically to resolve higher-level conflicts by adding characters, at the cost of densely sampling taxa to resolve lower-level relationships. No molecular study 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 estimate the phylogeny of 66 cetacean taxa and 24 outgroups based on Cytb sequences. We judge the reliability of our phylogeny based on the recovery of several deep-level benchmark clades. A Bayesian phylogenetic analysis recovered all benchmark clades and for the first time supported Odontoceti monophyly based exclusively on analysis of a single mitochondrial gene. The results recover the monophyly of all but one family level taxa within Cetacea, and most recently proposed super- and subfamilies. In contrast, parsimony never recovered all benchmark clades and was sensitive to a priori weighting decisions. These results provide the most detailed phylogeny of Cetacea to date and highlight the utility of both Bayesian methodology in general, and of Cytb in cetacean phylogenetics. They furthermore suggest that dense taxon sampling, like dense character sampling, can overcome problems in phylogenetic reconstruction.

Original languageEnglish
Pages (from-to)344-354
Number of pages11
JournalMolecular Phylogenetics and Evolution
Issue number2
Publication statusPublished - Feb 2006

Bibliographical note

Funding Information:
We thank Douglas Wartzok, Timothy Collins, Agnar Ingólfsson, Jim McGuire, and an anonymous reviewer for helpful comments on a version of the manuscript. Wayne P. Maddison helped with data analyses and provided computational support. Support for this study came to Laura May-Collado from Tinker Research Opportunities Award, American Natural History Museum (Lener-Gray Award), Animal Behavior Society (Cetacean Behavior and Conservation Award), STRI, Project Aware, Judith Parker Travel Grant, WWF-Russel E. Train Scholarship and Cetacean International Society, and a Killam Postdoctoral Fellowship to Ingi Agnarsson.

Other keywords

  • Balaneidae
  • Cetancodonta
  • Cetartiodactyla
  • Delphinidae
  • Delphinoidea
  • Euungulata
  • Iniidae
  • Missing data
  • Mitochondrial DNA
  • Monodentidae
  • Monophyly
  • Mysticeti
  • Odontoceti
  • Perissodactyla
  • Phocenidae
  • Phylogeny
  • Platanistidae
  • Taxon sampling
  • Ziphiidae


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