Phylogenetics of Baleen Whales


At present, there are 15 species of baleen whales that belong to the monophyletic suborder Mysticeti. The family‐level designations of Balaenidae (right and bowhead whales) and Neobalaenidae (pygmy right whales) are strongly supported and well resolved. However, family‐level designations and inter‐relationships among the remaining species and genera of Balaenopteridae (rorquals) and Eschrichtiidae (grey whales) are less well resolved. Taxonomic relationships vary between studies, reconstruction methods and marker types, despite strong morphological support for the placement of Eschrichtiidae as a sister group to the Balaenopteridae. This phylogenetic uncertainty appears to have originated from a rapid Miocene radiation of both families, which has resulted in incomplete sorting of genetic lineages and therefore conflicting phylogenetic signals among nuclear and mitochondrial loci. The earliest radiation of baleen whales (suborder Mysticeti) occurred in the Late Eocene. The fossil record of subsequent species diversifications has been strongly correlated with changes in fossil diatom diversity and isotopic oxygen levels over time.

Key Concepts:

  • The monophyletic suborder Mysticeti is composed of four families and 15 species of baleen whales.

  • Mysticete families Balaenidae and Neobalaenidae are strongly supported and well resolved.

  • Molecular genetic support for inter‐species relationships within and between Balaenopteridae and Eschrichtiidae is poorly resolved and suggests a rapid Miocene radiation of lineages at the origin of these families.

Keywords: baleen whales; Mysticeti; Balaenoptera; phylogeny; divergence times; fossil; calibration point; evolution

Figure 1.

A mysticete baleen comb. Copyright © 2007 David Monniaux.

Figure 2.

Phylogenetic hypotheses of evolutionary relationships among baleen whales. Studies supporting various evolutionary relationships (referred to by clade number) are summarised in Table . Phylogeny shown is as summarised by McGowen et al. . Cetacean illustrations copyright © Leaper and Miller.



Árnason Ú, Grétarsdóttir S and Widegren B (1992) Mysticete (baleen whale) relationships based on the sequence of the common cetacean DNA satellite. Molecular Biology and Evolution 9(6): 1018–1028.

Árnason U, Gullberg A and Janke A (2004) Mitogenomic analyses provide new insights into cetacean origin and evolution. Gene 333: 27–34.

Baker CS and Medrano‐González L (2002) Worldwide distribution and diversity of humpback whale mitochondrial DNA lineages. In: Pfeiffer CJ (ed.) Molecular and Cell Biology of Marine Mammals, pp. 84–99. Malabar, FL: Krieger Publishing Company.

Berger WH (2007) Cenozoic cooling, Antarctic nutrient pumps and the evolution of whales. Deep Sea Research. Part II, Topical Studies in Oceanography 54: 2399–2421.

Berubé M and Aguilar A (1998) A new hybrid between a blue whale, Balaenoptera musculus, and a fin whale, B. physalus: frequency and implications of hybridization. Marine Mammal Science 14(1): 82–98.

Bouetel V (2005) Phylogenetic implications of skull structure and feeding behavior in balaenopterids (Cetacea, Mysticeti). Journal of Mammalogy 86(1): 139–146.

Branch TA, Stafford KM, Palacios DM et al. (2007) Past and present distribution, densities and movements of blue whales Balaenoptera musculus in the Southern Hemisphere and northern Indian Ocean. Mammal Review 37(2): 116–175.

Cooper A and Fortey R (1998) Evolutionary explosions and the phylogenetic fuse. Trends in Ecology & Evolution 13: 151–156.

Deméré TA, Berta A and McGowen MR (2005) The taxonomic and evolutionary history of fossil and modern balaenopterid mysticetes. Journal of Mammalian Evolution 12(1/2): 99–143.

Deméré TA, McGowen MR, Berta A et al. (2008) Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales. Systematic Biology 57(1): 15–37.

Drummond AJ, Ho SYW, Phillips MJ et al. (2006) Relaxed phylogenies and dating with confidence. PLoS Biology 4(5): 699–710.

Fordyce RE (1980) Whale evolution and Oligocene southern ocean environments. Palaeogeography, Palaeoclimatology, Palaeoecology 31: 319–336.

Fordyce RE (1992) Cetacean evolution and Eocene/Oligocene environments. In: Prothero DR and Berggren WA (eds) Eocene‐Oligocene Climatic and Biotic Evolution, pp. 368–381. Princeton, NJ: Princeton University Press.

Fordyce RE (2002) Oligocene origins of skim‐feeding right whales: a small archaid balaenid from New Zealand. Journal of Vertebrate Paleontology 22(3, suppl.): 54a.

Fordyce RE (2003) Cetacean evolution and the eocene‐oligocene oceans revisited. In: Prothero DR, Ivany LC and Nesbitt EA (eds) From Greenhouse to Icehouse: The Marine Eocene‐Oligocene Transition. New York: Columbia University Press.

Fordyce RE (2009a) Cetacean evolution. In: Perrin WF, Würsig B and Thewissen JGM (eds) Encyclopedia of Marine Mammals, 2nd edn, pp. 201–207. Elsevier.

Fordyce RE (2009b) Cetacean fossil record. In: Perrin WF, Thewissen JGM and Würsig B (eds) Encyclopedia of Marine Mammals, pp. 207–215. San Diego: Elsevier.

Fortey R, Jackson JA and Strugnell J (2003) Phylogenetic fuses and evolutionary ‘explosions’: conflicting evidence and critical tests. In: Donoghue P and Smith P (eds) Telling the Evolutionary Time: Molecular Clocks and the Fossil Record. London and New York: Taylor and Francis.

Friedlaender AS, Halpin PN, Qian SS et al. (2006) Whale distribution in relation to prey abundance and oceanographic processes in shelf waters of the Western Antarctic Peninsula. Marine Ecology Progress Series 317: 297–310.

Gaines CA, Hare MP, Beck SE et al. (2005) Nuclear markers confirm taxonomic status and relationships among highly endangered and closely related right whale species. Proceedings. Biological Sciences/The Royal Society 272: 533–542.

Hatch LT, Dopman EB and Harrison RG (2006) Phylogenetic relationships among the baleen whales based on maternally and paternally inherited characters. Molecular Phylogenetics and Evolution 41: 12–27.

Iwanami K, Mita H, Yamamoto Y et al. (2006) cDNA‐derived amino acid sequences of myoglobins from nine species of whales and dolphins. Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology 145: 249–256.

Jackson JA, Baker CS, Vant M et al. (2009) Big and slow: phylogenetic estimates of molecular evolution in baleen whales (suborder Mysticeti). Molecular Biology and Evolution 26(11): 2427–2440. 10.1093/molbev/msp169.

Kimura M and Ozawa T (2002a) A new Cetothere (Cetacea: Mysticeti) from the early Miocene of Japan. Journal of Vertebrate Paleontology 22(3): 684–702.

Kimura T and Ozawa T (2002b) Rates of mitochondrial DNA evolution are slower in mysticete relative to odontocete cetaceans. In: Pfeiffer CJ (ed.) Molecular and Cell Biology of Marine Mammals, pp. 111–117. Malabar, FL: Krieger Publishing Company.

LeDuc RG, Dizon AE, Goto M et al. (2007) Patterns of genetic variation in Southern Hemisphere blue whales and the use of assignment test to detect mixing on the feeding grounds. Journal of Cetacean Research and Management 9(1): 73–80.

Martin AP and Palumbi S (1993) Body size, metabolic rate, generation time and the molecular clock. Proceedings of the National Academy of Sciences of the USA 90: 4087–4091.

Marx FG and Uhen MD (2010) Climate, critters and cetaceans: cenozoic drivers of the evolution of modern whales. Science 327: 993–996.

May‐Collado L and Agnarsson I (2006) Cytochrome b and Bayesian inference of whale phylogeny. Molecular Phylogenetics and Evolution 38: 344–354.

McDonald MA, Mesnick SL and Hildebrand JA (2006) Biogeographic characterisation of blue whale song worldwide: using song to identify populations. Journal of Cetacean Research and Management 8(1): 55–66.

McGowen MR, Spaulding M and Gatesy J (2009) Divergence date estimation and a comprehensive molecular tree of extant cetaceans. Molecular Phylogenetics and Evolution 53: 891–906.

Mitchell ED (1989) A new cetacean from the Late Eocene La Meseta Formation, Seymour Island, Antarctic Peninsula. Canadian Journal of Fisheries and Aquatic Sciences 46: 2219–2235.

Nabholz B, Glémin S and Galtier N (2008) Strong variations of mitochondrial mutation rate across mammals – the longevity hypothesis. Molecular Biology and Evolution 25(1): 120–130.

Nikaido M, Hamilton H, Makino H et al. (2006) Baleen whale phylogeny and a past extensive radiation event revealed by SINE insertion analysis. Molecular Biology and Evolution 23(5): 866–873.

Nishida S, Goto M, Pastene L et al. (2007) Phylogenetic relationships among cetaceans revealed by Y‐chromosome sequences. Zoological Science 24: 723–732.

Pastene L, Goto M, Kanda N et al. (2007) Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata. Molecular Ecology 16: 1481–1495.

Reeves RR, Perrin WF, Taylor BL et al. (2004) Report of the Workshop on Shortcomings of Cetacean Taxonomy in Relation to Needs of Conservation and Management. 30 April to 2 May, La Jolla, California. NOAA Technical Memorandum NMFS SWFSC‐363, 94pp.

Rice DW (1998) Marine mammals of the world: systematics and distribution. Marine Mammal Science (Special Publication) 4: 67–78.

Rosenbaum HC, Brownell RL Jr, Brown MW et al. (2000) World‐wide genetic differentiation of Eubalaena: questioning the number of right whale species. Molecular Ecology 9: 1793–1802.

Rychel AL, Reeder TW and Berta A (2004) Phylogeny of mysticete whales based on mitochondrial and nuclear data. Molecular Phylogenetics and Evolution 32: 892–901.

Sasaki T, Nikaido M, Hamilton H et al. (2005) Mitochondrial phylogenetics and evolution of mysticete whales. Systematic Biology 54(1): 77–90.

Sasaki T, Nikaido M, Wada S et al. (2006) Balaenoptera omurai is a newly discovered baleen whale that represents an ancient evolutionary lineage. Molecular Phylogenetics and Evolution 41: 40–52.

Smith AB and Peterson KJ (2002) Dating the time of origin of major clade: molecular clocks and the fossil record. Annual Review of Earth and Planetary Sciences 30: 65–88.

Steeman ME (2007) Cladistic analysis and a revised classification of fossil and recent mysticetes. Zoological Journal of the Linnean Society 150: 875–894.

Steeman ME, Hebsgaard MB, Fordyce RE et al. (2009) Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology 58(6): 573–585.

Thorne JL and Kishino H (2002) Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 51: 689–702.

Tynan CT (1998) Ecological importance of the southern boundary of the Antarctic circumpolar current. Nature 392(6677): 708–710.

Uhen MD (1998) Middle to late eocene basilosaurines and dorudontines. In: Thewissen JGM (ed.) The Emergence of Whales, pp. 29–61. New York: Plenum Press.

Uhen MD (1999) New species of protocetid Archaeocete whale, Eocetus wardii (Mammalia: Cetacea) from the middle Eocene of North Carolina. Journal of Paleontology 73(3): 512–528.

Utrecht WLV (1965) On the growth of the baleen plate of the fin whale and the blue whale. Bijdragen Tot De Dierkunde, uitgegeven door Koninklijk Zoölogisch Genootschap: ‘Natura Artis Magistra’ te Amsterdam 35: 3–38.

Wada S, Oishi M and Yamada TK (2003) A newly discovered species of living baleen whale. Nature 426: 278–281.

Walmsley R (1938) Some observations on the vascular system of a female fetal finback. Contributions to Embryology 27: 109–178.

Wilson DE and Reeder DM (2005) Mammal Species of the World. A Taxonomic and Geographic Reference, 3rd edn, p. 2142. Baltimore: Johns Hopkins University Press.

Further Reading

Bannister J (2009) Baleen whales (Mysticetes). In: Perrin WF, Thewissen JGM and Würsig B (eds) Encyclopedia of Marine Mammals, pp. 80–89. San Diego: Elsevier.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Jackson, Jennifer A(Dec 2010) Phylogenetics of Baleen Whales. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0022870]