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After its description by Brant in 1872, Cetotheriidae was used as a wastebasket taxon for baleen whales which were not assignable to extant whale families.
Comparing the cranial and mandibular morphology of 23 taxa (including late archaeocetes and both fossil and extant mysticetes),Bouetel & Muizon 2006 found Cetotheriidae in this traditional sense to be polyphyletic. Based on ten cranial characters, they also concluded that of the twelve included fossil baleen-bearing mysticetes, six formed a monophyletic group, Cetotheriidae sensu stricto.
Several phylogenetic studies since Bouetel & Muizon 2006 support the monophyly of a small group of core Cetotheriidae sensu stricto, archaic mysticetes with a cranium that have "a long ascending process of the maxilla with anteriorly diverging lateral border that interdigitates with the frontal" and some other characters. This group is limited to Cetotherium rathkii, Metopocetus durinasus, Mixocetus elysius, Herpetocetus scaldiensis, H. transatlanticus, H. bramblei, Nannocetus eremus, and Piscobalaena nana. The remaining genera placed in the family are considered Cetotheriidae sensu lato and are often referred to as the 'cetotheres'.
Bisconti, Lambert & Bosselaers 2013 considered the primitive 'cetothere' Joumocetus the most basal named taxon of their new superfamily Thalassotherii (Cetotheriidae s.l., Cetotheriidae s.s., Eschrichtiidae (gray whales) and Balaenopteridae (rorquals)) and suggested that the term "Cetotheriidae s.l." should be renamed "basal" or "stem thalassotherians".Fordyce & Marx 2013 found that the pygmy right whale formed a well-supported clade with Eschrichtiidae and Balaenopteridae based on molecular data, and that, within 'cetotheres', it was most closely related to the herpetocetines (Herpetocetus and Nannocetus) Bisconti et al. 2013, however, found, based on morphological data, it to be more closely related to Balaenidae (the bowhead and right whales), but added that additional specimens are expected to resolve these conflicting results within a few years.
Classification of Cetotheriidae according to Eli Adli et al. (2014) and the Fossilworks online database:
^El Adli, Joseph J.; Deméré, Thomas A.; Boessenecker, Robert W. (2014). "Herpetocetus morrowi (Cetacea: Mysticeti), a new species of diminutive baleen whale from the Upper Pliocene (Piacenzian) of California, USA, with observations on the evolution and relationships of the Cetotheriidae". Zoological Journal of the Linnean Society. 170 (2): 400-466. doi:10.1111/zoj.12108.
^Gol'din, Pavel; Startsev, Dmitry (2014). "Brandtocetus, a new genus of baleen whales (Cetacea, Cetotheriidae) from the late Miocene of Crimea, Ukraine". Journal of Vertebrate Paleontology. 34 (2): 419-433. doi:10.1080/02724634.2013.799482.
^Pavel Gol'din; Dmitry Startsev (2017). "A systematic review of cetothere baleen whales (Cetacea, Cetotheriidae) from the Late Miocene of Crimea and Caucasus, with a new genus". Papers in Palaeontology. Online edition. doi:10.1002/spp2.1066
^Tarasenko, K. K. (2014). "New Genera of Baleen Whales (Cetacea, Mammalia) from the Miocene of the Northern Caucasus and Ciscaucasia: 3. Zygiocetus gen. nov. (Middle Sarmatian, Adygea)". Paleontological Journal. 48 (5): 551-562. doi:10.1134/S0031030114050116.
^Bisconti, Michelangelo (2015). "Anatomy of a new cetotheriid genus and species from the Miocene of Herentals, Belgium, and the phylogenetic and palaeobiogeographical relationships of Cetotheriidae s.s. (Mammalia, Cetacea, Mysticeti)". Journal of Systematic Palaeontology. 13 (5): 377-395. doi:10.1080/14772019.2014.890136.
Kimura, T.; Hasegawa, Y. (2010). "A New Baleen Whale (Mysticeti: Cetotheriidae) from the Earliest Late Miocene of Japan and a Reconsideration of the Phylogeny of Cetotheres". Journal of Vertebrate Paleontology. 30 (2): 577-591. doi:10.1080/02724631003621912.
Steeman, M. E. (2010). "The extinct baleen whale fauna from the Miocene-Pliocene of Belgium and the diagnostic cetacean ear bones". Journal of Systematic Palaeontology. 8 (1): 63-80. doi:10.1080/14772011003594961.
Tarasenko, K. K.; Lopatin, A. V. (2012a). "New Baleen Whale Genera (Cetacea, Mammalia) from the Miocene of the Northern Caucasus and Ciscaucasia: 1. Kurdalagonus gen. nov. from the Middle-Late Sarmatian of Adygea". Paleontological Journal. 46 (5): 531-542. doi:10.1134/s0031030112050115. Lay summary (December 2013).
Tarasenko, K. K.; Lopatin, A. V. (2012b). "New Baleen Whale Genera (Cetacea, Mammalia) from the Miocene of the Northern Caucasus and Ciscaucasia: 2. Vampalus gen. nov. from the Middle-Late Miocene of Chechnya and Krasnodar Region". Paleontological Journal. 46 (6): 620-629. doi:10.1134/s003103011206010x. Lay summary (December 2013).