Relationships of Cetacea (Artiodactyla) among mammals: Increased taxon sampling alters interpretations of key fossils and character evolution

PLoS ONE

Volumn 4, Issue 9, 2009, Pages

  Spaulding, Michelle ^a,b   O'Leary, Maureen A ^c   Gatesy, John ^d  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^c STONY BROOK UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ARTIODACTYLA; CARNIVORE; CETACEA; EVOLUTION; EXTINCT SPECIES; FOSSIL ANIMAL; HERBIVORE; MOLECULAR BIOLOGY; MORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENETIC TREE; PHYLOGENY; TAXONOMY; ANIMAL; CLASSIFICATION; DOLPHIN; FOSSIL; MAMMAL; PHYSIOLOGY; PORPOISE; SPECIES EXTINCTION; WHALE;

ARTIODACTYLA; CETACEA; CREODONTA; HIPPOPOTAMIDAE; INSECTIVORA; MAMMALIA; MESONYCHIA;

ANIMALS; CETACEA; DOLPHINS; EVOLUTION; EXTINCTION, BIOLOGICAL; FOSSILS; MAMMALS; PHENOTYPE; PHYLOGENY; PORPOISES; WHALES;

EID: 70349622813     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007062     Document Type: Article

References (71)

1. O'Leary MA, Gatesy J (2008) Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): Combined analysis including fossils. Cladistics 24: 397-442.
2. Gatesy J, O'Leary MA (2001) Deciphering whale origins with molecules and fossils. Trends in Ecology and Evolution 16: 562-570.
3. Thewissen JGM, Cooper LN, Clementz MT, Bajpai S, Tiwari BN (2007) Whales originated from aquatic artiodactyls in the Eocene epoch of India. Nature 450: 1190-1195.
4. Gingerich PD, Haq MU, Zalmout IS, Khan IH, Malkani MS (2001) Origin of whales from early artiodactyls: Hands and feet of Eocene Protocetidae from Pakistan. Science 293: 2239-2242.
5. Thewissen JGM, Williams EM, Roe LJ, Hussain ST (2001) Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls. Nature 413: 277-281.
6. Hiiemae KM, Crompton AW (1985) Mastication, food transport and swallowing. In: Hildebrand M, Bramble DM, Liem KF, Wake DB, eds. Functional vertebrate morphology. Cambridge, MA: Harvard University Press. pp 262-290.
7. Radinsky LB (1987) The evolution of vertebrate design. Chicago: University of Chicago Press.
8. Luo Z, Gingerich PD (1999) Terrestrial Mesonychia to aquatic Cetacea: Transformation of the basicranium and evolution of hearing in whales. University of Michigan Papers on Paleontology 31: 1-98.
9. Geisler JH, Theodor JM (2009) Hippopotamus and whale phylogeny. Nature 458: E1-E4.
10. Thewissen JGM, Cooper LN, Clementz MT, Bajpai S, Tiwari BN (2009) Hippopotamus and whale phylogeny. Nature 458: E5.
11. Borenstein S (2007) Whales may be related to deer-like creature. Bellingham: Bellingham Herald.
12. Simpson GG (1945) The principles of classification and a classification of mammals. Bulletin of the American Museum of Natural History 85: 1-350.
13. Wyss AR, Flynn JJ (1993) A phylogenetic analysis and definition of the Carnivora. In: Szalay FS, Novacek MJ, McKenna MC, eds. Mammal phylogeny: Placentals, Volume 2. New York: Springer-Verlag. pp 32-52.
14. McKenna MC, Bell SK (1997) Classification of mammals above the species level. New York: Columbia University Press.
15. Gunnell GF (1998) Creodonta. In: Janis CM, Scott KM, Jacobs LL, eds. Evolution of Tertiary mammals of North America Volume 1: Terrestrial carnivores, ungulates and ungulate like mammals. Cambridge: Cambridge University Press. pp 91-109.
16. Flynn JJ, Wesley-Hunt GD (2005) Phylogeny and early diversification of the Carnivora. In: Archibald JD, Rose K, eds.The rise of placental mammals: Origins and relationships of the major extant clades. Baltimore: Johns Hopkins University Press.
17. Polly PD (1996) The skeleton of Gazinocyon vulpeculus gen. et comb. nov. and the cladistic relationships of Hyaenodontidae (Eutheria, Mammalia). Journal of Vertebrate Paleontology 16: 303-319.
18. Wesley-Hunt GD, Flynn JJ (2005) Phylogeny of the Carnivora: Basal relationships among the Carnivoramorphans, and assessment of the position of 'Miacoidea' relative to Carnivora. Journal of Systematic Palaeontology 3: 1-28.
19. Waddell PJ, Okada N, Hasegawa M (1999) Towards resolving the interordinal relationships of placental mammals. Systematic Biology 48: 1-5.
20. Ax P (1985) Stem species and the stem lineage concept. Cladistics 1: 279-287.
21. de Queiroz K, Gauthier JA (1990) Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names. Systematic Zoology 39: 307-322.
22. de Queiroz K, Gauthier JA (1992) Phylogenetic taxonomy. Annual Review of Ecology and Systematics 23: 449-480.
23. de Queiroz K (2007) Toward an integrated system of clade names. Systematic Biology 56: 956-974.
24. de Queiroz K, Gauthier JA, Cantino P, eds (In prep) Companion volume (to the PhyloCode).
25. Graur D, Higgins DG (1994) Molecular evidence for the inclusion of cetaceans within the order Artiodactyla. Molecular Biology and Evolution 11: 357-364.
26. Irwin DM, Arnason U (1994) Cytochrome b gene of marine mammals: Phylogeny and evolution. Journal of Mammalian Evolution 2: 37-55.
27. Gatesy J, Hayashi C, Cronin MA, Arctander P (1996) Evidence from milk casein genes that cetaceans are close relatives of hippopotamid artiodactyls. Molecular Biology and Evolution 13: 954-963.
28. Montgelard C, Catzeflis FM, Douzery E (1997) Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S RNA mitochondrial sequences. Molecular Biology and Evolution 14: 550-559.
29. O'Leary MA (2009) "Artiodactylans": Phylogeny and the fossil record. Journal of Mammalian Evolution 16: 65-67.
30. Ayoub N, McGowen M, Clark C, Springer M, Gatesy J (2009) Evolution and phylogenetic utility of the melanocortin-1 receptor gene (MC1R) in Cetartiodactyla. Molecular Phylogenetics and Evolution 52: 550-557.
31. Geisler JH, Theodor JM, Uhen MD, Foss SE (2007) Phylogenetic relationships of cetaceans to terrestrial artiodactyls. In: Prothero DR, Foss SE, eds. The evolution of artiodactyls. Baltimore: Johns Hopkins University Press. pp 19-31.
32. Brochu C, Wagner JR, Jouve S, Sumrall CD, Densmore LD (in press) A correction corrected: Consensus over the meaning of Crocodylia and why it matters. Systematic Biology.
33. Witmer LM (1995) The extant phylogenetic bracket and the importance of reconstructing soft tissues in fossils. In: Thomason JJ, eds. Functional morphology in vertebrate paleontology. New York: Cambridge University Press. pp 19-33.
34. Arnason U, Gullberg A, Gretasdottir S, Ursing B, Janke A (2000) The mitochondrial genome of the sperm whale and a new molecular reference for estimating eutherian divergence dates. Journal of Molecular Evolution 50: 569-578.
35. Bryant HN (1996) Explicitness, stability, and universality in the phylogenetic definition and usage of taxon names: A case study of the phylogenetic taxonomy of the Carnivora. Systematic Biology 45: 174-189.
36. Swofford DL (2002) PAUP* Phylogenetic analysis using parsimony (* and other methods), 4.0b10a. Sunderland, Massachusetts: Sinauer Associates.
37. Goloboff PA, Farris JS, Nixon K (2004) TNT, a free program for phylogenetic analysis. Version 1.1. Cladistics 24: 774-786.
38. Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, et al. (2001) Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351.
39. Asher RJ, Novacek MJ, Geisler JH (2003) Relationships of endemic African mammals and their fossil relatives based on morphological and molecular evidence. Journal of Mammalian Evolution 10: 131-194.
40. Coombs MC, Coombs WP (1977) Dentition of Gobiohyus and a reevaluation of the Helohyidae (Artiodactyla). Journal of Mammalogy 58: 291-308.
41. Stucky RK (1998) Eocene bunodont and bunoselenodont Artiodactyla ("dichobunids"). In: Janis CM, Scott KM, Jacob LL, eds. Evolution of Tertiary mammals of North America. New York: Cambridge Univ. Press. pp 358-374.
42. Osborn HF (1924) Andrewsarchus, giant mesonychid of Mongolia. American Museum Novitates 146: 1-5.
43. Cole R, Hariharan R (1996) An O(n log n) algorithm for the maximum agreement subtree problem for binary trees. Proceedings of the 7th annual ACM-SIAM Symposium on Discrete Algorithms. pp 323-332.
44. VanValen L (1966) The Deltatheridia, a new order of mammals. Bulletin of the American Museum of Natural History 132: 1-126.
45. Geisler JH, Luo Z (1998) Relationships of Cetacea to terrestrial ungulates and the evolution of cranial vasculature in Cete. In: Thewissen JGM, eds. The Emergence of Whales. New York: Plenum. pp 163-212.
46. O'Leary MA (1998) Phylogenetic and morphometric reassessment of the dental evidence for a mesonychian and cetacean clade. In: Thewissen JGM, eds. The Emergence of Whales. New York: Plenum Press. pp 133-161.
47. O'Leary MA, Geisler JH (1999) The position of Cetacea within Mammalia: Phylogenetic analysis of morphological data from extinct and extant taxa. Systematic Biology 48: 455-490.
48. Geisler JH (2001) New morphological evidence for the phylogeny of Artiodactyla, Cetacea, and Mesonychidae. American Museum Novitates 3344: 1-53.
49. Geisler JH, Uhen MD (2003) Morphological support for a close relationship between hippos and whales. Journal of Vertebrate Paleontology 23: 991-996.
50. Geisler JH, Uhen MD (2005) Phylogenetic relationships of extinct cetartiodactyls: Results of simultaneous analyses of molecular, morphological and stratigraphic data. Journal of Mammalian Evolution 12: 145-160.
51. Theodor JM, Foss SE (2005) Deciduous dentitions of Eocene cebochoerid artiodactyls and cetartiodactylan relationships. Journal of Mammalian Evolution 12: 161-181.
52. O'Leary MA (2001) The phylogenetic position of cetaceans: Further combined data analyses, comparisons with the stratigraphic record and a discussion of character optimization. American Zoologist 41: 487-506.
53. O'Leary MA, Allard M, Novacek MJ, Meng J, Gatesy J (2004) Building the mammalian sector of the tree of life. In: Cracraft J, Donoghue MJ, eds. Assembling the tree of life. New York: Oxford University Press. pp 490-516.
54. Cope ED (1875) On the supposed Carnivora of the Eocene of the Rocky Mountains. Proceedings of the Academy of Natural Sciences, Philadelphia 27: 444-449.
55. Thewissen JGM, Russell DE, Gingerich PD, Hussain ST (1983) A new dichobunid artiodactyl (Mammalia) from the Eocene of north-west Pakistan. Dentition and classification. Proceedings of the Koninklijke Nederlandse Akademie voor Wetenschappen, Series B 86: 153-180.
56. Russell DE, Thewissen, JGM, Sigogneau-Russell D (1983) A new dichobunid artiodactyl (Mammalia) from the Eocene of North-West Pakistan. Part II: Cranial osteology. Proceedings of the Koninklijke Nederlandse Akademie voor Wetenschappen, Series B 86: 285-300.
57. Bremer K (1994) Branch support and tree stability. Cladistics 10: 295-304.
58. Gatesy J (2000) Linked branch support and tree stability. Systematic Biology 49: 800-807.
59. Fitch WM (1971) Toward defining the course of evolution: Minimum change for a specific tree topology. Systematic Zoology 20: 406-416.
60. Bryant HN, Russell AP (1992) The role of phylogenetic analysis in the inference of unpreserved attributes of extinct taxa. Philosophical Transactions of the Royal Society B 337: 405-418.
61. Novacek MJ (1985) Evidence for echolocation in the oldest known bats. Nature 315: 140-141.
62. O'Leary MA, Uhen MD (1999) The time of origin of whales and the role of behavioral changes in the terrestrial-aquatic transition. Paleobiology 25: 534-556.
63. Barklow WE (2004) Amphibious communication with sound in hippos, Hippopotamus amphibius. Animal Behavior 68: 1125-1132.
64. Novacek MJ, the Mammal AToL Team (2008) A team-based approach yields a new matrix of 4,500 morphological characters for mammalian phylogeny. Journal of Vertebrate Paleontology 28, Supplement to Number 3: 121A.
65. O'Leary MA, Kaufman S (2007) MorphoBank 2.5: Web application for morphological systematics and taxonomy.
66. Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ (2001) Molecular phylogenetics and the origins of placental mammals. Nature 409: 614-618.
67. Kleineidam RG, Pesole G, Breukelman H, Beintema J, Kastelein R (1999) Inclusion of cetaceans within the order Artiodactyla based on phylogenetic analysis of pancreatic ribonuclease genes. Journal of Molecular Evolution 48: 360-368.
68. Delgado S, Girondot M, Sire J (2005) Molecular evolution of amelogenin in mammals. Journal of Molecular Evolution 60: 12-30.
69. Thompson J, Higgins D, Gibson T (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
70. Gilbert DG (1992) SeqApp, version 1.9a. Bloomington: Indiana University.
71. Nixon K (1999) The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15: 407-414.