Are the Dental Data Really at Odds with the Molecular Data? Morphological Evidence for Whale Phylogeny (Re)Reexamined

Systematic Biology

Volumn 52, Issue 6, 2003, Pages 853-864

  O'Leary, Maureen A ^a   Gatesy, John ^b   Novacek, Michael J ^c  

^a STONY BROOK UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTIODACTYLA; BIOLOGICAL MODEL; CETACEA; CLASSIFICATION; COMPARATIVE STUDY; FOSSIL; GENETICS; HISTOLOGY; METHODOLOGY; PHYLOGENY; REVIEW; TOOTH;

ANIMALS; ARTIODACTYLA; CETACEA; CLASSIFICATION; FOSSILS; MODELS, GENETIC; PHYLOGENY; RESEARCH DESIGN; TOOTH;

ANIMALIA; ARTIODACTYLA; CETACEA; MAMMALIA;

EID: 1642528334     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150390252279     Document Type: Review

References (63)

1. BARKER, F. K., AND F. M. LUTZONI. 2002. The utility of the incongruence length distance test. Syst. Biol. 51:625-637.
2. BLAINVILLE, H. M. D. DE. 1816. Prodrome d'une nouvelle distribution systématique du règne animal. Bull. Soc. Philom., 1816: 105.
3. BULL, J. J., J. P. HUELSENBECK, C. W. CUNNINGHAM, D. L. SWOFFORD, AND P. J. WADDELL. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:384-397.
4. CAIN, A. J. 1959. Function and taxonomic importance. Oxford Univ. Press, New York.
5. CUVIER, G. 1800. Leçons anatomie comparée. Baudouin, Imp. de l'Institut national des sciences et des arts, puis Genets, an VIII, Paris.
6. DARLU, P., AND G. LECOINTRE. 2002. When does the incongruence length difference test fail? Mol. Biol. Evol. 19:432-437.
7. DE QUEIROZ, A. 1993. For consensus (sometimes). Syst. Biol. 42:368-372.
8. DOWTON, M., AND A. D. AUSTIN. 2002. Increased congruence does not necessarily indicate increased accuracy - The behavior of the incongruence length difference test in mixed-model analysis. Syst. Biol. 51:19-31.
9. ESTABROOK, G. F., C. S. JOHNSON, AND F. R. MCMORRIS. 1976. A mathematical foundation for the analysis of cladistic character compatibility. Math. Biosci. 29:181-187.
10. FARRIS, J. S. 1969. A successive approximations approach to character weighting. Syst. Zool. 18:374-385.
11. FARRIS. J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5:417-419.
12. FARRIS, J. S., M. KÄLLERSJÖ, A. G. KLUGE, AND C. BULT. 1995. Constructing a significance test for incongruence. Syst. Biol. 44:570-572.
13. FARRIS, J. S., A. G. KLUGE, AND M. F. MICKEVICH. 1982. Immunological distance and the phylogenetic relationships of the Rana boylii species group. Syst. Zool. 31:479-491.
14. GATESY, J. 1998. Molecular evidence for the phylogenetic affinities of Cetacea. Pages 63-111 in The emergence of whales (J. Thewissen, ed.). Plenum, New York.
15. GATESY, J. 2002. Relative quality of different systematic data sets for cetartiodactyl mammals: Assessments within a combined analysis framework. Pages 45-68 in Molecular systematics and evolution: Theory and practice (R. DeSalle, W. Wheeler, and G. Giribet, eds.). Birkhäuser Verlag, Basel.
16. GATESY, J., C. HAYASHI, M. A. CRONIN, AND P. ARCTANDER. 1996. Evidence from milk casein genes that cetaceans are close relatives of hippopotamid artiodactyls. Mol. Biol. Evol. 14:537-543.
17. GATESY, J., C. MATTHEE, R. DESALLE, AND C. HAYASHI. 2002. Resolution of a supertree/supermatrix paradox. Syst. Biol. 51:652-664.
18. GATESY, J., M. MILINKOVITCH, V. WADDELL, AND M. STANHOPE. 1999. Stability of cladistic relationhips between Cetacea and higher-level artiodactyl taxa. Syst. Biol. 48:6-20.
19. GATESY, J., AND M. A. O'LEARY. 2001. Deciphering whale origins with molecules and fossils. Trends Ecol. Evol. 16:562-570.
20. GEISLER, J. 2001. New morphological evidence for the phylogeny of Artiodactyla, Cetacea, and Mesonychidae. Am. Mus. Novit. 3344:1-53.
21. GINGERICH, P. D., M. UL HAQ, I. S. ZALMOUT, I. H. KHAN, AND M. S. MALKANI. 2001. Origin of whales from early artiodactyls: Hands and feet of Eocene Protocetidae from Pakistan. Science 293:2239-2242.
22. HALL, B. K. 1995. Homology and embryonic development. Evol. Biol. 28:1-37.
23. HARRIS, S. R., D.J. GOWER, AND M. WILKINSON. 2003. Intraorganismal homology, character construction, and the phylogeny of aetosaurian archosaurs (Reptilia, Diapsida). Syst. Biol. 52:239-252.
24. HOLBROOK, L. 1999. The phylogeny and classification of tapiromorph perissodactyls (Mammalia). Cladistics 15:331-350.
25. JANIES, D., AND R. DESALLE. 1999. Development, evolution and corroboration. New Anat. 257:6-14.
26. JERNVALL, J. 2000. Linking development with generation of novelty in mammalian teeth. Proc. Natl. Acad. Sci. USA 97:2641-2645.
27. JERNVALL, J., T. ABERG, P. KETTUNEN, S. KERÄNEN, AND I. THESLEFF. 1998. The life history of an embryonic signaling center: BMP-4 induces p21 and is associated with apoptosis in the mouse tooth enamel knot. Development 125:161-169.
28. JERNVALL, J. A., AND I. THESLEFF. 2000. Reiterative signaling and patterning during mammalian tooth morphogenesis. Mech. Dev. 92:19-29.
29. KLUGE, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:7-25.
30. KLUGE, A. G. 1997. Testability and the refutation and corroboration of cladistics hypotheses. Cladistics 13:81-96.
31. KLUGE, A. G. 1998. Total evidence or taxonomic congruence: Cladistics or consensus classification. Cladistics 14:151-158.
32. KLUGE, A. G., AND J. S. FARRIS. 1969. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18:1-32.
33. LANGER, P. 2001. Evidence from the digestive tract on phylogenetic relationships in ungulates and whales. J. Zool. Syst. Evol. Res. 39:77-90.
34. LIU, F., M. MIYAMOTO, N. FREIRE, P. ONG, M. TENNANT, T. YOUNG, AND K. GUGEL. 2001. Molecular and morphological supertrees for eutherian (placental) mammals. Science 291:1786-1789.
35. LUCKETT, W. P., AND N. HONG. 1998. Phylogenetic relationships between the orders Artiodactyla and Cetacea: A combined assessment of morphological and molecular evidence. J. Mammal. Evol. 5:127-182.
36. LUO, Z.-X., R. L. CIFELLI, AND Z. KIELAN-JAWOROWSKA. 2001. Dual origin of tribosphenic mammals. Nature 409:53-57.
37. MADDISON, W. 1990. A method for testing the correlated evolution of two binary characters: Are gains or losses concentrated on certain branches of a phylogenetic tree? Evolution 44:539-557.
38. MATTHEE, C. A., J. D. BURZLAFF, J. F. TAYLOR, AND S. K. DAVIS. 2001. Mining the mammalian genome for artiodactyl systematics. Syst. Biol. 50:367-390.
39. MAYR, E. 1969. Principles of systematic zoology. McGraw-Hill, New York.
40. MIYAMOTO, M. M., AND W. M. FITCH. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44:64-76.
41. MURPHY, W., E. EIZRIK, W. JOHNSON, Y. ZHANG, O. RYDER, AND S. O'BRIEN. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
42. NAYLOR, G. J. P. AND D. C. ADAMS. 2001. Are the fossil data really at odds with the molecular data? Morphological evidence for Cetartiodactyla phylogeny reexamined. Syst. Biol. 50:444-453.
43. NAYLOR, G. J. P., AND W. M. BROWN. 1998. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst. Biol. 47:61-76.
44. NIXON, K. C., AND J. M. CARPENTER. 1996a. On simultaneous analysis. Cladistics 12:221-241.
45. NIXON, K. C., AND J. M. CARPENTER. 1996b. On consensus, collapsibility, and clade concordance. Cladistics 12:305-321.
46. NOVACEK, M. J. 1994. Morphological and molecular inroads to phylogeny. Pages 85-131 in Interpreting the hierarchy of life: From systematic patterns to evolutionary process theories (L. Grande and O. Rieppel, eds.). Academic Press, San Diego.
47. O'KEEFE, F. R., AND P. J. WAGNER. 2001. Inferring and testing hypotheses of cladistic character dependence by using character compatibility. Syst. Biol. 50:657-675.
48. O'LEARY, M. A. 1999. Parsimony analysis of total evidence from extinct and extant taxa and the cetacean-artiodactyl question (Mammalia, Ungulata). Cladistics 15:315-330.
49. O'LEARY, M. A. 2001. The phylogenetic position of cetaceans: Further combined data analyses, comparisons with the stratigraphic record and a discussion of character optimization. Am. Zool. 41:487-506.
50. O'LEARY, M. A., AND J. H. GEISLER. 1999. The position of Cetacea within Mammalia: Phylogenetic analysis of morphological data from extinct and extant taxa. Syst. Biol. 48:455-490.
51. PHILIPPE, H., AND E. DOUZERY. 1994. The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships. J. Mammal. Evol. 2:133-152.
52. SHARKEY, M. J., AND J. W. LEATHERS. 2001. Majority does not rule: The trouble with majority-rule consensus trees. Cladistics 17:282-284.
53. SIDDALL, M. E. 1997. Prior agreement: Arbitration or arbitrary. Syst. Biol. 46:766-770.
54. SIMPSON, G.G. 1945. The principles of classification and a classification of mammals. Bull. Am. Mus. Nat. Hist. 85:1-350.
55. SWOFFORD, D. L. 1993. PAUP: Phylogenetic analysis using parsimony, version 3.1.1. Illinois Natural History Survey, Champaign.
56. SWOFFORD, D. L. 1998. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer, Sunderland, Massachusetts.
57. TEMPLETON, A. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221-244.
58. THEWISSEN, J. G. M., E. M. WILLIAMS, L. J. ROE, AND S. T. HUSSAIN. 2001. Skeletons of terrestrial cetaceans and the relationships of whales to artiodactyls. Nature 413:277-281.
59. TUCKER, A. S., K. L. MATHEWS, AND P. T. SHARPE. 1998 Transformation of tooth type induced by inhibition of BMP signaling. Science 282:1136-1138.
60. TUCKER, A. S., AND P. T. SHARPE. 1999. Molecular genetics of tooth morphogenesis and patterning: The right shape in the right place. J. Dent. Res. 78:826-834.
61. WAGNER, G. P. 1989. The origin of morphological characters and the biological basis of homology. Evolution 43:1157-1171.
62. WOLLENBERG, K. R., AND W. R. ATCHLEY. 2000. Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. Proc. Natl. Acad. Sci. USA 97:3288-3291.
63. WRAY, G. A., AND C. J. LOWE. 2000. Developmental regulatory genes and echinoderm evolution. Syst. Biol. 49:28-51.