Phylogenetic tests for differences in shape and the importance of divergence times: Eldredge’s enigma explored

Morphology, Shape and Phylogeny

Volumn , Issue , 2003, Pages 220-242

  Polly, P David ^a,b  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 27544434322     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9780203165171     Document Type: Chapter

References (81)

1. Berg, H. C. (1993) Random walks in biology, Expanded edition, Princeton: Princeton University Press.
2. Bodenbender, B. E. (1995) ‘Morphological, crystallographic, and stratigraphic data in cladistic analyses of blastoid phylogeny’, Contributions from the Museum of Paleontology, University of Michigan, 29, 201-257.
3. Bookstein, F. L. (1991) Morphometric tools for landmark data: geometry and biology, Cambridge: Cambridge University Press.
4. Bown, T. M., Rose, K. D., Simons, E. L. and Wing, S. L. (1994) ‘Distribution and stratigraphic correlation of Upper Paleocene and Lower Eocene fossil mammal and plant localities of the Fort Union, Willwood, and Tatman Formations, southern Bighorn Basin, Wyoming’, US Geological Survey Professional Paper, 1540, 1-103.
5. Butler, R. F., Gingerich, P. D. and Lindsay, E. H. (1981) ‘Magnetic polarity stratigraphy and biostratigraphy of Paleocene and lower Eocene continental deposits Clark’s Fork Basin, Wyoming’, Journal of Geology, 102, 367-377.
6. Cheverud, J. M. and Dow, M. M. (1985) ‘An autocorrelation analysis of genetic variation due to lineal fission in social groups of rhesus macaques’, American Journal of Physical Anthropology, 67, 113-121.
7. Clyde, W. C. (1997) ‘Stratigraphy and mammalian paleontology of the McCullough Peaks, northern Bighorn Basin, Wyoming: implications for biochronology, basin development, and community reorganization across the Paleocene-Eocene boundary’, Ph.D. thesis, The University of Michigan.
8. Clyde, W. C. and Gingerich, P. D. (1994) ‘Rates of evolution in the dentition of early Eocene Cantius: comparison of size and shape’, Paleobiology, 20, 506-522.
9. Clyde, W. C., Stamatakos, J. and Gingerich, P. D. (1994) ‘Chronology of the Wasatchian Land-Mammal Age (Early Eocene): magnetostratigraphic results form the McCullough Peaks Section, Northern Bighorn Basin, Wyoming’, Journal of Geology, 102, 367-377.
10. Crompton, A. W. and Hiiemae, K. (1970) ‘Molar occlusion and mandibular movements during occlusion in American opossum, Didelphis marsupialis’, Zoological Journal of the Linnean Society, 49, 21-47.
11. Eisenberg, J. F. (1981) The mammalian radiations: an analysis of trends in evolution, adaptation, and behavior, Chicago: Chicago University Press.
12. Eldredge, N. (1979) ‘Cladism and common sense’, in Cracraft, J. and Eldredge, N. (eds) Phylogenetic analysis and paleontology, New York: Columbia University Press, pp. 165-198.
13. Eldredge, N. and Cracraft, J. (1980) Phylogenetic patterns and the evolutionary process: method and theory in comparative biology, New York: Columbia University Press.
14. Falconer, D. S. and Mackay, T. F. C. (1996) Introduction to quantitative genetics, 4th edn, Harlow: Addison Wesley Longman, Ltd.
15. Felsenstein, J. (1973) ‘Maximum-likelihood estimation of evolutionary trees from continuous characters’, American Journal of Human Genetics, 25, 471-492.
16. Felsenstein, J. (1978) ‘Cases in which parsimony or compatibility methods will be positively misleading’, Systematic Zoology, 27, 401-410.
17. Felsenstein, J. (1985) ‘Phylogenies and the comparative method’, The American Naturalist, 125, 1-15.
18. Felsenstein, J. (1988) ‘Phylogenies and quantitative methods’, Annual Review of Ecology and Systematics, 19, 445-471.
19. Fisher, D. C. (1992) ‘Stratigraphic parsimony’, in Maddison, W. P. and Maddison, D. R. (eds) MacClade: analysis of phylogeny and character evolution, version 3, Sunderland, Mass.: Sinauer and Associates, Inc., pp. 124-129.
20. Fisher, D. C. (1994) ‘Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process’, in Grande, L. and Rieppel, O. (eds) Interpreting the hierarchy of nature, New York: Academic Press, pp. 133-171.
21. Flynn, J. J. and Galiano, H. (1982) ‘Phylogeny of early Tertiary Carnivora, with a description of a new species of Protictis from the middle Eocene of northwestern Wyoming’, American Museum Novitates, 2725, 1-64.
22. Fortelius, M. (1985) ‘Ungulate cheek teeth: development, function, and evolutionary interactions’, Acta Zoologica Fennica, 180, 1-76.
23. Fox, D. L., Fisher, D. C. and Leighton, L. R. (1999) ‘Reconstructing phylogeny with and without temporal data’, Science, 284, 1816-1819.
24. Fox, R. C. and Youzwyshyn, G. P. (1994) ‘New primitive carnivorans (Mammalia) from the Paleocene of western Canada, and their bearing on the relationships of the order’, Journal of Vertebrate Paleontology, 14, 382-404.
25. Fricke, H. C., Clyde, W. C., O’Neil, J. R. and Gingerich, P. D. (1998) ‘Evidence for rapid climate change in North America during the latest Paleocene thermal maximum: oxygen isotope compositions of biogenic phosphate from the Bighorn Basin (Wyoming)', Earth and Planetary Science Letters, 160, 193-208.
26. Garland, T. Jr., Midford, P. E. and Ives, A. R. (1999) ‘An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral values’, American Zoologist, 39, 374-388.
27. Gingerich, P. D. (1980) ‘The Bighorn Basin - Why is it so important?', Papers on Paleontology, University of Michigan, 24, 1-5.
28. Gingerich, P. D. (1983) ‘Rates of evolution: effects of time and temporal scaling’, Science, 222, 159-161.
29. Gingerich, P. D. (1991) ‘Systematics and evolution of early Eocene Perissodactyla (Mammalia) in the Clarks Fork Basin, Wyoming’, Contributions from the Museum of Paleontology, The University of Michigan, 28, 181-213.
30. Gingerich, P. D. (1993a) ‘Quantification and comparison of evolutionary rates’, American Journal of Science, 293-A, 453-478.
31. Gingerich, P. D. (1993b) ‘Rates of evolution in Plio-Pleistocene mammals: six case studies’, in Martin, R. A. and Barnosky, A. D. (eds) Morphological change in quaternary mammals of North America, Cambridge: Cambridge University Press, pp. 84-106.
32. Gingerich, P. D. and Gunnell, G. F. (1995) ‘Rates of evolution in Paleocene-Eocene mammals of the Clarks Fork Basin, Wyoming, and a comparison with Neogene Siwalik lineages of Pakistan’, Palaeogeography, Palaeoclimatology, Palaeoecology, 115, 227-247.
33. Gingerich, P. D. and Klitz, K. (1985) ‘University of Michigan Paleocene and Eocene fossil localities in the Fort Union and Willwood Formations, Clark’s Fork Basin, Wyoming’, University of Michigan Museum of Paleontology, map, 1 sheet.
34. Gingerich, P. D. and Winkler, D. A. (1985) ‘Systematics of Paleocene Viverravidae (Mammalia, Carnivora) in the Bighorn and Clark’s Fork Basin, Wyoming’, Contributions from the Museum of Paleontology, University of Michigan, 27, 87-128.
35. Girondot, M. and Sire, J.-Y. (1998) ‘Evolution of the amelogenin gene in toothed and toothless vertebrates’, European Journal of Oral Science, 106, 501-508.
36. Harvey, P. H. and Pagel, M. D. (1991) The comparative method in evolutionary biology, Oxford: Oxford University Press.
37. Heinrich, R. E. and Rose, K. D. (1997) ‘Postcranial morphology and locomotor behavior of two early Eocene miacoid carnivorans, Vulpavus and Didymictis’, Palaeontology, 40, 279-305.
38. Hendry, A. P. and Kinnison, M. T. (1999) ‘Perspective: the pace of modern life: measuring rates of contemporary microevolution’, Evolution, 53, 1637-1653.
39. Herring, S. W. (1993) ‘Functional-morphology of mammalian mastication’, American Zoologist, 33, 289-299.
40. Hillis, D. M., Huelsenbeck, J. P. and Swofford, D. L. (1994) ‘Consistency: hobgoblin of phylogenetics?', Nature, 369, 363-364.
41. Huelsenbeck, J. P. and Rannala, B. (2000) ‘Using stratigraphic information in phylogenetics’, in Wiens, J. (ed.) Phylogenetic analysis of morphological data, Washington, D.C.: Smithsonian Institution Press, pp. 165-191.
42. Hunt, R. M. and Tedford, R. H. (1993) ‘Phylogenetic relationships within the aeluroid carnivora and implications of their temporal and geographic distribution’, in Szalay, F. S., Novacek, M. J. and McKenna, M. C. (eds) Mammal phylogeny: placentals, New York: Springer-Verlag, pp. 53-73.
43. Jernvall, J. (2000) ‘Linking development with generation of novelty in mammalian teeth’, Proceedings of the National Academy of Sciences of the United States of America, 97, 2641-2645.
44. Jernvall, J. (1995) ‘Mammalian molar cusp patterns: developmental mechanisms of diversity’, Acta Zoologica Fennica, 198, 1-61.
45. Jernvall, J., Aberg, T., Kettunen, P., Keränen, S. and Thesleff, I. (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.
46. Jernvall, J., Kettunen, P., Karavanova, I., Martin, L. B. and Thesleff, I. (1994) ‘Evidence for the role of the enamel knot as a control center in mammalian tooth cusp formation: non-dividing cells express growth stimulating Fgf-4 gene’, International Journal of Developmental Biology, 38, 463-469.
47. Kay, R. F. and Hiiemae, K. M. (1974) ‘Jaw movement and tooth use in recent and fossil primates’, American Journal of Physical Anthropology, 40, 227-256.
48. Keränen, S. V. E., Berg, T., Kettunen, P., Thesleff, I. and Jernvall, J. (1998) ‘Association of developmental regulatory genes with the development of different molar shapes in two species of rodent’, Development, Genes, and Evolution, 208, 477-486.
49. Kluge, A. G. (1997) ‘Testability and the refutation and corroboration of cladistic hypotheses’, Cladistics, 13, 81-96.
50. Kluge, A. G. and Farris, J. S. (1969) ‘Quantitative phyletics and the evolution of anurans’, Systematic Zoology, 8, 1-32.
51. Koch, P. L., Zachos, J. C. and Dettman, D. L. (1995) ‘Stable isotope stratigraphy and paleoclimatology of the Paleogene Bighorn Basin (Wyoming, USA)', Palaeogeography, Palaeoclimatology, Palaeoecology, 115, 61-89.
52. Koenigswald, W. von. (1982) ‘Enamel structure in the molars of Arvicolidae (Rodentia, Mammalia), a key to functional morphology and phylogeny’, in Kurtén, B. (ed.) Teeth: form, function, and evolution, New York: Columbia University Press, pp. 109-122.
53. Koenigswald, W. von. (1997a) ‘The variability of enamel structure at the dentition level’, in von Koenigswald, W. and Sander, P. M. (eds) Tooth enamel microstructure, Rotterdam: Balkema, pp. 193-202.
54. Koenigswald, W. von (1997b) ‘Brief survey of enamel diversity at the schmelzmuster level in Cenozoic placental mammals’, in von Koenigswald, W. and Sander, P. M. (eds) Tooth enamel microstructure, Rotterdam: Balkema, pp. 137-162.
55. Koenigswald, W. von and Clemens, W. A. (1992) ‘Levels of complexity in the microstructure of mammalian enamel and their application in studies of systematics’, Scanning Microscopy, 6, 195-218.
56. Kumar, S. and Hedges, S. B. (1998) ‘A molecular timescale for vertebrate evolution’, Nature, 392, 917-920.
57. Legendré, S. (1986) ‘Analysis of mammalian communities from the late Eocene and Oligocene of southern France’, Palaeovertebrata, 16, 191-212.
58. Maas, R. and Bei, M. (1997) ‘The genetic control of early tooth development’, Critical Reviews in Oral Biology and Medicine, 8, 4-39.
59. Maddison, W. P. (1991) ‘Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree’, Systematic Zoology, 40, 304-314.
60. Martins, E. P. and Hansen, T. F. (1997) ‘Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data’, American Naturalist, 149, 646-667.
61. Mathur, A. K. and Polly, P. D. (2000) ‘The evolution of enamel microstructure: how important is amelogenin?', Journal of Mammalian Evolution, 7, 23-42.
62. Pispa, J., Jung, H. S., Jernvall, J., Kettunen, P., Mustonen, T., Tabata, M. J., Kere, J. and Thesleff, I. (1999) ‘Cusp patterning defect in Tabby mouse teeth and its partial rescue by FGF’, Developmental Biology, 216, 521-534.
63. Polly, P. D. (1997) ‘Ancestry and species definition in paleontology: a stratocladistic analysis of Paleocene-Eocene Viverravidae (Mammalia, Carnivora) from Wyoming’, Contributions from the Museum of Paleontology, The University of Michigan, 30, 1-53.
64. Polly, P. D. (1998) ‘Variability, selection, and constraints: development and evolution in viverravid (Carnivora, Mammalia) molar morphology’, Paleobiology, 24, 409-429.
65. Popowics, T. E. (1998) ‘Ontogeny of postcanine tooth form in the Ferret, Mustela putorius (Carnivora, Mammalia), and the evolution of dental diversity within the Mustelidae’, Journal of Morphology, 237, 69-90.
66. Rodrigo, A. (2000) ‘Serial sample UPGMA’, hyperlink “http://www.cebl.auckland.ac.nz/" http://www.cebl.auckland.ac.nz/.
67. Rohlf, F. J. (1998) ‘tpsSmall: is shape variation small?', Stony Brook, New York: Department of Ecology and Evolution, State University of New York.
68. Rohlf, F. J. (1999) ‘Shape statistics: Procrustes superimpositions and tangent spaces’, Journal of Classification, 16, 197-223.
69. Rose, K. D. (1981) ‘The Clarkforkian Land-Mammal Age and mammalian faunal composition across the Paleocene-Eocene boundary’, University of Michigan Papers on Paleontology, 26: 1-196.
70. Savage, R. J. G. (1976) ‘Evolution in carnivorous mammals’, Palaeontology, 20, 237-271.
71. Schluter, D., Price, T., Mooers, A. O. and Ludwig, D. (1997) ‘Likelihood of ancestor states in adaptive radiation’, Evolution, 51, 1699-1711.
72. Siddall, M. E. and Kluge, A. G. (1997) ‘Probabilism and phylogenetic inference’, Cladistics, 13, 313-336.
73. Silva, M. and Downing, J. A. (1995) CRC handbook of mammalian body masses, Boca Raton: CRC Press.
74. Simpson, G. G. (1951) ‘The species concept’, Evolution, 5, 285-298.
75. Sokal, R. R. and Rohlf, F. J. (1995) Biometry, 3rd edn, New York: W. H. Freeman and Co.
76. Thesleff, I. and Sahlberg, C. (1996) ‘Growth factors as inductive signals regulating tooth morphogenesis’, Seminars in Cell and Developmental Biology, 7, 185-193.
77. Williams, W. T. (1971) ‘Principles of clustering’, Annual Review of Ecology and Systematics, 2, 303-326.
78. Wilson, A. C., Ochman, H. and Prager, E. M. (1987) ‘Molecular time scale for evolution’, Trends in Genetics, 3, 241-247.
79. Wolsan, M. (1989) ‘Dental polymorphism in the genus Martes (Carnivora, Mustelidae) and its evolutionary significance’, Acta Theriologica, 34, 545-593.
80. Wyss, A. R. and Flynn, J. J. (1993) ‘A phylogenetic analysis and definition of the Carnivora’, in Szalay, F. S., Novacek, M. J. and McKenna, M. C. (eds) Mammal phylogeny: placentals, New York: Springer-Verlag, pp. 32-52.
81. Zuckerkandl, E. and Pauling, L. (1962) ‘Evolutionary divergence and convergence in proteins’, in Bryson, V. and Vogel, H. J. (eds) Evolving genes and proteins, New York: Academic Press.