The flourishing diversity of models in theoretical morphology: From current practices to future macroevolutionary and bioenvironmental challenges

Paleobiology

Volumn 34, Issue 3, 2008, Pages 301-317

  Dera, Guillaume ^a   Eble, Gunther J ^a   Neige, Pascal ^a   David, Bruno ^a  

^a UNIVERSITÉ DE BOURGOGNE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EMPIRICAL ANALYSIS; MORPHOLOGY; MULTIVARIATE ANALYSIS; PALEONTOLOGY; TYPOLOGY;

EID: 50249150326     PISSN: 00948373     EISSN: None     Source Type: Journal    
DOI: 10.1666/07070.1     Document Type: Article

References (131)

1. Ackerly, S. C. 1989. Kinematics of accretionary shell growth, with the examples from brachiopods and molluscs. Paleobiology 15:147-164.
2. Ackerly, S. C. 1992. Morphogenetic regulation in the shells of bivalved organisms: evidence from the geometry of the spiral. Lethaia 25:249-256.
3. Aono, M., and T. L. Kunii. 1984. Botanical tree image generation. IEEE Computer Graphics and Application 4:1-34.
4. Batchelor, M. T., R. V. Burne, B. I. Henry, and M. J. Jackson. 2005a. A case for biotic morphogenesis of coniform stromatolites. Physica A 337:319-326.
5. Batchelor, M. T., R. V. Burne, B. I. Henry, and T. Slatyer. 2005b. Statistical physics and stromatolite growth: new perspectives on an ancient dilemma. Physica A 350:6-11.
6. Beck, M., G. Benko, G. J. Eble, C. Flamm, S. Müller, and P. F. Stadler. 2004. Graph grammars as models for the evolution of developmental pathways. Pp. 8-15 in U. Brüggerman, H. Schaub, and F. Detje, eds. The logic of artificial life: abstracting and synthesizing the principles of living systems. Proceedings of GWAL 2004, IOS Press, Bamberg, Germany.
7. Bell, A. D. 1986. The simulation of branching patterns in modular organisms. Philosophical Transactions of the Royal Society of London B 313:143-159.
8. Berger, W. H. 1969. Planktonic foraminifera: basic morphology and ecological implications. Journal of Paleontology 43:1369-1383.
9. Bookstein, F. L. 1991. Morphometric tools for landmark data geometry and biology. Cambridge University Press, New York.
10. Brasier, M. D. 1980. Microfossils. Allen and Unwin, London.
11. Cheetman, A. H., and L. C. Hayek. 1983. Geometric consequences of branching growth in adeoniform Bryozoa. Paleobiology 9:240-260.
12. Cheetman, A. H., L. C. Hayek, and E. Thomsen. 1980. Branching structure in arborescent animals: models of relative growth. Journal of Theoretical Biology 85:335-369.
13. Coen, E., A.-G. Rolland-Lagan, M. Matthews, A. Bangham, and P. Prusinkiewicz. 2004. The genetics of geometry. Proceedings of the National Academy of Sciences USA 101:4728-4735.
14. Cortie, M. B. 1989. Models for mollusc shape. South African Journal of Science 85:454-460.
15. D'Arcy Thompson, W. 1917. On growth and forms. Cambridge University Press, Cambridge.
16. De Renzi, M. 1988. Shell coiling in some larger foraminifera: general comments and problems, Paleobiology 14:387-400.
17. De Renzi, M. 1995. Theoretical morphology of logistic coiling exemplified by tests of genus Alveolina (larger foraminifera). Neues Jahrbuch für Geologie und Paläontologie, Abhandlungen 195: 241-251.
18. Dommergues, J.-L., B. Laurin, and C. Meister. 1996. Evolution of ammonoid morphospace during the Early Jurassic radiation. Paleobiology 22:219-240.
19. Dupraz, C., R. Pattisina, and E. P. Verrecchia. 2006. Translation of energy into morphology: simulation of stromatolite morphospace using a stochastic model. Sedimentary Geology 185: 185-203.
20. Eble, G. J. 2000. Theoretical morphology: state of the art. Paleobiology 26:520-528.
21. Eble, G. J. 2002. Developmental morphospace and evolution. Pp. 35-65 in J. P. Crutchfield and P. Schuster, eds. Evolutionary dynamics. Oxford University Press, Oxford.
22. Eckartne, S. U. K., and D. J. Crisp. 1983. A geometrical analysis of growth in gastropod shells, with particular reference to turbinate forms. Journal of the Marine Biological Association of the United Kingdom 63:777-797.
23. Erwin, D. H. 2007. Disparity: morphological pattern and developmental context. Paleontology 50:57-73.
24. Felsenstein, J. 1990. PHYLIP (Phylogeny inferences package), Version 3. 3. University of Washington, Seattle.
25. Ferreira Junior, S. C., M. L. Martins, and M. J. Vilela. 2002. A reaction-diffusion model for the growth of avascular tumor. Physical Review E 65:021907.
26. Fortey, R. A. 1983. Geometrical constraints in the construction of graptolite stipes. Paleobiology 13:116-125.
27. Fortey, R. A., and A. Bell. 1987. Branching geometry and function of multiramous graptoloids. Paleobiology 13:1-19.
28. Fowler, D. R., H. Meinhardt, and P. Prusinkiewicz. 1992. Modeling seashells. Computer Graphics 26:379-387.
29. Gardiner, A. R., and P. D. Taylor. 1980. Computer modelling of colony growth in a uniserial bryozoan. Journal of Geological Society, London 137:107.
30. Gardiner, A. R., and P. D. Taylor. 1982. Computer modelling of branching growth in the bryozoan Stromatopora. Neues Jahrbuch für Geologie und Paläontologie, Abhandlungen 163:389-416.
31. Gerber, S., G. J. Eble, and P. Neige. 2007. Combining ontogenetic and evolutionary scales of morphological disparity: a study of early Jurassic ammonites. Evolution and Development 9: 472-482.
32. Glass, G. V. 1976. Primary, secondary, and meta-analysis. Educational Researcher 5:3-8.
33. Gould, S. J., and M. Katz. 1975. Distribution of ideal geometry in the growth of receptaculitids: a natural experiment in theoretical morphology. Paleobiology 1:1-20.
34. Graus, R. R., and I. G. Macintyre. 1976. Light control of growth form in colonial reef corals: computer simulation. Science 193: 895-897.
35. Harary, F. 1969. Graph theory. Addison Wesley, Reading, Mass.
36. Harbaugh, J. W., and G. Bonham-Carter. 1970. Computer simulation in geology. Wiley, New York.
37. Hickman, C. S. 1993. Theoretical design space: a new program for the analysis of structural diversity. In A. Seilacher and K. Chinzei, eds. Progress in constructional morphology. Neues Jahrbuch für Geologie und Paläontologie, Abhandlungen 190: 169-182.
38. Hofmann, H. J. 1994. Quantitative stromatology. Journal of Paleontology 68:704-709.
39. Honda, H. 1971. Description of the form of trees by the parameters of the tree-like body: effects of the branching angle and the branch length on the shape of the tree-like body. Journal of Theoretical Biology 31:331-338.
40. Honda, H., and J. B. Fisher. 1978. Tree branch angle: maximizing effective leaf area. Science 199:888-890.
41. Hull, D. 1988. Science as a process. University of Chicago Press, Chicago.
42. Hutchinson, J. M. C. 1990. Control of gastropod shell form via apertural growth rates. Journal of Morphology 206:259-264.
43. Hutchinson, J. M. C. 1999. But which morphospace to choose? Trends in Ecology and Evolution 14:414.
44. Illert, C. 1982. The mathematics of gnomic seashells. Mathematical Bioscience 63:21-56.
45. Illert, C. 1989. Formulation and solution of the classical seashell problem. Il Nuovo Cimento D 11:761-780.
46. Kaandorp, J. A. 1995. Analysis and synthesis of radiate accretive growth in three dimensions. Journal of Theoretical Biology 175:39-55.
47. Kaandorp, J. A. 1996. Effect of nutrient diffusion and flow on coral morphology. Physical Review Letters 77:2328-2331.
48. Kaandorp, J. A. 2001. The algorithmic beauty of seaweeds, sponges and corals. Springer, Heidelberg.
49. Kaandorp, J. A., and R. Garcia Leiva. 2004. Morphological analysis of two- and three-dimensional images of branching sponges and corals. Pp. 83-94 in A. M. T. Elena, ed. Morphometrics: applications in biology and paleontology. Springer, Berlin.
50. Kaandorp, J. A., and P. M. A. Sloot. 1997. Parallel simulation of accretive growth and form in three dimensions. BioSystems 44:181-192.
51. Kaandorp, J. A., and P. M. A. Sloot. 2001. Morphological models of radiate accretive growth and the influence of hydrodynamics. Journal of Theoretical Biology 209:257-274.
52. Kershaw, S., and R. Riding. 1978. Parameterization of stromatoporoid shape. Lethaia 11:233-242.
53. Kohn, A. J., and A. C. Riggs. 1975. Morphometry of the Conus shell. Systematic Zoology 24:346-359.
54. Kozlovsky, Y., I. Cohen, I. Golding, and E. Ben-Jacob. 1999. Lubricating bacteria model for branching growth of bacterial colonies. Physical Review E 59:7025-7035.
55. Kruszynski, K. J., R. Van Liere, and J. A. Kaandorp. 2006. An interactive visualization system for quantifying coral structures. Pp. 1-8 in T. Ertl, K. Joy, and B. Santos, eds. Eurographics/IEEE-VGTC Symposium on visualization, Benidorm, Spain, January 2006.
56. Labaj, P., P. Topa, J. Tyszka, and W. Alda. 2003. 2D and 3D numerical models of the growth of foraminiferal shell. Lecture Notes in Computer Science 2657:669-678.
57. Lefebvre, B., G. J. Eble, N. Navarro, and B. David. 2006. Diversification of atypical Paleozoic echinoderms: a quantitative survey of patterns of stylophoran disparity, diversity, and geography. Paleobiology 32:483-510.
58. Løvtrup, S., and M. Løvtrup. 1988. The morphogenesis of molluscan shells: a mathematical account using biological parameters. Journal of Morphology 197:53-62.
59. Løvtrup, S., and B. Von Sydow. 1974. D'Arcy Thompson's theorems and the shape of the molluscan shell. Bulletin of Mathematical Biology 38:567-575.
60. McCartney, K., and D. E. Loper. 1989. Optimized skeletal morphologies of silicoflagellate genera Dictyocha and Distephanus. Paleobiology 15:283-298.
61. McGhee, G. R., Jr. 1978. Analysis of shell torsion phenomenon in Bivalvia. Lethaia 11:315-329.
62. McGhee, G. R., Jr. 1980. Shell form in the biconvex articulate Brachiopoda: a geometric analysis. Paleobiology 6:57-76.
63. McGhee, G. R., Jr. 1991. Theoretical morphology: the concept and its applications. In N. L. Gilinsky and P. W. Signor, eds. Analytical paleobiology. Short Course in Paleontology 4:87-102. Paleontological Society, Knoxville, Tenn.
64. McGhee, G. R., Jr. 1999. Theoretical morphology: the concept and its applications (Perspectives in Paleobiology and Earth History Series). Columbia University Press, New York.
65. McGhee, G. R., Jr. 2001. Exploring the spectrum of existent, nonexistent, and impossible biological form. Trends in Ecology and Evolution 16:172-173.
66. McGhee, G. R., Jr. 2007. The geometry of evolution: adaptative landscapes and theoretical morphospaces. Cambridge University Press, Cambridge.
67. McKinney, F. K., and D. M. Raup. 1982. A turn in the right direction: simulation of erect spiral growth in the bryozoans Archimedes and Bugula. Paleobiology 8:101-112.
68. Meinhardt, H. 1995. The algorithmic beauty of sea shells. Springer, Berlin.
69. Merks, R. M. H., A. G. Hoekstra, J. A. Kaandorp, and P. M. A. Sloot. 2003. Models of coral growth: spontaneous branching, compactification and the Laplacian growth assumption. Journal of Theoretical Biology 224:153-166.
70. Merks, R. M. H., A. G. Hoekstra, J. A. Kaandorp, and P. M. A. Sloot. 2004. Polyp oriented modelling of coral growth. Journal of Theoretical Biology 228:559-576.
71. Moseley, H. 1838. On the geometrical forms of turbinated and discoid shells. Philosophical Transactions of the Royal Society of London for 1838:351-370.
72. Navarro, N. 2003. MDA: a MATLAB-based program for morphospace-disparity analysis. Computers and Geosciences 29: 655-664.
73. Neige, P. 2003. Spatial patterns of disparity and diversity of the recent cuttlefishes (Cephalopoda) across the Old World. Journal of Biogeography 30:1125-1137.
74. Niklas, K. J. 2004. Computer models of early land plant evolution. Annual Review of Earth and Planetary Sciences 32:467-66.
75. Niklas, K. J., and V. Kerchner. 1984. Mechanical and photosynthetic constraints on the evolution of plant shape. Paleobiology 10:79-101.
76. Okamoto, T. 1984. Theoretical morphology of Nipponites (a heteromorph ammonoid). Kaseki (fossils). Palaeontological Society of Japan 36:37-51. [In Japanese.]
77. Okamoto, T. 1988. Analysis of heteromorph ammonoids by differential geometry. Palaeontology 31:35-52.
78. Papentin, F., and H. Röder. 1975. Feeding patterns: the evolution of a problem and a problem of evolution. Neues Jahrbuch für Geologie und Paläontologie, Monatshefte 1975:184-191.
79. Parkinson, J., Y. Brechet, and R. Gordon. 1999. Centric diatom morphogenesis: a model based on a DLA algorithm investigating the potential role of microtubules. Biochimica et Biophysica Acta 1452:89-102.
80. Plotnick, R. E. 2002. Ecological and L-system based simulations of trace fossils. Palaeogeography, Palaeoclimatology, Palaeoecology 192:45-58.
81. Prusinkiewicz, P. 1986. Graphical applications of L-systems. Proceedings of Graphics Interface 86:247-253.
82. Prusinkiewicz, P. 1993. Modeling and visualization of biological structures. Proceeding of Graphics Interface 93:128-137.
83. Prusinkiewicz, P. 1998. Modeling of spatial structure and development of plants: a review. Scientia Horticulturae 74:113-149.
84. Prusinkiewicz, P. 2004. Modeling plant growth and development. Current Opinion in Plant Biology 7:79-83.
85. Prusinkiewicz, P., and A. Lindenmayer. 1996. The algorithmic beauty of plants (2d printing.). Springer, Berlin.
86. Rasskin-Gutman, D. 2003. Boundary constraints for the emergence of form. Pp. 305-322 in G. Müller and S. Newman, eds. Origination of organismal form. MIT Press, Cambridge.
87. Rasskin-Gutman, D., and A. D. Buscalioni. 1996. Affine transformation as a model of virtual form change for generating morphospaces. In L. F. Marcus, M. Corti, A. Loy, G. J. P. Naylor, and D. Slice, eds. 1996. Advances in morphometrics. NATO ASI Series A 284:169-178. Plenum, New York.
88. Rasskin-Gutman, D., and A. D. Buscalioni. 2001. Theoretical morphology of the Archosaur (Reptilia: Diapsida) pelvic girdle. Paleobiology 27:59-78.
89. Rasskin-Gutman, D., and J-. C. Izpisúa-Belmonte. 2004. Theoretical morphology of developmental asymmetries. Bioessays 26:405-412.
90. Raup, D. M. 1966. Geometric analysis of shell coiling: general problems. Journal of Paleontology 40:1178-1190.
91. Raup, D. M. 1967. Geometric analysis of shell coiling: coiling in ammonoids. Journal of Paleontology 41:43-65.
92. Raup, D. M. 1968. Theoretical morphology of echinoid growth. Journal of Paleontology 42:50-63.
93. Raup, D. M. 1969. Modeling and simulation of morphology by computer. Proceedings of the North American Paleontological Convention, Part B:71-83.
94. Raup, D. M. 1972. Approaches to morphologic analysis. Pp. 28-44 in T. J. M. Schopf, eds. Models in paleobiology. Freeman, Cooper, San Francisco.
95. Raup, D. M. 1987. Neutral models in paleobiology. Pp. 121-132 in M. H. Nitecki and A. Hoffman, eds. Neutral models in biology. Oxford University Press, Oxford.
96. Raup, D. M., and A. Michelson. 1965. Theoretical morphology of the coiled shell. Science 147:1294-1295.
97. Raup, D. M., and A. Seilacher. 1969. Fossil foraging behavior: computer simulation. Science 166:994-995.
98. Reif, W.-E., and D. B. Weishampel. 1991. Theoretical morphology, an annotated bibliography 1960-1990. Courier Forschungsinstitut Senckenberg 142:1-140.
99. Rice, S, H. 1998. The bio-geometry of mollusc shells. Paleobiology 24:133-149.
100. Roy, K. and M. Foote. 1997. Morphological approaches to measuring biodiversity. Trends in Ecology and Evolution 12:277-281.
101. Saunders, W. B., and A. R. H. Swan. 1984. Morphology and morphospace diversity of mid-Carboniferous (Namurian) ammonoids in time and space. Paleobiology 10:195-228.
102. Saunders, W B., D. M. Work, and S. Nikolaeva. 2004. The evolutionary history of shell geometry in Paleozoic ammonoids. Paleobiology 30:19-43.
103. Savazzi, E. 1987. Geometric and functional constraints on bivalve shell morphology. Lethaia 20:293-306.
104. Savazzi, E. 1990. Biological aspects of theoretical shell morphology. Lethaia 23:195-212.
105. Schindel, D. E. 1990. Unoccupied morphospace and the coiled geometry of gastropods: architectural constraint or geometric covariation. Pp. 270-304 in R. M. Ross and W. M. Allmon, eds. Causes of evolution: a paleontological perspective. University of Chicago Press, Chicago.
106. Signes, M., J. Bijma, C. Hemleben, and R. Ott. 1993. A model for planktic foraminiferal shell growth. Paleobiology 19:71-91.
107. Starcher, R. W., and G. R. Jr. McGhee. 2000. Fenestrate theoretical morphology: geometric constraints on lophophore shape and arrangement in extinct Bryozoa. Paleobiology 26:116-136.
108. Starcher, R. W., and G. R. Jr. McGhee. 2003. Fenestrate graptolite theoretical morphology: geometric constraints on lophophore shape and arrangement in extinct Hemichordates. Journal of Paleontology 77:360-367.
109. Stolarski, J., E. Roniewicz, and T. Grycuk. 2004. A model for furcate septal increase in a Triassic scleractiniamorph. Acta Palaeontologica Polonica 49:529-542.
110. Stone J. R. 1995. Cerioshell: a computer program designed to simulate variation in shell form. Paleobiology 21:509-519.
111. Stone J. R. 1996. The evolution of ideas: a phylogeny of shell models. American Naturalist 148:904-929.
112. Stone J. R. 1997. The spirit of D'Arcy Thompson dwells in empirical morphospaces. Mathematical Biosciences 142:13-30.
113. Sumner, R. W. 2001. Pattern formation in lichen. M.S. thesis. Massachusetts Institute of Technology, Cambridge.
114. Swan, A. R. H. 1999. Computer models of fossils morphology. Pp. 157-179 in D. A. T. Harper, ed. Numerical palaeobiology. Wiley, Chichester, U.K.
115. Swan, A. R. H. 2003. Occupation of Morphospace. Pp. 157-161 in D. E. G. Briggs and P. R. Crowther, eds. Palaeobiology II. Blackwell Science, Oxford.
116. Swan, A. R. H., and S. Kershaw. 1994. A computer model for skeletal growth of stromatoporoids. Palaeontology 37:409-423.
117. Swan, A. R. H., and W. B. Saunders. 1987. Function and shape in late Paleozoic (mid-Carboniferous) ammonoids. Paleobiology 13:297-311.
118. Thomas, R. D. K., and W.-E. Reif. 1993. The skeleton space: a finite set of organic designs. Evolution 47:341-360.
119. Thomas, R. D., R. M. Shearman, and G. W. Stewart. 2000. Evolutionary exploitation of design options by the first animals with hard skeletons. Science 288:1239-1242.
120. Turing, A. M. 1952. The chemical basis of morphogenesis. Philosophical Transactions of the Royal Society of London B 237: 37-72.
121. Tyszka, J., and P. Topa. 2005. A new approach to modeling of foraminiferal shells. Paleobiology 31:326-541.
122. Tyszka, J., P. Topa, and K. Saczka. 2005. State-of-the-art in modelling of foraminiferal shells: searching for an emergent model. Studia Geologica Polonica 124:143-157.
123. Ubukata, T. 2000. Theoretical morphology of hinge and shell form in Bivalvia: geometric constraints derived from space conflict between umbones. Paleobiology 26:606-624.
124. Ubukata, T. 2003a. A theoretical morphologic analysis of bivalve ligaments. Paleobiology 29:369-380.
125. Ubukata, T. 2003b. Pattern of growth rate around aperture and shell form in Bivalvia: a theoretical morphological study. Paleobiology 29:480-491.
126. Ubukata, T. 2005. Theoretical morphology of bivalve shell sculptures. Paleobiology 31:643-655.
127. Usami, Y. 2006. Theoretical study on the body form and swimming pattern of Anomalocaris based on hydrodynamic simulation. Journal of Theoretical Biology 238:11-17.
128. Vermeij, G. J. 1971. Gastropod evolution and morphological diversity in relation to shell geometry. Journal of Zoology 163: 15-23.
129. Ward, P. 1980. Comparative shell shape distributions in Jurassic-Cretaceous ammonites and Jurassic-Tertiary nautilids. Paleobiology 6:32-43.
130. Waters, J. A. 1977. Quantification of shape by use of Fourier analysis: the Mississippian blastoid genus Pentremites. Paleobiology 3:288-299.
131. Webb, L. R, and A. R. H. Swan. 1996. Estimation of parameters of foraminiferal test geometry by image analysis. Palaeontology 39:471-475.