Identifying heterogeneity in rates of morphological evolution: Discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi)

Evolution

Volumn 66, Issue 2, 2012, Pages 330-348

  Lloyd, Graeme T ^a,b   Wang, Steve C ^c   Brusatte, Stephen L ^d  

^a DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^b SWARTHMORE COLLEGE   (United States)

^c DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^d Columbia University ^*  (United States)

Author keywords

Adaptive radiation; Evolutionary rates; Lungfish; Morphological evolution; Paleontology; Punctuated equilibrium

Indexed keywords

ADAPTIVE RADIATION; DATA SET; DEVONIAN; EVOLUTIONARY BIOLOGY; FISH; FOSSIL RECORD; HETEROGENEITY; MORPHOLOGY; PALEONTOLOGY; PHYLOGENETICS; QUANTITATIVE ANALYSIS;

ANIMAL; ARTICLE; CLASSIFICATION; EVOLUTION; FISH; FOSSIL; GENETICS; HISTOLOGY; PHYLOGENY;

ANIMALS; BIOLOGICAL EVOLUTION; FISHES; FOSSILS; PHYLOGENY;

DIPNOI; SARCOPTERYGII;

EID: 84856238797     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2011.01460.x     Document Type: Article

References (90)

1. Adams, D. C., C. M. Berns, K. H. Kozak, and J. J. Wiens. 2009. Are rates of species diversification correlated with rates of morphological evolution? Proc. R. Soc. Lond. B. 276:2729-2738.
2. Ahlberg, P. E., and M. M. Smith. 2006. Developmental plasticity and disparity in early dipnoan (lungfish) dentitions. Evol. Dev. 8:331-349.
3. Alfaro, M. E., F. Santini, C. Brock, H. Alamillo, A. Dornburg, D. L. Rabosky, G. Carnevale, and L. J. Harmon. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Natl. Acad. Sci. USA 106:13410-13414.
4. Alroy, J., M. Aberhan, D. J. Bottjer, M. Foote, F. T. Fursich, P. J. Harries, A. J. W. Hendy, S. M. Holland, L. C. Ivany, W. Kiessling, et al. 2008. Phanerozoic trends in the global diversity of marine invertebrates. Science 321:97-100.
5. Apesteguia, S., F. L. Agnolin, and K. Claeson. 2007. Review of Cretaceous dipnoan from Argentina (Sarcopterygii, Dipnoi) with descriptions of new species. Rev. Mus. Argentino Cienc. Nat. n.s. 9:27-40.
6. Benjamini, Y., and Y. Hochberg. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57:289-300.
7. Benton, M. J. 1987. Mass extinctions among families of non marine tetrapods: the data, Mém. Soc géol France n.s. 150:21-32.
8. Bininda-Emonds, O. R. P. 2004. perlRat. pl v1.0.9a. Program distributed by author. Institut fur Spezeille Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena.
9. Bromham, L., M. Woolfit, M. S. Y. Lee, and A. Rambaut. 2002. Tesonship between morphological and molecular rates along phylogenies. Evolution 56:1921-1930.
10. Brusatte, S. L., M. J. Benton, M. Ruta, and G. T. Lloyd. 2008. Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs. Science 321:1485-1488.
11. Brusatte, S. L. 2011. Calculating the tempo of morphological evolution: rates of discrete character change in a phylogenetic context. Pp. 53-74 in: A. M. T. Elewa, ed. Computational paleontology. Springer-Verlag, Heidelberg.
12. Brusatte, S. L., M. J. Benton, G. T. Lloyd, M. Ruta, and S. C. Wang. 2011. Macroevolutionary patterns in the evolutionary radiation of archosaurs (Tetrapoda: Diapsida). Earth Environ. Sci. Trans. R. Soc. Edinburgh 101:367-382.
13. Cavin, L., V. Suteethorn, E. Buffetaut, and H. Tong. 2007. A new Thai Mesozoic lungfish (Sarcopterygii, Dipnoi) with an insight into post-Palaeozoic dipnoan evolution. Zool. J. Linn. Soc. 149:141-177.
14. Chan, K. M. A., and B. R. Moore. 2002. Whole-tree methods for detecting differential diversification rates. Syst. Biol. 51:855-865.
15. Chan, K. M. A., and B. R. Moore. 2005. SymmeTREE: whole-tree analysis of differential diversification rates. Bioinformatics 21:1709-1710.
16. Chaloner, W. G., and A. Sheerin. 1979. Devonian macrofloras. Spec. Pap. Palaeontol. 23:145-161.
17. Collar, D. C., T. J. Near, and P. C. Wainwright. 2005. Comparative analysis of morphological diversity: does disparity accumulate at the same rate in two lineages of centrarchid fishes? Evolution 59:1783-1794.
18. Cooper, N., and A. Purvis. 2009. What factors shape rates of phenotypic evolution? A comparative study of cranial morphology of four mammalian clades. J. Evol. Biol. 22:1024-1035.
19. Darwin, C. 1859. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. J. Murray, London.
20. Dawkins, R. 2004. The ancestor's tale: a pilgrimage to the dawn of life. Weidenfeld Nicolson Illustrated, London.
21. Derstler, K. L. 1982. Estimating the rate of morphological change in fossil groups. Proc. Third N. Am. Paleo. Conv. 1:131-136.
22. Dollo, L. 1895. Sur la phylogenie des dipneustes. Bull. Soc. belge Geol. Pal. Hydr. 9: 979-128.
23. Eldredge, N., and S. J. Gould. 1972. Punctuated equilibria: an alternative to phyletic gradualism. Pp. 92-115 in T. J. M. Schopf, ed. Models in paleobiology. Freeman, Cooper and Co., San Francisco.
24. Fitzinger, L. J. 1837. Uber Lepidosiren. Archiv. Naturgesch. 2:232.
25. Foote, M., and J. J. Sepkoski. 1999. Absolute measures of the completeness of the fossil record. Nature 398:415-417.
26. Forey, P. L. 1988. Golden jubilee for the coelacanth Latimeria chalumnae. Nature 336:727-732.
27. Friedman, M. 2007. The interrelationships of Devonian lungfishes (Sarcopterygii: Dipnoi) as inferred from neurocranial evidence and new data from the genus Soederberghia Lehman, 1959. Zool. J. Linn. Soc. 151:115-171.
28. Garland, T. G. 1992. Rate tests for phenotypic evolution using phylogenetically independent contrasts. Am. Nat. 140:509-519.
29. Gatesy, J., C. Matthee, R. deSalle, and C. Hayashi. 2002. Resolution of a supertree-supermatrix paradox. Syst. Biol. 51:652-664.
30. Gatesy, J., R. H. Baker, and C. Hayashi. 2004. Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia. Syst. Biol. 53:342-355.
31. Gavrilets, S., and J. B. Losos. 2009. Adaptive radiation: contrasting theory with data. Science 323:732-737.
32. Gradstein, F. M., J. G. Ogg, and A. G. Smith. 2004. A geologic time scale. Cambridge Univ. Press, Cambridge.
33. Harmon, L. J., J. Melville, A. Larson, and J. B. Losos. 2008. The role of geography and ecological opportunity in the diversification of day geckos (Phelsuma). Syst. Biol. 57:562-573.
34. Hill, R. V. 2005. Integration of morphological data sets for phylogenetic analysis of Amniota: the importance of integumentary characters and increased taxonomic sampling. Syst. Biol. 54:530-547.
35. Hutcheon, J. M., and T. Garland. 2004. Are megabats big? J. Mammal. Evol. 11:257-277.
36. Jones, S. 1999. Almost like a whale. Doubleday, London.
37. Jones, K. E., O. R. P. Bininda-Emonds, and J. L. Gittleman. 2005. Bats, clocks, and rocks: diversification patterns in Chiroptera. Evolution 59:2243-2255.
38. Knopf, A. 1949. Time in Earth history. Pp. 1-9. in G. L. Jepsen, G. G. Simpson, E. Mayr, eds. Genetics, paleontology and evolution. Princeton Univ. Press, Princeton.
39. Krupina, N. I., and R. R. Reisz. 2000. Phylogeny of Devonian dipnoans, with special emphasis on forms from the Russian platform. Paleontol. J. 34:S147-S153.
40. Levinton, J. S. 2001. Genetics, paleontology, and macroevolution, 2nd ed. Cambridge Univ. Press, Cambridge.
41. Lloyd, G. T., K. E. Davis, D. Pisani, J. E. Tarver, M. Ruta, M. Sakamoto, D. W. E. Hone, R. Jennings, and M. J. Benton. 2008. Dinosaurs and the Cretaceous Terrestrial Revolution. Proc. R. Soc. Lond. B 275:2483-2490.
42. Marshall, C. R. 1986. Lungfish: phylogeny and parsimony. J. Morphol. Suppl. 1:151-162.
43. McConway, K. J., and H. J. Sims. 2004. A likelihood-based method for testing for non-stochastic variation of diversification rates in phylogenies. Evolution 58:12-23.
44. McKinney, M. L. 1990. Classifying and analyzing evolutionary trends. Pp. 28-58. in K. J. McNamara, ed. Evolutionary trends. Belhaven, London.
45. MindEll, D. P., and C. E. Thacker. 1996. Rates of molecular evolution: phylogenetic issues and applications. Annu. Rev. Ecol. Syst. 27:279-303.
46. Moore, B. R., and M. J. Donoghue. 2009. A Bayesian approach for evaluating the impact of historical events on rates of diversification. Proc. Natl. Acad. Sci. USA 106:4307-4312.
47. Nixon, K. C. 1999. The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15:407-414.
48. Oakley, T. H. 2003. Maximum likelihood models of trait evolution. Comments Theor. Biol. 8:1-17.
49. O'Meara, B. C., C. Ané, M. J. Sanderson, and P. C. Wainwright. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922-933.
50. Omland, K. 1997. Correlated rates of molecular and morphological evolution. Evolution 51:1381-1393.
51. Pagel, M. 1998. Inferring evolutionary process from phylogenies. Zool. Scripta 26:331-348.
52. Paradis, E., J. Claude, and K. Strimmer. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290.
53. Paul, C. R. C. 1982. The adequacy of the fossil record. Pp. 75-117. in K. A. Joysey and A. E. Friday, eds. Problems of phylogenetic reconstruction. Academic Press, London.
54. Pinto, G., D. L. Mahler, L. J. Harmon, and J. B. Losos. 2008. Testing the island effect in adaptive radiation: rates and patterns of morphological diversification in Caribbean and mainland Anolis lizards. Proc. R. Soc. Lond. B 275:2749-2757.
55. Pol, D., and M. A. Norell. 2006. Uncertainty in the age of fossils and the stratigraphic fit to phylogenies. Syst. Biol. 55:512-521.
56. Qiao, T., and M. Zhu. 2009. A new tooth-plated lungfish from the Middle Devonian of Yunnan, China, and its phylogenetic relationships. Acta Zool. 90(Suppl. 1):236-252.
57. R Development Core Team. 2010. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, Available at:.
58. Raup, D. M., and S. M. Stanley. 1978. Principles of paleontology, 2nd ed. W. H. Freeman and Company, San Francisco.
59. Raup, D. M., and J. J. Sepkoski. 1982. Mass extinctions in the marine fossil record. Science 215:1501-1503.
60. Ree, R. H. 2005. Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis. Evolution 59:257-265.
61. Revell, L. J., L. J. Harmon, and D. C. Collar. 2008. Phylogenetic signal, evolutionary process, and rate. Syst. Biol. 57:591-601.
62. Ricklefs, R. E. 2007. Estimating diversification rates from phylogenetic information. Trends Ecol. Evol. 22:601-610.
63. Ridley, M. 1996. Evolution, 2nd ed.. Blackwell Science, Oxford.
64. Ruta, M., P. J. Wagner, and M. I. Coates. 2006. Evolutionary patterns in early tetrapods. I. Rapid initial diversification followed by decrease in rates of character change. Proc. R. Soc. Lond. B 273:2107-2111.
65. Ruta, M., D. Pisani, G. T. Lloyd, and M. J. Benton. 2007. A supertree of Temnospondyli: cladogenetic patterns in the most species-rich group of early tetrapods. Proc. R. Soc. Lond. B 274:3087-3095.
66. Sahney, S., and M. J. Benton. 2008. Recovery from the most profound mass extinction of all time. Proc. R. Soc. Lond. B 275:759-765.
67. Schluter, D. 2000. The ecology of adaptive radiation. Oxford University Press, Oxford.
68. Schultze, H.-P. 1992. Fossilium Catalogus Animalia pars 131: Dipnoi. Kugler, Amsterdam.
69. Schultze, H.-P., and C. R. Marshall. 1993. Contrasting the use of functional complexes and isolated characters in lungfish evolution. Mem. Assoc. Austral. Palaeo. 15:211-224.
70. Schultze, H.-P., and J. Chorn. 1997. The Permo-Carboniferous genus Sagenodus and the beginning of modern lungfish. Cont. Zool. 67:9-70.
71. Schultze, H.-P. 2001. Melanognathus, a primitive dipnoan from the Lower Devonian of the Canadian Arctic and the interrelationships of Devonian dipnoans. J. Vert. Paleo. 21:781-794.
72. Schultze, H.-P. 2004. Mesozoic sarcopterygians. Pp. 463-492 in G. Arratia and A. Tintori, eds. Mesozoic Fishes 3-Systematics, paleoenvironments and biodiversity. Verlag Dr. Freidrich Pfeil, Munchen.
73. Sepkoski, J. J. 1978. A kinetic model of Phanerozoic taxonomic diversity, I: analysis of marine orders. Paleobiology 4:223-251.
74. Sepkoski, J. J. 1981. A factor analytic description of the Phanerozoic marine fossil record. Paleobiology 7:36-53.
75. Sepkoski, J. J. 1982. A compendium of fossil marine families. Milw. Pub. Mus. Cont. Biol. Geol. 51:1-156.
76. Sidlauskas, B. L. 2007. Testing for unequal rates of morphological diversification in the absence of a detailed phylogeny: a case study from characiform fishes. Evolution 61:299-316.
77. Simpson, G. G. 1944. Tempo and mode in evolution. Columbia Univ. Press, New York.
78. Simpson, G. G 1953. The major features of evolution. Simon and Schuster, New York.
79. Sims, H. J., and K. J. McConway. 2003. Non-stochastic variation of species-level diversification rates within angiosperms. Evolution 57:460-479.
80. Stanley, S. M. 1979. Macroevolution: pattern and process. W. H. Freeman and Company, San Francisco.
81. Swofford, D. L., and W. P. Maddison. 1987. Reconstructing ancestral character states under Wagner parsimony. Math. Biosci. 87:199-229.
82. Swofford, D. L. 2003. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods). Sinauer Associates, Sunderland.
83. Thomas, G. H., R. P. Freckleton, and T. Székely. 2006. Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds. Proc. R. Soc. Lond. B 273:1619-1624.
84. Tsuji, L. A., and J. Müller. 2009. Assembling the history of the Parareptilia: phylogeny, diversification, and a new definition of the clade. Fossil Record 12:71-81.
85. Wagner, G. P. 1980. Empirical information about the mechanism of typogenetic evolution. Naturwissenschaften 67:258-259.
86. Wagner, P. J. 1997. Patterns of morphologic diversification among the Rostroconchia. Paleobiology 23:115-150.
87. Wang, S. C., and P. Dodson. 2006. Estimating the diversity of dinosaurs. Proc. Natl. Acad. Sci. USA 103:13601-13605.
88. Westoll, T. S. 1949. On the evolution of the Dipnoi. Pp. 121-184 in G. L. Jepsen, G. G. Simpson, and E. Mayr, eds. Genetics, paleontology and evolution. Princeton Univ. Press, Princeton.
89. Wilkinson, M. 1994. Common cladistic information and its consensus representation: reduced Adams and reduced cladistic consensus trees and profiles. Syst. Biol. 43:343-368.
90. Young, G. C., and H.-P. Schultze. 2005. New osteichthyans (bony fishes) from the Devonian of Central Australia. Mitteil Mus Natur Berlin, Geowiss R 8:13-35.