Selective press extinctions, but not random pulse extinctions, cause delayed ecological recovery in communities of digital organisms

American Naturalist

Volumn 173, Issue 4, 2009, Pages

  Yedid, Gabriel ^a,b   Ofria, Charles A ^c   Lenski, Richard E ^d  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b NANJING INSTITUTE OF GEOLOGY AND PALAEONTOLOGY   (China)

^c Michigan State University   (United States)

^d Michigan State University   (United States)

Author keywords

Digital organisms; Experimental evolution; Mass extinction; Recovery; Selectivity

Indexed keywords

ADAPTATION; COMMUNITY RESPONSE; ECOLOGICAL IMPACT; ENVIRONMENTAL DISTURBANCE; EXPERIMENTAL STUDY; MASS EXTINCTION; PALEONTOLOGY; RESOURCE AVAILABILITY; TROPHIC LEVEL;

ADAPTATION; ARTICLE; COMPUTER SIMULATION; ECOSYSTEM; EVOLUTION; FOOD CHAIN; PHENOTYPE; PHYSIOLOGY; SPECIES EXTINCTION; THEORETICAL MODEL;

ADAPTATION, BIOLOGICAL; COMPUTER SIMULATION; ECOSYSTEM; EVOLUTION; EXTINCTION, BIOLOGICAL; FOOD CHAIN; MODELS, THEORETICAL; PHENOTYPE;

EID: 63449126094     PISSN: 00030147     EISSN: None     Source Type: Journal    
DOI: 10.1086/597228     Document Type: Article

References (87)

1. Amaral, L. A. N., and M. Meyer. 1999. Environmental changes, coextinction, and patterns in the fossil record. Physical Review Letters 82:652-655.
2. Arnold, A. J., D. C. Kelly, and W. C. Parker. 1995. Causality and Cope's rule: evidence from the planktonic foraminifera. Journal of Paleontology 69:203-210.
3. Bambach, R. K., A. H. Knoll, and J. J. Sepkoski Jr. 2002. Anatomical and ecological constraints on Phanerozoic animal diversity in the marine realm. Proceedings of the National Academy of Sciences of the USA 99:6854-6859.
4. Benton, M. J., and R. J. Twitchett. 2003. How to kill (almost) all life: the end-Permian extinction event. Trends in Ecology & Evolution 18:358-365.
5. Benton, M. J., V. P. Tverdokhlebov, and M. V. Surkov. 2004. Ecosystem remodeling among vertebrates at the Permian-Triassic boundary in Russia. Nature 432:97-100.
6. Botha, J., and R. M. H. Smith. 2006. Rapid vertebrate recuperation in the Karoo Basin of South Africa following the end-Permian extinction. Journal of African Earth Sciences 45:502-514.
7. Bottjer, D. J., and J.-C. Gall. 2005. The Triassic recovery, the dawn of the modern biota. Comptes Rendus Palevol 4:453-461.
8. Carr, T. R., and J. A. Kitchell. 1980. Dynamics of taxonomic diversity. Paleobiology 6:427-443.
9. Chow, S. S., C. O. Wilke, C. Ofria, R. E. Lenski, and C. Adami. 2004. Adaptive radiation from resource competition in digital organisms. Science 305:84-86.
10. Cooper, T., and C. Ofria. 2002. Evolution of stable ecosystems in populations of digital organisms. Pages 227-232 in R. K. Standish, M. A. Bedau, and H. A. Abbass, eds. Eighth International Conference on Artificial Life, December 9-13, Sydney, New South Wales. MIT Press, Cambridge, MA.
11. D'Hondt, S., P. Donaghay, J. C. Zachos, D. Luttenberg, and M. Lindinger. 1998. Organic carbon fluxes and ecological recovery from the Cretaceous-Tertiary mass extinction. Science 282:276-279.
12. Erwin, D. H. 1998a. After the end: recovery from extinction. Science 279:1324-1325.
13. -. 1998b. The end and the beginning: recoveries from mass extinctions. Trends in Ecology & Evolution 13:344-349.
14. -. 2000. Life's downs and ups. Nature 404:129-130.
15. -. 2001. Lessons from the past: biotic recoveries from mass extinctions. Proceedings of the National Academy of Sciences of the USA 98:5399-5403.
16. -. 2007. Increasing returns, ecological feedback, and the Early Triassic recovery. Palaeoworld 16:9-15.
17. Erwin, D. H., J. W. Valentine, and J. J. Sepkoski. 1987. A comparative study of diversification events: the early Paleozoic versus the Mesozoic. Evolution 41:1177-1186.
18. Fischer, A. G. 1981. Climatic oscillations in the biosphere. Pages 103-131 in M. H. Nitecki, ed. Biotic crises in ecological and evolutionary time. Academic Press, New York.
19. Foote, M. 1996. Ecological controls on the evolutionary recovery of post-Paleozoic crinoids. Science 274:1492-1495.
20. -. 1999. Morphological diversity in the evolution of Paleozoic and post-Paleozoic crinoids. Paleobiology 25(suppl.):1-115.
21. -. 2003. Origination and extinction through the Phanerozoic: a new approach. Journal of Geology 111:125-148.
22. -. 2005. Pulsed origination and extinction in the marine realm. Paleobiology 31:6-20.
23. Gould, S. J. 1989. Wonderful life: the Burgess shale and the nature of history. Norton, New York.
24. Grard, A., L. M. François, C. Dessert, B. Dupré, and Y. Goddéris. 2005. Basaltic volcanism and mass extinction at the Permo-Triassic boundary: environmental impact and modeling of the global carbon cycle. Earth and Planetary Science Letters 234:207-221.
25. Hallam, A., and P. B. Wignall. 1997. Mass extinctions and their aftermath. Oxford University Press, Oxford.
26. Hewzulla, D., M. C. Boulter, M. J. Benton, and J. M. Halley. 1999. Evolutionary patterns from mass originations and mass extinctions. Philosophical Transactions of the Royal Society B: Biological Sciences 354:463-469.
27. Holland, S. M. 1995. The stratigraphic distribution of fossils. Paleobiology 21:92-109.
28. -. 2000. The quality of the fossil record: a sequence stratigraphic perspective. Pages 148-168 in D. H. Erwin and S. L. Wing, eds. Deep time: paleobiology's perspective. Paleontological Society, Lawrence, KS.
29. Holland, S. M., and M. E. Patzkowsky. 2002. Stratigraphic variation in the timing of first and last occurrences. Palaios 17:134-146.
30. Jablonski, D. 1986. Evolutionary consequences of mass extinctions. Pages 313-330 in D. M. Raup and D. Jablonski, eds. Life science research reports. Vol. 36. Patterns and processes in the history of life. Springer, Berlin.
31. -. 1996. Body size and macroevolution. Pages 256-289 in D. Jablonski, D. H. Erwin, and J. H. Lipps, eds. Evolutionary paleobiology. University of Chicago Press, Chicago.
32. -. 2005. Mass extinctions and macroevolution. Paleobiology 31:192-210.
33. Jin, Y.-G., Y. Wang, W. Wang, Q.-H. Shang, C.-Q. Cao, and D. H. Erwin. 2000. Pattern of marine mass extinction near the Permian - Triassic boundary in south China. Science 289:432-436.
34. Kidwell, S. M., and S. M. Holland. 2002. The quality of the fossil record: implications for evolutionary analyses. Annual Review of Ecology and Systematics 33:561-588.
35. Kirchner, J. W. 2002. Evolutionary speed limits inferred from the fossil record. Nature 415:65-67.
36. Kirchner, J. W., and A. Weil. 2000a. Correlations in fossil extinction and origination rates through geological time. Proceedings of the Royal Society B: Biological Sciences 267:1301-1309.
37. -. 2000b. Delayed biological recovery from extinctions throughout the fossil record. Nature 404:177-180.
38. Knoll, A. H., R. K. Bambach, J. L. Payne, S. Pruss, and W. W. Fischer. 2007. Paleophysiology and end-Permian mass extinction. Earth and Planetary Science Letters 256:295-313.
39. LaBarbera, M. 1986. The evolution and ecology of body size. Pages 69-98 in D. M. Raup and D. Jablonski, eds. Life science research reports. Vol. 36. Patterns and processes in the history of life. Springer, Berlin.
40. Lenski, R. E., C. Ofria, T. C. Collier, and C. Adami. 1999. Genome complexity, robustness and genetic interactions in digital organisms. Nature 400:661-664.
41. Lenski, R. E., C. Ofria, R. T. Pennock, and C. Adami. 2003. The evolutionary origin of complex features. Nature 423:139-144.
42. Lindeman, R. 1942. The trophic-dynamic aspect of ecology. Ecology 23:399-418.
43. Looy, C. V., W. A. Brugman, D. L. Dilcher, and H. Visscher. 1999. The delayed resurgence of equatorial forests after the Permian-Triassic ecological crisis. Proceedings of the National Academy of Sciences of the USA 96:13857-13862.
44. Lu, P. J., M. Yogo, and C. R. Marshall. 2006. Phanerozoic marine biodiversity dynamics in light of the incompleteness of the fossil record. Proceedings of the National Academy of Sciences of the USA 103:2736-2739.
45. Martin, R. E. 1996. Secular increase in nutrient levels through the Phanerozoic: implications for productivity, biomass, diversity, and extinction of the marine biosphere. Paleontological Journal 30: 637-643.
46. McGhee, G. R., P. M. Sheehan, D. J. Bottjer, and M. L. Droser. 2004. Ecological ranking of Phanerozoic biodiversity crises: ecological and taxonomic severities are decoupled. Palaeogeography, Palaeoclimatology, Palaeoecology 211:289-297.
47. McKinney, M. L. 1997. Extinction vulnerability and selectivity: combining ecological and paleontological views. Annual Review of Ecology and Systematica 28:495-516.
48. Misevic, D., C. Ofria, and R. E. Lenski. 2006. Sexual reproduction reshapes the genetic architecture of digital organisms. Proceedings of the Royal Society B: Biological Sciences 273:457-464.
49. Myers, N., and A. H. Knoll. 2001. The biotic crisis and the future of evolution. Proceedings of the National Academy of Sciences of the USA 98:5389-5392.
50. Norris, R. D. 1991. Biased extinction and evolutionary trends. Paleobiology 17:388-399.
51. Odling-Smee, F. J., K. N. Laland, and M. W. Feldman. 2003. Niche construction: the neglected process in evolution. Princeton University Press, Princeton, NJ.
52. Ofria, C., and C. Wilke. 2004. Avida: a software platform for research in computational evolutionary biology. Journal of Artificial Life 10:191-229.
53. Pruss, S., and D. B. Bottjer. 2005. The reorganization of reef communities following the end-Permian mass extinction. Comptes Rendus Palevol 4:485-500.
54. Pruss, S., D. B. Bottjer, F. A. Corsetti, and A. Baud. 2006. A global marine sedimentary response to the end-Permian mass extinction: examples from southern Turkey and the western United States. Earth-Science Reviews 78:193-206.
55. Rampino, M. R., and K. Caldeira. 2005. Major perturbation of ocean chemistry and a "Strangelove Ocean" after the end-Permian mass extinction. Terra Nova 17:554-559.
56. Rampino, M. R., A. Prokoph, and A. Adler. 2000. Tempo of the end-Permian event: high-resolution cyclostratigraphy at the Permian-Triassic boundary. Geology 28:643-646.
57. Rhodes, M. C., and C. W. Thayer. 1991. Mass extinctions: ecological selectivity and primary production. Geology 19:877-880.
58. Roopnarine, P. D., K. D. Angielczyk, S. C. Wang, and R. Hertog. 2007. Trophic network models explain instability of Early Triassic terrestrial communities. Proceedings of the Royal Society B: Biological Sciences 274:2077-2086.
59. Ross, C. A., and J. R. P. Ross. 1995. Foraminiferal zonation of the late Paleozoic depositional sequences. Marine Micropaleontology 26:469-478.
60. Rozen, D. E., D. Schneider, and R. E. Lenski. 2005. Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism. Journal of Molecular Evolution 61: 171-180.
61. Russell, D. 1977. The biotic crisis at the end of the Cretaceous period. Syllogeus, National Museum of Natural Sciences of Canada 12: 11-23.
62. Sahney, S., and M. J. Benton. 2008. Recovery from the most profound mass extinction of all time. Proceedings of the Royal Society B: Biological Sciences 275:759-765.
63. Saunders, W. B., D. M. Work, and S. V. Nikovaeva. 1999. Evolution of complexity in Paleozoic ammonoid sutures. Science 286:760-763.
64. Schluter, D. 2000. The ecology of adaptive radiation. Oxford University Press, Oxford.
65. Schubert, J. K., and D. Bottjer. 1992. Early Triassic stromatolites as post mass extinction disaster forms. Geology 20:883-886.
66. Sepkoski, J. J. 1978. A kinetic model of Phanerozoic taxonomic diversity. 1. Analysis of marine orders. Paleobiology 4:223-251.
67. -. 1979. A kinetic model of Phanerozoic taxonomic diversity. 2. Early Phanerozoic families and multiple equilibria. Paleobiology 5:222-251.
68. -. 1984. A kinetic model of Phanerozoic taxonomic diversity. 3. Post-Paleozoic families and mass extinctions. Paleobiology 10: 246-267.
69. -. 1992. A compendium of fossil marine families. Milwaukee Public Museum Contributions to Biology and Geology 51:1-125.
70. -. 1997. Biodiversity: past, present, and future. Journal of Paleontology 71:533-539.
71. -. 2002. A compendium of fossil marine and animal genera. Bulletin of American Paleontology 363:1-563.
72. Simpson, G. G. 1944. Tempo and mode in evolution. Columbia University Press, New York.
73. -. 1953. The major features of evolution. Columbia University Press, New York.
74. Solé, R. V., J. M. Montoya, and D. H. Erwin. 2002. Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics. Philosophical Transactions of the Royal Society B: Biological Sciences 357:697-707.
75. Stanley, S., and X. Yang. 1994. A double mass extinction at the end of the Paleozoic era. Science 266:1340-1344.
76. Travisano, M., J. A. Mongold, A. F. Bennett, and R. E. Lenski. 1995. Experimental tests of the roles of adaptation, chance, and history in evolution. Science 267:87-90.
77. Twitchett, R. J. 2001. Incompleteness of the Permian-Triassic fossil record: a consequence of productivity decline? Geological Journal 36:341-353.
78. -. 2006. The palaeoclimatology, palaeoecology, and palaeoen-vironmental analysis of mass extinction events. Palaeogeography, Palaeoclimatology, Palaeoecology 252:190-213.
79. Twitchett, R. J., C. V. Looy, R. Morante, H. Visscher, and P. B. Wignall. 2001. Rapid and synchronous collapse of marine and terrestrial ecosystems during the end-Permian biotic crisis. Geology 29:351-354.
80. Urbanek, M. 1993. Biotic crises in the history of early Silurian graptoloids: a paleobiological model. Historical Biology 7:29-50.
81. Valentine, J. W. 1980. Determinants of diversity in higher taxonomic categories. Paleobiology 6:444-450.
82. Wagner, P. J., M. A. Kosnik, and S. Lidgard. 2006. Abundance distributions imply elevated complexity of post-Paleozoic marine ecosystems. Science 314:1289-1292.
83. Whittaker, R. H. 1977. Communities and ecosystems. Macmillan, New York.
84. Yedid, G., and G. Bell. 2001. Microevolution in an electronic microcosm. American Naturalist 157:465-487.
85. -. 2002. Macroevolution simulated with autonomously replicating computer programs. Nature 420:810-812.
86. Yedid, G., C. A. Ofria, and R. E. Lenski. 2008. Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms. Journal of Evolutionary Biology 21:1335-1357.
87. Yin, H.-F., Q.-L. Feng, X.-L. Lai, A. Baud, and J.-N. Tong. 2007. The protracted Permo-Triassic crisis and multi-episode extinction around the Permian-Triassic boundary. Global and Planetary Change 55:1-20.