Simulations of evolutionary radiations and their application to understanding the probability of a Cambrian explosion

Journal of Paleontology

Volumn 78, Issue 1, 2004, Pages 31-38

  Levinton, Jeffrey ^a   Dubb, Lindsey ^b   Wray, Gregory A ^c  

^a STONY BROOK UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAMBRIAN; EVOLUTION; PHYLOGENY;

AGNATHA; ANIMALIA; CHORDATA; ECHINODERMATA;

EID: 0346462953     PISSN: 00223360     EISSN: None     Source Type: Journal    
DOI: 10.1666/0022-3360(2004)078<0031:SOERAT>2.0.CO;2     Document Type: Article

References (43)

1. ABOUHEIF, E., R. ZARDOYA, AND A. MEYER. 1998. Limitations of metazoan 18S rRNA sequence data: implications for reconstructing a phylogeny of the animal kingdom and inferring the reality of the Cambrian explosion. Journal of Molecular Evolution, 47:394-405.
2. AGUINALDO, A. M. A., J. M. TURBEVILLE, L. S. LINFORD, M. C. RIVERA, J. R. GAREY, R. A. RAFF, AND J. A. LAKE. 1997. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature, 387: 489-493.
3. AYALA, F. J., A. RZHETSKY, AND F. J. AYALA. 1998. Origin of the metazoan phyla: molecular clocks confirm paleontological estimates. Proceedings of the National Academy of Science USA. 95:606-611.
4. BALAVOINE, G., AND A. ADOUTTE. 1998. One or three Cambrian radiations? Science, 280:397-398.
5. BOWRING, S. A., J. P. GROTZINGER, C. E. ISACHSEN, A. H. KNOLL, S. M. PELECHATY, AND P. KOLOSOV. 1993. Calibrating rates of Early Cambrian evolution. Science, 261:1293-1298.
6. BROMHAM, L., A. RAMBAUT, R. FORTEY, A. COOPER, AND D. PENNY. 1998. Testing the Cambrian explosion hypothesis using a new molecular dating technique. Proceedings of the National Academy of Science USA, 95:12386-12389.
7. DEROBERTIS, E. M., AND Y. SASAI. 1996. A common plan for dorsoventral patterning in Bilateria. Nature, 380:37-40.
8. FARRIS, J. S. 1970. Methods for computing Wagner trees. Systematic Zoology, 19:83-92.
9. FELSENSTEIN, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology, 27:401-410.
10. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17:368-376.
11. FELSENSTEIN, J. 1988. Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics, 22:521-565.
12. FELSENSTEIN, J. 1993. Phylip (Phylogeny Inference Package) 3.5c: Distributed by the author.
13. FORTEY, R. A., D. E. G. BRIGGS, AND M. A. WILLS. 1996. The Cambrian evolutionary 'explosion': decoupling cladogenesis from morphological disparity. Biological Journal of the Linnaean Society, 57:13-33.
14. GOULD, S. J. 1989. Wonderful Life. New York, Norton.
15. GOULD, S. J. 1995. Of it, not above it. Nature, 377:681-682.
16. GOULD, S. J. 1998. On embryos and ancestors. Natural History, p. 20-22, 58-63.
17. GU, X. 1998. Early metazoan divergence is about 830 million years ago. Journal of Molecular Evolution, 47:369-371.
18. HALANYCH, K. M. 1995. The phylogenetic position of the pterobranch hemichordates based on 18S rDNA sequence data. Molecular Phylogeny and Evolution, 4:72-76.
19. HAUSDORF, B. 2000. Early evolution of the bilateria. Systematic Biology, 49:130-142.
20. HENDY, M. D., AND D. PENNY. 1989. A framework for the quantitative study of evolutionary trees. Systematic Zoology, 38:297-309.
21. HILLIS, D. M. 1996. Inferring complex phylogenies. Nature, 383:130-131.
22. HILLIS, D. M., J. P. HUELSENBECK, AND D. L. SWOFFORD. 1994. Hobgoblin of phylogenetics? Nature, 369:363-364.
23. HUELSENBECK, J. P., AND D. M. HILLIS. 1993. Success of phylogenetic methods in the four-taxon case. Systematic Biology, 42:247-264.
24. KIM, J. 1996. General inconsistency conditions for maximum parsimony. Effects of branch lengths and of increasing numbers of taxa. Systematic Biology, 45:363-374.
25. KUHNER, M. K., AND J. FELSENSTEIN. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution, 11:459-468.
26. LEVINTON, J. S. 2001. Genetics, Paleontology, and Macroevolution. New York, Cambridge University Press, 617 p.
27. MCHUGH, D. 1997. Molecular evidence that echiurans and pogonophorans are derived annelids. Proceedings of the National Academy of Science USA, 94:8006-8009.
28. NIKOH, H., N. IWABE, K.-I. KUNA, M. OHNO, T. SUGIYAMA, Y. WATANABI, K. YASUI, Z. SHI-CUI, K. HORI, Y. SHIMURA, AND T. MIYATA. 1997. An estimate of divergence time of Parazoa and Eumetazoa and that of Cephalochordata and Vertebrata by aldolase and triose phosphate isomerase clocks. Journal of Molecular Evolution, 45:97-106.
29. OHNO, S. 1996. The notion of the Cambrian pananimalia genome. Proceedings National Academy of Science USA, 93:8475-8478.
30. PHILIPPE, H. C. A., AND A. ADOUTTE. 1994. Can the Cambrian explosion be inferred through molecular phylogeny. Development, 1994(Supplement):15-25.
31. POE, S., AND D. L. SWOFFORD. 1999. Taxon sampling revisited. Nature, 398:299-300.
32. RADINSKY, L. B. 1982. Evolution of skull shape in carnivores. 3. The origin and early radiation of the modern carnivore families. Paleobiology, 8:177-195.
33. RASSMUSSEN, B., S. BENGTSON, I. R. FLETCHER, AND N. J. MCNAUGHTON. 2002. Discoidal impressions and trace-like fossils more than 1200 million years old. Science, 296:1112-1115.
34. ROSENBERG, M. S., AND S. KUMAR. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proceedings National Academy of Science USA, 98:10751-10756.
35. SAITOU, N., AND M. NEI. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4:406-425.
36. SEILACHER, A., P. K. POSE, AND F. PFLUGER. 1998. Triploblastic animals more than 1 billion years ago: trace fossil evidence from India. Science, 282:80-83.
37. SIDDALL, M. 1998. Success of parsimony in the four-taxon case: long-branch repulsion by likelihood in the Farris Zone. Cladistics, 14:209-220.
38. VALENTINE, J. W., D. H. ERWIN, AND D. JABLONSKI. 1996. Developmental evolution of metazoan body plans: the fossil evidence. Developmental Biology, 173:373-381.
39. WANG, D. Y.-C., S. KUMAR, AND S. B. HEDGES. 1998. Divergence time estimates for the early history of animal phyla and the origin of plants, animals, and fungi. Proceedings of the Royal Society of London B, 266:163-171.
40. WINNEPENNINKX, B., T. BACKELJAU, AND R. D. WACHTER. 1995. Phylogeny of protostome worms derived from 18S rRna. Molecular Biology and Evolution, 12:641-649.
41. WRAY, G. A., J. S. LEVINTON, AND L. H. SHAPIRO. 1996. Molecular evidence for deep Precambrian divergences among metazoan phyla. Science, 274:568-573.
42. YANG, Z. 1993a. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Molecular Biology and Evolution, 10:1396-1401.
43. YANG, Z. 1993b. Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution, 11:367-372.