Maximum likelihood estimation of phylogeny using stratigraphic data

Paleobiology

Volumn 23, Issue 2, 1997, Pages 174-180

  Huelsenbeck, John P ^a   Rannala, Bruce ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FOSSIL RECORD; MAXIMUM LIKELIHOOD METHOD; PHYLOGENY; STRATIGRAPHIC RANGE;

EID: 0030776127     PISSN: 00948373     EISSN: None     Source Type: Journal    
DOI: 10.1017/S0094837300016778     Document Type: Article

References (34)

1. Benton, M. J. 1995. Testing the time axis of phylogenies. Philosophical Transactions of the Royal Society of London B 349: 5-10.
2. Benton, M. J., and G. W. Storrs. 1996. Diversity in the past: comparing cladistic phylogenies and stratigraphy. Pp. 19-40 in Aspects of the genesis and maintenance of biological diversity. M. E. Hochberg, J. Clobert, and R. Barbault, eds. Oxford University Press, Oxford.
3. Cox, D. R. 1961. Tests of separate families of hypotheses. Proceedings of the Fourth Berkeley Symposium. University of California Press, Berkeley.
4. _. 1962. Further results on tests of separate families of hypotheses. Journal of the Royal Society of London B 24:406-424.
5. Cox, D. R., and D. V. Hinkley. 1974. Theoretical statistics. Cambridge University Press, Cambridge.
6. Edwards, A. W. F. 1992. Likelihood. Johns Hopkins University Press, Baltimore.
7. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17:368-376.
8. _. 1995. PHYLIP (Phylogeny Inference Package) Version 3.57c. Distributed by the author. Department of Genetics, University of Washington, Seattle.
9. Fisher, D. C. 1982. Phylogenetic and macroevolutionary patterns within the Xiphosurida. Proceedings of the Third North American Paleontological Convention 1:175-180.
10. _. 1988. Stratocladistics: integrating stratigraphic and morphologic data in phylogenetic inference. Geological Society of America Abstracts with Program 20:A186.
11. _. 1991. Phylogenetic analysis and its application in evolutionary paleobiology. In N. L. Gilinsky and P. W. Signor, eds. Analytical paleobiology. Paleontological Society Short Courses in Paleontology No. 4:103-122. University of Tennessee, Knoxville.
12. _. 1992. Stratigraphic parsimony. Pp. 124-129 in W. P. Maddison and D. R. Maddison. MacClade: analysis of phylogeny and character evolution. Sinauer Associates, Sunderland, Mass.
13. Foote, M., and D. M. Raup. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121-140.
14. Furnas, G. W. 1984. The generation of random, binary, unordered trees. Journal of Classification 1:187-233.
15. Gauthier, J., A. Kluge, and T. Rowe. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105-209.
16. Gingerich, P. D. 1979. The stratophenetic approach to phylogeny reconstruction in vertebrate paleontology. Pp. 41-77 in J. Cracraft and N. Eldredge, eds. Phylogenetic analysis and paleontology. Columbia University Press, New York.
17. Goldman, N. 1993. Statistical tests of models of DNA substitution. Journal of Molecular Evolution 36:182-198.
18. Harper, C. 1976. Phylogenetic inference in paleontology. Journal of Paleontology 50:180-193.
19. Huelsenbeck, J. P. 1994. Comparing the stratigraphic record to estimates of phylogeny. Paleobiology 20:470-483.
20. Huelsenbeck, J. P., and J. J. Bull. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Systematic Biology 45: 92-98.
21. Huelsenbeck, J. P., and M. Kirkpatrick. 1996. Do phylogenetic methods produce trees with biased shapes? Evolution 50: 1418-1424.
22. Johnson, N. L., S. Kotz, and N. Balakrishnam. 1994. Continuous univariate distributions, Vol. 2. Wiley, New York.
23. Kendall, D. G. 1949. Stochastic processes and population growth. Journal of the Royal Statistical Society B 11:230-264.
24. Kirkpatrick, M., and M. Slatkin. 1993. Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution 47: 1171-1181.
25. Marshall, C. R. 1990. Confidence intervals on stratigraphic ranges. Paleobiology 16:1-10.
26. _. 1991. Estimation of taxonomic ranges from the fossil record. In N. L. Gilinsky and P. W. Signor, eds. Analytical paleobiology. Paleontological Society Short Courses in Paleontology No. 4:19-38. University of Tennessee, Knoxville
27. Norell, M. 1992. Taxic origin and temporal diversity: the effect of phylogeny. Pp. 89-118 in M. J. Novacek and Q. D. Wheeler, eds. Extinction and phylogeny. Columbia University Press, New York.
28. Norell, M., and M. Novacek. 1992. The fossil record and evolution: comparing cladistic and paleontologic evidence for vertebrate history. Science 255:1690-1693.
29. Raup, D. M. 1985. Mathematical models of cladogenesis. Paleobiology 11:42-52.
30. Raup, D. M., and S. M. Stanley. 1971. Principles of paleontology. W. H. Freeman, San Francisco.
31. Solow, A. R. 1996. Tests and confidence intervals for a common upper endpoint in fossil taxa. Paleobiology 22:406-410.
32. Strauss, D., and P. M. Sadler. 1989. Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Mathematical Geology 21:411-427.
33. Wagner, P. J. 1995. Stratigraphic tests of cladistic hypotheses. Paleobiology 21:153-178.
34. Yang, Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Molecular Biology and Evolution 10:1396-1401.