Missing data, incomplete taxa, and phylogenetic accuracy

Systematic Biology

Volumn 52, Issue 4, 2003, Pages 528-538

  Wiens, John J ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

Combining data; Computer simulations; Fossils; Incomplete taxa; Missing data; Phylogenetic accuracy; Supertrees

Indexed keywords

EID: 0042905752     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150390218330     Document Type: Article

References (32)

1. ANDERSON, J. S. 2001. The phylogenetic trunk: Maximal inclusion of taxa with missing data in an analysis of the Lepospondyli (Vertebrata, Tetrapoda). Syst. Biol. 50:170-193.
2. AX, P. 1987. The phylogenetic system: The systematization of organisms on the basis of their phylogenesis. Wiley, New York.
3. BININDA-EMONDS, O. R. P., AND M. J. SANDERSON. 2001. Assessment of the accuracy of matrix representation with parsimony analysis supertree reconstruction. Syst. Biol. 50:565-579.
4. DONOGHUE, M. J., J. A. DOYLE, J. GAUTHIER, A. G. KLUGE, AND T. ROWE. 1989. The importance of fossils in phylogeny reconstruction. Annu. Rev. Ecol. Syst. 20:431-460.
5. EBACH, M. C., AND S. T. AHYONG. 2001. Phylogeny of the trilobite subgenus Acanthopyge (Lobopyge). Cladistics 17:1-10.
6. GAO, K., AND M. A. NORELL. 1998. Taxonomic revision of Carusia (Reptilia: Squamata) from the Late Cretaceous of the Gobi Desert and phylogenetic relationships of anguimorphan lizards. Am. Mus. Novit. 3230:1-51.
7. GATESY, J., C. MATTHEE, R. DESALLE, AND C. HAYASHI. 2002. Resolution of a supertrees/supermatrix paradox. Syst. Biol. 51:652-664.
8. GAUTHIER, J. 1986. Saurischian monophyly and the origin of birds. Mem. Calif. Acad. Sci. 8:1-47.
9. GAUTHIER, J., A. G. KLUGE, AND T. ROWE. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105-209.
10. GRANDE, L., AND W. E. BEMIS. 1998. A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy, an empirical search for interconnected patterns of natural history. Soc. Vertebr. Paleontol. Mem. 4:1-690.
11. HILLIS, D. M. 1995. Approaches to assessing phylogenetic accuracy. Syst. Biol. 44:3-16.
12. HUELSENBECK, J. P. 1991. When are fossils better than extant taxa in phylogenetic analysis? Syst. Zool. 40:458-469.
13. JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (H. Munro, ed.). Academic Press, New York.
14. KEARNEY, M. 2002. Fragmentary taxa, missing data, and ambiguity: Mistaken assumptions and conclusions. Syst. Biol. 51:369-381.
15. LIU, F.-G., M. M. MIYAMOTO, N. P. FREIRE, P. ONG, M. R. TENNANT, T. S. YOUNG, AND K. F. GUGEL. 2001. Molecular and morphological supertrees for eutherian (placental) mammals. Science 291:1786-1789.
16. NIXON, K. C., AND Q. D. WHEELER. 1992. Extinction and the origin of species. Pages 119-143 in Extinction and phylogeny (M. J. Novacek and Q. D. Wheeler, eds.). Columbia Univ. Press, New York.
17. NOVACEK, M. J. 1992. Fossils, topologies, missing data, and the higher level phylogeny of eutherian mammals. Syst. Biol. 41:58-73.
18. PATTERSON, C. 1981. Significance of fossils in determining evolutionary relationships. Annu. Rev. Ecol. Syst. 12:195-223.
19. PENNY, D., AND M. D. HENDY. 1985. The use of tree comparison metrics. Syst. Zool. 34:75-82.
20. RANNALA, B., J. P. HUELSENBECK, Z. YANG, AND R. NIELSEN. 1998. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47:702-710.
21. ROWE, T. 1988. Definition, diagnosis, and origin of Mammalia. J. Vertebr. Paleontol. 8:241-264.
22. SANDERSON, M. J., A. PURVIS, AND C. HENZE. 1998. Phylogenetic supertrees: Assembling the tree of life. Trends Ecol. Evol. 13:105-109.
23. STEEL, M. A., AND D. PENNY. 1993. Distributions of tree comparison metrics - Some new results. Syst. Biol. 42:126-141.
24. SWOFFORD, D. L. 2001. PAUP*: Phylogenetic analysis using parsimony (* and other methods), version 4.068. Sinauer, Sunderland, Massachusetts.
25. SWOFFORD, D. L. 2003. http://paup.csit.fsu.edu/paupfaq/faq.html.
26. SWOFFORD, D. L., AND G. J. OLSEN. 1990. Phylogeny reconstruction. Pages 411-501 in Molecular systematics, 1st edition (D. M. Hillis and C. Moritz, eds.). Sinauer, Sunderland, Massachusetts.
27. WIENS, J. J. 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst. Biol. 47:625-640.
28. WIENS, J. J. 2001. Character analysis in morphological phylogenetics: Problems and solutions. Syst. Biol. 50:689-699.
29. WIENS, J. J. 2003. Incomplete taxa, incomplete characters, and phylogenetic accuracy: Is there a missing data problem? J. Vertebr. Paleontol. 23:297-310.
30. WIENS, J. J., AND T. W. REEDER. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Syst. Biol. 44:548-558.
31. WILKINSON, M. 1995. Coping with abundant missing entries in phylogenetic inference using parsimony. Syst. Biol. 44:501-514.
32. WILKINSON, M., AND M. J. BENTON. 1995. Missing data and rhynchosaur phylogeny. Hist. Biol. 10:137-150.