Generalizing Phylogenetic Parsimony from the Tree to the Forest

Systematic Biology

Volumn 47, Issue 3, 1998, Pages 414-426

  Dickerman, Allan W ^a  

^a NATIONAL CENTER FOR GENOME RESOURCES   (United States)

Author keywords

Algorithm; Forest; Gene trees; Hybridization; Hypertree; Parsimony; Phylogeny; Reticulation

Indexed keywords

EID: 0032333346     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/106351598260798     Document Type: Article

References (25)

1. ALROY, J. 1995. Continuous track analysis: A new phylogenetic and biogeographic method. Syst. Biol. 44:152-178.
2. BAUM, D., AND K. L. SHAW. 1995. Genealogical perspectives on the species problem. Monogr. Syst. Bot. 53:289-303.
3. BREMER, K., AND H. WANNTORP. 1979. Hierarchy and reticulation in systematics. Syst. Zool. 28:624-627.
4. DARWIN, C. 1859. On the origin of species by means of natural selection. J. Murray, London.
5. FARRIS, J. S. 1982. Ougroups and parsimony. Syst. Zool. 31:328-334.
6. FELSENSTEIN, J. 1993. PHYLIP (Phylogeny inference package) version 3.5c. Dept. of Genetics, Univ. of Washington, Seattle.
7. FITCH, W. M. 1971. Toward defining the course of evolution: Minimal change for a specific tree topology. Syst. Zool. 20:406-416.
8. FUNK, V. A. 1985. Phylogenetic patterns and hybridization. Ann. Mol. Bot. Gard. 72:681-715.
9. FURNIER, G. R., M. P. CUMMINGS, AND M. T. CLEGG. 1990. Evolution of the avocados as revealed by DNA restriction fragment variation. J. Hered. 81:183-188.
10. HEIN, J. 1990. Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci. 98:185-200.
11. HEIN, J. 1993. A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 36:396-405.
12. HENDY, M. D., AND D. PENNY. 1993. Spectral analysis of phylogenetic data. J. Classif. 10:5-24.
13. HENNIG, W. 1966. Phylogenetic systematics. Univ. of Illinois Press, Urbana.
14. HUMPHRIES, C. J. 1983. Primary data in hybrid analysis. Pages 89-103 in Advances in Cladistics, Volume 2. (N. I. Platnick and V. A. Funk, eds.). Columbia Univ. Press, New York.
15. MADDISON, W. P., AND D. R. MADDISON. 1992. Mac-Clade: Analysis of phylogeny and character evolution. Sinauer, Sunderland, Massachusetts.
16. MAYNARD SMITH, J. 1992. Analyzing the mosaic structure of genes. J. Mol. Evol. 34:126-129.
17. NELSON, G. 1983. Reticlulation in cladograms. Pages 105-111 in Advances in cladistics, Volume 2 (N. I. Platnick and V. A. Funk, eds.). Columbia Univ. Press, New York.
18. NELSON, G., AND N. I. PLATNICK. 1981. Systematics and biogeography: Cladistics and vicariance. Columbia Univ. Press, New York.
19. PAGE, R. D. M. 1994. Parallel phylogenies: Reconstructing the history of host-parasite assemblages. Cladistics 10:155-173.
20. SANKOFF, D., AND P. ROUSEAU. 1975. Locating the vertices of a Steiner tree in arbitrary space. Math. Progr. 9:240-246.
21. SAWYER, S. 1989. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6:526-538.
22. SNEATH, P. H. A. 1975. Cladistic representation of reticulate evolution. Syst. Zool. 24:360-368.
23. SNEATH, P. H. A., M. J. SACKIN, AND R. P. AMBLER. 1975. Detecting evolutionary incompatibilities from protein sequences. Syst. Zool. 24:311-332.
24. STEPHENS, J. C. 1985. Statistical methods of DNA sequence analysis: Detection of intragenic recombination or gene conversion. Mol. Biol. Evol. 2:539-556.
25. 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.