Brooks Parsimony Analysis: A valiant failure

Cladistics

Volumn 19, Issue 6, 2003, Pages 554-564

  Siddal, Mark E ^a   Perkins, Susan L ^b  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLADISTICS; HOST-PARASITE INTERACTION; PHYLOGENETICS;

EID: 0347530444     PISSN: 07483007     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2003.tb00388.x     Document Type: Article

References (60)

1. Bandoni, S.M., Brooks, D.R., 1987. Revision and phylogenetic analysis of the Amphilinidea Poche, 1922 (Platyhelminthes: Cercomeria: Cercomeromorpha). Can. J. Zool. 65, 1110-1128.
2. Brooks, D.R., 1979. Testing the context and extent of host-parasite coevolution. Syst. Zool. 28, 299-307.
3. Brooks, D.R., 1981. Hennig's parasitological method: a proposed solution. Syst. Zool. 30, 299-307.
4. Brooks, D.R., 1985. Historical ecology: a new approach to studying the evolution of ecological associations. Ann. Mo. Bot. Gard. 72, 660-680.
5. Brooks, D.R., 1988. Macroevolutionary comparisons of host and parasite phylogenies. Annu. Rev. Ecol. Syst. 19, 235-259.
6. Brooks, D.R., 1990. Parsimony analysis in historical biogeography and coevolution: methodological and theoretical update. Syst. Zool. 39, 14-30.
7. Brooks, D.R., McLennan, D.A., 1991. Phylogeny, Ecology, and Behavior: A Research Program in Comparative Biology. University of Chicago Press, Chicago.
8. Brooks, D.R., McLennan, D.A., 1993. Parascript: Parasites and the Language of Evolution. Smithsonian Press, Washington, DC.
9. Brooks, D.R., Van Veller, M.G.P., McLennan, D.A., 2001. How to do BPA, really. J. Biogeogr. 28, 345-358.
10. Charleston, M.A., 1998. Jungles: a new solution to the host/parasite phylogeny reconciliation problem. Math. Biosci. 149, 191-223.
11. Charleston, M.A., Page, R.D.M., 2002. TREEMAP 2.0β A Macintosh program for the analysis of how dependent phylogenies are related, by cophylogeny mapping. Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
12. Charleston, M.A., Perkins, S.L., 2003. Lizards, malaria and jungles in the Caribbean. In: Page, R.D.M. (Ed.), Tangled Trees: Phylogeny, Cospeciation, and Coevolution. University of Chicago Press, Chicago, pp. 65-92.
13. Cracraft, J., 1988. Deep-history biogeography: Retrieving the historical pattern of evolving continental biotas. Syst. Zool. 37, 221-236.
14. Dowling, A.P.G., 2002. Testing the accuracy of TreeMap and Brooks parsimony analyses of coevolutionary patterns using artificial associations. Cladistics 18, 416-435.
15. Dowling, A.P.G., 2003. Erratum to "Testing the accuracy of Tree Map and Brooks Parsimony analysis of coevolutionary patterns using artificial association." Cladistics 18, 416-435.
16. Ebach, M.C., Humphries, C.J., 2002. Cladistic biogeography and the art of discovery. J. Biogeogr. 29, 427-444.
17. Farris, J.S., Albert, V.A., Kallersjo, M., Lipscomb, D., Kluge, A.G., 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12, 99-124.
18. Felsenstein, J., 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401-410.
19. Felsenstein, J., 1982. Numerical methods for inferring evolutionary trees. Q. Rev. Biol. 57, 379-404.
20. Goldman, N., 1990. Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses. Syst. Zool. 39, 345-361.
21. Hennig, W., 1966. Phylogenetic Systematics. University of Illinois Press, Urbana, IL.
22. Hoberg, E.P., 1992. Congruence and synchronic patterns in biogeography and speciation among seabirds, pinnipeds, and cestodes. J. Parasitol. 78, 601-615.
23. Hoberg, E.P., Adams, A.M., 1992. Phylogeny, historical biogeography and ecology of Anophryocephalus spp. (Tetrabothriidae) among pinnipeds of the Holarctic during the late Tertiary and Pleistocene. Can. J. Zool. 70, 703-719.
24. Hovenkamp, P., 1997. Vicariance events, not areas, should be used in biogeographical analysis. Cladistics 13, 67-79.
25. Huelsenbeck, J.P., Hillis, D.M., 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42, 247-264.
26. Kishino, H., Hasegawa, M., 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29, 170-179.
27. Kluge, A.G., 1988. Parsimony in vicariance biogeography: A quantitative method and a Greater Antillean example. Syst. Zool. 37, 315-328.
28. Maddison, W., Maddison, D., 1992. MacClade: Analysis of Phylogeny and Character Evolution. Sinauer, Sunderland, MA.
29. Mindell, D.P., Schultz, J.W., Ewald, P.W., 1995. The AIDS pandemic is new, but is HIV new? Syst. Biol. 44, 77-92.
30. Morrone, J.J., Carpenter, J.M., 1994. In search of a method for cladistic biogeography: an empirical comparison of component analysis, Brooks parsimony analysis, and three-area statement. Cladistics 10, 99-153.
31. O'Grady, R.T., Deets, G.B., 1987. Coding multistate characters, with special reference to the use of parasites as characters of their hosts. Syst. Zool. 36, 268-279.
32. Page, R.D.M., 1988. Quantitative cladistic biogeography: Constructing and comparing area cladograms. Syst. Zool. 37, 254-270.
33. Page, R.D.M., 1990. Component analysis: a valiant failure? Cladistics 6, 119-136.
34. Page, R.D.M., 1993a. Genes, organisms, and areas: the problem of multiple lineages. Syst. Biol. 42, 77-84.
35. Page, R.D.M., 1993b. Parasites, phylogeny, and cospeciation. Int. J. Parasitol. 23, 499-506.
36. Page, R.D.M., 1994a. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43, 58-77.
37. Page, R.D.M., 1994b. Parallel "phylogenies": reconstructing the history of host-parasite assemblages. Cladistics 10, 155-173.
38. Page, R.D.M., 1995. TreeMap. Computer Program, distributed by the author. University of Glasgow, Glasgow.
39. Page, R.D.M., Charleston, M.A., 1998. Trees within trees: phylogeny and historical associations. Trends Ecol. Evol. 13, 356-359.
40. Perkins, S.L., Schall, J.J., 2002. A molecular phylogeny of malarial parasites recovered from cytochrome b gene sequences. J. Parasitol. 88, 972-978.
41. Planet, P.J., Kachlany, S.C., Fine, D.H., DeSalle, R., Figurski, D.H., 2003. The widespread colonization island of Actinobacillus actinomycetemcomitans. Nature Genetics 34, 193-198.
42. Pol, D., Siddall, M.E., 2001. Biases in maximum likelihood and parsimony: a simulation approach to a ten-taxon case. Cladistics 17, 266-281.
43. Ronquist, F., 1995. Reconstructing the history of host-parasite associations using generalized parsimony. Cladistics 11, 73-89.
44. Ronquist, F., 1998. Three-dimensional cost-matrix optimization and maximum cospeciation. Cladistics 14, 167-172.
45. Ronquist, F., 2000. TreeFitter, Computer Program, distributed by the author. University of Uppsala, Uppsala.
46. Ronquist, F., 2003. Parsimony analysis of coevolving species associations. In: Page, R.D.M. (Ed.), Tangled Trees: Phylogeny, Cospeciation, and Coevolution. University of Chicago Press, Chicago, pp. 22-64.
47. Ronquist, F., Nylin, S., 1990. Process and pattern in the evolution of species associations. Syst. Zool. 39, 323-344.
48. Saether, O.A., 1986. The myth of objectivity - post-Hennigian deviations. Cladistics 2, 1-13.
49. Saitou, N., Nei, M., 1987. The neighbor-joining method: A new method for constructing phylogenetic trees. Mol. Biol. Evol. 4, 406-422.
50. Shimodaira, H., Hasegawa, M., 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
51. Siddall, M.E., 1996. Phylogenetic covariance probability confidence and historical associations. Syst. Biol. 45, 48-66.
52. Siddall, M.E., 1997. The AIDS pandemic is new, but is HIV not new? Cladistics 13, 267-273.
53. Siddall, M.E., 2002. Phylogeny and revision of the leech family Erpobdellidae (Hirudinida: Oligochaeta). Invertebr. Taxon. In press.
54. Siddall, M.E., Kluge, A.G., 1997. Probabilism and phylogenetic inference. Cladistics 13, 313-336.
55. Siddall, M.E., Whiting, M.F., 1999. Long-branch abstractions. Cladistics 15, 9-24.
56. Stammer, H.J., 1957. Gedanken zu den parasitophyloetischen Regeln und zur Evolution der Parasiten. Zool. Anz. 159, 255-267.
57. Stoneking, M., Sherry, S.T., Vigilant, L., 1992. Geographic origin of human mitochondrial DNA revisited. Syst. Biol. 41, 384-391.
58. Swofford, D.L., Waddell, P.J., Huelsenbeck, J.P., Foster, P.G., Lewis, P.O., Rogers, J.S., 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50, 525-539.
59. Van Veller, M.G.P., Brooks, D.R., 2001. When simplicity is not parsimonious: a priori and a posteriori methods in historical biogeography. J. Biogeogr. 28, 1-12.
60. Van Veller, M.G.P., Kornet, D.J., Zandee, M., 2000. Methods in vicariance biogeography: assessment of the implementations of assumptions 0, 1, and 2. Cladistics 16, 319-345.