PACT: An efficient and powerful algorithm for generating area cladograms

Journal of Biogeography

Volumn 32, Issue 5, 2005, Pages 755-774

  Wojcicki, Maggie ^a   Brooks, Daniel R ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b Area de Conservacion Guancaste ^*  (Costa Rica)

Author keywords

Cladistic biogeography; Community evolution; Dispersal; Evolutionary radiations; Historical biogeography; Phylogenetic analysis; Phylogeny; Speciation; Taxon pulse; Vicariance

Indexed keywords

ALGORITHM; CLADISTICS; PHYLOGENY; SPECIATION (BIOLOGY);

EID: 20044385937     PISSN: 03050270     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2004.01148.x     Document Type: Article

References (39)

1. Bouchard, P. & Brooks, D.R. (in press) Effect of vagility potential on dispersal and speciation in rainforest insects. European Journal of Evolutionary Biology.
2. Bouchard, P., Brooks, D.R. & Yeates, D.K. (in press) Mosaic macroevolution in Australian wet tropics arthropods: community assemblage by taxon pulses. Rainforest: past, present, future (ed. by C. Moritz and E. Bermingham). University of Chicago Press, Chicago, IL.
3. Brooks, D.R. (1990) Parsimony analysis in historical biogeography and coevolution: methodological and theoretical update. Systematic Zoology, 39, 14-30.
4. Brooks, D.R. & McLennan, D.A. (1991) Phylogeny, ecology and behavior - a research program in comparative biology. University of Chicago Press, Chicago, IL.
5. Brooks, D.R. & McLennan, D.A. (2001) A comparison of a discovery-based and an event-based method of historical biogeography. Journal of Biogeography, 28, 757-767.
6. Brooks, D.R. & McLennan, D.A. (2002) The nature of diversity - an evolutionary voyage of discovery. University of Chicago Press, Chicago, IL.
7. Brooks, D.R., Van Veller, M.G.P. & McLennan, D.A. (2001) How to do BPA, Really. Journal of Biogeography, 28, 343-358.
8. Cormen, T.H., Leiserson, C.E., Rivest, R.L. & Clifford, S. (2001) Introduction to algorithms. McGraw-Hill, Toronto.
9. Cressey, R.F., Collette, B. & Russo, J. (1983) Copepods and scombrid fishes: A study in host-parasite relationships. Fisheries Bulletin, 81, 227-265.
10. Donoghue, M.J. & Moore, B.R. (2003) Toward an integrative historical biogeography. Integrative and Comparative Biology, 43, 261-270.
11. Endler, J.A. (1982) Problems in distinguishing historical from ecological factors in biogeography. American Zoologist, 22, 441-452.
12. Enghoff, H. (1996) Widespread taxa, sympatry, dispersal, and an algorithm for resolved area cladograms. Cladistics, 12, 349-364.
13. Erwin, T.L. (1979) Thoughts on the evolutionary history of ground beetles: hypotheses generated from comparative faunal analyses of lowland forest sites in temperate and tropical regions. Carabid beetles: their evolution, natural history, and classification (ed. by T.L. Erwin, G.E. Ball and D.R. Whitehead), pp. 539-592. W. Junk, The Hague.
14. Erwin, T.L. (1981) Taxon pulses, vicariance, and dispersal: an evolutionary synthesis illustrated by carabid beetles. Vicariance biogeography - a critique (ed. by G. Nelson and D.E. Rosen), pp. 159-196. Columbia University Press, New York.
15. Erwin, T.L. (1985) The taxon pulse: a general pattern of lineage radiation and extinction among carabid beetles. Taxonomy, phylogeny, and zoogeography of beetles and ants (ed. by G.E. Ball), pp. 437-472. W. Junk, Dordrecht.
16. Erwin, T.L. (1991) An evolutionary basis for conservation strategies. Science, 253, 750-752.
17. Erwin, T.L. & Adis, J. (1982) Amazonian inundation forests: their role as short-term refuges and generators of species richness and taxon pulses. Biological diversification in the tropics (ed. by G. Prance), pp. 358-371. Columbia University Press, New York.
18. Green, M., Van Veller, M.G.P. & Brooks, D.R. (2002) Assessing modes of speciation: range asymmetry and biogeographical congruence. Cladistics, 18, 112-124.
19. Halas, D., Zamparo, D. & Brooks, D.R. (2005) A historical biogeographical protocol for studying biotic diversification by taxon pulses. Journal of Biogeography, 32, 249-260.
20. Lieberman, B.S. (2000) Paleobiogeography. Plenum/Kluwer Academic Press, New York, NY.
21. Lieberman, B.S. (2001) Applying molecular phylogeography to test paleoecological hypotheses: a case study involving Amblema plicata (Mollusca: Unionidae). Evolutionary paleoecology (ed. by W.D. Allmon and D.J. Bottjer), pp. 83-103. Columbia University Press, New York, NY.
22. Lieberman, B.S. (2003a) Unifying theory and methodology in biogeography. Evolutionary Biology, 33, 1-25.
23. Lieberman, B.S. (2003b) Paleobigeography - the relevance of fossils to biogeography. Annual Review of Ecology, Evolution and Systematic, 34, 51-69.
24. McLennan, D.A. & Brooks, D.R. (2002) Complex histories of speciation and dispersal: an example using some Australian birds. Journal of Biogeography, 29, 1055-1066.
25. 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 Statements. Cladistics, 10, 99-153.
26. Platnick, N.I. & Nelson, G. (1978) A method of analysis for historical biogeography. Systematic Zoology, 27, 1-16.
27. Ronquist, F. (2002) Parsimony analysis of coevolving species associations. Tangled trees (ed. by R.D.M. Page), pp. 22-64. University of Chicago Press, Chicago, IL.
28. Siddall, M.E. & Perkins, S.L., (2003) Brooks parsimony analysis: a valiant failure. Cladistics, 19, 554-564.
29. Spironello, M. & Brooks, D.R. (2003) Dispersal and diversification in the evolution of Inseliellium, an archipelagic dipteran group. Journal of Biogeography, 30, 1563-1573.
30. Van Veller, M.G.P. & Brooks, D.R. (2001) When simplicity is not parsimonious: inductive and hypothetico-deductive approaches in historical biogeography. Journal of Biogeography, 28, 1-11.
31. Van Veller, M.G.P., Zandee, M. & Kornet, D.J. (1999) Two requirements for obtaining valid common patterns under different assumptions in vicariance biogeography. Cladistics, 15, 393-406.
32. Van Veller, M.G.P., Kornet, D.J. & Zandee, M. (2000) Methods in vicariance biogeography: assessment of the implementation of assumptions zero, 1 and 2. Cladistics, 16, 319-345.
33. Van Veller, M.G.P., Kornet, D.J. & Zandee, M. (2001) A posteriori and a priori methodologies for testing hypotheses of causal processes in vicariance biogeography. Cladistics, 7, 248-259.
34. Van Veller, M.G.P., Zandee, M. & Kornet, D.J. (2002) Testing hypotheses regarding general patterns in vicariance biogeography with a posteriori and a priori methods. Cladistics, 18, 207-217.
35. Wiley, E.O. (1981) Phylogenetics - the theory and practice of phylogenetic systematics. Wiley & Sons, New York.
36. Wiley, E.O. (1986) Methods in vicariance biogeography. Systematics and evolution (ed. by P. Hovenkamp), pp. 283-306. University of Utrecht Press, Utrecht.
37. Wiley, E.O. (1988a) Parsimony analysis and vicariance biogeography. Systematic Zoology, 37, 271-290.
38. Wiley, E.O. (1988b) Vicariance biogeography. Annual Review of Ecology and Systematics, 19, 513-542.
39. Zandee, M. & Roos, M.C. (1987) Component-compatibility in historical biogeography. Cladistics, 3, 305-332.