Are nonuniform clade priors important in Bayesian phylogenetic analysis? A response to Brandley et al.

Systematic Biology

Volumn 55, Issue 1, 2006, Pages 147-151

  Randle, Christopher ^a   Pickett, Kurt ^b  

^a UNIVERSITY OF KANSAS   (United States)

^b DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33644595199     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150500481630     Document Type: Short Survey

References (15)

1. Efron, B., E. Halloran, and S. Holmes. 1996. Bootstrap confidence levels for phylogenetic trees. Proc. Natl. Acad. Sci. USA 93:13429-13434.
2. Farris, J. S., V. A. Albert, M. Källersjö, D. Lipscomb, and A. Kluge. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12:99-124.
3. Fisher, R. A. 1912. On an absolute criterion for fitting frequency curves. Messenger of Mathematics 41:155-160.
4. Jeffreys, H. 1960. Theory of probability. Clarendon Press, Oxford.
5. Jordan, S., C. Simon, and D. Polhemus. 2003. Molecular systematics and adaptive radiation of Hawaii's endemic damselfly genus Megalagrion (Odonata: Coenagrionidae). Syst. Biol. 52:89-109.
6. Kiefer, A., F. Mayer, J. Kosuch, O. von Helversen, and A. Veith. 2002. Conflicting molecular phy logenies of European long-eared bats (Plecotus) can be explained by cryptic diversity. Mol. Phyl. Evol. 25:557-566.
7. Kluge, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Sys. Zool. 38:7-25.
8. Nixon, K. C., and J. M. Carpenter. 1996. On simultaneous analysis. Cladistics 12:221-241.
9. Pickett, K. M., and C. P. Randle. 2005. Strange Bayes indeed: Uniform topological priors imply non-uniform clade priors. Mol. Phyl. Evol. 34:203-211.
10. Rokas, A., G. Melika, Y. Abe, J. L. Nieves-Aldrey, J. M. Cook, and G. N. Stone. 2003. Lifecycle closure, lineage sorting, and hybridization revealed in a phylogenetic analysis of European oak gallwasps (Hymenoptera : Cynipidae : Cynipini) using mitochondrial sequence data. Mol. Phyl. Evol. 26:36-45.
11. Rydin, C., and M. Källersjö. 2002. Taxon sampling and seed plant phylogeny. Cladistics 18:485-513.
12. Simmons, M. P., K. M. Pickett, and M. Miya. 2004. How meaningful are Bayesian support values? Mol. Biol. Evol. 21:188-199.
13. Wheeler, W. C. 1991. Congruence among data sets: a Bayesian approach. Pages 334-346 in Phylogenetic analysis of DNA sequences (M. M. Miyamoto, and J. Cracraft, eds.). Oxford University Press, Oxford.
14. Yang, Z. H., and B. Rannala. 2005. Branch-length priors influences Bayesian posterior probability of phylogeny. Syst. Biol. 54:455-470.
15. Zwickl, D. J., and M. T. Holder. 2004. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst. Biol. 53:877-888.