Entomology/Genetics 606
Quantitative Phylogenetics
Spring 2008
Suggested Readings From Lectures
Introduction
Holder, M. and P.O. Lewis (2003). Phylogeny Estimation: Traditional and Bayesian Approaches. Nature Reviews, Genetics 4:275-284
Model Selection
Alfaro, M. E., and J. P. Huelsenbeck. 2006. Comparative performance of
Bayesian and AIC-based measures of phylogenetic model uncertainty. Systematic Biology 55:89-96.Sullivan, J., Z. Abdo, P. Joyce and D.L. Swofford (2005). Evaluating the performance of a successive approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Molecular Biology and Evolution 22(6): 1386-1392.
Kelchner, S.A. and M.A. Thomas (2006). Model use in phylogenetics: nine key questions. Trends in Ecology and Evolution 22(2): 87-94.
Gatesy, J. (2007). A tenth crucial question regarding model use in phylogenetics. Trends in Ecology and Evolution 22(10): 509-510.
Sullivan, J. and P. Joyce (2005). Model Selection in Phylogenetics. Annual Review of Ecology and Systematics 36: 445-466.
Posada, D. and T.R. Buckley (2004) Model selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests. Systematic Biology 53(5): 793-808.
Model-based Methods
Simon, C., T. R. Buckley, F. Frati, J. B. Stewart, and A. T. Beckenbach.
2006. Incorporating Molecular Evolution into Phylogenetic Analysis, and a New Compilation of Conserved Polymerase Chain Reaction Primers for Animal Mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics 37:545-579.Niehuis, O., S-H. Yen, C.M. Naumann, and B. Misof (2006). Higher phylogeny of zygaenid moths (Insecta: Lepidoptera) inferred from nuclear and mitochondrial sequence data and the evolution of larval cuticular cavities for chemical defense. Molecular Phylogenetics and Evolution 39: 812-829.
Castoe, T.A., M.M. Sasa, and C.L. Parkinson (2005). Modeling nucleotide evolution at the mesoscale: the phylogeny of the Neotropical pitvipers of the Porthidium group (Viperidae: Crotalinae). Molecular Phylogenetics and Evolution 37: 881-898.
Measures of Clade Support
Carpenter, J.M. (1996) Uninformative bootstrapping. Cladistics 12:177-181.
Erixon, P., B. Svennblad, T. Britton, and B. Oxelman. 2003. Reliability of
Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst Biol 52:665-73.Hillis, D. M., and J. J. Bull (1993) An empirical test of bootstrapping as
a method for assessing confidence in phylogenetic analysis. Syst. Biol.
42:182-192.
Hillis, D. M (1995) Approaches for Assessing Phylogenetic Accuracy.
Systematic Biology 44:3-16.Suzuki, Y., G. V. Glazko, and M. Nei. 2002. Overcredibility of molecular
phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci U S A 99:16138-43.Zharkikh, A., and W. H. Li. (1995) Estimation of confidence in phylogeny: the complete-and-partial bootstrap technique. Mol. Phylogenet. Evol. 4:44-63.
Randomization methods and null models
Carpenter, J.M. (1992) Random cladistics. Cladistics 8:147-153.
Goloboff, P. (1991) Random data, homoplasy, and information. Cladistics 7: 395-406.
Slowinski, J.B. and B.I. Crother (1998) Is the PTP test useful? Cladistics 14: 297-302.
Combining different data partitions
Wenzel, J.W. and M.E. Siddall (1999) Noise. Cladistics 15: 51-64.
Nylander, J.A.A., F. Ronquist, J.P. Huelsenbec and J. L. Nieves-Aldrey (2004). Bayesian Phylogenetic Analysis of Combined Data. Systematic Biology 53(3) 47-67.
Bayesian Methods
Ronquist, F. 2004. Bayesian inference of character evolution. Trends Ecol
Evol 19:475-81.Suchard, M. A., and B. D. Redelings. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 22:2047-8.
Molecular Clocks
Rutschmann, F. (2006). Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Diversity and Distributions 12: 35-48.
Bromham, L. and D. Penny (2003). The Modern Molecular Clock. www.nature.com/reviews/genetics 4: 216-224
Kumar, K. (2005.) Molecular clocks: four decades of evolution. www.nature.com/reviews/genetics 6: 654-662
Pybus, O.G. (2006). Model selection and the molecular clock. PLoS Biology (www.plosbiology.org) 4(5): 686-688.
Drummond, A.J., S.Y.W. Ho, M.J. Phillips, A. Rambaut (2006). Relaxed phylogenetics and dating with confidence. PLoS Biology (www.plosbiology.org) 4(5): 699-710.