Quantitative Phylogenetics

Spring 2012

Suggested Readings From Lectures


Week 1. Introduction

Goldman, N. and Z. Yang. (2008) Introduction. Statistical and computational challenges in molecular phylogenetics and evolution. Phil. Trans. R. Soc. B. 363:3889-3892.


Week 2. Sequence Alignment

Chapter 3, Multiple Sequence Alignment, Theory and Practice, Lemey et al. (2009), The Phylogenetic Handbook.

Morrison, D.A. (2006) Multiple sequence alignment for phylogenetic purposes. L.A.S. Johnson Review No. 8, Australian Systematic Botany 19:479-539.

Nuin, P.A., Z. Wang and E.R. Tiller (2006) The accuracy of several multiple sequence alignment programs for proteins. Bioinformatics 7: 471.


Parsimony Analysis and Search Strategies

Goloboff, P.A. (1999). Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15: 415-428.

Nixon, K.C. (1999). The parsimony ratchet: a new method for rapid parsimony analysis. Cladistics: 407-414.

 


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.

Posada D. (2008). jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25(7): 1253-1256.


Model-based Methods

Bergsten, J. (2005). A review of long-branch attraction. Cladistics 21:163-193.

Morrison, D.A. (2007). Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences. Systematic Biology 56(6): 988-1010.

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.

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.


SuperTrees

Semple, C. and M. Steel (2000). A supertree method for rooted trees. Disc. Appl. Math. 105: 147-158.

Page, R.D.M. (2002). Modified MinCut SuperTrees. ALGORITHMS IN BIOINFORMATICS, PROCEEDINGS 2452: 537-551