Papers for Discussion in Lectures
Questions for discussion. Everyone is required to email to us three questions for discussion, prior to class on Wed. Please do not send these to us while we are walking to class on Wednesday. An hour or two prior to class would be appreciated.
Week 4: Advanced Parsimony Analysis and Assessing Results
Wed. February 5
Discussion Leader: Drew
Paper: Emily and Alan Lemmon (2013). High-throughput genomic data in systematics and phylogenetics. Annual Review of Ecology, Evolution and Systematics 44:99-121.
Week 5: Phenetic Methods
Wed. February 12
Discussion Leader: Julian
Paper: Pamela and Doug Soltis (2003). Applying the bootstrap in phylogeny reconstruction. Statistical Science 18(2): 256-267.
Week 6: Maximum Likelihood, Model Selection
Wed. February 19
Discussion Leader: Elly
Papers: Scot Kelchner and Michael Thomas (2006). Model use in phylogenetics: nine key questions. Trends in Ecology and Evolution 22(2): 87-94 and John Gatesy (2007). A tenth crucial question regarding model use in phylogenetics. Trends in Ecology and Evolution 22(10): 509.
Week 7: Maximum Likelihood, Implementing an Analysis
Wed. Feb. 26
Discussion Leader: Taylor
Paper: Mark Simmons and Andrew Norton (2014) Divergent maximum-likelihood-branch-support values for polytomies. Molecular Phylogenetics and Evolution. 73: 87-96.
Week 8: Bayesian Methods
Wed. March 5
Discussion Leader: Xanthe
Paper: Jeremy Brown (2014) Detection of Implausible Phylogenetic Inferences using Posterior Predictive Assessment of Model Fit. Systematic Biology, In Press.
Week 9: Data Partitons
Wed. March 19
Discussion Leader: Adrian
Paper: Robert Lanfear et al. (2012) PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analysis. Mol. Biol. Evol. 29(6): 1695-1701.
Week 10: Gene Trees and Species Trees
Wed. March 26
Discussion Leader: Oona
Paper: Degnan and Rosenberg (2009) Gene tree discordance, phylogenetic inference and the multispecies problem. Trends in Ecology and Evolution 24(6): 332-340.
Another paper that develops the sources of incongruence between gene trees and species trees from first principles, and argues against concatenation of multi-gene data sets, is Edwards (2008) Is a new and general theory of systematics developing? Evolution 63(1): 1-19.
Week 11: Hypothesis Testing - Topology comparisons
Wed Apr. 2
Discussion Leader: Chang
Paper: Bergsten, J., A. N. Nilsson, and F. Ronquist. 2013. Bayesian tests of topology hypotheses with an example from diving beetles. Systematic Biology 62:660-73.
Week 12: Rate Heterogeneity and the Molecular Clock
Wed. April 9
Discussion Leader: Carl
Maria M. Bauzá-Ribot et al. (2012). Mitogenomic phylogenetic analysis supports continental-scale vicariance in subterranean Thalassoid crustaceans. Current Biology 22: 2069-2074.
Phillips et al. (2013) and Bauzá-Ribot et al. (2013). Critique and response.
Week 13: Hypothesis Testing, Comparative Analyses
Wed. April 16
Discussion Leader: Caitlin
Paper: Davis, R.B. et al. (2011). Disentangling determinants of egg size in the Geometridae (Lepidoptera) using an advanced phylogenetic comparative method. Evolutionary Biology 25: 210-219.
Week 14: Topic not yet assigned
Wed. April 23
Discussion Leaders: Mariana and Jim
Paper: To be determined, send us your suggestions!