Quantitative Phylogenetics

Spring 2014

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

Papers:

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!