Jack Sullivan 

Updated Spring, 2013

Biology 545 - Readings

January 16: Felsenstein 2001. A perspective from the champion of statistical approaches.

Optional: Siddall & Kluge 1997. An example of the arguments made against statistical approaches.

Question for discussion: Why is it that statistical approaches have become dominant?

January 30: Wu et al. 2012.

Question for discusion: Should we eliminate ambiguously aligned sites from our analyses? If so, how should we identify such sites?

February 13: Nei et al. 1998.

Questions for discussion: Do you trust the simulations conducted here? Under what conditions to you agree with the conclusion that it's a waste of time and effort to search for the optimal tree?

March 6: Steel 2005: Fitting and elephant.

Supplemental: Goldman 1993: The foundational paper in testing phylogenetic models.

Question for discussion: To what degree is the quality of inference under a model linked to the fit between that model and the data?

March 27: Rannala and Yang 1996: A foundational paper on Bayesian estimation of phylogenies.

Supplemental: Larget and Simon 1999: An early implementation of MCMC for Bayesian estimation of phylogenies.

Question for discussion: Are you willing to permit prior knowledge/beliefs into estimation procedures?

April 17: Thomas et al. 2013: A great empirical paper that coalesces lots of topic we've been discussing this semester.

Question for discussion: How would one conduct similar tests under a frequentist philosophy?