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?