Schedule for the rest of the course:
03/10 - Introduction to comparative methods (pdf notes) (3 per page)
Pagel, M. 1999 Inferring the historical patterns of biological evolution. Nature, 401, 877-884.
03/12 - Diversification I: Birth-death models (Fels. Ch. 33) (pdf notes) (3 per page)
Magallón, S., and M. J. Sanderson. 2001. Absolute diversification rates in angiosperm clades. Evolution 55:1762-1780.
Foote, M., J. P. Hunter, C. M. Janis, and J. J. Sepkoski Jr. 1999. Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals. Science 283:1310–1314.
Spring Break
03/23 - Lab: Simulating evolution (pdf of lab)
03/24 - Diversification II: lineage through time (pdf notes) (3 per page)
Nee, S. 2006. Birth-death models in macroevolution. Ann Rev Ecol Evol Syst 37: 1–17.
Nee, S., May, R. M. & Harvey, P. H. (1994) The reconstructed evolutionary process. Phil. Trans. Roy. Soc. Lond. B. 349, 25-31.
03/26 - Continuous characters I: Brownian motion (Fels. Ch. 23, 25a) (pdf notes) (3 per page)
Revell, L. J., L. J. Harmon, and D. C. Collar. 2008. Phylogenetic signal, evolutionary process, and rate. Systematic Biology 57: 591-601.
03/30 - Lab: Paper discussion (paper)
03/31 - Continuous characters II: Fitting likelihoods and multivariate models (pdf notes) (3 per page)
Felsenstein, J. (1973). Maximum-likelihood estimation of evolutionary trees from continuous characters. Amer. J. Human Genetics, 25:471-492.
Felsenstein, J. (1981). Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution, 35:1229-1242.
04/02 - Continuous characters III: other models (Fels. Ch. 24) (continue with previous notes; problem set; solutions)
04/05 - Lab: Fun with R (link)
04/07 - Discrete characters I: The Mk model (Fels. Ch. 25b) (pdf notes) (3 per page)
Lewis, P. O. 2001b. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50:913-925.
04/09 - Discrete characters II: Character correlations and ancestral states (pdf notes) (3 per page)
Pagel, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society (B) 255, 37-45.
04/13 - Lab: Paper discussion (paper)
04/14 - Quantitative genetics and comparative methods (pdf notes) (3 per page)
Felsenstein, J. 2005. Using the quantitative genetic threshold model for inferences between and within species. Philosophical Transactions of the Royal Society of London, series B 360: 1427-1434.
Felsenstein, J. 2008. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. American Naturalist 171: 713-725.
04/16 - Characters and diversification (pdf notes) (3 per page)
Maddison, W.P., P.E. Midford & S.P. Otto. 2007. Estimating a binary character's effect on speciation and extinction. Systematic Biology 56:701-710.
04/20 - Lab: Anolis Ecomorphs (lab report document: anoleMesquite.doc; data file: anolesLabdata.nex)
04/21 - Biogeography (Fels. Ch. 31) (pdf notes)
04/23 - Review (pdf notes; practice test)
04/27 - Lab: Poster presentations
04/28 - Applications in the Harmon lab (pdf notes)
04/30 - You Can't Take it With You (to be continued on Thursday morning; stay tuned)
5/5 - Exam II (practice test solutions; formula sheet)