Schedule

Back to the course homepage.

Analysis of comparative data

DateTopic Primary reading: Discussions Suggested reading
Sept. 6 and 8Introduction and Examples   Cardillo et al. (2005), Barker & Pagel (2005)
Sept. 13 Methods for categorical interspecific data   Ch.4, Maddison (1990)
Sept. 15 Methods for categorical data (cont.)   Pagel (1994),
Sept. 20 ANOVA methods for quantitative data   Ch.5: 5.4, 5.5 and 5.8.1, Bell (1989)
Sept. 22 Felsenstein's Independent Contrasts, with introduction to Brownian motion   Felsenstein (1985), interpretation of regression patterns (5.9), Maddison (1991)
Sept. 27 FIC (cont.) and Introduction to the Ornstein-Uhlenbeck process   
Sept. 29 Rescaling, assumption checking Garland et al. (1992) Grafen (1989), Diaz-Uriarte & Garland (1996)
Oct. 4 Introduction to the Ornstein-Uhlenbeck process (cont.)   Micro to macro-evolutionary models: Hansen & Martins (1996)
10/6 & 11 Generalized linear models    
Oct. 13 PGLS and GEE   Martins & Hansen (1997), Paradis & Claude (2002)
Oct. 18 Randomization tests (discussion), and brief overview of tree building methods from molecular data Garland et al. (1993)  
Oct. 20 Dealing with unresolved phylogenies ... Garland & Diaz-Uriarte (1999) by Genevieve Kozak
Purvis & Garland (1993), Martins (1996a)
Oct. 25 ... in a Bayesian framework Pagel et al. (2004) Huelsenbeck & Rannala (2003)
Oct. 27 PMM (mixed model)   Lynch (1991), Housworth et al. (2004)
Nov. 1 Comparing comparative methods Rolf (2001) by Oscar Perez

Martins et al. (2002) by Ivalú Cacho
 
Nov. 3 Ancestral state reconstruction Schluter et al. (1997) by Stacey Smith

Garland & Ives (2000) by Tim Grant
Pagel (1999)
Nov. 8 (Bret Larget) Analysis of discrete data using stochastic mapping Huelsenbeck et al. (2003) Nielsen (2002)
Nov. 10 Testing rates of evolution Garland (1992) by Flor Rodriguez  
Nov. 15 Testing adaptation, and Model selection (AIC, BIC)   Hansen (1997), Butler & King (2004)

Estimation of divergence times

DateTopic Primary reading: Discussions Suggested reading
Nov. 17The molecular clock, and local clocks   Britton et al. (2002), Cutler (2000), Yoder and Yang (2000), Rambaut (2000)
Nov. 22 Poisson process for changes in rate Huelsenbeck, Larget and Swofford (2000) by Heejung Shim  
Nov. 24No class (Thanksgiving)    
Nov. 29 Penalized likelihood   Sanderson (1997), Sanderson (2002)
Dec. 1 Penalized likelihood (cont.), Gradual models of rate change and bayesian estimation   Yang & Rannala (1997), Thorne,Kishino and Painter (1998), Kishino, Thorne and Bruno (2001),
Dec. 6 Gradual models of rate change and bayesian estimation (cont.)   Aris-Brosou & Yang (2002), Thorne & Kishino (2002), Yang & Yoder (2003)
Dec. 8 Choosing a method... Bell & Donoghue (2005) by JoungYoun Kim Korber et al. (2000), Graur & Martin (2004)
Dec. 13 Project presentations:
  • Floral diversification and pollination system evolution in Andean Solanaceae (by Stacey & Steve)
  • Brain size and group size in African antelopes (by Joung-Youn, Genny & Heejung)
Dec. 15
  • Revisiting climate and life-history evolution in evening primroses (by Ivalú & Tim)
  • Morphological relationships inside of the New World Croton's species (by Flor & Oscar)

Last modified: Tue Dec 6 16:47:58 CST 2005