| Date | Topic |
Primary reading: Discussions |
Suggested reading |
| Sept. 6 and 8 | Introduction 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) |
| Date | Topic |
Primary reading: Discussions |
Suggested reading |
| Nov. 17 | The 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. 24 | No 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) |
