Topic |
Handouts |
Reading |
Week 1 (11-Jan-08)
Intro and Variation |
Lecture slides
Lab handout (Assignment)
Brachiopod data
|
Cope, 1887, Evolution
Polly & Spang, 2002, History
Van Valen, 2005, Statistics
|
Week 2 (18-Jan-08)
Species and Speciation |
Lecture slides
Assignment |
De Queiroz, 2007, Species
Erwin & Anstey, 1995, Species
Gingerich, 1974, Species
Imbrie, 1955, Species
Simpson, 1951, Species
|
Week 3 (25-Jan-08)
Bootstrapping and similar tests, Geometric morphometric data
|
Lecture slides
Assignment
Brach photos |
Efron & Tibshirani, 1986, Bootstrap
Richtsmeier et al. 2002, Morphometrics
Rohlf & Slice, 1990, Procrustes
Rohlf, 1993, PCA
|
Week 4 (1-Feb-08)
Morphospaces, disparity, and phenotypic diversification |
Lecture slides
Assignment |
**Erwin, 2007, Disparity
**Richtsmeier et al. 2002, Morphometrics
Foote, 1997, Disparity
Gerber et al., 2007, Ontogeny and disparity
Wills, 1998**, Cambrian disparity |
Week 5 (8-Feb-08)
No meeting |
|
|
Week 6 (15-Feb-08)
Phyletic evolution, tempo, mode |
Assignment |
Bookstein et al., 1978, Tempo and mode
**Gingerich, 2001, Rates of evolution
Gingerich, 1993, Quantification of evolutionary rates |
Week 7 (22-Feb-08) More Phyletic evolution, tempo, mode
|
Slides
Assignment |
Eldredge & Gould, 1972, Punc. Equilibrium
**Gould & Eldredge, 1977, Punc. Equil. Reconsidered |
Week 8 (29-Feb-08) Phylogenetic tempo and mode, morphological modelling
|
Slides
Assignment |
Bookstein, 1988, Random walks
Polly, 2004, Morph Modelling |
Week 9 (7-Mar-08) Review and Synthesis
|
Slides
[No assignment] |
|
Spring Break (14-Mar-08)
|
|
|
| Week 10 (21 Mar 08) Ontogeny and Growth |
Assignment
Age / Size Data |
Goswami, 2006
Olson & Miller, 1951
LaBarbara, 1985
**Maynard Smith et al. 1985, Devl. Constr.
**Rudwick, 1968, Brach Growth
Pennington et al., 1999, Brach Development
Rice, 1998, shell coiling |
Week 11 (28 Mar 08) Character-based phylogenetics: parsimony cladistics, stratocladistics
|
|
Eldredge & Cracraft, 1980, Cladograms
Patterson, 1977, Palaeo and Phylogeny
Fox et al, 1999, Stratocladistics
(Fox & Marcot, 2008, Stratocladistic software
Donoghue et al., 1989, Importance of fossils in phylogeny reconstruction ) |
Week 12 (4 Apr 08) Quantitative phylogenetics: distance trees, stratophenetics, maximum-likelihood, and Bayesian techniques |
Assignment |
Felsenstein, 1981, evolutionary trees
Gingerich, 1979, Stratophenetics
Huelsenbeck & Rannala, 1997, ML and stratigraphy
Huelsenbeck, 2001, Bayesian
|
Week 13 (11 Apr 08) Phylogenetics and classification
|
|
De Queiroz and Gauthier, 1990, Phylogeny and classification
Forey, 2002, Phylocode: Pain, no Gain
Gingerich, 1979, Stratophenetics
Hull, 1979, Limits of Cladism
|
Week 14 (18 Apr 08)
Comparative phylogenetic and statistical methods
|
|
MacLeod, 2001, Phylogeny and quantitative analysis
Martins and Hansen, 1997, Phylogenies and the comparative method
Polly, 2001, Ancestral nodes and confidence intervals
|
Week 15 (25 Apr 08)
Biodiversity and extinction |
Slides
Assignment |
Van Valen, 1973, Red Queen
Raup, 1975, Survivorship and Van Valen's Law
Raup & Sepkoski, 1984, Periodicity in Extinction
Raup, 1985, Models of Cladogenesis
Alroy et al., 2001, Phanerozoic diversity
|
|
General Info
P. David Polly
513 Geol Sciences
pdpolly@indiana.edu
Syllabus
[pdf format]
R Functions
degrade()
disparity.univariate()
Diversity Functions
group.disparity()
groupdists()
individual.disparity()
longrandomwalk()
lri()
lriInt()
randomwalk()
read.tps()
Paleontology
Paleobiology: A Synthesis
The Paleobiology Database
R
A Short R Tutorial
Kickstarting R
Getting data from Microsoft to R |