Botany 940Seminar: Plant Systematics and Evolution
Mondays, 12:05-12:55pm |
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| Day | Presenter | Theme | Reading | Other material |
| 2/4 | Cecile Ane | Review | Part of Chapter 1 in Yang's book | slides |
| 2/11 | Bret Larget | Review | slides | |
| 2/18 | Evelyn Williams | Gene/Species trees | Carstens and Knowles (2007) Estimating Species Phylogeny from Gene-Tree Probabilities Despite Incomplete Lineage Sorting: An Example from Melanoplus Grasshoppers. | |
| 2/25 | Josh Sulman | Gene/Species trees | Edwards, Liu and Pearl (2007) High-resolution species trees without concatenation. | |
| 3/3 | Stephanie Lyon | Divergence times | Yang and Rannala (2006) Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. | Yang (2007) PAML 4: Phylogenetic Analysis by Maximum Likelihood. |
| 3/10 | Brian Walsh | Divergence times | Britton et al. (2007) Estimating divergence times in large phylogenetic trees. |
Drummond and Rambaut (2007)
BEAST: Bayesian evolutionary analysis by sampling trees.
Lepage et al. (2007) A general comparison of relaxed molecular clock models. Rannala and Yang (2007) Inferring speciation times under an episodic molecular clock. |
| 3/17 | Recess | |||
| 3/24 | Emily Butler | Trait evolution | Barker, Meade and Pagel (2007) Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. | |
| 3/31 | Andy Gardner | Trait evolution | Vanderpoorten and Goffinet (2006) Mapping Uncertainty and Phylogenetic Uncertainty in Ancestral Character State Reconstruction: An Example in the Moss Genus Brachytheciastrum. | Finarelli and Flynn (2006) Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): The effects of incorporating data from the fossil record. |
| 4/7 | Tim Smith | Trait evolution | Smith et al. (2008) The role of pollinator shifts in the floral diversification of Iochroma (Solanaceae). | |
| 4/14 | Kirk Grubbs | Alignement and phylogeny | Wong, Suchard, and Huelsenbeck (2008) Alignment uncertainty and genomic analysis | Rokas (2008) Lining up to avoid bias |
| 4/21 | Heejung Shim | Alignement and phylogeny | Redelings and Suchard (2005) Joint Bayesian Estimation of Alignment and Phylogeny | Suchard and Redelings (2007) BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny |
| 4/28 | Brent Berger | Software demo | Garli, the BEAUti and the BEAST | Garli manual, paper describing BEAST: Drummond and Rambaut (2007), |
| 5/5 | Ken Sytsma | Software demo | BayesTrait | manual, Friedman and Barrett (2008), Vallejo-Marin and O'Brien (2007), Moore and Donoghue (2007). |