Botany 940

Seminar: Plant Systematics and Evolution
New Advances in Phylogenetics Methods

Mondays, 12:05-12:55pm
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Schedule

DayPresenterThemeReadingOther material
2/4Cecile AneReviewPart of Chapter 1 in Yang's bookslides
2/11Bret LargetReview slides
2/18Evelyn WilliamsGene/Species trees Carstens and Knowles (2007) Estimating Species Phylogeny from Gene-Tree Probabilities Despite Incomplete Lineage Sorting: An Example from Melanoplus Grasshoppers.  
2/25Josh SulmanGene/Species trees Edwards, Liu and Pearl (2007) High-resolution species trees without concatenation.  
3/3Stephanie LyonDivergence 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.
3/10Brian WalshDivergence 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.
3/17Recess
3/24Emily ButlerTrait evolution Barker, Meade and Pagel (2007) Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes.  
3/31Andy GardnerTrait 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.
4/7Tim SmithTrait evolution Smith et al. (2008) The role of pollinator shifts in the floral diversification of Iochroma (Solanaceae).  
4/14Kirk GrubbsAlignement and phylogeny Wong, Suchard, and Huelsenbeck (2008) Alignment uncertainty and genomic analysis Rokas (2008) Lining up to avoid bias
4/21Heejung ShimAlignement 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
4/28Brent BergerSoftware demo Garli, the BEAUti and the BEAST Garli manual, paper describing BEAST: Drummond and Rambaut (2007),
5/5Ken Sytsma Software demo BayesTrait manual, Friedman and Barrett (2008), Vallejo-Marin and O'Brien (2007), Moore and Donoghue (2007).