This is a page hosting resources used in the Phylogenetics in Evolution and Ecology practical course taught by Faysal Bibi at the Museum für Naturkunde, Berlin.
Course is registered through the Institute of Biochemistry and Biology, University of Potsdam (since 2017). Letters/certificates of attendance can also be provided.
Day 1 – Phylogenetics. Tree thinking. Parsimony
Programs used: Pen and Paper!
Day 2 – Parsimony analysis. Morphological data
Programs used: TNT, Mesquite, Figtree
Presentation: Lecture 2 pdf
Anolis.tnt Extant anolis lizard DNA [Source: BEAST example file]
TNT command line instructions (all platforms)
Day 3 – Molecular data. Model testing. Maximum likelihood. Bayesian analyses
Programs used: jModelTest, Mesquite, PhyML (online), BEAST, Tracer, Figtree
Presentation: Lecture 3 pdf
Primates.nex – an alignment of molecular data from primates
Dembo_2015_beast.nex – the hominin fossil dataset cleaned up for beast (invariant characters and ambiguous codings removed).
Day 4 – Total Evidence Analysis. Fossil calibration and time-trees
Programs used: BEAST, Tracer, Figtree
Presentation: Lecture 4 pdf
Primates.nex (from yesterday)
Dembo_2015_beast.nex (from yesterday)
Dembo fossil ages – text file with tip ages for beauti.
Caprini_morph.nex – Caprini morphology matrix
Bears – an excellent tutorial on using the FBD model for dating
Day 5 – Guest Presentations
Programs used: MrBayes, TNT, Figtree, R, RStudio
Juan Cantalapiedra – Phylogenetics in the study of macroevolution
Roland Sookias – Character construction, outgroups, and data exploration
Day 6 – Phylogenetic networks. GenBank query. Alignment. Topological constraints.
Programs used: BLAST (online), Dendroscope, Densitree, Mesquite. MUSCLE, SplitsTree.
Presentation: Lecture 6 pdf
Day 7 – Total Evidence class exercise
Presentation: Lecture 7 pdf