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 and the Institute of Earth and Environmental Sciences, University of Potsdam (2017-2019). Letters/certificates of attendance can also be provided.
Instructors: FB: Faysal Bibi. JM: Johannes Müller. RS: Roland Sookias.
Day 1 – Phylogenetics. Cladistics. Tree thinking. Morphological characters. Parsimony. (FB)
Programs used: TNT, Mesquite, Figtree
Presentation: Lecture 1.pdf
Anolis.tnt Extant anolis lizard DNA characters. [Source: Beast example file]
TNT command line instructions (all platforms)
Day 2 – Molecular data. Model testing. Maximum likelihood. Bayesian analyses (FB)
Programs used: jModelTest, Mesquite, PhyML (online), BEAST, Tracer, Figtree
Presentation: Lecture 2.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).
Dembo fossil ages – text file with tip ages for beauti.
Day 3 – Total Evidence Analysis. Fossil calibration and time-trees (FB)
Programs used: BEAST, Tracer, Figtree
Presentation: Lecture 3.pdf
Primates.nex (from yesterday)
Dembo_2015_beast.nex (from yesterday)
Spaulding_2009mol.nex – molecular matrix of cetartiodactyls
Caprini_morph.nex – Caprini morphology matrix
More bears – an excellent tutorial on using the FBD model for dating
Day 4 – Phylogenetic comparative methods (JM)
Programs used: R, RStudio
Presentation: Lecture 4.pdf
Text file with today’s R script commands
Day 5 – Total evidence analyses and the Fossil Birth-Death tree prior. (FB)
Programs used: BEAST
Presentation: No new material (see Lecture 3 above)
Example files: Caprini, Bears, Penguins datasets from above.
Day 6 – DNA data query and alignment. Phylogenetic networks. Total Evidence class exercise.
Afternoon class exercise: 2 teams, 10 mammals – Total Evidence Analysis!
Programs used: BLAST (online), Dendroscope, Densitree, Mesquite. MUSCLE, SplitsTree.
Presentation: Lecture 6.pdf
Example files: Any trees files generated by previous Beast analyses (for network visualization)
Folder of Nexus files you made from the class exercise on mammal skulls
Day 7- Morphometric phylogenetics. Evolution of languages (RS)
Using geoometric morphometric data to generate phylogenies. Using comparative phylogenetic methods to study the evolution of languages.
Programs used: Rstudio, TNT, Figtree, GPSA, Landmark
Presentation: [ ]
Example files all here.
Day 8 – Phylomorphospace. Phylogenetic community structure. Phylogenetic model testing. Work on individual projects. (FB)
Program used: RStudio.
Phylo_PCO.R script for phylogenetic morphospace analyses
Comm_Structure.R script with all exercises for today (with thanks to Juan Cantalapiedra and John Rowan).
R script for evolutionary model testing
Additional resources: The picante tutorial pdf.
Day 9 – Work on individual projects. (FB)
Days 10 – Project presentations (FB)