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.
Software resources:
BEAST Dendroscope Figtree GPSA
Day 1 – Phylogenetics. Cladistics. Tree thinking. Morphological characters. Parsimony. (FB)
Programs used: TNT, Mesquite, Figtree
Presentation: Lecture 1.pdf
Example files:
Dembo_2015.tnt Morphological dataset of hominin taxa. Character list. Publication.
Anolis.tnt Extant anolis lizard DNA characters. [Source: Beast example file]
Spaulding_2009.tnt Extant and fossil artiodactyl morphology. Publication.
Bears.nex Extant and fossil bear morphology. Publication.
TNT command line instructions (all platforms)
TNT parsimony analysis – windows or pdf here
Day 2 – Molecular data. Model testing. Maximum likelihood. Bayesian analyses (FB)
Programs used: jModelTest, Mesquite, PhyML (online), BEAST, Tracer, Figtree
Presentation: Lecture 2.pdf
Example files:
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
Example files:
Primates.nex (from yesterday)
Dembo_2015_beast.nex (from yesterday)
Spaulding_2009morph.nex – morphological matrix of cetartiodactyls (Publication)
Spaulding_2009mol.nex – molecular matrix of cetartiodactyls
Caprini_cytb.nex – Caprini cytochrome b alignment (Publication)
Caprini_morph.nex – Caprini morphology matrix
More bears – an excellent tutorial on using the FBD model for dating
Penguins – Total evidence xml file for Beauti (Publication)
Day 4 – Phylogenetic comparative methods (JM)
Programs used: R, RStudio
Presentation: Lecture 4.pdf
Example files:
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.
Example files:
Phylo_PCO.R script for phylogenetic morphospace analyses
Dembo tree file. Primates tree file.
Cantalapiedra et al. files for ruminant phylogenetic structure. (Publication)
Comm_Structure.R script with all exercises for today (with thanks to Juan Cantalapiedra and John Rowan).
Rowan et al. files for African large mammal phylogenetic structure. (Publication)
R script for evolutionary model testing
Additional resources: The picante tutorial pdf.
Day 9 – Work on individual projects. (FB)
Days 10 – Project presentations (FB)
