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 (2017-2020). Letters/certificates of attendance can also be provided.
Instructors: FB: Faysal Bibi. IL: Ignacio Lazagabaster
Software resources:
Day 1 – Phylogenetics. Tree thinking. Parsimony. (FB)
Programs used: Pen and Paper!
Presentation: Lecture 1 pdf
Baum et al. 2005 Tree-thinking Quiz I
Baum et al. 2005 Tree-thinking Quiz II
Baum et al. 2005 Original paper
Day 2 – Parsimony analysis. Morphological data (FB)
Programs used: TNT, Mesquite, Figtree
Presentation: Lecture 2 pdf
Example files:
Dembo_2015.tnt Hominin morphological dataset (Character list & Publication)
Anolis.tnt Extant anolis lizard DNA [Source: BEAST example file]
Bears.nex Extant and fossil bear morphology. Publication
TNT command line instructions (all platforms)
TNT Windows instructions or pdf here
3D cranial specimens for morphological analysis
Day 3 – Molecular data. Model testing. Maximum likelihood. Bayesian analyses (FB)
Programs used: jModelTest, Mesquite, PhyML (online), BEAST, Tracer, Figtree
Presentation: Lecture 3 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).
Day 4 – Total Evidence Analysis. Fossil calibration and time-trees (FB)
Programs used: BEAST, Tracer, Figtree
Presentation: Lecture 4 pdf
Example files:
Primates.nex (from yesterday)
Dembo_2015_beast.nex (from yesterday)
Hedges et al. 2015 paper on molecular rates
Dembo fossil ages – text file with tip ages for beauti.
Caprini_cytb.nex – Caprini cytochrome b alignment (Publication)
Caprini_morph.nex – Caprini morphology matrix
Bears – an excellent tutorial on using the FBD model for dating
Penguins – Total evidence xml file for Beauti (Publication)
Day 5 – Phylogenetic comparative methods (IL)
Programs used: R, RStudio
Presentation: Lecture 5 pdf
Example files:
Day 6 – Phylogenetic signal. Modes of Evolution. (IL)
Programs used: R, RStudio
Presentation: Lecture 6 pdf
Example files: In Google drive folder here
Day 7 – GenBank query. Alignment. Phylogenetic networks. Total Evidence class exercise.
Programs used: BLAST (online), Dendroscope, Densitree, Mesquite. MUSCLE, SplitsTree.
Presentation: Lecture 7 pdf
Day 8 – Phylomorphospace. Phylogenetic community structure. 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.
