This is a page hosting resources used in the Phylogenetics in Evolution and Ecology practical course taught by Faysal Bibi & Johannes Müller at the Museum für Naturkunde, Berlin, through the Institute of Biochemistry and Biology and the Institute of Earth and Environmental Sciences, University of Potsdam (2017-2018).
Software resources:
BEAST Figtree Landmark Editor (PC only – sorry Macs)
PHYLIP SplitsTree GPSA MeshLab MrBayes
Day 1 – Parsimony. Obtaining and aligning DNA sequences. (FB)
Programs used: TNT, Mesquite, Figtree, BLAST (Genbank), Mesquite, MUSCLE
Presentation: Lecture 1 (pdf)
Example files:
Dembo_2015.tnt Morphological dataset of hominin taxa and character list. Source
Anolis.tnt Extant anolis lizard DNA characters. [Beast example file]
Spaulding_2009.tnt Extant and fossil artiodactyl morphology. Source.
Bears.nex Extant and fossil bear morphology. Source.
TNT parsimony analysis instructions – command line (all platforms)
TNT parsimony analysis – windows
Day 2 – Maximum likelihood and Bayesian analyses (FB)
Programs used: PhyML 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.
Spaulding_2009morph.nex – morphological matrix of cetartiodactyls (Source)
Spaulding_2009mol.nex – molecular matrix of cetartiodactyls
Day 3 – Fossil calibration and time-trees (JM, FB)
Programs used: BEAST, Tracer, Figtree
Presentation: Lecture 3 (pdf)
Example files:
From yesterday: Primates.nex (for node calibration) and Dembo_2015_beast.nex (for tip dating)
Penguins – ready to go xml file for Beauti, with fossils and tip dating (Source)
More bears – an excellent tutorial from tamingthebeast.org
Day 4 – Phylogenetic comparative methods (JM)
Programs used: R, RStudio
Presentation: Lecture 4 (pdf)
Example files:
Additional resources:
Phylogenetic signal demonstration
https://www.r-phylo.org/wiki/HowTo/Table_of_Contents
https://lukejharmon.github.io/ilhabela/postIndex
Day 5 – Phylogenetic community structure & class exercise (FB)
Programs used: Rstudio
Presentation: Lecture 5 (pdf)
Example files:
R script with all exercises for today (with thanks to Juan Cantalapiedra and John Rowan). The picante tutorial pdf.
Cantalapiedra et al. files for ruminant phylogenetic structure. (Source)
Rowan et al. files for African large mammal phylogenetic structure. (Source)
Afternoon class exercise: 2 teams, 10 mammals! Results of your work: here!
Day 6 – Geometric morphometrics and evolutionary model selection (MK, FB)
Programs used: Landmark, MorphoJ, RStudio.
Geometric morphometrics. PCA of GM data, PCO of morphological matrices. Testing models of evolution (OU, Brownian motion, etc.). Testing for phylogenetic signal.
Programs used: MorphoJ, Landmark Editor, RStudio (geomorph, OUwie)
Presentations: Lecture 6A (Geometric Morphometrics). Lecture 6B (Evolutionary Models).
Example files:
Geometric morphometric example files.
R script for evolutionary model testing
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: R; PHYLIP; Mesquite; TNT; SplitsTree; GPSA; MeshLab; MrBayes; BEAST and BEAUti (may not need these)
Presentation: Lecture 7 (pdf)
Example files:
Link to folder with files (alternately here)
Day 8 – Work on individual projects
[Days 9 & 10 – presentations and discussions]
Presenters:
FB: Faysal Bibi. JM: Johannes Müller. MK: Martin Kirchner. RS: Roland Sookias.
