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.
Software resources:
Day 1 – Phylogenetics. Tree thinking. Parsimony
Programs used: Pen and Paper!
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
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
A more in-depth tutorial on TNT (ppt)
3D cranial specimens for morphological analysis
Day 3 – Molecular data. Model testing. Maximum likelihood. Bayesian analyses
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
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 (Roy Ebel & Sarin Tiatragul)
Programs used: R, RStudio
Lecture & example files here
Day 6 – GenBank query. Alignment. Phylogenetic networks. Total Evidence class exercise.
Programs used: BLAST (online), Dendroscope, Densitree, Mesquite. MUSCLE, SplitsTree.
Presentation: Lecture 6 pdf
Day 7 – Phylogenetics with Phylogeneticists
10h: Alice Petzold (Museum für Naturkunde): Phylogenetics and Conservation – Past and Present Giraffe Biodiversity (based on Petzold & Hassanin 2020 and Petzold et al. 2020)
11h: Juan Cantalapiedra (Alcala University): Becoming a Megaherbivore
13h: Johannes Müller (Museum für Naturkunde): A total evidence analysis of lacertid lizards (based on Garcia-Porta, Müller, et al. 2019)
14h: Justus Hagemann (Uni. Potsdam): Dating phylogenies with a sparse fossil record and limited data
15h: Roland Sookias (Université de Liège): Introduction to culturolinguistic phylogenetics and phylogenetics from continuous data (related study Sookias et al. 2018)
Day 8 – Topological constraints & Work on individual projects
Meredith et al. 2011 Mammal DNA dataset
Day 9 – Work on individual projects
amniota.org 