This is a page hosting resources used in the Phylogenetics in Evolution and Ecology practical course taught by Faysal Bibi & Mozes Blom 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:
Aliview BEAST Figtree Geneious
Day 1 – Phylogenetics. Tree thinking. Parsimony. (Bibi)
Programs used: Pen and Paper!
Presentation: Day 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. Skulls exercise. (Bibi)
Programs used: TNT, Mesquite, Figtree
Presentation: Day 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)
Day 3 – Genetic data. Sequencing. Alignment. GenBank. Maximum likelihood. (Blom)
Programs used: Genious.
Presentation: [not public]
ML tutorial using Jupyter Notebook & Google Colab via Mozes Blom Github (requires a Google account)
Day 4 – Bayesian inference (Blom). Fossil calibration & time-trees (Bibi).
Programs used: BEAST, Tracer, Figtree
Presentation1: Bayesian inference [not public].
Presentation2: Fossil calibration & time-trees (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.
Bears – an excellent tutorial on using the FBD model for dating
Penguins – Total evidence xml file for Beauti (Publication)
Day 5 – Gene tree-species tree discordance, coalescent variation (Blom)
Programs used: Python via Google Colab
Presentation [not public]
Practical: Github tutorial run this via Google Colab (paste the GitHub URL into the GitHub tab)
Day 6 – Topological constraints. GenBank exercises. Guest Lectures. (Bibi, Blom, & guests)
Sofia Hayden Bofill – [tbd]
Roland Sookias – Culturolinguistic phylogeny
Presentation1: Topological constraints, GenBank, Troubleshooting (pdf)
Presentation2: Crocodile GenBank exercise (not public)
Day 7 – Total Evidence Class Exercise
Presentation: Total Evidence (pdf)
amniota.org 