Phylogenetics in Evolution and Ecology

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:

BEAST Dendroscope   Figtree

jModelTest  Mesquite 

MeshLab  MUSCLE

R   RStudio

Tracer   TNT  SplitsTree 

Day 1 – Phylogenetics. Tree thinking. Parsimony

Programs used: Pen and Paper!

Presentation: Lecture 1 pdf

Baum et al. 2005 Tree-thinking Quiz I

Cladisticules exercise

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 command line wiki page

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

Lecture 8 pdf

Meredith et al. 2011 Mammal DNA dataset

Day 9 – Work on individual projects

Days 10 – Project presentations