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 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:

BEAST Dendroscope   Figtree

jModelTest  Mesquite 

MeshLab  MUSCLE

R   RStudio

Tracer   TNT  SplitsTree 

Day 1 – Phylogenetics. Tree thinking. Parsimony. (FB)

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 (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 command line wiki page

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:

R script: R brief intro

Garland 1993 dataset.csv

R script: Carnivore-Ungulate

R script: Primate data

Primatedata.csv

Upham 2019 mammal tree

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.

Day 9 – Work on individual projects. (FB)

Days 10 – Project presentations (FB)