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 & 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)

Mesquite   MorphoJ   MUSCLE

R   RStudio   Tracer   TNT

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 command line wiki page

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:

R Script used

Anolis.phy

Anolis_Data.csv

Geospiza.nex

Geospiza.txt

Geospiza_Mesquite.nex

 

Additional resources:

Phylogenetic signal demonstration

Arborworkflows

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.