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 (2017-2019). Letters/certificates of attendance can also be provided.

Instructors: FB: Faysal Bibi. JM: Johannes Müller. RS: Roland Sookias.

Software resources:

BEAST Dendroscope   Figtree GPSA

jModelTest Landmark (PC only)

 Mesquite  MeshLab MUSCLE

PHYLIP R   RStudio

Tracer   TNT  SplitsTree 

Day 1 – Phylogenetics. Cladistics. Tree thinking. Morphological characters. Parsimony. (FB)

Programs used: TNT, Mesquite, Figtree

Presentation: Lecture 1.pdf

Example files:

Dembo_2015.tnt Morphological dataset of hominin taxa. Character list. Publication.

Anolis.tnt  Extant anolis lizard DNA characters. [Source: Beast example file]

Spaulding_2009.tnt  Extant and fossil artiodactyl morphology. Publication.

Bears.nex Extant and fossil bear morphology. Publication.

TNT command line instructions (all platforms)

TNT command line wiki page

TNT parsimony analysis – windows or pdf here

Day 2 – Molecular data. Model testing. Maximum likelihood. Bayesian analyses (FB)

Programs used: jModelTest, Mesquite, PhyML (online), 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.

Day 3 – Total Evidence Analysis. Fossil calibration and time-trees (FB)

Programs used: BEAST, Tracer, Figtree

Presentation: Lecture 3.pdf

Example files:

Primates.nex (from yesterday)

Dembo_2015_beast.nex (from yesterday)

Spaulding_2009morph.nex – morphological matrix of cetartiodactyls (Publication)

Spaulding_2009mol.nex – molecular matrix of cetartiodactyls

Caprini_cytb.nex – Caprini cytochrome b alignment (Publication)

Caprini_morph.nex – Caprini morphology matrix

More bears – an excellent tutorial on using the FBD model for dating

Penguins – Total evidence xml file for Beauti (Publication)

Day 4 – Phylogenetic comparative methods (JM)

Programs used: R, RStudio

Presentation: Lecture 4.pdf

Example files:

Geospiza_Mesquite.nex

Geospiza.nex

Geospiza.txt

Text file with today’s R script commands

Day 5 – Total evidence analyses and the Fossil Birth-Death tree prior. (FB)

Programs used: BEAST

Presentation: No new material (see Lecture 3 above)

Example files: Caprini, Bears, Penguins datasets from above.

Day 6 – DNA data query and alignment. Phylogenetic networks. Total Evidence class exercise.

Afternoon class exercise: 2 teams, 10 mammals – Total Evidence Analysis!

Programs used: BLAST (online), Dendroscope, Densitree, Mesquite. MUSCLE, SplitsTree.

Presentation: Lecture 6.pdf

Example files: Any trees files generated by previous Beast analyses (for network visualization)

Folder of Nexus files you made from the class exercise on mammal skulls

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: Rstudio, TNT, Figtree, GPSA, Landmark

Presentation: [ ]

Example files all here.

Day 8 – Phylomorphospace. Phylogenetic community structure. Phylogenetic model testing. 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)