Exercise 2: Coding with pizza

Exercise 2: Coding with pizza

1. Reconstruct ancestral states for snout-vent length (SVL) for Phelsuma geckos.

2. Is there a standard correlation between ln(SVL) and ln(jaw) across the species of Phelsuma geckos? Is there an evolutionary correlation? What do you conclude?

3. Day geckos can be classified by island group, as listed below. Use ancestral state reconstructions to investigate the dispersal of geckos across islands.

Species	Island
abbotti	Seychelles
astriata	Seychelles
borbonica	Mauritius
cepedianaA	Mauritius
dubia	Madagascar
guentheri	Mauritius
guttata	Madagascar
laticauda	Madagascar
lineata	Madagascar
grandis	Madagascar
mutabilis	Madagascar
ornata	Mauritius
quadriocellata	Madagascar
longinsulae	Seychelles
standingi	Madagascar
sunbergi	Seychelles
barbouri	Madagascar
guimbeaui	Mauritius
comorensis	Comoros
robertmertensi	Comoros

Exercise 1: Comparative data in R

Exercise 1: Comparative data in R

1. Read in the data phelsuma.csv. Describe the data set. How many species are included? How many variables?

2. Read in the tree phel2.phy. Plot the tree. Is it ultrametric?

3. Do the names match in the two data sets? If not, make a tree and data set that do match using treedata().

4. Reroot the tree using the species “ornata” as an outgroup.

Comparative methods workshop - 18 May 2016 Leipzig

Comparative Methods in R
18 May, 2016
iDiv, Leipzig, Germany

Welcome to this short course in comparative methods in R. The course materials can be found here.

Files you will need:

anolisDataAppended.csv
anolis.phy
multiple_trees.phy
phel2.phy
phelsuma.csv

Review materials:

basics.R
Also see this intro to basic R.

My files from the day
zip file

Schedule

9:00 - 9:30 AM 
Lecture 1: What is the point of comparative methods? pdf

9:30 - 10:00 AM 
Demonstration 1: Reading trees into R, matching tip data R script

10:00 - 10:30 AM 
Exercise 1: Comparative data in R
answer is here - along with all of the things I did in the morning session!

10:30 - 10:45 AM - Coffee break

10:45 - 11:00 AM
Lecture 2: What is a phylogenetic correlation? pdf

11:00 - 11:30 AM
Demonstration 2: PICs, PGLS, and ancestral states R script

11:30 - 12:30 AM
Exercise 2: Coding with pizza

12:30 - 2:00 PM - Lunch

2:00 - 2:30 PM
Lecture 3: Fitting macroevolutionary models to data pdf

2:30 - 3:00 PM
Demonstration 3: Fitting models using geiger code

3:00 - 3:30 PM
Exercise 3: Which model is the best exercise

3:30 - 3:45 PM - Coffee break

3:45 - 4:15 PM
Demonstration 4: Plotting using phytools code

4:15 - 5:00 PM

Wrap-up exercise: lightning analysis

5:15 - 5:30 PM
Presentations of lightning analysis