Basically I am trying to teach myself how to calculate diversification rates. While there are some R tutorials most of them use simulated data. What I would like to do is either load in an actual tree file or consensus chronogram and use that. I am not that gifted with R.
You can use Bayesian Analysis of Macroevolutionary Mixtures (BAMM) to quantify heterogeneity in speciation, extinction and trait evolution rates. More information in the links below (including a detailed documentation about using the method):
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089543
http://bamm-project.org/index.html
TreeBase is a good source of data. http://treebase.org/treebase-web/search/ Researchers deposit both the data matrices and the trees in this database, along with PDFs of the publications describing the work. Many authors deposit data in the data DRYAD http://datadryad.org/ and some of those sets include trees and the data used to build the trees.
NCBI/GenBank of course also has many data sets, but the trees are not included with the data, and the PopSets (population data sets) need a bit of reformatting and alignment to get them ready for phylogenetic analyses.
I would recommend exploring several data sets, such as one that is from organisms with a similar evolution to your organism (viruses and bacteria evolve a bit differently than diploid eukaryotes for example), one that is from a gene set similar to the set you plan to work with (mitochondrial DNA has a different history than genes in the nucleus for eukaryotes), and one that uses methods similar to the method you plan to use.
http://treebase.org/treebase-web/search/study/summary.html?id=10278
Divergence times and colonization of the Canary Islands by Gallotia lizards.
is one example from TreeBase
http://datadryad.org/resource/doi:10.5061/dryad.35321
Phylogenetic structure of vertebrate communities across the Australian arid zone
is one example from the data DRYAD.
Hi,
I agree that GEIGER is probably the best way to do this. The following link should help you get a handle on how to run the package in R:
http://cran.r-project.org/web/packages/geiger/geiger.pdf
http://informatics.nescent.org/wiki/R_Hackathon/Diversification
My best recommendation would be to just spend some time reading this and trying it out. It will take a while to get it to work right, but you'll have picked up a nice skill and will be able to do it next time without any problem.
BAMM is also a really exciting new package that does some different things. You can find a ton of documentation for it here:
http://bamm-project.org/index.html
I have also attached the original paper (Harmon et al.) for GEIGER.
I hope that helps!
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