Suggested Reading

Unix & R

Some computational skills will be needed to make the most out of the Workshop. We’ll provide introductions to both Unix and the R programming environment, but if you’re not familiar with these tools yet, we recommend a look at the very helpful tutorials provided by the folks from the Software Carpentry workshop:

Ortholog identification

Two recent papers by Toni Gabaldón and co-workers provide a good overview of the subject:

Phylogenetic inference

Joe Felsenstein’s “Inferring Phylogenies” is one of the most important books in the field and a great (albeit voluminous) read:

Maximum Likelihood and Bayesian inference, reviewed by Paul Lewis and others:

Software-specific publications for Workshop programs:

Coalescent theory

We recommend reading the following two reviews:

Gene trees / Species trees

In Kubatko & Degnan (2007), Laura Kubatko showed that concatenation of multi-marker datasets can lead to inconsistent phylogenies. A great introduction to the subject is provided by Laura’s book “Estimating Species Trees: Practical and Theoretical Aspects” (the first chapter of which can be downloaded for free):

Time calibration

Relaxed clock models, presented by Alexei Drummond and colleagues:

Recent approaches for the integration of fossil and molecular data, by Tanja Stadler and others:

Trait evolution

An important paper on the use of the Ornstein-Uhlenbeck model for trait evolution, and the presentation of geiger 2.0 by Matt Pennell:

Diversification rate estimation

A review on diversification models and a recent paper by Tanja Stadler on likelihood-based diversification rate estimation: