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:
- Gabaldón & Koonin (2013) Functional and evolutionary implications of gene orthology
- Sonnhammer et al. (2014) Big data and other challenges in the quest for orthologs
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:
- Huelsenbeck et al. (2001) Bayesian inference of phylogeny and its impact on evolutionary biology
- Holder & Lewis (2003) Phylogeny estimation: traditional and Bayesian approaches
Software-specific publications for Workshop programs:
- Bazinet et al. (2014) A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0
- Bouckaert et al. (2014) BEAST 2: a software platform for Bayesian evolutionary analysis
- Drummond & Bouckaert (2014) Bayesian evolutionary analysis with BEAST 2.
Coalescent theory
We recommend reading the following two reviews:
- Rosenberg & Nordborg (2001) Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
- Wakeley (2013) Coalescent theory has many new branches
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):
- Kubatko & Degnan (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence
- Knowles & Kubatko (2010) Estimating Species Trees: Practical and Theoretical Aspects
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:
- Ronquist et al. (2012) A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera
- Heath et al. (2014) The fossilized birth-death process for coherent calibration of divergence-time estimates
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:
- Butler & King (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution
- Pennell et al. (2014) geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
Diversification rate estimation
A review on diversification models and a recent paper by Tanja Stadler on likelihood-based diversification rate estimation: