Suggested Reading

Population genetics theory

Theoretical evolutionary genetics by Joe Felsenstein, available online:


 

Basic unix tutorial

A summary of basic unix commands and knowledge as preparation for novices can be found here:

 

Likelihood and Bayesian Inference theory

A review of relevant probability models for population genomics and their application to low coverage sequence data:

 

Models for locus-specific introgression and admixture

A review describing statistical models and applications to estimate genetic ancestry:

 

Natural selection / adaptation

 

Coalescent analyses with BEAST

The extended Bayesian Skyline plot, introduced by Joseph Heled and Alexei Drummond:

 

Species tree inference from SNP data

The model implemented in the BEAST add-on SNAPP, by David Bryant and colleagues:

 

Measuring divergence and gene flow between species

Examples of genome-wide analyses of speciation and gene flow, using Heliconius butterflies and Ficedula flycatchers as models:

 

Inference of population structure

Core methodological publications: