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

Assessments of the ABBA BABA statistic and topology weighting as tools to identify introgression:

Examples of genome-wide analyses of speciation and gene flow, using Heliconius butterflies as a model system:


Inference of population structure

Core methodological publications: