Suggested Reading

Population genetics theory

An excellent online resource on general population genetics, with R code examples:


Basic UNIX tutorial

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


Bayesian inference

Easy-to-follow visual explanations of likelihood and Bayesian inference can be found in Paul Lewis’ phyloseminars available on Youtube:


Models for locus-specific introgression and admixture

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


Natural selection / adaptation

Two reviews on the identification of signals of selection:


Genome-wide genealogy inference

The paper on Relate by Speidel et al. and a commentary by Kelley Harris:


Inference of population structure

Publications describing the methodology used in tools like STRUCTURE:


The multi-species coalescent

A review on the model and a paper on tree discordance:


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: