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: