Suggested Reading

Population genetics theory

Theoretical evolutionary genetics by Joe Felsenstein, available online:

Some background literature about the ‘omics’ era in evolutionary biology:

 

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

 

Genome scan methods (BayeScan / BayeScEnv)

 

Coalescent analyses with BEAST

The extended Bayesian Skyline plot, introduced by Joseph Heled and Alexei Drummond, and the structured coalescent approximation implemented in the BEAST2 add-on BASTA, by Nicola De Maio and colleagues:

 

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:

Evolutionary population genomics

Background for Daniel Berners lecture:

Interesting recent application paper that illustrates interpretation issues of admixture model: