Workshop on Population and Speciation Genomics Preparation

Population genetics theory

Theoretical evolutionary genetics by Joe Felsenstein, available online:

• Joe Felsenstein, Theoretical evolutionary genetics (1978-2015)

 

Basic unix tutorial

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

• Evomics unix tutorial

 

Likelihood and Bayesian Inference theory

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

• Buerkle & Gompert (2012) Population genomics based on low coverage sequencing: how low should we go?

 

Models for locus-specific introgression and admixture

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

• Gompert & Buerkle (2013) Analyses of genetic ancestry enable key insights for molecular ecology

 

Natural selection / adaptation

• Jensen, Wong, Aquadro (2007) Approaches for identifying targets of positive selection
• Nielsen (2005) Molecular Signatures of Natural Selection

 

Coalescent analyses with BEAST

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

• Heled & Drummond (2008) Bayesian inference of population size history from multiple loci

 

Species tree inference from SNP data

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

• Bryant et al. (2012) Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis

 

Measuring divergence and gene flow between species

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

• Martin et al. (2015) Evaluating the use of ABBA–BABA statistics to locate introgressed loci
• Martin and van Belleghem (2017) Exploring evolutionary relationships across the genome using topology weighting

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

• The Heliconius Genome Consortium (2012) Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
• Martin et al. (2013) Genome-wide evidence for speciation with gene flow in Heliconius butterflies

 

Inference of population structure

Core methodological publications:

• Pritchard et al.(2000) Inference of population structure using multilocus genotype data
• Lawson et al.(2012) Inference of Population Structure using Dense Haplotype Data