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)

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

• Hans Ellegren (2014) Genome sequencing and population genomics in non-model organisms

 

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

 

Genome scan methods (BayeScan / BayeScEnv)

• Villemereuil & Gaggiotti (2015) A new FST-based method to uncover local adaptation using environmental variables
• Foll et al. (2014) Widespread Signals of Convergent Adaptation to High Altitude in Asia and America
• Foll & Gaggiotti (2008) A Genome-Scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective
• Vatsiou et al (2015) Detection of selective sweeps in structured populations: a comparison of recent methods

 

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:

• Heled & Drummond (2008) Bayesian inference of population size history from multiple loci
• De Maio et al. (2015) New routes to phylogeography: a Bayesian structured coalescent approximation

 

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

Examples of genome-wide analyses of speciation and gene flow, using Heliconius butterflies and Ficedula flycatchers as models:

• The Heliconius Genome Consortium (2012) Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
• Martin S. H. et al. (2013) Genome-wide evidence for speciation with gene flow in Heliconius butterflies
• Burri R. et al. (2015) Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

 

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

Evolutionary population genomics

Background for Daniel Berners lecture:

• Roesti et al.(2014) The genomic signature of parallel adaptation from shared genetic variation

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

• van Dorp et al.(2015) Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference