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:
- Lewis (2018) Primer part 1 (introduction of likelihood starts at minute 19)
- Lewis (2018) Primer part 3a
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:
- Jensen, Wong, Aquadro (2007) Approaches for identifying targets of positive selection
- Nielsen (2005) Molecular signatures of natural selection
Genome-wide genealogy inference
The paper on Relate by Speidel et al. and a commentary by Kelley Harris:
- Speidel, Forest, Chi, Myers (2019) A method for genome-wide genealogy estimation for thousands of samples
- Harris (2019) From a database of genomes to a forest of evolutionary trees
Inference of population structure
Publications describing the methodology used in tools like STRUCTURE:
- Pritchard et al. (2000) Inference of population structure using multilocus genotype data
- Lawson et al. (2012) Inference of population structure using dense haplotype data
The multi-species coalescent
A review on the model and a paper on tree discordance:
- Degnan and Rosenberg (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent
- Wang and Hahn (2018) Speciation genes are more likely to have discordant gene trees
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