Here you will find lecture slides and learning activities for the 2018 Workshop on Population and Speciation Genomics.
These activities are designed by the faculty and the workshop team and will be updated during the workshop.
Week I
Workshop introduction and orientation
- Introduction to the Evomics workshop series by Scott Handley
- Information from Daniel Kinzl of the Cesky Krumlov tourist information
- Introduction to the Workshop on Population and Speciation Genomics
Computer lab and UNIX introduction
- Connecting to Amazon EC2 instances
- Unix Activity
- The VCF format, filtering, and first analyses
- (extra) Detecting population structure with smartPCA
Likelihood and Bayesian inference
Population structure
- Lecture slides by Daniel Falush: The palette of human ancestry
- Lecture slides by Daniel Falush: A tutorial on how (not) to overinterpret STRUCTURE/ADMIXTURE bar plots
- fineRADstructure activity
- fineSTRUCTURE activity
Exploring genome data
Demography and admixture
- Lecture slides by Richard Durbin
- PSMC and MSMC activity
- Demography analysis with BEAST 2
- ANGSD and NGSadmix activities
- Lecture slides by Anders Albrechtsen: PCA, admixture, and SFS for low depth NGS data
- Lecture slides by Anders Albrechtsen: SFS inference from NGS data to detect recent adaptive selection
- Exercise slides by Anders Albrechtsen: ANGSD
- Lecture slides by Vitor Sousa_Part_I
- Lecture slides by Vitor Sousa_Part_II
- Fastsimcoal2 activity
- Lecture slides by Tim Vaughan: EBSP and Structured coalescent analyses with BEAST2
- Structured coalescent analyses with BEAST
The genomics of organismal diversification
Week II
Selection
Species tree inference
Adaptation
Species delimitation
Mutation spectrum evolution
Species networks
Introgression scans
- Speciation with gene flow lecture slides by Chris Jiggins
- ABBA BABA intro slides by Simon Martin
- ABBA BABA statistics
- Topology weighting intro slides by Simon Martin
- Topology weighting
Population and Speciation Genomics for Dummies