2016 Population and Speciation Genomics

Here you can find lecture slides and learning activities from the 2016 Workshop on Population and Speciation Genomics.

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Week I

Workshop introduction

• Workshop introduction – lecture slides

Computer lab and UNIX

• • Connecting to the Cloud
  • UNIX introduction / UNIX example data / UNIX example data2

File formats, VCFtools, Plink

• File formats, VCFtools, Plink exercise

R and adegenet, STRUCTURE, smartpca

• R and adegenet exercise
• STRUCTURE exercise
• smartpca exercise

Bayesian and Likelihood Inference

• Bayesian and Likelihood Inference – lecture slides

Genotype and SNP calling

• Genotype and SNP calling – lecture slides
• ANGSD exercise / ngsTools exercise

Introgression and Admixture Modelling

• Introgression and admixture exercise

Natural selection and Adaptation

• • Scans of Selection – lecture slides
  • Local Adaptation – lecture slides
  • BayeScan and BayeScEnv exercises

Population demography

• Demographic inference – lecture slides
• Python introduction
• δaδi exercise

Genomics of Organismal diversification

• Genomics of Organismal diversification – lecture slides

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Week II

Ancient genomics

• Lecture slides – part 1
• Lecture slides – part 2

Analyses of demography, population structure, and species delimitation with BEAST2

• Bayesian coalescent inference of population size history -introduction slides
• BEAST2 exercises

Evolutionary population genomics

• Daniel Berners Lecture slides
• Background for the lecture Roesti et al.(2014) The genomic signature of parallel adaptation from shared genetic variation
• R RADseq exercise
• Exploring selective sweeps exercise

Detecting selective sweeps

• Genetic basis and signatures of selection around loci underlying adaptation and speciation
• SweeD exercise

Introgression

• Painting chromosomes – lecture slides
• How to over-interpret Structure – a manual
• fineSTRUCTURE exercise

Divergence and gene flow between species

• Divergence and gene flow – lecture slides
• Why study speciation and genomics
• Divergence and gene flow exercise