Day 1
Participants arrive
Dinner, logistics, introductions
Day 2
Experimental design: traditional markers and NGS; avoiding pitfalls
Overview of NGS approaches Reduced representation sequencing (RADseq, UCEs, exomes), whole genome sequencing/re-sequencing, target enrichment methods, RNAseq
Pipelines; QC-filtering; assembly and mapping; storage (use mitogenomes as example)
Computer demo/exercises
Evening speaker 1
Day 3
Mining markers from NGS data I (variant discovery)
Computer demo/exercises
Mining markers from NGS data II (variant interpretation)
Computer demo/exercises
Evening speaker 2
Day 4
Genetic diversity and inbreeding I
Computer demo/exercises
Genetic diversity and inbreeding II
Computer demo/exercises
Evening speaker 3
Day 5
Genetic structure/isolation: PCA, STRUCTURE/ADMIXTURE, allele trees
Computer demo/exercises
Gene flow and admixture
Computer demo/exercises
Evening speaker 4
Day 6
Field trip
Mid-course dinner & party
Day 7
Effective population size/Historical demography I
Computer demo/exercises
Effective population size/Historical demography II
Computer demo/exercises
Evening speaker 5
Day 8
Local adaptation: SNPs that matter
Computer demo/exercises
Local adaptation: genes that matter
Computer demo/exercises
Evening speaker 6
Day 9
Estimating relatedness I
Computer demo/exercises
Estimating relatedness II
Computer demo/exercises
Evening speaker 7
Day 10
Phylogenetics: Alignments and Networks
Computer demo/exercises
Phylogenetics: Trees
Computer demo/exercises
Evening speaker 8
Day 11
Phylogenetics: Applications – barcoding, metagenomics, eDNA
Genetic management of ex situ populations of endangered species
Postdoctoral fellowships, careers
Course evaluation, group photo
Closing party
Day 12
Participants depart