Population Genomics Course

Learning Goals

• Identification of lineage-specific genomic changes of pathogens
• Estimate recombination, mutation, and selection in natural pathogen populations

Learning outcomes

• Be able to construct genome trees using genome-wide SNPs
• Use genome trees to identify orthologs and paralogs, and gene gains and losses
• Detecting recombination among bacterial genomes
• Use of coalescence tree to describe process of microbial genome evolution

Syllabus

Part 1. Introduction & Overview

• Lecture (45 min) o Bacterial population structure: B. burgdorferi in Northeast US o Phylogenetic vs. coalescent trees o Bioinformatics pipeline/protocol • In-Class Exercise (15 min): Tree Puzzles

Part 2. Building genome phylogeny/Geographic structuring/Population growth?

• Data: cp26 plasmids from ~20 B. burgdorferi sensu lato genomes • Demo (15 min) o Genome alignment: MUGSY o Alignment viewer: Gmaj o Genome tree: FastTree o Tree viewer: R package APE • In-Class Exercise (45 min)

Part 3. Estimation of recombination rate

• Data: three pairs of sister-group cp26 plasmids • Demo (15 min): o LAMAC o LDhat o Own script for sister-group counts? • In-Class Exercise (45 min)

Part 4. Simulation of natural selection & Summary

• Data: • Demo (20 min): BacSim • In-Class Exercise (45 min):