Population Genomics Course

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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: 8:30-9:30
  • Population processes
    • Recombination: Muller's Rachet; Hill-Roberson effect
    • Recombination and natural selection: Background selection & selective sweeps
  • Applications
    • GWAS
    • Population history: phylogeny, structuring, gene flow, and selective sweeps (e.g., Neandertal genomes; Borrelia burgdorferi in Northeast US)
    • Genomic surveillance of infectious diseases
  • Bioinformatics pipeline/protocol
  • In-Class Exercise: Software setup & data download

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

  • In-class exercise: 10:00-11:30
  • Data set: cp26 plasmids from 23 B. burgdorferi sensu lato genomes
  • Genome alignment: MUGSY & Alignment viewer: Gmaj
  • Genome tree: FastTree
  • Tree re-rooting: R package APE see syllabus
  • Interactive tree viewer: trexonline

Part 3. Estimation of recombination rate

  1. Download and Install:
    svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean
  2. Data: cp26.ss.fas
  3. Convert to LDhat file format:
    ../ldhat/convert -seq cp26.ss.fas -2only -prefix cp26
  4. In RStudio:
    source("http://ldhat.sourceforge.net/R/coalescent.r")
  • Own script for sister-group counts? (D statistics)

Part 4. Simulation of natural selection & Summary

  • In-class exercise: 3:30-5
  • ms, seq-gen; Genomes
  • BacSim

Assignment & Assessment