An introduction to population genomics

Image: Science 350:1493-1498

Workshop background

This workshop will start with a short lecture introduction to population genomics (~15mins), followed by hands-on experience on how to handle and visualize population genomic data (largely) using a published data set (Malinsky, et al. 2015. Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake Science 350: 1493-1498).

Participants who have their own population genomic data sets are encouraged to bring them, and we can brainstorm ways to analyze these data as a group.

The workshop will cover:

  • How to calculate basic summary statistics from population genomic data.
  • How to infer population structure in population genomic data.
  • How to infer demographic histories for population genomic data.
  • Hopefully (!), how to start identifying targets of selection in population genomic data.
  • Common pitfalls when analyzing population genomic data.

Prerequisites:

  • We assume no prior experience with population genomics - i.e., it is okay if you don't know what a VCF is!
  • However, you should understand basics of how high-throughput sequencing works.
  • Basic familarity with R is useful, though not required.

Target audience:

  • Graduate students, postdocs, and other researchers interested in population genetics

There are a few things you need to do to be prepared:

Brush up your R skills.

Pull up and bring along any data sets you might have.

Programs to download:

Note: if you cannot download & install any of these programs, do not worry. We will figure out alternatives on the day. Please do try to download R, though, at a minimum.

For those who use Brew on Macs or Linux, installing programs (RAxML, VCFtools, R) can be speedier.

brew tap homebrew/science

brew install zlib

brew install gsl

brew install homebrew/science/raxml

brew install homebrew/science/vcftools

brew install homebrew/science/openblas

brew install homebrew/science

 

To install R:

brew install cask

brew cask install xquartz

brew tap homebrew/science

brew install r

 

Data to Download

 

Workshop schedule:

  • ~3 hours, with a short break for tea.
  • We appreciate you taking the time to register (it's free) - it gives us an idea of who’s attending our TEA Talks, and the presenters some background on their audience. We will also provide morning tea, so numbers are needed for catering.

 

Workshop slides:

  • can be downloaded from here, and tutorial here.

 

Hosted by the Centre for Biodiversity Analysis, TEA Talks (Techniques in Evolutionary Analysis) are a monthly series of short workshops that introduce a range of current methods and analytical approaches in phylogenetics, bioinformatics and macroevolution. 

 

Date & time

9am–12pm 7 April 2017

Location

ANU Sciences Teaching Building 136 Linnaeus Way, Seminar Rm 1, top floor...

Speakers

Sonal Singhal, University of Michigan

Event series

Contacts

 Claire Stephens

Updated:  19 November 2017/Responsible Officer:  Director/Page Contact:  Coordinator