There are two GSA workshops taking place on Sunday 1st July from 9:00 am to 2:00 pm. The registration fee is $25 which includes morning tea and lunch.
Introduction to phylogenetic analysis (Simon Ho and David Duchene) Register here
This workshop will provide an introduction to phylogenetic analysis. Talks will cover the principles of phylogenetics, phylogenetic methods and models, Bayesian phylogenetics, and molecular dating. Hands-on exercises will involve the use of the freely available software MEGA and BEAST. Prior knowledge of basic phylogenetics is helpful but not essential.
Analysis of SNP data from reduced representation sequencing (Bernd Gruber and Arthur Georges) Register here
Great technological advances have been made in terms of the availability of genome wide genetic markers (such as single nucleotide polymorphism SNP). This advances comes at the cost that the analysis of this kind of data becomes more and more challenging in terms of computer power and also complexity. It is now feasible to genotype hundreds of individuals at thousands of loci within weeks at moderate costs.
Dozens of software packages do exist to support the analysis of this kind of data in terms of answering questions on the population dynamics, population structure and evolutionary processes of such populations. Often the analysis requires profound data juggling skills to reformat data into the appropriate structure to be handled by the program. In addition new methods and ways to analyse such kind of data do pop-up constantly, hence researchers are faced to learn new software packages regularly.
R has become the dominant platform in science to analyse data, and several R packages do exist already. The advantages of R as an analysing tool are manifold: new methods are most likely implemented in R first, a single platform can perform (almost) all kind of analysis out there and therefore the researcher has not to relearn different software packages and their often very specific syntax.
In this workshop we provide an overview on the use of a recently developed R-package (dartR) that aims to integrate as many as possible ways to analyse SNP data sets. We will cover topics such as:
- loading data sets into R
- how to quality filter and subset your data set
- visualise population structure (PCoA, IBD, phylogenetic trees)
- assign individuals to populations
- export data set for other specialized software packages (e.g. STRUCTURE, fastSTRUCTURE, NewHybrid)
The format of the workshop will be a mixture between short lectures on the different topics to explain the idea of an approach and the type of analysis followed by computer exercises how to implement and interpret such an analysis.
To avoid a lengthy installation session of all the required packages we will use prepared university computers to run the packages and also bring sample data set. For an overview of the ability of the package you should read: Gruber et al. (2018), DartR: An R package to facilitate analysis of SNP data generated from reduced representation genome sequencing. DOI: 10.1111/1755-0998.12745)