Demographic inference for comparative phylogeography using Next-Gen sequence data

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Model-based statistical inference of demographic histories for comparative phylogeographic purposes using Next-Generation sequencing data

This workshop will focus on foundational concepts underlying and practical application of select population genomic methods for phylogeographic-scaled inference, particularly for a comparative context.

Broad topics that will be covered include:

• Cutting-edge software for model-based demographic inference from population genomic-scale data;
• Constructing and testing demographic models;
• Probabilistic inferential frameworks currently popular in population genetics;
• The site frequency spectrum; and
• Basic scripting.

The workshop will start with an overview of phylogeography as a field, its central goals, how these goals have been met traditionally (i.e. via summary statistics), and how a model-based approach can alternatively achieve these goals.

This will be followed by a discussion of the site frequency spectrum (SFS), a widely used summarization of genome-scale data, and statistical inferential frameworks that are often paired with the SFS (i.e. approximate Bayesian computation and optimization of a composite likelihood function).

The workshop will then move toward a more practical, hands-on environment, starting with an introduction to/crash course in scripting (including bash i.e. terminal/command line, R, python), specifying and running demographic models in the open-access software packages fastsimcoal2, abc package in R, and dadi.

The workshop will conclude with a tutorial of currently-developing software packages for comparative and spatially-explicit demographic inference assuming population genomic data, preceded by a basic introduction of the underlying mechanics.

Registration

This workshop is FREE, but you need to register your intention to attend by 11 Sept 2015 as places are limited. Please send your Name, Status (PhD student, post doc, etc), Lab, Division, etc. to claire.stephens@anu.edu.au.

The workshop is now full, but we will take names for the waiting list.

Information for registered participants

• The workshop will run over two mornings (9am-1pm) with a morning tea break each morning.
• Please bring your laptop (Mac or Linux preferred but not strictly necessary) to the workshop with the R (3.1.3) packages abc and SparseM including all dependencies) and fastsimcoal2 installed. You will also need python and the python package dadi.
• The room will be open from 8.30am. Please make sure you are ready to start at 9am.