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Australian Centre for Ancient DNA
School of Earth & Environmental Sciences
Darling Building
THE UNIVERSITY OF ADELAIDE
SA 5005
AUSTRALIA
Email

Telephone: +61 8 8313 3952
Facsimile: +61 8 8313 4364

Adelaide Phylogenetics Workshop, April 6th -9th, 2010

The Australian Centre for Ancient DNA will repeat the extremely successful Phylogenetics Workshop 09 for graduate students (or early career researchers). This workshop is run prior to the Phylogenetics Workshop Conference at Pt Elliot, South Australia April 12-16.

This small workshop (limited to 20 attendees) features an intensive 4 day hands-on training from 4 international experts, in leading software packages for the analysis of genetic data: Dr. Alexi Drummond (BEAST), Prof. Peter Lockhart (Phylogenetic methods),  Christian Anderson (Serial SimCoal), and Andrew Storfer (Landscape Genetics). These leading experts will provide detailed instruction on the analysis of model and actual datasets, and there is a strong demand for places. Interested graduates are encouraged to apply for travel funds from their host institutions. Workshop participants are strongly encouraged to attend and present at the Port Elliot  Conference where they have free registration.

Registration

As at 9/3/2010 only 3 seats remaining. Please contact the workshop organiser before registering

Registration fees:

  • Phylogentics Workshop registration Early Bird $500.00 AUD (includes training manual, welcome breakfast and free entry to the Pt Elliot Conference).
    [Non Early Bird $550.00] Early Bird rate closes Feb 28th, 2010
  • NO SINGLE DAY REGISTRATION AVAILABLE

To register your interst now, click here
Deadline date: your registration plus full payment must reach our office no later than March 5, 2010. Late payment does not guarantee a placing.

Registration Payment form available here

Completed registration payment form can be returned via fax or post, with payment to:
Ms Maria Lekis, The University of Adelaide, School of Earth & Environmental Sciences
Darling Building, North Terrace Campus
South Australia 5005 AUSTRALIA

Ph: +61 8 8303 3952 | Fax: +61 8 8303 4364 | or via email to: Maria Lekis At adelaide.edu.au

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Program

Workshop participants have free entry to the Pt Elliot Phylogenetics Conference, which is run the following week.

The 4 day training program will include introduction to tree building/alighment, phylogenetic trees and networks, work on programs such as BEAST and MRBAYES, Coalescence, SIR and ABC methods and will comprise of a combination of lectures and hands-on computer training.

Presenters

Peter Lockhart

Professor Peter Lockhart

Peter is an expert on the molecular evolution of plants and holds the 2010 New Zealand James Cook Research Fellow in Biological Sciences. His current research is focused on mRNA (microarray and Illumina GAII sequencing)  projects investigating hybridization and adaptation in New Zealand alpine plants. He has been an Associate Editor of  Systematic Biology (2000-2004) and Molecular Biology and Evolution (2004-2010) and has more than 20 years experience in phylogenetic analyses.  He is has published on the evolutionary properties of molecules – understanding their importance when tree building, model misspecification and phylogenetic networks. He will provide an introduction to modern phylogenetic methodology.
Alexei Drummund

A/Professor Alexei Drummond

Alexei specializes in bioinformatics and coalescent methods and has created the Bayesian phylogenetic software analysis package BEAST, which can be used to construct phylogenetic trees, estimate rates of evolution, estimate Ne of populations, and detect bottlenecks.

Christian Anderson

Christian Anderson, a PhD student in marine biology at the University of San Diego wrote the program code for Serial SimCoal, an extension of Excoffier’s SimCoal that allows serial sampling through time.  He will lead a tutorial on the newly released Bayesian Serial SimCoal, which is useful for both contemporary and ancient samples.

 C. Anderson

A/Professor Andrew Storfer

Andrew  specializes in evolutionary and population genetics of amphibians.  Andrew’s lab for the past several years has been involved in the development of landscape genetics methods.

 Andrew Storfer

Schedule

Tuesday 6, April: 9:00am -10am Welcome + Student Introductions (5mins each), morning tea provided. Venue: Mawson Building, Field Geology Room, click here for map download, ref 11B on page 2
10am. Start. Professor Peter Lockhart
  • An overview of phylogenetic methods and what they are useful for
  • Building Evolutionary Models: UPGMA and Neighbor

Lunch break at 1pm - 2pm

  • Substitution models
  • Maximum Parsimony, rates and long branch attraction I
  • Maximum Likelihood, model misspecification and long branch attraction II
  • Measures of convergence and support

Finish around 5pm.

Audio podcasts below:

 

 

 

Part 1 click here

Part 2 click here

Part 3 click here

Lecture notes download


Unweighted pair group method

Hypothesis testing

Parsimony and search

Distances Methods

Trees can be unrooted or rooted

Questions to aks when building Evolutionary Models
Wednesday 7, April:

9:30am - 5pm A/Professor Alexei Drummond (breaks at 11am and 1pm)

  • “Trees with time scales” inferring topologies, dates and rates
  • Simple Bayesian approaches to discrete-location phylogeography.

Lunch break at 1pm - 2pm

  • Single-population coalescent inference using Bayesian Skyline plot
  • Coalescent inference of species trees from gene trees
Using software: BEAST, MRBAYES and MIGRATE

Part 1 click here

Part 2 click here

Part 3 click here

Bayesian Phylogenetics Lecture notes

Multi Species Coalescent Lecture notes
Thursday 8, April:

9:30am - 5pm Christian Anderson

  • Why use a model-based approach - A general rubric for demographic inference using aDNA
  • Constructing demographic models with many populations

Lunch break 1pm - 2pm

  • Bayesian techniques for parameterizing models
  • Picking the best model, methods old

Using sofTware: R and BayeSSC

Part 1 available only click here

Lecture notes

Lab notes
Friday 9, April: 9:30am - 5pm A/Professor Andrew Stofer
  • What is landscape genetics?
  • Applications
  • Sampling methods

Lunch break 1pm -2pm

  • Data analysis techniques (Assignment methods, paternity analysis, ordination, resistance surfaces, continuous surfaces)
  • Landscape genomics

Part 1 click here

Part 2 click here

Part 3 click here

Intro Lecture

Lecture 2

Lecture 3

Lecture 4

Recommended Reading prior to the workshop, click here

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Accommodation in Adelaide

For accommodation in Adelaide during the workshop, we recommend the below options for their close proximity to the University and affordability:

1)Mantra on Frome. approx 10mins walk to the University. Contact phone +61 8 8412 3333. Standard rooms range from AUD$110-130

2) Adelaide Riviera Hotel, North Terrace, City. Standard room is around AUD $125.00 and approx 10mins walk to the University. Contact phone +61 8231 8000 or Toll free in Australia only # 1800 061 300

3) The Vines or Grand Apartments in North Adelaide City. Standard rooms range from AUD $79-$100. approx 10mins walk to the University. Contact phone Toll free in Australia only #1300 668 400

4) The Oaks Embassy 96 North Terrace, Adelaide. 1 bedroom apartment from AUD $134.00.

4) Try the site Backpacker and Youth/Student Hostels in Adelaide where a listing of local backpackers is provided.

5) Another site for students who are willing to share accommodation - check EasyRoommate or Adelaide Backpackers Accommodation

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Venue

The Venue for this workshop is The University of Adelaide, North Terrace Campus South Australia 5005

Mawson Lecture Theatre and Computer Suite, Rms G12-13

Click here for map, ref B11

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Site seeing in South Australia