Genetic analysis for population studies

Date & time

9am 1 July – 3.30pm 5 July 2013

Location

ANU | Sciences Teaching Building (136) Seminar Rm 1 | Southern entrance, Level 3 (top floor)

Event series

Contacts

 Rod Peakall
 02-612 50022

A national workshop for graduate students and other scientists offered by Professor Rod Peakall (ANU) and Professor Peter Smouse (Rutgers University, USA).

Jointly sponsored by CBA and ANU.

We are pleased to announce the 6th and final workshop in this popular series on analytical methods for the analysis of population genetic patterns. The course will cover a wide range of standard and new statistical procedures for the population analysis of single-locus codominant markers (e.g. microsatellites and SNPs), multiple-locus dominant markers (e.g. AFLPs), and haploid markers (e.g. mtDNA and cpDNA sequences). The course is designed to ensure that students fully understand the procedures involved. For many analyses, students will learn to calculate the various statistics by hand, before attempting the self-paced, computer-based tutorial examples, pursuing further understanding and interpretation of the results. Lectures, with examples drawn from a wide range of organisms, will illustrate both statistical analyses and biological interpretations of real data sets. In an update to the course, we will also briefly explore the issues and challenges in population genetic analysis that arise with next-generation-sequencing (NGS) based data sets.

The workshop will commence on Monday 1 July and will run through to Friday, 5 July. Similar courses were offered in 1996, 1998, 2001, 2006 and 2009, and were very popular. This new version is being offered in response to continuing requests for another workshop. This will be the final workshop in this series. As the tutorial sessions involve considerable 'hands-on' computer-aided analysis of real data sets, under the active guidance of the instructors, the number of places available is strictly limited.

All participants need to bring a laptop computer with Excel 2011 (MacOS) or Excel 2007 or higher (MS Windows). GenAlEx software and supporting documentation is freely available online from ANU.  

 

 

 

Cost and registration

ANU graduate students $150 | Other graduate students $250 | Others $500

Registration includes morning and afternoon teas and light lunches.

Workshop registration is from 3 May - 10 June 2013. Places are limited and registrations will close once all places are filled. Registrations will be processed in order of receipt.

REGISTER HERE ONLINE

 

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Accommodation

We have reserved a small number of rooms at Burton & Garren Hall on campus for five nights - check in Sunday 30 June, check out Friday 5 July. Cost $300 - book and pay online at registration. Single rooms are supplied with linen, towels, internal telephone access and a study desk. Guests have access to shared bathroom, kitchen and self-­service laundry facilities (need to supply own front load laundry detergent).

Other accomodation options

 

Canberra and surrounding regions

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Venue

ANU, Canberra | Sciences Teaching Building | Southern entrance, Level 3 (top floor)

MAP

 

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Topics to be covered include:

  1. A brief overview of the laboratory methods for the genetic analysis of natural populations, including NGS methods.
  2. Interpretation and scoring of genetic markers.
  3. Allele frequency-based analyses of genetic variation, including F-statistics and new [0,1]-standardized estimators of population genetic structure such as G’ST, G’’ST and Jost’s D.
  4. Genetic distance metrics and distance matrices, as used in population analysis.
  5. Procedures for exploring population genetic patterns, including Analysis of Molecular Variance (AMOVA), Mantel tests and Principal Coordinates procedures.
  6. Spatial-autocorrelation methods for micro-spatial genetic structure analysis.
  7. Principles for good experimental design and smart sampling strategies.
  8. Optional afternoon sessions will provide participants with the opportunity to explore their own data sets.

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Why offer this workshop?

Course evaluations from our previous Australian workshops have revealed that more than 90% of the participants would strongly recommend the course if it were offered again. In the words of one participant: "This course provides a much needed analysis of basic issues in population genetics. It fills a genuine void. Perhaps this workshop is essential for most graduate students?" Another participant wrote: "I learnt heaps! All wonderfully taught in lectures and tutorials at a great pace. Thanks also for some new project inspiration. I've got to run back to my lab now ... so I can get to the fun bit - data analysis (which I was dreading only last week). Now I am ready for it! Thanks!"

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About the software

The course will utilise the popular software package GenAlEx (Genetic Analysis in Excel). This software package was initially developed by the authors for teaching, but also offers a wide range of advanced features for research (Peakall and Smouse 2006, 2012). GenAlEx is designed as a user-friendly package with an intuitive and consistent interface that allows users to analyse a wide range of population genetic data within a software environment with which most users will have some familiarity (MS Excel). GenAlEx is now widely used by university teachers at both undergraduate and graduate levels in Australia, North America, South America, and Europe. The software also offers a wide range of analysis options for researchers, including some spatial analysis options not available elsewhere. More than 6000 registered users, representing over 60 countries, have used the software. According to ISI, the first paper describing the software was cited more than 2800 times in the period 2006 to 2012.
 
GenAlEx offers analysis of codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance- based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. GenAlEx 6.5 (released in 2012) offers new features including calculation of new estimators of population structure: G’ST, G’’ST, Jost’s Dest, and F’ST via AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data, and heterogeneity tests for spatial autocorrelation analysis. Data export is provided to more than 30 other software packages.
 
Peakall, R. and Smouse P.E. (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28, 2537-2539. Freely available as an open access article.
Peakall, R. and Smouse P.E. (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes. 6, 288-295.
 
GenAlEx software and supporting documentation is freely available online from ANU.
 

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About the lecturers

Rod Peakall is a Professor in Evolutionary Biology in the Research School of Biology at The Australian National University. His research team employs multidisciplinary approaches spanning the fields of ecology, genetics, molecular biology and chemical ecology for investigating a range of pure and applied questions in evolutionary biology, conservation biology and chemical ecology. His research programs presently falls into two primary themes. The first theme concerns the evolution of specialised pollinator interactions and the role of pollinators in plant speciation. The target species for this theme are Australian orchids and their pollinators. The second theme concerns the analysis of genetic structure in natural populations, and its implications for dispersal, mating systems and conservation. The target species for this theme have been diverse, spanning microorganisms, plants, birds, small mammals and whales. Professor Peakall has previously offered similar workshops in Australia, Denmark, Finland and USA.
 
Peter Smouse is a Professor in Theoretical & Applied Genetics in the Department of Ecology, Evolution & Natural Resources at Rutgers University, New Jersey, USA. As a theoretical and statistical population geneticist, he has worked on both theoretical and empirical aspects of population structure analysis in a wide variety of organisms, including forest trees, agronomic crops, bacteria, marine and freshwater fish, insects, and humans. His current research interests are centered on the analysis of plant mating systems and of propagule flow across anthropogenically altered landscapes. Professor Smouse has previously offered similar workshops in Argentina, Australia, Denmark, Israel and Spain.

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An Introduction to GenAlEx: Genetic Analysis in Excel

A free one-day workshop, An Introduction to GenAlEx: Genetic Analysis in Excel by Professor Rod Peakall (ANU) and sponsored by the Genetics Society of AustralAsia Inc. (GSA), will also be offered as part of the Annual GSA Conference in Sydney 14-17 July, 2013.

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Updated:  29 July 2017/Responsible Officer:  Director/Page Contact:  Coordinator