SNPs in population- and phylo-genomics

Have you got large SNP datasets and now are wondering how best to filter the data, to infer population diversity or structure, adaptation, or to delimit species and estimate their relationships? Do you have a bioinformatics or analytical pipeline that you would like to see used by empiricists? 

With increasing access to large-scale SNP data (e.g. from ddRAD, GbS or DArT screens), many of us now need to understand the nuances of cleaning and filtering data, and then analyzing the data. 

This 3-day workshop will include lectures and hands-on training from Australian and international experts spanning bioinformatics, population genomics and phylogenetics with SNP data.

Emphasis will be on applications for non-model species, but there will also be examples of how to exploit genome assemblies from related taxa should these be available.

There will also be opportunity for both empiricists and developers of methods to present posters in order to build a community that can continue to interact to get the most out of such datasets.  

How to attend: There are a limited number of places available for this workshop. To apply, please submit an expression of interest form by 12 October, 2018. Successful applicants will notified as soon as possible after this date and will be sent a link to register and pay online.

ECR grants: The CBA is also offering several Early Career Researcher grants of $150 AUD each to cover registration costs. Please note in your application if you would like to be considered for one of these.

Cost: $150 for 3 days (includes morning and afternoon teas and lunches). A social function (Mexican food and drinks) will also be held on the Wednesday evening ($45 per head).

Information on casual parking at UC can be found here.

Participants will need to bring their own laptops. More detailed instructions about the workshop will be emailed to those selected to attend.

Preliminary program

TUESDAY 4 DECEMBER 2018

9:00 LECTURE Welcome & overview on applications of SNP data: Craig Moritz (Australian National University)
   Day 1: Getting the data & quality assurance
9:45 LECTURE DArT pipeline: Arthur Georges (University of Canberra)
10:15 LECTURE Pre-analysis - From reads to SNPs: Sam Banks (Charles Darwin University)
10:45 Coffee break
11:00 Computer setup (Groups A & B)
11:15 TUTORIAL (Groups A & B) dartR Introduction - quality filtering, data structures: Arthur Georges/Bernd Gruber (University of Canberra)
13:00 Lunch
14:00 TUTORIAL (Group A) dartR Introduction cont.: Bernd Gruber
14:00 TUTORIAL (Group B) Set up/clean data: Sam Banks & Renee Catullo (ANU)
15:15 Coffee break
15:45 TUTORIAL (Group A) Set up/clean data: Sam Banks & Renee Catullo
15:45 TUTORIAL (Group B) dartR Introduction cont.: Bernd Gruber
17:00 KDdart demonstration: Andrzej Kilian (DArT)
   

WEDNESDAY 5 DECEMBER 2018

  Day 2: Population genomics
9:00 LECTURE Population structure & landscape genetics: Bernd Gruber
9:45 LECTURE Adaptation, GWAS & GEA: Luciano Beheregaray (Flinders University)
10:30 Coffee break
11:00 TUTORIAL (Group A) Population structure & landscape genetics: Bernd Gruber
11:00 TUTORIAL (Group B) Adaptation, GWAS & GEA: Chris Brauer (Flinders University)
12:30 Lunch
13:30 TUTORIAL (Group A) Adaptation, GWAS & GEA: Chris Brauer
13:30 TUTORIAL (Group B) Population structure & landscape genetics: Bernd Gruber
15:00 Coffee break
15:30 LECTURE Adaptation genomics: Justin Borevitz (ANU)
16:15 LECTURE dartR phylogeny: Arthur Georges
17:00 Posters and drinks
18:30 Social function (Mexican dinner & drinks)
   

THURSDAY 6 DECEMBER 2018

  Day 3: Systematics
9:00 LECTURE Species delimitation: Adam Leache (University of Washington)
9:45 LECTURE Species tree inference: Adam Leache
10:30 Coffee break
11:00 TUTORIAL (Group A) Species tree inference: Adam Leache
11:00 Analyse your own data (Group B) 
12:30 Lunch
13:30 Analyse your own data (Group A) 
13:30 TUTORIAL (Group B) Species tree inference: Adam Leache
15:00 Coffee break
15:30 TUTORIAL (Group A) Species delimitation: Adam Leache
15:30 Analyse your own data (Group B) 
16:30 Analyse your own data (Group A) 
16:30 TUTORIAL (Group B) Species delimitation: Adam Leache
17:30 Workshop ends

Date & time

9am 4 December – 5pm 6 December 2018

Location

University of Canberra, Bruce, ACT

Speakers

Adam Leaché (U Washington), Luciano Beheregaray, Chris Brauer (Flinders), Sam Banks (CDU), Bernd Gruber, Arthur Georges (UC), Craig Moritz, Justin Borevitz (ANU)

Event series

Contacts

 Claire Stephens

Updated:  18 October 2018/Responsible Officer:  Director/Page Contact:  Coordinator