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.  

Registration: Closes 22 November, 2018. Register online here. Please note - registration has now closed and the workshop is at capacity.

Participants will need to bring their own laptops. More detailed instructions regarding software, data, etc. will be emailed to prior to the workshop. A pre-workshop survey for registered participants can be found here.

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 all morning and afternoon teas and lunches, and drinks on Tuesday evening). A social function (Mexican food and drinks) will also be held on the Wednesday evening ($45 per head).

Venue maps & information:

* Free workshop parking has been arranged at parking areas P7 & P17 (see map). Press the intercom button at the gate, state your name and that you are a “CBA workshop participant”. Then see Bernd Gruber at the workshop who will give you a ticket to leave the car park.

 

Program

Download Program

TUESDAY 4 DECEMBER 2018

 

Introduction

9:00

LECTURE Welcome & overview on applications of SNP data - Craig Moritz (slides)

9:45 LECTURE DArT pipeline - Andrzej Kilian (slides)
10:15 LECTURE Population genomics introduction - Sam Banks (slides)
10:45 Morning tea break

 

11:00

Filtering SNPs with dartR

Computer setup dartR (Groups A & B) dartR requirements for workshop

11:15 TUTORIAL (Groups A & B) Introduction to dartR  - quality filtering, data structures - Arthur Georges/Bernd Gruber/ Renee Catullo
13:00 Lunch (20 min DArT tours in groups of 10)
14:00 TUTORIAL (Group A) dartR introduction cont. (basic analyses) - Bernd Gruber (tutorial downloads)
14:00 TUTORIAL (Group B) QA & filtering your own data - Sam Banks & Renee Catullo (tutorial downloads)
15:15 Afternoon tea break
15:45 TUTORIAL (Group A) QA & filtering your own data - Sam Banks & Renee Catullo (tutorial download)
15:45 TUTORIAL (Group B) dartR introduction cont. (basic analyses) - Bernd Gruber (tutorial downloads)
17:00 KDDArT informatics - Andrzej Kilian (slides)
18:00

Welcome mixer / CBA end-of-year drinks. All welcome.

 

WEDNESDAY 5 DECEMBER 2018

 

Population genomics

9:00 LECTURE Population structure & landscape genetics - Bernd Gruber (slides)
9:45 LECTURE Adaptation, GWAS & GEA - Luciano Beheregaray (slides)
10:30 Morning tea break
11:00 TUTORIAL (Group A) Population structure & landscape genetics - Bernd Gruber (tutorial downloads)
11:00 TUTORIAL (Group B) Adaptation, GWAS & GEA - Chris Brauer (tutorial downloads)
12:30 Lunch (poster presentations)
13:30 TUTORIAL (Group A) Adaptation, GWAS & GEA - Chris Brauer (tutorial downloads)
13:30 TUTORIAL (Group B) Population structure & landscape genetics - Bernd Gruber (tutorial downloads)
15:00 Afternoon tea break
15:30 LECTURE Adaptation genomics - Justin Borevitz (slides)
16:15 LECTURE dartR phylogeny - Arthur Georges (slides)
17:30 Social function (Mexican dinner & drinks), Coopers Lodge Rooftop. Pre-paid ticket-holders only.
   

THURSDAY 6 DECEMBER 2018

 

Systematics

9:00 LECTURE Species tree inference - theory - Remco Bouckaert (slides)
9:45 LECTURE Species tree inference - examples - Adam Leache (slides)
10:30 Morning tea break
11:00 TUTORIAL Species tree inference - SNAPP demonstration - Adam Leache/Remco Bouckaert
12:30 Lunch
13:30 LECTURE Species delimitation - theory & examples - Adam Leache/Remco Bouckaert (slides)
15:00 Afternoon tea break
15:30 TUTORIAL Species delimitation - Adam Leache/Remco Bouckaert
17:30

Workshop ends

We would appreciate you filling in our post-workshop survey. Workshop photo.

 

 

 

Date & time

9am 4 December – 5.30pm 6 December 2018

Location

Building 6, Level B, Rooms 3 & 4, University of Canberra, Bruce, ACT

Speakers

Adam Leaché (Washington)
Remco Bouckaert (Auckland)
Luciano Beheregaray (Flinders)
Chris Brauer (Flinders)
Sam Banks (CDU)
Bernd Gruber (Canberra)
Arthur Georges (Canberra)
Renee Catullo (ANU)
Justin Borevitz (ANU)
Craig Moritz (ANU)
Andrzej Kilian (DArT)

Event series

Contacts

 Claire Stephens

Updated:  12 December 2018/Responsible Officer:  Director/Page Contact:  Coordinator