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Population genetics inference with ‘Migrate’ (PGMG01)

16th March 2020 - 20th March 2020

£275.00 – £570.00
Population genetics inference with ‘Migrate’ (PGMG01)

Event Date

Monday, March 16th, 2020

Course Format

This is a ‘LIVE COURSE’ – the instructor will be delivering lectures and coaching attendees through the accompanying computer practical’s via video link, a good internet connection is essential.

Course Program

TIME ZONE – UTC+2 – however all sessions will be recorded and made available allowing attendees from different time zones to follow a day behind with an additional 1/2 days support after the official course finish date (please email oliverhooker@prstatistics.com for full details or to discuss how we can accommodate you).

Course Details
This 5-day course will cover population genetics data analysis using the software Migrate. Students will learn to operate the software to infer gene flow and population divergence model using sequence data and microsatellite marker data and compare and choose among different population genetics models. The course has two major components: a theoretical and a hands-on component where participants will use the software on their own computers. In the theoretical section, we will review coalescence theory and discuss concepts of genetic drift, gene flow and migration, population divergence estimation, Bayesian inference, Markov chain Monte Carlo methods, and Model selection. In the practical section, students will learn to operate the program, set options, define population models, compare these models, and also learn to assess whether the *migrate*-analyses were run sufficiently well to guarantee that the results are meaningful.
Intended Audiences
Research postgraduates, practicing academics and primary investigators in genetical ecology, biogeography, phylogenetics of closely related species, conservation genetics, spatial ecology, and management and environmental professionals in government and industry.
Venue

Venue – PR statistics head office, 53 Morrison Street, Glasgow, G5 8LB Google Map

Course Information
Availability – 20 places

Duration – 5 days

Contact hours – Approx. 35 hours

ECT’s – Equal to 3 ECT’s

Language – English
Packages

We offer COURSE WITH FREE ACCOMMODATION, COURSE ONLY and ACCOMMODATION PACKAGES;
• COURSE WITH FREE ACCOMMODATION – includes everything listed below (only eligible for persons in academia)
• COURSE ONLY – Includes lunch and refreshments.
• ACCOMMODATION PACKAGE (to be purchased in addition to the course only option) – Includes breakfast, lunch, refreshments and welcome dinner Monday evening. Self-catering facilities are available in the accommodation. Accommodation is multiple occupancy (max 3- 4 people) single sex en-suite rooms. Arrival Sunday 15th May (after 5pm) and departure Friday 20th May (accommodation must be vacated by 09:15).

To book ‘COURSE ONLY’ with the option to add the additional ‘ACCOMMODATION PACKAGE’ please scroll to the bottom of this page.

Other payment options are available please email oliverhooker@prstatistics.com

PLEASE READ – CANCELLATION POLICY: Cancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered, contact oliverhooker@prstatistics.com. Failure to attend will result in the full cost of the course being charged. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees (and accommodation fees if booked through PR statistics) will be credited. However, PR statistics will not be held responsible/liable for any travel fees, accommodation costs or other expenses incurred to you as a result of the cancellation. Because of this PR statistics strongly recommends any travel and accommodation that is booked by you or your institute is refundable/flexible and to delay booking your travel and accommodation as close the course start date as economical viable.

Teaching Format
This course will be hands-on and workshop based. Each day will start with a lecture on theoretical concepts that then lead to a mixture of program-specific presentations and hands-on sections.

Assumed quantitative knowledge

We assume basic knowledge of population genetics, for example, the small primer by *John Gillespie*, **a concise guide to population genetics** [John Hopkins University Press] would be perfect preparation. Some basic knowledge of probability theory will be beneficial but is not required to understand the concepts of Bayesian inference, because we will introduce the essential mathematical concepts.

Assumed computer background

We will use command style based program execution (*Migrate* does not have a Graphical User interface) therefore UNIX experience is desirable but not essential because, during the first day of the workshop, we will give an introduction to UNIX-style shell commands.

Equipment and software requirements

A laptop computer with the latest operating system installed and with the possibility to start a command-line tool; on Macintosh laptops, we will use the *Terminal.app*, and on Windows 10 (64bit) laptops we will use the Linux *bash* shell. If you have another system, please let us know before the workshop, we will be able to help you to install a viable command-line tool.

UNSURE ABOUT SUITABLILITY THEN PLEASE ASK oliverhooker@prstatistics.com

Assumed quantitative knowledge

Coming soon..

Assumed computer background

Coming soon..

Equipment and software requirements

Attendees will need to install/update R/RStudio and various additional R packages.

This can be done on Macs, Windows, and Linux.

R – https://cran.r-project.org/

RStudio – https://www.rstudio.com/products/rstudio/download/

Tickets

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PLEASE READ – CANCELLATION POLICY

Cancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered, contact oliverhooker@prstatistics.com. Failure to attend will result in the full cost of the course being charged. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees will be credited.

If you are unsure about course suitability, please get in touch by email to find out more

info@clovertraining.co.uk

COURSE PROGRAMME

Sunday 15th

Meet at Flat 2/1, 43 Cook Street, Glasgow G5 8JN between 17:00 – 21:00.

Monday 16th – Classes from 09:30 to 17:30

Module 1: Introduction to population genetics and population genetic inference using DNA sequences: What do we estimate? Why do we estimate these parameters?
Module 2: Basic Coalescence theory, mutation models
Module 3: **Guided Hands-on** Commandline tools and preparation of data

Tuesday 17th – Classes from 09:30 to 17:30

Module 4: Bayesian inference and Markov chain Monte Carlo
Module 5: **Guided Hands-on** Introduction to Migrate

Wednesday 18th – Classes from 09:30 to 17:30

Module 6: **Guided Hands-on** Gene flow analysis; discussion of setting up specific population models, in-depth examination of quality assessment of results
Module 7: **Guided Hands-on** Population divergence analysis;

Thursday 19th – Classes from 09:30 to 17:30

Module 8: Model selection introduction
Module 9: **Guided Hands-on** Tutorial on how to differentiate among population models, and how to choose among the models.

Friday 20th – Classes from 09:30 to 16:00

Module 10: Parallelizing *migrate* for cluster computer or multicore systems.
Module 11: Things to come, glimpse into the ‘fractional coalescent’ with a tutorial.

Course Instructor


 

Dr. Antoine Becker-Scarpitta

Works at – University of Helsink
Teaches – Multivariate analysis of ecological communities in R with the VEGAN package (VGNR03)
Antoine is a plant community ecologist working as a postdoctoral researcher at the University of Helsinki and as a postdoctoral fellow at the Institute of Botany of the Academy of the Czech Republic. Antoine holds a degree in Conservation Biology from the University of Paris-Sud-Orsay, and from the Natural History Museum of Paris, he obtained his PhD in Biology/Ecology from the University of Sherbrooke (Canada). Antoine’s research focuses on the temporal dynamics of biodiversity with a particular focus on the forest and Arctic vegetation. Antoine has taught community ecology, plant ecology and evolution, linear and multivariate statistics assisted on R.

Details

Start:
16th March 2020
End:
20th March 2020
Cost:
£275.00 – £570.00
Event Category:

Venue

PR statistics head office
53 Morrison Street
Glasgow, Scotland G5 8LB United Kingdom
+ Google Map
Phone:
07966500340
View Venue Website

Tickets

The numbers below include tickets for this event already in your cart. Clicking "Get Tickets" will allow you to edit any existing attendee information as well as change ticket quantities.
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