Population genetics inference with ‘Migrate’ (PGMG01)
16th March 2020 - 20th March 2020£275.00 - £550.00
This 5-day course will cover population genetics data analysis using the software <i>Migrate</i>. 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.
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 – PR statistics head office, 53 Morrison Street, Glasgow, G5 8LB – Google Map
Availability – 20 places
Duration – 5 days
Contact hours – Approx. 35 hours
ECT’s – Equal to 3 ECT’s
Language – English
We offer COURSE ONLY and ACCOMMODATION PACKAGES;
• COURSE ONLY – Includes lunch and refreshments.
• ACCOMMODATION PACKAGE (to be purchased in addition to the course only option) – Includes breakfast, lunch, welcome dinner Monday evening, farewell dinner Thursday evening, refreshments and accommodation. Self-catering facilities are available in the accommodation. Accommodation is approximately a 6-minute walk from the PR informatics head office. 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).
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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 firstname.lastname@example.org. 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.
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.
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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.
The instructors were excellent and clearly were the reasons for my previous comments. They both combined a deep understanding of statistics and ecology at the same level.Any questions or queries I’ve had, were thus first answered with an ecological point of view and then translated into statistical consideration thereby making much more sense on both side.In addition the course was very well organised, the course director and the two instructors were very friendly as well as professional. On the top of learning many useful things, I’ve also had a very good time during the week there.” Clement Garcia,
Spatial ecologist, Centre For Environment, Fisheries & Aquaculture Science (CEFAS), England
(Attended ADVR course)