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Modelling Forest Complexity Summer School 2015
Introduction to Landscape Genetics
Instructor: Patrick James (patrick.ma.james@gmail.com)



Summary
The objective of this short course is to introduce students to the rapidly developing field of landscape genetics. Landscape genetics is a synthetic discipline that requires background in multiple disciplines including population genetics, landscape ecology, and spatial statistics. We will briefly cover each of these topics and address what sort of questions we can address using a landscape-genetics approach. 

* Prior to arriving at SBL, please read the first three papers listed below (i.e., those that start with "0___". Also, please check section 2 below to see which specific landscape genetics paper you have been assigned for your group project. *

See you soon!

Patrick.


 Schedule

  DAY TIME 
 SUBJECT

Thursday

8:30

Section 1 – Introduction to landscape ecology and connectivity

Section 2 – Group work: paper review

10:00

Coffee break

10:30

Section 2 cont. – Group presentations

Section 3 – A primer on population genetics

12:00

Lunch

1:30

Section 3 – Genetic distances

3:00

Coffee Break

3:30

Section 4 – Geographic and  effective distances

~4:30

Finish for the day!

Friday

8:30

Section 5 – Statistical methods

10:00

Coffee break

10:30

Section 6 Hands-on application in R

12:00

Lunch / end.


Detailed course outline

THURSDAY AM

Section 1Introduction to landscape genetics 1: connectivity, fragmentation, and movement of organisms.

Objectives: The goal of this section is to present the motivation for investigating gene flow and the movement of organisms using spatial genetic methods and how the contemporary processes of fragmentation and habitat loss affect structural and functional (i.e., genetic) connectivity. This section will present the fundamental concepts and logic underlying the field of landscape genetics.

Obligatory Readings (attached below):

  1. Tischendorf L, Fahrig L. 2000. On the usage and measurement of landscape connectivity. Oikos, 90(1): 7-19
  2. Holderegger R, Wagner HH. 2008. Landscape Genetics. BioScience, 58, 199
  3. Wagner HH, M-J Fortin. 2013. A conceptual framework for the spatial analysis of landscape genetic data. Conservation Genetics, 14: 253-261
  4. http://www.molecularecologist.com/2015/03/reviewing-the-reviews-twelve-years-of-landscape-genetics/

Section 2 – Introduction to landscape genetics 2: paper review

Objectives: The goal of this section is to work in small group to analyze a scientific article on landscape genetics. Through this exercise, we will examine the goals, methods, strengths, and limitations of the discipline. This also give you an opportunity to practice your presentation skills.

Methods: Each student will be assigned one of three landscape genetics papers prior to the course (see table below). Together with the others who have read the same paper, you will summarize the article using the following outline:
  • Objective/question
  • Taxa
  • Molecular markers used
  • Method of analysis (statistics)
  • Main findings and interpretations
After ~30 minutes of working with your team, together you will present your combined summary to the rest of the class. This will be an oral presentation of around 10 minutes using the chalk-board as needed. After all three groups have given a presentation we will discuss the question of “What is landscape genetics?” Consider your replies in the context of the readings assigned above. 

 GROUPMembers Assigned Paper 
 1Chrystelle Fournier, Paul Mayrand, Emeline Chaste Spear et al. 2005
 2Gabriel Letendre, Fanny Senez-Gagnon, Clémentine Ols Murphy et al. 2010
 3Christian Riuz, Nicolas Coallier, Isabelle Laforest-Lapointe, Alice Antonio Garroway et al. 2011.



Section 3 – Fundamentals of population genetics.

Objective: Learn some fundamentals of population genetics including the essentials of DNA, chromosomes, loci / alleles, molecular markers, neutral genetic variation, and Hardy-Weinberg equilibrium. 

THURSDAY PM

Section 4 – Genetic Distances

Objective: Develop a familiarity with Wright's F-statistics (i.e., Fst). We will learn how to calculate pair-wise genetic distances between populations manually and using software (R). We will also learn how to visualize these genetic distance matrices using ordination (e.g., PCA, PCoA) .


Section 5 – Effective geographic distances

Objective: In this section we will consider landscape genetic data as spatial graphs comprised of nodes and links. We will discuss isolation by distance (IBD), isolation by resistance (IBR) and how to calculate effective distances between populations using least cost paths.


FRIDAY AM

Section 6 – Methods of analysis

Objective: Here, we will see how to model genetic distance as a function of geographic / effective distance(s). Methods presented will include Mantel tests and constrained ordination (i.e., RDA & db-RDA).


Section 7 – Hands-on application

Objective: in this final section we will get some hands-on experience in manipulating genetic and spatial data and modelling their relationships using R. For this section we will use the landgenreports function of the PopGenReports package

Please install the R package PopGenReports and all associated dependencies prior to arrival at the summer school.


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Patrick James,
19 May 2015, 10:06
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Patrick James,
19 May 2015, 10:06
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Patrick James,
19 May 2015, 10:06
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Patrick James,
19 May 2015, 09:47
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LG_DistMetrics_R_2.zip
(170k)
Patrick James,
27 May 2015, 19:30
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Patrick James,
29 May 2015, 17:59
Ċ
Patrick James,
19 May 2015, 09:47
Ċ
Patrick James,
19 May 2015, 09:48
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