"Genetic data analysis/exploration using R" (GDAR03)
This course will be delivered by Dr. Thibaut Jombart who authors the
adegenet package and Dr. Zhian Kamvar.
This course will run from the 23rd - 27th October at Margam discovery
in Wales, United Kingdom.
This course provides a comprehensive introduction to exploratory
statistical methods used in population genetics and molecular ecology.
Participants will become proficient in a range of approaches for
genetic structures from usual genetic data including most genetic
(e.g. microsatellites, SNPs, AFLP) and genetic sequences (DNA or amino-
acid). After covering different types of phylogenetic reconstruction,
basic population genetics tests, a strong emphasis will be put on using
factorial methods (e.g. Principal Component Analysis) for investigating
genetic diversity. In particular, we will focus on the identification
description of genetic clusters, and on characterising spatial genetic
patterns. The last day of the course will be an open problem day, where
participants will be able to analyse their own data.
Intro to phylogenetic reconstruction.
Module 1a: Reconstructing phylogenies from genetic sequence data. Three
main approaches covered: distance-based phylogenies; maximum parsimony;
Module 1b: Short R refresher.
Practical 1: Phylogenetic reconstruction using R. Three main approaches
plus rooting a tree; assessing/testing for a molecular clock; and
Main packages: ape, phangorn.
Intro to multivariate analysis of genetic data
Module 2: Key concepts in multivariate analysis. Focus on using
methods for genetic data analysis.
Practical 2: Basics of multivariate analysis of genetic data in R.
include: data handling, population genetic tests of population structure
Main packages: adegenet, ade4, ape.
Exploring group diversity
Module 3: Approaches to identifying and describing genetic clusters.
include: hierarchical clustering, K-means, population-level multivariate
analysis (between-group-PCA, DA, DAPC).
Practical 3: Applying the approaches covered in morning lecture and
emphasising their strengths and weaknesses.
Main packages: adegenet, ade4.
Spatial genetic structures
Module 4: Discussing the origin and significance of spatial genetic
patterns, and how to test for them.
Practical 4: Visualising and analysing spatial genetic data. Topics:
spatial density estimates, Moran/Mantel tests, mapping principal
in PCA, spatial PCA.
Main packages: adegenet, adehabitat, ade4.
Using R for reproducible science.
Module 5: Using R for reproducible science
Practical 5: Practical session based on morning lecture
Main packages: knitr, Sweave, rmarkdown
If you have any questions please email [hidden email] or
To book online go to http://www.prstatistics.com/course/genetic-data-
Other up-coming courses are as follows
PR statistics other courses
1. MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA #MASE
19th – 23rd June, Canada, Prof. Subhash Lele, Dr. Peter Solymos
2. TIME SERIES MODELS FOR ECOLOGISTS USING R (JUNE 2017 #TSME
26th – 30th June, Canada, Dr. Andrew Parnell
3. META-ANALYSIS IN ECOLOGY, EVOLUTION AND ENVIRONMENTAL SCIENCES
24th – 28th July, Scotland, Prof. Julia Koricheva, Prof. Elena
4. SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R #SPAE
7th – 12th August 2017, Scotland, Prof. Jason Matthiopoulos, Dr. James
5. ECOLOGICAL NICHE MODELLING USING R #ENMR
16th – 20th October 2017, Scotland, Dr. Neftali Sillero
6. GENETIC DATA ANALYSIS AND EXPLORATION USING R #GDAR
23rd – 27th October, Wales, Dr. Thibaut Jombart, Zhian Kavar
7. STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY
BIOLOGISTS USING R #SEMR
23rd – 27th October, Wales, Prof Jarrett Byrnes, Dr. Jon Lefcheck
8. LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R #LNDG
6th – 10th November, Wales, Prof. Rodney Dyer
9. APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS #ABME
20th - 25th November 2017, Scotland, Prof. Jason Matthiopoulos, Dr. Matt
10. INTRODUCTION REMOTE SENSING AND GIS APPLICATIONS FOR ECOLOGISTS
27th Nov – 1st Dec, Wales, Dr Duccio Rocchini, Dr. Luca Delucchi
11. ADVANCING IN STATISTICAL MODELLING USING R #ADVR
11th – 15th December 2017, Wales, Dr. Luc Bussiere, Dr. Tom Houslay,
Dr. Ane Timenes Laugen,
12. INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING #IBHM
29th Jan – 2nd Feb 2018, Scotland, Dr. Andrew Parnell
13. ANIMAL MOVEMENT ECOLOGY (February 2018) #ANME
19th – 23rd February 2018, Wales, Dr Luca Borger, Dr. John Fieberg
14. GEOMETRIC MORPHOMETRICS USING R #GMMR
5th – 9th June 2017, Scotland, Prof. Dean Adams, Prof. Michael
Collyer, Dr. Antigoni Kaliontzopoulou
15. FUNCTIONAL ECOLOGY FROM ORGANISM TO ECOSYSTEM: THEORY AND
5th – 9th March 2018, Scotland, Dr. Francesco de Bello, Dr. Lars
Götzenberger, Dr. Carlos Carmona
16. ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R
Prof. Pierre Legendre, Dr. Olivier Gauthier - Date and location to be
17. STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR #SIMM
Dr. Andrew Parnell, Dr. Andrew Jackson – Date and location to be
18. NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA
Dr. Marco Scotti - Date and location to be confirmed
19. MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV0
Prof David Warton - Date and location to be confirmed
20. PHYLOGENETIC DATA ANALYSIS USING R (TBC) #PHYL
Dr. Emmanuel Paradis – Date and location to be confirmed
PR informatics other courses
1. BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS #BIGB
3rd – 7th July 2017, Scotland, Dr. Nic Blouin, Dr. Ian Misner
2. INTRODUCTION TO BIOINFORMATICS USING LINUX #IBUL
16th – 20th October, Scotland, Dr. Martin Jones
3. INTRODUCTION TO PYTHON FOR BIOLOGISTS #IPYB
27th Nov – 1st Dec, Wales, Dr. Martin Jones
4. INTRODUCTION REMOTE SENSING AND GIS APPLICATIONS FOR ECOLOGISTS #IRMS
27th Nov – 1st Dec, Wales, Dr Duccio Rocchini, Dr. Luca Delucchi
5. DATA VISUALISATION AND MANIPULATION USING PYTHON #DVMP
11th – 15th December 2017, Wales, Dr. Martin Jones
6. EUKARYOTIC METABARCODING
23rd – 27th July 2018, Scotland, Dr. Owen Wangensteen
7. CODING, DATA MANAGEMENT AND SHINY APPLICATIONS USING RSTUDIO FOR
EVOLUTIONARY BIOLOGISTS AND ECOLOGISTS #CDSR
Dr. Aline Quadros
Oliver Hooker PhD.
2017 publications -
Ecosystem size predicts eco-morphological variability in post-glacial
diversification. Ecology and Evolution. In press.
The physiological costs of prey switching reinforce foraging
specialization. Journal of animal ecology.
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