Similaire à THEME – 4 Detecting Selection Along Environmental Gradients: Analysis of Eight Methods and Their Effectiveness for Outbreeding and Selfing Populations
Similaire à THEME – 4 Detecting Selection Along Environmental Gradients: Analysis of Eight Methods and Their Effectiveness for Outbreeding and Selfing Populations (20)
Pests of mustard_Identification_Management_Dr.UPR.pdf
THEME – 4 Detecting Selection Along Environmental Gradients: Analysis of Eight Methods and Their Effectiveness for Outbreeding and Selfing Populations
1. Detecting Selection Along Environmental
Gradients:
Analysis of Eight Methods and Their Effectiveness for
Outbreeding and Selfing Populations
Yves Vigouroux
Institut de Recherche pour le Développement
Montpellier, France
International Workshop on
“Applied Mathematics and Omics Technologies for Discovering Biodiversity and Genetic Resources for
Climate Change Mitigation and Adaptation to Sustain Agriculture in Drylands”
Rabat - Morocco, 24-27 June 2014
4. Principle of differentiation selection
scan
Environment – spatial variation
Neutral allele: variation due
to demographic/gene
flow/history effects
Selected gene: variation due
to demographic/gene
flow/history effects and
selectionDifferentiation
FST
5. • Methods: use or not environmental data?
• Sampling design?
• Impact of the reproduction system (selfing)?
Exemple of
environmental
gradient in
Niger, Africa
Environmental Gradients
6. Software QuantiNEMO [Neuenschwander et al. 2008 Bioinformatics]
Simulations =
- time-forward
- individual
- modèle flexible
100 populations - 2N = 200
100 unlinked neutral locus
1 linked selected locus
Selfing: {0.0, 0.95}
Different sampling strategy
Model
si
13. Methods studied
Name Reference Data
FDIST Beaumont et al. 2006 Population
DETSEL Vitalis et al. 2001 Pairs of population
FLK Bonhomme et al. 2010 Population
BAYSCAN Foll et al. 2008 Population
BAYENV Coop et al. 2010 Population
SAM Joost et al. 2006 Individual
GEE Poncet et al. 2010 Individual
Differentiation-
based methods
Correlation
based
methods
Use of
environ.
data
14. Evaluation of the methods
• Simulation of neutral and selected locus
• Use of the method to calculate the
proportion of loci detected
Simulated % of loci detected
selected
Neutral Percentage of false
positive
Expected 5%
Selected Percentage of true
positive
Expected close to 100%
20. Conclusion
- Methods based on differentiation are conservative
- Methods based on correlation more powerfull / efficient
- Requiere to have good environmental data...
- New development: non parametric correlation
- Sampling more population is the most efficient
De Mita et al., 2013, Molecular Ecology
De Mita et Siol, 2012, BMC Genetics
22. Work going on using this approach
Medicago truncatulaRice
(Oriza sp)
Natural populationTraditionnal varieties in Guinea
and Madagascar
Selfing
selfing
23. Acknowledgement
IRD, Montpellier On ongoing project:
S De Mita UAM Niamey
AC Thuillet Y Bakasso
JL Pham IS Ousseini
C Berthouly
CIRAD, Montpellier ISRA Sénégal
N Ahmadi N Kané
INRA Montpellier
L Gay
Université de Provence
S Manel
ARCAD Project
Agropolis Researcher Center for Crop Diversity and Adapation