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  4. Sampling strategy optimization to increase statistical power in landscape genomics: a simulation-based approach
 
research article

Sampling strategy optimization to increase statistical power in landscape genomics: a simulation-based approach

Selmoni, Oliver Michele  
•
Vajana, Elia  
•
Guillaume, Annie Sandrine  
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2020
Molecular Ecology Resources

An increasing number of studies are using landscape genomics to investigate local adaptation in wild and domestic populations. The implementation of this approach requires the sampling phase to consider the complexity of environmental settings and the burden of logistic constraints. These important aspects are often underestimated in the literature dedicated to sampling strategies. In this study, we computed simulated genomic datasets to run against actual environmental data in order to trial landscape genomics experiments under distinct sampling strategies. These strategies differed by design approach (to enhance environmental and/or geographic representativeness at study sites), number of sampling locations and sample sizes. We then evaluated how these elements affected statistical performances (power and false discoveries) under two antithetical demographic scenarios. Our results highlight the importance of selecting an appropriate sample size, which should be modified based on the demographic characteristics of the studied population. For species with limited dispersal, sample sizes above 200 units are generally sufficient to detect most adaptive signals, while in random mating populations this threshold should be increased to 400 units. Furthermore, we describe a design approach that maximizes both environmental and geographical representativeness of sampling sites and show how it systematically outperforms random or regular sampling schemes. Finally, we show that although having more sampling locations (between 40 and 50 sites) increase statistical power and reduce false discovery rate, similar results can be achieved with a moderate number of sites(20 sites). Overall, this study provides valuable guidelines for optimizing sampling strategies for landscape genomics experiments.

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Type
research article
DOI
10.1111/1755-0998.13095
Web of Science ID

WOS:000491213100001

Author(s)
Selmoni, Oliver Michele  
Vajana, Elia  
Guillaume, Annie Sandrine  
Rochat, Estelle  
Joost, Stéphane  
Date Issued

2020

Published in
Molecular Ecology Resources
Volume

20

Issue

1

Start page

154

End page

169

Subjects

Sampling strategy

•

Landscape genomics

•

Statistical power

•

False discovery rate

•

Sample size

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LASIG  
Available on Infoscience
September 20, 2019
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/161430
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