Detecting Adaptive Differentiation in Structured Populations with Genomic Data and Common Gardens

Adaptation in quantitative traits often occurs through subtle shifts in allele frequencies at many loci-a process called polygenic adaptation. While a number of methods have been developed to detect polygenic adaptation in human populations, we lack clear strategies for doing so in many other system...

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Bibliographic Details
Published in:Genetics (Austin) 2019-03, Vol.211 (3), p.989-1004
Main Authors: Josephs, Emily B, Berg, Jeremy J, Ross-Ibarra, Jeffrey, Coop, Graham
Format: Article
Language:English
Subjects:
Adaptation
Adaptation, Physiological - genetics
Agricultural practices
Bioinformatics
Corn
Datasets
Divergence
Domestication
Ecosystem
Evolution, Molecular
Gardens & gardening
Gene frequency
Genetics
Genome, Plant
Genomes
Germplasm
Government agencies
Human populations
Inbreeding
Investigations
Models, Genetic
Multifactorial Inheritance
Polygenic inheritance
Population
Population structure
Populations
Quantitative genetics
Quantitative Trait, Heritable
Zea mays - genetics
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Summary:Adaptation in quantitative traits often occurs through subtle shifts in allele frequencies at many loci-a process called polygenic adaptation. While a number of methods have been developed to detect polygenic adaptation in human populations, we lack clear strategies for doing so in many other systems. In particular, there is an opportunity to develop new methods that leverage datasets with genomic data and common garden trait measurements to systematically detect the quantitative traits important for adaptation. Here, we develop methods that do just this, using principal components of the relatedness matrix to detect excess divergence consistent with polygenic adaptation, and using a conditional test to control for confounding effects due to population structure. We apply these methods to inbred maize lines from the United States Department of Agriculture germplasm pool and maize landraces from Europe. Ultimately, these methods can be applied to additional domesticated and wild species to give us a broader picture of the specific traits that contribute to adaptation and the overall importance of polygenic adaptation in shaping quantitative trait variation.
ISSN:1943-2631
0016-6731
1943-2631
DOI:10.1534/genetics.118.301786