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Fig. 1 | Genome Biology

Fig. 1

From: Modularity of genes involved in local adaptation to climate despite physical linkage

Fig. 1

Conceptual framework for evaluating the modularity and pleiotropy of genetic architectures adapting to the environment. In this example, each gene (identified by numbers) contains two causal SNPs (identified by letters) where mutations affect fitness in potentially different aspects of the environment. The two aspects of the environment that affect fitness are aridity and freezing. a The true underlying genetic architecture adapting to multiple aspects of climate. The left column represents a modular genetic architecture in which any pleiotropic effects of genes are limited to a particular aspect of the environment. The right column represents a non-modular architecture, in which genes have pleiotropic effects on multiple aspects of the environment. Universal pleiotropy occurs when a gene has effects on all the multiple distinct aspects of the environment. Genes in this example are unlinked in the genome, but linkage among genes is an important aspect of the environmental response architecture. b Hierarchical clustering is used to identify the “co-association modules,” which jointly describe the groups of loci that adapt to a distinct aspects of climate as well as the distinct aspects of climate to which they adapt. In the left column, the “aridity module” is a group of SNPs within two unlinked genes adapting to aridity, and SNPs within these genes show associations with both temperature and climate-moisture deficit. In the right column, note how the aridity module is composed of SNPs from all four unlinked genes. c Co-association networks are used to visualize the results of the hierarchical clustering with regards to the environment, and connections are based on similarity in SNPs in their associations with environments. In both columns, all SNPs within a module (network) all have similar associations with multiple environmental variables. d Pleiotropy barplots are used to visualize the results of the hierarchical clustering with regards to the genetic architecture, represented by the proportion of SNPs in each candidate gene that affects different aspects of the environment (as defined by the co-association module)

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