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Table 1 Overview of terminology used in the literature regarding pleiotropy and modularity

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

Term Meaning References
Genetic architecture Genetic architecture refers to the pattern of genetic effects that build and control a facet of the organism (character, trait, or fitness). A description of genetic architecture includes statements about gene and allele number, the distribution of allelic and mutation effects, patterns of pleiotropy, and recombination rates among causal loci on chromosomes [1]
Selectional pleiotropy The number of separate components of fitness a mutation effects. Traits are defined by the action of selection and not by the intrinsic attributes of the organism [8]
Antagonistic pleiotropy at a single allele In the context of this study, an allele exhibits antagonistic pleiotropy if it has different effects on fitness at different extremes of an environmental variable (e.g., positive effects on fitness in cold environments and negative effects in warm environments), which results in an association between the allele frequency and the environmental variable [9]
Environmental pleiotropy Genes affect fitness in multiple distinct aspects of the multivariate environment, where each aspect is defined by the action of selection This study
Modularity or modular genetic architecture A modular unit is a complex of elements (characters or genes) that (1) collectively serve a similar functional role, (2) are tightly integrated by strong pleiotropic effects of genetic variation, and (3) are relatively independent from other such units. Pleiotropic effects may be on traits or on fitness, and are limited to elements within a module, with a suppression of pleiotropic effects between different modules (Fig. 1a, left column). Genes within a module may or may not be physically linked [25]
Co-association network analysis An application of network theory used to identify modules of loci that are similar in their associations across many variables This study
Co-association module A group of SNPs that show associations with a distinct selective environmental factor. These modules can be thought of as “variational” modules (sensu [19]), which are composed of features that vary together and are relatively independent of other such sets of features. In practice, co-association modules are inferred by their similarity in associations with multiple variables This study
Selective environmental factors The specific aspect of the multivariate environment to which a SNP adapts on a geographic landscape. In practice, these are inferred by the environmental variables that associate with candidate SNPs within co-association modules This study