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1. Introduction
Although primary sex determining genes are responsible for the initial sex determining cues in the gonad, most of the heritable differences in morphology, behavior, and life history between males and females are the result of different expression levels of genes present in both sexes [1, 2]. Sex-biased genes, which comprise up to 50% of metazoan transcriptomes [3–7], are the product of sexually antagonistic selection for different male and female optima [8, 9]. This antagonism is resolved with the emergence of sex-specific transcriptional regulatory elements that decouple expression between the sexes, thereby allowing separate female and male phenotypes to emerge from a shared genome. Sex-biased genes behave according to the evolutionary predictions for sexually selected and sexually antagonistic traits [10–18], and the study of sex-biased gene expression is emerging as a method to connect sex-specific selection pressures, which act on the whole organism, to the encoding loci.
This connection between sex-biased genes and sexually dimorphic traits offers a way to study the complex interactions between the phenotype to the underlying genome. Most studies of sex-biased gene expression treat individual genes as independent units, ignoring correlated expression that results from the interactive nature of genetic pathways and networks. This simplification compresses the multidimensional nature of the transcriptome. However, because many sexually dimorphic phenotypes are complex amalgams of numerous genes [5, 19, 20], we require a way to study the interactions of the genes underlying them if we wish to understand the constraints acting on these traits and how they respond to selection. In addition to this complexity, many genes contribute to more than one phenotype, pathway, or subnetwork. This pleiotropy is likely an important factor in the evolution of sex-biased gene expression which may ameliorate intralocus sexual conflict acting on a given gene [9].
For genes with high levels of pleiotropy, the many functions of a single locus result in strong evolutionary constraints hindering change due to selection pressure for any single function [21]. This is important for studies of sex-biased genes, as sex-biased gene expression patterns resulting from sexually antagonistic selection for any single...