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This book studies the interplay between gene regulatory networks, phenotype and evolution via a combination of concept, theory and experiment. At the conceptual level, the author demonstrates thatgenes in regulatory networks group into surprisingly well-defined evolutionary modules with distinctive rates of evolution and conserved patterns of gene expression. At the theoretical level, the authordevelops a a novel probabilistic model for estimating the phylogeny of a pathway. Finally, the author analyses experimental data to reveal that genes sharing expression patterns (transcriptional modules) are not always evolutionarily conserved, but that genes sharing phylogenetic patterns (evolutionary modules) are typically co-expressed. These comparative approaches begin the attempt towardsa system-level understanding of how evolution is linked to the design and dynamics of regulatory networks, and how these networks functionacross timescales from microseconds to eons.