Understanding the Genotype-Phenotype Map: Contrasting Mathematical Models

In this chapter, we review and compare existing theoretical models of the relationship between genetic and phenotypic variation or genotype-phenotype map (GPM). By doing that, we introduce the reader to concepts and assumptions of evolutionary genetics and contrast them with concepts and models coming from developmental biology. Although these two approaches can be regarded as complementary to study the same underlying problem, phenotypic variation and evolution, they contradict each other in a number of ways. The evolutionary genetics models on the GPM consider genetic interactions but not epigenetic interactions. This simplicity has been used to argue that they are the most general (Wagner, Trends Ecol Evol 26: 577–584, 2011). We argue, in contrast, that epigenetic factors are crucial to understand the GPM. We understand epigenetic factors as nongenetic factors that are instrumental in building the phenotype during development (Waddington, Beyond reductionism, 1968). We argue that models including epigenetic factors exhibit features found in real GPMs that are not found in purely genetic models. Since these features are widely found in real GPMs, no model can be considered general without those and, then, models including epigenetic factors are more general than purely genetic models, even when the details of the former are specific of certain types of phenotypes.