Bottom-up’ evolution in the gene regulatory pathways of the C. elegans embryo

Extensive gene regulatory pathways are deployed throughout the cell lineages of an embryo to pattern the body architecture with cell fates. Evolution of these gene pathways is inherently intertwined with their function, since development both reflects past constraints and biases possible pathway evolution. Models have been proposed to account for the principles of pathway evolution, positing accumulated changes to their top, middle, or bottom, however they have not been generally tested in a large-scale developmental system. Here, we infer the evolutionary mode of developmental gene pathways by studying the ages of genes expressed throughout the C. elegans embryo, from the 1- to 102-cell stage, as identified and characterized by single-cell RNA-Seq. We find that the age of transcription factors (TFs) is inversely correlated with their temporal expression, such that evolutionarily newer genes are biased towards early expression across the developmental lineages. In contrast, genes involved in other functional groups generally exhibit the opposite relationship, suggesting that TFs are uniquely poised for ‘bottom-up’ evolution of regulatory pathways. Both within and across TF gene family expansions contribute to this pattern: recently duplicated genes of the same family are expressed earlier and genes of specific DNA binding families have characteristic lineage and temporal expressions. Bottom-up evolution of TF hierarchies provides a framework for understanding the robust and redundant construction of developmental pathways. Our work reveals an evolutionary principle and provides insight into the plastic nature of developmental pathways over evolutionary timescales.