Mapping gene expression in two Xenopus: evolutionary constraints and developmental flexibility

Variation in gene expression is known to be important for morphological evolution, however little is known about its general propensity. Here we examine a pair of frogs – Xenopus laevis and Xenopus tropicalis – with highly similar embryology, and ask how their transcriptomes compare. Despite separation for over ~30-90 million years we found a strong conservation in gene expression in the vast majority of the expressed orthologs. There were a significant number of changes in the level of expression of genes. Changes in timing of expression, heterochrony, were much less common, and were often found in genes and pathways that reflect responses to selective features of the environment. Differences in gene expression levels were concentrated in the earliest embryonic stages. We propose that different evolutionary rates across developmental stages may be explained by the stabilization of cell fate determination pathways in later stages.