Polyps in different locations on individual stony coral colonies experience variation in numerous environmental conditions including flow and light that potentially may lead to transcriptional and physiological differences across the colony. In this paper, using high resolution tissue and skeleton measurements and differential gene expression from multiple locations within a single colony of
Stylophora pistillata we observed a broad transcriptional responses in both the host and photosymbiont in response to polyp position within the colony. For example, biomolecular mechanisms of biomineralization appear more active toward branch tips that maybe responsible for fine-scale structural differences in corallites observed along the colony branches. Each part of the colony appears to have distinct functional roles related to polyps’ differential exposure to environmental conditions.