Developmental system drift and modular gene regulatory networks shape gastrulation in <i>Acropora</i>

Although gastrulation is a conserved morphogenetic process in animals, the cellular mechanisms underlying it are highly variable. This raises important questions regarding the extent to which conserved or divergent gene regulatory programs (GRNs) control gastrulation in phylogenetically distant taxa. We compared gene expression profiles during gastrulation of <i>Acropora digitifera</i> and <i>Acropora tenuis</i>, species that diverged ∼50 million years ago. Despite the morphological similarity, each species uses divergent GRNs, supporting the concept of developmental system drift. Consistently, orthologous genes showed significant temporal and modular expression divergence, indicating GRN diversification rather than conservation. Yet, we identified a subset of 370 differentially expressed genes that were up-regulated at the gastrula stage in both species, with roles in axis specification, endoderm formation, and neurogenesis, suggesting a conserved regulatory "kernel" for the process. We also identified species-specific differences in paralog usage and alternative splicing patterns that indicate independent peripheral rewiring of this conserved module. Interestingly, although <i>A. digitifera</i> exhibits greater paralog divergence, consistent with neofunctionalization, <i>A. tenuis</i> shows more redundant expression, suggesting the regulatory robustness of developmental programs in this species.