The elusive genomic signature of tadpole shrimps’ ancient morphology

The tempo of evolutionary change varies widely across the tree of life, with some lineages undergoing extensive morphological diversification while others remain remarkably static. Notostraca, or tadpole shrimps, exemplify the latter, displaying minimal morphological change for hundreds of millions of years. To investigate the molecular basis of this exceptional stasis, we generated high-quality genome assemblies for Triops granarius and Triops simplex. These genomes, combined with data from 18 additional branchiopod species representing Notostraca and Onychocaudata, were employed for phylogenetic reconstruction and time estimation and support the emergence of Notostraca and their general morphology in the Devonian (approx. 390 Ma). We identified genes with significantly reduced rates of protein evolution in Notostraca compared to their more morphologically diverse sister group, Onychocaudata. Functional annotation linked these genes to morphogenesis and development, but we also detected genes with accelerated protein evolution associated with similar developmental processes. Notably, genes undergoing a decelerated evolution in their protein-coding sequences lack signatures of evolutionary constraints in their non-coding regions. In addition, sequence evolution and gene family expansion/contraction dynamics appear decoupled from the rate of protein evolution, suggesting that genes can undergo reduced evolutionary change in one aspect, but not in others. Our findings reveal a complex interplay between genomic and phenotypic evolution and suggest that morphological stasis is maintained by multiple molecular processes rather than by a single, overarching mechanism.