Tracing the Roots of Vertebrate Head Evolution through Single-Cell Transcriptomics and Regulatory Analysis in Amphioxus. BraFloSC

The evolutionary origin of the vertebrate head is a central theme in chordate evolutionary developmental biology. At the heart of this enigma are the neural crest, placodes, and prechordal plate — integral elements believed to be pivotal in the evolution of the vertebrate head, yet seemingly absent in the amphioxus, a close relative of basal chordates. To unravel this mystery, we employed single-cell transcriptomic analysis to scrutinize embryonic cells from four developmental stages. Utilizing the Seurat pipeline to identify the cell populations and a diffusion-based computational approach to explore cell fate transition probabilities, we revealed the prechordal plate and neural crest-like populations in the developing amphioxus embryo. Our careful investigation revealed regulatory-stage homology in the development of prechordal plate in chordates and highlighted the critical role of Nodal and Shh pathways in head development, similar to vertebrates. Our findings suggest that the key features of vertebrate head development go back to the common ancestor of all chordates.