Gutierrez, E. B. | Search bioRxiv

bioRxiv2025

Phylogenetic discordance and genic innovation at the emergence of modern cephalochordates

Cephalochordates (also known as amphioxus or lancelets) are a group of marine invertebrates occupying a critical phylogenetic position as the sister group to the remaining members of the chordate phylum (vertebrates and tunicates). As such, amphioxus have been key to help understanding the origin and evolution of vertebrate genomes, the evolution of their development and the diversification of their anatomy. However, out of the three genera of amphioxus currently known (Branchiostoma, Asymmetron and Epigonichthys), most studies have focused exclusively on Branchiostoma species. Indeed, all amphioxus genomes published to date belong to the Branchiostoma genus. This implies that our understanding of cephalochordate biology is limited to findings from Branchiostoma alone. It is consequently difficult to infer from the currently available Branchiostoma genomes, what aspects of their gene composition and structure are genus-specific or ancestral to cephalochordates. Here, we provide new high-quality genome assemblies and annotations from representatives of both Asymmetron and Epigonichthys. Genome-wide phylogenetic analyses reveal that, in contrast to previous mitogenomic studies, Branchiostoma is the sister group to Asymmetron and Epigonichthys. We further uncover discordant gene histories between these three genera, with notable asymmetry in the distribution of gene trees with minority topologies. Lastly, we find that extensive gene births and duplications preceded the origin of modern cephalochordates.

evolutionary biology↗

bioRxiv2021

Restricted proliferation during neurogenesis contributes to regionalization of the amphioxus nervous system.

The central nervous system of the cephalochordate amphioxus consists of a dorsal neural tube with an anterior brain. Two decades of gene expression analyses in developing amphioxus embryos have shown that despite the lack of overt segmentation the amphioxus neural tube is highly regionalized at the molecular level. However, little is known about the mechanisms that generate such precise regionalization. Proliferation is a key driver of pattern formation and cell type diversification, but in amphioxus it has never been studied in detail nor in the specific context of neurogenesis. Here, we describe the dynamics of cell division during the formation of the central nervous system in amphioxus embryos and its contributions to the regionalization of the neural axis. We show that after gastrulation, proliferation pauses to become spatially restricted to the anterior and posterior ends of the neural tube at neurula stages. Only at the onset of larval life, proliferation resumes in the central part of the nervous system. By marking specific populations and inhibiting cell division during neurulation, we demonstrate that proliferation in the anterior cerebral vesicle is required to establish the full cell type repertoire of the frontal eye complex and the putative hypothalamic region of the amphioxus brain, while posterior proliferating progenitors, which were found here to derive from the dorsal lip of the blastopore, contribute to elongate the caudal floor plate. Between these proliferative domains, we find trunk nervous system differentiation is independent from cell division, which decreases during neurulation and resumes at the early larval stage. Taken together, our results highlight multiple roles for proliferation in shaping the amphioxus nervous system.

developmental biology↗