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.