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Amphioxus is increasingly important as a model for ancestral chordates. Nevertheless, it is secondarily modified in various ways, especially in the larva, whose small size has resulted in a rescaling and repositioning of structures. This is especially pronounced in the head region, where the mouth opens asymmetrically on the left side, leading to speculation that the mouth is secondarily derived, e.g. from a gill slit, and is hence not homologous with mouths in other animals. The available evidence does not, in the author's view, support this interpretation. A second issue is raised concerning the identity and function of the midbrain homolog, whose extent depends on whether greater weight is given to dorsal landmarks in the nerve cord or ventral ones. The presence of two sets of dorsal photoreceptors, the lamellar body and Joseph cells, functionally links the region they occupy to the vertebrate midbrain. The midbrain is currently suggested to be the brain region in which primary consciousness emerged during early vertebrate evolution, so the origin of its constituent cells is of special interest. Possible amphioxus homologs include the anterior-most group of dorsal bipolar cells (ADBs), which are apico-basally inverted (i.e. synapse-bearing neurites arise from the apical cell compartment) in the same fashion as cortical neurons in vertebrates. This may have been a crucial innovation for chordates, responsible for both improved sensory processing and, eventually, consciousness.

Interpreting amphioxus, and thoughts on ancestral chordate mouths and brains