In Agnatha the pharyngeal arch complex is present in it's primitive state.
Agnatha possess a series of pharyngeal arches that may vary from eight clefts and nine arches in lampreys, to fifteen clefts and sixteen arches in hagfish and extinct ostracoderms.
The ancestor of gnathostomes appears to have been limited to five clefts and six arches, a feature that is definitive of the gnathostomes.
In early gnathostomes the first arch components are modified to form components of the newly evolved jaws and sympathetic-trigeminal system.
The first pharyngeal arch components split into two divisions, maxillary (upper jaw) and mandibular (lower jaw).
In primitive gnathostomes:
In more advanced gnathostomes the first dorsal pharyngeal arch cartilage becomes divided into the palatoquadrate and the quadrate cartilages of the upper jaw.
In more advanced gnathostomes the first ventral pharyngeal arch cartilage becomes divided into the the mandibular and the articular cartilages of the lower jaw.
In more advanced gnathostomes the second dorsal pharyngeal arch cartilage is transformed into the hyomandibular cartilage and provides additional support for the upper jaw.
The second ventral pharyngeal arch cartilage is transformed into the hyoid cartilage.
In tetrapods the other arches become extensively modified or vestigial as the transition to land progresses.
The columella of the reptilian auditory system is derived from the second dorsal pharyngeal arch cartilage.
The incus of the mammalian auditory system is derived from the articular end of the first dorsal pharyngeal arch cartilage.
The malleus of the mammalian auditory system is derived from the articular end of the first ventral pharyngeal arch cartilage.
The stapes of the mammalian auditory system is derived from the second dorsal pharyngeal arch cartilage.
The striated muscle of the first pharyngeal arch gives rise to the followin muscles: