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Through Anatomy and Thyroid

Possible external relationships

This taxon is often included in the paraphyletic infraphylum Agnatha, which also includes several groups of extinct armored fishes called ostracoderms. Most fossil agnathans, such as galeaspids, thelodonts, and osteostracans, are more closely related to vertebrates with jaws (called gnathostomes) than to cyclostomes.

Biologists historically disagreed on whether cyclostomes are a clade. The "vertebrate hypothesis" held that lampreys are more closely related to gnathostomes than they are to the hagfish. The "cyclostome hypothesis", on the other hand, holds that lampreys and hagfishes are more closely related, making Cyclostomi monophyletic.

Most studies based on anatomy have supported the vertebrate hypothesis, while most molecular phylogenies have supported the cyclostome hypothesis.

There are exceptions in both cases, however. Similarities in the cartilage and muscles of the tongue apparatus also provide evidence of sister-group relationship between lampreys and hagfishes. At least one molecular phylogeny has supported the vertebrate hypothesis. The embryonic development of hagfishes was once held to be drastically different from that of lampreys and gnathostomes, but recent evidence suggests that it is more similar than previously thought, which may remove an obstacle to the cyclostome hypothesis.

Several groups of Palaeozoic jawless fish have been suggested to be more closely related to cyclostomes than to jawed fish, including conodonts and anaspids. The presence of mineralised elements in these jawless fish, like the oral conodont elements and the armoured body covering of anaspids and scutes on other species like Lasanius suggests that mineralised tissues were present in the last common ancestor of all vertebrates, but were secondarily lost in hagfish and lampreys.

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