Specimens of Archaeopteryx resembling a flying squirrel. After conducting an embryological comparison with modern birds, he noticed a similarity between "Archaeopteryx" and the embryonic stage of birds, concluding that the former was likely an "archetype", or created kind, of the bird lineage. Owen's monograph presented a description of the osteology and the plumage, though he missed a number of elements. Owing to its overall similarity to the structure of modern birds, Owen postulated a toothless, horny beak-like instrument "fitted for preening", and misinterpreted the fragment of an upper jaw with teeth, located next to the pelvis on the specimen, as the remains of
Archaeopteryx be related particularly closely to "Anchiornis" and "Xiaotingia", which were recovered as basal troodontids instead. Agnolín and Novas (2013) found "Archaeopteryx" and (possibly synonymous) "Wellnhoferia" to be the basalmost avialans (Avialae being defined by the authors as including "Archaeopteryx lithographica" and "Passer", their most recent common ancestor and all of its descendants), with Microraptoria, Unenlagiinae, and the clade containing "Anchiornis" and "Xiaotingia" being successively closer outgroups to the Avialae. Another phylogenetic study by Godefroit, "et al.", using a more inclusive matrix than the one from the analysis in the description of "Eosinopteryx brevipenna", also found "Archaeopteryx" to be a member