Protoavis are well preserved, and they are astonishingly non-avian. The distal carpals, while long, are in no way similar to those observed in the urvogel or other archaic birds. There is no semilunate element, and the structure of the radiale and ulnare would have limited the flexibility of the wrist joint. The manus is not tridactyl, and metacarpal V is present. In even the most basal avialian, "Archaeopteryx", there is no vestige of the fifth metacarpal and its presence in "Protoavis" seems incongruous with the claim that it is a bird, let alone one more derived than "Archaeopteryx". Chatterjee claims that
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