And it nests with
the extinct great auk (Pinguinus) in the large reptile tree (LRT, 1217 taxa). No wonder it seems so different than other living birds! It is.
Figure 1. Black skimmer (genus: Rynchops) in vivo.
These, in turn
are close to the puffin (Fratercula), which also has large keratinous extensions of the rostrum and mandible, and not one, but two mandibular fenestrae.
Figure 2. Skull of the the black skimmer (Rynchops niger) with bones colorized. Note the large keratinous extension extending the mandible. Note the slight differences in the two presented skulls.
Rynchops niger (Linneaus 1758; up to 50 cm in length) is the extant black skimmer, famous for having a longer lower bill than upper. It flies low on still waters to skim for fish near the surface. Close relatives include the auk, Pinguinus and the puffin, Fratercula, all derived from skuas and petrels.
Figure 3. Pinguinus the great auk skull. This flightless extinct bird nests closest to the black skimmer in the LRT. Note the two mandibular fenestra, The curved and expanded premaxilla that extends no further posteriorly than the naris, the pinched rostrum, the tiny ascending process of the retroarticular process, the quadratojugal that extends to the antorbital fenestra,
Prum et al. 2015
nested Rynchops with the black-headed gull (Chroicocephalus) using DNA data. They did not test the extinct Pinguinius. In the LRT, the black-headed gull nests with another clade of wading birds, beginning with the limpkin, Aramus.
Figure 4. Chroicocephalus, the black-headed sea gull in vivo and as a skeleton. This taxon nests with hummingbirds, both derived from stilts and other wading birds like the limpikin (Aramus).
References
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
wiki/Atlantic_puffin
wiki/Great_auk
wiki/Black_skimmer
The Pterosaur Heresies 
Hello,
I see you are using photopraph material obtained from skullsite.com, without referencing the source, and without permission. Please mention the source of the photographs on your page, and next time please ask for permission to use material.
Regards,
Jan Jansen, skullsite.com
Thanks for the note, Jan Jansen. With 4400 posts, I ask you to report the photos individually via email: davidpeters@att.net You should know that US copyright law permits not for profit usage, e.g. if for education, criticism, argument, science, etc. To your point, I credit digimorph.org so I am onboard with your request.
Have you tested Terns yet? are they Rynchops sisters?
Yes, some time ago. Not sisters, but distantly related in the LRT. This needs to be tested in trait analysis. See: http://reptileevolution.com/thalasseus.htm