To jog everyone's memory, Hou et al.'s paper provided details on Confuciusornis, Liaoningornis and Chaoyangia and was interesting in that it included a cladogram with matrix for birds, not before (or since?) done by the Birds Are Not Dinosaurs (BAND) crowd. This cladogram supported the BAND concept of Sauriurae including Confuciusornis and enantiornithines, and supposedly used Petrolacosaurus as an outgroup. Hou et al. claim "The use of a coelurosaurian dinosaur like Velociraptor as the outgroup would make no difference for character states." Really? The figured cladogram also oddly differed from the matrix in adding 'Modern Birds' as sister to Ichthyornis and replacing Cathayornis with Enantiornithes. The figure has a similar but different character list than the matrix (note my old post dealt with the figure's character list, so the numbers don't match up with my new critique). The authors' phylogeny was-
|--outgroup (Petrolacosaurus) `--Aves |--Sauriurae | |--Archaeopteryx | `--+--Confuciusornis | `--Cathayornis `--Ornithurae |--Liaoningornis `--+--Chaoyangia `--+--Hesperornis `--Ichthyornis
Correcting and re-running the matrix
Go here to read commentary on all of the characters and codings. This analysis is hindered by its small size, several characters based on fictional morphologies, others that are the opposite of other characters, and some which are based on developmental assumptions that cannot be coded in adult specimens. This leaves only seventeen characters that are valid and phylogenetically informative. The anatomy of Archaeopteryx has been greatly misunderstood by BANDits for decades, which spread somewhat to Confuciusornis. Hou et al. also ascribed unsupported referred specimens to Cathayornis and Chaoyangia, negating many of the codings for those taxa. Petrolacosaurus was coded 0 for everything, including characters it actually has state 1 for, those which are unpreserved, and even those based on structures it lacks. Ichthyornis meanwhile was coded as if it were a complete ornithurine, despite not preserving several elements. These examples show Hou et al. coded taxa as idealized hypothetical examples instead of actual specimens. In total, 43% (110/256) of characters were miscoded, though this is somewhat exaggerated by the several deleted characters. Once corrected, the consensus is-
|--Petrolacosaurus `--Eosuchia to Ornithes |--Archaeopteryx `--Ornithurae |--Enantiornithes | |--Cathayornis | `--Liaoningornis `--Pygostylia |--Confuciusornis `--+--Chaoyangia `--Ornithuromorpha |--Hesperornis `--Ichthyornis
This differs from the original tree in having a paraphyletic 'Sauriurae', though differs from the modern consensus in placing Confuciusornis closer to Aves than enantiornithines. This is no doubt due to the low number of characters, and as noted on my site, changed with only 2 extra steps. Liaoningornis moved to Enantiornithes, matching O'Connor's (2012) redescription. Hou et al.'s original flawed matrix finds Pygostylia and Ornithothoraces instead of Sauriurae with only 3 extra steps, so doesn't even support their own hypothesis strongly. Indeed, my conclusion is that the matrix is too small to strongly reject any proposed hypothesis.
What about Petrolacosaurus?
It's very odd that Hou et al. would choose Petrolacosaurus as their avian outgroup. I mean, even BANDits think birds are archosaurs, so why not use Euparkeria or Ornithosuchus? As noted above, they state "The use of a coelurosaurian dinosaur like Velociraptor as the outgroup would make no difference for character states" compared to their supposed use of Petrolacosaurus. Well let's check that.
If Velociraptor is added, there are in fact nine characters that are coded differently. Velociraptor is known to have feathers (based on ulnar quill knobs) whereas Petrolacosaurus' integument is unpreserved though originally miscoded as known. Petrolacosaurus is inapplicable for hypocleidium length, anterior sternal groove presence and sternal length (all originally miscoded), due to lacking a furcula or ossified sternum, unlike Velociraptor. Velociraptor has uncinate processes, unlike Petrolacosaurus or even Archaeopteryx. Velociraptor has an ectocondylar tuber on its femur like Archaeopteryx, though Hou et al. view the latter's structure as a non-homologous structure. Petrolacosaurus' pedal unguals are not enlarged (again miscoded by Hou et al.), but Velociraptor has pedal ungual II enlarged so is polymorphic. Most amusingly, Petrolacosaurus actually has a dorsolaterally grooved clavicle and proximodorsal ischial process like some basal birds (but unlike Velociraptor), though Hou et al. miscoded these in assuming it was a generic diapsid. That's right. The BANDits had data to support their hypothesis, but didn't realize it due to their own laziness and evolutionary assumption that these were derived sauriurine characters instead of symplesiomorphies.
References- Reisz, 1981. A diapsid reptile from the Pennsylvanian of Kansas. University of Kansas Museum of Natural History. Special Publication 7, 74 pp.
Hou, Martin, Zhou and Feduccia, 1996. Early adaptive radiation of birds: Evidence from fossils from northeastern China. Science. 274, 1164-1167.