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Our current understanding of Mesozoic bird phylogeny

David's recent Gansus question reminded me of this study I did a couple months ago. And yes, his question gets answered towards the end.

While updating my website, I noticed the lack of rigorously tested phylogenies for basal birds, especially enantiornithines. While my ongoing analysis will eventually answer this question to my satisfaction, I wanted an idea of their relationships now, as opposed to months in the future. So over the last few weeks, I've hastily combined Clarke's (2002, 2004, etc.) matrix with Chiappe's (2001, 2002, etc.) and Chiappe et al.'s (2006), coded almost all relevent taxa, and added several more characters from other sources. This includes all characters that have been used in the past for numerical analyses of enantiornithine interrelationships, and most that have been used for bird relationships at levels between Avialae and Neornithes. The downsides are that I didn't check my or the authors' codings as rigorously as I do for my big analysis, so miscodings are no doubt present. Also, a lot of characters are divided into coarser states than need be, since that's how nearly every one is defined in the literature at this time. This is the current understanding of bird phylogeny, not the future understanding. ;)

What characters did I include?
1-202 of Norell and Clarke (2001), as used subsequently in Clarke and Norell (2002), Clarke's (2002) thesis, her (2004) Ichthyornis paper, the new Yixianornis paper (Clarke et al., 2006) and the descriptions of Jeholornis (Zhou and Zhang, 2002), Sapeornis (Zhou and Zhang, 2002), Jinfengopteryx (Ji et al., 2005), Hongshanornis (Zhou and Zhang, 2005), and Archaeorhynchus (Zhou and Zhang, 2006). Clarke et al. (2006) had four extra characters that were also included.
The 19 characters from Chiappe et al. (2006) enantiornithine analysis in the Elsornis paper which weren't used in the above.
Three characters from Chiappe and Walker's (2002) euenantiornithine analysis which weren't used in the above.
The 37 characters from Chiappe (2001, 2002) which weren't present in the above and weren't only used for inter/relationships of alvarezsaurids.
Two characters of my own (median sternal process expanded distally; mtIV longer than mtIII) that I thought might affect enantiornithine relationships.
I also altered some of these characters. Cervical centrum morphology is only evaluated for anterior cervicals, since in several taxa posterior cervicals are still amphicoelous when anterior ones are semiheterocoelous. Dorsal vertebral count was divided so that 12 and 13 were different states. Dorsal parapophysis placement was only evaluated in posterior dorsals, since anterior dorsals can maintain the plesiomorphic anterior placement in some taxa (e.g. Iberomesornis). Caudal vertebral count was revised to be a total count and not just of free vertebrae. I quantified the ulnohumeral ratio to be more objective. I divided manual phalanx II-2/II-1 ratios into more states as in my analysis. I ordered posterior trochanter size. I quantified and added a state to tibiotarsal medial/lateral condyle width ratios. I separated distal tarsal fusion from metatarsal fusion. I made each possible number of phalanges in manual digit III its own state.
Characters were ordered where morphological gradients existed.

What taxa did I exclude?
I excluded some non-pygostylian taxa like Wellnhoferia, Jixiangornis, Yandangornis, Dalianraptor, Omnivoropteryx, as well as controversially basal bird taxa like Hulsanpes, Jinfengopteryx, Unenlagia, Buitreraptor, Rahonavis and scansoriopterygids. Any useful analysis of these taxa would have to include other paravians and is outside the scope of this analysis. The analyses I used for characters were largely designed to test relationships within Pygostylia, so Sapeornis and Shenzhouraptor (=Jeholornis) are decent outgroups, along with Archaeopteryx and a Dromaeosauridae that could no doubt stand to be coded better. Also excluded were taxa which probably fall inside Pygostylia but cannot be coded for more than a couple characters (endocast- Cerebavis; sacrum- Kuszholia, Lenesornis, Platanavis, Zhyraornis, Z? logunovi, Guildavis, Gargantuavis; distal radius- "Paleopteryx"; feather- Cretaaviculus, Illerdopteryx, Praeornis; undescribed or illustrated- "Holbotia"). I don't have the descriptions or good illustrations of "Cathayornis" aberransis, Eurolimnornis or Palaeocursornis, so these were excluded as well. Neither Horezmavis nor hesperornithines besides Baptornis and Hesperornis were included, though I could try this in the future. Everything else (66 taxa) has been included, plus 5 unnamed specimens. Finally, Jinzhouornis wasn't included, as I had previously concluded the two species are junior synonyms of Confuciusornis, and probably C. sanctus itself.

The analysis
I ran the analysis with all taxa except Dapingfangornis and those described by Hou (1997) - Jibeinia, "Cathayornis" caudatus, Longchengornis, Cuspirostrisornis, Largirostrornis. This is because Hou's descriptions of other taxa in that work (Confuciusornis, etc.) are inaccurate and the illustrations are of very low quality. For instance, Confuciusornis is described as having a septomaxilla, prefrontal, patella and a free distal tarsal, contra Chiappe et al. (1999). Because every taxon affects every other taxon's placement, I didn't want inaccurate codings for Hou's taxa to change character distribution and topology of the whole tree. Dapingfangornis has a similarly bad illustration, and the authors' interpretation of the skull at least seems to be flawed (see http://dml.cmnh.org/2006Apr/msg00170.html). Each of these taxa was subsequently added individually to test for its placement in the cladogram, but these must be viewed with caution due to the numerous probable miscodings.
Of course the large amount of missing data resulted in huge polytomies, but it was important to include even fragmentary taxa (as long as they had unique character combinations) in order to get a tree with the best character distribution and topology for all taxa. Fragmentary taxa were then excluded from the tree (but not the analysis) until a fully resolved tree was present. Each taxon was then reintroduced to the tree separately to determine the possible places it could go in the phylogeny.
The resulting cladogram is shown below. It uses the same format as my website, with an asterisk meaning the taxon is incertae sedis within the node it's placed at. Most clade names have been phylogenetically defined, with the exception of the enantiornithine families and subfamilies (except Avisauridae).

`--Ornithurae sensu Gauthier
        |  |--Changchengornis
        |  |--Proornis
        |  `--Confuciusornis
           |  |*-Abavornis
           |  |*-Catenoleimus
           |  |*-Explorornis nessovi
           |  |*-Sazavis
           |  |--Wyleyia
           |  `--+?-Cuspirostrisornis
           |     |?-Largirostrornis
           |     |?-Longchengornis
           |     |--Vorona
           |     |--Elsornis
           |     `--+*-Explorornis? walkeri
           |        |*-Incolornis
           |        |*-Nanantius
           |        |--Protopterygidae
           |        |  |--Noguerornis
           |        |  `--+--Protopteryx
           |        |     `?-Jibeinia
           |        `--+*-Alexornis
           |           |*-Kizylkumavis
           |           |*-Liaoxiornis
           |           |--Iberomesornis
           |           `--Euenantiornithes
           |              |*?"Cathayornis" caudatus
           |              |*-Eoenantiornis
           |              |*-Gurilynia
           |              |*-Lebanon
           |              |--Longipterygidae
           |              |  |--Longipteryx
           |              |  `--Longirostravis
           |              `--+*-Dalingheornis
           |                 |--IVPP V14238
           |                 |?-Jibeinia adult
           |                 `--+*-Enantiornis
           |                    |*-Halimornis
           |                    |*-Otogornis
           |                    |*-+--Eocathayornis
           |                    |  `?-Dapingfangornis
           |                    `--+--+--Yungavolucris
           |                       |  |--Hebeiornis
           |                       |  |--LP-4450-IEI
           |                       |  `--+--GMV 2158
           |                       |     `--GMV-2159
           |                       `--+--Gobipterygidae
           |                          |  |--Boluochia
           |                          |  `--Gobipteryx
           |                          `--Avisauridae
           |                             |*-Avisaurinae
           |                             |  |--Avisaurus
           |                             |  `--Soroavisaurus
           |                             |--Sinornis
           |                             `--+--Liaoningornithinae
           |                                |  |--Eoalulavis
           |                                |  `--Liaoningornis
           |                                `--Concornithinae
           |                                   |--Concornis
           |                                   `--Neuquenornis
                 |  |--Hongshanornis
                 |  `--+--Archaeorhynchus
                 |     `--Chaoyangia
                    `--Ornithurae sensu Gauthier and deQuieroz
                       |  |--Yanornis
                       |  `--+--Yixianornis
                       |     `--Songlingornis
                          `--Ornithurae sensu Chiappe
                             |  |--Baptornis
                             |  `--Hesperornis
                                            |  |--Lithornis
                                            |  `--Crypturellus
                                               |  |--Chauna
                                               |  `--Anas

I initially wanted to include diagnoses for the clades found here, but they would make the post far too long. So diagnoses will be on my website once I update it with this phylogeny. The tree above (without Hou's taxa and Dapingfangornis) is 857 steps long. I examined a number of proposed alternative phylogenies to determine how much longer they were, giving a rough idea of their probability.

Virtually impossible
895 steps- Patagopteryx as a palaeognath
This was the original position proposed for Patagopteryx by Alvarenga and Bonaparte (1992) and also by Kurochkin (1995), though Chiappe rejected it as early as 1989.
892 steps- Confuciusornithids as euornithines and archaeopterygids as sauriurines
This was suggested by Kurochkin (2006), whose paper I critiqued here- http://dml.cmnh.org/2006Oct/msg00467.html . Of course, since he also has all non-bird theropods more closely related to sauriurines than to euornithines, his phylogeny is even less parsimonious than can be shown here (as non-bird theropods besides dromaeosaurids are not included).
891 steps- Archaeopteryx and confuciusornithids as sauriurines
This goes back to Hou et al.'s (1995) description of Confuciusornis, and is still supported by MANIACs like Martin and Feduccia.
880 steps- Sinornis outside of Enantiornis + Passer
This kind of paraphyletic Enantiornithes was found by Chatterjee (1999) and also supported as a possibility by myself over the years, but seems not to be true. In Chatterjee's case, it was due to a large number of incorrect codings.

Highly unlikely
875 steps- Otogornis as a euornithine ambiortiform
This is Kurochkin's (1999) idea, based on his reinterpretation of the material. Even if I were to grant Kurochkin's alternative morphology (coracoid tubercle = procoracoid process), the tree would still be 873 steps or so, showing Kurochkin's identifications for these are probably wrong.
874 steps- Liaoningornis as a euornithine
This was proposed by Hou (1997) and still followed as recently as Zhou and Zhang (2006). As I noted in http://dml.cmnh.org/2005Dec/msg00237.html , the cladistic disagreements are largely due to different interpretations of morphology. I used Clarke's (2002) codings here.
874 steps- Hebeiornis as a protopterygid
Remember that Hebeiornis is the correct name for Vescornis, as I detailed here- http://dml.cmnh.org/2006Dec/msg00079.html. Zhou and Zhang (2006) placed it together with Protopteryx and Jibeinia in the Protopterygidae, without justification.
871 steps- Protopteryx and Longipteryx successively closer to Ornithothoraces
This kind of paraphyletic Enantiornithes was proposed by me back in 2001 on the DML, based on six characters, all of which were examined here. Notably, far more enantiornithine characters have been described in it now than were proposed by Zhang et al. (2001). I now officially reject this hypothesis.
871 steps- Patagopteryx as a hesperornithine
Chatterjee (1999) found this result, which was based on several characters, some miscodings and others due to reduced forelimbs.
870 steps- Patagopteryx outside of Ornithothoraces
I've noticed several characters that are remarkably basal in Patagopteryx, such as the unreduced proximal coracoid and brevis shelf, but apparently these are near certainly reversals.

Not likely, but possible
867 steps- Iberomesornis outside of Enantiornithes + Euornithes
This idea was popular prior to Sereno (2000) and Chiappe (2001), due largely to several misinterpretations of Iberomesornis. Indeed, Sanz et al. (2002) continue to make some of them- five sacrals, unfused astragali and distal tarsals, unfused metatarsals.
867 steps- Euornithiformes sensu Kurochkin 1996
Kurochkin proposed a basal clade of Enantiornithes containing Iberomesornis, Noguerrnis, Concornis, Sinornis and Boluochia, but excluding the Lecho taxa, Alexornis, Gobipteryx, Nanantius, Kizylkumavis and Sazavis. This was based on seven characters, most of which are vague and flawed (as in his other enantiornithine clades, see here- http://dml.cmnh.org/2001Feb/msg00618.html). Euornithiformes fails largely due to the avisaurid characters in Sinornis and Concornis.
867 steps- Gansus as a hesperornithine
This has never been suggested in the literature, but I was curious how unparsimonious grouping these aquatic taxa together would be.
867 steps- Ambiortus as a palaeognath
This goes back to Kurochkin (1985), and was still entertained by him in 1999 at least.
865 steps- Chaoyangia as a confuciusornithid
Though near universally identified as a euornithine (=ornithurine of older workers), Clarke (2002) found that Chaoyangia grouped with Confuciusornis instead and might even be synonymous with that taxon. The analysis of more characters makes this unlikely.
865 steps- Protopteryx outside of Ornithothoraces
This idea was developed by me on the DML in 2000. It was based on eleven characters, nine of which were included in this analysis. One of the others (maxillary fenestra) is now known in some enantiornithines anyway. Of the included characters, some are now known in basal euornithines (two phalanges on manual digit III) or derived enantiornithines (gastralia; extensor process absent).
865 steps- Alexornithiformes sensu Kurochkin 1996
This is the sister taxon to Kurochkin's Euornithiformes, with the opposite taxon distribution than described for the latter clade. It is slightly more likely, as alexornithiform taxa are more poorly known and generally more derived.
865 steps- Aberratiodontus as an enantiornithine
This was suggested in the original description by Gong et al. (2004), but wasn't supported by many characters. The few mentioned were plesiomorphies (elongate pygostyle; posterolateral sternal processes; narrow posteromedian process; unfused carpometacarpus; distally unfused tarsometatarsus) or misinterpretations (well developed postorbital; short sternum). The addition of several euornithine characters makes the taxon appear as a basal member of that clade, but a more detailed description could certainly change its placement.
865 steps- Ambiortus as an ichthyornithine
This is an idea proposed by Martin (1987), though not supposed in any explicit cladistic analysis published to date.
863 steps- Otogornis sister to Longirostravis
This was proposed by Zhou and Zhang (2006) without justification. It is possible primarily due to the fragmentary nature of Otogornis.

Very possible
862 steps- confuciusornithids as enantiornithines
Surprisingly, this reduced version of Sauriurae (which shouldn't be termed Sauriurae, as it lacks Archaeopteryx) is highly parsimonious. The addition of Chiappe's characters makes it slightly less so than the traditional (western) ornithothoracine view.
862 steps- Chaoyangia as an enantiornithine
This was found by Clarke (2002) to be equally parsimonious to topologies where it was a confuciusornithid. When more characters are added, this possibility becomes more likely and almost as likely as those in which it is a euornithine.
861 steps- Noguerornis as an iberomesornithid
This was proposed by Chiappe (2001) based on one character- a non-procoelous sacrum. Similarly, the present position sister to Protopteryx is only based on the elongate ulna in both taxa. Noguerornis' relationship is hard to pin down, though it does seem to be a relatively basal enantiornithine.
861 steps- Alexornithidae sensu Kurochkin 1996
Kurochkin proposed a family uniting Neuquenornis, Alexornis, Gobipteryx, Nanantius, Kizylkumavis and Sazavis to the exclusion of the Lecho taxa and Early Cretaceous enantiornithines he was aware of. As these taxa are especially poorly known (except for Gobipteryx and Neuquenornis), they can easily switch positions to form a clade. However, Kurochkin's proposed synapomorphies for this clade are almost entirely invalid, as shown in my post linked to above.
861 steps- Nanantius as a gobipterygid
Kurochkin (1996) felt that the most complete specimen of Gobipteryx was in fact a new species of Nanantius- N. valifanovi. This was based on tibiotarsal characters that are mostly not included in this analysis, nor possible to compare with most enantiornithine taxa. The present position as an iberomesornithid is only due to the completely fused tibiotarsus, which is possibly ontogenetic. A more derived position for Nanantius, such as one in Gobipterygidae, is therefore quite possible.
861 steps- Enantiornithidae sensu Kurochkin 1996
Kurochkin's Enantiornithidae contains Avisaurus, Soroavisaurus and Enantiornis. While the first two taxa are closely related, Enantiornis cannot be compared to either of them, being known only from forelimb and pectoral elements. Although Enantiornis is here excluded from Avisauridae due to the non-compressed distal humerus, it doesn't take many extra steps to make it an avisaurine.
861 steps- Neuquenornis as an avisaurine
Sanz et al. (1995), based on Chiappe (1993), conducted a phylogenetic analysis of enantiornitines based on pedal characters, with the topology (Lectavis,Yungavolucris (Concornis (Neuquenornis (Soroavisaurus, Avisaurus)))). This agrees with the present analysis except that Neuquenornis is an avisaurine instead of a concornithine.
861 steps- Chaoyangia sister to Songlingornis
Originally (Hou et al., 1996), Songlingornis was described as a specimen of Chaoyangia. The two holotype are not comparable though, besides some fragmentary portions. This position is less parsimonious than its current one sister to Archaeorhynchus mainly because Chaoyangia has a low number of sacrals and lacks a completely fused pelvis.
861 steps- Odontornithes
Another surprisingly likely possibility is that Hesperornithes and Ichthyornithes are sister taxa, more closely related to each other than to neornithines. It's especially surprising given the large amount of characters supporting Carinatae and Gansus+Carinatae, though several are unknown in hesperornithines or perhaps reversed due to their reduced wings.
860 steps- "Proornis" as an archaeopterygid
This is the classic position for "Proornis", though never supported by synapomorphies. The reason it changes position with so few steps is merely because so few (11) characters could be scored for it, and only two confuciusornithid synapomorphies (manual ungual II much smaller than manual ungual I; manual phalanx III-2 >150% of III-1 in length) were identifiable. No archaeopterygid synapomorphies were identified.
860 steps- Elsornis closer to Euenantiornithes than Protopteryx
This was suggested by Chiappe et al. (2006). Supporting my basal placement of Elsornis are the absent capital groove, short ulna, distally terminating intermetacarpal space and unkeeled hypocleideum. It's possible these are the result of neoflightlessess however. Supporting Chiappe et al.'s arrangement are the laterally convex coracoid and concave central portion of the humeral head. The addition of taxa like Iberomesornis which are more derived but lack these characters makes the latter topology less likely though.
860 steps- Yanornis basal to Songlingornithidae + Ornithurae
This was proposed by Zhou and Zhang (2005), though it should be noted their codings for most basal euornithines differ from those of Clark et al. (2006).
860 steps- Apsaravis closer to Carinatae than Hesperornithes
This was suggested in the original description of Apsaravis (Norell and Clarke, 2001), but found to be slightly less parsimonious by Clarke and Norell (2002). The change was due to correcting a few codings between papers.
860 steps- Apatornis as an ichthyornithine
Only one more step is needed to support this position, originally suggested by Marsh (1873), though there are no synapomorphies supporting it. As with "Proornis", few steps are needed because Apatornis can be coded for so few (2) characters.
859 steps- Eocathayornis as an avisaurid
Zhou (2002) suggested both Eocathayornis and Sinornis (=Cathayornis) belong in the same family. This was based on several characters, none of which are included in this analysis. The more basal position shown here is due to the less angled dorsal humeral condyle, apparently non-concave proximal deltopectoral crest, elongate manus and manual phalanx III-2 present.

Mickey Mortimer