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Thoughts on the biggest morphological bird analysis

Livezey and Zusi, 2007. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zoological Journal of the Linnean Society. 149 (1), 1-95.

Well, Livezey and Zusi's massive effort is finally published, and I do mean massive. 2954 characters, from all areas of morphology, make this the largest bird morphological analysis by over an order of magnitude. In addition, nearly every non-passeriform family of living bird is included, as well as a huge amount of outgroups and a few subfossil taxa. The paper is freely available here- http://www.blackwell-synergy.com/toc/zoj/149/1 , and I strongly recommend reading it. Their Consistancy Index of 0.2432 is very reassuring, as it indicates unplanned results (as well it should, with so many characters). Ordering seems to have been done properly, and taxon choice seems commendable. This is THE way to do a morphological analysis. I'm extremely impressed.

Livezey and Zusi used 35 outgroups, most of which are theropods. It's at this point I wish I had the companion paper, which describes the characters used, because I don't know if the authors included characters traditionally diagnostic of nodes like Coelurosauria or Theropoda, or if they analyzed non-avians in an avian matrix. The outgroup phylogeny is fairly standard, with the exception of Phytodinosauria (58% bootstrap), Troodontidae as Avialae (<50%), Alvarezsauridae as close to birds as Archaeopteryx (98%), Rahonavis in Ornithothoraces (69%), Hesperornithes sister to Ichthyornis (62%) and Lithornis outside Aves (91%). The position of troodontids and hesperornithines is quite possible in my opinion, but clearly oddities here "reflect missing key taxa and poor preservation of those coded", as noted by the authors. A number of taxa were pruned and merged (pg. 9), but surely Shuvuuia should have been merged into Alvarezsauridae, Segnosaurus and Erlikosaurus into Therizinosauroidea, and Gobipteryx into Enantiornithes (instead these four genera were pruned). For those fans of taxonomy, we get a lot of new names. Troodontoidea, Dromaeosauroidea and Alvarezsauroidea are all used where their familial counterparts should have been. Also named are Rahonaviformes, Rahonavidae, Apsaraviformes and Apsaravidae. I'm not sure of the use of these, as Rahonavis is probably a dromaeosaurid, unenlagiid or jeholornithid, while Apsaravis is quite possibly an ambiortid. Another new name is Palaeoaves, which seems to be a paraphyletic grade of taxa from Archaeopteryx to Apsaravis. Why Livezey and Zusi use so many paraphyletic groups outside of Aves I'm not sure (e.g. Archaeopteryx and Confuciusornis are joined in Archaeornithes; Apsaravis and Rahonavis in Euenantiornithes- gag), but I don't approve. In any case, non-avians were not the point of this analysis, so I digress.

The avian phylogeny is very well structured in the strict consensus tree, but many nodes (especially deeper ones) have terrible bootstrap support. Bootstraps have their problems, but with most every avian known from complete specimens in this analysis, they should be an accurate report of rearrangment liklihood. I find it funny that Livezey and Zusi say things like "The present data set (Livezey & Zusi, 2006) supports the rejection of this novel proposal involving the grebes and flamingos, and suggests that the taxonomic proposal for the couplet by Sangster (2005) is premature", when they name taxa like Terrestrornithes which has a bootstrap of <50% and a Bremer support of 1! Indeed, their taxonomic scheme overflows with redundant taxa, several of which are newly named- Casuariimorphae, Struthionimorphae, Hemiprocni, Trogonomorphae/Trogones, Pico-clamatores. I agree with David regarding their taxonomic disaster. If we hold Livezey and Zusi's analysis to the same standards as huge molecular analyses in regards to support (say 95% bootstrap liklihood), nearly all the major nodes collapse-

|--Tinamidae
|--Ratitae
|  |--Apterygidae
|  |--Struthioniformes
|  |  |--Struthionidae
|  |  `--Rheidae
|  `--Casuariiformes
|     |--Casuariidae
|     `--Dromaiidae
`--Neognathae
  |--Galloanserae
  |  |--Anseriformes
  |  |  |--Anhimidae
  |  |  `--Anseres
  |  |     |--Anseranatidae
  |  |     `--Anatidae
  |  `--Galliformes
  |     |--Megapodiidae
  |     |--Cracidae
  |     `--Phasiani
  |        |--Meleagridae
  |        `--Phasianidae
  `--Neoaves
     |--Pygopodo-tubinares
     |  |--Gaviomorphae
     |  |  |--Gaviidae
     |  |  `--Podicepididae
     |  |--Spheniscidae
     |  `--Procellariiformes
     |     |--Pelecanoididae
     |     |--Oceanitidae
     |     `--Procellariidae (incl. Diomedeidae)
     |--+--Balaenicipitidae
     |  `--Pelecaniformes
     |     |--Phaethontidae
     |     |--Fregatidae
     |     |--Pelecanidae
     |     |--Sulidae
     |     `--Phalacrocoracoidea
     |        |--Phalacrocoraciidae
     |        `--Anhingidae
     |--Ardeiformes
     |  |--Cochleariidae
     |  `--Ardeidae
     |--Scopidae
     |--Threskiornithoidea
     |  |--Threskiornithidae
     |  `--Plateleidae
     |--Ciconiidae
     |--Phoenicopteridae
     |--Cariamae
     |  |--Otididae
     |  `--Cariamidae
     |--Eurypygidae
     |--Rhynochetidae
     |--Aptornithidae
     |--Grues
     |  |--Psophiidae
     |  `--Gruoidea
     |     |--Aramidae
     |     `--Gruidae
     |--Turnicidae
     |--Mesitornithidae
     |--Ralliformes
     |  |--Heliornithidae
     |  `--Rallidae
     |--Charadriiformes
     |  |--Pedionomidae
     |  |--Parrae
     |  |  |--Jacanidae
     |  |  `--Rostratulidae
     |  |--Dromadidae
     |  |--Thinocoridae
     |  |--Scolopacidae
     |  |--Phalaropodidae
     |  |--Charadriidae
     |  |--Glareolidae
     |  |  |--Glareolinae
     |  |  `--Cursoriinae
     |  |--Burhinidae
     |  |--Haematopodinae
     |  |--Ibidorhynchinae
     |  |--Himantopodini
     |  |--Cladorhynchini
     |  |--Chionididae
     |  `--+--Alcidae
     |     `--Laroidea
     |        |--Stercorariidae
     |        |--Rhynchopidae
     |        |--Larinae
     |        `--Sterninae
     |--Strigiformes
     |  |--Tytonidae
     |  `--Strigidae
     |--Falconiformes
     |  |--Cathartidae
     |  |--Sagittariidae
     |  `--Falconides
     |     |--Accipitridae
     |     `--Falconoidea
     |        |--Pandionidae
     |        `--Falconidae
     |--Cuculimorphae
     |  |--Opisthocomidae
     |  |--Musophagidae
     |  `--Cuculidae
     |--Psittaciformes
     |  |--Nestoridae
     |  |--Psittacidae
     |  |--Cacatuidae
     |  `--Loriinidae
     |--Columbiformes
     |  |--Pteroclididae
     |  `--Columbidae (incl. Raphidae)
     |--Aegothelidae
     |--Caprimulgidae
     |--Nyctibiidae
     |--Steatornithidae
     |--Podargidae
     |--Apodiformes
     |  |--Hemiprocnidae
     |  |--Trochilidae
     |  `--Apodidae
     |--Coliidae
     |--Trogonidae
     `--Passeromorphae
        |--Bucerotes
        |  |--Bucerotidae
        |  `--Upupides
        |     |--Upupidae
        |     `--Phoeniculidae
        |--Halcyones
        |  |--Motmotidae
        |  |--Todidae
        |  `--Alcedinidae
        |--Meropidae
        |--Coraciides
        |  |--Coraciidae
        |  `--Leptosomatoidea
        |     |--Leptosomatidae
        |     `--Brachypteraciidae
        |--Galbulae
        |  |--Galbulidae
        |  `--Bucconidae
        |--Capitonidae
        |--Ramphastidae
        |--Indicatoridae
        |--Picidae
        |  |--Jynginae
        |  `--Picinae
        `--Passeriformes
           |--Menura
           `--Passeres
              |--Pittidae
              |--Tyrannidae
              |--Ptilonorhynchidae
              |--Corvidae
              |--Bombycillidae
              `--+--Paridae
                 `--Passeridae

What this says to me is that the relationships of major neoavian taxa may be forever beyond morphological resolution if only recent taxa are included. Interestingly, there are only a few areas in which this disagrees with the largest current molecular analysis of Neoaves (Ericson et al., 2006; 5007 characters) if the latter is evaluated at 95% (Bayesian posterior probability this time). Ericson et al. had similar taxon sampling to Livezey and Zusi, except they included less Charadriiformes and outgroups.
- Grebes are related to loons instead of flamingos. It takes 146 more steps to get Mirandornithes in Livezey and Zusi's matrix, even though I assume Mayr's (2004) characters were included. The present authors foresaw my opinion- "it is predictable that strong confirmation of a sister-group relationship between the Gaviiformes and Podicipediformes herein will engender concerns of artefactual pairing by convergence". I agree with many of Livezey and Zusi's points, that many previous criticisms of the loon-grebe clade (newly named Gaviomorphae by the authors) were flawed, and that the comparatively poor morphological evidence for Mirandornithes would surely lead to its rejection if morphology were all we had. Yet Ericson et al.'s support for Mirandornithes is impressive, as is that for the five additional clades separating grebes and loons in his topology. Furthermore, comparison with mammalian phylogenies suggest that convergent taxa group together in morphological analyses, sometimes with large support indices. In Asher et al. (2003), two of the best supported clades are bats plus flying lemurs, and pangolins plus anteaters. Much as I'll continue to support these groups being convergent, I'll support grebes and loons being convergent too.
- Albatrosses are derived procellariids instead of diving petrels being derived procellariids and albatrosses being the basal procellariiformes.
- Tropicbirds are pelecaniformes instead of metornithines.
- The shoebill is a pelecaniform sister group instead of a hammerkop relative. It only takes 30 steps to move the showbill inside Pelecaniformes, presumedly by pelicans. Placing the hammerkop by or inside of Pelecaniformes only takes 23 steps. Neither of these is precisely congruent with Ericson et al.'s topology, but it does seem to indicate the taxa are fairly labile.
- Pelecans are with traditional pelecaniforms instead of by the shoebill and hammerkop.
- Seriamas are sister to bustards instead of parrots+falcons+passeriforms.
- Buttonqail are outside Charadriiformes instead of nested inside it. Here the large amount of Charadriiformes included by Livezey and Zusi (21 vs. 3 in Ericson et al.) may make you think the position of buttonquail is an artifact, but more extensive molecular analyses of charadriiformes (e.g. Paton and Baker, 2006; 12902 characters) agree they are the sister group of Lari, with 100% posterior probabilities in almost every node.
- Falcons are related to other diurnal predatory birds instead of seriamas+parrots+passeriformes.
- The hoatzin is sister to cuculids and musophagids instead of a metornithine.
- Passeriformes are in a trichotomy with piciforms and coraciiforms instead of seriamas, falcons and parrots.
- Cuckoo-rollers are coraciiformes instead of more basal.

Even many of the larger clades which aren't well supported in Livezey and Zusi's work correspond to clades in Ericson et al. though.
Though the former did not recover Metaves, it recovered Cypselomorphae at 75%. Within that clade, Apodiformes is well supported at 100%. It only takes 31 more steps to get Daedalornithes. Other supported metornithine clades are Columbiformes (100%) and Eurypygae (77%). Thus Metornithes really does seem to be the Afrotheria of birds, as afrotherian clades (Tenrecoidea, Paenungulata, Tethytheria) are recovered morphologically though there's no known morphological support for Afrotheria as a whole.
As noted above, Charadriiformes is recovered (97%; albeit without Turnicidae). Yet, turnicids are a possible charadriiform sister group in Livezey and Zusi's tree, with only ralliforms more closely related (at <50% certainty). Within Charadriiformes, recurvirostrids and haematopodids are sister taxa at 64%, with the other Charadrii not separated by nodes of over 50%. Rostratulids and jacanids are strongly supported sister taxa (99%) with the other Scolopaci all placed as the most basal members of the order. So this is probably a rooting problem. Lari (99%), Laroidea (100%), and the larid+sternid+rhynchopid clade (91%) are all well supported, with glareolids not separated by nodes of over 50%.
Grues (100%) and Gruoidea (100%) are both well supported, as is Ralliformes (100%) and are located nearby on the cladogram with otidids. Cuculids and musophagids are weakly joined (66%) and are potential sister taxa in Ericson et al.. Besides the two metornithine families, Livezey and Zusi's Natatores (<50%) corresponds to a clade in Ericson et al.. Procellariiformes is well supported (100%), with the Procellariiformes+Sphenisciformes clade (88%) and the clade joining this to Gaviiformes (100%) are not contradicted by the molecular data. Phalacrocoracoidea (100%) and Sulida (87%) are supported. Livezey and Zusi's Ciconiimorphae (78%) is mostly represented by the molecular data, though missing Pelecanidae and Balaenicipitidae, and with Ciconiidae itself only a possible member. But balaenicipitids are the most basal members of the ciconiimorph's sister taxon in Livezey and Zusi, so they're not far away.
Besides the metavian Cypselomorphae, Opisthocomidae and Columbiformes, and the gruiform-related Cuculiformes, Livezey and Zusi's Dendrornithes (58%) is represented in the molecular data. Ericson et al.'s Cariamidae+Falconidae+Psittaciformes+Passeriformes clade is another one which receives no morphological support, though its components do (Falconidae 99%, Psittaciformes 100%, Passeriformes 100%).
Strigiformes (100%), Sagittariidae+Accipitridae+Pandionidae (89%), and Accipitridae+Pandionidae (100%) are all recovered, and the molecular data leaves the possibility of Raptores (72%) and Accipitriformes (100%) open. Thus the entire topology of raptorial birds could correspond, excepting Falconidae's absence. Livezey and Zusi's Trogones+Pico-Clamatores clade (74%) is represented in Ericson et al. except for the absence of Passeriformes in the latter. Coliidae and Trogonidae are joined in Livezey and Zusi's tree (78%), and are potential sister taxa in Ericson et al.'s. Bucerotes (98%) and Upupides (100%) are found in both. A Halcyones+Coracii clade (76%; though minus leptosomids), Coraciides (96%; though minus leptosomids), and Halcyones (97%) are found in both. Coracii (63%) is not contradicted by the molecular data. The entire topology of Piciformes (88%) is shared by the two studies- Galbulae (100%), Pici (89%), Capitonoidea (<50%), and Picoidea (51%).

I have to agree with David regarding Livezey and Zusi's fear of missing data. There's no reason Dinornithiformes and Aepyornthiformes should be excluded when we have complete skeletons. Taxa don't cluster together due to missing data, and inserting them a posteriori won't let their unique character combinations improve the tree. I think adding fossils to this tree will be extremely interesting, especially if the molecular data is added and analyzed simultaneously. Fossils are the morphologist's only hope at combating such detailed convergence.

Mickey Mortimer