Competing bird phenomics: Livezey and Zusi 2007

From the Livezey and Zusi 2007 abstract:
“This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees.”

Sounds like the methods used in the large reptile tree (LRT, 2338 taxa),
but with fewer theropod (including bird) taxa. Will that make a difference?

368 LRT taxa are theropods (including birds) vs 185 in Livezey and Zusi.
200 LRT taxa are Archaeopteryx or thereafter.

“2954 morphological characters were defined;
a total solution set of 97 well-resolved, most-parsimonious trees (MPTs).”

235 characters are tested in this subset of the LRT, less than ten percent of those tested by Livezey and Zusi. resulting in a total solution of 16 well-resolved, MPTs.

“Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively,

The LRT confirms that recovery.

“and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves).”

Here’s the problem: In Livezey and Zusi Chauna, the extant screamer, is recovered as basal to geese and ducks = anseriformes. On the other hand, Megapodius the tinimou = megapode, is recovered basal to guinea fowl and chickens = galliformes.

That differs from the LRT (Fig 1), which nests palaeognathid-like Megapodius basal to all other extant birds and their extinct relatives, far from all other ‘galliformes’.

Likewise the LRT nests Chauna far from all other ‘anseriformes’ (Fig 1).

This is what can happen when more taxa are added.

“Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds;”

By contrast, the LRT nests terrestrial and aerial predators next.
Water and shoreline birds appear in the middle and most derived nodes.

“(ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested;”

The LRT confirms that recovery. In other words, traits recover grebes with loons – not close to flamingos, as recently suggested in genetic studies.

(iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic;

The LRT confirms that recovery.

“(iv) traditional Ciconiiformes are monophyletic;”

The LRT confirms that recovery.

“(v) Strigiformes and Falconiformes are sister-groups;”

The LRT confirms that recovery.

“(vi) Cathartidae is the sister-group of the remaining Falconiformes;”

The LRT confirms that recovery, but nests vultures basal to falcons, owls and terror birds on one branch, the rest of living birds on the other branch.

“(vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade;”

The LRT confirms that recovery.

“(viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae);”

The LRT nests the hoatzin (Opisthocomus, Fig 1) between chickens and parrots.

“(ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes;”

The LRT confirms that recovery.

“(x) Trogoniformes are the sister-group of Coliiformes;”

The LRT confirms that recovery.

“(xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related;”

In the LRT kingfishers, woodpeckers and sparrows are not related to one another. Freshwater-diving kingfishers arise from sea-diving terns.
Woodpeckers arise from trunk clinging nuthatches – and they from crows.
Seed-eating sparrows are close to seed-eating chickens and parrots.

“and (xii) the Galbulae are retained within the Piciformes.”

Not tested in the LRT.

“Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes.”

These are all resolved in the LRT.

“The remaining polytomies were among outgroups.”

The LRT resolves theropod outgroups.

References
Livezey BC and Zusi RL 2007. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zoological Journal of the Linnean Society149(1):1–95, https://doi.org/10.1111/j.1096-3642.2006.00293.x

Source: https://pterosaurheresies.wordpress.com/2025/03/28/competing-bird-phenomics-livezey-and-zusi-2007/