Molecules vs. morphology in bird phylogeny: Prum et al. 2015

As readers know
DNA cladograms do not match morphology cladograms, like the large reptile tree (LRT, 1124 taxa). Today we’ll be looking at some of the ‘strange bedfellows‘ that the Prum et al. 2015 DNA cladograms produced.

The LRT outgroups
include a long line of taxa extending through theropods and Jurassic birds, like Archaeopteryx), and other taxa going all the way back to Devonian tetrapods. That’s a solid out group. At every node the taxa document a gradual accumulation of traits. 76+ (the number may grow) Euornithine birds comprise the in group.

Figure 2. Basal Euornithes/horizontal. Click to enlarge.

Figure 1. Basal Euornithes. Click to enlarge this horizontal view of figure 1.

The Prum et al. cladogram employed 198 euornithine birds,
and nested the ones genetically closest to crocs at the base: Struthio, the ostrich + (Leipoa, the megapode + Chauna, the screamer).

Prum et al. chose two outgroup taxa:
Two crocodilians. No theropods were included. No Jurassic birds were included.

Crocs don’t have feathers.
Their forelimbs are not transformed into wings. Morphologically crocs are not good outgroups for euornithine birds, but, when using DNA, there are no better taxa living today. Unfortunately they do not provide a readily visible gradual accumulation of traits. For those we have pertinent taxa recovered by the LRT (Figs. 1, 2).

Figure 1. Basal euornithes to scale as recovered by the LRT.

Figure 2. Basal euornithes to scale as recovered by the LRT. Basal birds, for the most part, were long-legged forms. Short forms arrive easily by way of neotony as bird hatchlings have short legs. Yanornis is Early Cretaceous.

LRT Clades 1 and 2: Tinamous and Ratites
In the LRT the first clade includes an early Eocene tinamou-like bird, Pseudocrypturus + Apteryx, the kiwi. In the next clade mid-sized tinamous are basal to giant ratites – and all other extant birds.

Prum et al. Clade 1: Ratites and Tinamous
In the Prum et al. cladogram, the giant derived ostrich splits off first, then the smaller rhea, then the even smaller kiwi (Fig. 1), then the giant cassowary and giant emu. These last two are sisters to the clade of tinamous and all members of the Palaeognathae in the DNA study. In the Prum et al. tree, the ostrich is basal to all known ratites – and all other extant birds.

This may strike you as odd.
Generally basal taxa are average to small in size (Fig. 1) and without unusual traits, but the opposite is the case in the Prum et al. cladogram.

LRT Clade 3: Toothed Birds
The next clade in the LRT includes extinct toothed birds, a clade that, perforce, has to be ignored by the Prum et al. DNA study and, for that matter, has little bearing on extant bird evolution. This clade came and went without affecting the living birds. The presence of teeth are a secondary appearance, an atavism in this clade. The basalmost taxon, Changzuiornis, had tiny teeth and most closely resembled the long-snouted, long-legged outgroup tinamous. Later toothed birds had larger teeth, shorter legs and the most derived toothed bird, Hesperornis, had vestigial wings.

Teeth in birds,
whether true teeth with dentine and enamel, or false teeth made of bone or keratin also reappear most obviously in ducks, flamingoes and Pelagornis, the giant petrel. Less obviously tiny bill projections can be found in several other bird bills on close examination.

Prum et al. Clade 2: Neognathae + Galloanseriformes
In the Prum et al cladogram the first neognath clade includes megapodes and chickens on one branch and screamers and ducks in the other. In the LRT megapodes are indeed close to chickens, but ducks are far removed from screamers. Importantly, neither screamers nor megapodes are skeletally similar to the ostrich, their proximal outgroup in Prum et al.

LRT Clade 4: Birds of Prey
Generally tinamous are infrequent flyers and so are basal members of the next clade in the LRT, the long-legged, hooked beak predators, Cariama and Sagittarius. The latter gives rise to short-legged aerial predators like Pandion (ospreys),  Falco (falcons) + Targas (Old World vultures) and Tyto (owls) + Apus (swifts).

Figure 2. Which taxa share more traits? Phoenicopterus, the flamingo nests with Cariama, the seriema in the LRT, but with Gavia in the Prum et al. DNA study. Gavia nests with Thalasseus, the tern in the LRT.

Figure 3. Which taxa share more traits? Phoenicopterus, the flamingo nests with Cariama, the seriema in the LRT, but with Gavia in the Prum et al. DNA study. Gavia nests with Thalasseus, the tern in the LRT.

Phoenicopterus, the derived flamingo is a frequent flyer, but eats while standing with a strongly hooked beak and nests with the similarly gracile basal Cariama. In summary, and heretically, swifts and flamingos nest with birds of prey in the LRT. Prum et al. nest flamingos with short-limbed, straight-billed grebes, like Gavia, and all other shorebirds (Fig. 3). The LRT nests Gavia with short-limbed, straight-billed terns and only a few other shorebirds.

More later.
It’s a big subject.

References
Prum et al. (6 co-authors) 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526:569–573. online

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