Molecular evolution and the origin of Aves

In this book, we've emphasized the fossil record as the means oftelling when events occurred, mainly because this book deals with extinct organisms, the only record ofwhich has historically been the fossil record. But in those cases in which we are dealing with living organisms, a whole different type of technique is available for study: molecular evolution.

Molecular evolution involves measuring the timing of molecular changes. So, for example, take two somewhat closely related living organisms, A and B. Now, choose a particular protein that they share, say, serum albumin (a protein in their blood). Their serum albumins might be quite closely related, but if some time has elapsed since A and B last shared a common ancestor, the exact molecules may have evolved and now differ slightly, in either form or composition. Ifwe knew the rate at which the molecules diverged, we would know how distantly in the past the A and B shared a single common ancestor (whose serum albumin composition and form were the ancestral ones). This very technique (and indeed this very molecule) was used in the case of humans and chimpanzees to show that the two shared a most recent common ancestor only 5 million years ago, instead of the 15 million that had been inferred from the geological record.

More recently, molecular biologists have been using a technique called DNA hybridization. This technique works similarly to the one described above for proteins, except that it compares two strands ofDNA (instead of proteins). In the same species, the strands ofDNA should be virtually identical. DNA hybridization allows molecular biologists to measure the differences between the two strands. Knowing what rate substitutions (or changes) occur in the DNA allows us to calculate how long ago two different creatures shared identical DNA. That number should equal the time of divergence from a common ancestor.

And what of birds? Molecular estimates ofthe earliest Aves have consistently been somewhat earlier than has been inferred from the fossil record. In general, the fossil record has shown that the major radiation of birds took place after the K/T extinction. Yet, the fossil record of birds is, as we have seen, rather spotty, and perhaps most trustworthy only in its broadest outlines.

Estimates of the radiation of Aves, based on molecular data - primarily DNA hybridization - have put the time of the radiation well within the Cretaceous, before the boundary. How to resolve this contradiction?

Recently, the fossil record has begun to support the mol ecular record . . . a little bit. The fossil record of modern bird groups in the Cretaceous now includes the ancestral relatives of ducks, chickens, and large, flightless birds such as ostriches and emus. Even with these new-found discoveries, however, whether or not the major radiations of birds took place before or after the Cretaceous-Tertiory boundary remains unclear. Our best guess, a compromise between the molecular and fossil data, is that the origins of many modern groups were in the Late Cretaceous, but their radiations took place after the Cretaceous-Tertiary boundary.

Molecular evidence has also been used in an entirely different context. A study published in April, 2008, compared proteins from 21 different living creatures, including an alligator, an ostrich, a chicken, and two extinct creatures T. rex and a mammoth. The Tyrannosaurus proteins were types of collagen extracted from an unaltered femur (see Chapter 1 and Chapter 9, footnote 3). The results were unequivocal: the proteins showed that the mammoth and an elephant were phylogeneti-cally close and, more relevant for our story, that the Tyrannosaurus and the birds were close - closer to each other than either is to an alligator.

If it were only that easy! Exciting as that study was, it has not gone unchallenged. The question has been whether the molecular evidence was really of Cretaceous age - or whether it was actually much younger. Some researchers have recently suggested that the collagen extracted originated from modern biofilms: layers of bacteria that grew in the last 50 years or so in the holes of the fossil bone. What those proteins are - and are not - is certainly going to be an active topic of research, and perhaps controversy, in the coming years.

not well-known for Mesozoic Aves. Likewise, no Cenozoic toothed bird is known, although the fossil record of birds in the earliest Cenozoic is also very poor. Teeth - that final step in getting to be a modern-style bird - somehow got lost during the Mesozoic-Cenozoic transition (Box 11.1).

Cold cases

But it's by no means all figured out. Flightless birds such as emus and ostriches appear to retain in the skull primitive features whose origin may be found in Mesozoic birds. Unfortunately,

Figure 11.8. Mononykus, an alvarez-saurid from the Late Cretaceous of

Figure 11.8. Mononykus, an alvarez-saurid from the Late Cretaceous of

the rarity of the skulls of Mesozoic birds has made connecting them with modern birds both complex and controversial. How such flightless modern birds fit into the rest of modern birds and into our understanding of Mesozoic bird history - is a story that must await another day.

Enigmata. One small evolutionary radiation, known as Alvarezsauridae, from the Late Cretaceous, has been difficult to place in the phylogenetic scheme we've outlined here. This is largely due to unusual specializations of their skeletons. Take Mononykus for example, a Late Cretaceous theropod that evidently apparently lived in a Late Cretaceous Sahara-like sand sea (Figure 11.8).

From its pelvis backward, Mononykus looks like a typical ho-hum theropod, with strong, elongate, well-developed hindlimbs, and a long straight tail. But the hands are fused into a short, powerful carpometacarpus, and the arms are stout and short, with a large pro cess (the olecranon process) for developing power at the elbow joint. Among its avian-like characters is a mildly keeled sternum. Perhaps it used its shortened, yet strong, arms for burrowing.

Subsequent years have seen the discovery of other alvarezsaurids - Parvicursor and Shuvuuia from the Gobi Desert in Mongolia, and Alvarezsaurus and Avisaurus from Argentina and the USA. No feathers are preserved with any alvarezsaurid - if they were ever present.

Figure 11.9. Two interpretations of the position of Alvarezsauridae. (a) Alvar-ezsaurids as birds; (b) alvarezsaurids as relatives of Ornithomimosauria.

Maniraptora

Figure 11.9. Two interpretations of the position of Alvarezsauridae. (a) Alvar-ezsaurids as birds; (b) alvarezsaurids as relatives of Ornithomimosauria.

Maniraptora

The position of alvarezsaurids within Theropoda is still utterly unclear (Figure 11.9). Are the carpometacarpus and keeled sternum homologous with those of birds? If so, what a mess that is for the cladograms we've presented: it would call for a comparatively primitive theropod evolutionary throwback (at least, from the pelvis backward) in the middle of a group of animals that are very bird-like.

If these features are not homologous, is it unparsimonious for them to have evolved twice: once in ornithothoracans (where they would be homologous with the carpometacar-pus and keeled sternum of living birds) and once in some more basal eumaniraptoran, thero-pod lineage, in which their appearance would be utterly unique?

This story, too, must await another day for its final telling.

While Archaeopteryx was clearly important in identifying the relationship between Aves and dinosaurs, there were still a number of evolutionary steps to take before the anatomical condition seen in Aves (see Chapter 10) was achieved. Despite their rarity as fossils, the fossil record of birds indicates the general order in which these evolutionary events occurred.

The improvement of flight capability was a driving force in post-Archaeopteryx bird evolution. Pneumatic foramina became better developed, along with, sequentially, the pygostyle, a reduction in the number of trunk vertebrae, modifications of the shoulder, and the development of the carpometacarpus. Still, some primitive characters such as gas-tralia, were retained. All these features were present in Cretaceous ornithothoracan birds, including the small, comparatively common Enantiornithes, and the line leading to Aves, Ornithuromorpha.

Within Ornithuromorpha, several highly evolved birds appeared, notably the diving hesperornithiformes and the seagull-like ichthyornithiformes. These birds, for all their advancement, were not exactly like living birds, lacking a number of features diagnostic for Aves, including loss of teeth. The earliest fossil record of Aves is very fragmentary, but goes back into the Late Cretaceous.

Some forms exist that do not fit into the evolutionary scenario proposed above. These include the enigmatic alvarezsaurids, whose stout carpometacarpus, if homologous

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