I'm afraid I'm going to be descending into cattiness for a moment later. I apologise in advance for any unwarranted snarkiness.
A paper (citation above) has appeared in today's edition of Science that adds to the ongoing debate on bird phylogeny. It is a fairly significant paper, giving the results of the largest molecular phylogenetic analysis to date for birds. As such, it largely supersedes the previous front-runner, the analysis of Ericson et al. (2006). However, most of the results of Hackett et al. (2008) are largely congruent with those from Ericson et al. (2006). So I'm a little bemused to read Chuck Hagner commenting that "What wasn’t expected was an apparent sister relationship between Passeriformes and Psittaciformes" and expressing surprise that Falconidae should cluster with that clade instead of with Accipitridae, when both these results had been reported in the 2006 paper. What is significant is that both these studies, conducted independently (no shared authors), found such similar results. Both studies (and the earlier Fain & Houde, 2004) found the same six major clades - Palaeognathae (ratites and tinamous), Galloanserae (gamebirds and waterfowl), Metaves (I'll explain in a minute), the "higher water-birds and allies" clade (including 'Ciconiiformes' and 'Pelecaniformes' intermixed), Charadriiformes and the "higher land-birds" (Passeriformes, Piciformes, Coraciiformes and allies).
Metaves is one of the most controversial groupings of birds to have been proposed in recent years. It first made an appearance in a 2004 paper by Fain and Houde published in the journal Evolution. These authors coined the name Metaves for a clade containing nightjars, swifts and hummingbirds, pigeons and doves, sunbitterns, the kagu, mesites, tropicbirds and the hoatzin that was well-supported in an analysis of the β-fibrinogen gene. This clade was then completely unexpected - perviously, its members had been scattered among an assortment of other bird orders, and the only thing a number of them had previously had in common was that they had always looked a little out of place. In a message forwarded to the DML shortly after the publication of the 2004 paper, Peter Houde commented that the results had been so heterodox that it had been very difficult to get them published. The Charadriiformes, higher land-birds and higher water-birds together formed a clade that Fain and Houde dubbed "Coronaves". The Fain and Houde analysis did resolve the Charadriiformes and higher water-birds, but support was not great.
Ericson et al. (2006) increased the number of genes analysed to five, and again found the Metaves-Coronaves division of Fain & Houde (2004). They were also better able to resolve relationships within the major clades. However, the support for Metaves was completely reliant on the inclusion of the β-fibrinogen gene. If this gene was left out of the analysis, the clade collapsed.
Not too long after Ericson et al. (2006), a counter-sally from the morphological fort appeared in the form of the long-awaited Livezey & Zusi (2007) analysis. Using an awe-inspiring 2954 characters over 150 taxa, this morphological über-analysis bravely fought off the molecular novelties and called stridently for a return to more traditional relationships.
It is into this clash between the molecular data of Ericson et al. (2006) and the morphological data of Livezey & Zusi (2007) that Hackett et al. (2008) make their entrance. Hackett et al. increase the number of analysed genes to 19, and once again recover the much-maligned Metaves. Once again, though, the presence of this clade is dependent solely on the β-fibrinogen gene. The hoatzin abandons the Metaves and attaches itself to the base of the higher water-bird clade. I'm inclined to describe this as unsurprisingly surprising - once again, Opisthocomus is just being a prick. There seems to be a visible trail of respectability here - four years ago, Metaves had to fight its way for recognition in a respectable journal. With the publication of a paper supporting it in Science, it seems to have become a respectable hypothesis.
And that, really, is the source of my irritation. Nature and Science are widely regarded as the ultimate science journals, but it's difficult to escape the observation that many papers that appear in the two are, well, kind of crap. This is not the fault of the contributing authors, but results from the severe space restrictions on articles in these journals. At five very densely-written pages, Hackett et al. is a fairly long paper for Science, but the reader is left frustrated by the need to know about stuff that the authors were evidently forced to leave out. What happens when the analysis parameters change? If a given clade is collapsed, how does this affect the rest of the tree? Some of this is alluded to in the article, but there simply isn't the time for it to be explored properly. And was it lack of space that caused the authors to write clangers such as "flighted tinamous arose within the flightless Struthioniformes", which sounds to be suggesting that tinamous evolved or regained flight independently of other birds, rather than the far more likely scenario that flight was lost multiple times within the ratites? Nature and Science papers have been referred to as "extended abstracts" Sometimes, no matter how extended, an abstract just doesn't substitute for a paper.
Don't get me wrong, this is a very significant paper, and one that will provide a base-line for many future studies. It doesn't completely overthrow previous studies, but in the end that is exactly what is so fantastic about it - not that the results are completely unexpected, but that as more and more data is added, we can say more and more about the picture that has been developing over the past few years.
Ericson, P. G. P., C. L. Anderson, T. Britton, A. Elzanowski, U. S. Johansson, M. Källersjö, J. I. Ohlson, T. J. Parsons, D. Zuccon & G. Mayr. 2006. Diversification of Neoaves: integration of molecular sequence data and fossils. Biology Letters 2 (4): 543-547.
Fain, M. G., & P. Houde. 2004. Parallel radiations in the primary clades of birds. Evolution 58 (11): 2558-2573.
Livezey, B. C., & R. L. 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.