In a recent paper Hackett et al., present a phylogenomic analysis of birds based on 19 genes sampled from 169 species. The phylogenies are amazingly well supported and reflect many traditional groupings. However, this new phylogeny offers several surprises. For example, parrots and passeriforms (perching birds) are sister lineages.
The analyses were based on concatenated datasets. We at dechronization are sure that species tree proponents interested in birds (e.g. Scott Edwards at Harvard) will be analyzing this wonderful dataset using the new and cutting edge methods being developed to estimate species trees. These are exciting times for phylogenetics.
Hackett, S. J., R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M. J. Bruan, J. L. Chonjnowski, W. A. Cox, K.-L. Han, J. Harshman, C. J. Huddleston, B. D. Marks, K. J. Miglia, W. S. Moore, F. H. Sheldon, D. W. Steadman, C. C. Witt and T. Yuri 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320: 1763-1768.