The new family tree of birds rests on whole-genome analysis. Phylogeny for birds and other organisms always has been based on painstaking evaluation of the few available fossils, buttressed since the 1970s by molecular comparisons of selected proteins or a handful of shared genes. But this new tree is based on scanning every last letter of DNA, 1.2 billion letters of genes and non-genes, in forty-eight bird species representing every major order.
For example, you could draw a pretty convincing family tree of American automobiles by just comparing tail lights and steering wheels, a small, but distinguishing sample of their total parts. By contrast, whole-genome analysis is like having the serial number of every one of the 30,000 parts in each vehicle. By comparing these huge data sets carefully with big computers and some purposebuilt statistical algorithms, you’d be able to see that a Ford pickup and a Ford Mustang share many parts and had a common ancestor in the past. You might puzzle over how a Chevy pickup and a Ford pickup ended up being so similar despite having come from different lineages. And you’d probably struggle to sort out features like all the cupholders in those minivans. Do they look alike because they all came from the same parent, or did they independently evolve to the same basic shape?
So it is with whole-genome analysis of the birds. The picture has changed but is still far from resolved, and the arguments and reanalysis will persist for quite a while.