H5N1 in Nigeria and the importance of phylogenetics

Those of you who have followed creationism/intelligent design literature over the years have probably felt as if you're living in an alternate universe sometimes. In that literature, many times it seems as if "up" means "down" and "highly supported by the evidence" means "a theory in crisis." You may not have been following the comments to this post on AIDS denial (and lord, I can't blame you), but if you have been, you've seen a similar phenomenon, where it's suggested that mutations found in RNA viruses are just due to sloppy lab work, essentially blowing off an entire field of research. This, of course, has implications far beyond HIV. Phylogenetic analyses based on genetic mutations are used to determine relationships for all kinds of organisms--including humans. In infectious disease epidemiology, they can be used to pinpoint the origin of a virus, or to track and predict its spread, as I've written about previously. A new paper in Nature uses similar methodology to examine the introduction of influenza H5N1 into Nigeria. (Continued at Aetiology).