Thursday, May 8, 2008

Strange happenings in a strange animal

The platypus genome is out. The coolest result is that the venom produced by the male platypus is derived from some of the same gene families that were coopted for venom production in reptiles. An amazing example of independent evolution, to be sure.

I was really excited to see some phylogenies in this paper and looking forward to learning all about how they were made. After browsing the paper and skimming through the copious supplemental material, however, I have yet to find any information on how the tree in Figure 1 was obtained (see image). A program called NJTree (since renamed TreeBest) is mentioned in the supplemental material, but it's not clear which analyses this program was used for, or which of its algorithms were used (it seems capable of building trees via both neighbor-joining [a distance-based method that is decades old and riddled with problems] and 'extended' maximum likelihood [a method that I've never run across]). Since we can't learn anything from methods that don't exist, we're left to ponder just one question: How can a paper with ~100 authors not include a single meaningful sentence about the methods used to produce at least two of its five figures?

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