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Re: Shaking up the bird family tree

Well, Science, like Nature, is an extended-abstract publication, so one has to read the supplementary information immediately.

Best quote from there:

"MrBayes v.3.11 (S23) was used for BI searches. We attempted both partitioned (with unlinked rate parameters across the 19 gene regions, while branch lengths remained linked) and unpartitioned analysis. We used two different strategies for the partitioned analysis, both of which were unsuccessful in approaching stationarity. First we tried two simultaneous runs with six heated chains each for 10 million generations, saving each 500th generation (Analysis A). Next we conducted a search with six runs of two chains each, one cold and one heated, for 10 million generations (Analysis B). Both searches, performed at the supercomputing facilities at the Illinois Bio-grid at DePaul University, took over 2 months each. In the end, none of the different runs had either converged or reached stationarity (Fig. S3). Failure of Bayesian analyses to satisfactorily complete a phylogenetic analysis of large datasets has also been demonstrated recently by (S24), though that study included more taxa and fewer gene partitions. Unpartitioned analyses of our data set always immediately crashed, regardless of the memory capacity of the computers used. Undoubtedly, Bayesian analysis of large datasets is a complex problem such that the number of rearrangements needed to find optimal trees may be so large (on the order of hundreds of millions to billions of generations for a dataset of our size) (S25) that is it not currently computationally feasible."

Interestingly, Metaves and Coronaves are found, but not supported, perhaps because of the pesky hoatzin. The interesting part is that only two of the 19 loci find it, but, in spite of this, the other 17 do not manage to overcome this signal.

Regarding the flightlessness question, here's Palaeognathae (impressionistic rather than to scale):


(The individual tinamous have very long branches of their own, too.)

I smell long-branch attraction between the ostrich and the root, and perhaps even long-branch repulsion between the ostrich and the tinamous. We need moa sequences, pun intended, and elephantbird sequences... and a good morphological analysis with *Palaeotis* and *Eleutherornis* and *Remiornis* and *Diogenornis* and lithornithids and whatnots wouldn't hurt either.