Re: Shaking up the bird family tree

[David Marjanovic <david.marjanovic@gmx.at>]

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):

--+---------------------*Struthio*
  `----------+------------------*Rhea*
            `--+-----------------------------------Tinamidae
               `--+--------*Apteryx*
                  `---------------+--*Casuarius*
                                  `--*Dromaius*

(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.