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Combined answer Re: Avian origins: new analysis confirms ancient beginnings



----- Original Message -----
From: "evelyn sobielski" <koreke77@yahoo.de>
Sent: Wednesday, February 06, 2008 4:15 AM

The provisional PDF version is here:
http://www.biomedcentral.com/content/pdf/1741-7007-6-6.pdf

Thanks a lot. I have now read the paper. The two external calibration points have both minimal and maximal ages, but all 18 internal ones have minimal ages only. I think that explains something (Marjanovic & Laurin 2007).


Having established the major flaw, I'll heap some praise on the paper. It is huge. To estimate molecular divergence date estimates, you need a data matrix, a tree, and a program. The paper uses a matrix (almost 5000 base pairs from the mitochondrial genome of no less than 135 species, plus at least one alligator and at least one caiman as outgroups), two trees -- one assembled from the literature, the other derived from the dataset --, and four programs*, resulting in eight analyses. Although they agree in putting lots of divergences into the Cretaceous and in putting the origin of Neornithes into the Early Cretaceous, the results differ quite drastically -- two programs put the first divergences in two sister clades at the same age, while the other two put one up to 40 Ma before the other.

The tree derived from the dataset contains numerous bizarrities, like Caprimulgiformes being broken into three parts that are scattered almost all over the tree, or having Falconiformes paraphyletic to Pterocleidae and Coliiformes + something else entirely or having ostrich and kiwi as sister-groups. But the dates derived from the two trees differ only by a very small amount, the sign of which depends on the program. The tree based on the literature unavoidably contains many polytomies, but apart from this, it is rather unremarkable.

In summary, this paper is almost how to do it. If the authors had used more maximum ages, and perhaps a few more calibration points in general, it would be ideal. They even went to the trouble of bootstrapping the dates that the program r8s found -- and that's not implemented in r8s, instead you have to make every single bootstrap matrix yourself and then run them all through the program. This huge amount of work may explain why our paper isn't in the enormous list of references even though it was published early enough.

Of course, as the authors mention, the addition of nuclear genes could only help, but that's another story...

* Including MultiDivTime, which is completely unusable unless you have l33t Unix sgillz. My respect.

----- Original Message ----- From: "evelyn sobielski" <koreke77@yahoo.de>
Sent: Wednesday, February 06, 2008 10:35 PM


And nearly half a decade ago (which seems like an
eternity in avian phylogeny and evolution studies) they
quite confidently could state:

"Molecular, morphological and fossil data all indicate
that the early history of modern birds began in the
Cretaceous and did not involve 'transitional
shorebirds'."

The question is when in the Cretaceous -- just before its end, or around the time the Yixian Fm was deposited???


----- Original Message -----
From: "Tim Williams" <twilliams_alpha@hotmail.com>
Sent: Wednesday, February 06, 2008 11:10 PM

Whoops, my bad. At least six lineages. (Any other stem-anseriforms
we're forgetting?)

Dromornithids?

And *Brontornis*, which used to be considered a phorusrhacoid, but was recently redescribed as an anseriform in a paper that I still haven't read. (Actually I'm waiting for Darren to blog about it. :-> )


Of course, two or three of these lineages of heavy-bodied big-skulled huge flightless birds could be the same, though the geography makes this rather improbable, I suppose.