Re: [dinosaur] Dinosaur Origins + Neoavian Radiation

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

> You are implying that phylogenomicists actually think in terms of organism, 
> and of taxonomy, and of tree-based thinking outside of genomes...

They do engage in tree-thinking, it's just all messed up. I have complained 
twice before on this list about this paper 
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_nature03025&d=DwIBaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=5rVTfiEmFIHSk0rBpmeoRnV0mdBxVX7YopQP4IK4QmU&s=9lnmksW7DRxEONdCBA9exeQFnGQTQnNjUzAJNhriymk&e=
  , whose "early vertebrate proto-karyotype" of the title is revealed to be 
"the basic structure of the ancestral bony vertebrate genome" in the abstract 
and "the karyotype of their osteichthyan (bony vertebrate) ancestor" later in 
the paper, after "the ray-finned fish (actinopterygians) lineage after its 
separation from tetrapods" is mentioned, turning lungfish and coelacanths into 
tetrapods just because their bloated genomes hadn't been sequenced in 2004.

On the other hand, I hope the same paper's repeated implicit restriction of 
"fish(es)" to Actinopterygii (...though not to just *Takifugu* and 
*Tetraodon*...) actually catches on.