Re: New paper on Neoaves

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

----- Original Message -----
From: "Tim Williams" <twilliams_alpha@hotmail.com>
Sent: Monday, August 14, 2006 5:13 PM

> Definitely.  But as you can you see from your example, it is relatively 
> easy to identify the source of potential homoplasy in morphology.  In this 
> case, it is characters related to foot-propelled diving shared by grebes 
> and loons.  Similarly, penguins and plotopterids (to use David's example) 
> might be being pulled together by characters associated with their 
> underwater lifestyle (as interpreted by Olson), or they could reflect a 
> common ancestry (as Mayr proposed more recently, based on his phylogenetic 
> analysis).  This is a tricky business, sorting convergence from common 
> ancestry - but I like to think that, given enough characters, the latter 
> wins out.  But the potential sources of homoplasy in molecular phylogenies 
> are more subtle, and require further analyses to identify.

Things like base frequency biases (like increased GC content) or codon usage 
are similar to highly specialised lifestyles: they produce correlated 
characters. In morphology, the trick is to count the correlated characters 
as a single character. With molecules only statistical approaches to this 
problem seem to be possible... right?

> Compositional bias may affect the entire
> genomes of prokaryotes, as well as mitochondria and chloroplasts.

The extreme case are hyperthermophilic archaea with very high GC contents, 
apparently an adaptation to avoid that the DNA strands fall apart in the 
heat.