Re: New paper on Neoaves

[Tim Williams <twilliams_alpha@hotmail.com>]

David Marjanovic wrote:

> Things like base frequency biases (like increased GC content) or codon 
> usage are similar to highly specialised lifestyles: they produce correlated 
> characters.

Yes; except that, for base composition, there may not be any functional 
correlation to this homoplasy.  It just may happen that two lineages evolve 
the same bias independently.  Unlike the feet of grebes, loons and 
hesperornithids, which converged due to the same adaptations for the same 
lifestyle.  Or else, like your example of certain thermophilic microbes, 
there may be an adaptive component.

There is quite a deal of base-compositional heterogeneity among mammal 
nuclear genomes (check out Bernardi's work).  Bats (Chiroptera) were once 
said to have a lower-than-average GC content by mammalian standards, which 
was attributed to an elevated metabolism (i.e., this character was 
flight-related); but further studies indicated that it really isn't that 
low.

Also, certain amino acids (especially the hydrophobic ones) seem to evolve 
rapidly and (worse) sometimes give off a homoplastic signal of their own 
that competes with the phylogenetic signal - especially if the lineage is 
long, and the phylogenetic signal has eroded over time as a result.

> 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?

More or less.  It also helps to understand the secondary and tertiary 
structure of proteins, to see what interactions might be constraining 
evolutionary change in the molecule.

> 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.

Makes perfect sense, and this is true for many thermophiles.  _Thermus 
aquatic_, who provides us with Taq polymerase enzyme for PCR, has a GC 
content around 67%.  However, some hyperthermophilic archaea actually have 
low GC contents (e.g., _Sulfolobus_ species: ~33-37%).  Apparently these 
archaea have proteins that help stabilize the DNA, and the tRNA's are 
high-GC; but I don't know much more apart from that.  Just when we think we 
understand these little guys, they come up with more surprises.

Cheers

Tim