[Taxacom] The difference

[Richard Pyle]

Hi Richard, 

> After 10 years of mulling over the difference between 
> morphological and molecular phylogenetic analysis, and the 
> great disparity between sizes of data sets of each, it 
> finally occurred to me that morphological traits are based on 
> genes, and shared apomorphic morphological traits imply 
> shared apomorphic DNA base sequences. 

I was struck by a similar epiphany several years ago. It may be out of place
to use the word "epiphany" for something so obvious that any high-school
student with a grade of "C" or better in introductory biology should know,
but I think it representes a fundamental cognition of something we all know
to be factually true, but haven't quite itegrated it into our mental
abstraction of biodiversity to the point where it shapes our perspective of
the world around us. I know that sounds largely like gobble-dee-gook, but
there is something real in there about interpreting the world in a new way
after putting an otherwise obvious fact into proper context (I had a similar
experience late one night the first time I saw the moon as a 3-dimentional
object floating in space, rather than a big disk).

In any case, the equally obvious (and equally underappreciated) logical
conclusion in the case of morphology/molecules is that absolutely everything
that is phylogentically informative about morphology exists somewhere in the
genome.  Most of us don't think this way on a day-to-day basis, because we
still live in a world where what we understand about the information
contained within the genetic code of an organism is VASTLY less than what we
do not understand about it.  The exciting thing to me is that, within my
lifetime, we may very-well cross the threshold of understanding about
genomics/proteinomics/etc.  -- at which point the connection between
genotype and phenotype will be better understood.

For the time being, though I think it is indeed helpful to think of
morphology as a course surrogate to the underlying genetic information that
lies behind.

However....

> Can we come up with some average or standard value of 
> expected shared DNA bases per shared morphological trait? 

I don't think there's a practical way to quantitatively build this
connection. Too many variables, too much variation, and above all, too much
we simply don't understand yet.

Nevertheless...

> Even if we can't, it is clear that morphological data is 
> given short shrift when combined on an even basis with 
> molecular data, and therefore morphological and molecular 
> data sets should always be evaluated separately.

I do wholeheartedly agree with this point, and I believe it's silly to
assign equal weight to an apomorphic DNA substitution as to an apomorphic
morphological character.  In most cases, I think, the morphological
apomorphy should be seen as a surrogate for what could end up being hundreds
of substitutions spread across dozens of genes (in any case, likely
representative of much more than one DNA substitution).  Of course, this
needs to be balanced against those cases where the DNA substitution should
count for *more* than a morphological character (i.e., in cases where the
character is not phylogenetically informative -- e.g. when the purported
morphological "apomorphy" is a response to environmental factors, or a
function of ontological development, etc.).

Aloha,
Rich