Re: What goes around comes around

> > When we look at all the cases, common descent is less simple, as it
> > must draw on a common mechanisms hypothesis, and we have no
> > compelling, theory-neutral reason to limit that hypothesis to the
> > cases that common descent doesn't handle.

However, common mechanism does not negate common descent. Evolutionary
studies are selective, not to ignore data that disagree but to ignore
data that don't tell anything. (Plus the fact that you can't examine
everything at once, especially unfunded.)

For example, I'm using ITS1, a noncoding spacer region, in looking at
some confamilial species of mussels. Other bivalve families have so
much difference with these that there's not much point in trying to
align the sequences, much less analyze them. In some other organisms,
the variation in ITS1 within an individual is higher than the differnce
between individuals of related species, so it's not much use. On the
ohter hand, I know someone who tried using 28S within a "genus" (a
wastebasket taxon of random things within a tribe) of mussels and found
only a dozen variable sites out of about 1000 base pairs. There's not
enough variation to analyze.

Another example: I recently generated some COI sequences for mussels.
Two of them looked different from the others. One was just a little
more different. Afterwards I checked and saw that I had forgotten that
one sample was from a different tribe from the others. However, the
remaining sequence was highly divergent. Before trying to analyze it,
I plan to search and see if it matches a parasite or other plausible
contaminant better than it matches mussels. No one has data for the
species, so I can't rule out that the strange sequence is valid, but I
have doubts.

Another example: Oysters have some similarities (e.g., larval form) to
pearl oysters and some similarities to scallops (e.g., shell
structure). Fossil oysters have shell structure closer to the general
primitive bivalve condition after ancestral scallops already started
changing their shell structure. There is both the example of parallel
shell changes in other bivalve lineages and the selective forces that
could favor shell structure change in favor of possible parallel
evolution. Further discoveries turned up a pearly layer in some of the
oldest fossil oysters. The first DNA analyses tended to weakly group
oysters with a totally different group of bivalves, but when more data
were obtained for additional species (more oysters, the first pearl
oyster data, additional genes, etc.), oysters have consistently grouped
with pearl oysters. The COI sequence data is sufficiently randomized
to not provide very strong support, but there is a unique pattern of
deletions in COI for the oyster/pearl oyster group relative to other
mollusks. Close common ancestry of oysters and pearl oysters is thus
strongly supported; there are also some common mechanisms at work.

-- 
Dr. David Campbell
425 Scientific Collections Building
Department of Biological Sciences
Biodiversity and Systematics
University of Alabama, Box 870345
Tuscaloosa AL 35487-0345  USA