There are a variety of possible complications for DNA.  Because
mollusks, like most invertebrates (echinoderms being one of the most
familiar exceptions) have determinate cleavage in development, you
can't get a fusion between two embryos to make a new individual with
composite DNA.  Also, given how intensively humans have been studied,
we have a good ideas as to what DNA sequences vary widely from
individual to individual and which are fairly consistent across humans
but differ relative to other species, etc.  Although it's possible
(though very rare) for a person to have chimeric cells, DNA from cells
deriving from originally different embryos is going to be extremely
similar.  Especially as both embryos almost always derive from the
same two parents, the difference will usually be evident only by very
specialized testing.

However, there are a number of other factors that do pose a challenge
for using DNA for species identification.  Many mollusks release male
and sometimes female gametes to be transported in the water, making
half-siblings commonplace; even those with mating may not be
monogamous, so there may be some analagous issues to this one.

The biggest problem is that we usually don't have the data to know
what bits of DNA vary between species, what varies within species, and
what doesn't vary much at all.  You have to build up data on the
populations you are interested in, as well as on related ones outside
your study focus, to find out what works, although there are a number
of genes known to usually show higher or lower variation.  It's
definitely important to look for correlation from other
evidence-multiple genes, anatomy, shell form, geographic patterns,
etc.  This problem applies to studying physical characters, too-one
species always shows a particular color pattern, another is quite
variable, etc.

Another problem is that there might be multiple versions of a
particular gene within an individual or within a population.  For
example, most bivalves so far examined have male-inherited
mitochondria as well as the normal female-inherited ones.  If you
sequenced the female version in two species and the male in another,
you could be misled about the relationship.  (Often, it will be
obvious that something is wrong if you consider the possibility, but
molecular papers don't always consider error enough).

Then there's always the same sorts of mistakes that can occur in any
type of study-mixed up samples, contamination, etc.

--
Dr. David Campbell
425 Scientific Collections
University of Alabama
"I think of my happy condition, surrounded by acres of clams"

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