So, right:  genetic evidence that the human population was never down to 
two.

This is exactly true, and very hard to argue with.  Here's the main bit of 
evidence that I know:

There are genes that encode your immune system, and one of them in 
particular, the Major Histocompatibility Complex or MHC 
(http://en.wikipedia.org/wiki/Major_histocompatibility_complex) that has a 
unique selection profile.  And let me explain selection profile first:

For every gene in your body, you have two copies, or alleles.  Usually, 
you have two options for how much good they do you:  either one allele is 
better than the other, in which case having one copy is good and having 
two copies is great, or they make no difference, in which case it doesn't 
matter which copy you have.  The first drives natural selection, the 
second drives drift--two populations will gradually diverge from one 
another just due to chance because one copy of the allele will happen, by 
chance, to come to dominate.

However, in rare situations, no one copy can be said to be 'better' than 
another, and having two *different* copies is better than having two 
*identical* copies.  In the case of MHC, this is because each variant 
protects you from one disease, or type of disease.  If you have two copies 
of the same variant, you are resistant to that disease.  If you have two 
different copies, you are resistant to two different diseases.  This is 
known as 'balancing selection' 
(http://en.wikipedia.org/wiki/Balancing_selection)

So, as you might expect, this process drives the abundance of MHC 
variants.  There are always mutations that arise over time, but some of 
them are so different from each other that they must have diverged a long, 
long, time ago:  before humans diverges as a species, in fact.  If you 
look at the variations themselves, in fact, you can see classes of 
MHCs--lots of people around the world have MHC-alpha (I'll call it--I 
assume there are actual names for these things, but I don't know what the 
nomenclature is), which clearly shares a common ancestor to all the other 
MHC-alphas out there.

And here's the rub:  there are several dozen of these variants (I don't 
remember the number, sadly) that are shared by both humans and apes.  So 
any population bottleneck that humans might have gone through would have 
had to be large enough to have at least one individual in the population 
with each of the variants.  Otherwise, the variant would have disappeared 
in humans entirely, and we wouldn't see it today in both humans and apes.

So, if you go to two people, at two copies each, that gets you four 
possible different MHCs.  You have to add a handful more people to 
maintain the genetic line for the other dozen+.  I forget the numbers, but 
I think it's theoretically possible for that to have been accomplished in 
the other human bottleneck recorded in the Bible, that of the flood, since 
in that case you had Noah and his wife and the wives of his sons (his 
direct sons would have had to had only Noah and his wife's genes).  That's 
five people, so that gets you 10 MHC classes.  Maybe throw in an 
unmentioned servant or two if you need a few more.  Plus divine 
intervention to get the exact right group of people who had exactly the 
right diversity of MHCs.

But Adam and Eve alone?  That's basically impossible.  From a genetic 
standpoint.

But if you imagine Adam and Eve as originally part of a wandering family 
of proto-humans, which God 'awakens' by breathing his spirit into them, it 
makes sense that even though they're not mentioned directly in the Bible, 
there would have been other genetically compatible almost-humans around to 
become spouses for their kids.  Cain's 'whoever finds me' and his 
casually-mentioned wife could have been these members of their former 
tribe/pack/whatever.  Assuming being spiritually awakened by God is a 
dominant trait, all their kids then become human, and off you go.

So that's my best guess about what the genetic evidence means, and its 
literal implications for the story of Genesis.  I also don't think it 
impacts the *spiritual* implications for the story of Genesis one bit ;-)

Feel free to ask followup questions!

-Lucian