But that is a lot of variability, especially for two individuals. And if a trait is governed by more than one gene each of which has four alleles, as human skin color is governed by four genes, then you have a great deal of variability in a mere two individuals. This was probably the case on the ark although by now there's no reason to expect that much genetic variability in any creature.
But it's really not a lot of variability when you think about it. This has to account for variations within species as well as between species of the same kind. As I understood from your argument, and please correct me if I'm wrong, but the creation of species within a kind is a result of populations splitting off with a subset of this diversity. So as more species occur within a kind this diversity will rapidly go down, so many of these gene loci will tend towards a single allele.
I do agree with you many traits are influenced by a number of genes interacting with each other. Now let's take human skin colour as an example since you brought it up. There are 3 main genes common to all humans, with additional genes getting involved depending if you are from European or East Asian descent. However one of the main genes is MC1R which regulates melanin production. It has been documented that there are 90 nonsynonymous, frameshift or stop mutations known to affect the activity of the protein and 8 of these are found in more than 1% of the population. So just to reiterate, for this one gene there are 90 alleles with 8 of these alleles in greater than 1% of the population. Where did these additional alleles come from if not from individuals on the ark?
Source
There's no need for a fallback if two individuals have as much genetic variability at one gene locus as you postulate. Besides, junk DNA is really just dead or half-dead DNA, not of use for any constructive purpose.
As I said above, it is not much genetic variability, but I've read creationists arguments before that the missing genetic variability is hidden in the junk DNA. If you are not one of these creationists I apologise.
I wouldn't quite describe junk DNA as dead, but it is non-coding DNA. This means it does not directly affect an individuals survival so it accrues random mutations which are neither advantageous or detrimental. However, from a scientific point of view it does serve a constructive purpose since when you compare these regions between two species you can identify by how much they have diverged from a common ancestor and how long ago this occurred. This is all based on current rates of mutation as seen today.
The other structures I mentioned which I managed to confuse you with, the ERVs and pseudogenes, can also be used to identify relationships. This is because two organisms with the same genetic sequences at the same location, with the same mutations, could only have resulted if they shared a common ancestor. But I don't expect you to accept this, and my original reason for bringing them up was in case you thought further variability was in junk DNA, so won't push you further on this.
Which of course is a wild fantasy as all those dating estimates are.
And of course the rate of mutations has nothing to do with genetic variation, being either useless or destructive.
Which dating estimates are you referring to? As I said above it is simply comparing genetic sequences of a number species, identifying how many differences there are and how long it would take for those differences to accumulate based on current mutation rates. With the dogs
here is one study comparing the mitochondrial DNA between different breeds and they found that breeds diverged greater than the 14,000 years of the last known archaeological evidence of domesticated dogs known at the time. Of course mitochondrial DNA is highly conserved and any destructive mutations would be fatal to the individual, so this is based on neutral mutations and the rate in which they accumulate.
The study on the big cats you can read about
here. In this case they looked at two genes, EGLN1 and TYR and again compared the number of differences between different species. Interestingly TYR as well as being associated with light fur in cats is also involved in light skin colour in european humans. It is involved in transport of tyrosine which is a precursor to melanin production.
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