Earlier this week I hinted that I had a priori genetic reasons for being skeptical of a "two wave" theory for the peopling of the New World. Well, I was going to do some literature searches and slap something together that was meaty, but I don't have time, so I'll just offer up an attenuated but sufficient outline of what my issue is. First, look at this map and note the "Amerindians" and other populations. Now, look at this table and note the level of heterozygosity of Amerindians vs. other populations. In short, Amerindians are notoriously genetically homogenous on the MHC loci compared to other human populations. This is a key point, the MHC loci and the HLA variants associated with them are extremely polymorphic, and either overdominance or frequency dependent selection maintains alleles which should be extinct. Some of the alleles predate the human species, that is, there are ancient genes floating around which we share with our anthropoid cousins. There are cases where your HLA profile might resemble a chimpanzee more than your cousin, and that is because many variants span the species. Why is this diversity preserved? The standard answer is The Red Queen Hypothesis. In relation to this post I've pointed out how depauperate Native Americans are not because this is news, anyone who researchers the massive die offs that occurred with the arrival of Europeans in the 16th century knows that the homogeneity of native peoples on these loci was fatal. Rather, I want to emphasize that there is a strong drive toward maintaining diversity on the MHC loci, and only something like a population bottleneck can expunge this variation (selection maintains it, but it can be swamped out by drift). The fact that the Native Americans remained homogenous implies that they had no new genetic inputs. In relation to the "two wave" theory, that is, there were ancient peoples who predate the current Native Americans that resembled Australian Aboriginals and Melanesians (or, they were "unspecialized moderns"), I believe that the HLA diversity is just too low to fit into this model.
The invaders would have to have zero interbreeding to not diversify their HLA pool
, diversity is selected for, so even if the interbreeding was minor one would assume that the frequency dependent selection would favor new alleles. So that's it.