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Although I am a probable Biology major and my biology class this past semester was heavily about population genetics.
Let me quickly address your point about ethnic heritage - that was a poor choice of words on my part. What I meant was the whole idea of genetically pure heritages for various "nations" has been shown very much to be false.
Mitochondrial DNA studies and Y-chromosome studies all show that there has been tremendous gene flow throughout the human population, at least of the Old World. The key factor in human populations is isolation-by-distance. Yes, someone from England in 1500 would not have interbred with someone from China. But over the course of generations, there has been a great deal of gene flow through neighboring populations. That is illustrated by studies of DNA, particularly mitochondrial DNA and Y-chromosomal DNA, which illustrate patterns of migration and gene flow. And particularly when you're talking about Europe alone, the idea of a single mutation spreading through the population over 400 generations is VERY credible. It doesn't need to be a lot of people - just some. Even if most people never left the village, a small group of people doing so would result in a high degree of gene flow in populations. As for you cats and dogs example, cats and dogs aren't a good example because domestic cats and dogs are not subdivided into multiple species - they're all classified as different breeds selected by human beings. As for birds - try to mate a South American bird with an African bird. Most likely, they will not be able to produce viable offspring, or any offspring at all.
Now, with the New World there of course was a long time when there was little contact, but they've been in contact with Old-World humans for centuries by now. Mathematical models indicate that the most recent common ancestor of all (or at least the vast majority) of human beings lived between 3000 BC and 1000 AD. This doesn't of course mean that that's the only human line - just that that individual line is in all human beings. Obviously, as you say, that's more speculative. But most population biologists find that credible.
I don't think the scientists are claiming that this is the only mutation affecting skin color. And as they say, this only explains about 1/3 the shift. The point is, however, that there's no reason it couldn't be. But even with just a few individuals from neighboring communities exchanging genes and interbreeding, gene flow is strong. And considering that the founder populations of most Europeans was probably a contingent of only 1,000 or so by most estimates, it's not at all difficult to see how a mutation that arose in one could have, over a few generations, have become widespread. Environmental pressures will play a major role in determining phenotype. But genetic factors play a role too. It simply isn't credible genetically that the same phenotype would arise in multiple individuals due to the same or even different mutations. Most likely, if different genes were altered, different phenotypes would result.
I don't think anybody is claiming that we know exactly what happened with skin color. What I'm trying to get at is that you don't seem to think that a single mutational event a few hundred thousand years ago that could have spread to all Europeans. What I'm saying is that's not true - it very well could have. Mathematical and computer models illustrate how it could have happened and DNA evidence largely proves that large-scale gene flow patterns exist and have existed throughout human history.
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