The idea that an avalanche of European and African pathogens would select for Amerindian alleles makes no sense 
 
Maybe the Amerindian genome was too alien for the European and African pathogens to infect? At least with the ancestors of the Puerto Ricans, anyway.

Since auto-immune disorders are often more common in blacks than in whites, it is possible that eumelanin is a risk factor for auto-immune diseases. Therefore, lighter skin may have been favored because those people would have been less likely to suffer from auto-immune problems.

Consider that agriculture became normative in Sweden about 5,000 years ago, 5,000 years after it was the dominant mode of production in the eastern Mediterranean 
 
Over 10,000 years ago, everyone in the world lived the hunter-gatherer lifestyle - even the people of the eastern Mediterranean - so it is likely that most humans would do well on such a Paleolithic diet. 
 
Modern-day hunter-gatherers exploit wild starch sources 
 
But that may be because they don't have alternative food sources. 
 
Note that Sweden is also the epicenter lactose tolerance (thought that seems to have become the norm after agriculture arrived on the scene), suggesting a priori expectation of localized adaptations 
 
And yet the research shows that the Swedes do better without dairy.

Mosquitoes proliferate in wet northern lands, like Minnesota and Alaska 
 
But do the mosquitos in those areas carry diseases that are harmful to humans?

How do the researchers know that any of the descendants of the Etruscans survived into modern times?