A great introduction to the evidence of widespread pre-Columbian civilizations in North Central and South America is 1491 by Charles C. Mann.

You can also Google/Bing 1491 and read up on the general topic, as a popular science author Mann has been published everywhere including Science and The Atlantic Monthly. Its not Mann's theory at stake, he reports in an accessible way on the findings of numerous archaeologists anthropologists and other scientific types. Most of the science has been distilled down to what they can agree to, which is fascinating. 1491 is full of revelations and insights, which like most good science is bound and intended to be revised by additional good science to come. Check it out, you'll love it.

I think the current theory on the diseases that decimated most of the American societies at first contact with Euros was that it was mostly smallpox, although it included almost anything the early Euros brought along even those they didn't understand - diphtheria, typhus, influenza and smallpox and other pox were all detected at epidemic levels in early 1500s Hispaniola and elsewhere in the Americas. Records documented extreme fatalities among natives, wiping them out. Remember also, the Euros brought new animal species that carried diseases with little if any resistance among natives. They didn't have any immune resistance, so they were wiped out by things the Euros were mostly immune to and lived with for generations. Diseases spread far in advance of the march of the De Soto and the explorations of others. This accounts for the largely vacant park-like atmosphere early North American settlers and explorers observed in the early 1600s but which was quite grown over by the time of greater settlement.

The debate of how many natives and civilizations occupied the Americas goes on, last I heard as many as 90 to 115 million, which would out pace Europe by a bit, although this number continues to be revised and debated. At least 25-30 million in the Mexican highlands, that's a lock. In general though, with additional discoveries of advanced societies in South and Central America, the range of estimates goes up, not down. Fascinating stuff!

Related to this is the whole theory, when were the Americas first settled. Most scientists feel that it was by the Clovis people about ~12,000 years ago. Recent discoveries in caves in Oregon however have pushed that back to at least 13,000 (and additional archaeological evidence in Chile etc), an important difference as it would point to a source other than the land bridge that wasn't there for entry across what's now Canada. So natives came from someplace else, TBD. As is its function, science resists new evidence and supports the Clovis findings until they are superseded. There should be no holy cows in science, although predictably there will be scientists who can't keep from protecting a lifetime of theory and work - their life's work. I think we'll see a whole new theory of American population in 20 years or so, created by folks looking for evidence in places we never thought of.

1491 is one of the better books of I've ever read - its right up there with revelations about plate tectonics in the 1970-80s (who knew) and hot blooded dinosaurs around the same time. It goes to show you never knew everything about what went on before or what goes on around you.