Why were the natives exterminated in some regions, ut not in others?

Recent comments raise a new question:
Why were the East-Coast North American Indians, sitting on pretty good land less advanced than the Mexicans?

North American natives had very little in the way of useful indigenous crops that could be domesticated. Most of the crops associated with the Eastern Agricultural Complex were abandoned after Mesoamerican crops spread that far north - Today many of them are considered weeds (like sumpweed, pigweed). They're characterized as having small yields that are very labor-intensive to harvest and some of them are even major allergens. The only ones that are still cultivated to any significant degree today are sunflowers, squashes, and gourds (though the latter two were also domesticated elsewhere as well, leaving sunflowers as the only major contribution).

Wild rice has also been long been cultivated around the Great Lakes region, but it has a pretty limited range from what I understand. There's also a variety of indigenous plants that are widely-cultivated today (maple, cranberries, blueberries, Concord grapes, Jerusalem artichokes, pecans, black walnuts, mesquite pods, etc) but they're not enough to power large populations of people by themselves.

Most of the productive food crops in the New World that could support large populations originated south of the United States and had to spread north over many different climate regions (desert, plains, mountains, woodlands, etc), which slowed their dispersion and crippled the development of North American native civilization.
 
Recent comments raise a new question:
Why were the East-Coast North American Indians, sitting on pretty good land less advanced than the Mexicans?

Because the technological level was lower than that in Mexico, while people relative to land were also rather thinner on the ground. Even the largest estimates of pre-Columbian population don't have an extremely dense population north of the Rio, while for that matter US demographics has an enormous number of people on both coasts, but very few (comparatively) in the interior.
 
In the Americas the Aztecs, Incas and Maya had a high level of techology the Aztecs nearly beating Cortez in fact the Spaniards largely won through alliances with other groups who were opposed to the Aztecs and Incas. In Patagonia a stone age culture was largely wiped out. A lot of the Indian nations in North America were hunting communities.

Umm...the Aztecs were in the Stone Age technologically. They had clubs and obsidian weapons. The Incas were only in the Bronze Age, which isn't that much more impressive when you consider that a bronze sword versus a steel sword is no contest at all. No indigenous American civilization that I'm aware of ever advanced to the Iron Age. And you seem to be ignoring the fact that Patagonian peoples remained independent for centuries, whereas Mesoamericans and Andeans, while still alive today, were institutionally subjected to Spanish rule very soon after the arrival of the Europeans. It's much harder to subjugate a nomadic or semi-nomadic people and a whole lot easier to control sedentary populations.
 
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