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It has been estimated that much of the Indian population (as much as 90%) were wiped out by European diseases. The native population never had immunity to diseases such as mumps, measles, or small pox, and these diseases proved deadly to the native Americans.
The Aztecs originally defeated Cortez and his Indian allies on June 1, 1520. However, after interacting with the Spanish, the Aztecs experienced a series of devastating plagues. These plagues severely weakened the Aztecs, and the next spring, the Spanish and their allies once again attacked Tenochtitlan. This time defeating the Aztecs and destroying their capital city.
By the time the Pilgrims landed at Plymouth in the 17th century, the Wampanoag had already been ravaged by small pox. The original Plymouth colony was setup in an abandoned Indian village. There were unburied skeletons around. The weakened state of the local Indian population may have been one of the reasons that the English were able to settle New England.
I don’t believe that most of this devastation was done on purpose, but was simply the result of the natural transmission of disease. By the time of Colonel Henry Bouquet in the 18th century, the devastation had already occurred. it is likely that those Indians who remained by the 18th century were about as immune to small pox as the Europeans. Using blankets to infect the Indians would not have the devastating effect he would have hoped, and certainly could have easily backfired onto the colonists themselves.
The big question is why was this such a one-way transmission? Why didn’t the Europeans get sick and wiped out from native American diseases? Why was there no small pox American equivalent?
Jarad Diamond proposes a solution in Guns, Germs, and Steel on why the Europeans were the conquerers and not the Aztecs, and why diseases wiped out the native Americans, but not the Europeans.
Most of the devastating diseases were originally animal diseases. The Europeans had cows, pigs, chickens, horses, goats, and all sorts of domesticated animals. These diseases had previously revenged the Eurasian populations and the population that was left were capable of defending themselves from these diseases.
The native Americans didn’t have this wide spread animal domestication. The few animals that were domesticated (such as Llamas) lived in the fields while many Europeans would share their living quarters with their animals during cold winters. Thus, the Europeans have learned to live with these devastating diseases, but the native American populations never did.