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While growing up we were told in school that plagues, carried over by the Europeans, decimated the Native American population. We were also taught about the black plague in Europe and a few other historical epidemics.

My question is threefold.

First, what are some of the main methods that historians use to determine that an epidemic really did in fact occur?

Second, why do we believe that Europeans carried diseases to the Americas and those decimated the native population.

Third, is there a specific name for the field of study which attempts to uncover the fact that epidemics occurred in history and study them in detail?

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I don't think there is a separate "historical epidemiology" field.

Sources

Major epidemics are chronicled just like wars - written record is the main source of information. Death records - both papers (when preserved) and cemetery headstones - may provide additional statistical evidence.

For prehistorical deceases, the main sources of information are the genetic analyses of pathogens and the human immune systems. Epidemics in the modern sense did not occur because humans lived in mostly isolated communities.

Research

Recurring epidemics, like flu, are subject to intensive medical research; e.g.:

In June 2010, a team at the Mount Sinai School of Medicine reported the 2009 flu pandemic vaccine provided some cross-protection against the 1918 flu pandemic strain.

Decease transfer by colonizers

As for the Europeans carrying diseases to the Americas, you might want to take a look at Guns, Germs, and Steel.

Basically, the European conquest of America is sufficiently recent for ample written record to exist, including the famous episode when the Europeans attempted to pass smallpox-infected blankets to the Indians (the transfer of blankets was in the summer, the smallpox outbreak among the Indians - in the spring. I am not a physician, but the connection seems tenuous).

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    and don't forget bone damage as a result of some diseases, which shows in the archeological record.
    – jwenting
    Dec 27, 2013 at 12:52
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Although it doesn't comprehensively answer your question, the December 2013 issue of the BBC history magazine contains an article in which John Hatcher explores the impact of the Black Death on the Suffolk village of Walsham le Willows

The article touches on some of the ways that epidemics are studied.

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