chilies are smoked jalapeno
Chipotles date back to a region that is now northern Mexico City, prior to the Aztec civilization. It is conjecture that the Aztecs smoked the chilies because the thick, fleshy jalapeno was difficult to dry and prone to rot. The Aztecs used the same "smoke drying" process for the chilies as they used for drying meats. This smoking allowed the chilies to be stored for a substantial period of time.
Today chipotles are used widely throughout Mexico as well as in the United States. Quite popular in the South Western U.S. and California, the chipotle measures between 5,000 and 10,000 Shu's on the Scoville scale.