What fundamental differences were readily apparent when comparing England's New England, Middle and Southern colonies?

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Although formed under the umbrella of England's North American colonies, these three regions developed into very different parts of the country, foreshadowing, in some respects, the differences that would develop as the nation expanded west later on, not to mention the differences that would ultimately lead to a war between the states.  The New England colonies were first established by the Pilgrims, but became primarily Puritan in religious background, and although the popular notion is that the Puritans came to practice religious freedom, more accurately it might be said that they came to practice their religion freely, but without a great deal of patience for dissenters.  Massachusetts, of course, was the setting for the horrific Salem witchcraft trials, and the Puritans were also the galvanizing force for the formation of Rhode Island, which was founded by Roger Williams after they threw him out of Massachusetts Bay, and then Thomas Hooker, who founded Connecticut after deciding he could no longer deal with church and government politics as they were being handled.  New England was a difficult place to farm, given the thin rocky soil, but fishing thrived, and colonists were generally able to trade with the Mother Country for needed item. 

The Middle Colonies, known also as the "Breadbasket Colonies" are usually associated with people like William Penn, who founded Pennsylvania on the Quaker model of religious freedom.  The term "breadbasket" refers to the grains that grew plentifully there, and politics and religion both tended toward a more liberal philosophical bent than the uptight New Englanders. 

The Southern colonies were always most closely tied to, and loyal to England, a sentiment that became especially obvious during the American Revolution.  Southerners, who embraced what they perceived to be the "genteel" lifestyle of affluent Europeans had a particularly difficult time letting go of their tea when friction with the mother country became problematic up North.  The plantation system developed in the Deep South with the success of cash crops like rice, indigo, tobacco, and of course, what would ultimately become known as "King Cotton", and as slavery was dying out in New England and the Middle Colonies, it would begin to flourish in the years leading up to the Civil War.