The Jacobites believed that being King was a God given right and passed on through heredity and were opposed to parliamentary interference with the line of succession to the throne. They saw this interference as being illegal. People were expected to swear allegiance to their King and his authority. Jacobites wouldn't swear allegiance since William was not a direct descendant of James, while Charles Stuart (Bonnie Prince Charlie) was. Hoping to reinstate the Stuart regime, the Jacobites rose in rebellion on a number of occasions, notably in 1715 and in 1745.
Beginning in 1716, Jacobites were rounded up, imprisoned and subsequently transported to the Americas. Approximately 1,500 Jacobite prisoners were exiled to the American Plantations. Since Jacobites were charged with Treason they were tried before the High Court. Documents pertaining to the Jacobites, for genealogical purposes, are Royal Warrants, Letters, and a variety of letters.
While there are some records contained within the High Court records at the National Archives in Scotland, the primary repository is the National Archives in London.
There are also registers of ships that were used for transportation. PDF listings of Jacobite prisoners for various regions of Scotland can be found here: http://www.jacobites.net/lists.html
Hugh Tornabene, a volunteer for the Immigrant Ships Transcribers Guild has uncovered the
passenger lists for the ships that were used to transport the Jacobites. He has transcribed the lists for the 10 ships that arrived in the Americas.
There are another 8 ships that went to the Caribbean (Barbados and the Leeward Islands). Here is the website to view the transcriptions of the 10 ships (there are 13 lists, with two of the ships having made the voyage more than once) that Hugh has transcribed: