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The Kerrs continued to oppose one another during the 16th century and on the death of James IV, when his widow Margaret Tudor remarried the Douglas Earl of Angus, the Kers of Cessford supported the English Queen-mother and the Kerrs of Ferniehurst the young King, James V. Cessford was forced to flee to England when Angus was exiled only to return on the death of James V in 1542 when Sir John Kerr of Ferniehurst lost his castle. The castle was recaptured in 1549 and the English who had repeatedly raped the Kerr women, rather than being killed, were captured and horribly tortured. The rivalry continued when Sir Thomas of Ferniehurst fought for Mary Queen of Scots at Langside and Sir Walter Cessford on the side of James VI. The feud was resolved on the political level by the Union of the Crown and by the marriage of Anne Ker of Cessford to William Kerr of Ferniehurst.
From this couple descend the Earls and Marquesses of Lothian. Sir Robert Cessford, son of Sir Walter mentioned above was created Lord Roxburgh in 1637. By marraige to the heiress of the Earl of Roxburgh, Sir William Drummond became 2nd Earl of Roxburgh and assumed the name of Kerr. His descendant, John, 5th Earl was created Duke of Roxburgh. Following the failure of the line with the death of John, 3rd Duke of Roxburgh the title passed to Sir James Innes of that Ilk who was 25th Chief of the Innes who adopted the name of Kerr. The chief of the Clan Kerr is the Marquess of Lothian and the Duke of Roxburgh is the Chief of the Innes.