Gen. Allen is slated to replace Adm. Jim Stavridis in the spring, and Marine Gen. Joseph Dunford, the assistant Marine commandant, would take the top Afghanistan job. The changes must be confirmed by the Senate.
Mr. Obama said in a statement that Gen. Allen has served with distinction as U.S. commander in Afghanistan, helping the country through a critical period as the U.S. prepares to withdraw its troops, starting in mid-2013.
Gen. Allen is expected to provide recommendations by the end of the year on the pace and number of U.S. troops leaving Afghanistan. Gen. Dunford has been assistant commandant since October 2010. Gen. Allen took over the Afghanistan job in July 2011.
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