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When Jacob blessed Joseph's two sons and made them part of the twelve-tribe confederacy in place of Joseph, why is it that the number of tribes does not now add up to thirteen?
The answer to this question will be worked out in the history of Israel. But in general it involved the curse of Simeon and Levi being dispersed among the tribes of Judah and Israel (Gen 48:5-7) for their savagery when they killed all the inhabitants of the small town of Shechem as revenge for the rape of their sister Dinah (Gen 34), even after the men of the town had agreed to be circumcised.
Depending on the period of history, Simeon tended to be absorbed into Judah both in territory and name, while Levi, which never was assigned any landed territory, turned the curse into a means of ministering to all twelve tribes. Thus Joseph's two sons, Ephraim and Manasseh, take not only Joseph's place in the list of the twelve, but also either that of Levi, or at other times, when Levi is also listed, the place of Simeon.