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Stephen E. Hughes, Sarah Ellen Hughes, and John S. Hughes were the children of John H. Hughes (24 Aug. 1823-04 Nov. 1847) and Amanda Simpson (18 Feb. 1820-living Dec. 1890 in Madison Co. Indiana). John H. Hughes was son of Stephen Hughes (1797-1889) and Sarah Henry (1802-1839). Stephen Hughes was son of John Hughes and Sarah Scrogham.
After the death of John H. Hughes in 1847, Amanda moved in with her father-in-law. He had had two other marriages since Sarah Henry died, both ending in divorce. His two youngest sons by Sarah, William and Hamilton, were afflicted "with fits," so having Amanda come run the household was a benefit to them both. In 1852, Amanda Simpson Hughes married Stephen Hughes; they had 3 more children: Amanda, Bellfield, and Elizabeth.
I researched this family in 2001 for a descendant of your Stephen E. Hughes' sister, Sarah Ellen who m. Moses Gant. Contact me directly for family group sheets, photo of old Stephen, misc. documentation, etc. Donna Kuhlman, email@example.com.