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Since you know when and where Thomas died, get a copy of his death certificate. It should show the names and birth locations of his parents.
J.P. may have married again, and Ophelia Hay, who d 1914, might be a second wife. J.P. would have needed a woman to raise the young Thomas. Etta could be a sister to Thomas, and married someone named Shaw. Could be a dau of Margaret, or even Ophelia, if she is second wife.
I would check Soundex for TN 1880 census for J.P. If he remarried, second wife would most likely be on that census.