Nathaniel had at least 2 wives. Mary Ann Bruce who died around 1814 in Newberry, South Carolina and Ann--?? Inman, widow of Joshua Inman.
Sources
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DNA Connections
It may be possible to confirm family relationships with Nathaniel by comparing test results with other carriers of his Y-chromosome or his mother's mitochondrial DNA.
However, there are no known yDNA or mtDNA test-takers in his direct paternal or maternal line.
It is likely that these autosomal DNA test-takers will share some percentage of DNA with Nathaniel:
Somehow there is a duplicate name for the wife of Nathaniel Thomas. The Mary Ann Bruce and the Mary Ann Bruce Thomas is the same lady. There was only one marriage between Nathaniel Thomas and Mary Ann Bruce Thomas.
It's been suggested that his parents have yet to be proven conclusively.