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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:
On page 25 of of Hale, House and Related Families by Jacobus and Waterman (https://archive.org/details/halehouserelated00jaco/page/24/mode/2up), it says, ""Bennezer Hale of Wethersfield conveyed 4 Nov 1732 to 'my well beloved son Nath'll Hale' of Wethersfield, his house lot of one acre and one rod, with his dwelling house, barn and fruit trees, together with two acres of meadow, to take effect 'Immediately upon & after my Decease.'" From that, I would say that Nathaniel is the son of Bennezer (Ebenezer), not Thomas.