I notice that the media has started reporting that scientific genealogy has now established to a great extent the likely origin of the Melungeons. You can find the original paper online. The gist is that the Melungeons seem to exhibit a large proportion of Sub-Saharan African origin Y chromosomal lineages, and European mtDNA lineages. The lack of Amerindian ancestry in the generality is also notable. But, this does not entail that the origins of the Melungeons is from the union of free black males and white women necessarily, at least on purely genetic grounds (the paper itself has a wealth of genealogical evidence pointing to this likelihood). The Melungeons are an endogamous community, and so have a low effective population. African or Amerindian mtDNA lineages may simply have been lost by chance over the past few hundred years.
But I point to the story of the Melungeons because it is a nice counter-point to that of the Hispanos of the Southwest. This is a case where historians and anthropologists who made the case for the false construction of a mythical Middle Eastern ancestry for the Melungeons as a way in which to escape the bounds of the American racial caste system were correct. In contrast, this model was not totally supported for the Hispanos, who do seem to have some grounds to argue for genuine connection to Jewishness. In other words, genetic evidence is an important complement to other methodologies.