James Horn is the vice president for research and historical interpretation at the Colonial Williamsburg Foundation and one of the scholars involved in the recent discovery of Jane’s remains. He is the author of “A Land as God Made It: Jamestown and the Birth of America.”

IN the bitterly cold winter of 1607, Capt. John Smith was captured by a large war party of Pamunkey Indians on the banks of the Chickahominy River, in what is now Virginia. Smith was led by his captors to a nearby hunting village, where he was taken to a long house and given enough venison and bread to feed 20 men. The food he did not eat was placed in baskets and tied on a pole over his head. About midnight they set the food before him once more and then in the morning brought as much food again, which made the fearful captain, later describing his capture in the third person, “think they would fat him to eat him.”

That Smith wondered whether the Indians were cannibals is unsurprising — it was part of the received wisdom among colonists that Indians they encountered might be ferocious wild men, marked above all by their predilection for human flesh. And while that received wisdom was utterly wrong, popular history has long portrayed the early colonial era as a meeting of civilized Europeans and savage, if noble, Indians.

The discovery, announced this week, of the cannibalized remains of a young settler at Jamestown greatly complicates that story. It reminds us that the first European settlements were no Eden, and that the initial contact of peoples in the New World — native people, Europeans and then, very soon, Africans — was fraught from the first....