The paper that most clearly articulated the Population Y signal and brought it to broad scientific attention was published in Nature in 2015, by Pontus Skoglund and a large team of co-authors including David Reich, Eske Willerslev, and others.

The paper analyzed genome-wide data from a large number of Native American populations, both ancient and modern, and applied a range of statistical tests to characterize the genetic relationships among them.

The paper’s central finding regarding American settlement was that all Native American populations shared a common founding ancestry — consistent with the Beringian dispersal model — but that the data from certain South American populations and certain ancient samples showed an additional signal that could not be explained by that founding ancestry alone.

This additional signal was named Population Y — using Y not to indicate the male Y chromosome but as a variable name in the statistical model, the unknown element whose characteristics needed to be determined.