We further tested the presence of differential affinity of ancient Brazilian individuals to present-day Papuans, Onge and Australians, as well as the 40,000-year-old Tianyuan genome-wide data from China77 using f4 statistics of the form f4(Mbuti, Papuan/Onge/Australian/Tianyuan; Ancient Brazilian A, Ancient Brazilian B). Only the JabuticabeiraII_~2400BP group reaches significant attraction to both Onge and Papuans, and only in comparison to LapaDoSanto_9600BP (ref. 63). This suggests either that the Population Y signal is equally widespread in most tested ancient individuals from Brazil or that previously reported attractions to non-American ancestries62,77,78 are exacerbated by the use of present-day Mexican populations in comparison to ancient groups (Supplementary Data 7).
The Population Y signal related to Andamanese and Australasian populations could not be detected in the early Holocene Capelinha_10400BP individual or in the Amazonian Palmeiras Xingu_500BP individual. However, we report this signal in individuals from the southern sambaqui sites of Cabeçuda_3200BP and JabuticabeiraII_~2400BP. The latter is the only pre-colonial group exhibiting higher affinity to non-American ancestries even in direct comparison to another ancient Brazilian group (Supplementary Data 7). If confirmed, the sporadic identification of the Population Y signal in ancient individuals with different ancestries, locations and time periods across Brazil—where this signal was first described—suggests a higher probability that it derives from genetic structure in the founding Native American population65,77 than from multiple independent migrations into the Americas62,82.
https://dx.doi.org/10.1038/s41559-023-02114-9