Given that the above analyses provide an inference of temporal genetic affinity in the Andes from roughly 4000 years BP, and perhaps extending to 7000 years, we tested for strict continuity. Here, continuity is defined as a genetic affinity between two temporal populations without external gene flow. We performed the test for continuity using the method described in Schraiber (49). We find that when the Rio Uncallane individuals are tested against the 25 modern Aymara, the test fails to show strict continuity (230,649 SNPs: t1 = 0.00443, t2 = 0.04189; log LRT P = −∞). However, this test might be inappropriate for the region, since it assumes no outside gene flow between populations. Several civilizations rose and fell in the region between the two time periods represented by the ancient and modern populations. These civilizations, such as the Wari and Incas, built elaborate trade networks throughout the Andes, and it is likely that the ancestral populations leading to the Aymara experienced regional admixture before European contact.

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