Fig. 3: aProportion and source of Native American admixture in Rapanui.

a, ADMIXTURE-estimated proportions assuming K = 5 and K = 6 ancestry components. For K = 5, we considered five reference populations (African (Yoruba), European (CEU), Asian (Japan), Native American (Bolivia and Totonac) and Near Oceanian (New Guinea Highlands)). To minimize the effect of strong drift in Remote Oceanians (Fijians and Polynesians), we ran ADMIXTURE separately for each Remote Oceanian (n = 78), including the Ancient Rapanui (n = 15), present-day Rapanui (n = 8) and the Ancient Polynesians from an unknown island (n = 2). For K = 6, we included all Fijians and present-day Polynesians (excluding present-day Rapanui) in all runs. Wider bars represent ancient individuals (pseudohaploid calls). b, D-statistics testing for Native American and European admixture in ancient and present-day Rapanui and the two Ancient Polynesians from an unknown island. Totonac represent Native American ancestry and Utah residents (CEU) represent European ancestry. Points represent D-statistics. Error bars represent about 3.3 standard errors (P ≈ 0.001 in a Z test; 755,094 SNPs in 5-Mb blocks). Under each axis, we indicate the pair of populations with excess allele sharing, depending on the sign of D. To maximize the test sensitivity, we considered imputed diploid genotypes for the ancient individuals (Supplementary Information section 5). c, f₃-statistics showing the genetic affinities between the Native American tracts in Ancient Rapanui and ancient and present-day Native American populations. For each Ancient Rapanui, we masked Polynesian ancestry tracts and pooled Native American ancestry tracts to estimate f₃-statistics. Lighter colours represent greater shared drift between a Native American population (X) and the Ancient Rapanui. We label the five Native American populations that lead to the largest f₃-statistics. Point shapes represent the age of Native American populations in years before present. Points with a darker outline correspond to point estimates overlapping with the 95% confidence interval of the highest f₃-statistic (illustrated in Extended Data Fig. 2).