1.22 applied to the two different datasets described in Section 2.4 above. Three different approaches were used
to search for evidence of migration into the Ecuadorian population: first, the three-population test , second, the maximum-likelihood tree approach implemented in TREEMIX v.1.1  (performed on the two datasets) considering from 0 to 12 migration events; and third, a method based on the decay of linkage disequilibrium implemented in ALDER v 1.03, which also provides an estimate of the time of admixture . We first used simulations to evaluate our power to detect recent admixture (in the last MS-275 price few generations) or more ancient admixture (∼6 Kya) as suggested in the previous study , compared with a non-admixed population established 15–20 Kya. Then we examined newly-generated data from the Ecuadorian population to determine
whether or not any admixture was detectable. For the recent admixture model, we found that we could detect ∼50% or ∼20% of Japanese ancestry in all the individuals in the 50% or 20% artificial admixed simulations, respectively. With lower proportions of admixture, there was more variation between individuals, but we identified 3–14% Japanese ancestry in all but one individual in the 10% artificial admixed simulation. We detected 1–9% of Japanese ancestry in about half of the individuals in the 5% artificial admixed simulations, and 1–2% in two individuals in the simulations of 1% artificial admixture (Fig.
2A). So we are well-powered for detecting recent admixture, selleck kinase inhibitor and detect it in some individuals from a population sample of 16 even at 1% admixture. We then simulated a scenario where the admixture had occurred 6 Kya, using the demographic parameters estimated from the linkage disequilibrium pattern as described previously , shown in Fig. 2B and Supplementary Table 2. A single pulse of migration out was set at 0%, 1%, 5% and 10%. Due to genetic drift in the relatively small population, after 6 Ky the population average level of admixture in the present-day population was much less than the starting amount. The power to detect ancient admixture at these levels therefore depends on the sensitivity to detect the reduced admixture in the present-day population. For example, if 0.1% mean population admixture can be detected in the present-day population, we have ∼80% power to detect 5% ancient admixture and ∼100% power to detect 10% ancient admixture. If, instead, we could only detect 0.5% mean admixture in the present-day population, we have ∼0 power to detect 5% ancient admixture and ∼35% power to detect 10% ancient admixture ( Fig. 2C). With these population mean levels of admixture, the admixture in different individuals in the population can vary substantially. Immediately after a pulse of 10% migration, almost all individuals in the Admixed population have >5% and >1% admixture ( Fig. 2D, middle section), as also seen in Fig. 2A.