the autosomal data, estimates of the mean time since admixture in the 13 Mestizo populations range between ∼6–14 generations (Table S3), in agreement with independent estimates made in some of the populations examined here [14],[24] and consistent with the notion that most admixture in these populations is likely to have occurred in colonial times[16]. These age estimates are obtained based on the inferred mean frequency of transitions in ancestry along the genome, under the assumption of a single past admixture event[25]. These estimates should be viewed with caution, as it is doubtful that such as model applies in the populations we examined and the added complication of a non-negligible three-way admixture in some of these populations (Figure 2). The observed variation in the estimated age of admixture in different populations is in fact likely to be influenced by variable levels of historical gene flow in different regions[26]: the relatively more isolated populations (e.g. CVCR)[27],[28] tend to show older age estimates, while populations in the vicinity of large local native populations (e.g. Salta, in Northern Argentina)[29] or near areas of recent European immigration (e.g. RGS, in Southern Brazil)[30] show younger estimates, consistent with more recent gene flow and possibly ongoing admixture.
