g. [8] and [9]). The most comprehensive study of indigenous South American Y chromosomes thus far surveyed 1011 individuals and found that while most of them belonged to haplogroup Q as expected, 14 individuals from two nearby populations in Ecuador carried haplogroup C3*(xC3a-f) chromosomes (henceforth C3*), with this haplogroup reaching 26% frequency in the Kichwa sample and 7.5% in the Waorani [10]. The estimated TMRCA for the combined Ecuadorian C3* chromosomes was 5.0–6.2 Kya. The finding of this ABT-199 datasheet haplogroup in Ecuador was surprising because C3* is otherwise unreported from the

Americas (apart from one example in Alaska), but is widespread and common in East Asia. Three scenarios might explain the presence of C3* Smad pathway chromosomes

at a mean frequency of 17% in these two Ecuadorian populations [10], Fig. 1. First, they might represent recent admixture with East Asians during the last few generations. This possibility was considered unlikely because the Waorani discouraged contact with outsiders using extreme ferocity until peaceful links were established in 1958, and known male ancestors (fathers, grandfathers) of C3* carriers were born before this date. Second, C3* might have been another founding lineage entering the Americas 15–20 Kya, and have drifted down to undetected levels in all populations examined except the Ecuadorians. This was also considered unlikely because the populations of North and Central America have in general experience less drift and retained more diversity than those in South America [2], and so it would be surprising to lose C3* from North/Central Americans but not South Americans. Third, Benzatropine C3* could have been introduced into Ecuador from East Asia at some intermediate date by a direct route that bypassed North America. In support of this third scenario, archaeologists have identified similarities in pottery between the middle Jōmon culture of Kyushu (Japan) and the Valdivia culture of coastal Ecuador dating to 5.3–6.4 Kya; notably, like

the C3* chromosomes, such a ceramic complex in the Americas was unique to Ecuador and was not reported from North or Central America or elsewhere from South America [11]. We refer to these three scenarios as ‘recent admixture’, ‘founder plus drift’ and ‘ancient admixture’, respectively. In this follow-up study, we set out to revisit the three hypotheses for the origin of the C3* Y chromosomes in Ecuador. One possibility would be to sequence the Ecuadorian C3* Y chromosomes, and compare them with existing or additional East Asian C3* chromosome sequences, to determine the divergence time. However, the limited quantity and quality of DNA available did not allow this. We therefore followed another possibility, using genome-wide autosomal SNP genotyping.