Hierarchical Y-SNP assay to study the hidden diversity and phylogenetic relationship of native populations in South America. Forensic Sci Int Genet. 2011 Mar;5(2):100-4.
Studying the Y chromosomes of indigenous tribes of Ecuador revealed a lack of strategic SNP assays to examine the substructure of South American native populations. In most studies dealing with South American samples so far only the most common Y-SNP M3 of haplogroup Q was analyzed, because this is known to define a founder group in South America. Studies of SNPs ancestral to Q-M3 (Q1a3a) to confirm the results or the typing of Q subclades have often been neglected. For this reason we developed a SNaPshot assay, which allows first for a hierarchical testing of all main haplogroups occurring in South American populations and second for a detailed analysis of haplogroups Q and C thought having ancient Asian descent. We selected 16 SNPs from the YCC haplogroup tree and established two multiplexes. The first multiplex ("SA Major") includes 12 Y-SNPs defining the most frequent haplogroups occurring in South America (M42, M207, M242, M168, M3, M145, M174, M213, RPS4Y711, M45, P170, and M9). The second multiplex ("SA SpecQ") contains Y-SNPs of haplogroup Q, especially of the subclade Q-M3 (M19, M194, P292, M3, and M199). Within our Ecuadorian sample, haplogroup Q-M3 (xM19, M194, P292, and M199) was predominant, but we also found haplogroup E and R, which can be attributed to recent admixture. Moreover, we found four out of 65 samples, which were tested to be haplogroup C3* (C-M217) the modal haplogroup in Mongolians and widespread in indigenous populations of the Russian Far East as well as in Eastern Asia. This haplogroup is not known to be the result of recent admixture and has been found only one time before in South America. Since haplogroup C occurs in Asia and in North America (C3b or C-P39), we assume that these C-lineages are ancient as well. Therefore, we established a third multiplex ("SA SpecC"), which allows the further subtyping of haplogroup C, mainly of subclade C3 defined by the Y-SNP M217 (M407, M48, P53.1, M217, P62, RPS4Y711, M93, M86, and P39). Altogether, these three multiplexes cover the most frequent haplogroups in South America and allow for a maximal resolution of the Y-chromosomal SNP diversity in Amerindian population samples.
Mitochondrial diversity in Amerindian Kichwa and Mestizo populations from Ecuador. Int J Legal Med. 2012 Mar;126(2):299-302.
This study presents mitochondrial DNA (mtDNA) data from 107 unrelated individuals from two of the major ethnic groups in Ecuador: Amerindian Kichwas (n = 65) and Mestizos (n = 42). We characterized the diversity of the matrilineal lineages of these Ecuadorian groups by analyzing the entire mtDNA control region. Different patterns of diversity were observed in the two groups as result of the unique historical and demographic events which have occurred in each population. Higher genetic diversity values were obtained for the Mestizo group than for the Amerindian group. Interestingly, only Native American lineages were detected in the two population samples, but with differences in the haplogroup distribution: Kichwa (A, 49%; B, 3%; C, 8%; and D, 40%) and Mestizo (A, 33%; B, 33%; C, 10%; and D, 24%). Analysis of the complete mtDNA control region proved to be useful to increase the discrimination power between individuals who showed common haplotypes in HVSI and HVSII segments; and added valuable information to the phylogenetic interpretation of mtDNA haplotypes.