Abstract
Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible.
Highlights
Population genetic studies on modern-day Native American populations have described the presence of five haplogroups, termed A, B, C, D and X [1,2,3]
Native American populations can be distinguished from their East Siberian source populations by exhibiting distinct sub-haplogroups, which can only be found in the Americas
Optimization of the multiplex protocol The AmericaPlex26 assay was initially tested with default concentrations of 0.017 mM for each primer (3 mL of 25 mM stock) and 0.015 mM for each Single Base Extension (SBE) primer (3 mL of 50 mM stock) to assess the generic efficiency of primers or probes when used in the multiplex assay
Summary
Population genetic studies on modern-day Native American populations have described the presence of five haplogroups (hgs), termed A, B, C, D and X [1,2,3]. These five hgs are shared with East Asian populations and support an entry route to the Americas via the Bering landmass. Native American populations can be distinguished from their East Siberian source populations by exhibiting distinct sub-haplogroups (sub-hgs), which can only be found in the Americas. The low genetic variation found in modern Native American groups is believed to be due to either population bottlenecks or genetic drift [8,9]
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