title: AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas.
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.
authors.affiliation: Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Coutinho
authors.affiliation: Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: Guido
authors.initials: G
authors.lastname: Valverde
authors.affiliation: Historical Anthropology and Human Ecology, Johann-Friedrich-Blumenbach Department of Zoology and Anthropology, University Goettingen, Goettingen, Germany; Department of Anthropology, University of California Santa Cruz, Santa Cruz, California, United States of America.
authors.forename: Lars
authors.initials: L
authors.lastname: Fehren-Schmitz
authors.affiliation: Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: Alan
authors.initials: A
authors.lastname: Cooper
authors.affiliation: Museo de Sitio Huaca Pucllana, Miraflores, Lima, Perú
authors.forename: Maria Inés
authors.initials: MI
authors.lastname: Barreto Romero
authors.affiliation: Museo de Sitio Huaca Pucllana, Miraflores, Lima, Perú
authors.forename: Isabel Flores
authors.initials: IF
authors.lastname: Espinoza
authors.affiliation: Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: Bastien
authors.initials: B
authors.lastname: Llamas
authors.affiliation: Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Haak
mesh_terms: D018703:Founder Effect; D050259:Genes, Mitochondrial; D005826:Genetics, Medical; D054629:Genome, Mitochondrial; D060005:Genotyping Techniques / Q000379:methods*; D006239:Haplotypes; D006801:Humans; D007199:Indians, South American / Q000235:genetics*; D060885:Multiplex Polymerase Chain Reaction; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity