title: Identification of new SNPs in native South American populations by resequencing the Y chromosome.
abstract: The Y-chromosomal genetic landscape of South America is relatively homogenous. The majority of native Amerindian people are assigned to haplogroup Q and only a small percentage belongs to haplogroup C. With the aim of further differentiating the major Q lineages and thus obtaining new insights into the population history of South America, two individuals, both belonging to the sub-haplogroup Q-M3, were analyzed with next-generation sequencing. Several new candidate SNPs were evaluated and four were confirmed to be new, haplogroup Q-specific, and variable. One of the new SNPs, named MG2, identifies a new sub-haplogroup downstream of Q-M3; the other three (MG11, MG13, MG15) are upstream of Q-M3 but downstream of M242, and describe branches at the same phylogenetic positions as previously known SNPs in the samples tested. These four SNPs were typed in 100 individuals belonging to haplogroup Q.
authors.affiliation: Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité - Universitätsmedizin Berlin, Germany. Electronic address: maria.geppert@charite.de.
authors.forename: M
authors.initials: M
authors.lastname: Geppert
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom.
authors.forename: Q
authors.initials: Q
authors.lastname: Ayub
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom.
authors.forename: Y
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Universidade Federal do Pará, Laboratório de Genética Humana e Médica, Belém, Pará, Brazil.
authors.forename: S
authors.initials: S
authors.lastname: Santos
authors.affiliation: Universidade Federal do Pará, Laboratório de Genética Humana e Médica, Belém, Pará, Brazil.
authors.forename: Â
authors.initials: Â
authors.lastname: Ribeiro-dos-Santos
authors.affiliation: BIOMICs Research Group, Universidad del País Vasco, Vitoria, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Baeta
authors.affiliation: BIOMICs Research Group, Universidad del País Vasco, Vitoria, Spain.
authors.forename: C
authors.initials: C
authors.lastname: Núñez
authors.affiliation: Department of Legal Medicine, University of Zaragoza, Spain.
authors.forename: B
authors.initials: B
authors.lastname: Martínez-Jarreta
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom.
authors.forename: C
authors.initials: C
authors.lastname: Tyler-Smith
authors.affiliation: Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité - Universitätsmedizin Berlin, Germany.
authors.forename: L
authors.initials: L
authors.lastname: Roewer
mesh_terms: D041322:Chromosomes, Human, Y; D006801:Humans; D007199:Indians, South American / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
keywords: Ecuador; Kichwa; NGS; South America; Y chromosome; Y-SNPs