title: New native South American Y chromosome lineages.
abstract: Many single-nucleotide polymorphisms (SNPs) in the non-recombining region of the human Y chromosome have been described in the last decade. High-coverage sequencing has helped to characterize new SNPs, which has in turn increased the level of detail in paternal phylogenies. However, these paternal lineages still provide insufficient information on population history and demography, especially for Native Americans. The present study aimed to identify informative paternal sublineages derived from the main founder lineage of the Americas-haplogroup Q-L54-in a sample of 1841 native South Americans. For this purpose, we used a Y-chromosomal genotyping multiplex platform and conventional genotyping methods to validate 34 new SNPs that were identified in the present study by sequencing, together with many Y-SNPs previously described in the literature. We updated the haplogroup Q phylogeny and identified two new Q-M3 and three new Q-L54*(xM3) sublineages defined by five informative SNPs, designated SA04, SA05, SA02, SA03 and SA29. Within the Q-M3, sublineage Q-SA04 was mostly found in individuals from ethnic groups belonging to the Tukanoan linguistic family in the northwest Amazon, whereas sublineage Q-SA05 was found in Peruvian and Bolivian Amazon ethnic groups. Within Q-L54*, the derived sublineages Q-SA03 and Q-SA02 were exclusively found among Coyaima individuals (Cariban linguistic family) from Colombia, while Q-SA29 was found only in Maxacali individuals (Jean linguistic family) from southeast Brazil. Furthermore, we validated the usefulness of several published SNPs among indigenous South Americans. This new Y chromosome haplogroup Q phylogeny offers an informative paternal genealogy to investigate the pre-Columbian history of South America.Journal of Human Genetics advance online publication, 31 March 2016; doi:10.1038/jhg.2016.26.
authors.affiliation: Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Marilza S
authors.initials: MS
authors.lastname: Jota
authors.affiliation: Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Daniela R
authors.initials: DR
authors.lastname: Lacerda
authors.affiliation: Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.|Instituto de Genética y Biología Molecular, Universidad San Martin de Porres, Lima, Peru.
authors.forename: José R
authors.initials: JR
authors.lastname: Sandoval
authors.affiliation: Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Pedro Paulo R
authors.initials: PP
authors.lastname: Vieira
authors.affiliation: Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Dominique
authors.initials: D
authors.lastname: Ohasi
authors.affiliation: Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: José E
authors.initials: JE
authors.lastname: Santos-Júnior
authors.affiliation: Instituto de Genética y Biología Molecular, Universidad San Martin de Porres, Lima, Peru.
authors.forename: Oscar
authors.initials: O
authors.lastname: Acosta
authors.affiliation: Facultad de Bioquímica, Universidad Mayor de San Andrés, La Paz, Bolivia.
authors.forename: Cinthia
authors.initials: C
authors.lastname: Cuellar
authors.affiliation: Facultad de Bioquímica, Universidad Mayor de San Andrés, La Paz, Bolivia.
authors.forename: Susana
authors.initials: S
authors.lastname: Revollo
authors.affiliation: Instituto de Investigaciones Biomédicas, Universidad de las Americas, Quito, Ecuador.
authors.forename: Cesar
authors.initials: C
authors.lastname: Paz-Y-Miño
authors.affiliation: Instituto de Genética y Biología Molecular, Universidad San Martin de Porres, Lima, Peru.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Fujita
authors.affiliation: Universidad del Tolima, Ibagué, Colombia.
authors.forename: Gustavo A
authors.initials: GA
authors.lastname: Vallejo
authors.affiliation: Department of Anthropology, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Theodore G
authors.initials: TG
authors.lastname: Schurr
authors.affiliation: Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Eduardo M
authors.initials: EM
authors.lastname: Tarazona-Santos
authors.affiliation: Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Sergio Dj
authors.initials: SDj
authors.lastname: Pena
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Qasim
authors.initials: Q
authors.lastname: Ayub
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
authors.affiliation: Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Fabrício R
authors.initials: FR
authors.lastname: Santos
mesh_terms: D000483:Alleles; D041322:Chromosomes, Human, Y; D019143:Evolution, Molecular; D005828:Genetics, Population; D005838:Genotype; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007199:Indians, South American / Q000235:genetics*; D018895:Microsatellite Repeats; D009154:Mutation; D020641:Polymorphism, Single Nucleotide