• An Erratum to this article was published on 25 July 2016

This article has been updated

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.

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Change history

  • 31 March 2016

    This article has been corrected since Advance Online Publication, and an erratum is also printed in this issue.

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Acknowledgements

We thank Joice Pedroso, Fabiano Assunção and Sibelle T Vilaça for technical help in some experiments and analysis, and to Davidson Campos for drawing of map figures. We thank the Laboratório Multiusuário de Genômica of Universidade Federal de Minas Gerais (Brazil) for the use of the BeadXpress. We received financial support from the National Geographic Society (USA) and the National Research Council (CNPq) and Fundação de Apoio à Pesquisa de Minas Gerais (FAPEMIG) (Brazil). QA and CTS are supported by The Wellcome Trust (098051), and FRS by CNPq.

Author information

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Affiliations

  1. Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil

    • Marilza S Jota
    • , Daniela R Lacerda
    • , José R Sandoval
    • , Pedro Paulo R Vieira
    • , Dominique Ohasi
    • , José E Santos-Júnior
    • , Eduardo M Tarazona-Santos
    •  & Fabrício R Santos
  2. Instituto de Genética y Biología Molecular, Universidad San Martin de Porres, Lima, Peru

    • José R Sandoval
    • , Oscar Acosta
    •  & Ricardo Fujita
  3. Facultad de Bioquímica, Universidad Mayor de San Andrés, La Paz, Bolivia

    • Cinthia Cuellar
    •  & Susana Revollo
  4. Instituto de Investigaciones Biomédicas, Universidad de las Americas, Quito, Ecuador

    • Cesar Paz-y-Miño
  5. Universidad del Tolima, Ibagué, Colombia

    • Gustavo A Vallejo
  6. Department of Anthropology, University of Pennsylvania, Philadelphia, PA, USA

    • Theodore G Schurr
  7. Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil

    • Sergio DJ Pena
  8. The Wellcome Trust Sanger Institute, Hinxton, UK

    • Qasim Ayub
    •  & Chris Tyler-Smith

Consortia

  1. The Genographic Consortium

    The Genographic Consortium Li Jin, Hui Li, & Shilin Li (Fudan University, Shanghai, China); Pandikumar Swamikrishnan (IBM, Somers, New York, United States); Asif Javed, Laxmi Parida & Ajay K Royyuru (IBM, Yorktown Heights, New York, United States); R John Mitchell (La Trobe University, Melbourne, Victoria, Australia); Pierre A Zalloua (Lebanese American University, Chouran, Beirut, Lebanon); Arun Kumar, Ganesh Prasad, Ramasamy Pitchappan, Arun Varatharajan Santhakumari (Madurai Kamaraj University, Madurai, Tamil Nadu, India); R Spencer Wells and Miguel G Vilar (National Geographic Society, Washington, District of Columbia, United States); Himla Soodyall (National Health Laboratory Service, Johannesburg, South Africa); Elena Balanovska & Oleg Balanovsky (Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia); Jaume Bertranpetit, Marc Haber, Marta Melé, & David Comas (Universitat Pompeu Fabra, Barcelona, Spain); Christina J Adler, Alan Cooper, Clio S I Der Sarkissian & Wolfgang Haak (University of Adelaide, South Australia, Australia); Matthew E Kaplan & Nirav C Merchant (University of Arizona, Tucson, Arizona, United States); Colin Renfrew (University of Cambridge, Cambridge, United Kingdom); Andrew C Clarke & Elizabeth A Matisoo-Smith (University of Otago, Dunedin, New Zealand); Jill B Gaieski (University of Pennsylvania, Philadelphia, Pennsylvania, United States).

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https://doi.org/10.1038/jhg.2016.26

Supplementary Information accompanies the paper on Journal of Human Genetics website (http://www.nature.com/jhg)

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