Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders

Thomaz Pinotti, Anders Bergström, Maria Geppert, Matt Bawn, Dominique Ohasi, Wentao Shi, Daniela R. Lacerda, Arne Solli, Jakob Norstedt, Kate Reed, Kim Dawtry, Fabricio González-Andrade, Cesar Paz-y-Miño, Susana Revollo, Cinthia Cuellar, Marilza S. Jota, José E. Santos, Qasim Ayub, Toomas Kivisild, José R. SandovalRicardo Fujita, Yali Xue, Lutz Roewer, Fabrício R. Santos, Chris Tyler-Smith

Research output: Contribution to journalArticlepeer-review

49 Scopus citations

Abstract

The Americas were the last inhabitable continents to be occupied by humans, with a growing multidisciplinary consensus for entry 15–25 thousand years ago (kya) from northeast Asia via the former Beringia land bridge [1–4]. Autosomal DNA analyses have dated the separation of Native American ancestors from the Asian gene pool to 23 kya or later [5, 6] and mtDNA analyses to ∼25 kya [7], followed by isolation (“Beringian Standstill” [8, 9]) for 2.4–9 ky and then a rapid expansion throughout the Americas. Here, we present a calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C [10], with four major conclusions. First, we identify three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C3-P39/Z30536 in North America. Second, from the divergence times and Eurasian/American distribution of lineages, we estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky, according to alternative models, and entry south of the ice sheet after 19.5 kya. Third, we describe the star-like expansion of Q-M848 (within Q-M3) starting at 15 kya [11] in the Americas, followed by establishment of substantial spatial structure in South America by 12 kya. Fourth, the deep branches of the Q-CTS1780 lineage present at low frequencies throughout the Americas today [12] may reflect a separate out-of-Beringia dispersal after the melting of the glaciers at the end of the Pleistocene.

Original languageEnglish
Pages (from-to)149-157.e3
JournalCurrent Biology
Volume29
Issue number1
DOIs
StatePublished - 7 Jan 2019

Bibliographical note

Funding Information:
Foremost, the authors would like to thank all Native Americans who collaborated in the Genographic Project of South America and the EQ Genetics Project, which made this historical genetics research possible. This work is dedicated to them. The authors would also like to thank Pedro Paulo R. Vieira, Oscar Acosta, Donaldo Pinedo, and Paulo Robles-Ruiz for participating in the fieldwork in Peru and Ecuador and Marc Haber, Elena Arciero, Maria Cátira Bortolini, Rafael Bisso-Machado, Tábita Hünemeier, David Comas, and Ray Banks for helpful comments and discussion. We also thank Vladimir Gurianov, Vadim Urasin, and the YFull team for their detailed phylogeny online and Rui Martiniano, Christiana Scheib, Swapan Mallick, Michelle Lee, and David Reich for facilitating access to published sequences. T.P. and F.R.S. were supported by the National Geographic Society of the United States, FAPEMIG, CAPES, and CNPq of Brazil; A.B., Y.X., and C.T.-S. were supported by Wellcome grant number 098051.

Funding Information:
Foremost, the authors would like to thank all Native Americans who collaborated in the Genographic Project of South America and the EQ Genetics Project, which made this historical genetics research possible. This work is dedicated to them. The authors would also like to thank Pedro Paulo R. Vieira, Oscar Acosta, Donaldo Pinedo, and Paulo Robles-Ruiz for participating in the fieldwork in Peru and Ecuador and Marc Haber, Elena Arciero, Maria Cátira Bortolini, Rafael Bisso-Machado, Tábita Hünemeier, David Comas, and Ray Banks for helpful comments and discussion. We also thank Vladimir Gurianov, Vadim Urasin, and the YFull team for their detailed phylogeny online and Rui Martiniano, Christiana Scheib, Swapan Mallick, Michelle Lee, and David Reich for facilitating access to published sequences. T.P. and F.R.S. were supported by the National Geographic Society of the United States, FAPEMIG , CAPES , and CNPq of Brazil ; A.B., Y.X., and C.T.-S. were supported by Wellcome grant number 098051 .

Publisher Copyright:
© 2018 The Authors

Keywords

  • Beringia
  • Native Americans
  • Y chromosome lineages
  • phylogeography
  • pre-Columbian settlement of Americas

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