Dataset Information

Reconstructing the Deep Population History of Central and South America.

ABSTRACT: We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ?9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ?4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

SUBMITTER: Posth C

PROVIDER: S-EPMC6327247 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Reconstructing the Deep Population History of Central and South America.

Posth Cosimo C Nakatsuka Nathan N Lazaridis Iosif I Skoglund Pontus P Mallick Swapan S Lamnidis Thiseas C TC Rohland Nadin N Nägele Kathrin K Adamski Nicole N Bertolini Emilie E Broomandkhoshbacht Nasreen N Cooper Alan A Culleton Brendan J BJ Ferraz Tiago T Ferry Matthew M Furtwängler Anja A Haak Wolfgang W Harkins Kelly K Harper Thomas K TK Hünemeier Tábita T Lawson Ann Marie AM Llamas Bastien B Michel Megan M Nelson Elizabeth E Oppenheimer Jonas J Patterson Nick N Schiffels Stephan S Sedig Jakob J Stewardson Kristin K Talamo Sahra S Wang Chuan-Chao CC Hublin Jean-Jacques JJ Hubbe Mark M Harvati Katerina K Nuevo Delaunay Amalia A Beier Judith J Francken Michael M Kaulicke Peter P Reyes-Centeno Hugo H Rademaker Kurt K Trask Willa R WR Robinson Mark M Gutierrez Said M SM Prufer Keith M KM Salazar-García Domingo C DC Chim Eliane N EN Müller Plumm Gomes Lisiane L Alves Marcony L ML Liryo Andersen A Inglez Mariana M Oliveira Rodrigo E RE Bernardo Danilo V DV Barioni Alberto A Wesolowski Veronica V Scheifler Nahuel A NA Rivera Mario A MA Plens Claudia R CR Messineo Pablo G PG Figuti Levy L Corach Daniel D Scabuzzo Clara C Eggers Sabine S DeBlasis Paulo P Reindel Markus M Méndez César C Politis Gustavo G Tomasto-Cagigao Elsa E Kennett Douglas J DJ Strauss André A Fehren-Schmitz Lars L Krause Johannes J Reich David D

Cell 20181108 5

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains a ...[more]

PMID: 30415837

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Project description:The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse--which today is reflected by shorter, older ancestry tracts--consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse--reflected by longer, younger tracts--is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.

Dataset Information

Reconstructing the Deep Population History of Central and South America.

Publications

Reconstructing the Deep Population History of Central and South America.

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