Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the AmericasBastien Llamas1,*,†, Lars Fehren-Schmitz2,†, Guido Valverde1, Julien Soubrier1, Swapan Mallick3,4,5, Nadin Rohland3,4,5, Susanne Nordenfelt3,4,5, Cristina Valdiosera6, Stephen M. Richards1, Adam Rohrlach7, Maria Inés Barreto Romero8, Isabel Flores Espinoza8, Elsa Tomasto Cagigao9, Lucía Watson Jiménez9,10, Krzysztof Makowski9, Ilán Santiago Leboreiro Reyna11, Josefina Mansilla Lory11, Julio Alejandro Ballivián Torrez12, Mario A. Rivera13, Richard L. Burger14, Maria Constanza Ceruti15,16, Johan Reinhard17, R. Spencer Wells17,‡, Gustavo Politis18, Calogero M. Santoro19, Vivien G. Standen19, Colin Smith6, David Reich3,4,5, Simon Y. W. Ho20, Alan Cooper1,*,§ and Wolfgang Haak1,*
AbstractThe exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.
http://advances.sciencemag.org/content/2/4/e1501385.full