Genomic insights into the origin and diversification of late maritime hunter-gatherers from the chilean Patagonia

Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia similar to 15,000-20,000 y ago. Despite recent genomic approaches to reconstruct the continental evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia (n = 61) and four ancient maritime individuals from Patagonia (similar to 1,000 y old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native Patagonian Kaweskar and Yamana showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1,000 y before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the ancient maritime individuals were genetically equidistant to a similar to 200-y-old terrestrial hunter-gatherer from Tierra del Fuego, which supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups.Comision Nacional de Investigacion Cientifica y Tecnologica Grant USA2013-0015 Fondo Nacional de Ciencia y Tecnologia 1140544 1170726 Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica-Universidad Nacional Autonoma de Mexico IA206817 Swiss National Science Foundation PZ00P3_154717 European Research Council 679330 International Center for Genetic Engineering and Biotechnology Grant CRP/MEX15-04_EC Fund of Scientific and Technological Equipment (FONDEQUIP) EQM14015

Native American mitochondrial lineages in admixed populations from Chile: detecting recent migrations during post-Columbian times using geographically restricted lineages

Objectives: To analyze the mitochondrial diversity in three admixed populations and evaluate the historical migration effect of native southern population to Santiago (capital of Chile). The intensity of migration was quantified using three mitochondrial lineages restricted to South-Central native groups.Methods: D-loop sequences were genotyped in 550 unrelated individuals from San Felipe-Los Andes (n=108), Santiago (n=217) and Concepción (n=225). Sequence processing, alignment and haplogroup inference was carried out, and different genetic structure analyses were performed for haplogroup frequencies and D-loop sequences. Results: The Native lineages B2i2, C1b13 and D1g were the most frequent haplogroups in our sample, especially in Santiago (71,8%). Despite the distance, this city showed a higher genetic affinity with southern populations, including Concepción ( ~500km distant) and native groups, rather than with those from San Felipe-Los Andes (<100km distant). In fact, there was a negative correlation between geographical and genetic distance among these cities (r corr= -0,6342, p-value= 0,8315). Network analysis revealed shared haplotypes between Santiago, Concepción and other southern populations. Finally, we found lineages from Concepción acting as ancestral nodes in the northern clade.Conclusions: Considering Santiago is farther away from Concepción than from the cities of San Felipe-Los Andes, the results were not consistent with a model of genetic isolation by geographic distance, revealing the effects of a historical migration process from the south to the capital. We also show evidence of possible north-to-south migration during admixture onset in Concepción and most importantly, we were able to identify previously unreported mitochondrial diversity in urban populations that became lost in Native groups post-European contact.Fil: Pezo, Patricio. Universidad de Chile. Facultad de Medicina.; ChileFil: Orellana Soto, Michael. Universidad de Chile. Facultad de Medicina.; ChileFil: de la Fuente, Constanza. University of Chicago; Estados UnidosFil: Leiva, Ximena. Universidad de Chile. Facultad de Medicina.; ChileFil: Herrera, Luisa. Universidad de Chile. Facultad de Medicina.; ChileFil: Flores Alvarado, Sandra. Universidad de Chile. Facultad de Medicina.; ChileFil: Galimany, Jacqueline. Universidad de Chile. Facultad de Medicina.; ChileFil: de Saint Pierre, Michelle. Universidad de Chile; ChileFil: Bravi, Claudio Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; ArgentinaFil: Moraga, Mauricio. Universidad de Chile. Facultad de Medicina.; Chil