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

Abstract

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.