Reconstructed Lost Native American Populations from Eastern Brazil Are Shaped by Differential Jê/Tupi Ancestry.

Alex Mas-Sandoval,Francisco M Salzano,David Comas,Maria Cátira Bortolini,Alexandre C Pereira,Eduardo Tarazona-Santos,Maria Fernanda Lima-Costa,Mauricio L Barreto,Bernardo L Horta,Lara R Arauna,Tábita Hünemeier,Mateus H Gouveia,Kirk Lohmueller

doi:10.1093/gbe/evz161

Abstract

After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African, and the Native American. The study of the Native American genetic history is challenged by the lack of availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies, and the low proportions of the Native American component in the admixed Brazilian populations (on average 7%). We analyzed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North-East), Bambui (South-East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui, and 197 in Pelotas). We compared the reconstructed populations with nonadmixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê-speaking ancestry related groups. We also show evidence of a decrease of the diversity of nonadmixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.

Highlights

Genetic evidence shows that the Native peoples of South America trace their origins to an ancestral population that populated North America from Beringia around 15,000 years ago and reached South America in a few hundred years (Bonatto and Salzano 1997; Hey et al 2005; Tamm et al.ß The Author(s) 2019
The genetic structure of the admixed Brazilian populations is driven by the admixture proportions of Native American, European, and sub-Saharan African components
As previously shown (Kehdy et al 2015), individuals from Salvador present, on average, higher amounts of sub-Saharan African ancestry than individuals from Pelotas and Bambui, there is a high variability in the admixture proportions within each population

Summary

Introduction

Genetic evidence shows that the Native peoples of South America trace their origins to an ancestral population that populated North America from Beringia around 15,000 years ago and reached South America in a few hundred years (Bonatto and Salzano 1997; Hey et al 2005; Tamm et al.ß The Author(s) 2019. European historical records describe a population scenario of Brazil during the 16th century in which Tupi populations from the TupiGuarani linguistic family were living along the coast, whereas non-Tupi populations named generically Tapuia (mostly Macro-J^e-speaking populations) inhabited the hinterlands This coastal Tupi continuum was broken by Tapuia in the mouth of the Paraıba River, in the Southern Bahia, and in the Maranh~ao areas (Soares de Souza 1879; Metraux 1927; Carneiro da Cunha 1998). It is claimed that these non-Tupi populations occupied a wider coastal extension before Tupi populations expelled them out of the coastal regions (Cardim 1925; Metraux 1927; Carneiro da Cunha 1998)

Methods

Results

Conclusion