Genome-Wide Analysis in Brazilian Xavante Indians Reveals Low Degree of Admixture

Patricia C Kuhn,José Maurício Sanches,Regina S Moises,Luciana Franco,João Paulo B Vieira Filho,Laercio Joel Franco,Andréa R V Russo Horimoto,Amaury Dal Fabbro,Alexandre C Pereira,Dennis O’Rourke

doi:10.1371/journal.pone.0042702

Patricia C Kuhn, José Maurício Sanches + Show 8 more

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https://doi.org/10.1371/journal.pone.0042702

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Abstract

Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise Fst statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders.

Highlights

Knowledge of genetic diversity patterns of human populations provides important insights of their evolutionary history and is useful in genetic mapping studies of complex diseases and their component traits [1,2,3]
The earliest contact of Xavante with western culture was during the 18th century in the Brazilian Central Plateau and this period was marked by epidemics, armed conflicts and forced labor imposed by the Portuguese colonial government
The aim of the present study was to characterize the genetic structure in Xavante Indians providing valuable baseline data for future genetic studies and to compare it with a Southeast Brazilian population [8], populations of the Human Genome Diversity Panel (HGDP-CEPH) [9], and populations of the HapMap Project, Phase III [10], which include individuals of Asian, African, European, and Mexican Ancestry

Summary

Introduction

Knowledge of genetic diversity patterns of human populations provides important insights of their evolutionary history and is useful in genetic mapping studies of complex diseases and their component traits [1,2,3]. In this context, isolated populations are of particular interest since they may overcome some of the challenges in genetic investigations. The earliest contact of Xavante with western culture was during the 18th century in the Brazilian Central Plateau and this period was marked by epidemics, armed conflicts and forced labor imposed by the Portuguese colonial government. Despite of the interaction with the outsiders, the Xavante maintain their own complex social organization and cultural values that were preserved over the years [5,6,7]

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