Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study

Sung K Kim,Annette Lum-Jones,Laurence N Kolonel,Jeffrey D Wall,Daniel O Stram,Christopher A Haiman,Loic Le Marchand,Richa Saxena,Christopher R Gignoux,Iona Cheng,Brian E Henderson,Hansong Wang,Gary K Chen

doi:10.1371/journal.pone.0047881

Abstract

The population genetic structure of Native Hawaiians has yet to be comprehensively studied, and the ancestral origins of Polynesians remain in question. In this study, we utilized high-resolution genome-wide SNP data and mitochondrial genomes of 148 and 160 Native Hawaiians, respectively, to characterize their population structure of the nuclear and mitochondrial genomes, ancestral origins, and population expansion. Native Hawaiians, who self-reported full Native Hawaiian heritage, demonstrated 78% Native Hawaiian, 11.5% European, and 7.8% Asian ancestry with 99% belonging to the B4 mitochondrial haplogroup. The estimated proportions of Native Hawaiian ancestry for those who reported mixed ancestry (i.e. 75% and 50% Native Hawaiian heritage) were found to be consistent with their self-reported heritage. A significant proportion of Melanesian ancestry (mean = 32%) was estimated in 100% self-reported Native Hawaiians in an ADMIXTURE analysis of Asian, Melanesian, and Native Hawaiian populations of K = 2, where K denotes the number of ancestral populations. This notable proportion of Melanesian admixture supports the “Slow-Boat” model of migration of ancestral Polynesian populations from East Asia to the Pacific Islands. In addition, approximately 1,300 years ago a single, strong expansion of the Native Hawaiian population was estimated. By providing important insight into the underlying population structure of Native Hawaiians, this study lays the foundation for future genetic association studies of this U.S. minority population.

Highlights

Population structure and genetic ancestry of Native Hawaiians, a racial/ethnic minority group within the U.S, have been understudied
Previous reports of the genetic admixture of Native Hawaiians have been largely based on ancestry informative markers (AIMs), which can be limited in their resolution in providing accurate estimates of the genetic contribution of ancestral populations [1,2]
ADMIXTURE analysis at K = 6 suggests that these 100% self-reported Native Hawaiians have an average of 78% of their genomes classified as Native Hawaiian ancestry with 11.5% and 7.8% classified as European and admixed Native Hawaiians with European (Asian) ancestry, respectively (Figure 2B)

Summary

Introduction

Population structure and genetic ancestry of Native Hawaiians, a racial/ethnic minority group within the U.S, have been understudied. Previous reports of the genetic admixture of Native Hawaiians have been largely based on ancestry informative markers (AIMs), which can be limited in their resolution in providing accurate estimates of the genetic contribution of ancestral populations [1,2]. Individuals with mixed ancestry such as Native Hawaiians can be used to map susceptibility loci for complex traits via admixture mapping This is a powerful approach for localizing risk loci of traits that have a higher prevalence in one ancestral population than another [5,6,7,8,9,10,11]. Future admixture mapping studies in Native Hawaiians may be informative for chronic diseases such as cardiovascular disease, diabetes, and breast cancer for which Native Hawaiians demonstrate a higher incidence than other Asian and European populations [12,13,14,15,16]

Methods

Results

Conclusion