Genome-wide Analysis Indicates More Asian than Melanesian Ancestry of Polynesians

Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
The American Journal of Human Genetics (Impact Factor: 10.93). 02/2008; 82(1):194-8. DOI: 10.1016/j.ajhg.2007.09.010
Source: PubMed


Analyses of mitochondrial DNA (mtDNA) and nonrecombining Y chromosome (NRY) variation in the same populations are sometimes concordant but sometimes discordant. Perhaps the most dramatic example known of the latter concerns Polynesians, in which about 94% of Polynesian mtDNAs are of East Asian origin, while about 66% of Polynesian Y chromosomes are of Melanesian origin. Here we analyze on a genome-wide scale, to our knowledge for the first time, the origins of the autosomal gene pool of Polynesians by screening 377 autosomal short tandem repeat (STR) loci in 47 Pacific Islanders and compare the results with those obtained from 44 Chinese and 24 individuals from Papua New Guinea. Our data indicate that on average about 79% of the Polynesian autosomal gene pool is of East Asian origin and 21% is of Melanesian origin. The genetic data thus suggest a dual origin of Polynesians with a high East Asian but also considerable Melanesian component, reflecting sex-biased admixture in Polynesian history in agreement with the Slow Boat model. More generally, these results also demonstrate that conclusions based solely on uniparental markers, which are frequently used in population history studies, may not accurately reflect the history of the autosomal gene pool of a population.

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    • "It is important to fully specify the models and which components are being tested - for example, there are at least seven independent components to the ‘express train’ model including three related to Taiwan (language, associated culture, and the maternal genetics from mitochondrial DNA), three related to the rate of movement (including a relatively rapid movement, no significant breaks after leaving Taiwan until reaching Western Polynesia, little displacement of existing peoples), and finally the question of ongoing genetic contact with other peoples in the region – including differences between introgression of males and females [12]. Also, different models can have the same name; an example being the ‘slow boat’ models of Kayser et al. [13] and of Oppenheimer and Richards [14]. While we do not attempt to formally evaluate the main models here (but see Hurles et al, 2003 [2]), it is important to be aware that most models have several compon that can be evaluated independently, and by using data from a range of disciplines. "
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    ABSTRACT: Many details surrounding the origins of the peoples of Oceania remain to be resolved, and as a step towards this we report seven new complete mitochondrial genomes from the Q2a haplogroup, from Papua New Guinea, Fiji and Kiribati. This brings the total to eleven Q2 genomes now available. The Q haplogroup (that includes Q2) is an old and diverse lineage in Near Oceania, and is reasonably common; within our sample set of 430, 97 are of the Q haplogroup. However, only 8 are Q2, and we report 7 here. The tree with all complete Q genomes is proven to be minimal. The dating estimate for the origin of Q2 (around 35 Kya) reinforces the understanding that humans have been in Near Oceania for tens of thousands of years; nevertheless the Polynesian maternal haplogroups remain distinctive. A major focus now, with regard to Polynesian ancestry, is to address the differences and timing of the 'Melanesian' contribution to the maternal and paternal lineages as people moved further and further into Remote Oceania. Input from other fields such as anthropology, history and linguistics is required for a better understanding and interpretation of the genetic data.
    PLoS ONE 12/2012; 7(12):e52022. DOI:10.1371/journal.pone.0052022 · 3.23 Impact Factor
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    • "Evidence in support of this hypothesis includes archaeological evidence [26] and Y chromosome data [27]–[30]. Previous genome-wide surveys [31]–[33] that addressed the ancestral origins of Polynesians have yielded conflicting results over these two hypotheses with the majority of studies focusing on microsatellite (short-tandem repeat) markers [31], [32]. These discrepancies may be due to the use of microsatellite markers, which have inherently high mutation rates and a mutation model that is difficult to model [34]–[36]. "
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    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.
    PLoS ONE 11/2012; 7(11):e47881. DOI:10.1371/journal.pone.0047881 · 3.23 Impact Factor
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    • "However, Y-DNA and mtDNA are both inherited effectively as single " linkage block " owing to the absence of recombination, while other genomic regions could be expected to have different lineages or histories (Hey & Machado, 2003). Recently available data on genome-wide high-density single nucleotide polymorphisms (SNPs), and the advent of whole-genome sequencing data for human populations, have demarcated a transition from single-locus based studies to genomics analysis of human population structure and relationship (Rosenberg et al., 2002, 2005; The International HapMap Consortium, 2005, 2007; Friedlaender et al., 2008; Jakobsson et al., 2008; Kayser et al., 2008; Li et al., 2008; The HUGO Pan-Asian SNP Consortium, 2009). Apart from the significant increase in the number of loci or markers , the accumulated recombination events in the genome are expected to provide additional information for human genetic relationship studies. "
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    ABSTRACT: The vast amount of recombination information in the human genome has long been ignored or deliberately avoided in studies on human population genetic relationships. One reason is that estimation of the recombination parameter from genotyping data is computationally challenging and practically difficult. Here we propose chromosome-wide haplotype sharing (CHS) as a measure of genetic similarity between human populations, which is an indirect approach to integrate recombination information. We showed in both empirical and simulated data that recombination differences and genetic differences between human populations are strongly correlated, indicating that recombination events in different human populations are evolutionarily related. We further demonstrated that CHS can be used to reconstruct reliable phylogenies of human populations and the majority of the variation in CHS matrix can be attributed to recombination. However, for distantly related populations, the utility of CHS to reconstruct correct phylogeny is limited, suggesting that the linear correlation of CHS and population divergence could have been disturbed by recurrent recombination events over a large time scale. The CHS we proposed in this study is a practical approach without involving computationally challenging and time-consuming estimation of recombination parameter. The advantage of CHS is rooted in its integration of both drift and recombination information, therefore providing additional resolution especially for populations separated recently.
    Annals of Human Genetics 11/2011; 75(6):694-706. DOI:10.1111/j.1469-1809.2011.00678.x · 2.21 Impact Factor
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