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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    • "Oceanian population variation is further complicated by indications of a recent relationship between the Indian subcontinent and some Aboriginal Australian populations [36] [37]. Lastly, a small number of studies using autosomal markers [38] [39] [40] indicate low genetic diversity in Remote Oceania and high diversity in Melanesia, with Polynesian variation closer to East Asia than Melanesia. This study describes a new multiplex of 29 ancestry-informative SNPs (AIM-SNPs) termed Pacifiplex that is focused on Oceanian population variation. "
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    ABSTRACT: The analysis of human population variation is an area of considerable interest in the forensic, medical genetics and anthropological fields. Several forensic single nucleotide polymorphism (SNP) assays provide ancestry-informative genotypes in sensitive tests designed to work with limited DNA samples, including a 34-SNP multiplex differentiating African, European and East Asian ancestries. Although assays capable of differentiating Oceanian ancestry at a global scale have become available, this study describes markers compiled specifically for differentiation of Oceanian populations. A sensitive multiplex assay, termed Pacifiplex, was developed and optimized in a small-scale test applicable to forensic analyses. The Pacifiplex assay comprises 29 ancestry-informative marker SNPs (AIM-SNPs) selected to complement the 34-plex test, that in a combined set distinguish Africans, Europeans, East Asians and Oceanians. Nine Pacific region study populations were genotyped with both SNP assays, then compared to four reference population groups from the HGDP-CEPH human diversity panel. STRUCTURE analyses estimated population cluster membership proportions that aligned with the patterns of variation suggested for each study population's currently inferred demographic histories. Aboriginal Taiwanese and Philippine samples indicated high East Asian ancestry components, Papua New Guinean and Aboriginal Australians samples were predominantly Oceanian, while other populations displayed cluster patterns explained by the distribution of divergence amongst Melanesians, Polynesians and Micronesians. Genotype data from Pacifiplex and 34-plex tests is particularly well suited to analysis of Australian Aboriginal populations and when combined with Y and mitochondrial DNA variation will provide a powerful set of markers for ancestry inference applied to modern Australian demographic profiles. On a broader geographic scale, Pacifiplex adds highly informative data for inferring the ancestry of individuals from Oceanian populations. The sensitivity of Pacifiplex enabled successful genotyping of population samples from 50-year-old serum samples obtained from several Oceanian regions that would otherwise be unlikely to produce useful population data. This indicates tests primarily developed for forensic ancestry analysis also provide an important contribution to studies of populations where useful samples are in limited supply.
    No preview · Article · Oct 2015 · Forensic Science International: Genetics
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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.
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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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