REPORT Genome-wide Analysis Indicates More Asian than Melanesian Ancestry of Polynesians Manfred Kayser, 1,8, * Oscar Lao, 1,8 Kathrin Saar, 2 Silke Brauer, 1,3 Xingyu Wang, 4 Peter Nu ¨ rnberg, 5 Ronald J. Trent, 6 and Mark Stoneking 7 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. Previous analyses of mtDNA and NRY variation in Polyne- sians have demonstrated a dramatic discrepancy in the or- igins of the Polynesian mtDNA and NRY gene pools: 1–4 about 94% of Polynesian mtDNAs are of East Asian origin and only 6% are of Melanesian origin (consisting of main- land New Guinea and surrounding islands, also known as Near Oceania), whereas 66% of Polynesian Y chromo- somes are of Melanesian origin and only 28% are of East Asian origin. 4 To explain this discrepancy, the Slow Boat hypothesis for Polynesian origins was formulated, according to which the ancestors of Polynesians migrated from East Asia/Taiwan through New Guinea and Island Melanesia, mixing extensively with the local populations as they did so, before continuing eastward to colonize Remote Oceania/Polynesia. 2,4 This mixing was sex biased, involving many more Melanesian males than females admixing with East Asian newcomers, consistent with the view that ancestral Polynesian society may have been matrilocal in residence (men move to their wife’s land) and matrilineal in descent (clans are inherited through the mothers line). 4–6 This large discrepancy between the mtDNA and NRY genetic contributions of East Asian and Melanesian ancestors to Polynesians raises the question as to the constitution of the autosomal gene pool of Polynesians. To address this question, we genotyped 377 genome-wide distributed autosomal short tandem repeat (STR) loci in 47 Polynesians (10 Cook Islanders, 10 Tongans, 18 Samoans, 5 Tokelau Islanders, and 4 Nuie Islanders), 44 Han Chinese from Beijing, and 24 Papua New Guineans from the interior highlands (15 from the Eastern Highlands, 9 from the Southern Highlands). Geno- typing was performed essentially as described elsewhere. 7 Additional STR loci were chosen to reduce the average dis- tance between markers to 8.8 cM; the genotype data are available from the authors. Some basic statistics of genetic diversity in these three groups, based on the 377 STR loci, are presented in Table 1 and indicate that diversity in the Polynesians is interme- diate between that of Chinese and New Guineans. Previous evidence from NRY and mtDNA data indicates that Poly- nesians have NRY and mtDNA haplogroups of both East Asian and Melanesian origins. 1–4,8–12 We therefore hy- pothesized that East Asians and Melanesians represent the parental populations of Polynesians, and we estimated the genome-wide autosomal proportion of the East Asian (represented by the Chinese samples) and Melanesian (rep- resented by the PNG samples) contribution to Polynesians. However, the estimation of the East Asian and Melanesian components in the current Polynesian autosomal gene pool is potentially complicated by the severe bottlenecks that accompanied the migrations to and through the Pa- cific (Remote Oceania), as well as the relatively long period since the admixture occurred, approximately 3500 years ago. 13 Several methods have been proposed for estimating the amount of admixture of a hybrid population, 14 of which two seem to be more robust to departures from model as- sumptions. These are the maximum likelihood method proposed by Wang 15 as implemented in the program LEADMIX and the coalescent approach proposed by 1 Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands; 2 Gene Mapping Center, Max Delbru ¨ck Center for Molecular Medicine (MDC), Robert-Ro ¨ ssle-Strasse 10, 13092 Berlin, Germany; 3 Department of Biology, Nether- lands Forensic Institute, PO Box 24044, 2490 AA Den Haag, The Netherlands; 4 Beijing Hypertension League Institute, Fu Wai Hospital, 167 Beilishi, 100037 Beijing, China; 5 Cologne Center for Genomics, University of Cologne, Zuelpicher Strasse 47, 50674 Ko ¨ ln, Germany; 6 Department of Molecular and Clinical Genetics, Royal Prince Alfred Hospital and Central Clinical School, The University of Sydney, Missenden Road, Camperdown, NSW 2050, Australia; 7 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany 8 These authors contributed equally to this work. *Correspondence: m.kayser@erasmusmc.nl DOI 10.1016/j.ajhg.2007.09.010. ª2008 by The American Society of Human Genetics. All rights reserved. 194 The American Journal of Human Genetics 82, 194–198, January 2008