Ancient Voyaging and Polynesian Origins
2011; Elsevier BV; Volume: 88; Issue: 2 Linguagem: Inglês
10.1016/j.ajhg.2011.01.009
ISSN1537-6605
AutoresPedro Soares, Teresa Rito, J. Tréjaut, Maru Mormina, Catherine Hill, Emma Tinkler‐Hundal, Michelle Braid, Douglas J. Clarke, Jun-Hun Loo, Noel Thomson, Tim Denham, Mark Donohue, Vincent Macaulay, Marie Lin, Stephen Oppenheimer, Martin Richards,
Tópico(s)Linguistics and language evolution
ResumoThe “Polynesian motif” defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ∼4000 years ago (4 ka), but the chronological resolution of existing control-region data is poor, and an East Indonesian origin has also been proposed. By analyzing 157 complete mtDNA genomes, we show that the motif itself most likely originated >6 ka in the vicinity of the Bismarck Archipelago, and its immediate ancestor is >8 ka old and virtually restricted to Near Oceania. This indicates that Polynesian maternal lineages from Island Southeast Asia gained a foothold in Near Oceania much earlier than dispersal from either Taiwan or Indonesia 3–4 ka would predict. However, we find evidence in minor lineages for more recent two-way maternal gene flow between Island Southeast Asia and Near Oceania, likely reflecting movements along a “voyaging corridor” between them, as previously proposed on archaeological grounds. Small-scale mid-Holocene movements from Island Southeast Asia likely transmitted Austronesian languages to the long-established Southeast Asian colonies in the Bismarcks carrying the Polynesian motif, perhaps also providing the impetus for the expansion into Polynesia. The “Polynesian motif” defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ∼4000 years ago (4 ka), but the chronological resolution of existing control-region data is poor, and an East Indonesian origin has also been proposed. By analyzing 157 complete mtDNA genomes, we show that the motif itself most likely originated >6 ka in the vicinity of the Bismarck Archipelago, and its immediate ancestor is >8 ka old and virtually restricted to Near Oceania. This indicates that Polynesian maternal lineages from Island Southeast Asia gained a foothold in Near Oceania much earlier than dispersal from either Taiwan or Indonesia 3–4 ka would predict. However, we find evidence in minor lineages for more recent two-way maternal gene flow between Island Southeast Asia and Near Oceania, likely reflecting movements along a “voyaging corridor” between them, as previously proposed on archaeological grounds. Small-scale mid-Holocene movements from Island Southeast Asia likely transmitted Austronesian languages to the long-established Southeast Asian colonies in the Bismarcks carrying the Polynesian motif, perhaps also providing the impetus for the expansion into Polynesia. The colonization of Polynesia has been debated for several centuries, but for the last few decades, the “out of Taiwan” model, based in the first instance on linguistic arguments, has remained the most widely favored explanation. This model suggests that the Austronesian-speaking populations of Island Southeast Asia (ISEA), Near Oceania, and Remote Oceania (including Polynesians) have a common origin among early Taiwanese agricultural groups who dispersed into ISEA ∼4000 years ago (4 ka), reaching Near Oceania ∼3.5 ka.1Bellwood P. First Farmers: The Origins of Agricultural Societies. Blackwell Publishing, Oxford2005Google Scholar, 2Spriggs M. The Neolithic and Austronesian expansion within Island Southeast Asia and into the Pacific.in: Chiu S. Sand C. From Southeast Asia to the Pacific: Archaeological Perspectives on the Austronesian Expansion and the Lapita Cultural Complex. Academia Sinica, Taipei, Taiwan2007: 104-140Google Scholar These people are often considered largely responsible for the Lapita phenomenon, a cultural complex including finely decorated dentate-stamped pottery, obsidian tools, and shell ornaments that first appeared on the coasts of the Bismarck Archipelago ∼3.5 ka, spreading into Remote Oceania ∼3 ka. Alternative models propose that there have been maritime contacts between Southeast Asia and Near Oceania from the end of the Pleistocene ∼12 ka,3Solheim W.G. Archaeology and Culture in Southeast Asia: Unraveling the Nusantao. University of Philippines Press, Quezon City, The Philippines2006Google Scholar or at least before the mid-Holocene, by ∼6 ka,4Terrell J.E. The ‘sleeping giant’ hypothesis and New Guinea's place in the prehistory of Greater Near Oceania.World Archaeol. 2004; 36: 601-609Crossref Scopus (19) Google Scholar leading to the formation of spheres of interaction along a “voyaging corridor” between Near Oceania and ISEA.5Terrell J.E. Welsch R.L. Lapita and the temporal geography of prehistory.Antiquity. 1997; 71: 548-572Google Scholar, 6Torrence R. Swadling P. Social networks and the spread of Lapita.Antiquity. 2008; 82: 600-616Google Scholar, 7Irwin G. The Prehistoric Exploration and Colonisation of the Pacific. Cambridge University Press, Cambridge1992Crossref Google Scholar Hybrid models suggest involvement of both incoming Austronesian speakers from ISEA and indigenous populations in the Bismarck Archipelago.8Green R.C. The Lapita horizon and traditions: Signature for one set of oceanic migrations.in: Sand C. Pacific Archaeology: Assessments and Prospects. Service des Musées et du Patrimoine, Nouméa, New Caledonia2003Google Scholar Recently, it has been suggested that Taiwan's role as source of the Austronesian languages may have emerged as it became incorporated into the periphery of maritime networks centered farther to the south, with minimal gene flow.9Donohue M. Denham T. Island Southeast Asia during the mid-Holocene: Reframing Austronesian history.Curr. Anthropol. 2010; 51: 223-256Crossref Scopus (99) Google Scholar Questions about prehistoric dispersals can be addressed more directly by archaeogenetics than by either archaeology or linguistics. The “Polynesian motif” and its descendants comprise a clade of mtDNA lineages that together account for >90% of Polynesian mtDNAs.10Kayser M. Brauer S. Cordaux R. Casto A. Lao O. Zhivotovsky L.A. Moyse-Faurie C. Rutledge R.B. Schiefenhoevel W. Gil D. et al.Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific.Mol. Biol. 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Genet. 1998; 63: 1807-1823Abstract Full Text Full Text PDF PubMed Scopus (98) Google Scholar However, most of the data so far available come from the first hypervariable segment of the mtDNA control region (HVS-I), the interpretation of which has been highly controversial because of its poor phylogeographic resolution. Some have argued that its variation supports the “out of Taiwan” model for Pacific maternal lineages,10Kayser M. Brauer S. Cordaux R. Casto A. Lao O. Zhivotovsky L.A. Moyse-Faurie C. Rutledge R.B. Schiefenhoevel W. Gil D. et al.Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific.Mol. Biol. Evol. 2006; 23: 2234-2244Crossref PubMed Scopus (177) Google Scholar, 11Redd A.J. Takezaki N. Sherry S.T. McGarvey S.T. Sofro A.S.M. Stoneking M. Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific.Mol. Biol. Evol. 1995; 12: 604-615PubMed Google Scholar, 12Sykes B. Leiboff A. Low-Beer J. Tetzner S. Richards M. The origins of the Polynesians: An interpretation from mitochondrial lineage analysis.Am. J. Hum. Genet. 1995; 57: 1463-1475PubMed Google Scholar, 15Pierson M.J. Martinez-Arias R. Holland B.R. Gemmell N.J. Hurles M.E. Penny D. Deciphering past human population movements in Oceania: Provably optimal trees of 127 mtDNA genomes.Mol. Biol. Evol. 2006; 23: 1966-1975Crossref PubMed Scopus (50) Google Scholar, 16Melton T. Clifford S. Martinson J. Batzer M. Stoneking M. Genetic evidence for the proto-Austronesian homeland in Asia: mtDNA and nuclear DNA variation in Taiwanese aboriginal tribes.Am. J. Hum. Genet. 1998; 63: 1807-1823Abstract Full Text Full Text PDF PubMed Scopus (98) Google Scholar whereas others have argued for an origin for the motif—and therefore the maternal ancestry of the vast majority of islanders themselves—before the mid-Holocene in Wallacea, Eastern Indonesia.13Richards M. Oppenheimer S. Sykes B. mtDNA suggests Polynesian origins in Eastern Indonesia.Am. J. Hum. Genet. 1998; 63: 1234-1236Abstract Full Text Full Text PDF PubMed Scopus (79) Google Scholar, 14Oppenheimer S.J. Richards M. Polynesian origins. Slow boat to Melanesia?.Nature. 2001; 410: 166-167Crossref PubMed Scopus (76) Google Scholar, 17Hill C. Soares P. Mormina M. Macaulay V. Clarke D. Blumbach P.B. Vizuete-Forster M. Forster P. Bulbeck D. Oppenheimer S. Richards M. A mitochondrial stratigraphy for Island Southeast Asia.Am. J. Hum. Genet. 2007; 80: 29-43Abstract Full Text Full Text PDF PubMed Scopus (177) Google Scholar Molecular-clock estimates based on the genetic diversity accumulated within founder lineages—that is to say, the level of variation that has arisen since a particular lineage arrived in a particular location—can be used as a proxy for colonization times.18Richards M. Macaulay V. Hickey E. Vega E. Sykes B. Guida V. Rengo C. Sellitto D. Cruciani F. Kivisild T. et al.Tracing European founder lineages in the Near Eastern mtDNA pool.Am. J. Hum. Genet. 2000; 67: 1251-1276Abstract Full Text Full Text PDF PubMed Scopus (745) Google Scholar However, HVS-I sequences, and indeed synonymous sites from complete coding-region sequences, lack the chronological resolution needed to distinguish models that differ in predicted dispersal times by only a few thousand years. To provide the necessary precision, we calibrated the mutation rate for the entire mtDNA genome, and to be confident of the accuracy of the clock, we also corrected for the effects of purifying selection.19Soares P. Ermini L. Thomson N. Mormina M. Rito T. Röhl A. Salas A. Oppenheimer S. Macaulay V. Richards M.B. Correcting for purifying selection: An improved human mitochondrial molecular clock.Am. J. Hum. Genet. 2009; 84: 740-759Abstract Full Text Full Text PDF PubMed Scopus (504) Google Scholar We then applied the improved clock, with both the simple unbiased ρ statistic and maximum likelihood (ML), to the analysis of 157 complete mtDNA genomes (81 new to this study; see Table S1 available online) belonging to haplogroup B4 from mainland East and Southeast Asians, aboriginal Taiwanese, Island Southeast Asians, and Near and Remote Oceanians (as well as two Native Americans). For our purposes, ISEA includes the Philippines, Indonesia, and Malaysian Borneo; Near Oceania (the western Pacific) includes New Guinea, the Bismarck Archipelago, Bougainville, and the Solomon Islands; and Remote Oceania includes Island Melanesia southeast of the Solomons (including Vanuatu and Fiji), Polynesia, and Micronesia (Figure 1). DNA sequencing at the University of Leeds used an ABI 16-capillary 3130XL DNA Analyzer and the protocol of Torroni et al.,20Torroni A. Rengo C. Guida V. Cruciani F. Sellitto D. Coppa A. Calderon F.L. Simionati B. Valle G. Richards M. et al.Do the four clades of the mtDNA haplogroup L2 evolve at different rates?.Am. J. Hum. Genet. 2001; 69: 1348-1356Abstract Full Text Full Text PDF PubMed Scopus (161) Google Scholar and DNA sequencing at Taipei used an ABI 48-capillary 3730/3730X DNA Analyzer. The work was approved by the University of Leeds, Faculty of Biological Sciences Ethics Committee and the Human Experiment Committee of the Mackay Memorial Hospital in Taipei, and the samples were collected with the appropriate informed consent of the subjects. We generated 16 of the 81 new mtDNA genomes by denaturing high-performance liquid chromatography (dHPLC) and hybridization with a previously sequenced root-type B4a1a1a sequence;21Meierhofer D. Mayr J.A. Ebner S. Sperl W. Kofler B. 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Mitochondrial portraits of human populations using median networks.Genetics. 1995; 141: 743-753PubMed Google Scholar with the Network 4.5 software with a total of 164 sequences (Figure S1). These included all of the available B4a sequences (34–157 in Table S1), additional sequences representing the overall structure of the B4 tree (1–33 in Table S1), and seven sequences to root the B4 network and represent the roots of haplogroups B, R, and N (unnumbered sequences in Table S1). To provide the maximum possible detail about the phylogeography of the lineages, we also analyzed 4793 HVS-I sequences, including published sequences from Taiwan,17Hill C. Soares P. Mormina M. Macaulay V. Clarke D. Blumbach P.B. Vizuete-Forster M. Forster P. Bulbeck D. Oppenheimer S. Richards M. A mitochondrial stratigraphy for Island Southeast Asia.Am. J. Hum. Genet. 2007; 80: 29-43Abstract Full Text Full Text PDF PubMed Scopus (177) Google Scholar, 23Trejaut J.A. Kivisild T. Loo J.H. Lee C.L. He C.L. Hsu C.J. 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Some of the data did not include the full stretch of HVS-I that we used in the analysis (positions 16051–16400), but the available stretches included >90% of the variation, and their inclusion greatly strengthened the analysis because of their key locations. We tested all of the unclassified B4a samples in the Leeds laboratory at positions 6719, 10238, 12239, and 15745, defining haplogroup B4a1a by direct sequencing. Position 6719 was determined by restriction analysis in Taipei by using the enzyme NalIII, whereas position 10238 was determined by direct sequencing. Almost all of the samples fell into B4a1a (Figure S1), the offshore clade identified by Trejaut et al.23Trejaut J.A. Kivisild T. Loo J.H. Lee C.L. He C.L. Hsu C.J. Lee Z.Y. Lin M. Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations.PLoS Biol. 2005; 3: e247Crossref PubMed Scopus (171) Google Scholar The published HVS-I sequences, except for the Philippine data of Tabbada et al.,25Tabbada K.A. Trejaut J. Loo J.H. Chen Y.M. Lin M. Mirazón-Lahr M. Kivisild T. De Ungria M.C. Philippine mitochondrial DNA diversity: A populated viaduct between Taiwan and Indonesia?.Mol. Biol. Evol. 2010; 27: 21-31Crossref PubMed Scopus (93) Google Scholar had not been tested for any marker for B4a1a, but we can safely assume that the great majority of B4a∗ (that is, excluding B4a1a1) lineages in ISEA and Taiwanese Austronesian-speaking aboriginals belong to B4a1a. With the exception of B4a2, which can be identified from its HVS-I motif, all of the B4a samples we tested from aboriginal Taiwanese Austronesian-speakers, and >93% of the ISEA samples analyzed, belonged to this clade. All of the available samples in the Leeds laboratory, and most of those in Taipei, were also tested by sequencing for the transition at position 14022 that defines B4a1a1 (Table S2). All of the B4a1a∗ samples (with transitions at HVS-I positions 16189, 16217, and 16261) tested from the north coast of New Guinea (except for one [Table S2], plus a published B4a1a1∗ sequence from the Trobriand Islands), the south coast of New Guinea, and the Bismarck Archipelago were from B4a1a1. One sample in ISEA (from Ujung Pandang) was from B4a1a1∗ (Table S2), and two from the Philippines (one from Mindanao and one from an undetermined location) have also been detected.25Tabbada K.A. Trejaut J. Loo J.H. Chen Y.M. Lin M. Mirazón-Lahr M. Kivisild T. De Ungria M.C. Philippine mitochondrial DNA diversity: A populated viaduct between Taiwan and Indonesia?.Mol. Biol. Evol. 2010; 27: 21-31Crossref PubMed Scopus (93) Google Scholar For variation within New Guinea and the Pacific in published data (not tested for 14022), we assumed that the samples belong mainly to the B4a1a1 clade, because 98.6% of the samples that we tested were from this clade. We estimated clade ages for both complete genomes and HVS-I19Soares P. Ermini L. Thomson N. Mormina M. Rito T. Röhl A. Salas A. Oppenheimer S. Macaulay V. Richards M.B. Correcting for purifying selection: An improved human mitochondrial molecular clock.Am. J. Hum. Genet. 2009; 84: 740-759Abstract Full Text Full Text PDF PubMed Scopus (504) Google Scholar and analyzed different data sets independently in order to explore different geographical aspects of the diversity in the B4a1a tree. We excluded Remote Pacific sequences from clade age estimates because they have undergone severe founder effects and redispersals (although they were used to calculate founder ages for the locations concerned). For ML analyses, four different trees were used, including the same set of deeper lineages, but differing in the B4a1a data included: tree 1 included all the available B4a1a complete mtDNAs from Taiwan, ISEA, and Near Oceania, tree 2 included only the B4a1a data set from Taiwan, tree 3 included only the B4a1a data set from ISEA, and tree 4 included only the B4a1a1 data set from the Bismarck Archipelago. The sequences used in each tree are shown in Table S1. We carried out founder analysis to estimate settlement times as we previously did, using the f1 criterion to identify founder sequence types by screening out likely back-migration and back-mutation.18Richards M. Macaulay V. Hickey E. Vega E. Sykes B. Guida V. Rengo C. Sellitto D. Cruciani F. Kivisild T. et al.Tracing European founder lineages in the Near Eastern mtDNA pool.Am. J. Hum. Genet. 2000; 67: 1251-1276Abstract Full Text Full Text PDF PubMed Scopus (745) Google Scholar, 37Forster P. Harding R. Torroni A. Bandelt H.-J. Origin and evolution of Native American mtDNA variation: A reappraisal.Am. J. Hum. Genet. 1996; 59: 935-945PubMed Google Scholar, 38Soares P. Trejaut J.A. Loo J.-H. Hill C. Mormina M. Lee C.-L. Chen Y.-M. Hudjashov G. Forster P. Macaulay V. et al.Climate change and postglacial human dispersals in southeast Asia.Mol. Biol. Evol. 2008; 25: 1209-1218Crossref PubMed Scopus (140) Google Scholar Founder age estimates use only the ρ statistic because no way yet exists of employing ML for this purpose. Cross-comparison of age estimates via both approaches (e.g., Table 1) shows that they give comparable results, albeit with wider confidence intervals for ρ.Table 1Age Estimates for B4a1a1 and B4a1a1aIndonesia (yr)Bismarcks (yr)Overall (yr)B4a1a1Maximum likelihood6000 (3400; 8650)8400 (4850; 12,050)6800 (4950; 8700)Complete genome clock, ρ5650 (1050; 10,400)9300 (3600; 15,200)7900 (3450; 12,450)Synonymous, ρ4300 (850; 7750)8550 (1500; 15,600)6500 (2000; 11,000)Control region, ρaCorresponds to paragroup B4a1a1∗.0 (0)12250 (0; 25,650)9300 (2250; 16,350)B4a1a1aMaximum likelihood4000 (2000; 6000)6650 (4500; 8850)5300 (4050; 6600)Complete genome clock, ρ3900 (1950; 5850)6950 (3600; 10,400)5850 (3850; 7800)Synonymous, ρ4750 (950; 8500)9050 (800; 17,350)7150 (1750; 12,550)Control region, ρ3450 (250; 6600)12,000 (5350; 18,650)7700 (4300; 11,100)B4a1a1 and B4a1a1a are defined by the “pre-motif” and the Polynesian motif, respectively. Estimates with associated 95% confidence limits are shown for Indonesia, the Bismarck Archipelago, and the overall data set via maximum likelihood (complete genomes) and ρ for three different molecular clocks, two of them with independent sources of variation (control region and synonymous clocks).a Corresponds to paragroup B4a1a1∗. Open table in a new tab B4a1a1 and B4a1a1a are defined by the “pre-motif” and the Polynesian motif, respectively. Estimates with associated 95% confidence limits are shown for Indonesia, the Bismarck Archipelago, and the overall data set via maximum likelihood (complete genomes) and ρ for three different molecular clocks, two of them with independent sources of variation (control region and synonymous clocks). We calculated haplotype diversity as before17Hill C. Soares P. Mormina M. Macaulay V. Clarke D. Blumbach P.B. Vizuete-Forster M. Forster P. Bulbeck D. Oppenheimer S. Richards M. A mitochondrial stratigraphy for Island Southeast Asia.Am. J. Hum. Genet. 2007; 80: 29-43Abstract Full Text Full Text PDF PubMed Scopus (177) Google Scholar and calculated the mean number of pairwise differences (π) and the ρ statistic with Network 4.5. We also used ρ, usually presented as a measure of time depth, as a diversity index for different geographic regions. Note that the associated age estimates in these cases do not correspond to the time of arrival of the clade into each geographic region, because in most cases diversity is carried over from the source to the sink and must be excluded from any age estimates, as is done systematically in a founder analysis. Thus, in the founder analyses, a founder age, corresponding to a ρ value that excludes any diversity present in the hypothetical source population or populations, was used to approximate the arrival time of a clade in a geographic region. There is one particular case, however, in which the raw age estimate calculated from the diversity of a clade is meaningful in terms of time depth: this is the case for the region in which the clade first arose. In this case, the time to the most recent common ancestor also estimates the time in which it has been evolving within that region. The Polynesian motif defines a recent, geographically restricted subclade, B4a1a1a, of haplogroup B4 (Figure 2; for more detail, see Figure S1). Haplogroup B4 itself arose ∼44 ka, most likely on the East Asian or Southeast Asian mainland, where it is dispersed especially around the coastal regions from Vietnam to Japan. It subdivided ∼35 ka into three main subclades: B4a, B4b'd, and B4c (with a subclade of B4b, B2, found uniquely in Native Americans and dating to ∼15 ka19Soares P. Ermini L. Thomson N. Mormina M. Rito T. Röhl A. Salas A. Oppenheimer S. Macaulay V. Richards M.B. Correcting for purifying selection: An improved human mitochondrial molecular clock.Am. J. Hum. Genet. 2009; 84: 740-759Abstract Full Text Full Text PDF PubMed Scopus (504) Google Scho
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