Origins and dispersals of Pacific peoples: Evidence from mtDNA phylogenies of the Pacific rat E. Matisoo-Smith† and J. H. Robins Department of Anthropology and Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, P.B. 92019, Auckland, New Zealand Communicated by R. C. Green, University of Auckland, Auckland, New Zealand, May 5, 2004 (received for review March 16, 2004) The human settlement of the Pacific in general, and the origin of the Polynesians in particular, have been topics of debate for over two centuries. Polynesian origins are most immediately traced to people who arrived in the Fiji, Tonga, and Samoa region Ϸ3,000 B.P. and are clearly associated with the Lapita Cultural Complex. Although this scenario of the immediate origins of the Polynesians is generally accepted, the debate on the ultimate origin of the Polynesians and the Lapita cultural complex continues. Our previ- ous research has shown that analyses of mtDNA variation in the Pacific rat (Rattus exulans), often transported as a food item in the colonizing canoes, are valuable for tracing prehistoric human migration within Polynesia. Here we present mtDNA phylogenies based on Ϸ240 base pairs of the D-loop from both archaeological and modern samples collected from Island Southeast Asia and the Pacific. We identify three major haplogroups, two of which occur in the Pacific. Comparing our results with Lapita models of Oceanic settlement, we are able to reject two often cited but simplistic ANTHROPOLOGY models, finding support instead for multifaceted models incorpo- rating a more complex view of the Lapita intrusion. This study is unique and valuable in that R. exulans is the only organism associated with the Lapita dispersal for which there are sufficient Fig. 1. Map of the Pacific showing the Wallace Line (A) and the line ancient and extant populations available for genetic analysis. By delineating Near and Remote Oceania (B). Arrows mark the proposed routes tracking population changes through time, we can understand of dispersal of R. exulans according to Tate (2). Wallacea is shown in gray. more fully the settlement process and population interactions in BIOLOGY both Near and Remote Oceania. POPULATION (1, 4). After a pause of Ϸ500–1,000 years, Polynesians then Oceania ͉ Lapita ͉ prehistory ͉ ancient DNA ͉ phylogeography settled the rest of the Polynesian Triangle (1). In a recent review of the role of Lapita in Pacific prehistory, Green (4) outlines current models for Lapita in both Near and he history of human settlement in the island Pacific can Remote Oceania. For Lapita origins in Near Oceania, Green generally be divided into two major phases: the settlement of T identifies four sets of models: set A, or the ‘‘Express Train to Near Oceania, which commenced Ϸ40,000 B.P., and that of Polynesia’’ (ETP), focuses on a rapid dispersal from Southeast Remote Oceania, which began only Ϸ3,100 B.P. (1) (see Fig. 1). Asia (Taiwan) ultimately to Polynesia, with little or no contact The initial settlement of Near Oceania involved the peopling of with indigenous populations in between; set B, or the ‘‘Bismarck greater New Guinea followed by colonization of the Bismarck Archipelago Indigenous Inhabitants’’ (BAII), the other extreme archipelago by 33,000 B.P. and the Solomon Islands by 29,000 perspective, argues that there is no need to consider any major B.P., if not before. Many modern-day descendants of these migration into Near Oceania to account for the appearance of people speak what is often termed ‘‘Papuan’’ languages, which includes a remarkably diverse group of languages quite distinct the Lapita cultural complex, rather that it can be explained as an from the more recently introduced Austronesian languages. The indigenous development; set C, the ‘‘Slow Boat to the Bis- introduction of the Oceanic subgroup of Austronesian languages marcks’’ (SBB) focuses on interactions within a ‘‘voyaging cor- is associated by many with the appearance of the Lapita cultural ridor stretching from eastern Indonesia to the Bismarck and Solomon Islands’’ from 6,000 to 3,500 B.P., followed by rapid complex into previously uninhabited coastal sites and on small Ϸ off-shore islands in Near Oceania at Ϸ3,500–3,300 B.P. (3). The expansion out into Remote Oceania 3,100 B.P.; and set D, the Lapita cultural complex is currently identified not only by the ‘‘Voyaging Corridor Triple I’’ (VC Triple-I), seen by some (5) as distinctive ‘‘Lapita’’ pottery and other artifacts, but also by the a ‘‘compromise solution’’ builds on the SBB model but allows for introduction of a number of plant and animal species, apparently various components of the Lapita cultural complex to be the including the Pacific rat, Rattus exulans. result of intrusion of new components along with the integration Within a few hundred years of the initial appearance of the of materials from indigenous inhabitants in Near Oceania and Lapita cultural complex in Near Oceania, the voyaging barrier beyond it into Remote Oceania was breached, and Lapita ͞ Abbreviations: ETP, Express Train to Polynesia; BAII, Bismark Archipelago Indigenous settlements appear from the Reef Santa Cruz group east of the Inhabitants; SBB, Slow Boat to the Bismarcks; VC Triple-I, Voyaging Corridor Triple-I; NJ, Solomon chain through as far as Fiji, Samoa, and Tonga, on the neighbor joining. western edge of the Polynesian Triangle, defined by the apices of Data deposition: The sequences reported in this paper have been deposited in the GenBank Hawaii, Easter Island, and New Zealand. It is generally believed database (accession nos. AY604202–AY604233). that these phenotypically Oceanic ‘‘Lapita people’’ from Vanu- †To whom correspondence should be addressed. E-mail: [email protected]. atu, New Caledonia, and Fiji are the ancestors of the Polynesians © 2004 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0403120101 PNAS ͉ June 15, 2004 ͉ vol. 101 ͉ no. 24 ͉ 9167–9172 Downloaded by guest on October 2, 2021 innovation or development of new, unique components. For other samples in this study. Sample information is available in Lapita settlement of Remote Oceania, Green presents set E, Table 1, which is published as supporting information on the which describes a rapid and rather unstable process he identifies PNAS web site. as a Mobile Founding Migrant category of models. Using DNA was extracted from bones by using a modified silica͞ mtDNA phylogenies of the commensal Pacific rat, we can test guanidinium thiocyanate method (10). Fresh tissues were ex- these models of Lapita origins for both Near and Remote tracted as described (9). We amplified and sequenced Ϸ240 base Oceania. pairs of the hypervariable mitochondrial control region; see The Pacific rat, R. exulans, is the third most widely dispersed Supporting Text, which is published as supporting information on rat species, with a distribution that ranges from mainland the PNAS web site, for specific methods. Southeast Asia, throughout Island Southeast Asia and across the All extraction and pre-PCR processing of bone material was Pacific as far as Easter Island. It is believed to originate in island conducted in a separate, dedicated ancient DNA laboratory with or peninsular southeast Asia (2, 6) and was not in Near Oceania all precautions taken to avoid and identify any potential con- before the Holocene (7). Rattus exulans skeletal remains first tamination (11). In addition, a randomly chosen subsample of appear in Remote Oceania in Lapita settlements, generally in specimens representing each identified haplogroup was repli- the earliest layers, and are present in all archaeological sites cated in an independent laboratory at Massey University (Palm- associated with both Lapita and with the later Polynesian erston North, New Zealand). From each of these specimens, a settlement. The ubiquitous distribution and the fact that skeletal second bone was removed from an articulated cranial sample, remains occur in large numbers in archaeological middens and sent for DNA extraction, PCR amplification, and direct suggests that R. exulans was intentionally introduced, possibly as sequencing. All resulting sequences were identical to those a food item. These rats do not swim so cannot self disperse (8). obtained originally. Ancient DNA sequences were also com- Therefore a phylogeographic analysis of R. exulans populations pared to those obtained from fresh tissue in each of the major should provide evidence of the origins of the canoes that geographic regions (Southeast Asia, New Guinea, and Polyne- transported the animals, and thus shed light on the origins of sia), to confirm their ‘‘phylogenetic sense’’ (11). both the Polynesians and the Lapita peoples. A total of 32 distinct haplotypes with 27 variable sites were In addition to R. exulans, people associated with the Lapita identified. We constructed an unrooted neighbor-joining (NJ) horizon also introduced dogs (Canis familiaris), pigs (Sus sp.), tree (12) by using the distance matrix calculated by the Kimura and jungle fowl (Gallus gallus) to the islands they settled. Unlike two-parameter model of evolution (13) as implemented in the R. exulans, these animals were the same species carried by PAUP* software package (v 4.0b10; ref. 14). A bootstrap analysis Europeans as they moved into the Pacific. Thus, just as with using 1,000 pseudoreplicates was performed on the resulting humans, there has been substantial admixture between Pacific tree. Trees were also estimated by using maximum likelihood and European populations over the intervening 300 plus years. with the general time reversible model of evolution. Eleven R. exulans, on the other hand, is a distinct species from the rats equally likely trees were found and had nearly identical topol- introduced by Europeans (Rattus rattus and Rattus norvegicus), ogies to that of the NJ tree. A strict consensus parsimony tree and so does not interbreed with them.