Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania

Abstract

Human settlement of Oceania marked the culmination of a global colonization process that began when humans first left Africa at least 90,000 years ago. The precise origins and dispersal routes of the Austronesian peoples and the associated Lapita culture remain contentious, and numerous disparate models of dispersal (based primarily on linguistic, genetic, and archeological data) have been proposed. Here, through the use of mtDNA from 781 modern and ancient Sus specimens, we provide evidence for an early human-mediated translocation of the Sulawesi warty pig (Sus celebensis) to Flores and Timor and two later separate human-mediated dispersals of domestic pig (Sus scrofa) through Island Southeast Asia into Oceania. Of the later dispersal routes, one is unequivocally associated with the Neolithic (Lapita) and later Polynesian migrations and links modern and archeological Javan, Sumatran, Wallacean, and Oceanic pigs with mainland Southeast Asian S. scrofa. Archeological and genetic evidence shows these pigs were certainly introduced to islands east of the Wallace Line, including New Guinea, and that so-called "wild" pigs within this region are most likely feral descendants of domestic pigs introduced by early agriculturalists. The other later pig dispersal links mainland East Asian pigs to western Micronesia, Taiwan, and the Philippines. These results provide important data with which to test current models for human dispersal in the region.

Fig. 1.

Bayesian (Monte Carlo–Markov chain) consensus tree of 249 Sus mtDNA control region haplotypes rooted by a common warthog (Phacochoerus aethiopicus). Gray (basal) and green (derived) clusters on the tree correspond to general regions on the map where the majority of pigs possess haplotypes within that cluster. The yellow clade represents the Pacific Clade. Yellow stars represent islands on which at least one specimen possessing Pacific Clade haplotypes was identified. The yellow star in Southeast Asia represents the two mainland Asian wild boar samples in Vietnam that possessed this haplotype. Regions on the map are: Mal, peninsular Malaysia; Bor, Borneo; Sum, Sumatra; Jav, Java; Sul, Sulawesi; F, Flores; T, Timor (both in the Lesser Sundas); Mol, Moluccas Islands; PI, Philippines; Tai, Taiwan; NG, New Guinea. The dashed red line labeled WL represents the Wallace Line. The black dashed arrow leading to the more derived portion of the tree illustrates the natural movement of wild Sus out of ISEA and into mainland Asia. See SI Fig. 4 for a more detailed version of the tree.

Fig. 2.

Map of East Asia and the Pacific depicting only the distributions of Pacific Clade (yellow) and East Asian haplotypes (light blue). Ancient pigs on the island of Kosrae possess both haplotypes, as do modern pigs from Hawaii, although the East Asian haplotypes on Hawaii are likely the result of postcontact introductions.

Fig. 3.

Scatter plot of the first two factorial axes of principal components analysis calculated from elliptic Fourier coefficients extracted from third lower molar (M₃) occlusal outlines of modern and archaeological pigs from Southeast Asia. The distribution of specimens shows a unique signature for the introduced domestic pigs. The reconstructed outlines depicted on the borders of the plot represent the shape changes corresponding to the component axes. Samples labeled with an F and a cross are modern Sus from Flores, and those labeled with LB and an open circle are archeological pigs from Liang Bua cave also on Flores. The drawing depicts a left third lower molar (M₃) in occlusal view (ant, anterior; ling, lingual).