Population Turnover in Remote Oceania Shortly after Initial Settlement

Abstract

Ancient DNA from Vanuatu and Tonga dating to about 2,900-2,600 years ago (before present, BP) has revealed that the "First Remote Oceanians" associated with the Lapita archaeological culture were directly descended from the population that, beginning around 5000 BP, spread Austronesian languages from Taiwan to the Philippines, western Melanesia, and eventually Remote Oceania. Thus, ancestors of the First Remote Oceanians must have passed by the Papuan-ancestry populations they encountered in New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture [1]. However, all present-day populations in Near and Remote Oceania harbor >25% Papuan ancestry, implying that additional eastward migration must have occurred. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu from 2900-150 BP, as well as 185 present-day individuals from 18 islands. We find that people of almost entirely Papuan ancestry arrived in Vanuatu by around 2300 BP, most likely reflecting migrations a few hundred years earlier at the end of the Lapita period, when there is also evidence of changes in skeletal morphology and cessation of long-distance trade between Near and Remote Oceania [2, 3]. Papuan ancestry was subsequently diluted through admixture but remains at least 80%-90% in most islands. Through a fine-grained analysis of ancestry profiles, we show that the Papuan ancestry in Vanuatu derives from the Bismarck Archipelago rather than the geographically closer Solomon Islands. However, the Papuan ancestry in Polynesia-the most remote Pacific islands-derives from different sources, documenting a third stream of migration from Near to Remote Oceania.

Keywords: Lapita; Near Oceania; Pacific Islanders; Remote Oceania; ancient DNA; migration.

Figure 1. Locations and broad-scale genetic structure of analyzed populations

(A) ADMIXTURE results with K=8 clusters for selected populations (full results in Figure S1). The analysis suggests three primary Papuan components (black maximized in New Guinea, blue in New Britain in the Bismarck Islands, and red maximized in the Solomon Islands) and a component maximized in First Remote Oceanians (green). (B) Population locations with colored clusters assigned based on the ratio of Papuan ancestry components in ADMIXTURE. We loosely adopt the color scheme from ADMIXTURE, with black indicating a New Guinea-like profile, blue a New Britain-like profile, red a Solomon Islands-like profile, and purple a profile mixed between New Britain and Solomon Islands. Level of fill in the bars indicates Papuan ancestry proportion. The map was plotted in R using the ‘maps’ package with data from http://www.naturalearthdata.com/. (C) Close-up of Vanuatu labeling islands for which new data are reported. Islands with ancient samples are indicated in red (for Efate and Ifira, both present-day and ancient individuals). The map was downloaded from http://www.maphill.com/vanuatu/simple-maps/blank-map/no-labels/. (D) Papuan ancestry proportions for ancient samples over time; Efate island is used to represent the present. See also Figure S2 and Data S1.

Figure 2. Ancestry proportions and dates of admixture in Vanuatu

Black points represent the 20 present-day populations with the most confident admixture date estimates from ALDER (as measured by Z-score for difference from zero), assuming 28 years per generation and showing one standard error in each direction. The red point represents a pair of ancient individuals with a mean calibrated date of 1283 BP (18 ± 6 generations, or 1800 ± 160 years BP). Gray shading indicates the Lapita period in Vanuatu (~3000-2700 BP). See also Data S1.

Figure 3. Inferred admixture graph model with diverse present-day Oceanian populations

Dotted lines denote admixture events. For five populations, the proportions of four fitted ancestry sources maximized in First Remote Oceanians (green), Solomon Islands (red), Bismarck Archipelago (blue) and New Guinea (black) are shown. Papuan ancestry is inferred to be highly simlar in the Tolai and in the Tongan pouplation, allowing Tongan to be fit as a mixture of a group with ancestry similar to Tolai and additional ancestry from First Remote Oceanians. Colors are chosen to be correlated to the components inferred from ADMIXTURE (Figure S1), but the ADMIXTURE components represent combinations of the sources given here, and hence the ratios differ between the methods. Full model parameters for the admixture graph are shown in Figure S3.