Language continuity despite population replacement in Remote Oceania

Abstract

Recent genomic analyses show that the earliest peoples reaching Remote Oceania-associated with Austronesian-speaking Lapita culture-were almost completely East Asian, without detectable Papuan ancestry. However, Papuan-related genetic ancestry is found across present-day Pacific populations, indicating that peoples from Near Oceania have played a significant, but largely unknown, ancestral role. Here, new genome-wide data from 19 ancient South Pacific individuals provide direct evidence of a so-far undescribed Papuan expansion into Remote Oceania starting ~2,500 yr BP, far earlier than previously estimated and supporting a model from historical linguistics. New genome-wide data from 27 contemporary ni-Vanuatu demonstrate a subsequent and almost complete replacement of Lapita-Austronesian by Near Oceanian ancestry. Despite this massive demographic change, incoming Papuan languages did not replace Austronesian languages. Population replacement with language continuity is extremely rare-if not unprecedented-in human history. Our analyses show that rather than one large-scale event, the process was incremental and complex, with repeated migrations and sex-biased admixture with peoples from the Bismarck Archipelago.

Fig. 1. Spatial and genetic distribution of ancient and present-day individuals.

(a) Principal component analysis of modern-day East Asian and Near and Remote Oceanian populations genotyped on the Affymetrix Human Origins Array, with 23 ancient individuals projected. Ancient samples are indicated by filled symbols – the new data from this study have a black border – and present-day samples are indicated by open symbols. (b) Regional map, showing locations of Near and Remote Oceanian sample populations and ancient individuals.

Fig. 2. Admixture proportions of Papuan- vs. Lapita-related ancestry in ancient and present-day populations using 1240K genome-wide data.

(a) Unsupervised ADMIXTURE analyses of present-day global populations and ancient Pacific individuals, with 5 ancestral components. (b) Austronesian ancestry proportion (modeled by indigenous Taiwanese population Ami) in ancient and present-day Vanuatu individuals estimated through qpAdm analyses. Symbol legend is given in Fig. 1, and standard errors are indicated by black lines if larger than the symbol (see also Supplementary table 8).

Fig. 3. Demographic history of ancient Vanuatu individuals.

(a) qpGraph model that fits observed allele frequency patterns with branch lengths representing drift in F_ST*1000 units and edge percentages indicating admixture proportions. Ancient samples or groups are indicated with a red border. (b) ALDER analyses estimating the date of Papuan and East Asian admixture, converted into years with a generation time of 28.1 years. Standard error bars are shown for date estimates, while sample ages for the two ancient groups (Futuna and Malakula) are averaged radiocarbon dating confidence interval (CI) midpoints. As the earliest ancient Vanuatu individual with unadmixed Near Oceanian ancestry, TAN002 is included for age comparison, with error bar indicating the 95.4% radiocarbon dating CI.