Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas

Rapa Nui (Easter Island), at the eastern edge of the Polynesian Triangle, is among the most isolated inhabited places on Earth. Archaeological and genetic evidence indicate Polynesian settlement around 1150–1280 CE, with subsequent development of a distinctive culture including moai statues and ahu platforms. European contact occurred in 1722 and was followed by violence, disease, and 1860s Peruvian slave raids and smallpox, reducing the population to an estimated ~110 individuals. Two central pre-contact demographic questions remain contentious: (1) whether the Rapanui experienced a severe, human-mediated population collapse in the 1600s (“ecocide” hypothesis) following deforestation and resource depletion; and (2) whether Polynesians and Native Americans made trans-Pacific contact prior to European arrival. This study addresses both questions using genome-wide data from 15 radiocarbon-dated ancient Rapanui individuals.

The ecocide hypothesis posits extensive deforestation and overexploitation culminating in famine, warfare (the ‘Huri Moai’ phase), cannibalism, and a population crash from ~15,000 to 1,500–3,000 by the 1700s. Multiple archaeological, bioanthropological, and historical studies have challenged this scenario, suggesting resilience and small but stable pre-contact populations. Regarding Native American contact, material culture and biotic evidence (for example, sweet potato dispersal, putative pre-Columbian chickens in Chile) have been debated. Genetic studies of present-day Rapanui report Native American and European admixture, with the Native American component dated to 13th–15th centuries CE, predating European admixture. Broader analyses detected Native American gene flow across several Polynesian islands with dates spanning ~1150–1380 CE. However, prior ancient DNA studies from Rapa Nui (mtDNA from 12 individuals; ultra-low depth whole-genome data from 5 individuals) did not detect Native American ancestry, potentially due to low sequencing depth limiting statistical power.

Community engagement included presentations and consultations with Rapanui community representatives and Chilean commissions, with approvals and ongoing communication of results. Samples: 15 individuals labeled as Rapanui from Muséum national d’Histoire naturelle (Pinart 1877 and Métraux 1935 collections). Sampling followed minimally invasive protocols using petrous bones (60–120 mg powder; n=11) and loose teeth when available (n=4). Radiocarbon dating was performed at Oxford Radiocarbon Accelerator Unit and Bristol Radiocarbon Accelerator Mass Spectrometer, with δ13C correction and calibration including marine reservoir effects; calibrated dates broadly span 1670–1950 CE and predate museum collection dates. Whole-genome sequencing yielded mean coverage 0.4–25.6× with <5% contamination per library. Genotype imputation: GLIMPSE used to generate diploid genotypes, validated via benchmarking and downsampling; analyses replicated with pseudohaploid calls where appropriate. Comparative datasets included SNP arrays from present-day Rapanui and genome data from two ancient Polynesians (unknown island). Population structure and relatedness: Multidimensional scaling on 755,094 SNPs; f-statistics f(Yoruba; X, Ancient Rapanui) for worldwide and Oceanian panels; IBD inference with IBDseq and ancIBD to quantify sharing with Remote Oceanians. Kinship and inbreeding: READ and NGSrelate for kinship; runs of homozygosity inferred with hapROH (pseudohaploid) and PLINK (imputed, transitions excluded). Demography: Effective population size trajectory over last ~100 generations using HapNe-LD; extensive coalescent simulations using msprime modeling two bottlenecks (peopling and putative ecocide collapse) and post-bottleneck growth (parameters Tb1, Sb1, Tb2, Sb2, α). Model fit assessed by distances between HapNe-LD curves and ROH summaries. Admixture analyses: ADMIXTURE (K=5,6) run per Remote Oceanian to minimize drift effects; D-statistics testing excess allele sharing with Native Americans and Europeans; f-ratio to estimate Native American admixture proportion. Local ancestry with RFMix to identify Polynesian, Native American, and European tracts; source affinity of Native American tracts assessed with f-statistics and corroborating D-statistics. Admixture dating: ALDER and DATES for weighted LD decay; tract-length-based dating from RFMix tracts under a two-way Polynesian–Native American model. Bayesian modeling combined individual genetic admixture-date estimates with reservoir-corrected radiocarbon phases (Pinart 1877, Métraux 1935) to infer a population-level calendar-date for admixture assuming 25–30-year generation times.

• All 15 ancient individuals cluster within Polynesian genetic diversity and share the most drift and longest IBD segments with present-day Rapanui, confirming Rapanui origin and supporting museum records; useful for repatriation efforts. - Relatedness: No first- or second-degree relatives; only one pair shows third–fourth-degree relatedness by IBD; pairwise inbreeding coefficients <0.01 (GL-based) / <0.02 (imputed). - ROH: Ancient Rapanui exhibit large total ROH compared to many world populations (average total length ~198 cM vs ~25 cM in Eurasia with hapROH), but predominantly short segments (≈80% of ROH <12 cM), indicating low long-term effective population size without evidence of frequent close-kin unions pre-1860s. - Demography: HapNe-LD shows a decline to a minimum ~28 generations (~800 years) before average birth time, followed by steady increase; simulations favor models without a 1600s collapse (bottleneck 2 strength ~0%) and modest growth (α < 0.3% per year). Strong/intermediate post-peopling bottlenecks (≤50% remaining) are inconsistent with observed data (permutation P < 1e-5); ROH distributions also reject very strong bottleneck scenarios (Sb2 ≤ 0.2). - Admixture proportions: ADMIXTURE and D-statistics detect ~10% Native American ancestry in Ancient Rapanui (estimated 6.5–12.4% by f-ratio) and no European ancestry; present-day Rapanui carry similar Native American (~8–10%) plus European components. - Source of Native American ancestry: f-statistics restricted to Native American tracts indicate the closest affinity to ancient and present-day Central Andean Highlands populations, robust to reference panel variations. - Admixture timing: Weighted LD decay (DATES/ALDER) and tract-based inference indicate admixture 15–17 generations before the mean birth date of the ancient individuals. Bayesian integration with radiocarbon phases estimates a calendar date of 1336–1402 CE (68.3% probability) and 1246–1425 CE (95.4%), i.e., centuries before European contact (1722) and well before Columbus. - Reanalysis of prior ultra-low-depth ancient Rapanui genomes explains earlier null results as lack of power; using the current pipeline, weak Native American-like components are detectable in 3/5 prior individuals by ADMIXTURE.

The genomic data directly address two long-standing debates. First, demographic inference from LD and ROH, supported by simulations, finds no evidence of a severe Rapanui population collapse in the 1600s attributable to ecocide. Instead, the population appears small but demographically resilient, with effective size increasing gradually from initial settlement until the upheavals of the 19th century. While environmental impacts (e.g., deforestation, rat introductions) are documented, the genomic record does not support a pre-contact demographic crash. Second, consistent Native American ancestry (~10%) in all ancient individuals, absence of European ancestry, Andean source affinity, and admixture dates centered in the 13th–15th centuries together provide strong evidence for pre-European trans-Pacific contact between Polynesians and Native Americans. The overlap of admixture timing with or shortly after the peopling of Rapa Nui suggests contact near this period; concordant signals across ancient and present-day Rapanui imply sustained or repeated contacts may have occurred in Polynesia. Directionality and number of voyages cannot be resolved solely from these data, but archaeological and oral histories attest to Polynesian voyaging capabilities. The confirmation that these remains are Rapanui ancestors has implications for community-led repatriation.

This study presents 15 radiocarbon-dated ancient Rapanui genomes, demonstrating close affinity to present-day Rapanui and enabling robust demographic and admixture inferences. The results refute a 1600s population collapse prior to European contact and establish pre-European admixture with Native Americans, likely from Central Andean Highlands groups, dated to approximately 1250–1430 CE. These findings highlight demographic resilience on Rapa Nui and substantiate trans-Pacific contacts before European arrival. Future research should: (1) expand ancient genomic sampling across Polynesian islands to resolve the timing, frequency, and geography of contacts; (2) broaden pre-contact genomic coverage in Central and South America (particularly Pacific coastal regions, e.g., Ecuador, Colombia, Peru) to better identify source populations; and (3) integrate genomic, archaeological, linguistic, and paleoenvironmental data for a comprehensive reconstruction of Rapa Nui’s population and environmental history. The genomic confirmation of Rapanui origin supports ongoing repatriation initiatives.

• The genomic data illuminate demographic history but cannot directly quantify ecological impacts or causality of environmental change; absence of a genomic collapse signal does not preclude significant ecological transformations. - Source resolution for Native American ancestry is limited by sparse and uneven pre-contact genomic sampling in Central and South America; short internal divergences among Native American groups further limit phylogeographic precision. - Admixture analyses cannot determine the number or directionality of voyages; signals are consistent with single or multiple events. - HapNe-LD trajectories are used comparatively rather than for absolute effective population sizes; translating Ne to census sizes is inherently uncertain. - Present-day Rapanui demography is harder to model due to heterogeneous post-contact ancestry. - Temporal coverage: most ancient individuals postdate initial European contact, though they predate the 1860s demographic shocks; sample size is 15 individuals. - Prior low-depth ancient datasets lack power for formal tests, complicating direct comparisons.