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

Rapa Nui, renowned for its iconic moai statues, is one of the most isolated inhabited places globally. Its history has been debated, with two main points of contention: the 'ecocide' theory, proposing a major population collapse due to resource overexploitation, and the possibility of pre-Columbian trans-Pacific contact with the Americas. The ecocide theory posits that the Rapanui population, once estimated at 15,000, drastically declined due to deforestation and resource depletion, leading to famine, warfare, and cannibalism in the 1600s. This would have resulted in a dramatic population decrease to a mere 10-20% of the original size before European contact in 1722. The theory of pre-Columbian contact posits that Polynesian voyagers reached the Americas before Columbus, leaving behind genetic traces in the Rapanui population. Previous genetic studies on modern Rapanui have shown Native American admixture, but ancient DNA studies yielded conflicting results. This study aims to resolve these controversies through high-coverage whole-genome sequencing of ancient Rapanui individuals, allowing for a robust investigation of population dynamics and admixture events.

The ecocide theory, popularized by Jared Diamond, has been challenged by various lines of bioanthropological, archaeological, and historical evidence. Studies have questioned the extent of deforestation and its impact on the population. Furthermore, the existence of pre-Columbian trans-Pacific contacts has been supported by archaeological findings such as the presence of sweet potatoes in Polynesia and genetic evidence suggesting Native American admixture in some Polynesian populations. However, previous ancient DNA studies on Rapa Nui yielded mixed results, with some failing to find evidence of Native American ancestry, even in samples post-dating the inferred admixture time. This discrepancy highlighted the need for a more comprehensive analysis of ancient Rapanui genomes with high-quality sequencing data.

The researchers analyzed whole-genome sequencing data from 15 ancient Rapanui individuals obtained from the Muséum national d’Histoire naturelle, France, and radiocarbon dated them (1670–1950 CE). Minimally invasive sampling methods were used to extract DNA from petrous bone and teeth. Whole genomes were sequenced to an average depth of 0.4–25.6×, with contamination estimated at <5%. Imputation techniques were used to improve the quality and completeness of the ancient genomes. The researchers employed several analytical approaches: (1) they compared the ancient Rapanui genomes to a panel of worldwide populations using multidimensional scaling and f-statistics to establish genetic relationships and ancestry; (2) they used HapNe-LD to reconstruct the effective population size of the Rapanui through time, testing for population bottlenecks consistent with the ecocide theory; (3) they employed ADMIXTURE and D-statistics to quantify and date Native American admixture in ancient and modern Rapanui individuals; (4) they used local ancestry inference with RFMix to identify and analyze Native American ancestry tracts in Ancient Rapanui genomes; (5) Finally they combined genetic and radiocarbon dating using a Bayesian approach to pinpoint the timing of the admixture event more precisely with ALDER and DATES, using admixture linkage disequilibrium and tract length distribution to estimate the admixture date. Extensive population genetic simulations were conducted to assess the consistency of the observed data with various demographic scenarios.

The study yielded several key findings: (1) the ancient Rapanui genomes were closely related to present-day Rapanui, confirming their ancestral connection. This will contribute to repatriation efforts; (2) effective population size reconstructions rejected the scenario of a severe population bottleneck in the 1600s proposed by the ecocide theory. Instead, the data suggested a small but steadily growing population; (3) both ancient and present-day Rapanui showed similar proportions of Native American admixture (approximately 10%). A Bayesian approach incorporating genetic and radiocarbon data placed the admixture event between 1250–1430 CE; (4) The source of the Native American admixture was most likely from the Central Andean Highlands, supporting pre-Columbian trans-Pacific contact; (5) The re-analysis of the publicly available data from Fehren-Schmitz et al., (2017), showed that the low-depth sequencing data used previously lacked the power to detect the Native American admixture statistically.

The findings directly address the long-standing debates about the Rapanui population history. The rejection of the ecocide theory suggests that the Rapanui population displayed resilience in the face of environmental change. This is contrary to the commonly accepted notion of environmental collapse. While acknowledging the impact of human activity on the environment, the study emphasizes the population's capacity to adapt and persist. The confirmation of pre-European contact with Native Americans reveals the extent of Polynesian voyaging and intercultural exchange across the Pacific. The estimated timing of admixture, significantly before European arrival, underscores the importance of considering the historical context when interpreting genetic patterns. The findings highlight the limitations of low-depth ancient DNA data and the importance of high-quality data for robust population genetic inferences.

This study provides compelling evidence against the ecocide theory and strongly supports pre-Columbian trans-Pacific contact between Polynesians and Native Americans. The high-quality ancient Rapanui genomes offer invaluable insights into the population's resilience and complex history. Future research could focus on expanding the ancient DNA dataset from other Polynesian islands to refine the understanding of trans-Pacific interactions and explore other possible admixture events. Further work may also be needed to better understand the environmental changes faced by the Rapanui population and their adaptability and resilience.

The study's focus on a limited number of ancient individuals may not fully represent the entire range of genetic diversity in the Rapanui population throughout history. The accuracy of the admixture dating relies on several modeling assumptions and parameters, like generation time, that inherently have some uncertainty associated with them. The resolution of the reference dataset used for the identification of the source population of Native American admixture might influence the precision of the ancestry identification. More ancient DNA data, especially from other Polynesian islands and wider sampling of Native American populations, would enhance the study's power and precision.