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

Rapa Nui (also known as Easter Island) is one of the most isolated inhabited places in the world. It has captured the imagination of many owing to its archaeological record, which includes iconic megalithic statues called moai1. Two prominent contentions have arisen from the extensive study of Rapa Nui. First, the history of the Rapanui has been presented as a warning tale of resource overexploitation that would have culminated in a major population collapse—the ‘ecocide’ theory2–4. Second, the possibility of trans-Pacific voyages to the Americas pre-dating European contact is still debated5–7. Here, to address these questions, we reconstructed the genomic history of the Rapanui on the basis of 15 ancient Rapanui individuals that we radiocarbon dated (1670–1950 ce) and whole-genome sequenced (0.4–25.6×). We find that these individuals are Polynesian in origin and most closely related to present-day Rapanui, a finding that will contribute to repatriation efforts. Through effective population size reconstructions and extensive population genetics simulations, we reject a scenario involving a severe population bottleneck during the 1600s, as proposed by the ecocide theory. Furthermore, the ancient and present-day Rapanui carry similar proportions of Native American admixture (about 10%). Using a Bayesian approach integrating genetic and radiocarbon dates, we estimate that this admixture event occurred about 1250–1430 ce.


Statistics
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Software and code
Policy information about availability of computer code Data collection DNA libraries were sequenced in Illumina HiSeq 4000 and NovaSeq instruments.Radiocarbon measurements were undertaken at the ORAU (Oxford Radiocarbon Accelerator Unit) and BRAMS (Bristol Radiocarbon AMS) facilities.

Data analysis
Here we list the software that was used in this work.References for each software are included in the main text and supplementary information.
-Relatedness between individuals was estimated using READ commit f541d55 and ngsRelate v2 commitc327f744d76a17e1d17ecac88fd92b3ac82a0b07.
-Radiocarbon date calibration and admixture dating bayesian modelling were performed using OxCal 4.4.
For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers.We strongly encourage code deposition in a community repository (e.g.GitHub).See the Nature Portfolio guidelines for submitting code & software for further information.

Data Policy information about availability of data
All manuscripts must include a data availability statement.This statement should provide the following information, where applicable: -Accession codes, unique identifiers, or web links for publicly available datasets -A description of any restrictions on data availability -For clinical datasets or third party data, please ensure that the statement adheres to our policy Following consultation with the Comisión Asesora de Monumentos Nacionales (CAMN), the 'Ancient Rapanui' sequencing data will be made available upon request to the corresponding authors.Access requests will be managed jointly with CAMN representatives.'Ancient Rapanui' sequencing data is not available for public posting, medical research or commercial purposes.
Publicly available data was obtained from the following sources: - Research involving human participants, their data, or biological material Policy information about studies with human participants or human data.See also policy information about sex, gender (identity/presentation), and sexual orientation and race, ethnicity and racism.

Reporting on sex and gender
We determined the chromosomal sex of the ancient individuals by comparing the depth of coverage in the autosomes and the X-chromosome.We highlight that our findings on chromosomal sex do not provide any information on the gender identity of the individuals we sequenced in this study.We do not carry any analyses where we stratify the data by chromosomal sex.
Reporting on race, ethnicity, or other socially relevant groupings We refer to the 15 ancient individuals that were sequenced in this study as 'Ancient Rapanui'.This is based on the museum records indicating these individuals were sampled in Rapa Nui and our results showing the ancient individuals are most closely related to present-day Rapanui.For the publicly available reference data, we use labels that describe their broad continental genomic ancestry as established in their original publications.

Recruitment
Following strict museum guidelines, we sampled petrous bone and teeth material from 15 individuals-labelled as Rapanuifrom the Musée National d'Histoire Naturelle, France, Pinart (1877) and Métraux (1935) collections using a minimallyinvasive method.This included the retrieval of loose teeth whenever the remains were sufficiently well preserved and enough teeth were present (four individuals) and up to 120mg (60-120mg) of petrous bone powder in other cases (11 individuals).

Ethics oversight
Throughout the course of the study, we met with representatives of the Rapanui community on the island, the Comisión de Desarrollo Rapa Nui (CODEIPA) and the Comisión Asesora de Monumentos Nacionales (CAMN), where we presented our research goals and ongoing results.Both commissions voted in favour of us continuing with the research and the results of our study have been communicated to the community prior to the first submission of our manuscript.Furthermore, we presented the research project in public talks, a short video and radio interviews on the island giving us the opportunity to inquire about the questions that are most relevant to the Rapanui community.These discussions have informed the research