Local ancestry analysis of Rapanui and the Ancient Polynesian using phased shapeit2106: results from the phased 1000 Genomes project

Rapanui and the Ancient Polynesian people were used with the Hap Map genetic map in order to conduct local ancestry inference. For all individuals in this analysis, we phased their diploid genotypes using shapeit2106 with the phased 1000 Genomes project. The description of this analysis and validation experiments is presented in Supplementary Information section 13. 38 and 40.

We used PLINK v 1.9.2020071247 to detect ROH. hapRoh was used to find ROH in haploid mode. To do so, we used pileupCaller (https://github.com/stschiff/sequenceTools) following ref. 103 to generate pseudohaploid calls at the 1240K sites with output in eigenstrat format, as required by hapROH. Following ref. 104, we ran PLINK with the following command to detect ROH in imputed ancient genomes and high-coverage present-day genomes: plink –bfile input –homozyg –homozyg-kb 500 –homozyg-gap 100 –homozyg-density 50 –homozyg-snp 50 –homozyg-window-het 1 –homozyg-window-snp 50 –homozyg-window-threshold 0.05 –out output. We restricted this analysis to transversion SNPs and filtered imputed genotypes (MAF > 1% and GP ≥ 0.99). We describe these analyses in detail in Supplementary Information section 10 and present validation results in Supplementary Figs. 25–27 and Supplementary Tables 17–21.

We used genetic admixture dates and radiocarbon dates to estimate the time of a particular event for each individual. We were able to model two separate phases with the help of OxCal29, which took into account the time the human remains were collected. For each dated individual, we used the mean number of generations elapsed since introgression based on the per-individual tracts estimates as a constraint to calculate an ‘introgression’ date in the Bayesian model. Supplementary Information section 15 contains model specifications.

Laboratory Work in the Rapanui Archaeologistics Using GLIMPSE v.1.1.131 (Lambda Papua New Zealand)

We had meetings with representatives of the Rapanui community on the island. During these meetings we presented our research goals and preliminary results and enquired and discussed about research questions of particular interest to the Rapanui community (see below). The commissions voted in favor of the research. The meeting minutes can be found in the summaries of these meetings. We presented our findings and interpretations to the public in a lecture at the Rapa Nui Museum, as well as giving a presentation to the Rapanui community. The staff of the Rapa Nui Museum helped us with these activities.

We used GLIMPSE v1.1.131 to impute whole-genome sequencing data using the 1000 Genomes v5 phase 3100,101 as a reference panel following ref. 99. A description of our imputation validation is presented in Supplementary Information section 5.

We called majority rule mtDNA consensus sequences for each individual and used HaploGrep288 to assign mtDNA haplogroups. To call the Y-chromosome haplogroups, we used pathPhynder89 and the ISOGG Y-chromosome reference data.

The Globe Institute has dedicated clean laboratory facilities for ancient DNA work. We started by taking the saliva from teeth and then continued on to take the bone powder. We generated double-stranded73,76 and single-stranded77 libraries from standard and USER-treated78 DNA extracts and sequenced the whole genomes from the 15 Ancient Rapanui individuals using Illumina HiSeq and NovaSeq instruments. Supplementary information section 1 has a detailed description of the laboratory work.

We used the v 1.5.409 to trim the Illumina adaptor sequence, leading N bases, trailing quality-2 runs and collapse reads over 11 bases. Collapsed reads were mapped without seeding following ref. It was 81. We retained mapped reads with a mapping quality greater than 30, removed PCR duplicates using picard MarkDuplicates (http://picard.sourceforge.net), carried out local realignment using GATK82 and computed the MD tag and extended BAQ for each read using the samtools calmd command. The data processing procedures are described in Supplementary Information section 3 and mapping statistics are included in Supplementary Table 1.

The Last Nail in the Collapse Narrative of Rapa Nui’s Early Indigenous Peoples: Evidence from Ancient Genomes from Their Descendants

Now, a study of ancient genomes from descendants of these voyagers has answered key questions about the island’s history, dispelling the idea of a population collapse hundreds of years ago, and confirming precolonial contact with Indigenous Americans.

The author of Collapse said that Rapa Nui’s early Indigenous inhabitants caused its population to crash before the Europeans arrived, but other scholars have since criticized that theory.

The latest analysis, published on 11 September in Nature1, “serves as the final nail in the coffin of this collapse narrative”, says Kathrin Nägele, an archaeogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. It is changing the image of Indigenous people.

Rapa Nui was settled by the ancient Polynesian people around 1200, which is when they started to develop their culture of stone statues.

When Europeans first reached the island in 1722, they estimated that it had a population of between 1,500 and 3,000 people and found a landscape denuded of the palm-tree forests that would have once covered the island. By the 19th century, the Rapanui population had dwindled to less than 100 people because of a disease and the abduction of a third of them from their homes.

The ‘ecocide’ theory, that a pre-contact population of 15,000 or more plundered the once-pristine island’s resources, has been challenged by researchers who have questioned humans’ role in deforestation and its effects on food production, as well as the large estimates for the population.

Vctor Moreno-Mayar and Anna-Sapfo Malaspinas are both evolutionary geneticists with the University of Lausanne, Switzerland, and they hope that ancient Rapanui DNA can address the ecocide theory.

Both ancient and modern genomes carry information about how a population’s size has changed over time. When the population is small, segments of DNA shared between individuals — which are inherited from a common ancestor — tend to be longer and more abundant, compared with DNA segments from periods when numbers are higher.

The genetic data might not be consistent with a drop from as many as 15,000 to fewer than 3000 people in the 18th century. “There’s no strong collapse,” says Malaspinas. We are pretty sure that it didn’t happen.

It will come as no surprise to Polynesian people, says Keolu Fox, a genome scientist at the University of California, San Diego. “We’re confirming something we already knew,” he says. “Do you think that a community that found things like Hawaii or Tahiti would miss a whole continent?”

Malaspinas and her colleagues got approval for the study from committees that oversee land use and cultural heritage on the island. Malasipinas regrets that the researchers requested their permission to sample the remains in Paris. “I would do things differently if I had started the project today,” she says, adding that her team was prepared to shelve the work if the committees had said no.

Nägele, who works in Polynesia, thinks the researchers did a good job of engaging with people in Rapa Nui. But she adds that scientists should have a stronger role in pressuring foreign institutions to return Indigenous remains to their place of origin.