Pre-European contact with the Americas is revealed by the Rapanui genomes

Exploring the genetic ancestry of the Ancient Rapanui using multidimensional scaling: PLINK and hapROH analyses and Bayesian modelling

We explored the broad continental genetic affinities of Ancient Rapanui individuals using multidimensional scaling. There is aSupplementary Information section 6. As a complementary approach, we explored the genetic ancestry components of the Ancient Rapanui using ADMIXTURE55. To reduce the effect of strong drift in Polynesian individuals, we ran separate treatments for each individual. For every run, we considered 20 independent replicates and present the results for the replicate with the highest likelihood. We present a detailed description of our ADMIXTURE analyses in Supplementary Information section 12 and estimated admixture proportions in Supplementary Table 25.

We used PLINK and hapROH46 to detect ROH. The model that we used to find ROH was the haploid model. We used pileup Caller to generate pseudohaploid calls at the 1240k sites, 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. The analysis was restricted to transversion SNPs and imputed genotypes. In section 10, we describe the analyses and present the validation results. 25–27 and Supplementary Tables 17–21.

We used a new Bayesian modelling approach to estimate admixture times using genetic admixture dates and radiocarbon dates for each individual jointly. Using OxCal29, we modelled two separate dated phases with termini ante quem corresponding to the time human remains were collected, accounting for their marine C intake and consequent reservoir offsets. The per-individual tracts estimates are used to estimate the mean number of generations elapsed since the start of introgression. Model specifications are presented in Supplementary Information section 15.

Preliminary results of the 1000 Genomes v5 phase 3100,101 at the Rapa Nui Museum and the present-day presence of Human DNA contamination

A draft of this manuscript was shared with representatives from the Rapa Nui museum before submission. Following peer review, the published manuscript will be stored at the Rapa Nui Museum Library and results will be summarized in an outreach poster that will be displayed at the Rapa Nui Museum. Finally, we will submit a report with a summary of the published results to both commissions.

The 1000 Genomes v5 phase 3100,101 was imputeed as a reference panel following ref. 99. There is a description in the Supplementary Information section and validation results presented in the Supplementary Table 3.

We determined the chromosomal sex of the Ancient Rapanui individuals by examining the depth of coverage ratio on the X chromosome and the autosome (Supplementary Fig. 2). We assessed the authenticity of the sequencing data by inspecting the length distributions and misincorporation patterns of the mapped reads using bamdamage36 (Supplementary Fig. 3). We computed type-specific error rates using ANGSD v0.93083. We estimated the proportion of present-day human mtDNAContamination using contamMix84 and a majority rule consensus for each individual. We estimated the proportion of present-day human nuclear DNA contamination in XY individuals using contaminationX86 on reads with a mapping quality ≥30, bases with quality ≥20, sites with depth between 3 and 20 and the HapMap CEU allele frequencies87. A detailed description of the authentication procedures is included in Supplementary Information section 3.

Ancient DNA work was conducted in dedicated clean laboratory facilities at the Globe Institute, University of Copenhagen. We extracted DNA from teeth and petrous bone powder following ref. 73 and refs. 74,75, respectively. We were able to sequence the whole genomes from the 15 Ancient Rapanui individuals using the Illumina HiSeq and NovaSeq instruments. There is a description of the lab work in the Supplementary Information section.

We used AdapterRemoval v1.5.379 to trim Illumina adaptor sequences, leading N bases and trailing quality-2 runs and collapse paired-end reads overlapping over ≥11 bases. The collapsed reads were mapped with bwa aln. There is a column called 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. A detailed description of the data processing procedures is presented in Supplementary Information section 3 and mapping statistics are included in Supplementary Table 1.

The Final Nails in Rapa Nui’s Collapse Narration: DNA Evolution Across the Different Ages and Population Trajectories

The study of ancient genomes from descendants of the voyagers has answered a number of important questions about the history of the island, with the most important being the idea that there was no decline in population hundreds of years ago.

The theory that the natives of Rapa Nui decimated the island’s flora and fauna before the arrival of Europeans in the 18th century was popularized in the 2006 book Collapse, but some other scholars have since criticized it.

The analysis published on September 11, in Nature1, serves as the final nail in the coffin of the collapse narrative, according to Kathrin Ngele. “It’s correcting the image of Indigenous people.”

Rapa Nui gave birth to a thriving culture famous for its hundreds of stone statues, called moai.

Europeans first came to the island in 1718, estimating that it had as many as 3000 people and finding a landscape devoid of palm- tree forests. The Indigenous population, called the Rapanui, had dwindled to a small number by the late 19th century due to disease and the kidnapping of one-third of the inhabitants.

The 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.

An evolutionary geneticist and a population geneticist at the University of Lausanne, Switzerland, were hoping ancient Rapanui DNA was able to address the ecocide theory.

Information about how a population has changed over time can be found in both ancient and modern genomes. 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.

Translating these trajectories into actual population numbers is not straightforward, but further modelling suggested that the genetic data are not consistent with, for example, a drop from 15,000 to 3,000 people before the eighteenth century. “There’s no strong collapse,” says Malaspinas. “We’re quite confident that it did not happen.”

Keolu Fox, a genome scientist at the University of California, San Diego, says the finding that Rapanui reached the Americas will come as no surprise to Polynesian people. “We’re confirming something we already knew,” he says. Do you think the community that found Hawaii or Tahiti would miss a big part of the world?

Malaspinas and her colleagues got approval for the study from committees that oversee land use and cultural heritage on the island. The researchers sought their permission after sampling the remains in Paris — something Malasipinas now regrets. “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. She thinks that the scientists should have more of a role to play in getting Indigenous remains returned to their place of origin.