Paths and timings of the peopling of Polynesia inferred from genomic networks

In the paper

“Meanwhile, ancient DNA studies have sequenced only four samples from one island in western Polynesia and three near-modern samples from one island in eastern Polynesia, all with low genotype density, still lower between-sample genotype overlap, and different time frames17,18.”

What the sources say

• Disputed

  The paper’s ancient-DNA passage (section labeled Abstract; page unavailable) explicitly places its four sequenced individuals on two islands: three on Efate, Vanuatu, and one on Tongatapu, Tonga—not four on one western Polynesian island. It reports 139,461–231,944 covered SNPs per individual, but does not report three near-modern eastern Polynesian samples or the claimed between-sample genotype overlap. (LLM, conf=0.88)

  Checked by a reasoning model — may be wrong.

  cites [17] Skoglund, P. et al. Genomic insights into the peopling of the Southwest Pacific. Nature 538, 510–513 (2016). sourceExperimental — accuracy not yet measured
• Partly supported

  The Results (‘Different genetic trajectory in Polynesia’; page unavailable) report three genome-wide samples from Ra’iātea, eastern Polynesia, dated to the 18th century. The paper also reports three Tongan samples, but does not establish the claimed total of four western Polynesian samples from one island; nor does it state that all samples had low genotype density or quantify between-sample overlap. (LLM, conf=0.84)

  cites [18] Posth, C. et al. Language continuity despite population replacement in Remote Oceania. Nat. Ecol. Evol. 2, 731–740 (2018). sourceExperimental — accuracy not yet measured

In the paper

“Standard errors for all allele frequency based statistics were computed using the block-bootstrap using 100 replicates and a block size of 1000 markers86.”

What the sources say

• Disputed

  The Methods Summary (page not available in our copy) says standard errors were computed using a Block Jackknife, not a block bootstrap. It does not give the claimed 100 replicates or 1,000-marker block size. (LLM, conf=0.89)

  Checked by a reasoning model — may be wrong.

  cites [86] Patterson, N. et al. Reconstructing Indian population history. Nature 461, 489–494 (2009). sourceExperimental — accuracy not yet measured

In the paper

“Previous region-wide Polynesian genetics studies have considered only globin gene polymorphisms14, or have been restricted to near (western) Polynesia15 and the Society Islands16 and lacked an ancestry-specific approach.”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [14] Hill, A. V. S. et al. Polynesian origins and affinities: globin gene variants in eastern Polynesia. Am. J. Hum. Genet. 40, 453–463 (1987).
• ?Not checked — no full text of the sourcecites [15] Wollstein, A. et al. Demographic history of Oceania inferred from genome-wide data. Curr. Biol. 20, 1983–1992 (2010). source
• Supported

  The Results (Data; page unavailable) identify this as a genomic study of individuals from the Leeward Society Islands. The Materials and Methods (Autosomal analysis; page unavailable) describe analyses of combined genomic data rather than an ancestry-specific approach. The globin-gene and western-Polynesia clauses are attached to other citations, not this source. (LLM, conf=0.84)

  cites [16] Hudjashov, G. et al. Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles. Sci. Rep. 8, 1823 (2018). source

In the paper

“Geological analyses of Polynesian trade goods, particularly adzes, indicate that the remote Polynesian islands remained in trade contact with one another for several centuries25,28,29.”

What the sources say

• ?Not checked — no full text of the sourcecites [25] Kirch, P. V. et al. Human ecodynamics in the Mangareva Islands: a stratified sequence from Nenega-Iti Rock Shelter (site AGA-3, Agakauitai Island). Archaeol. Oceania 50, 23–42 (2015). source
• Supported

  The Abstract reports geochemical sourcing of adze material imported to Mangaia from several distant archipelagos for more than 300 years, beginning in the early AD 1300s. The Conclusions describe this as an interaction network involving at least three archipelagos, supporting the claim of sustained contact through exchange. (LLM, conf=0.92)

  cites [28] Weisler, M. I. et al. Cook Island artifact geochemistry demonstrates spatial and temporal extent of pre-European interarchipelago voyaging in East Polynesia. Proc. Natl Acad. Sci. USA 113, 8150–8155 (2016). source
• ?Not checked — no full text of the sourcecites [29] Collerson, K. D. & Weisler, M. I. Stone adze compositions and the extent of ancient Polynesian voyaging and trade. Science 317, 1907–1911 (2007). source

In the paper

“The Polynesians are predominantly descended from Austronesian-speaking voyagers17”

What the sources say

• Partly supported

  The paper’s ancestry-model passage (labelled Abstract in our copy; no page given) identifies a population related to the First Remote Oceanians as the primary component in present-day Polynesians, and describes seafaring settlement of Remote Oceania. It does not establish that those ancestral voyagers spoke Austronesian languages; the Extended Data table labels some present-day sampled populations Austronesian-speaking, but not the ancient voyagers. (LLM, conf=0.82)

  cites [17] Skoglund, P. et al. Genomic insights into the peopling of the Southwest Pacific. Nature 538, 510–513 (2016). sourceExperimental — accuracy not yet measured

In the paper

“Our date for the settlement of Rapa Nui is consistent with Wilmshurst and Mulrooney and also agrees closely with the date found by Hunt et al. (1200 CE) based on analyses of pollen in lake cores and soil erosion patterns42, as well as with recent radiocarbon dates of archaeological sites43.”

What the sources say

• ?Could not verify

  The Radiocarbon Dating Results from Fa’ahia section describes dates from Huahine, while General points discusses colonization estimates for other East Polynesian island groups. Searches for Rapa Nui or Easter Island settlement, Wilmshurst, Mulrooney, and Hunt’s 1200 CE estimate found no passage assessing the claimed agreement with Rapa Nui archaeological dates. (LLM, conf=0.74)

  cites [42] Anderson, A. J., Conte, E., Smith, I. & Szabo, K. New excavations at Fa’ahia (Huahine, Society Islands) and chronologies of central East Polynesian colonization. J. Pac. Arch. 10, 1–14 (2019). sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [43] Hunt, T. L. & Lipo, C. P. Evidence for a shorter chronology on Rapa Nui (Easter Island). J. Island Coast. Archaeol. (2008). source

In the paper

“Meanwhile, the archaeological estimates for settlement dates remain debated, and have recently been revised forward across eastern Polynesia by up to a millennium2–4,12,13.”

What the sources say

• ?Not checked — no full text of the sourcecites [2] Kirch, P. V. On the Road of the Winds (Univ. of California Press, 2017). source
• ?Not checked — no full text of the sourcecites [3] Mulrooney, M. A., Bickler, S. H., Allen, M. S. & Ladefoged, T. N. High-precision dating of colonization and settlement in East Polynesia. Proc. Natl Acad. Sci. USA 108, E192–E194 (2011). source
• ?Not checked — no full text of the sourcecites [4] Schmid, M. M. E. et al. How 14C dates on wood charcoal increase precision when dating colonization: the examples of Iceland and Polynesia. Quat. Geochronol. 48, 64–71 (2018). source
• Partly supported

  The introduction says East Polynesian settlement dates remain debated, with long and short chronologies differing by 400–1,000 years. The Results and Discussion report a revised, later colonization chronology, but say it shortens the estimated age by up to 2,000 years relative to some earlier claims. Thus the stated ceiling of a millennium does not capture the full range reported by this source. (LLM, conf=0.84)

  cites [12] Wilmshurst, J. M., Hunt, T. L., Lipo, C. P. & Anderson, A. J. High-precision radiocarbon dating shows recent and rapid initial human colonization of East Polynesia. Proc. Natl Acad. Sci. USA 108, 1815–1820 (2011). sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [13] Spriggs, M. & Anderson, A. Late colonization of east Polynesia. Antiquity 67, 200–217 (1993). source

In the paper

“Unlike earlier methods69, this method permits the use of all samples, rather than only a panel of reference samples, for the completion step; thus, far more data is used allowing for more accurate completion.”

What the sources say

• ?Could not verify

  The Introduction describes Procrustes analysis for comparing spatial maps, including plots whose sample sets only partially overlap. Searches for matrix completion, reference panels, missing entries, and imputation found no passage about using all samples in a completion step or improving completion accuracy. Page numbers were not provided in our copy. (LLM, conf=0.75)

  cites [32] Wang, C. et al. Comparing spatial maps of human population-genetic variation using procrustes analysis. Stat. Appl. Genet. Mol. Biol. 9, 13 (2010). sourceExperimental — accuracy not yet measured
• ?Could not verify

  The passage on reference panels (section labeled Abstract; page unavailable) concerns haplotype sharing in Mexican samples, not a matrix-completion method. Searches for matrix completion, the completion step, and missing-data imputation found no passage saying that all samples can be used for completion or that doing so improves accuracy. (LLM, conf=0.76)

  cites [68] Moreno-Estrada, A. et al. The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science 344, 1280–1285 (2014). sourceExperimental — accuracy not yet measured

In the paper

“Native American ancestry, particularly from emigration of admixed Hispanic individuals from Chile, which annexed Rapa Nui (Easter Island), and African ancestry also entered32.”

What the sources say

• ?Could not verify

  The Introduction discusses comparisons of genetic-variation maps and CNV datasets, but does not address ancestry entering Polynesia. Searches for Rapa Nui, Chilean migration, Native American ancestry, and African admixture found no passage supporting the claim in our copy. (LLM, conf=0.76)

  cites [32] Wang, C. et al. Comparing spatial maps of human population-genetic variation using procrustes analysis. Stat. Appl. Genet. Mol. Biol. 9, 13 (2010). sourceExperimental — accuracy not yet measured

In the paper

“This gives better variance estimates than the jackknife for these pairwise allele frequency comparisons34.”

What the sources say

• ?Could not verify

  The Methods Summary describes leave-one-out cross-validation, and the Methods describe SNP filtering and association simulations. Neither those passages nor searches for “block bootstrap,” “jackknife,” and “variance estimates” address a comparison of the two methods for pairwise allele-frequency comparisons. (LLM, conf=0.75)

  cites [34] Novembre, J. et al. Genes mirror geography within Europe. Nature 456, 98–101 (2008). sourceExperimental — accuracy not yet measured

In the paper

“(A 0.1 or lower minor allele frequency was required in the merged Tonga, Samoa, Fiji outgroup samples, yielding 228,262 SNPs, as opposed to the more stringent requirement of minor alleles being fixed in the Taiwan outgroup samples, following the procedure of Zhan et. al37, which yielded only 137,383 SNPs.)”

What the sources say

• ?Could not verify

  The Results > Application section describes an analysis of human populations using several hundred thousand loci, but gives neither of the claimed SNP counts. Searches for the Tonga–Samoa–Fiji and Taiwan outgroups, the two counts, and the stated allele-frequency criteria found no passage addressing those filters. (LLM, conf=0.76)

  cites [37] Peter, B. M. & Slatkin, M. Detecting range expansions from genetic data. Evolution 67, 3274–3289 (2013). sourceExperimental — accuracy not yet measured

In the paper

“European ancestries entered Polynesia during the colonial period with the first European explorer (Magellan) arriving in the 16th century and significant immigration commencing in the early 19th century64.”

What the sources say

• ?Could not verify

  The Materials and Methods section (‘Real datasets’; page unavailable) describes cohorts in Europe and Uganda, while the other retrieved passages concern haplotype phasing or references. Searches for Polynesia, Magellan, colonial-era European ancestry, and 19th-century immigration found no passage in our copy addressing the claim. (LLM, conf=0.77)

  cites [64] O’Connell, J. et al. A general approach for haplotype phasing across the full spectrum of relatedness. PLoS Genet. 10, e1004234 (2014). sourceExperimental — accuracy not yet measured

In the paper

“Stretching across central eastern Polynesia, the Tuamotu Archipelago was previously hypothesized to have served as a regional voyaging hub20,25,28, and our analysis indicates that it was from this hub that settlers made their way north to the Marquesas Islands (Nuku Hiva and Fatu Hiva in our dataset) and south to the Gambier Islands (Mangareva in our dataset) beginning in the mid-1100s CE.”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [20] Emory, K. P. The Tuamotuan creation charts by Paiore. J. Polynesian Soc. 48, 1–29 (1939).
• ?Not checked — no full text of the sourcecites [25] Kirch, P. V. et al. Human ecodynamics in the Mangareva Islands: a stratified sequence from Nenega-Iti Rock Shelter (site AGA-3, Agakauitai Island). Archaeol. Oceania 50, 23–42 (2015). source
• Supported

  The citation is attached to the prior hypothesis that the Tuamotus served as a regional voyaging hub. The Conclusions (page unavailable) call the archipelago “the navigational crossroads of central East Polynesia,” supporting that characterization. The proposed settlement routes and mid-1100s date are explicitly presented as the citing authors’ own analysis, not as findings attributed to this source. (LLM, conf=0.86)

  cites [28] Weisler, M. I. et al. Cook Island artifact geochemistry demonstrates spatial and temporal extent of pre-European interarchipelago voyaging in East Polynesia. Proc. Natl Acad. Sci. USA 113, 8150–8155 (2016). source

In the paper

“It is also notable that it is only on islands that we infer were settled via the Tuamotus that pre-colonial Native American genetic contact has been identified, and its timing corresponds closely with our voyaging dates for this region32.”

What the sources say

• ?Could not verify

  The Introduction compares worldwide genetic and geographic maps using Procrustes analysis; it does not discuss settlement through the Tuamotus. Searches for Native American genetic contact, Polynesian islands, and voyaging dates found no passage addressing the claimed locations or timing. (LLM, conf=0.78)

  cites [32] Wang, C. et al. Comparing spatial maps of human population-genetic variation using procrustes analysis. Stat. Appl. Genet. Mol. Biol. 9, 13 (2010). sourceExperimental — accuracy not yet measured

In the paper

“(Admixture between populations stemming from these two sources occurred on Vanuatu and other Melanesian islands in the thousand years before the settlement of Polynesia and was carried into Polynesia during its settlement17,79.)”

What the sources say

• Partly supported

  The paper’s Abstract (page unavailable) dates Papuan–First Remote Oceanian mixture to roughly 1,500–2,300 years before present and finds Papuan ancestry in present-day Polynesians. It does not locate that mixture on Vanuatu or other Melanesian islands, or establish that an already admixed population carried it into Polynesia during settlement. Instead, the ancient Vanuatu and Tongan individuals had little or no Papuan ancestry, and the paper infers later movements into Remote Oceania. (LLM, conf=0.86)

  cites [17] Skoglund, P. et al. Genomic insights into the peopling of the Southwest Pacific. Nature 538, 510–513 (2016). sourceExperimental — accuracy not yet measured
• ?Could not verify

  The Introduction (pp. 1–2) discusses self-organizing maps, not population history. Searches for admixture on Vanuatu and other Melanesian islands, and for Papuan–Austronesian ancestry and Polynesian settlement, found no passage in our copy addressing the claim. (LLM, conf=0.78)

  cites [79] Wittek, P., Gao, S. C., Lim, I. S. & Zhao, L. Somoclu: an efficient parallel library for self-organizing maps. J. Stat. Softw. 78, https://doi.org/10.18637/jss.v078.i09 (2017). sourceExperimental — accuracy not yet measured

In the paper

“In addition, the model of IBD segment independence holds only for (N >> T) with N the population size and T the number of generations97.”

What the sources say

• ?Could not verify

  The Results section discusses detecting and comparing IBD segments, and Materials and Methods describes a sample-size correction. Neither states when IBD segments can be treated as independent; searches for segment independence and the N >> T condition found no supporting passage. Page numbers were not available in our copy. (LLM, conf=0.73)

  cites [97] Botigué, L. R. et al. Gene flow from North Africa contributes to differential human genetic diversity in southern Europe. Proc. Natl Acad. Sci. USA 110, 11791–11796 (2013). sourceExperimental — accuracy not yet measured

In the paper

“If we are considering recombination segments shared between two present day individuals stemming from the same common ancestor, that is IBD segments, we must adjust the rate for the number of recombination events per unit length that have occurred down both sides of the pedigree from this common ancestor, which gives a λ of 2T total92,95,98.”

What the sources say

• ?Not checked — no full text of the sourcecites [92] Ceballos, F. C., Joshi, P. K., Clark, D. W., Ramsay, M. & Wilson, J. F. Runs of homozygosity: windows into population history and trait architecture. Nat. Rev. Genet. 19, 220–234 (2018). source
• Supported

  The Abstract (page unavailable) says an ancestral haplotype reaches two kth-generation descendants through 2k meioses and gives the expected shared-segment length as 100/(2k) cM. Its reciprocal is a decay rate of 2k per Morgan, or k/50 per cM, matching the claim with T = k. (LLM, conf=0.88)

  cites [95] Gusev, A. et al. Whole population, genome-wide mapping of hidden relatedness. Genome Res. 19, 318–326 (2009). source
• Supported

  In “Sharing between Remote Relatives” (page unavailable), the paper says IBD segment length depends on transmissions from the shared ancestor and is exponentially distributed. Its stated mean of 50 cM/(k+1) for k-th cousins corresponds to a decay rate of (k+1)/50 per cM, or 2T per Morgan when the ancestor is T=k+1 generations back on each side. (LLM, conf=0.90)

  cites [98] Atzmon, G. et al. Abraham’s children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern ancestry. Am. J. Hum. Genet. 86, 850–859 (2010). source

In the paper

“This recursive algorithm for building the branching settlement path of the Pacific islands is a form of the Chu-Liu-Edmonds algorithm, which is guaranteed to produce the minimum spanning tree of a directed acyclic graph (see Supplementary Discussion ‘On tree-building’)87,88.”

What the sources say

• ?Could not verify

  The Methods section on Nei’s FST and the Results sections on SNP ascertainment and FST estimators discuss population-genetic estimates, not settlement-path construction. Searches for the Chu-Liu-Edmonds algorithm, Pacific Islands tree-building, and directed graphs found no passage in our copy addressing the claim. (LLM, conf=0.78)

  cites [87] Bhatia, G., Patterson, N., Sankararaman, S. & Price, A. L. Estimating and interpreting FST: the impact of rare variants. Genome Res. 23, 1514–1521 (2013). sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [88] Nei, M. & Roychoudhury, A. K. Sampling variances of heterozygosity and genetic distance. Genetics 76, 379–390 (1974). source

In the paper

“Only in the settlement of the Marquesas Island group, dated by Mulrooney to the late 1100s CE, and the Southern Cook Islands, dated even later by Wilmshurst to the mid-1200s CE, do we find different (earlier) dates.”

In the paper

“Because the originating islands have much greater diversity (as discussed below), they dominate the first principal component when included in the PCA (Supplementary Fig. 3).”

In the paper

“we find that Polynesian population structure exhibits high dimensionality (Supplementary Fig. 1) not at all reflective of geography (Fig. 1a)”

In the paper

“Rarotonga and Palliser appear at the center of the eastern Polynesian islands with the other eastern islands radiating out from them.”

In the paper

“(Projections onto fewer dimensions yielded similar results, with some clusters beginning to disappear in the range 12–15 dimensions, as predicted by the Tracy-Widom analysis.)”

In the paper

“This filtering resulted in the loss of 60,377 SNPs (8.75% of the total 689,899 SNPs), leaving 629,522 SNPs across all populations for computation of population allele frequency statistics.”

In the paper

“The latter calculation reduced the standard errors for the range expansion statistic on islands settled subsequent to western Polynesia, i.e. the eastern Polynesian islands; nevertheless, the general ordering of islands in the range expansion was the same for both calculations (see comparison Supplementary Fig. 14).”

In the paper

“As discussed above, modern Pacific islanders are often admixed, possessing European and occasionally Native American and African ancestries (Supplementary Fig. 32).”

In the paper

“our settlement dates (1140 CE on Fatu Hiva in the Marquesas, or 28.4 generations before 1989) agree with the genealogical oral histories of many Pacific islanders themselves (1005 CE, or 29 generations before 1875, on Fatu Hiva) 27. In the Tuamotus our dates (1110 CE, or 29.3 generations before 1989) agree even more closely with island’s oral histories (1125 CE, or 28 generations before 1965)44.”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [27] Handy, E. S. C. The Native Culture in the Marquesas (The Bishop Museum, 1923).
• ?Not checked — no full text of the sourcecites [44] Mulrooney, M. A. An island-wide assessment of the chronology of settlement and land use on Rapa Nui (Easter Island) based on radiocarbon data. J. Archaeol. Sci. 40, 4377–4399 (2013). source

In the paper

“A few Pacific island individuals, particularly in the Marquesas, were found to also have >5% East Asian ancestry in the ADMIXTURE results.”

In the paper

“We find deviations from our settlement tree only for 3 of its branches: Mangareva – Raivavae (migration from Tahiti), Mangareva – Palliser (migration from Tahiti), and North Marquesas – Palliser (migration from Tahiti and also from the Cooks).”

In the paper

“An elbow61 was found in the cross-validation error plot at K = 7 clusters, with larger numbers of clusters delivering little improvement (Supplementary Fig. 32).”

In the paper

“We have shown that these particular islands also have high levels of homozygosity (Supplementary Figs. 25–27), which should increase the power to detect trait associations, and significant IBD, enabling IBD mapping, another useful approach51.”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [51] Buck Te Rangi Hīroa, P. H. Vikings of the Sunrise (J. B. Lippincott, 1938).

In the paper

“The number of significant (p > 0.05) dimensions for the genotype frequency matrix, described above, was determined (n = 14) using a Tracy-Widom distribution57 and verified via a scree plot70.”

In the paper

“The pattern confirms the results of our drift statistics; Mangareva is the island most recently connected to Rapa Nui, while Samoa, the root of the expansion into remote Polynesia, is the most archaic connection.”

In the paper

“Trends of increasing IBD sharing along the course of the inferred settlement chain (see the map in Extended Data Fig. 5) are evident, but there is significant noise.”

In the paper

“Not removing these outliers does not change our island settlement dates significantly, but, by distorting the tail of the exponential decay distributions, does increase our standard error”

In the paper

“Begin with the island with the most potential parents (at the end of the range expansion) (Fig. 2B) or in other words the largest ψ, Rapa Nui.”

In the paper

“Removing all entries corresponding to λ values that have standard errors above .07 (representing errors larger than 15% of the average λ value), creates a matrix of more precise generation values, but with some missing entries.”

In the paper

“although the same settlement sequence is also returned when using the latter metric instead (Supplementary Fig. 12)”

In the paper

“finally to the widely separated, but genetically connected, megalithic statue-building cultures of the Marquesas (Te Henua ‘Enana) Islands in the north, Raivavae in the south, and Easter Island (Rapa Nui), the easternmost of the Polynesian islands, settled in approximately 1200 CE via Mangareva.”

In the paper

“The Austronesian-speaking settlers of the western Pacific (Fiji, Tonga, and Samoa) went on to people the widely dispersed islands in the vast ocean to their east through extraordinary voyages of exploration and settlement2,20.”

What the sources say

• ?Not checked — no full text of the sourcecites [2] Kirch, P. V. On the Road of the Winds (Univ. of California Press, 2017). source
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [20] Emory, K. P. The Tuamotuan creation charts by Paiore. J. Polynesian Soc. 48, 1–29 (1939).

In the paper

“who trace their linguistic origins to Taiwan9”

What the sources say

• ?Not checked — no full text of the sourcecites [9] Gray, R. D., Drummond, A. J. & Greenhill, S. J. Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science 323, 479–483 (2009). source

In the paper

“Recent movement between islands, such as post-settlement trade contact, can introduce small numbers of longer, inter-island IBD segments, shifting the estimated divergence time towards the present, so we fit a truncated exponential.”

In the paper

“Instead, each successive principal component captures the genetic drift of a particular island or island group (Fig. 1b, c and Supplementary Fig. 2), illustrating that genetic variance between these islands is dominated by their founder effects, not by diffusion clines or migration gradients.”

In the paper

“When constructing a population tree, this means that our dataset contains not only the terminal (leaf) nodes, but also the internal nodes, and we know their hierarchy from the ψ-statistic.”

In the paper

“Quality control filters were applied across all sampled individuals using the Plink 1.9 package53, removing individuals with >1% of genotyped sites missing (mind .01), removing genotyped sites missing in >1% of individuals (geno .01), and removing sites (18 SNPs) with extreme deviations from Hardy-Weinberg equilibrium (p-value less than 10e-110).”

In the paper

“REAP55 was used to determine kinship coefficients using the ADMIXTURE clustering results discussed below; individuals with a kinship coefficient of >.2 (first degree relatives) were iteratively removed.”

In the paper

“This final leg had been suggested by some based on similarities between the Mangarevan and Rapanui languages48, and by similarities in their traditional stone ceremonial platforms49.”

What the sources say

• ?Not checked — no full text of the sourcecites [48] Dickinson, W. Pacific atoll living: how long already and until when. Geol. Soc. Am. Today 19, 4–10 (2009). source
• ?Not checked — no full text of the sourcecites [49] Fischer, S. R. Mangarevan doublets: preliminary evidence for proto-southeastern Polynesian. Ocean. Linguist. 40, 112–124 (2001). source

In the paper

“Settlers also fanned out from Rarotonga northeast to the Society Islands (represented by Tahiti in our dataset but also containing the culturally significant island Raʻiātea) around 1050 CE, thence northeast to the Tuamotu Archipelago (represented by Mataiva in the Palliser group in our dataset) by 1110 CE.”

In the paper

“Local approvals for engagement with the Rapa Nui community were obtained from the mayor (Pedro Pablo Edmunds Paoa) of the municipality of Easter Island, and the study was registered with the National Corporation for Indigenous Development (CONADI), in accordance with the indigenous law No. 19.253.”

In the paper

“The guidelines of the UNESCO International Declaration on Human Genetic Data and the Declaration of Helsinki were followed throughout the study.”

In the paper

“Note that our reconstruction of the settlement path is independent of these date estimates, which are overlaid upon it, and is more robust to later sporadic contact than IBD distributions are”

In the paper

“No statistical methods were used to predetermine sample size.”

In the paper

“This study was also approved by the Council of Polynesian Elders for the community of Rapa Nui, along with local educational institutions, including the Lyceum Hoŋa’a o te Mana and the Lorenzo Baeza school for adults.”

In the paper

“At this time the widely scattered Tuamotu hub and other critical atolls in the expansion path (e.g. Nororotu in the Austral group), would have only recently emerged above falling sea levels (900 CE) and finished solidifying their topsoil and forests44,47”

What the sources say

• ?Not checked — no full text of the sourcecites [44] Mulrooney, M. A. An island-wide assessment of the chronology of settlement and land use on Rapa Nui (Easter Island) based on radiocarbon data. J. Archaeol. Sci. 40, 4377–4399 (2013). source
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [47] Walworth, M. The Language of Rapa Iti (Univ. Hawaii, 2015).

In the paper

“From this base, we find that settlers continued south around 1190 CE to Rapa Iti (a branch recently hypothesized from linguistic evidence46) and, separately, east to the smaller Cook Islands (Mauke and Atiu in our dataset).”

What the sources say

• ?Not checked — no full text of the sourcecites [46] Di Piazza, A., Di Piazza, P. & Pearthree, E. Sailing virtual canoes across Oceania: revisiting island accessibility. J. Archaeol. Sci. 34, 1219–1225 (2007). source

In the paper

“These clouds on its prominent mountain make the island visible for long distances at sea and probably facilitated its discovery45.”

What the sources say

• ?Not checked — no full text of the sourcecites [45] Pirazzoli, P. A. & Montaggioni, L. F. Late Holocene sea-level changes in the northwest Tuamotu islands, French Polynesia. Quat. Res. 25, 350–368 (1986). source

In the paper

“After merging reference sequence data with sample genotyped data, strand inconsistencies were flipped when unambiguous, while ambiguous SNPs were removed, leaving 689,899 SNP sites.”

In the paper

“research/ethics approval and permits were obtained from the following institutions: Stanford University Institutional Review Board (IRB approval No. 20839), Oxford University Tropical Research Ethics Committee (reference No. 537–14), and the Scientific Ethics Committee of the Catholic University of Chile (reference No. 1971092).”

In the paper

“The average call rate was 98.5% for all newly genotyped samples.”

In the paper

“Written informed consent was obtained from all participants”

In the paper

“Community engagement, including pre-participation presentations and post-participation return of results, were conducted throughout the project.”

In the paper

“Because allele frequencies drifted during the Pacific island settlement process, some minor alleles in Taiwan would have become major alleles by the time the settlers reached western Polynesia (see Supplementary Discussion ‘On psi‘), so the intermediate repolarization using Tonga, Samoa, and Fiji as an outgroup increased the resolution of the range expansion statistic (reduced standard errors) for”

In the paper

“Thus, a genome-wide haplotype vector constructed by assembling all chromosomes sequentially into a single row vector will switch phase arbitrarily across chromosome boundaries and so is already a mixture of an individual’s two true parental haplotypes.”

In the paper

“Because ancestries fully (or partially) introduced via colonial settlement did not necessarily follow the same island settlement process (or founder sizes and dates) as the original Polynesian settlement, such ancestries need to be distinguished, necessitating an ancestry-specific approach65, cf. Supplementary Figs. 10, 20.”

What the sources say

• ?Not checked — no full text of the sourcecites [65] D’Arcy, P. The Chinese Pacifics: a brief historical review. J. Pacific Hist. 49, 396–420 (2014). source

In the paper

“Together with even more distant North and South Marquesas and Rapa Nui, each also with inferred settlement stemming from the Tuamotus, Raivavae had an ancient tradition of carving monumental anthropomorphic statues in stone. No other Austral island had these50; indeed, such immense sculptures are found only on those far-flung islands that we now, however, show to had a common genetic source in the”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [50] Flenley, J. & Bahn, P. The Enigmas of Easter Island (Oxford Univ. Press, 2003).

In the paper

“From western Polynesia, Polynesian voyagers reached Rarotonga in the Cook Islands around 830 CE, having passed from Samoa along a route shared with the settlement of Fiji and Tonga.”

In the paper

“The independence of drift between these separated, small island populations leads us to expect some deviation from Hardy-Weinberg in Polynesia, so we do not apply a typical threshold here.”

In the paper

“The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment.”

In the paper

“Fortunately, our dataset has T values of 25–30 generations and N values in the thousands21, so we do not fall into these problematic regimes.”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [21] Hunt, T. & Lipo, C. The Statues that Walked (Free Press, 2011).

In the paper

“consistent with Tahiti’s recent role as the capital of French Polynesia.”

In the paper

“This works because the per generation recombination rate is constant over time, so the distance from an ancestral population to any of its sampled contemporary descendants is the same when measured by segment length distributions.”

In the paper

“In addition, the shape of the IBD length distribution (decay rate) changes steadily each generation. It does not depend, as genetic drift does, on the fluctuations, which are generally unknown, of the historical population sizes.”

In the paper

“The model of a Poisson process of recombination events along a continuous genome holds for small IBD segment lengths, viz. T > 5, but for more recent relatedness, leading to very long IBD segments, one must consider the finite size of the chromosomes themselves when computing the IBD length distribution101.”

What the sources say

• ?Not checked — no full text of the sourcecites [101] Palamara, P. F., Lencz, T., Darvasi, A. & Pe'er, I. Length distributions of identity by descent reveal fine-scale demographic history. Am. J. Hum. Genet. 91, 809–822 (2012). source

In the paper

“This alters the amplitude, but not the decay rate shape parameter λ, of the exponential in Supplementary Fig. 22A, or, equivalently, the intercept, but not the slope of the lines in Supplementary Fig. 22B; thus demonstrating graphically that λ is robust to noise (errors) in ancestry normalization.”

In the paper

“However, because of the founding bottlenecks for each island, there is some intra-island IBD shared between pairs of individuals on the island (Supplementary Figs. 25, 26), so some recombination events will be non-productive.”

In the paper

“This holds in our case because all samples were taken from contemporary populations, and so all are leaf nodes of the ancestry tree dating to the same period (the present).”

In the paper

“The markers are bootstrapped together as long contiguous blocks to preserve the effects of linkage on the variance of the estimates35.”

What the sources say

• ?Not checked — no full text of the sourcecites [35] Nei, M. & Kumar, S. Molecular Evolution and Phylogenetics (Oxford Univ. Press, 2000). source

In the paper

“That our graph is acyclic can be shown (proof derived in Supplementary Discussion ‘On the acyclicity of psi’) from the formal definition of ψ, which defines our edge directionality.”