Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A genetic history of the pre-contact Caribbean


Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago1,2,3. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population that is closest to Central and northern South American individuals; contrary to previous work4, we find no support for ancestry contributed by a population related to North American individuals. Archaic-related lineages were >98% replaced by a genetically homogeneous ceramic-using population related to speakers of languages in the Arawak family from northeast South America; these people moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools that reflect small effective population sizes, which we estimate to be a minimum of 500–1,500 and a maximum of 1,530–8,150 individuals on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the individuals who we analysed lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous pan-Caribbean estimates of hundreds of thousands of people are too large5,6. Confirming a small and interconnected Ceramic Age population7, we detect 19 pairs of cross-island cousins, close relatives buried around 75 km apart in Hispaniola and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland, but instead reflected interactions within an interconnected Caribbean world1,8.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Geography and genetic structure.
Fig. 2: Genetic affinities of ancient Caribbean people.
Fig. 3: Estimates of Ne from shared haplotypes.

Data availability

The aligned sequences are available through the European Nucleotide Archive under accession number PRJEB38555. Genotype data used in analysis are available at Any other relevant data are available from the corresponding authors upon reasonable request.

Code availability

The custom code used in this study is available from


  1. Rouse, I. The Tainos: Rise & Decline of the People who Greeted Columbus (Yale Univ. Press, 1992).

  2. Maggiolo, M. V. La Isla de Santo Domingo antes de Colón (Banco Central de la Republica Dominicana, 1993).

  3. Keegan, W. F. & Hofman, C. L. The Caribbean before Columbus (Oxford Univ. Press, 2017).

  4. Nägele, K. et al. Genomic insights into the early peopling of the Caribbean. Science 369, 456–460 (2020).

    ADS  PubMed  Google Scholar 

  5. Cook, S. F. & Borah, W. Essays in Population History Vol. 1, 376–410 (Univ. California Press, 1971).

  6. Henige, D. On the contact population of Hispaniola: history as higher mathematics. Hisp. Am. Hist. Rev. 58, 217–237 (1978).

    Google Scholar 

  7. Wilson, S. M. The Archaeology of the Caribbean (Cambridge Univ. Press, 2007).

  8. Rodríguez Ramos, R. in Oxford Handbook of Caribbean Archaeology (eds Keegan, W. F. et al.) 155–170 (Oxford Univ. Press, 2013).

  9. Bérard, B. About boxes and labels: a periodization of the Amerindian occupation of the West Indies. Journal of Caribbean Archaeology 19, 51–67 (2019).

    Google Scholar 

  10. Callaghan, R. T. in Oxford Handbook of Caribbean Archaeology (eds Keegan, W. F. et al.) 285–295 (Oxford Univ. Press, 2013).

  11. Siegel, P. E. et al. Paleoenvironmental evidence for first human colonization of the eastern Caribbean. Quat. Sci. Rev. 129, 275–295 (2015).

    ADS  Google Scholar 

  12. Oliver, J. R. The Archaeological, Linguistic and Ethnohistorical Evidence for the Expansion of Arawakan into Northwestern Venezuela and Northeastern Colombia. PhD thesis, Univ. Illinois at Urbana-Champaign (1989).

  13. Reich, D. et al. Reconstructing Native American population history. Nature 488, 370–374 (2012).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  14. Eisenmann, S. et al. Reconciling material cultures in archaeology with genetic data: The nomenclature of clusters emerging from archaeogenomic analysis. Sci. Rep. 8, 13003 (2018). 

  15. Greenberg, J. H. Language in the Americas (Stanford Univ. Press, 1987).

  16. Salzano, F. M., Hutz, M. H., Salamoni, S. P., Rohr, P. & Callegari-Jacques, S. M. Genetic support for proposed patterns of relationship among lowland South American languages. Curr. Anthropol. 46, S121–S128 (2005).

    Google Scholar 

  17. Schroeder, H. et al. Origins and genetic legacies of the Caribbean Taino. Proc. Natl Acad. Sci. USA 115, 2341–2346 (2018).

    CAS  PubMed  Google Scholar 

  18. Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Chinique de Armas, Y., Roksandic, M., Suárez, R. R., Smith, D. G. & Buhay, W. M. in Cuban Archaeology in the Circum-Caribbean Context (ed. Roksandic, I.) 125–146 (Univ. Press Florida, 2016).

  20. Lovén, S. E. Origins of the Tainan Culture, West Indies (Elanders, 1935).

  21. Nieves-Colón, M. A. et al. Ancient DNA reconstructs the genetic legacies of precontact Puerto Rico communities. Mol. Biol. Evol. 37, 611–626 (2020).

    PubMed  Google Scholar 

  22. Moreno-Estrada, A. et al. Reconstructing the population genetic history of the Caribbean. PLoS Genet. 9, e1003925 (2013).

    PubMed  PubMed Central  Google Scholar 

  23. Narasimhan, V. M. et al. The formation of human populations in South and Central Asia. Science 365, eaat7487 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Ross, A. H., Keegan, W. F., Pateman, M. P. & Young, C. B. Faces divulge the origins of Caribbean prehistoric inhabitants. Sci. Rep. 10, 147 (2020).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  25. Ringbauer, H., Novembre, J. & Steinrucken, M. Human parental relatedness through time - detecting runs of homozygosity in ancient DNA. Preprint at (2020).

  26. 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).

    CAS  Google Scholar 

  27. Frankham, R. Effective population size/adult population size ratios in wildlife: a review. Genet. Res. 89, 491–503 (2007).

    PubMed  Google Scholar 

  28. Browning, S. R. & Browning, B. L. Accurate non-parametric estimation of recent effective population size from segments of identity by descent. Am. J. Hum. Genet. 97, 404–418 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Fortes-Lima, C. et al. Exploring Cuba’s population structure and demographic history using genome-wide data. Sci. Rep. 8, 11422 (2018).

    ADS  PubMed  PubMed Central  Google Scholar 

  30. Toro-Labrador, G., Wever, O. R. & Martínez-Cruzado, J. C. Mitochondrial DNA analysis in Aruba: strong maternal ancestry of closely related Amerindians and implications for the peopling of northwestern Venezuela. Caribb. J. Sci. 39, 11–22 (2003).

    Google Scholar 

  31. Mendizabal, I. et al. Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba. BMC Evol. Biol. 8, 213 (2008).

    PubMed  PubMed Central  Google Scholar 

  32. Vilar, M. G. et al. Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies. Am. J. Phys. Anthropol. 155, 352–368 (2014).

    PubMed  Google Scholar 

  33. Benn Torres, J. et al. Genetic diversity in the Lesser Antilles and its implications for the settlement of the Caribbean basin. PLoS ONE 10, e0139192 (2015).

    PubMed  PubMed Central  Google Scholar 

  34. The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015).

    Google Scholar 

  35. Hofman, C. L. & Reid, B. A. in Encyclopedia of Caribbean Archaeology (eds Reid, B. & Gilmore, G.) 300–303 (Univ. Press Florida, 2014).

  36. Roksandic, I. & Roksandic, M. in New Perspectives on the Peopling of the Americas (eds Harvati, K. et al.) 199–223 (Kerns, 2018).

  37. Keegan, W. The People Who Discovered Columbus (Univ. Press Florida, 1992).

  38. Anderson-Córdova, K. F. Surviving Spanish Conquest: Indian Fight, Flight, and Transformation in Hispaniola and Puerto Rico (Univ. Alabama Press, 2017).

  39. Pinhasi, R. et al. Optimal ancient DNA yields from the inner ear part of the human petrous Bone. PLoS ONE 10, e0129102 (2015).

    PubMed  PubMed Central  Google Scholar 

  40. Pinhasi, R., Fernandes, D. M., Sirak, K. & Cheronet, O. Isolating the human cochlea to generate bone powder for ancient DNA analysis. Nat. Protocols 14, 1194–1205 (2019).

    CAS  PubMed  Google Scholar 

  41. Sirak, K. et al. Human auditory ossicles as an alternative optimal source of ancient DNA. Genome Res. 30, 427–436 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).

    ADS  CAS  PubMed  Google Scholar 

  43. Korlević, P. et al. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. Biotechniques 59, 87–93 (2015).

    PubMed  Google Scholar 

  44. Rohland, N., Glocke, I., Aximu-Petri, A. & Meyer, M. Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing. Nat. Protocols 13, 2447–2461 (2018).

    CAS  PubMed  Google Scholar 

  45. Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. Lond. B 370, 20130624 (2015).

    Google Scholar 

  46. Gansauge, M.-T., Aximu-Petri, A., Nagel, S. & Meyer, M. Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nat. Protocols 15, 2279–2300 (2020).

    CAS  PubMed  Google Scholar 

  47. Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010).

    PubMed  Google Scholar 

  48. Fu, Q. et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  50. Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  51. Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  52. Behar, D. M. et al. A “Copernican” reassessment of the human mitochondrial DNA tree from its root. Am. J. Hum. Genet. 90, 675–684 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).

    PubMed  PubMed Central  Google Scholar 

  54. Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics 15, 356 (2014).

    PubMed  PubMed Central  Google Scholar 

  55. Nakatsuka, N. et al. ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium. Genome Biol. 21, 199 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Kennett, D. J. et al. Archaeogenomic evidence reveals prehistoric matrilineal dynasty. Nat. Commun. 8, 14115 (2017).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  57. Lohse, J. C., Culleton, B. J., Black, S. L. & Kennett, D. J. A precise chronology of Middle to Late Holocene bison exploitation in the far southern Great Plains. J. Texas Arch. Hist. 1, 94–126 (2014).

    Google Scholar 

  58. Bronk Ramsey, C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009).

    Google Scholar 

  59. Reimer, P. J. et al. The IntCal20 northern hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 62, 725–757 (2020).

    CAS  Google Scholar 

  60. Passariello, I. et al. Characterization of different chemical procedures for 14C dating of buried, cremated, and modern bone samples at Circe. Radiocarbon 54, 867–877 (2012).

    CAS  Google Scholar 

  61. Lindo, J. et al. The genetic prehistory of the Andean highlands 7000 years BP though European contact. Sci. Adv. 4, eaau4921 (2018).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  62. Moreno-Mayar, J. V. et al. Early human dispersals within the Americas. Science 362, eaav2621 (2018).

    ADS  PubMed  Google Scholar 

  63. Scheib, C. L. et al. Ancient human parallel lineages within North America contributed to a coastal expansion. Science 360, 1024–1027 (2018).

    ADS  CAS  PubMed  Google Scholar 

  64. Posth, C. et al. Reconstructing the deep population history of Central and South America. Cell 175, 1185–1197.e22 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Raghavan, M. et al. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349, aab3884 (2015).

    PubMed  PubMed Central  Google Scholar 

  66. Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  67. Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).

    PubMed  PubMed Central  Google Scholar 

  68. Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  69. Skoglund, P. et al. Genetic evidence for two founding populations of the Americas. Nature 525, 104–108 (2015).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  70. Olalde, I. et al. The genomic history of the Iberian peninsula over the past 8000 years. Science 363, 1230–1234 (2019).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  71. Nakatsuka, N. et al. A paleogenomic reconstruction of the deep population history of the Andes. Cell 181, 1131–1145.e21 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Skoglund, P. et al. Genomic insights into the peopling of the southwest Pacific. Nature 538, 510–513 (2016).

    ADS  PubMed  PubMed Central  Google Scholar 

  73. Harney, É. et al. Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation. Nat. Commun. 9, 3336 (2018).

    ADS  PubMed  PubMed Central  Google Scholar 

  74. Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).

    PubMed  PubMed Central  Google Scholar 

  75. Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Alexander, D. H. & Lange, K. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12, 246 (2011).

    PubMed  PubMed Central  Google Scholar 

  77. Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015).

    PubMed  PubMed Central  Google Scholar 

  78. Fu, Q. et al. The genetic history of Ice Age Europe. Nature 534, 200–205 (2016).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  79. Lipson, M. Applying f4-statistics and admixture graphs: theory and examples. Mol. Ecol. Resour. 00, 1–10 (2020).

    Google Scholar 

  80. Harney, É., Patterson, N., Reich, D. & Wakeley, J. Assessing the performance of qpAdm: a statistical tool for studying population admixture. Preprint at (2020).

  81. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    PubMed  PubMed Central  Google Scholar 

Download references


We acknowledge the ancient people who were the source of the skeletal material analysed in this study, as well as modern people from the Caribbean who have a genetic or cultural legacy from some of the ancient populations we analysed. This work was supported by a grant from the National Geographic Society to M. Pateman to facilitate analysis of skeletal material from The Bahamas and by a grant from the Italian ‘Ministry of Foreign Affairs and International Cooperation’ (Italian archaeological, anthropological and ethnological missions abroad, DGPSP Ufficio VI). D.R. was funded by NSF HOMINID grant BCS-1032255, NIH (NIGMS) grant GM100233, the Paul Allen Foundation, the John Templeton Foundation grant 61220 and the Howard Hughes Medical Institute. We thank J. Avilés, J. Acayaguana Delvalle, J. Estevez, D. T. Golding Frankson, J. Gregory, L. A. Guitar, L. Kelly, G. A. Lopez Castellano, K. R. Nibonri and O. Patterson for comments on early versions of this manuscript and discussions that improved the presentation of this work; V. A. Forbes-Pateman and N. Albury for their assistance compiling descriptions for archaeological sites in The Bahamas; E. Harney, R. Maier and N. Nakatsuka for help with data processing; and M. Chintalapati, P. Moorjani and N. Patterson for advice on analysis. We dedicate this article to the memory of F. Luna Calderon, who would have been a co-author had he not passed away in the course of the work for this study.

Author information

Authors and Affiliations



W.F.K., A. Coppa, M. Lipson, R.P. and D.R. supervised the study. J.S., O.C., C.A.A., E.V.C., R.C., A. Cucina, F.G., C.K., F.L.P., M. Lucci, M.V.M., C.T.M., C.M., I.P., M.P., T.M.S., C.G.S. and M.V. provided skeletal materials and/or assembled and interpreted archaeological and anthropological information. C.A.A., E.V.C., C.K., M.V.M., C.T.M., C.M., I.P., M.P., T.M.S. and C.G.S. contributed local perspectives to the interpretation and contextualization of new genetic data. B.M.-T. provided data from present-day populations. N.R., M.M., S.M., N.A., R.B., G.B., N.B., O.C., K.C., F.C., L.D., K.S.D.C., S.F., A.M.L., K.M., J.O., K.T.Ö., C.S., R.S., K.S. and F.Z. performed ancient DNA laboratory and/or data-processing work. B.J.C., R.J.G., L.E., F.M., W.C.M., F.T. and D.J.K. performed radiocarbon analysis and stable isotope work; D.J.K. supervised this work. D.M.F., K.A.S., H.R., M.M., S.M., I.O. and M. Lipson analysed genetic data. D.M.F., K.A.S., W.F.K. and D.R. wrote the manuscript with input from all co-authors.

Corresponding authors

Correspondence to Alfredo Coppa, Ron Pinhasi or David Reich.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature thanks John Lindo, Alice Samson and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 Temporal distribution of newly reported individuals and overview of population structure.

a, Numbers represent individuals from each site; thick lines denote direct 14C dates (95.4% calibrated confidence intervals); thin lines denote archaeological-context dating; grey area identifies the first arrivals of ceramic users in the Caribbean. Colours and labels are consistent with Fig. 1. b, PCA plot with ancient individuals shown as solid squares or circles for Archaic- or Ceramic-associated individuals, respectively. Newly reported individuals are outlined in black; genetic outliers are outlined in red; and individuals with <30,000 SNPs are outlined in blue. Individuals are separated by subclades, and three individuals from the site of Cueva Roja (Dominican Republic) who were excluded from clading analysis analysis are labelled *Dominican_Archaic (Cueva Roja) and coloured magenta. Individual PDI009, previously assessed elsewhere as an outlier11, is denoted with a cross. Three previously published ancient Caribbean individuals9,10 are shown as inverted triangles outlined in grey and coloured for the subclade that encompasses the geographical region with which they are associated. This plot focuses on ancient individuals and does not show some present-day populations; a full plot is provided as Supplementary Fig. 17. c, ADMIXTURE analysis best supports K = 6 ancestral elements. Newly reported and co-analysed individuals are clustered by subclade; all newly reported individuals are identified by a black bar to the side of the plot. The same three previously published individuals9,10 shown in b are included, and three present-day populations (Suruí, Cabécar and Piapoco) are shown for reference.

Extended Data Fig. 2 FST distances.

a, b, Average pairwise FST distances and standard errors (×100) between clades (a) and sites with more than two unrelated individuals (b), demonstrating both overall high levels of genetic similarity between the *Caribbean_Ceramic subclades and the sites composing them, as well as the magnitude of genetic differentiation between those and the groups with Archaic- and Venezuela-related ancestries.

Extended Data Fig. 3 Maximum-likelihood population tree from allele frequencies using Treemix.

The *Caribbean_Ceramic subclades are inferred to be on the same branch as modern Arawak-speaking groups (Palikur and Jamamadi). Orange arrows represent admixture events, although observations from other analyses (for example, qpAdm admixture modelling) suggest that the indicated direction of admixture may be inaccurate (for example, we believe it is more likely that there is *GreaterAntilles_Archaic admixture into *Haiti_Ceramic than the reverse scenario (Supplementary Information section 9)).

Extended Data Fig. 4 Estimated effective population sizes.

a, Estimates per site are based on ROH blocks 4–20 cM long using a likelihood model (Supplementary Information section 7). Colours as per subclades; numbers denote the count of analysed individuals. Highly consanguineous individuals with a sum of ROH > 20 above 50 cM were excluded. b, As in a, but for IBD segments 8–20 cM long shared on the X chromosome between all pairs of males. Closely related pairs of individuals with a sum of IBD X > 20 above 25 cM were excluded. Numbers denote counts of all remaining pairs. In a, b, points represent maximum-likelihood estimate and vertical bars represent 95% confidence interval.

Extended Data Fig. 5 Conditional heterozygosity by clade.

Conditional heterozygosity in the ancient Caribbean was similar to that of contemporaneous groups from Peru71, except for the Archaic-associated groups and *Venezuela_Ceramic. First- and second-degree relatives were excluded from the analysis, including the pair of related individuals who represent *Haiti_Ceramic. Coloured circles represent point estimates (colour scheme matching Fig. 1); bars represent three s.e.

Extended Data Fig. 6 Pairwise kinship estimates for all individuals from sites where close relatives were identified using autosomal data.

Dotted lines identify family clusters and intersite relationships; bottom rows correspond to relationships per individual.

Extended Data Table 1 Ne values for each site
Extended Data Table 2 Subset of cross-site relatives from different islands, identified through IBD analysis
Extended Data Table 3 Ancestry proportion estimates using qpAdm for present-day Caribbean individuals from Cuba (and its provinces), Dominican Republic and Puerto Rico
Extended Data Table 4 Statistics testing for an Australasian link

Supplementary information

Supplementary Information

This file contains an Ethics Statement, Supplementary Information sections 1-17, and Supplementary Figures, Supplementary Tables, and Supplementary References.

Reporting Summary

Supplementary Data

This file contains Supplementary Data 1-15.

Peer Review File

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Fernandes, D.M., Sirak, K.A., Ringbauer, H. et al. A genetic history of the pre-contact Caribbean. Nature 590, 103–110 (2021).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing