Skip to main content

Thank you for visiting nature.com. 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.

  • Article
  • Published:

Medieval DNA from Soqotra points to Eurasian origins of an isolated population at the crossroads of Africa and Arabia

Nature Ecology & Evolution volume 8, pages 817–829 (2024)Cite this article

Subjects

Abstract

Soqotra, an island situated at the mouth of the Gulf of Aden in the northwest Indian Ocean between Africa and Arabia, is home to ~60,000 people subsisting through fishing and semi-nomadic pastoralism who speak a Modern South Arabian language. Most of what is known about Soqotri history derives from writings of foreign travellers who provided little detail about local people, and the geographic origins and genetic affinities of early Soqotri people has not yet been investigated directly. Here we report genome-wide data from 39 individuals who lived between ~650 and 1750 ce at six locations across the island and document strong genetic connections between Soqotra and the similarly isolated Hadramawt region of coastal South Arabia that likely reflects a source for the peopling of Soqotra. Medieval Soqotri can be modelled as deriving ~86% of their ancestry from a population such as that found in the Hadramawt today, with the remaining ~14% best proxied by an Iranian-related source with up to 2% ancestry from the Indian sub-continent, possibly reflecting genetic exchanges that occurred along with archaeologically documented trade from these regions. In contrast to all other genotyped populations of the Arabian Peninsula, genome-level analysis of the medieval Soqotri is consistent with no sub-Saharan African admixture dating to the Holocene. The deep ancestry of people from medieval Soqotra and the Hadramawt is also unique in deriving less from early Holocene Levantine farmers and more from groups such as Late Pleistocene hunter–gatherers from the Levant (Natufians) than other mainland Arabians. This attests to migrations by early farmers having less impact in southernmost Arabia and Soqotra and provides compelling evidence that there has not been complete population replacement between the Pleistocene and Holocene throughout the Arabian Peninsula. Medieval Soqotra harboured a small population that showed qualitatively different marriage practices from modern Soqotri, with first-cousin unions occurring significantly less frequently than today.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Overview of Soqotri burials with analysis of shared drift between medieval Soqotri and present-day groups.
Fig. 2: Qualitative analyses of medieval Soqotri DNA.
Fig. 3: Medieval Soqotri had fewer long ROH than expected from modern ethnographic studies.

Similar content being viewed by others

Data availability

The aligned sequences are available through the European Nucleotide Archive under accession number PRJEB66485. Genotype data are available at https://reich.hms.harvard.edu/datasets. Any other relevant data are available from the corresponding authors upon reasonable request.

Code availability

The custom code used in this study is available at https://github.com/DReichLab/ADNA-Tools.

References

  1. Jansen van Rensburg, J. et al. The Soqotra Heritage Project (2017–2020). Bull. Soc. Arab. Stud. 22, 26–27 (2022).

    Google Scholar 

  2. Strauch, I. Foreign Sailors on Socotra: The Inscriptions and Drawings from the Cave Hoq (Hempen, 2012).

  3. Naumkin, V. V. A. Island of the Phoenix: An Ethnographic Study of the People of Socotra (Paul & Company Pub Consortium, 1993).

  4. Weeks, L., Morris, M., McCall, B. & Al-Zubairy, K. A recent archaeological survey on Soqotra. Report on the preliminary expedition season, January 5th–February 2nd 2001. Arab. Archaeol. Epigr. 13, 95–125 (2002).

    Article  Google Scholar 

  5. Casson, L. The Periplus Maris Erythraei: Text with Introduction, Translation, and Commentary (Princeton Univ. Press, 1989).

  6. Doe, B. Socotra: Island of Tranquillity (Immel, 1992).

  7. Morris, M., Watson, J. C. E. & Eades, D. A Comparative Cultural Glossary across the Modern South Arabian Language Family (Oxford Univ. Press, 2019).

  8. Evers, K. Cave of revelations: Indian Ocean trade in light of the Socotran graffiti. J. Indian Ocean Archaeol. 10, 19–37 (2014).

    Google Scholar 

  9. Bent, J. T. Southern Arabia (Smith, Elder and Co., 1900).

  10. Doe, B. Socotra; an Archaeological Reconnaissance in 1967 (Field Research Projects, 1970).

  11. Jansen van Rensburg, J. Rock art of Soqotra, Yemen: a forgotten heritage revisited. Arts 7, 99 (2018).

    Article  Google Scholar 

  12. Naumkin, V. V. & Sedov, A. V. Monuments of Socotra. Topoi Orient-Occident 3, 569–623 (1993).

    Google Scholar 

  13. Shinnie, P. L. Socotra. Antiquity 34, 100–110 (1960).

    Article  Google Scholar 

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

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Vyas, D. N., Al-Meeri, A. & Mulligan, C. J. Testing support for the northern and southern dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations. Am. J. Phys. Anthropol. 164, 736–749 (2017).

    Article  PubMed  Google Scholar 

  18. Hellenthal, G. et al. A genetic atlas of human admixture history. Science 343, 747–751 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Fedele, F. G. in The Evolution of Human Populations in Arabia: Paleoenvironments, Prehistory and Genetics (eds Petraglia, M. D. & Rose, J. I.) 215–236 (Springer, 2010).

  20. McCorriston, J., & Martin, L. in The Evolution of Human Populations in Arabia: Paleoenvironments, Prehistory and Genetics (eds Petraglia, M. D. & Rose, J. I.) 237–250 (Springer, 2010).

  21. Uerpmann, H.-P., Potts, D., & Uerpmann, M. in The Evolution of Human Populations in Arabia: Paleoenvironments, Prehistory and Genetics (eds Petraglia, M. D. & Rose, J. I.) 205–214 (Springer, 2010).

  22. Almarri, M. A. et al. The genomic history of the Middle East. Cell 184, 4612–4625. e4614 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lazaridis, I. et al. The genetic history of the Southern Arc: a bridge between West Asia and Europe. Science 377, eabm4247 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Lazaridis, I. et al. Ancient DNA from Mesopotamia suggests distinct pre-pottery and pottery Neolithic migrations into Anatolia. Science 377, 982–987 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419–424 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Černý, V. et al. Internal diversification of mitochondrial haplogroup r0a reveals post-last glacial maximum demographic expansions in South Arabia. Mol. Biol. Evol. 28, 71–78 (2011).

    Article  PubMed  Google Scholar 

  27. Agranat-Tamir, L. et al. The genomic history of the bronze age southern levant. Cell 181, 1146–1157 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Harney, É. et al. Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation. Nat. Commun. 9, 1–11 (2018).

    Google Scholar 

  29. Lazaridis, I. et al. A genetic probe into the ancient and medieval history of Southern Europe and West Asia. Science 377, 940–951 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. van de Loosdrecht, M. et al. Pleistocene north African genomes link near eastern and sub-Saharan African human populations. Science 360, 548–552 (2018).

    Article  PubMed  Google Scholar 

  31. Soares, P. The expansion of mtDNA haplogroup L3 within and out of Africa. Mol. Biol. Evol. 29, 915–927 (2012).

    Article  CAS  PubMed  Google Scholar 

  32. Černý, V., Čížková, M., Poloni, E. S., Al-Meeri, A. & Mulligan, C. Comprehensive view of the population history of Arabia as inferred by mtDNA variation. Am. J. Phys. Anthropol. 159, 607–616 (2016).

    Article  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Shinde, V. et al. An ancient Harappan genome lacks ancestry from steppe pastoralists or Iranian farmers. Cell 179, 729–735 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Derenko, M. et al. Complete mitochondrial DNA diversity in Iranians. PLoS ONE 8, e80673 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Al-Abri, A. et al. Pleistocene–Holocene boundary in southern Arabia from the perspective of human mtDNA variation. Am. J. Phys. Anthropol. 149, 21–28 (2012).

    Article  Google Scholar 

  37. Černý, V. et al. Out of Arabia—the settlement of Island Soqotra as revealed by mitochondrial and Y chromosome genetic diversity. Am. J. Phys. Anthropol. 138, 439–447 (2009).

    Article  PubMed  Google Scholar 

  38. Gandini, F. et al. Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes. Sci. Rep. 6, 25472–25472 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Ringbauer, H., Novembre, J. & Steinrücken, M. Parental relatedness through time revealed by runs of homozygosity in ancient DNA. Nat. Commun. 12, 5425 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. 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).

    Article  CAS  PubMed  Google Scholar 

  41. Cadenas, A. M., Zhivotovsky, L. A., Cavalli-Sforza, L. L., Underhill, P. A. & Herrera, R. J. Y-chromosome diversity characterizes the Gulf of Oman. Eur. J. Hum. Genet. 16, 374–386 (2008).

    Article  CAS  PubMed  Google Scholar 

  42. Ariano, B. et al. Ancient maltese genomes and the genetic geography of neolithic Europe. Curr. Biol. 32, 2668–2680.e6 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Wellsted, J. R. Travels to the City of the Caliphs, Along the Shores of the Persian Gulf and the Mediterranean: Including a Voyage to the Coast of Arabia, and a Tour on the Island of Socotra (2 volumes) (Henry Colburn, 1840).

  44. Luciani, M., Binder, M. & Alsaud, A. S. Life and living conditions in north-west Arabia during the Bronze Age: first results from the bioarchaeological work at Qurayyah. Proceedings of the Seminar Arabian Studies 48, 185–20 (2018).

    Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Dridi, H. Indiens et proche-orientaux dans une grotte de Suquṭrā (Yemen). J. Asiatique 290, 565–610 (2002).

    Article  Google Scholar 

  47. Dridi, H. & Gorea, M. Au IIIe siècle de notre ère: le voyage d’Agbar à Suqutra. Archeologia 396, 48–57 (2003).

  48. Robin, C. J. & Gorea, M. Les vestiges antiques de la grotte de Hôq (Suqutra, Yémen)(note d’information). C. R. Séances Acad. Inscr. B.-Lett. 146, 409–445 (2002).

    Article  Google Scholar 

  49. Strauch, I. & Bukharin, M. Indian inscriptions from the Cave Ḥoq on Suquṭrā. Ann. dell’Istituto Universitario Orient. Napoli 64, 121–138 (2004).

    Google Scholar 

  50. Strauch, I. in Ports of the Ancient Indian Ocean (eds. Boussac, M.-F. et al.) 79–97 (Primus Books, 2016).

  51. Al-Mujāwir, I., & ibn Ya’qūb, Y. A Traveller in Thirteenth-Century Arabia: Ibn al-Mujāwir’s Tārīkh al-Mustabṣir (Ashgate, 2008).

  52. Bittles, A. H., & Hamamy, H. A. in Genetic Disorders among Arab Populations (ed. Teebi, A. S.) 85–108 (Springer, 2010).

  53. Korotayev, A. Parallel-cousin (FBD) marriage, islamization, and arabization. Ethnology 39, 395–407 (2000).

    Article  Google Scholar 

  54. Stern, G. H. Marriage in Early Islam (Royal Asiatic Society, 1939).

  55. Yule, H., & Cordier, H. The Travels of Marco Polo: The Complete Yule-Cordier Edition: Including the Unabridged Third Edition (1903) of Henry Yule’s Annotated Translation, as Revised by Henri Cordier, Together with Cordier’s Later Volume of Notes and Addenda (1920) (Dover Publications/Constable, 1993).

  56. Hansen, H. B. et al. Comparing ancient DNA preservation in petrous bone and tooth cementum. PLoS ONE 12, e0170940 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  58. 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. Protoc. 13, 2447–2461 (2018).

    Article  CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. USA 110, 2223–2227 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Lohse, J. C., Madsen, D. B., Culleton, B. J. & Kennett, D. J. Isotope paleoecology of episodic mid-to-late Holocene bison population expansions in the Southern Plains, USA. Quat. Sci. Rev. 102, 14–26 (2014).

    Article  Google Scholar 

  70. Van Klinken, G. J. Bone collagen quality indicators for palaeodietary and radiocarbon measurements. J. Archaeol. Sci. 26, 687–695 (1999).

    Article  Google Scholar 

  71. Santos, G. M., Southon, J. R., Druffel-Rodriguez, K. C., Griffin, S. & Mazon, M. Magnesium perchlorate as an alternative water trap in AMS graphite sample preparation: a report on sample preparation at KCCAMS at the University of California, Irvine. Radiocarbon 46, 165–173 (2004).

    Article  CAS  Google Scholar 

  72. Stuiver, M. & Polach, H. A. Discussion reporting of 14C data. Radiocarbon 19, 355–363 (1977).

    Article  Google Scholar 

  73. Bronk Ramsey, C. & Lee, S. Recent and planned developments of the program OxCal. Radiocarbon 55, 720–730 (2013).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  75. Brielle, E. S. et al. Entwined African and Asian genetic roots of medieval peoples of the Swahili coast. Nature 615, 866–873 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Fan, S. et al. African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biol. 20, 1–14 (2019).

    Google Scholar 

  77. Fregel, R. et al. Ancient genomes from north Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. Proc. Natl Acad. Sci. USA 115, 6774–6779 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  78. Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Gallego-Llorente, M. et al. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 350, 820–822 (2015).

    Article  CAS  PubMed  Google Scholar 

  80. Jones, E. R. et al. Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nat. Commun. 6, 8912 (2015).

    Article  CAS  PubMed  Google Scholar 

  81. Kılınç, G. M. et al. The demographic development of the first farmers in Anatolia. Curr. Biol. 26, 2659–2666 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  82. Lipson, M. et al. Ancient West African foragers in the context of African population history. Nature 577, 665–670 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Lipson, M. et al. Ancient DNA and deep population structure in sub-Saharan African foragers. Nature 603, 290–296 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Prendergast, M. E. et al. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science 365, eaaw6275 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014).

    Article  PubMed  Google Scholar 

  87. Raghavan, M. et al. Upper palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014).

    Article  PubMed  Google Scholar 

  88. Schlebusch, C. M. et al. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 358, 652–655 (2017).

    Article  CAS  PubMed  Google Scholar 

  89. Schuenemann, V. J. et al. Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nat. Commun. 8, 1–11 (2017).

    Article  Google Scholar 

  90. Sirak, K. A. et al. Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia. Nat. Commun. 12, 7283 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Skoglund, P. et al. Reconstructing prehistoric African population structure. Cell 171, 59–71 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Biagini, S. A. et al. People from Ibiza: an unexpected isolate in the Western Mediterranean. Eur. J. Hum. Genet. 27, 941–951 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  94. Broushaki, F. et al. Early Neolithic genomes from the eastern Fertile Crescent. Science 353, 99–503 (2016).

    Article  Google Scholar 

  95. Changmai, P. et al. Indian genetic heritage in Southeast Asian populations. PLoS Genet. 18, e1010036 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Flegontov, P. et al. Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America. Nature 570, 236–240 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Jeong, C. et al. The genetic history of admixture across inner Eurasia. Nat. Ecol. Evol. 3, 966–976 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  98. Lipson, M. et al. Ancient genomes document multiple waves of migration in Southeast Asian prehistory. Science 361, 92–95 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Liu, D. et al. Extensive ethnolinguistic diversity in Vietnam reflects multiple sources of genetic diversity. Mol. Biol. Evol. 37, 2503–2519 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. López, S. et al. Evidence of the interplay of genetics and culture in Ethiopia. Nat. Commun. 12, 3581 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  101. Nakatsuka, N. et al. The promise of discovering population-specific disease-associated genes in South Asia. Nat. Genet. 49, 1403–1407 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  PubMed  PubMed Central  Google Scholar 

  103. Pickrell, J. K. et al. The genetic prehistory of southern Africa. Nat. Commun. 3, 1143 (2012).

    Article  PubMed  Google Scholar 

  104. Qin, P. & Stoneking, M. Denisovan ancestry in east Eurasian and Native American populations. Mol. Biol. Evol. 32, 2665–2674 (2015).

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  PubMed Central  Google Scholar 

  106. Wang, C.-C. et al. Genomic insights into the formation of human populations in East Asia. Nature 591, 413–419 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Weissensteiner, H. et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  PubMed  PubMed Central  Google Scholar 

  111. Consortium, T. G. P. A global reference for human genetic variation. Nature 526, 68–74 (2015).

    Article  Google Scholar 

Download references

Acknowledgements

We thank N. Adamski, R. Bernardos and Z. Zhang for contributions to data generation, processing and curation. We acknowledge the help and support we received from the Soqotra Heritage Project team, including A. E. A. S. Al-Rumali, M. T. H. Ali, A. S. S. A. Al-Ameri and S. M. O. Sulaiman. We thank N. Salem for translation of the manuscript title and abstract to Arabic. The work of J. Jansen van Rensburg in Soqotra was supported by the National Geographic Society (NGS-61123R-19). D. Reich is an Investigator of the Howard Hughes Medical Institute (HHMI), and the ancient DNA laboratory work and analyses were also supported by National Institutes of Health grant HG012287, by John Templeton Foundation grant 61220, by the Allen Discovery Center program, which is a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation, and by a gift from J.-F. Clin. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 licence to the public and a sublicensable licence to HHMI in their research articles. Pursuant to those licences, the author-accepted manuscript of this article can be made freely available under a CC BY 4.0 licence immediately upon publication.

Author information

Authors and Affiliations

  1. Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA

    Kendra Sirak, Esther Brielle, Bowen Chen, Iosif Lazaridis, Harald Ringbauer, Matthew Mah, Swapan Mallick & David Reich

  2. Department of Genetics, Harvard Medical School, Boston, MA, USA

    Kendra Sirak, Esther Brielle, Iosif Lazaridis, Matthew Mah, Swapan Mallick, Adam Micco, Nadin Rohland, Kimberly Callan, Elizabeth Curtis, Aisling Kearns, Ann Marie Lawson, J. Noah Workman, Fatma Zalzala & David Reich

  3. Chronicle Heritage, Phoenix, AZ, USA

    Julian Jansen Van Rensburg

  4. Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

    Harald Ringbauer

  5. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA

    Matthew Mah, Swapan Mallick, Adam Micco, Kimberly Callan, Elizabeth Curtis, Aisling Kearns, Ann Marie Lawson, J. Noah Workman, Fatma Zalzala & David Reich

  6. Broad Institute of Harvard and MIT, Cambridge, MA, USA

    Matthew Mah, Swapan Mallick, Nadin Rohland & David Reich

  7. General Organisation for Antiquities and Museums (GOAM), Hadiboh, Republic of Yemen

    Ahmed Saeed Ahmed Al-Orqbi

  8. Arab Regional Centre for World Heritage, Manama, Kingdom of Bahrain

    Esmail Mohammed Ahmed Salem

  9. Environmental Protection Agency on Soqotra (EPA), Hadiboh, Republic of Yemen

    Ali Mohammed Salem Hasan

  10. Independent Researcher, London, UK

    Daniel Charles Britton

Authors
  1. Kendra Sirak
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Julian Jansen Van Rensburg
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Esther Brielle
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Bowen Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Iosif Lazaridis
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Harald Ringbauer
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Matthew Mah
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Swapan Mallick
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Adam Micco
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Nadin Rohland
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Kimberly Callan
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Elizabeth Curtis
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Aisling Kearns
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Ann Marie Lawson
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. J. Noah Workman
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Fatma Zalzala
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Ahmed Saeed Ahmed Al-Orqbi
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Esmail Mohammed Ahmed Salem
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Ali Mohammed Salem Hasan
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Daniel Charles Britton
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. David Reich
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

K.S., J.J.V.R. and D.R. designed the research. J.J.V.R., A.S.A.A.-O., E.M.A.S., A.M.S.H. and D.C.B. excavated and/or contributed to the acquisition and description of the osteological and archaeological data. K.S., E.B., B.C., I.L., D.R. and H.R. carried out population genetics analyses. M.M., S.M., A.M. and A.K. contributed to data generation, processing and curation. K.C., E.C., A.M.L., J.N.W. and F.Z. performed laboratory work under the supervision of N.R. K.S. and J.J.V.R wrote and revised the manuscript with input from all co-authors.

Corresponding authors

Correspondence to Kendra Sirak or Julian Jansen Van Rensburg.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Ecology & Evolution thanks Diyendo Massilani, Miranda Morris and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

Additional information

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

Extended data

Extended Data Fig. 1 Heatmap of pairwise qpWave tests for 32 medieval Soqotri individuals with sufficient SNP coverage.

Data are in Supplementary Data 4 and details are in Supplementary Note 4. We interpret pairwise model p-values > 0.01 (colored cells) to be consistent with the two individuals forming a clade relative to the reference population set, and p-values < 0.01 (grey cells) to be inconsistent.

Supplementary information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sirak, K., Jansen Van Rensburg, J., Brielle, E. et al. Medieval DNA from Soqotra points to Eurasian origins of an isolated population at the crossroads of Africa and Arabia. Nat Ecol Evol 8, 817–829 (2024). https://doi.org/10.1038/s41559-024-02322-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41559-024-02322-x

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research