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 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history


Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world’s most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 bc in the Levant1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, 14C dated to the New Kingdom, 1130–1000 bc. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.

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

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Emmer wheat husks in accession UC10164 and the sequenced specimens.
Fig. 2: The relationship between UC10164 and modern emmer wheat.
Fig. 3: Phylogenetic analysis of UC10164 and 64 modern emmer wheats.
Fig. 4: Haplotype sharing between UC10164 and modern emmer wheat within loci associated with selection under domestication.

Data availability

Sequence data are deposited in the ENA with study accession number PRJEB31103. The genotype calls are also provided as the source data for Fig. 2. The database of archaeobotanical observations is provided as the source data for Extended Data Fig. 1. Source data are available for Figs. 24 and Extended Data Figs. 15.


  1. Arranz-Otaegui, A., Colledge, S., Zapata, L., Teira-Mayolini, L. C. & Ibáñez, J. J. Regional diversity on the timing for the initial appearance of cereal cultivation and domestication in southwest Asia. Proc. Natl Acad. Sci. USA 113, 14001–14006 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Fuller, D. Q., Willcox, G. & Allaby, R. G. Early agricultural pathways: moving outside the ‘core area’ hypothesis in southwest Asia. J. Exp. Bot. 63, 617–633 (2012).

    CAS  PubMed  Google Scholar 

  3. Fuller, D. Q. & Lucas, L. in Encyclopedia of Global Archaeology (Ed. Smith, C.) 7812–7817 (Springer, 2014).

  4. McClatchie, M. et al. Neolithic farming in north-western Europe: archaeobotanical evidence from Ireland. J. Archaeol. Sci. 51, 206–215 (2014).

    Google Scholar 

  5. Mascher, M. et al. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nat. Genet. 48, 1089–1093 (2016).

    CAS  PubMed  Google Scholar 

  6. Ramos-Madrigal, J. et al. Genome sequence of a 5,310-year-old maize cob provides insights into the early stages of maize domestication. Curr. Biol. 26, 3195–3201 (2016).

    CAS  PubMed  Google Scholar 

  7. Vallebueno-Estrada, M. et al. The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding. Proc. Natl Acad. Sci. USA 113, 14151–14156 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Kistler, L. et al. Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science 362, 1309–1313 (2018).

    CAS  PubMed  Google Scholar 

  9. Smith, O. et al. A domestication history of dynamic adaptation and genomic deterioration in sorghum. Nat. Plants 5, 369–379 (2018).

    Google Scholar 

  10. Palmer, S. A., Smith, O. & Allaby, R. G. The blossoming of plant archaeogenetics. Ann. Anat. 194, 146–156 (2012).

    CAS  PubMed  Google Scholar 

  11. Bilgic, H., Hakki, E. E., Pandey, A., Khan, M. K. & Akkaya, M. S. Ancient DNA from 8400 year-old Çatalhöyük wheat: implications for the origin of neolithic agriculture. PLoS ONE 11, e0151974 (2016).

    PubMed  PubMed Central  Google Scholar 

  12. Purugganan, M. D. & Fuller, D. Q. The nature of selection during plant domestication. Nature 457, 843–848 (2009).

    CAS  PubMed  Google Scholar 

  13. Avni, R. et al. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357, 93–97 (2017).

    CAS  PubMed  Google Scholar 

  14. Nalam, V. J., Vales, M. I., Watson, C. J. W., Kianian, S. F. & Riera-Lizarazu, O. Map-based analysis of genes affecting the brittle rachis character in tetraploid wheat (Triticum turgidum L.). Theor. Appl. Genet. 112, 373–381 (2006).

    CAS  PubMed  Google Scholar 

  15. Pourkheirandish, M. et al. Evolution of the grain dispersal system in barley. Cell 162, 527–539 (2015).

    CAS  PubMed  Google Scholar 

  16. Fuller, D. Q. Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the old world. Ann. Bot. 100, 903–924 (2007).

    PubMed  PubMed Central  Google Scholar 

  17. Harlan, J. R., de Wet, J. M. J. & Price, E. G. Comparative evolution of cereals. Evolution 27, 311–325 (1973).

    PubMed  Google Scholar 

  18. Salamini, F., Özkan, H., Brandolini, A., Schäfer-Pregl, R. & Martin, W. Genetics and geography of wild cereal domestication in the near east. Nat. Rev. Genet. 3, 429–441 (2002).

    CAS  PubMed  Google Scholar 

  19. Horovitz, A. The soil seed bank of wild emmer. In Proc. International Symposium on In situ Conservation of Plant Genetic Diversity (eds Zencirci, N. et al.) 185–188 (Central Research Institute for Field Crops, 1998).

  20. Nave, M., Avni, R., Ben-Zvi, B., Hale, I. & Distelfeld, A. QTLs for uniform grain dimensions and germination selected during wheat domestication are co-located on chromosome 4B. Theor. Appl. Genet. 129, 1303–1315 (2016).

    CAS  PubMed  Google Scholar 

  21. Allaby, R. G., Stevens, C., Lucas, L., Maeda, O. & Fuller, D. Q. Geographic mosaics and changing rates of cereal domestication. Proc. R. Soc. B 372, 20160429 (2017).

    Google Scholar 

  22. Crawford, D. J. Food: tradition and change in Hellenistic Egypt. World Archaeol. 11, 136–146 (1979).

    CAS  PubMed  Google Scholar 

  23. Caton-Thompson, G. & Gardner, E. W. The Desert Fayum (Royal Anthropological Institute of Great Britain and Ireland, 1934).

  24. Nesbitt, M. & Samuel, D. From stable crop to extinction? The archaeology and history of the hulled wheats. In Proc. First International Workshop on Hulled Wheats (eds Padulosi, S. et al.) 41–100 (International Plant Genetic Resources Institute, 1996).

  25. Wetterstrom, W. in The Archaeology of Africa (eds Andah, B., Okpoko, A., Shaw, T. & Sinclair, P.) 165–226 (Routledge, 1993).

  26. Zaharieva, M., Ayana, N. G., Al Hakimi, A., Misra, S. C. & Monneveux, P. Cultivated emmer wheat (Triticum dicoccon Schrank), an old crop with promising future: a review. Genet. Resour. Crop Evol. 57, 937–962 (2010).

    Google Scholar 

  27. Brunton, G. & Caton-Thompson, G. The Badarian Civilization and Predynastic Remains Near Badari (British School of Archaeology in Egypt, 1928).

  28. Günther, T. & Nettelblad, C. The presence and impact of reference bias on population genomic studies of prehistoric human populations. PLoS Genet. 15, 1008302 (2019).

    Google Scholar 

  29. Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. MapDamage2.0: fast approximate bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).

    PubMed  PubMed Central  Google Scholar 

  30. IWGSC. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361, eaar7191 (2018).

    Google Scholar 

  31. Golenberg, E. M. Outcrossing rates and their relationship to phenology in Triticum dicoccoides. Theor. Appl. Genet. 75, 937–944 (1988).

    Google Scholar 

  32. Fuller, D. Q. Agricultural origins and frontiers in south Asia: a working synthesis. J. World Prehist. 20, 1–86 (2006).

    Google Scholar 

  33. Stevens, C. J. et al. Between China and south Asia: a middle Asian corridor of crop dispersal and agricultural innovation in the bronze age. Holocene 26, 1541–1555 (2016).

    PubMed  PubMed Central  Google Scholar 

  34. 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 

  35. van der Veen, M. Consumption, Trade and Innovation: exploring the Botanical Remains from the Roman and Islamic Ports at Quseir al-Qadim, Egypt (Africa Magna Verlag, 2011).

  36. Murray, M. A. in Ancient Egyptian Materials and Technology (eds Nicholson, P. T. & Shaw, I.) 505–536 (Cambridge Univ. Press, 2000).

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

    PubMed  PubMed Central  Google Scholar 

  38. Marcussen, T. et al. Ancient hybridizations among the ancestral genomes of bread wheat. Science 345, 1250092 (2014).

    PubMed  Google Scholar 

  39. Olsen, K. M. et al. Selection under domestication: evidence for a sweep in the rice waxy genomic region. Genetics 173, 975–983 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Walsh, B. & Lynch, M. Evolution and Selection of Quantitative Traits (Oxford Univ. Press, 2018).

  41. Fuller, D. Q., Lucas, L., Gonzalez Carretero, L. & Stevens, C. From intermediate economies to agriculture: trends in wild food use, domestication and cultivation among early villages in southwest Asia. Paleorient 44, 59–74 (2018).

    Google Scholar 

  42. Badaeva, E. D. et al. Chromosomal passports provide new insights into diffusion of emmer wheat. PLoS ONE 10, e0128556 (2015).

    PubMed  PubMed Central  Google Scholar 

  43. Luo, M. C. et al. The structure of wild and domesticated emmer wheat populations, gene flow between them, and the site of emmer domestication. Theor. Appl. Genet. 114, 947–959 (2007).

    PubMed  Google Scholar 

  44. Wengrow, D., Dee, M., Foster, S., Stevenson, A. & Ramsey, C. B. Cultural convergence in the neolithic of the Nile Valley: a prehistoric perspective on Egypt’s place in Africa. Antiquity 88, 95–111 (2014).

    Google Scholar 

  45. Fuller, D. & Hildebrand, E. in The Oxford Handbook of African Archaeology (eds Mitchell, P. & Lane, P.) 507–525 (Oxford Univ. Press, 2013).

  46. Hasel, M. G. Domination and Resistance: Egyptian Military Activity in the Southern Levant, ca. 1300–1185 B.C. (Brill, 1998).

  47. Civáň, P., Ivaničová, Z. & Brown, T. A. Reticulated origin of domesticated emmer wheat supports a dynamic model for the emergence of agriculture in the fertile crescent. PLoS ONE 8, e81955 (2013).

    PubMed  PubMed Central  Google Scholar 

  48. He, F. et al. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat. Genet. 51, 896–904 (2019).

    CAS  PubMed  Google Scholar 

  49. Di Donato, A., Filippone, E., Ercolano, M. R. & Frusciante, L. Genome sequencing of ancient plant remains: findings, uses and potential applications for the study and improvement of modern crops. Front. Plant Sci. 9, 441 (2018).

    PubMed  PubMed Central  Google Scholar 

  50. Zohary, D., Hopf, M. & Weiss, E. Domestication of Plants in the Old World (Oxford Univ. Press, 2012).

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

    Google Scholar 

  52. Reimer, P. J. et al. IntCal13 and Marine13 radiocarbon age calibration curves 0–50,000 years cal BP. Radiocarbon 55, 1869–1887 (2013).

    CAS  Google Scholar 

  53. Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 6, pdb.prot5448 (2010).

    Google Scholar 

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

    Google Scholar 

  55. Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).

    PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Meyer, M. et al. A high coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2013).

    Google Scholar 

  58. Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Jordan, K. W. et al. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol. 16, 48 (2015).

    PubMed  PubMed Central  Google Scholar 

  61. Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Vavilov, N. I. Origin and Geography of Cultivated Plants (Cambridge Univ. Press, 1989).

  64. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. R Core Team R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2017).

  66. Lee, T. H., Guo, H., Wang, X., Kim, C. & Paterson, A. H. SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genom. 15, 162 (2014).

    Google Scholar 

  67. Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).

    Google Scholar 

  68. Kaplan, N. L., Hudson, R. R. & Langley, C. H. The hitchhiking effect revisited. Genetics 123, 887–899 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Haldane, J. B. S. The combination of linkage values and the calculation of distances between the loci of linked factors. J. Genet. 8, 299–309 (1919).

    Google Scholar 

  70. Cabrera, C. P. et al. Uncovering networks from genome-wide association studies via circular genomic permutation. G3 2, 1067–1075 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references


We thank Y. Diekmann, D. O’Rourke and A. Garnett for helpful discussions. M.F.S. and R.M. are supported by RCUK BBSRC grant BB/M011585/1. R.M. is also supported by RCUK BBSRC grant BB/P024726/1; L.R.B. by the Spanish Ministry of Economy and Competitiveness Severo Ochoa Programme for Centres of Excellence in R&D 2016-2019 (SEV-2015-0533) and CERCA Programme, Generalitat de Catalunya; M.G.T. and S.B. by a Wellcome Trust Senior Research Fellowship, grant 100719/Z/12/Z. D.Q.F. and C.S. are supported by the ERC ComPag project, grant number 323842. V.E.M. and S.B. are partially supported by the RCUK NERC grant NE/P012574/1. UCL computing infrastructure was supported by BBSRC grant BB/R01356X/1.

Author information

Authors and Affiliations



L.R.B., M.F.S., R.M., D.Q.F., C.S., A.S. and M.G.T. designed and coordinated the study. M.F.S. designed and performed data analysis. L.R.B., S.B. and V.E.M. performed experiments. C.S. obtained image data. M.F.S. and R.M. coordinated the sequencing. D.Q.F. coordinated the carbon dating. M.G.T. supervised access to the ancient DNA laboratory. D.Q.F., A.S. and C.S. collated archaeobotanical data. M.F.S. and R.M. wrote the manuscript. All of the authors edited and approved the manuscript.

Corresponding authors

Correspondence to Michael F. Scott or Richard Mott.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer Review Information Nature Plants thanks Thomas Gilbert, James Breen and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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

Extended data

Extended Data Fig. 1 Map showing archaeobotanical observations of emmer wheat from 9000 – 1000 BCE in Northeast Africa and South West Asia.

Map showing archaeobotanical observations of emmer wheat from 9000 – 1000 BCE in Northeast Africa and South West Asia. The collection location for the sequenced accession (UC10164) is labelled.

Extended Data Fig. 2 Summary of sequencing data from UC10164 samples S1 and S2.

Summary of sequencing data from UC10164 samples S1 and S2. Panel A shows the C to T and G to A misincorporations of alignments against the emmer wheat reference genome as output by MapDamage. Both samples show a small excess of these misincorporations in the 2 bp at each fragment end, as expected for partially UDG treated aDNA libraries. Panel B shows the distribution of fragment sizes after the overlapping paired-end reads were collapsed and adapter sequence was removed using AdapterRemoval. Panel C shows coverage and subgenome representation for different minimum mapping quality scores after these fragments were aligned to the hexaploid bread wheat reference genome. Panel D shows the coverage obtained from alignment to the emmer wheat reference genome, split by minimum mapping quality filters. The exonic SNP sites (at which genotypes are called) have a much lower percentage of ambiguous alignments with low mapping quality scores.

Extended Data Fig. 3 (a) phylogeny of modern emmer wheat accessions and (b) source population proportions inferred by the ADMIXTURE model for various number of source populations (K parameter).

(a) phylogeny of modern emmer wheat accessions and (b) Source population proportions inferred by the ADMIXTURE model for various number of source populations (K parameter). The maximum likelihood phylogeny in (a) was constructed from the full set of SNPs called among modern accessions, excluding UC10164. Bootstrap support for each node is shown where it is less than 100 (based on 1000 bootstraps). In (b), the majority of the ancestry proportion inferred for the ancient Egyptian accession (UC10164) across K values is from the same population that predominates among the “Indian Ocean” subgroup (green accession names). Furthermore, the ancient Egyptian accession has a relatively high proportion of ancestry inferred to come from population groups that are common among modern wild Southern Levant emmer wheats (light blue accession names).

Extended Data Fig. 4 Heatmap of the genotypic similarity between each pair of accessions across 86,594 SNP sites that were called in the ancient Egyptian accession (UC10164).

Heatmap of the genotypic similarity between each pair of accessions across 86,594 SNP sites that were called in the ancient Egyptian accession (UC10164). Below the diagonal, we plot similarity using identity by state. Above the diagonal, we plot haplotypic similarity, which is defined as the fraction of sliding windows of 50 SNP sites that are more than 95% concordant.

Extended Data Fig. 5 Differences between each modern accession and the ancient Egyptian accession (UC10164) across the genome.

Differences between each modern accession and the ancient Egyptian accession (UC10164) across the genome. The fraction of genotypic differences from UC10164 is calculated within sliding windows of 50 SNPs (moved in intervals of 25 SNPs). Each modern accession is plotted as a line and coloured according to its subgroup membership. Below zero we plot the ancestry mosaic inferred for each SNP site called in UC10164. The dissimilarity within sliding windows is plotted against the median physical map position of the SNPs in the sliding window. Each chromosome has a large region around the centromere that has low exonic SNP density and low recombination rate, resulting in long haplotypes.

Supplementary information

Reporting Summary

Supplementary Tables 1–5

Supplementary Table 1: table of alignment statistics for S1 and S2 after various filters have been applied. Supplementary Table 2: concordances between UC10164 and modern accessions, split by chromosome and accession subgroup. Supplementary Table 3: D statistics calculated for the phylogeny (outgroup, (Southern Levant Accession, (Indian Ocean, UC10164))). Supplementary Table 4: raw radiocarbon dating results. Supplementary Table 5: at SNP genotype sites called in UC10164, the proportion of substitutions that are C to T and G to A, relative to the outgroup genotype, and the ratio of transitions to transversions.

Source data

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Scott, M.F., Botigué, L.R., Brace, S. et al. A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. Nat. Plants 5, 1120–1128 (2019).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


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