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The genetics of an early Neolithic pastoralist from the Zagros, Iran

Gallego-Llorente, M., Connell, S., Jones, E. R., Merrett, D. C., Jeon, Y., Eriksson, A., Siska, V., Gamba, C., Meiklejohn, C., Beyer, R., Jeon, S., Cho, Y. S., Hofreiter, M., Bhak, J., Manica, A., Pinhasi, R.·2016·Scientific Reports
DOI 10.1038/srep31326PMC PMC4977546

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Abstract

The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an economy based on goat herding, ca. 10,000 BP. We show that Western Iran was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus, but distinct from the Neolithic Anatolian people who later brought food production into Europe. The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting those of the Central Zagros were somewhat isolated from other populations of the Fertile Crescent. Runs of homozygosity are of a similar length to those from Neolithic farmers, and shorter than those of Caucasus and Western Hunter-Gatherers, suggesting that the inhabitants of Ganj Dareh did not undergo the large population bottleneck suffered by their northern neighbours. While some degree of cultural diffusion between Anatolia, Western Iran and other neighbouring regions is possible, the genetic dissimilarity between early Anatolian farmers and the inhabitants of Ganj Dareh supports a model in which Neolithic societies in these areas were distinct.

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Figure 1 GD13a appears to be related to Caucasus Hunter Gatherers and to modern South Asian populations. (A) PCA loaded on modern populations (represented by open symbols). Ancient individuals (solid symbols) are projected onto these axes. (B) Outgroup f3(X, GD13a; Dinka), where Caucasus Hunter Gatherers (Kotias and Satsurblia) share the most drift with GD13a. Ancient samples have filled circles whereas modern populations are represented by empty symbols. (C) ADMIXTURE using K = 17, where GD13a appears very similar to Caucasus Hunter Gatherers, and to a lesser extent to modern south Asian populations.
Figure 1 GD13a appears to be related to Caucasus Hunter Gatherers and to modern South Asian populations. (A) PCA loaded on modern populations (represented by open symbols). Ancient individuals (solid symbols) are projected onto these axes. (B) Outgroup f3(X, GD13a; Dinka), where Caucasus Hunter Gatherers (Kotias and Satsurblia) share the most drift with GD13a. Ancient samples have filled circles whereas modern populations are represented by empty symbols. (C) ADMIXTURE using K = 17, where GD13a appears very similar to Caucasus Hunter Gatherers, and to a lesser extent to modern south Asian populations.CC BY · PubMed Central
Figure 2 GD13a did not undergo a recent large population bottleneck. (A) GD13a has similar runs of homozygosity (ROH) lengths to Neolithic individuals, while Caucasus Hunter Gatherers (Kotias and Satsurblia), like European Hunter Gatherers (Loschbour and Bichon), underwent recent large population bottlenecks potentially associated withthe LGM. (B) Map showing geographical location of Anatolian Neolithic samples, Caucasus Hunter Gatherers (CHG) and GD13a. Background colours indicate mean temperature (°C) of coldest quarter during the LGM (data from the worldclim database60 generated by the CCSM4 model)60, with LGM sea levels. Map of populations was generated with MATLAB R2015b (Mathworks, http://www.mathworks.com/)61.
Figure 2 GD13a did not undergo a recent large population bottleneck. (A) GD13a has similar runs of homozygosity (ROH) lengths to Neolithic individuals, while Caucasus Hunter Gatherers (Kotias and Satsurblia), like European Hunter Gatherers (Loschbour and Bichon), underwent recent large population bottlenecks potentially associated withthe LGM. (B) Map showing geographical location of Anatolian Neolithic samples, Caucasus Hunter Gatherers (CHG) and GD13a. Background colours indicate mean temperature (°C) of coldest quarter during the LGM (data from the worldclim database60 generated by the CCSM4 model)60, with LGM sea levels. Map of populations was generated with MATLAB R2015b (Mathworks, http://www.mathworks.com/)61.CC BY · PubMed Central

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Research works printed but not linked: 38

  1. Blockley, S. P. E. & Pinhasi, R. A revised chronology for the adoption of agriculture in the Southern Levant and the role of Lateglacial climatic change. Quaternary Science Reviews 30, 98–108 (2011). · DOI
  2. Goring-Morris, A. N. & Belfer-Cohen, A. Neolithization Processes in the Levant: The Outer Envelope. Current Anthropology 52, S195–S208 (2011). · DOI · Paper page
  3. Omrak, A. et al. Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool. Current Biology 26, 270–275 (2016). · DOI
  4. Zeder, M. A. & Hesse, B. The Initial Domestication of Goats (Capra hircus) in the Zagros Mountains 10,000 Years Ago. Science 287, 2254–2257 (2000). · DOI
  5. Zeder, M. A. Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact. PNAS, doi: 10.1073/pnas.0801317105 (2008). · DOI
  6. Zeder, M. A. The Origins of Agriculture in the Near East. Curr Anthrop 52, 221–235 (2011). · DOI
  7. Smith, P. E. L. Architectural Innovation and Experimentation at Ganj Dareh, Iran. World Archaeology 21, 323–335 (1990). · DOI
  8. Merrett, D. C. Bioarchaeology in Early Neolithic Iran: assessment of health status and subsistence strategy. Unpublished Ph.D. Dissertation. (University of Manitoba, 2004).
  9. van Zeist, W., Smith, P. E. L., Palfenier-Vegter, R. M., Suwijn, M. & Casparie, W. A. An archaeobotanical study of Ganj Dareh Tepe, Iran. Palaeohistoria 26, 201–224 (1984).
  10. Reidla, M. et al. Origin and Diffusion of mtDNA Haplogroup X. Am J Hum Genet 73, 1178–1190 (2003). · DOI
  11. Richards, M. et al. Tracing European founder lineages in the Near Eastern mtDNA pool. Am. J. Hum. Genet. 67, 1251–1276 (2000). · DOI
  12. Cassidy, L. M. et al. Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome. PNAS 113, 368–373 (2016). · DOI
  13. Olalde, I. et al. A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures. Mol Biol Evol msv181, doi: 10.1093/molbev/msv181 (2015). · DOI · Paper page
  14. Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009). · DOI · Paper page
  15. Green, R. E. et al. A Draft Sequence of the Neandertal Genome. Science 328, 710–722 (2010). · DOI · Paper page
  16. Harris, D. R. et al. Origins of Agriculture in Western Central Asia: An Environmental-Archaeological Study. (University of Pennsylvania Press, 2010). · DOI
  17. Gangal, K., Sarson, G. R. & Shukurov, A. The Near-Eastern Roots of the Neolithic in South Asia. PLoS ONE 9, e95714 (2014). · DOI
  18. Kirin, M. et al. Genomic Runs of Homozygosity Record Population History and Consanguinity. PLOS ONE 5, e13996 (2010). · DOI
  19. Matthews, R. & Nashli, H. F. The Neolithisation of Iran. 3, (Oxbow Books, 2013). · DOI
  20. Weeks, L. et al. The Neolithic Settlement of Highland SW Iran: New Evidence from the Mamasani District. Iran 44, 1–31 (2006). · DOI
  21. Whitlam, J., Ilkhani, H., Bogaard, A. & Charles, C. In The Earliest Neolithic of Iran: 2008 Excavations at Sheikh-e Abad and Jani (eds Matthews, R., Matthews, W. & Mohammadifar, Y. ) Ch. 15, 175–184 (2013). · DOI
  22. Gamba, C. et al. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. Mol Ecol Resour 16, 459–469 (2016). · DOI
  23. Meyer, M. & Kircher, M. Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing. Cold Spring Harb. Protoc. 2010, pdb.prot5448 (2010). · DOI
  24. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal 17, pp. 10–12 (2011). · DOI · Paper page
  25. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009). · DOI · Paper page
  26. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). · DOI · Paper page
  27. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010). · DOI · Paper page
  28. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010). · DOI · Paper page
  29. Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. USA 104, 14616–14621 (2007). · DOI · Paper page
  30. Brotherton, P. et al. Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Res. 35, 5717–5728 (2007). · DOI
  31. Gallego Llorente, M. et al. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 350, 820–822 (2015). · DOI · Paper page
  32. Sánchez-Quinto, F. et al. Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers. Curr. Biol. 22, 1494–1499 (2012). · DOI · Paper page
  33. Skoglund, P., Storå, J., Götherström, A. & Jakobsson, M. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J. Archaeol. Sci. 40, 4477–4482 (2013). · DOI · Paper page
  34. Vianello, D. et al. HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment. Hum. Mutat. 34, 1189–1194 (2013). · DOI
  35. 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). · DOI · Paper page
  36. Browning, S. R. & Browning, B. L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084–1097 (2007). · DOI
  37. Consortium, T. 1000 G. P. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012). · DOI · Paper page
  38. Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G. & Jarvis, A. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25, 1965–1978 (2005). · DOI

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Metadata

Authors
Gallego-Llorente, M., Connell, S., Jones, E. R., Merrett, D. C., Jeon, Y., Eriksson, A., Siska, V., Gamba, C., Meiklejohn, C., Beyer, R., Jeon, S., Cho, Y. S., Hofreiter, M., Bhak, J., Manica, A., & Pinhasi, R.
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2016-08-09
Volume
6
Issue
1
ISSN
2045-2322
DOI
10.1038/srep31326
PMC
PMC4977546
Cited by
73
References
18
Language
en
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CoChat. (2026). Citation check: The genetics of an early Neolithic pastoralist from the Zagros, Iran. https://app.cochat.ai/papers/10.1038/srep31326
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Gallego-Llorente, M., Connell, S., Jones, E. R., Merrett, D. C., Jeon, Y., Eriksson, A., Siska, V., Gamba, C., Meiklejohn, C., Beyer, R., Jeon, S., Cho, Y. S., Hofreiter, M., Bhak, J., Manica, A., & Pinhasi, R. (2016). The genetics of an early Neolithic pastoralist from the Zagros, Iran. Scientific Reports. https://doi.org/10.1038/srep31326