Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices

English version

Autoři: Sally Wasef ^aff001; Sankar Subramanian ^aff001; Richard O’Rorke ^aff001; Leon Huynen ^aff001; Samia El-Marghani ^aff003; Caitlin Curtis ^aff001; Alex Popinga ^aff004; Barbara Holland ^aff005; Salima Ikram ^aff006; Craig Millar ^aff008; Eske Willerslev ^aff009; David Lambert ^aff001
Působiště autorů: Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Brisbane, Australia ^aff001; Ancient DNA Laboratory, Learning Resource Center, Kasr Al-Ainy Faculty of Medicine, Cairo University, Cairo, Egypt ^aff002; Ministry of Antiquities, Cairo, Egypt ^aff003; Centre for Computation Evolution, Department of Computer Science, University of Auckland, Auckland, New Zealand ^aff004; School of Natural Sciences, University of Tasmania, Hobart, Australia ^aff005; Department of Sociology, Egyptology, and Anthropology, American University in Cairo, Cairo, Egypt ^aff006; Ancient Studies Department, Stellenbosch University, Stellenbosch, South Africa ^aff007; School of Biological Sciences, University of Auckland, Auckland, New Zealand ^aff008; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, England, United Kingdom ^aff009; Department of Zoology, University of Cambridge, Cambridge, England, United Kingdom ^aff010; Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark ^aff011
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pone.0223964

Souhrn

The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from ~600BC. Although it is known that a very large number of these ‘votive’ mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ~2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild migratory Sacred Ibis for the ritual yearly demand.

Klíčová slova:

Sequence alignment – Species diversity – Birds – Egypt – Paleogenetics – Ancient DNA – Tuna – Feathers

Zdroje

1. Gilbert MT, Barnes I, Collins MJ, Smith C, Eklund J, Goudsmit J, et al. Long-term survival of ancient DNA in Egypt: response to Zink and Nerlich (2003). Am J Phys Anthropol. 2005;128(1):110–4; discussion 5–8. doi: 10.1002/ajpa.20045 15714514.

2. Zink AR, Nerlich AG. Long-term survival of ancient DNA in Egypt: Reply to Gilbert et al. American Journal of Physical Anthropology. 2005;128(1):115–8. doi: 10.1002/ajpa.20046

3. Zivie A, Lichtenberg R. The cats of the goddess Bastet. In: Ikram S, editor. Divine Creatures: Animal Mummies in Ancient Egypt Cairo: The American University in Cairo Press; 2005. p. 106–19.

4. Zink AR, Sola C, Reischl U, Grabner W, Rastogi N, Wolf H, et al. Characterization of Mycobacterium tuberculosis complex DNAs from Egyptian mummies by spoligotyping. J Clin Microbiol. 2003;41(1):359–67. doi: 10.1128/JCM.41.1.359-367.2003 12517873; PubMed Central PMCID: PMC149558.

5. Zink AR, Grabner W, Reischl U, Wolf H, Nerlich AG. Molecular study on human tuberculosis in three geographically distinct and time delineated populations from ancient Egypt. Epidemiology and Infection. 2003;130(2):239–49. doi: 10.1017/s0950268802008257 12729192

6. Zink A, Nerlich AG. Molecular analyses of the “Pharaos:” feasibility of molecular studies in ancient Egyptian material. American journal of physical anthropology. 2003;121(2):109–11. doi: 10.1002/ajpa.10213 12740953

7. Ikram S. Divine Creatures: Animal Mummies in Ancient Egypt. Cairo: Amercain University in Cairo Press; 2005.

8. Hancock JA, Kushlan JA, Kahl MP. Storks, Ibises and Spoonbills of the World. London: Academic Press; 1992.

9. Ray JD. Observations on the Archive of Ḥor. Journal of Egyptian Archaeology. 1978;64:113–20.

10. Wade AD, Ikram S, Conlogue G, Beckett R, Nelson AJ, Colten R. Backroom Treasures: CT Scanning of Two Ibis Mummies from the Peabody Museum Collection. 2011.

11. Massiera M, Mathieu B, Rouffet F. Speculations on the Role of Animal Cults in the Economy of Ancient Egypt. Apprivoiser le sauvage/Taming the Wild. 2015;11:211–28.

12. Ikram S. An Eternal Aviary, Bird Mummies from Ancient Egypt. In: Bailleul Le-Suer R, editor. Between Heaven and Earth: Birds in Ancient Egypt. Chicago: The Oriental Institute of the University of Chicago; 2012. p. 41–8.

13. Wasef S, Wood R, El Merghani S, Ikram S, Curtis C, Holland B, et al. Radiocarbon dating of Sacred Ibis mummies from ancient Egypt. Journal of Archaeological Science: Reports. 2015;4:355–61. doi: 10.1016/j.jasrep.2015.09.020

14. Richardin P, Porcier S, Ikram S, Louarn G, Berthet D. Cats, Crocodiles, Cattle, and More: Initial Steps toward Establishing a Chronology of Ancient Egyptian Animal Mummies. Radiocarbon. 2017;59(2):595–607. doi: 10.1017/Rdc.2016.102 WOS:000400598700030.

15. Davies S, Smith HS. Sacred Animal Temples at Saqqara. In: Quirke S, editor. The Temple in Ancient Egypt: New Discoveries and Recent Research. London1997. p. 112–31.

16. Martin GT. The Sacred Animal Necropolis at North Saqqâra: The Southern Dependencies of the Main Temple Complex. London: 1981.

17. Zaghloul HO. Fruhdemotische Urkunden aus Hermupolis. Bulletin of the Center of Papyrological Studies. Cairo1985.

18. Kessler D, Nur el-Din A. Tuna al-Gebel. In: Ikram S, editor. Divine Creatures: Animal Mummies in Ancient Egypt. Cairo: Amercain University in Cairo Press; 2005. p. 120–63.

19. Kessler D, Nur el-Din A. Der Tierfriedhof von Tuna el-Gebel. Antike Welt. 1994;3:252–65.

20. Cuvier G. Discourse of the revolutions on the surface of the earth: determination of the birds called ibis by the ancient Egyptians1825.

21. Kessler D, el-Din AeHN. Tuna al-Gebel. divine creatures: animal mummies in ancient egypt. 2005;7948:120.

22. Meeks D. Les couveuses artificielles en Egypte. Travaux du Centre Camille Jullian. 1997:132–4.

23. Moodie RL. Roentgenologic studies of Egyptian and Peruvian mummies. Field Museum Press. 1931.

24. Dabney J, Knapp M, Glocke I, Gansauge MT, Weihmann A, Nickel B, et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci U S A. 2013;110(39):15758–63. doi: 10.1073/pnas.1314445110 24019490; PubMed Central PMCID: PMC3785785.

25. Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor protocols. 2010;2010(6):pdb.prot5448. Epub 2010/06/03. doi: 10.1101/pdb.prot5448 20516186.

26. Wasef S, Huynen L, Millar CD, Subramanian S, Ikram S, Holland B, et al., editors. ‘Fishing’ for mitochondrial DNA in mummified Sacred Ibis: Development of a targeted enrichment protocol resolves the ancient Egyptian DNA survival debate. the International Symposium of Animals in Ancient Egypt, ISAAE 1; 2016 2018; Lyon, France: Leiden: Sidestone Press.

27. Wasef S, Huynen L, Millar CD, Subramanian S, Ikram S, Holland B, et al. Fishing for Mitochondrial DNA in The Egyptian Sacred Ibis Mummies. bioRxiv. 2018.

28. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–60. doi: 10.1093/bioinformatics/btp324 19451168; PubMed Central PMCID: PMC2705234.

29. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. doi: 10.1093/bioinformatics/btp352 19505943; PubMed Central PMCID: PMC2723002.

30. Okonechnikov K, Conesa A, Garcia-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2015. doi: 10.1093/bioinformatics/btv566 26428292.

31. Jonsson H, Ginolhac A, Schubert M, Johnson PL, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics. 2013;29(13):1682–4. doi: 10.1093/bioinformatics/btt193 23613487; PubMed Central PMCID: PMC3694634.

32. Miller MA, Pfeiffer W, Schwartz T, editors. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE), 2010; 2010: Ieee.

33. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25(11):1451–2. doi: 10.1093/bioinformatics/btp187 19346325.

34. Nei M. Molecular Evolutionary Genetics. NY: Columbia University Press; 1987.

35. http://www.fluxus-engineering.com/. Network 4.6.1.1. ed: Fluxus Technology Ltd; 2015.

36. Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu CH, Xie D, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2014;10(4):e1003537. Epub 2014/04/12. doi: 10.1371/journal.pcbi.1003537 24722319; PubMed Central PMCID: PMC3985171.

37. Bouckaert RR, Drummond AJ. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evol Biol. 2017;17(1):42. Epub 2017/02/09. doi: 10.1186/s12862-017-0890-6 28166715; PubMed Central PMCID: PMC5294809.

38. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9. doi: 10.1093/molbev/mst197 24132122; PubMed Central PMCID: PMC3840312.

39. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586–91. doi: 10.1093/molbev/msm088 17483113.

40. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of molecular evolution. 1980;16(2):111–20. doi: 10.1007/bf01731581 7463489

41. Paradis E. Analysis of Phylogenetics and Evolution with R. Springer. New York. 2012.

42. Wickham H. ggplot2: an Implementation of the Grammar of Graphics, Version 0.8. 8. 2010.

43. Sorenson MD, Quinn TW. Numts: A challenge for avian systematics and population biology. Auk. 1998;115(1):214–21. doi: 10.2307/4089130 WOS:000071487100026.

44. Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME, Sikora M, et al. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am J Hum Genet. 2013;93(5):852–64. doi: 10.1016/j.ajhg.2013.10.002 24568772; PubMed Central PMCID: PMC3824117.

45. Enk JM, Devault AM, Kuch M, Murgha YE, Rouillard J-M, Poinar HN. Ancient Whole Genome Enrichment Using Baits Built from Modern DNA. Molecular Biology and Evolution. 2014;31(5):1292–4. doi: 10.1093/molbev/msu074 WOS:000335914400021. 24531081

46. Bandelt H-J, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Molecular biology and evolution. 1999;16(1):37–48. doi: 10.1093/oxfordjournals.molbev.a026036 10331250

Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices

Souhrn

Klíčová slova:

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