Saturday, October 05, 2019

Methodological Problems With The Nature Study Of Ancient Egypt - SOY Keita Let's Them Have It

COMMENT - This is a response to a study published in Nature titled Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods, which claims that the Ancient Egyptians were genetically the same as the people of North Africa/Middle East. There are many problems with these interpretations, and professor S.O.Y Keita lays them bare one by one. - MrK

Ancient Egyptian Genomes from northern Egypt: Further discussion

Jean-Philippe Gourdine1,4, S.O.Y Keita2,4, Jean-Luc Gourdine3 and Alain Anselin4*1
Oregon Health & Science University, 2Smithsonian Institution, 3National Institute of Agricultural Research, France(Guadeloupe), 4Ankhou/Cahiers Caribéens d'Égyptologie (Guadeloupe, Martinique),*corresponding author:

Schuenemann et al.1 seemingly suggest, based largely on the results of an ancient DNA study of later period remains from northern Egypt, that the ‘ancient Egyptians’ (AE) as an entity camefrom Asia (the Near East, NE), and that modern Egyptians “received additional sub-Saharan African (SSA) admixtures in recent times” after the latest period of the pharaonic era due to the “trans-Saharan slave trade and Islamic expansion.” In spite of the implied generalization about ‘origins’ the authors do offer the caveat that their findings may have been different if samples had been used from southern Egypt, and this is a significant admission. Their conclusions deserve further discussion from multiple perspectives which cannot be fully developed due to space limitations.

There are alternative interpretations of the results but which were not presented as is traditionally done, with the exception of the admission that results from southern Egyptians may have been different.

The alternative interpretations involve three major considerations:

1) sampling and methodology,
2) historiography and
3) definitions as they relate to populations,origins and evolution.

1) Sampling and methodological strategyThe samples can be questioned as to their representativeness of Egypt in terms of size, spatio-temporal and socio-cultural aspects.

●All of the samples are from the northern half of Egypt, from one nome which is 2.4% (1/42) of AE nomes. Ancient Egyptian culture originated southern Upper Egypt2.

●The socio-cultural dynamics are not fully considered: the information on the origin andsocial status is incomplete, or unknowable in fact. The mummies are clearly assumed tobe representative of the local population based on an incomplete archaeological report, in1
spite of the historical information provided about northern Egypt’s interaction with theNear East since the Predynastic, and the known settlements of Greeks, and others, innorthern Egypt in later periods.

●The timeline is not representative of AE history ~ 3,000 years is missing (e.g.Predynastic, Early Dynastic, Old Kingdom, Middle Kingdom

2) The samples cannot be convincingly said to represent true breeding populations or thosethat truly integrate historical information.

●The authors use Bayesian reconstruction of population size changes through time with BEAST, for which there is generally a discrepancy between the marginal prior and theoriginal prior distribution. The available information on the comparison between original and marginal priors, and on prior and posterior distributions, does not take into account possible population substructure.

Sex-biased sampling (mtDNA) cannot recover population demography of the whole country unless the sample size is large enough and representative in terms of chronology, regional variation, “ethnicities” (including the foreign presence), class and geography. It suffers from many biases that can affect the assessment of the effective population size: population size changes, mutation bias, and natural selection.

●The whole genome sample size is too small (n=3) to accurately permit a discussion of allEgyptian population history from north to south.2) Historiography and misinterpretation

●The authors do not consider explanations based on historical narrative, although theypresent historical information. NE input in AE could also be explained by old mercantile2 relationships with Lower Egypt (e.g. Maadi-Buto complex ~4,000 BC3), EgyptianizedAsiatic rulers and migrants (e.g. Hyksos ~1,650 BC), NE prisoners of war (e.g. from Thutmose III’s military campaign in NE ~ 1,490 BC), from diplomatic marriages2 (e.g.Amenhotep III and Mitanni princess, Gilukhipa~ 1,380 BC), etc.

The authors completely dismiss the results of PCR methods used on AE remains. As a Habicht et al.4 states, PCR based methods were used successfully on mummified Egyptian cats and crocodiles without creating extensive debate. Results that are likely reliable are from studies that analyzed short tandem repeats (STRs) from Amarna royal mummies5 (1,300 BC), and of Ramesses III (1,200 BC)6; Ramesses III had the Y chromosome haplogroup E1b1a, an old African lineage7. Our analysis of STRs from Amarna and Ramesside royal mummies with pop Affiliator18 based on the same published data 5,6 indicates a 41.7% to 93.9% probability of SSA affinities (see Table 1); most of the individuals had a greater probability of affiliation with “SSA” which is notthe only way to be “African” a point worth repeating.

●There are some philosophical issues as well for which space does not permit a full discussion. Conceptually what genetic markers are considered to be “African” or “Asian” needs discussion--and of what “defines” Africa as well. For example, the E1b1b1 (M35/78) lineage found in one Abusir el-Meleq sample is found not only in northern Africa, but is also well represented in eastern Africa7 and perhaps was taken to Europe across the Mediterranean before the Holocene (Trombetta, personal communication). E lineages are found in high frequency (>70%) among living Egyptians in Adaima9. The authors define all mitochondrial M1 haplogroups as “Asian” which is problematic. Gene history is not population history: ultimate “origins” and later sources to a specific region/3 population are conceptually different. Gene history is not also ethnic or linguistic history. M1 has been postulated to have emerged in Africa10, and there is no convincing evidence supporting an M1 ancestor in Asia: many M1 daughter haplogroups (M1a) are clearly African in origin and history10. The M1a1, M1a2a, M1a1i, M1a1e variants found in the Abusir el-Meleq samples1 predate Islam and are abundant in SSA groups10, particularly in East Africa. Furthermore, SSA groups indicated to have contributed to modern Egypt donot match the Muslim trade routes that have been well documented11 as SSA groups from the great lakes and southern African regions were largely absent in the internal trading routes that went north to Egypt. It is important to note that “SSA” influence may not bedue to a slave trade, an overdone explanation; the green Sahara is to be considered as Egypt is actually in the eastern Sahara. SSA affinities of modern Egyptians from AbusirEl-Meleq might be attributed to ancient early settlers as there is a notable frequency of the “Bushmen canine”- deemed a SSA trait in Predynastic samples dating to 4,000 BC9from Adaima, Upper Egypt. Haplogroup L0f, usually associated with southern Africans,is present in living Egyptians in Adaima9 and could represent the product of an ancient“ghost population” from the Green Sahara that contributed widely. Distributions and admixtures in the African past may not match current “SSA” groups12.

3) On the Definition of African

Schuenemann et al.1 seem to implicitly suggest that only SSA equals Africa and that there are no interconnections between the various regions of Africa not rooted in theslave trade, a favorite trope. It has to be noted too that that in the Islamic armies that entered Egypt that there were a notable number of eastern Africans. It is not clear why there is an emphasis on ‘sub-Saharan’ when no Saharan or supra-Saharan population4 samples--empirical or modelled are considered; furthermore, there is no one way to be“sub-Saharan.” In this study northern tropical Africans, such as lower and upper Nubians and adjacent southern Egyptians and Saharans were not included as comparison groups,as noted by the authors themselves.

4) Conclusion

The paleolithic past has to be distinguished from the biocultural emergence in the Holocene of any society, including Europe. Egypt long before the pyramids was culturally and linguistically African as evidenced by numerous studies3,13,14 based on standard research which accept Egypt’s place in the Nile corridor as having local origins. The symbolism found in the Badarian or Naqadan graves, etc. nor the pyramids werebrought from Asia (Near East). The Egyptian Neolithic cannot be shown as an entity to have come from Asia, although some domesticates were borrowed on local terms into asystem of indigenous foraging in the Fayum2. Historical linguistics shows ancientEgyptian to be Afroasiatic with borrowings from other African language phyla15.

Archaeological data would seem to indicate an early integration of the eastern delta, in northern Egypt, by early Upper Egyptian rulers since Iry Hor from Abydos (~3,250 BC),who already wrote royal inscriptions in Egyptian2 in a script and symbolic system that used African flora and fauna3,13. This region of Egypt, and northern Egypt had long had social intercourse with the Near East. The ancient Egyptians in “origin” were not settler colonists akin to the European colonists in Africa. Schuenemann et al.1 study is best seen as a contribution to understanding a local population history in northern Egypt as opposed to a population history of all Egypt from its inception. 5

Table 1: Geographical region affinities of Amarna and Ramesside mummies based onpopAffiliator 18 analysis of 8 pairs of STR 8/13 pairs of STR from Combined DNA Index System were used by Hawass et al.5,6,nevertheless, data suggest main sub-Saharan affinities of pharaonic mummies from the 18th and20th dynasty (circa 1,300 BC), far in the past before Islamic slave trade. Disclaimer:Thegeographical regions affinities were defined according to popAffiliator8, we acknowledge theremight be problems with any type of classification.(* data from Hawass et al.5,6 available here )ContributionsJ-P.G and S.O.Y Keita performed the PopAffialiator analysis, drew tables, wrote and reviewed the maingenetic, statistical, anthropological and Egyptology portions of the article. J-L. G wrote and review thestatistical portion. A.A wrote and reviewed Egyptological/linguistics portion. Competing interestsThe authors declare no competing financial interestsAbout the authors:Jean-Philippe Gourdine, Ph.D is a metabolomics and glycomics data analyst at Oregon Health & Science University and member of editorial board of the Ankhou/Cahiers Caribéens d'Égyptologie. Email: jpgourdine@gmail.comSOY Keita, MD, D.Phil is a research affiliate of the department of anthropology, Smithsonian Institution and member of editorial board of the Ankhou Cahiers Caribéens d'Égyptologie.Email: soykeita@yahoo.comJean-Luc Gourdine, Ph.D, is a researcher in quantitative genetics at the National Institute of Agricultural Research, France (Guadeloupe)Email: jean-luc.gourdine@inra.fr6

Alain Anselin, Ph.D is the editor of the peer reviewed Egyptological journals Cahiers Caribéens d'Égyptologie & electronic papyrus i-Medjat (, and director of the research group Ankhou

Email: alain.anselin@gmail.comReferences1.Schuenemann, V. J. et al.Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nat. Commun.8, 15694 (2017).2.Agut-Labordère, D. & García, J. C. M. L’Égypte des pharaons: de Narmer à Dioclétien :3150 av. J.C.- 284 apr. J.-C. (Belin, 2016).3.Teeter, E. Before the Pyramids: The Origins of Egyptian Civilization. (Oriental Institute ofthe University of Chicago, 2011)., M. E., Bouwman, A. S. & Rühli, F. J. Identifications of ancient Egyptian royalmummies from the 18th Dynasty reconsidered. Am. J. Phys. Anthropol.159, S216–31(2016).5.Hawass, Z. et al. Ancestry and pathology in King Tutankhamun’s family. JAMA303, 638–647 (2010).6.Hawass, Z. et al. Revisiting the harem conspiracy and death of Ramesses III:anthropological, forensic, radiological, and genetic study. BMJ345, e8268 (2012).7.Rowold, D. et al. At the southeast fringe of the Bantu expansion: genetic diversity andphylogenetic relationships to other sub-Saharan tribes. Meta Gene2, 670–685 (2014).8.Pereira, L. et al. PopAffiliator: online calculator for individual affiliation to a majorpopulation group based on 17 autosomal short tandem repeat genotype profile. Int. J. LegalMed.125, 629–636 (2011).9.Crubézy, E. Le peuplement de la vallée du Nil. Archéo-Nil20, 25–42 (2010).7

10.Pennarun, E. et al.Divorcing the Late Upper Palaeolithic demographic histories of mtDNAhaplogroups M1 and U6 in Africa. BMC Evol. Biol.12, 234 (2012).11.Lovejoy, P. E. Transformations in Slavery: A History of Slavery in Africa. (CambridgeUniversity Press, 2011).12.Busby, G. B. et al. Admixture into and within sub-Saharan Africa. Elife5, (2016).13.Anselin, A. Some Notes about an Early African Pool of Cultures from which Emerged theEgyptian Civilisation. in Egypt in its African Context. Proceedings of the Conference held atThe Manchester Museum, University of Manchester (ed. Exell, K.) 43–53 (Oxford, BARInternational, 2009).14.Wengrow, D., Dee, M., Foster, S., Stevenson, A. & Ramsey, C. B. Cultural convergence inthe Neolithic of the Nile Valley: a prehistoric perspective on Egypt’s place in Africa.Antiquity88, 95–111 (2014).15.Takács, G. Sibilant and velar consonants of South Cushitic and their regular correspondencesin Egyptian and other Afro-Asiatic branches. in Afroasiatica Tergestina. Papers from the 9thItalian Meeting of Afro-Asiatic (Hamito-Semitic) Linguistics, Trieste 393–426 (1998).8



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