Saturday, October 17, 2020

Beaker-like H4a1 in Southern Egypt (Takabuti, the priest's daughter)

This slightly built woman named Takabuti has yielded an H4a1 result at around 90% certainty.

Unlikely most Egyptian women, her reddish-auburn hair was not shaved during the preparations, instead it was styled and curled.  I'll assume this is due to the religious significance of red hair in ancient Egypt and the broader Near East.  (things like dwarfism, gigantism, blue eyes, twins seemed to attract bug-eyed people holding snakes)

You will remember that "Ginger" from outside Heliopolis in a pre-dynastic setting was also a redhead.  So the question you may have, and I have had for a long time, is when exactly did these lineages and phenotypes enter Southern Egypt.  It may be a mistake to believe that this and other atypical lineages were only recently introduced in Bronze Age.  

While Tutakhamen's paternal lineage is more plausibly due to (*update *what the hell was I thinking?) potential mercenary lineage in the army, that may not necessarily be the case.  It's quite possible, as I've suspected since the beginning of this blog, that the mid-4th millennium circum-Pontic region was spinning immigrants out in all directions, including the North Africa and the entire Middle East.  This is not to say that these were PIE, most certainly not, probably Upper Mesopotamians here.  (apparently you can not utter these words in a university without getting kicked in the balls and beaten like a brand new chimpanzee)

This reminds me of the original Rostaluu paper concerning the origin of H mtdna sequences.  Probably worth a review.  We're not talking about a lot of people in relation to the population density

*I teased this back some time ago.  I think the Tutankhamun paternal lineage probably extends through the entire 18th dynasty at least past Ahmose I.  The question I want to know is how far back it went into the 17th.  


  1. A little frustrating that the mtDNA read is not more specific, as she almost certainly had mutations more recent than H4a1, which would have better identified her likely sphere of origin.

    The study omits to mention the earliest H4a1 sample (H3C6, dated 5,335 BC), which is SE Iberian Cardial, and is not much later than its grandmother H4's 7,400 BC estimated age. The most likely inception point for H4a1 is therefore somewhere close to Greece, where the Cardial people seem to have originated.

    It's difficult to tell how Takabuti's maternal ancestor arrived in Southern Egypt - perhaps via the Hyksos, the Phoenicians or plundered from the Sea Peoples? But a mid-4th millennium BC origin from near the entrance to the Black Sea is not at all out of the question. Although I cannot detect any autosomal DNA with this kind of profile in ancient Egyptians, there appears to be plenty of it across the Mahgreb. Perhaps pre-Beaker journeymen on their way round the Mediterranean traded some of their fair-haired females with the bug-eyed locals there?

    1. There are some hints in Black Sea petroglyphs that Egyptian expeditions made it that far north. Why wouldn't the bring a few of the folks they encountered home with them?

    2. That's interesting. There are some signs of Egyptian-like DNA as far North as Lake Sevan c. 1,550 BC. Whereabouts on the Black Sea are the petroglyphs?

      On the other hand, Egyptian expeditions westwards into Libya might alternatively have picked up some folk of European ancestry there.

    3. I was thinking of Gobustan although my memory was faulty and it was the Caspian and not the Black Sea.

    4. Oh wow, Ok "Cova de l'Or". Well, certainly we've already seen Iberian (and European-specific) mtdna in a North African Phoenician burial

      So it is quite possible that Iron Age movements could account for its spread, if it spread from Iberia. I don't think you could discount the possibility it spread from Chacolithic pre-Beaker Iberia into North Africa or even early with the Neolithic movements into Egypt. I suspect it's more recent though, probably Bronze Age.

    5. The oldest U5b2b5 sample is from the same area in Spain, about 18km away, dated to c.3500 BC. U5b2b5 is the mtDNA lineage of Djehutynakht, a Middle Kingdom nomarch from Upper/Middle Egypt (2000 BC).

      I've made a list of the earliest U5b2b5 and H4a1 samples:

      They're found in Neolithic Spain, Portugal, Sardinia and Switzerland, including in Megalithic burials, and H4a1 has also been found in Neolithic Scotland.

      H4a1e has been found in indigenous Guanche samples from the Canary Islands. The Guanches practised mummification and some Guanche mummies have red hair. U5 has also been found in Guanche samples.

      This can't be a coincidence. I think these might be original Egyptian lineages. They might have migrated to Egypt together from the west. Probably along with Y-DNA R1b-V88. Maybe also T1a. I-M170 has also been found in Guanche samples and in modern samples from Nubia.

      And we have DNA evidence of migration from Iberia into North Africa c.5000-3700 BC.

    6. The oldest samples of the African subclade of R1b-V88 have also been found in Spain and Sardinia, dated to c.5200 and 3200 BC respectively.

      Y-DNA T1a was found in the Neolithic samples from Morocco (3700 BC - the migrants from Iberia), it has apparently also been found in Guanche samples.

      “We observe five different H sub-lineages in the indigenous people of the Canary Islands: H1cf, H1e1a9, H2, H3 and H4a1e. … The presence of lineages derived of H1e1a and H4a1 in both European Neolithic and the Canary Islands ancient samples corresponds with Eurasian prehistoric intrusions in North Africa. (…) Our data are in agreement with recent aDNA data from Morocco and further evidence of a complex pattern of Mediterranean migrations in North Africa. Archaeological records in the Maghreb support this result, and also suggest further European intrusions during the Chalcolithic and Bronze Age eras. (…) U5 was more frequent in the indigenous population of the eastern islands, including the island of Lanzarote”

      (Fregel et al. 2019)

      R1b-V88 and U5b are both found at a relatively high frequency (28% and 17%) in the Siwa Berbers in western Egypt.

  2. Couldn't find a link in the OP.

  3. Yes, Gobustan is close to Armenia, and this is probably connected to the Egyptian campaign against the Hyksos.
    Quite possible. On balance, I think she is slightly more likely to be ancestrally connected to the Sea Peoples, such as the Sherden or Shekelesh, or the Mekwesh, coming in from the North West.

    1. mtDNA H4a1 has also been found in indigenous Guanche samples from the Canary Island. The Guanches practised mummification and some Guanche mummies have red hair, like Takabuti.

      The oldest U5b2b5 sample has been found in the same area in Spain, dated to c.3500 BC, about 18 kms away from the oldest H4a1 sample. Both lineages are also found in Neolithic Portugal, Switzerland and Sardinia (EBA Sardinia in the case of H4a1).

    2. Very interesting. The Guanches certainly have a large pre-Islamic Berber contribution, possibly something else emanating from Late Neolithic SW Europe or something in-between. The Canaries are fascinating, especially to see how large their impact may have been on Puerto Rico on this side of the pond.

  4. An elite Egyptian male (high status priest) from the Middle Kingdom (c.2000-1800 BC) in Upper/Middle Egypt, apparently had Y-DNA H2:

    (from Ted Kendall of Open Genomes)

    "Everyone, meet Nakht-Ankh from Shashotep, Egypt. He lived sometime between 1991 BCE – 1802 BCE. He was the son of the Lady Khnum-Aa, and the older brother of Khnum-Nakht.

    He's Y-DNA H-Y21618* and mtDNA M1a1* + G8251A, G16145A.

    He's the earliest person who we can name in all of human history whose Y and mtDNA haplogroups we can identify. Nakht-Ankh was a contemporary of the Bell Beakers in Britain, the Minoans, and the Indus Valley Civilization in South Asia. He lived 100 years before Hammurabi of Babylon.

    I reanalyzed his Y SNPs using the YFull haplogroups and he's derived for 2 F* SNPs, Z19004 and Z18865 in H-P96, and BY44412 in H-Y21618. He's ancestral for G*, IJ* and K* SNPs and for Z19117 in H-Y19962 which is the immediate subgroup of H-Y21618.

    Haplogroup H2-P96 may be a very surprising result for Egypt. It's never been seen among Egyptians today. H2 is closely associated with the Northwest Anatolian and European Neolithic. However, H2 was also found in a Pre-Pottery Neolithic C Levantine individual from about 9000 ybp. It seems like some Levantine Neolithic and Chalcolithic people made it to Egypt at the start of Egyptian civilization. Since he's ancestral for H-Y19962, he's not in the European subclade of H-P96.

    The study wasn't able to identify his or his brother Khnum-Nakht's Y haplogroups, but they were able to get their mtDNA haplotype, proving that they were at least half-brothers.


    Copied from

    H2 has been found in Megalithic burials in Spain (La Mina, c.3900 BC) and Ireland (Linkardstown cists, c.3500 BC). In fact it's the only non-I-M70 male lineage that has been found in Megalithic burials. It has also been found in the Vinca culture, c.5500 BC.

    1. I trace South European DNA profiles at their heaviest concentrations in Tunisia, with strongest matches to Southern Italy and Sardinia. They are spread across the Mahgreb, but oddly show no significant signs in ancient Egyptian samples. Also oddly, the Levant-like contribution appears small, suggesting this DNA is largely neither of Roman nor Phoenician origin. I would accordingly suggest an older intrusion into Berber DNA, perhaps Nuragic, Sea People, early South European Bell Beaker, pre-Bell Beaker, or possibly a mixture of all of these. Some of its ancient DNA might have leaked into Egypt without leaving a substantial trace.

    2. 'Ancient genomes from North Africa evidence prehistoric migrations from both the Levant and Europe' (Fregel et al 2018)

      “The acquisition of agricultural techniques during the so-called Neolithic revolution has been one of the major steps forward in human history. Using next-generation sequencing and ancient-DNA techniques, we directly test whether Neolithization in North Africa occurred through the transmission of ideas or by demic diffusion. We show that Early Neolithic Moroccans (∼5,000 BC) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. (…)

      Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BC) and Levantine Pre-Pottery Neolithic farmers (∼6,500 BC). … However, Late Neolithic individuals from North Africa are admixed, with a North African and a European component. Our results support the idea that the Neolithization of North Africa involved both the development of Epipaleolithic communities and the migration of people from Europe … The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb. (…) Our analyses strongly support that at least some of the European ancestry observed today in North Africa is related to prehistoric migrations, and local Berber populations were already admixed with Europeans before the Roman conquest. (…)

      Mitochondrial DNA (mtDNA) and Y chromosome haplogroups obtained for IAM (Moroccan Early Neolithic) and KEB (Moroccan Late Neolithic) suggest either a population replacement or an important genetic influx into Morocco between 5,000 and 3,000 BCE. IAM samples belong to the mtDNA haplogroups U6a and M1—both of which are associated with the back migration to Africa from Eurasia in Upper Paleolithic times and observed in Moroccan Later Stone Age individuals—whereas KEB samples belong to haplogroups K1, T2, and X2, which are prominently found in Anatolian and European Neolithic samples. Regarding the paternal lineages, IAM individuals carry Y chromosomes distantly related to the typically North African E-M81 haplogroup, while the Y chromosome from KEB belongs to the T-M184 haplogroup; although scarce and broadly distributed today, this haplogroup has also been observed in European Neolithic individuals. (…)

      Ancient samples were projected on a principal components analysis (PCA) space, which was built using sub-Saharan African, North African, European, and Middle Eastern populations from the Human Genome Diversity Project dataset … In the PCA, IAM (Moroccan Early Neolithic, c.5000 BC) samples are placed close to Mozabites (A Berber group inhabiting the Mʾzab oases of Algeria), while Iberian Neolithic samples fall close to southern European populations … KEB (Moroccan Late Neolithic, 3700 BC) is placed in an intermediate position, with ∼50% each of European Early Neolithic and North African ancestries.”

  5. Looking at Egyptian history, we see three invasion attempts from the Libyan Meshwesh between 1,181 and 1,175 BC. In the second assault, they were accompanied by the Sherden (Sardinians). Over the next couple of centuries, we see Meshwesh settling in Egypt and eventually ruling as Pharoahs in Thebes (Southern Egypt) from 837 BC until 716 BC - only 20 years before Takabuti was estimated to have been born.

    Two of the Meshwesh Pharaohs Takelot I and II bore a similar-looking name to hers.

    There seems a good chance that Takabuti's ancestors were from somewhere in the Western Mediterranean where we find her mtDNA, such as Sardinia.

    The question is - were Sea People like the Sherden descended from seafaring Bell Beakers a millennium or so earlier?

    1. Interesting. Well, I think partly. In Sardinia the Beakers greatly influenced the subsequent Bronze Age culture, but I think their genetic impact was largely restricted to the North part of the island and generally came from Iberia. So it's quite possible.

    2. This comment has been removed by the author.

    3. This comment has been removed by the author.

    4. We already have 'Iberian' U5b2b5 in an Egyptian nomarch c.2000 BC. Long before any of the things you've mentioned.

      The oldest H4a1 sample is from the same area in Spain as the oldest U5b2b5 sample, just 18km away.

    5. Yes, I agree, links between South West Europe and Egypt may have gone back a lot longer. I am just indicating another more recent possible association.

      Looking at modern Sardinian DNA profiles, they are distinctive, quite unlike other Italian profiles:
      1. They are the only profiles I can find that suggest clear Iberian Beaker roots (perhaps 50% or more)
      2. Curiously, the best fit for their profiles also includes a substantial chunk of ancient Egyptian DNA (I don't see the same concentration elsewhere in Italy, nor in Spain).

      Not really sure what to make of it.

    6. I just noticed that Cassidy et al. 2020 has three H4a1 samples from Neolithic/Megalithic Ireland, the oldest dated 3940-3700 cal BC. Two are males, with ydna I2a1b and I2a1a. One of the samples is from a megalithic portal tomb/dolmen, the other is from a megalithic court tomb.

      Cassidy et al. 2020 is the paper about the incestuous dynastic 'god-king' buried at Newgrange. He had ydna I2a1b and mtDNA U5b:

      "we report a single extreme out-lier interred within the Newgrange passage tomb — a focal point of the monumental landscape of Brú na Bóinne, a United Nations Educational, Scientific and Cultural Organization world heritage site. Incorporating over 200,000 tonnes of earth and stone, this megalithic mound is one of the most spectacular of its kind known from Europe. Although externally designed for public consumption, the interior of the tomb consists of a single narrow passage with a specialized ritual inventory, the winter-solstice solar alignment of which would have been viewed by only a select few. Unburnt, disarticulated human bone was found concentrated within the most elaborately decorated recess of the terminal cruciform chamber, including the cranial remains of an adult male (designated NG10). The exceptional location of these remains is matched by a genomic heritage that — to our knowledge — is unprecedented in ancient genomics. He possessed multiple long runs of homozygosity, each com-prising large fractions of individual chromosomes, and totalling to a quarter of the genome (inbreeding coefficient = 0.25). This marks him as the offspring of a first-order incestuous union, which is a near-universal taboo for entwined biological and cultural reasons. However, given the nature of the interment, his parentage was very likely to have been socially sanctioned. Although simulations cannot distinguish whether his parents were full siblings or parent and offspring, the only known definitive acceptances of such mating occur among siblings —specifically within polygynous elites — as part of a rarely observed phenomenon known as ‘royal’ or ‘dynastic’ incest. In all of these documented cases (for example, in pre-contact Hawaii, the Inca empire and ancient Egypt) this behaviour co-occurs with the deification of political leaders and is typically limited to ruling families"

      I've added the Irish H4a1 samples to my list:

    7. As noted above, Y-DNA H2 has been identified in an Egyptian elite male from c.1900 BC.

      H2 has also been found in megalithic burials in Ireland (c.3500 BC), Spain (c.3900 BC), and the Vinca culture (c.5000 BC).

    8. The Irish H2 samples were found in 'Linkardstown cist' burials. The blogger oldeuropeanculture has an intriguing article about these burials and their possible relation to the Balkans:

    9. Yes, the idea of elite (possibly incestual) dynasties dispersed over a huge area covering Egypt, Iberia, the Balkans and Ireland is an intriguing one. If there were very little mixing with the indigenous populations, this could explain the lack of an autosomal trail.

      There are clear indications that some dynasties have risen to prominence along paternal lines, but would this have occurred in the same way along maternal lines, such as H4a1 and U5b2b5?

    10. I don't know if there were 'elite dynasties dispersed over a huge area covering Egypt, Iberia, the Balkans and Ireland', but there seem to be lots of connections and there is clear evidence of migration from Europe into North Africa.

      "the lack of an autosomal trail" Do you mean a lack of European autosomal ancestry in Egypt, or North Africa? What do you mean exactly?

    11. Just that I do not see much evidence of early European autosomal DNA profiles arising to any discernable degree in Egyptian profiles. There are occasional signs of North African and Levantine DNA within some European profiles, but we do not see these very often and when we do they are generally minor. That's why I wonder whether such people might have been aristocratic elites who did not generally mix into the local populations.

    12. Not sure if there is a good basis for this, but I've read that guanches followed a hereditary matrilineal autocracy, so perhaps mtDNA trails from Europe to North Africa are significant.

      Guanches are perhaps a good proxy for ancient North African, as their DNA is less affected by Arabian and other relatively modern introgressions. My estimates are that ancient South European (mainly Iberian) DNA provides a closer contributory fit for guanche than modern Iberian - a mix of Beaker and pre-Beaker. Morocco comes out similarly, but in lower concentrations. Accordingly, I would suggest that early Cardial and/or Beaker migrations from Iberia into North West Africa look likely to be the main sources of the European DNA there.

      Tunisians' European DNA component looks a little closer to early South East European than Iberian DNA, so I would suggest this is likely to be due to a separate early introgression from Italy or Greece, rather than Iberia.

      Yes, I think I would agree that Berbers look to have been infused with South European DNA at a very early stage.

    13. R1b-V88 and T1a migrated into Africa from Europe. T1a also came into Africa from the Middle East.

      R1B-V88 modern distribution estimates:

      28% Siwa Berbers from western Egypt.
      15% Copts + southern Egyptians
      16% Sudanese Arabs
      10% Nubians
      10% Northern Egyptians

      19% Kabyle Berbers
      8-34% Tuareg

      50% Kanembu
      47% Hausa
      34% Toubou
      18-54% Fulani
      30-95% Chadic speakers in northern Nigeria + Cameroon


      Upper Egyptians 10.3%
      Siwi Berbers 8.2%
      Tuareg 6%

      Daza 44%
      Toubou 31%
      Fulani 18%
      N’Djamena (Chadic) 9%

      T1a is also found in East Africa/the Horn.


      Kelif el Boroud (KEB), Morocco c. 3700 BC had ydna T1a.

      According to Genetiker T1a is also found in Guanche samples:


      I-M170 has been found in Guanches, and in a couple of modern samples from Nubia.



      It's also found in other parts of North Africa (I2a1a).

    14. Regarding R1b-V88 migration into Africa:

      “we detected R1b-V88 equivalent markers in 11 out of 30 ancient Sardinian males from the Middle Neolithic to the Nuragic with Y haplogroup calls. Two ancient individuals carried derived markers of the clade R, but we could not identify more refined subclades due to their very low coverage. … At present, R1b-V88 is prevalent in central Africans, at low frequency in present-day Sardinians, and extremely rare in the rest of Europe. By inspecting our reference panel of western Eurasian ancient individuals, we identified R1b-V88 markers in 10 mainland European ancient samples, all dating to before the Steppe expansion (>3k years BCE). Two very basal R1b-V88 (with several markers still in the ancestral state) appear in Serbian hunter-gatherers (HGs) as old as 9,000 BCE, which supports a Mesolithic origin of the R1b-V88 clade in or near this broad region. The haplotype appears to have become associated with the Mediterranean Neolithic expansion – as it is absent in early and middle Neolithic central Europe, but found in an individual buried at the Els Trocs site in the Pyrenees (modern Aragon, Spain), dated 5,178-5,066 BCE and in eleven ancient Sardinians of our sample. Interestingly, markers of the R1b-V88 subclade R1b-V2197, which is at present day found in Sardinians and most African R1b-V88 carriers, are derived only in the Els Trocs individual and two ancient Sardinian individuals (3370-3110 BCE, and 1220-1050 BCE).

      This configuration suggests that the V88 branch first appeared in eastern Europe, mixed into Early European farmer individuals (after putatively sex-biased admixture), and then spread with EEF to the western Mediterranean. … A west Eurasian R1b-V88 origin is further supported by a recent phylogenetic analysis that puts modern Sardinian carrier haplotypes basal to the African R1b-V88 haplotypes. The putative coalescence times between the Sardinian and African branches inferred there fall into the Neolithic Subpluvial (“green Sahara”, about 7,000 to 3,000 years BCE). Previous observations of autosomal traces of Holocene admixture with Eurasians for several Chadic populations provide further support for a speculative hypothesis that at least some amounts of EEF ancestry crossed the Sahara southwards. … Overall, our analysis provides evidence that R1b-V88 traces back to eastern European Mesolithic hunter gatherers and later spread with the Neolithic expansion into Iberia and Sardinia.” [And from there into Africa]

    15. Another question is whether there was also some R1b-M269 within one or more of these migrations. Many of their associated autosomal best fits estimate significant contributions from Smyadovo and Atapuerca 3, both of which had positive reads for SNPs within M269.

      Unlike with R1b-V88, I don't see any indicators of R1b-M269 with the early Cardial migrations, but signs of its likely presence do seem to arise in relation to subsequent migrations from the same sorts of geographical areas.

    16. Perfect timing:

      'Insights from ancient DNA analysis of Egyptian human mummies: clues to disease and kinship' (Gad et al. 2020)

      “An investigative study was carried out on the familial relationships of a number of late 18th dynasty mummies (ca. 1550–1295 B.C.), including that of Tutankhamen. The study was based on the analysis of the autosomal and Y-chromosome STR markers in addition to mitochondrial hypervariable region 1 sequences. A 4- generation pedigree of Tutankhamun’s immediate lineage and the identity of his ancestors were established. The Royal male lineage was the Y-chromosome haplogroup R1b that was passed from the grandparent [Amenhotep III] to the father [KV55, Akhenaten] to the grandchild [Tutankhamen]. The maternal lineage, the mitochondrial haplogroup K, extended from the great-grandmother [Thuya] to the grandmother [KV35 Elder lady, Queen Tiye] to the yet historically-unidentified mother [KV35 Younger lady] to Tutankhamen.”


      (Published online 15th Oct 2020)

  6. This comment has been removed by a blog administrator.

  7. Beaker Blogger check it out:

    Perfect timing:

    'Insights from ancient DNA analysis of Egyptian human mummies: clues to disease and kinship' (Gad et al. 2020)

    “An investigative study was carried out on the familial relationships of a number of late 18th dynasty mummies (ca. 1550–1295 B.C.), including that of Tutankhamen. The study was based on the analysis of the autosomal and Y-chromosome STR markers in addition to mitochondrial hypervariable region 1 sequences. A 4- generation pedigree of Tutankhamun’s immediate lineage and the identity of his ancestors were established. The Royal male lineage was the Y-chromosome haplogroup R1b that was passed from the grandparent [Amenhotep III] to the father [KV55, Akhenaten] to the grandchild [Tutankhamen]. The maternal lineage, the mitochondrial haplogroup K, extended from the great-grandmother [Thuya] to the grandmother [KV35 Elder lady, Queen Tiye] to the yet historically-unidentified mother [KV35 Younger lady] to Tutankhamen.”


    (Published online 15th Oct 2020)

    1. Dude, wow. That has literally been at least 7 years in the making. Thanks!