K = 14 admixture analysis of ancient Egyptian genomes

At the bottom of this post is a plot for a K = 14 admixture analysis that includes three genomes from ancient Egypt. The table above the plot gives some information for these samples.

The brown and black Negroid components are completely absent in the two Pre-Ptolemaic samples, while the Ptolemaic sample is 1.99% Negroid. This contrasts with the modern Egyptian samples, which are on average 10.93% Negroid.

Among the other ancient samples, the ancient Egyptian samples are most similar to the Bronze Age samples from Jordan in the Levant. Note that the Pre-Ptolemaic samples JK2134 and JK2911 belong to the same J1a2a2-Z2324 and J2b1-PF7314 Y haplogroups that the Bronze Age Levant samples I1705 and I1730 belong to.

Among the modern samples, the ancient Egyptian samples are most similar to the Saudi and Yemenite Jew samples.

These results are hardly surprising, as it has been well understood since the early 19th century, based on the cranial morphology of Egyptian mummies, the hair of Egyptian mummies, and also on the ancient Egyptians’ artistic representations of themselves, that they were predominately Caucasoid rather than Negroid. For example, on page 19 of Samuel George Morton’s 1844 work Crania Ægyptiaca, there’s a table showing that of 100 ancient Egyptian crania, 84 of them belong to different types of unmixed Caucasoids. On the next page, he gives the following quote from an earlier study of ancient Egyptian crania performed by Georges Cuvier (1769–1832):

I have examined in Paris, and in the various collections of Europe, more than fifty heads of mummies, and not one amongst them presented the characters of the Negro or Hottentot.

For ancient Egyptians’ depictions of themselves, see the following two images, which are from murals illustrating the Book of Gates in the tomb of pharaoh Seti I, who ruled Egypt from 1290 to 1279 BC. The first image shows, from left to right, four Libyans, a Nubian, a Semite, and an Egyptian. The second image shows, from bottom to top and from left to right, Horus, four Egyptians, four Semites, four Nubians, and four Libyans. The Nubians are clearly Negroid, while the Egyptians are clearly Caucasoid. The Libyans look more like modern Northern Europeans than modern Northwest Africans.

The three ancient Egyptian genomes leave important questions unanswered. Since they’re from middle-class people, one such question is how the ancient Egyptian elite might have differed from the rest of the population genetically.

This 2012 paper presented Y-STR data for the pharaoh Ramesses III, who ruled from 1186 to 1155 BC. The authors used Whit Athey’s haplogroup predictor to predict that Ramesses III belonged to the Negroid haplogroup E1b1a, which was the cause of much jubilation among Afrocentrists. But this thread casts doubt on the correctness of the Y-STR data, and, in any case, I’ve analyzed the data with the newer NevGen haplogroup predictor, which uses a more sophisticated methodology than Athey’s predictor, and it determined that Ramesses III belonged to the Caucasoid haplogroup E1b1b, with a 97.3% probability. This result makes a lot more sense, because as the below images show, neither paintings of Ramesses III nor his mummy show any Negroid features.

The most important question to be answered is how the ancient Egyptian civilization originated. In the early 1900s the English Egyptologist Sir William Flinders Petrie developed the Dynastic Race theory of the civilization’s origins, and it was the dominant mainstream theory until the late 1960s, when it, like so many other good ideas, became a politically incorrect taboo subject. According to this theory, the Egyptian civilization was founded by people from the Uruk period (4000–3100 BC) of southern Mesopotamia, who sailed in reed boats through the Persian Gulf, around the Arabian Peninsula, and up the Red Sea, and who then moved west over land into the Nile valley, where they introduced the arts of civilization, including writing, and established the first pharaonic dynasty.

Part of what led Petrie to his theory is the appearance of clear Mesopotamian influences in Egypt’s Naqada II period (3500–3200 BC) which were absent in the preceding Naqada I period (4400–3500 BC). These influences include architectural styles, pottery styles, cylinder seals, artwork, and rock and tomb paintings depicting Mesopotamian-style boats, symbols, and figures. You can read this page and this page for an overview of the Dynastic Race theory. The second page discusses the Mesopotamian influences of the two predynastic Egyptian artifacts shown below. The first is the ivory handle of the Gebel el-Arak knife, dated to the Naqada II period. Depicted at the top of the back side of the handle is a man (the “Master of Animals”) wearing Mesopotamian clothing flanked by two upright lions. The second artifact is the Narmer Palette, dated to the Naqada III period (3200–3000 BC, also known as the Protodynastic period or Dynasty 0). It is thought to depict the unification of Upper and Lower Egypt by Narmer, the first pharaoh of Egypt. The back side of the palette shows two serpopards with their necks intertwined. Below the photograph of the Narmer Palette is a photograph of a cylinder seal from the Uruk period of Mesopotamia, showing a very similar serpopard design.

The other major piece of evidence that led Petrie to his theory is that the people of the Naqada I and Naqada II cultures were distinctly different in both their burial styles and in the physical types of their remains. An important paper on the craniometry of these remains is “The Dynastic Race in Egypt” by Douglas Derry, published in 1956. Below are two excerpts from this paper:

The Predynastic people are seen to have had narrow skulls with a height measurement exceeding the breadth, a condition common also in negroes. The reverse is the case in the Dynastic Race, who not only had broader skulls but the height of these skulls, while exceeding that in the Predynastic Race, is still less than the breadth. This implies a greater cranial capacity and of course a larger brain in the invading people.

It is also very suggestive of the presence of a dominant race, perhaps relatively few in numbers but greatly exceeding the original inhabitants in intelligence; a race which brought into Egypt the knowledge of building in stone, of sculpture, painting, reliefs, and above all writing; hence the enormous jump from the primitive Predynastic Egyptian to the advanced civilization of the Old Empire.

In 1977–78 Thor Heyerdahl and his crew sailed the Tigris, a Mesopotamian-style reed boat like those depicted in Naqada II period Egyptian rock paintings, from the Persian Gulf to Pakistan, and then to the Red Sea, to demonstrate the possibility of seaborne contact between the Mesopotamian, Indus Valley, and Egyptian civilizations. Below is a photograph of the Tigris, and a map showing its voyage.

The Sumerian language spoken in southern Mesopotamia was at one time widely held to be an Indo-European language. This 2009 paper reviews 30 Sumerian and Proto-Indo-European words that show some kind of relationship. And this 2008 paper by Gordon Whittaker presents his theory that an Indo-European language he calls Euphratic was spoken in southern Mesopotamia before Sumerian was spoken there, and that the earliest proto-cuneiform tablets of the Late Uruk period (3350–3100 BC) are written in this Indo-European language. It’s possible that these Indo-Europeans of southern Mesopotamia belonged to Y haplogroup R1b-M269, and that their Y chromosomes were transmitted by the Dynastic Race of Egypt through the centuries to Tutankhamun, who is reported to have belonged to R1b-M269.

Sample  Period         Date BC
JK2134  Pre-Ptolemaic  776–569
JK2911  Pre-Ptolemaic  769–560
JK2888  Ptolemaic      97–2

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Phenotype SNPs from ancient Egypt

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for genomes from ancient Egypt. Nonzero derived allele counts are in bold. Note that small derived allele counts may be due to DNA damage.

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/3
JK2888  Ptolemaic      97–2     0/1

IRF4, rs12203592, light hair and eyes, freckling

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/1

KITLG, rs12821256, blond hair

Sample  Period         Date BC  D/T
JK2134  Pre-Ptolemaic  776–569  0/1
JK2911  Pre-Ptolemaic  769–560  0/2

MC1R, rs1110400, red hair

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/3
JK2888  Ptolemaic      97–2     0/6

MC1R, rs11547464, red hair

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/2
JK2888  Ptolemaic      97–2     0/3

MC1R, rs1805005, blond hair, fair skin

Sample  Period     Date BC  D/T
JK2888  Ptolemaic  97–2     0/1

MC1R, rs1805006, red hair, fair skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/4

MC1R, rs1805007, red hair, fair skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  1/4
JK2888  Ptolemaic      97–2     0/5

MC1R, rs1805008, red hair, fair skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/3
JK2888  Ptolemaic      97–2     0/1

MC1R, rs1805009, red hair, fair skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/3
JK2888  Ptolemaic      97–2     0/1

MCM6, rs4988235, ability to digest milk

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/10

OCA2/HERC2, rs12913832, blue eyes

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/2

SLC24A5, rs1426654, Caucasoid light skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  2/2
JK2888  Ptolemaic      97–2     1/1

SLC45A2, rs16891982, Caucasoid light skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/7

TYR, rs1042602, light skin, absence of freckles

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/4
JK2888  Ptolemaic      97–2     1/1

TYR, rs1393350, blond hair, blue eyes

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/2
JK2888  Ptolemaic      97–2     0/2
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Y-SNP calls from ancient Egypt

In the table below are links to Y-SNP calls for samples from ancient Egypt.

Sample  Period         Date BC  Haplogroup
JK2134  Pre-Ptolemaic  776–569  J1a2a2-Z2329    calls
JK2911  Pre-Ptolemaic  769–560  J2b1-PF7314     calls
JK2888  Ptolemaic      97–2     E1b1b1a1b2-V22  calls
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Chinchorro DNA paper published on bioRxiv

I’ve written a paper on my discovery of European admixture in a Chinchorro mummy DNA sample, and it’s now published on bioRxiv:

European admixture in Chinchorro DNA

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K = 14 admixture analysis of Neolithic Estonian genomes

Below is a plot for a K = 14 admixture analysis that includes seven genomes from Neolithic Estonia. The table above the plot gives some information for these samples.

The hunter-gatherer samples from the Comb Ware culture are similar to the Comb Ware sample from Latvia, the earlier hunter-gatherer samples from Karelia and Samara in Russia, and the earlier Mesolithic and Dnieper-Donets samples from Ukraine. All of these samples are made up mostly of the medium blue Eastern component, but also have significant amounts of the dark blue Western component. The Baltic Comb Ware samples have more of the Western component than the Russian samples, but less than the Ukrainian samples.

The Estonian Corded Ware samples are indistinguishable from the other Corded Ware samples from Germany and Poland. They differ from the Corded Ware sample from Latvia, which lacks the light blue early farmer component.

Sample       Culture      Date BC
Kudruküla 2  Comb Ware    3831–3426
Kudruküla 3  Comb Ware    3950–1850
Ardu 1       Corded Ware  2850–2050
Ardu 2       Corded Ware  2921–2555
Kunila 1     Corded Ware  2850–2050
Kunila 2     Corded Ware  2626–2390
Sope         Corded Ware  2625–2400

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Phenotype SNPs from Neolithic Estonia

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for genomes from Neolithic Estonia. Nonzero derived allele counts are in bold. Note that small derived allele counts may be due to DNA damage.

ASIP, rs2424984, Veddoid brown skin

Sample    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  0/1
Ardu 2    Corded Ware  2921–2555  1/1
Kunila 2  Corded Ware  2626–2390  8/8

ASIP, rs6058017, Veddoid brown skin

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  1/1
Kunila 2  Corded Ware  2626–2390  5/5
Sope      Corded Ware  2625–2400  1/1

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample       Culture       Date BC    D/T
Kudruküla 2  Comb Ceramic  3831–3426  0/1
Ardu 2       Corded Ware   2921–2555  0/1
Kunila 1     Corded Ware   2850–2050  0/1
Kunila 2     Corded Ware   2626–2390  0/8
Sope         Corded Ware   2625–2400  0/1

IRF4, rs12203592, light hair and eyes, freckling

Sample    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  1/1
Ardu 2    Corded Ware  2921–2555  0/1
Kunila 1  Corded Ware  2850–2050  0/3
Kunila 2  Corded Ware  2626–2390  2/3

KITLG, rs12821256, blond hair

Sample    Culture      Date BC    D/T
Kunila 2  Corded Ware  2626–2390  0/2

MC1R, rs1110400, red hair

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/4
Kunila 1  Corded Ware  2850–2050  0/2
Kunila 2  Corded Ware  2626–2390  0/16
Sope      Corded Ware  2625–2400  0/1

MC1R, rs11547464, red hair

Sample       Culture       Date BC    D/T
Kudruküla 2  Comb Ceramic  3831–3426  0/1
Ardu 1       Corded Ware   2850–2050  0/3
Ardu 2       Corded Ware   2921–2555  0/2
Kunila 1     Corded Ware   2850–2050  0/2
Kunila 2     Corded Ware   2626–2390  1/12

MC1R, rs1805005, blond hair, fair skin

Sample    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  0/1
Ardu 2    Corded Ware  2921–2555  0/1
Kunila 2  Corded Ware  2626–2390  0/12
Sope      Corded Ware  2625–2400  0/2

MC1R, rs1805006, red hair, fair skin

Sample       Culture       Date BC    D/T
Kudruküla 2  Comb Ceramic  3831–3426  0/1
Kudruküla 3  Comb Ceramic  3950–1850  0/1
Ardu 1       Corded Ware   2850–2050  0/1
Ardu 2       Corded Ware   2921–2555  0/1
Kunila 1     Corded Ware   2850–2050  0/2
Kunila 2     Corded Ware   2626–2390  0/11

MC1R, rs1805007, red hair, fair skin

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/4
Kunila 1  Corded Ware  2850–2050  0/2
Kunila 2  Corded Ware  2626–2390  1/13
Sope      Corded Ware  2625–2400  0/1

MC1R, rs1805008, red hair, fair skin

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/6
Kunila 2  Corded Ware  2626–2390  0/19

MC1R, rs1805009, red hair, fair skin

Sample    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  0/1
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 1  Corded Ware  2850–2050  0/2
Kunila 2  Corded Ware  2626–2390  0/2
Sope      Corded Ware  2625–2400  0/2

MCM6, rs182549, ability to digest milk

Sample    Culture      Date BC    D/T
Kunila 1  Corded Ware  2850–2050  0/1
Kunila 2  Corded Ware  2626–2390  0/7
Sope      Corded Ware  2625–2400  0/1

MCM6, rs4988235, ability to digest milk

Sample    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  0/1
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 1  Corded Ware  2850–2050  0/1
Kunila 2  Corded Ware  2626–2390  0/2

OCA2, rs1800407, green or hazel eyes

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 1  Corded Ware  2850–2050  0/2
Kunila 2  Corded Ware  2626–2390  0/6

OCA2, rs1800414, Mongoloid light skin

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 2  Corded Ware  2626–2390  0/1

OCA2/HERC2, rs12913832, blue eyes

Sample       Culture       Date BC    D/T
Kudruküla 3  Comb Ceramic  3950–1850  0/1
Kunila 1     Corded Ware   2850–2050  1/2
Kunila 2     Corded Ware   2626–2390  0/2
Sope         Corded Ware   2625–2400  1/2

SLC24A5, rs1426654, Caucasoid light skin

Sample       Culture       Date BC    D/T
Kudruküla 3  Comb Ceramic  3950–1850  1/2
Ardu 2       Corded Ware   2921–2555  2/2
Kunila 1     Corded Ware   2850–2050  2/2
Kunila 2     Corded Ware   2626–2390  7/7
Sope         Corded Ware   2625–2400  2/2

SLC45A2, rs16891982, Caucasoid light skin

Sample    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  1/1
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 1  Corded Ware  2850–2050  0/5
Kunila 2  Corded Ware  2626–2390  0/4

TYR, rs1042602, light skin, absence of freckles

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 1  Corded Ware  2850–2050  0/1
Kunila 2  Corded Ware  2626–2390  0/2

TYR, rs1393350, blond hair, blue eyes

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  1/2
Kunila 2  Corded Ware  2626–2390  0/2

TYRP1, rs2733831, light hair and eyes

Sample  Culture      Date BC    D/T
Ardu 2  Corded Ware  2921–2555  0/2
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Y-SNP calls from Neolithic Estonia

In the table below are links to Y-SNP calls for samples from Neolithic Estonia.

Sample       Culture       Date BC    Haplogroup
Kudruküla 3  Comb Ceramic  3950–1850  R1a1-YP1335      calls
Ardu 1       Corded Ware   2850–2050  R1a1a1b-Z645     calls
Ardu 2       Corded Ware   2921–2555  R1a1a1b1-Z283    calls
Kunila 1     Corded Ware   2850–2050  R1a1a1b-Z645     calls
Kunila 2     Corded Ware   2626–2390  R1a1a1b1a-Y2395  calls
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