Private Alleles Reveal Admixture in Cherokee Indians
The Ancient One Gene dramatically captures the shared deep ancestry of Native Americans with Mongols, Siberians and East Asians, with low levels in the rest of the world. It is a good example of how a single haplotype can reveal ancient migrations and point to world ethnic divisions
Named for the 12,000-year-old skeleton of a baby boy found in 1968 on a Montana ranch, the distribution of the Ancient One Gene reflects the earliest migrations of North Asiatic peoples into the Americas. Its pattern shows a path of entry from Siberia to Alaska and a spread down the Pacific Coast to the extreme tip of South America. Such are the compelling conclusions we can sometimes safely draw from a single haplotype.
Native Americans, as a population, have the smallest number of private alleles per locus; Africa has the highest. That means Native Americans have the least diversity and Africans the most.[1] The classic instance of a Native American private allele is D9S1120=9—a location, as it happens, that is not one of the CoDIS markers or part of a standard array of loci, so few people test for it. By definition, it is private to Native American (and Western Beringia) populations and very low or entirely lacking in most others. Native Americans have it in a frequency of 31.7%. No Africans, on the contrary, have it or if they do, only at extremely low levels. The genetic strand associated with it has been dubbed the American Modal Haplotype.[2]
The U.S. Department of Justice has published a list of Native American private alleles by tribe.[3] What can they tell us about Native American tribal population structure? Mutation is not the cause of these unusual readings but rather the combined action over time of migration, admixture and genetic drift.
- vWA=21
Said to occur in Chippewas at a frequency of 2.4%, this is truly a world-diffused gene originating in Africa. It is mostly absent in the Northern Hemisphere. We found that though it is “private” to the Chippewas, as the Department of Justice study states, it is found in other indigenous populations as well. The Huichols of Durango enjoy the highest frequency at 5.3%. It is also scattered sparsely throughout various unrelated populations, with an overall world average of 0.4 %. The top ten matches are shown below. Other than an origin in Africa, disappointingly little can be deduced from such a seemingly random pattern of occurrence. One suspects its highs and lows are an effect of various unrelated migration events, plus genetic drift.
| 520 | Mexico- Huichols- Durango (n=57) | 1 |
| 416 | Bali (n = 79) | 2 |
| 470 | U.S. Chippewa Indians (n = 22) | 3 |
| 501 | India – Mahadev Koli (n = 65) | 4 |
| 86 | India – Indo-Mongoloid – Naga (n = 106) | 5 |
| 259 | Ecuadorian – Black (n = 104) | 6 |
| 392 | Russia – Pskov (n = 62) | 7 |
| 495 | India – Balmiki (n = 62) | 8 |
| 105 | Spanish – Black – Central West African (n = 132) | 9 |
| 55 | Spanish Moroccan Arabs (n = 47) | 10 |
- CSF1PO=12.1 The next private allele on the government’s list is said to crop up only among the Apache, at a very low frequency (0.6%). In reality, it is also found among the following populations:
| 1 | Dubai (n = 224) |
| 2 | Native American – Arizona – Navajo (n = 93) |
| 3 | U.S. Apache and Mojave Indians (n = 88) |
| 4 | Italian (n = 1,541) |
| 5 | North American Native Americans (n = 533) |
If we ignore Dubai and Italian (which seem to have no relationship to each other, or to Apaches, Navajos and Mojaves), we could say that this is a private allele deeply embedded in Southwestern desert tribes, though of minimal frequency. Its appearance without any African roots or world migration background makes us believe it was a kind of de novo or “off-ladder” mutation—perhaps a change from CSF1PO=12. A value of 12 STRs at this location represents a very common and quite evenly distributed allele, one found abundantly among Native Americans, including Southwest desert tribes.
- TPOX=6 The next two TPOX variants are assigned as private alleles to the Cherokee (3%) and are very interesting and informative. The first of the pair is clearly African, not only in origin but in its principal places of expansion. It presumably embodies the recent spread of blacks in the age of Atlantic slavery. On a map it lights up every African population. Guinea Bissau in West Africa has it at the highest level, 13%. African Americans have it in equal measure. The world average is 2.4%. There is little or no Northern Hemisphere distribution (as with vWA=21, above). Among indigenous North American groups that have it, we find not only the Cherokee but also Chontal in Oaxaca (5.2%), Florida Native Americans (Creek, Seminole, 1.0%), Euchee and Lumbee (0.5%)—all tribes historically documented to have a small but important degree of African admixture.
Enrolled Cherokee and Euchee appear in the top matches, which are otherwise nearly all African and African American populations.
| Rank | World Population Matches |
| 1 | Guinea-Bissau C (n = 92) |
| 2 | South African – Bantu (n = 63) |
| 3 | Mozambique – Maputo (n = 154) |
| 4 | Mozambique (n = 110) |
| 5 | Black – U.S. (n = 258) |
| 6 | Guinea-Bissau B (n = 100) |
| 7 | Namibia – Windhoek (n = 195) |
| 8 | Tanzanian (n = 272) |
| 9 | Black – Trinidad (n = 43) |
| 10 | Angolan – Cabinda (n = 110) |
| 11 | Black – Minnesota (n = 75) |
| 12 | South African – Black – Capetown (n = 98) |
| 13 | Black – U.S. (n = 105) |
| 14 | Equatorial Guinea (n = 134) |
| 15 | Black – Virginia (n = 100) |
| 16 | Black – Minnesota (n = 157) |
| 17 | Euchee (n=6) |
| 18 | Black – U.S. (n = 195) |
| 19 | Black – Florida (n = 50) |
| 20 | Black – Florida (n = 100) |
| 21 | Black – Virginia (n = 194) |
| 22 | Black – U.S. (n = 3,927) |
| 23 | Colombian – North Pacific Coast (n = 123) |
| 24 | Black – Connecticut (n = 182) |
| 25 | Black – Alabama (n = 62) |
| 26 | Black – Jamaica (n = 122) |
| 27 | Black – Kentucky (n = 357) |
| 28 | Black – Bahamian (n = 81) |
| 29 | Black – North Carolina (n = 383) |
| 30 | Black – New York (n = 75) |
| 31 | Black – California (n = 100) |
| 32 | Black – Canadian (n = 179) |
| 33 | Egyptian Berbers – Siwa (n = 98) |
| 34 | Brazilian – Black – Florida (n = 117) |
| 35 | Mexico – Oaxaca – Chontal (n=29) |
| 36 | Rwandan – Hutu (n = 52) |
| 37 | Equatorial Guinea (n = 129) |
| 38 | Black – Illinois (n = 78) |
| 39 | Rwandan – Tutsi (n = 63) |
| 40 | Madagascar (n=67) |
| 41 | Ecuadorian – Black (n = 104) |
| 42 | India – Dhangar (n = 80) |
| 43 | Colombian – Caribbean Coast (n = 243) |
| 44 | U.S. Cherokee Enrolled (n = 33) |
| 45 | Brazilian – Rio de Janerio (n = 300) |
| 46 | Venezuelan – Maracaibo (n = 203) |
| 47 | Brazilian – Bahia (n = 150) |
| 48 | Venezuelan – Caracas (n = 255) |
| 49 | Egyptian Muslims – Adaima (n = 99) |
| 50 | Hispanic – Virginia (n = 183) |
- TPOX=7 is a predominantly African gene like the previous one. The Cherokee exhibit it at the rate of 1.5%—8.7% if we look at admixed rather than enrolled. It is a compelling pattern and the evidence is hard to dismiss.
Striking African features are visible in War Chief (Koranu, Raven) Oconostota (d. after 1809), Donald Yates’ 8th-great-grandfather. His picture comes from Isaac Basire’s engraving made in London in 1730 on the occasion of seven Cherokees’ visit to meet King George II. Oconostota is wearing the British officer’s uniform given to him by the King; he treasured it during his long life and according the his descendant Narcissa Owens it was passed down in the family. He was a son of John Beamer and grandson of James Beamor (Moytoy), a Sephardic Jew. His mother was known as Quatsie (Patsy or Betsy), a mulatto. He was thus called a Mustee—a sign of some degree of African blood in the line. John Beamer’s grandson, Thomas Beamer, was also known as a Mustee. Derived from Mestizo, this term was used of admixtures of the Indian and Negro races.
“By the year 1730, there was a significant degree of admixture among the Cherokee. The potpourri included French, English, Portuguese, Spanish, Moroccan, Scottish, Irish, Dutch, Armenian, Turkish, African and Jewish strains. All of these nationalities crop up in the autosomal results of Cherokee descendants. This admixture appears to be concentrated in the ruling families at the former Apalache capital of Melilot in the Nacoochee Valley, which had previously received strong French Huguenot, Portuguese, English, Irish, Templar/Maltese and Croatian influences.”[4]
- D21S11=24.2 Miwok 1.5%
Maltese is top; it is lacking in most of world. We might hazard that since its distribution, like the Helen Gene, favors islands, it is seaborne. Its presence could stem from Miwok land acting as a haven historically for European and other voyagers to resupply their water, repair ships and enjoy some shore leave with the local women. According to Gunnar Thompson, who has studied the voyages of Francis Drake, a brass plate with Drake’s inscription was brought to light in the San Francisco Bay area in 1936, and in 1974, an archeologist found an Elizabethan silver coin at a Miwok village site near San Francisco. It bore the date 1577 and the image of Queen Elizabeth.[5] Archeological, historical and genetic evidence converges to tell another compelling story that is completely left out of the history books.
- D21S11=27 Miwok 4.6%
This common haplotype has almost all African matches, and with no other Native American tribe. If we follow the line of reasoning used in the previous allele, we might see in it the signature of African shipmates. Drake’s ship was carrying hundreds of black slaves he had liberated from Spain in the Caribbean. Their exact fate was never known for sure. Did some remain with the Miwok?
- D21S11=29.2 Apache 1.1%
Worldwide rare gene, no patterns (?). The top match is Bali. It occurs also in the Shawnee and Mexican Mestizos.
- D21S11=35.2 Yavapai 1.0%
Other Native American tribes that have this allele are Florida Native Americans, Oaxaca Zoque and others, so it is not strictly considered an allele peculiar to the Yavapai but could be classified as one private to Native Americans. Its presence in South American Indians (e.g. Belem Amazonian Indians and Kichwas) shows the rough unity of New World indigenous peoples.
- D18S51= 9 Cherokee 3% (3% is one bi-allele, 1.5% is both alleles or double). Once again the highly mixed Cherokee carry the day:
- D18S51=10 Cherokee 1.5%. As widespread as D18=9, with Enrolled Cherokee (n=33) occupying rank #40. Some Cherokee must have had the value of 9,10 on this locus.
- D18=11.2 Apache 0.6%
Tonga is highest. Only found worldwide in 11 pops, one of the rarest alleles recorded.
Top 3 matches (the only ones that are high):
| Pop. 420 | Tonga (n=51) |
| Pop. 468 | U.S. Apache and Mojave Indians (n = 88) |
| Pop. 112 | Mozambique (n = 110) |
- D18=13.2 Cherokee 1.5%
Another rare widely distributed haplotype with African origin and persistence among recent African Americans. Almost no Northern Eurasian distribution. No Sundaland or Asian or Australian distribution. The Cherokee probably incorporated it into tribal gene pool with black admixture as seen above. The likely time of the gene flow was seventeenth to eighteenth century. Mustees, Mestizos, Mulattoes and Black Cherokees, including many black slaves, were removed with other Cherokees in the 1830s and all enjoyed rights in Indian Territory. In the 1860s, the slaves among them became Freedmen. Controversially, these Freedmen and their descendants were then stricken from the rolls. The action is still being litigated.
| 1 | India – Indo-Mongoloid – Naga (n = 106) |
| 2 | India – Indo-Mongoloid – Meitei (n = 105) |
| 3 | India – Indo-Mongoloid – Garo (n = 110) |
| 4 | India – Indo-Caucasoid – Kayastha (n = 103) |
| 5 | Argentinian – Salta/Puna/Cobres (n = 100) |
| 6 | India – Indo-Caucasoid – Brahmin (n = 110) |
| 7 | Tibet – Luoba (n = 93) |
| 8 | Rwandan – Tutsi (n = 63) |
| 9 | Chinese Han – Shaanxi (n = 203) |
| 10 | Black – Minnesota (n = 75) |
| 11 | Mexico – Nayarit and Jalisco – Huichol (n = 30) |
| 12 | Black – Minnesota (n = 157) |
| 13 | U.S. Cherokee Enrolled (n = 33) |
| 14 | Angolan – Cabinda (n = 110) |
| 15 | Spanish – Cantabria (n = 158) |
| 16 | Brazilian – Cape Verde (n = 120) |
| 17 | Moroccan Berbers (n = 64) |
| 18 | Mongolia – Ulaanbaatar – Lai (n = 92) |
| 19 | Guinea-Bissau (n = 92) |
| 20 | Guinea-Bissau (n = 92) |
| 21 | Native American – Arizona – Apache (n = 99) |
| 22 | Black – New York (n = 75) |
- D18S51=23 Huichol 1.7%, U.S. Creek 8.3% (top match), Chinanteco 3.8%, Mixtec 3.3%, Huichols 2.6%. World average is extremely low (0.6%). Primarily an Asian (Turkic, Mongolian, Siberian, Chinese) and Native American private allele.
- D19S433=11 Yavapai 1.0%
Top Euro match is Ireland at 8.6%. European average is only 0.7%.
- D19S433=17 Miwok 1.5%
Top Euro match is Estonia (1.3%) followed by Norway and Northern Ireland.
- THO1=10.3 Cora 1.6%
Very rare, detected only in West Mexican Cora Indians, Russia Oryol, Hungarians, Czechs.
| 1 | Pop. 473 | Mexico – Nayarit and Jalisco – Cora (n = 64) | High Match |
| 2 | Pop. 356 | Russia – Oryol (n = 72) | Medium Match |
| 3 | Pop. 467 | North American Native Americans (n = 533) | Medium Match |
| 4 | Pop. 402 | Hungarian (n = 4213) | Weak Match |
- FGA=17 Cora 0.8%
An Old World Gene associated with India – Pallar (6.1%). Compare to Oaxaca rare alleles. Worldwide average is 0.5%. Metapopulations South India, West India, Melungeon, Andean, Indian, West Central Asia, North American Native Americans. On the basis of rare alleles among Oaxaca Indians, we have theorized that some gene flow occurred by sea from India to the Americas, especially in the 5th to 9th centuries. See Indians from India in Old Mexico (blog post, Aug. 20, 2023).
- FGA = 22.2 Miwok 3%
World gene, another intrusive type in Miwok.
- FGA=26.2 Chippewa 2.4%
Top result is Native American – Northern Ontario (4.3%). A few other Native American populations have it.
- FGA=29 Cora 0.8%
Plausibly, an old African gene that shows up in minimal frequencies in the Americas. Egyptian Copts show a high incidence (5.5%), as do many other African populations. Choles (of Maya stock living in Chiapas) have 0.5%. The world average is 0.6%.
- D7S820=15 Cherokee 1.5%
Only 43 populations worldwide have this private allele of the Cherokee. #1 India Meitei (6.1%), #5 Cherokee. Metapopulations: #1 East Indian, #2 Native American. Megapopulations: #1 South Asian, #2 American Indian, #3 African.
In conclusion, we have explored the origins and long history of 21 private alleles reported by Kanthaswarmy et al five years ago. We suggested several of them are markers of minor ancestry in American Indian tribes. These inferences make a lot of sense and are reasonable by statistical measures as well as plausible on historical grounds. All alleles in existence worldwide are related and they do not mutate or change, practically speaking. The patterns presented in our analysis should not be dismissed as random and meaningless. If there is an alternative explanation for any of the private alleles identified in Native American populations, we would be happy to consider it.
[1] S. Wang et al, “Genetic Variation and Population Structure in Native Americans.” PLoS Genetics 3/11 (2007, with good bibliog.): Genetic Variation and Population Structure in Native Americans.
[2] K.B. Schroeder et al, “A private allele ubiquitous in the Americas,” Biology Letters (2007) 3, 218-223.
[3] S. Kanthaswarmy et al, “The Enhancement of the Native American Codis STR Database for Use in Forensic Casework,” July 2019.
[4] Donald N. Yates and Teresa A. Yates, Cherokee DNA Studies II: More Real People Who Proved the Geneticists Wrong, DNA Consultants Series on Consumer Genetics 4 (Longmont: Panther’s Lodge, 2021), p. 214.
[5] Gunnar Thompson, Secret Voyages (Raleigh: Lulu, 2010), p. 220.
Read More
Indians from India in Ancient Mexico (blog post, Aug. 20, 2023)
Reading the Ht Leaves (blog post, Aug. 24, 2024)
Evolution and Ancestry: DNA Mutation Rates (blog post, Oct. 23, 2013)
Private Alleles Reveal Minor Ancestry (blog post, April 21, 2024)
Basic Haplotype Report (new test)
Single Haplotype Report (new test)
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