The Lone Ranger and Tonto Fistfight on Facebook

A Short Guide to Detecting All the Crap about American Indian DNA

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It’s a familiar dispute in genealogy. Take the Short/Shortt List. One member (let’s call her Sally for short) spells the ancestral surname one way (the Short way), while another (call her Diane) acknowledges variants, including Shortt, which she says can be Melungeon or even Cherokee. Sally claims the family tree never had a single Native American leaf or twig. Short descendants are as devoid of American Indian blood as the driven snow is of moccasin tracks. Test results for herself and numerous Short acquaintances show zero or little percentage Native American ancestry from 23&me, Family Tree DNA and Could three big companies with millions of customers be wrong?

Diane argues with Sally, finds fault with her logic, with her methods, criticizes the companies and adduces cases of Native American matches in other people’s test results. Sally insists that Diane is deluded by fantasies of playing Indian and is a victim of bad science and false advertising on the Internet.

Why all the intensity? What explains the partisan passions? Why is this discussion not more open-minded and civil? We suggest it has to do with a bad conscience about treating Indians as nobodies in history. In effect, Sally is toeing party lines, extinguishing Indian title, and fighting the Indian wars all over. She is a genetic determinist and purist to a fault.

There are three DNA tests to detect American Indian ancestry or admixture. Ideally, all would be taken before a firm decision is made. Several family members should be included. Moreover, DNA storylines are evolving on several levels and should always be combined with genealogical clues and other evidence and testimony.

Did I mention that no DNA test can get you enrolled in an American Indian tribe? No DNA test can get you enrolled in an American Indian tribe. This bears saying three times. The commercially available tests are all for personal knowledge only. No DNA test can get you enrolled in an American Indian tribe. That said, here are the major types.

  1. Uniparental haplotype testing. These tests underpinned the DNA testing phenomenon that began with the publications of Martin Richards, Bryan Sykes and others in the runup to the Human Genome Project’s completion and culminated in the launch of Oxford Ancestors and Family Tree DNA around 2000. Haplotype testing is still the gold standard for determining your female-only maternal line (which often corresponds to your ethnic origins) as well as your male-only father’s pedigree (which usually follows the surname). Female-line tests are based on a diagnostic set of mutations in the mitochondrial DNA, usually mutations found in the standard control section known as Hypervariable Regions I & II. If the full sets of mutations detected in two individuals perfectly match, the two individuals belong to the same lineage. Their female lines go back to the same European, Asian, African or Native American ancestress a few thousand years ago. The male-line depends on the Y chromosome haplotype, which can be characterized with as few as 12 and as many as 1,000 Y-STRs. They are not the same as autosomal STRs but mutate much more rapidly and are thus well suited for recent history. The latter, like mitochondrial DNA, have a slower mutation rate and are best for deep ancestry.
  2. STR testing. Short tandem repeats or forensic markers were first used by the FBI for establishing identity in police work. The same method was applied to commercial paternity testing (Identigene, 1993). It also has applications in immigration and ancestry. DNA Consultants is the leading company for ancestry at present. Its DNA Fingerprint Plus was introduced in 2006. DNA profiling was pioneered by Sir Alec Jeffreys over 30 years ago. One of the standard texts today is John M. Butler, Fundamentals of Forensic DNA Typing, National Institute of Standards and Technology (Gaithersburg, Maryland: Academic Press, 2010). One of Butler’s chapters, “Statistical Interpretation: Evaluating the Strength of Forensic DNA Evidence,” gives STR allele frequencies according to race and ethnicity for populations around the world, discusses such tools as the Hardy-Weinberg Equilibrium formula and has an extensive bibliography (pp. 259-258 ).
  3. Autosomal genomic testing. Also known as the SNP chip method, this form of high-throughput, high-output personal genome testing was pioneered by Illumina and served as the basis for 23&me’s entry into the field in 2006. The cost of full genomic testing started out at over $950 and rapidly fell to around $150. Some super-sale prices today go as low as $29 as companies like and Family Tree DNA compete for customers.

Some Genetic and Genealogical Fallacies

What qualifies for being Indian DNA is an ever-changing proposition. Unsurprisingly, some tests appear to be sensitive for some Indians or their descendants and others seem to strike out completely. Let us divide the quality control into two aspects, reliability and validity.

Haplotype testing is arguably the most reliable, the most expensive and most time-consuming. But it has some challenges on grounds of validity. If reliability consists in repeatability, thoroughness and accuracy—in getting the same raw result twice—haplotype testing is the most trustworthy. It doesn’t matter whether your haplogroup/haplotype was found with a spit test or buccal specimen or blood.

As for validity, mitochondrial H, just like Y chromosomal R, is typically European, the L’s (L0, L1, L2, L3, L4, L5 L6) point to Sub-Saharan African ancestry and so forth. Notoriously, female lineages A, B, C, D and sometimes X are Native American. In fact, in the eyes of both the scientific establishment and generality of consumers, they are the only Native American mitochondrial haplotypes. But this doesn’t mean they are the only proof of Native American lines in your family tree.

By the rule of doubling for each generation, if you go back eight generations you have as many as 256 ancestors. One hundred twenty-seven of them could have a different female lineage from your mother’s direct female line, and 127 of them could have a different male haplotype than your father’s direct male type. Your mother’s haplotype may not represent the majority of haplotypes, and your father’s type may not reflect the general pattern of the past.

To return to our Facebook fracas, Sally found out her mitochondrial haplotype was a form of H1. Since H’s are not considered to be Native American in origin (only A, B, C, D and sometimes X), she insists that this line, which others have traced in strict mother-to-daughter fashion to a Mary Greenblanket, Seneca, is European, and that Mary Greenblanket’s descendants have no right to claim American Indian heritage. Diane has two objections.

—Maybe Mary Greenblanket’s H1 is, after all, a Native American type. Early genetic surveys found H in the Cherokee among other Eurasian types (Theodore G. Schurr, “Mitochondrial DNA and the Peopling of the New World,” American Scientist 88 [2000] 246-53). Online DNA sites confirm the findings of Yates and Yates’ 2013 study and assign uniformly large frequencies to “non-Native” haplotypes like H, T, J, U and N across the Eastern U.S. tribes, including Lumbee, Creek, Shawnee and others. Mal’ta Boy, the link discovered in 2014 between ancient North Eurasians and Native Americans, had haplogroup U2, a “non-Native” type.

—Even so, maybe there’s clear Native American elsewhere in the family tree. After the admixture process started, didn’t part-Indians marry part-Indians? Her results from STR testing spoke volumes about Native roots, with significant matches to Cherokee, Chippewa and Mexican Indian tribes.

The Basic American Indian DNA test was introduced this fall and is sold on Amazon, where it has been well received. As can be seen, its STR method is completely reliable, being used in other contexts to imprison and free individuals charged with serious crimes. No two individuals have the same multi-locus profile. Even though genetic markers are received equally from mother and father, siblings have slightly different values and results. Only identical twins have the same numbers.

The STR method enjoys important advantages in validity over both mitochondrial analysis and autosomal SNP chip tests. Its matches are not based on fraught evolutionary genetic theories, complicated projections and biased comparisons with a captive database. They come purely from the computations and published reference samples of forensic science. No other company takes the same approach.

The Basic American test, like all the others on offer from DNA Consultants, does not give percentages, only rankings. But its sixty-plus Native American reference populations are the maximal number available in forensic science. Included are all the following in the table shown below.

Algonquian Indians

Amazonian Indians

Andean Indians



Atocpan Indians

Belem Amazonians

Brazilian Indians

Cherokee Indians

Chihuahua Indians

Chippewa Indians

Choctaw Indians


Cochimi Indians

Cora Indians

Cree Indians

Creek Indians

Cucupa/Cocobah Indians

Cuetzalan Indians

Diegueno Indians

Dogrib Indians



Guatemalan Mestizo

Guerrero Mestizo

Hualapai and Yavapai Indians

Huichol Indians

Huichols – Durango

Huichols – Jalisco

Huichols – Nayarit


Kichwa Indians

Kiliwa Indians

Kumeyaa Indians

Lumbee Indians

Mayo – Sonora

Mexicaneros – Durango

Miwok Indians

Mojave Indians

Muskogean Indians

Native American – Michigan

Native American – Minnesota

Native American – Northern Ontario

Native American – Saskatchewan

Native American – Florida


Ojibwe Indians

Orinoquian Indians

Otomi Indians

PaiPai Indians

Paraguayan Indians

Raramuri Indians

Salishan Indians

Seminole Indians

Seri Indians

Sioux Indians

Tarahumara Indians

Tepehuanos – Durango

Yuman Indians


What this means if you get a high match to, say, Enrolled Cherokee, is that your DNA profile, unique, practically speaking, to you alone, is relatively common in the Enrolled Cherokee reference sample. Presumably, the only way your profile could match Cherokee profiles is if you share a high degree of ancestry with Cherokee people. (It is fair to point out that this is an inference, not an observation or fact, though the same came be said of haplotype and genomic testing.)

It also means that thirty-three Cherokee men and women responded to a call for volunteers, showed up a few years ago at a clinic, raised their hands, and said, “Yep, I’m an enrolled member of the Eastern Band of Cherokee Indians, and here’s my DNA.” Academics at the Molecular Anthropology Laboratory of the University of California at Davis then published the data as part of a survey of 533 Native Americans in 29 different tribes. The article was S. Kanthaswamy et al, “Native American Population Data Based on the Globalfiler Autosomal STR loci,” Forensic Science International: Genetics 24 (2016):e12-e13. Such STR matches are thus similarities to living, contemporary populations, not to hypothetical types in the past—another clear edge.

Sally and Diane feud a lot about where American Indians “came from” and when they began to mix with Europeans and Africans. Everyone’s understanding of American Indian genetics underwent a sea change several years ago when ancient DNA began to be available for the first time. Many people still cherish endangered theories, such as that of the Bering land-bridge and single-entry migration into the Americas. This brief guide can’t go into all that, but we will leave both Sally and Diane with the following questions to ponder.

—Why do people seem to think there might be only one Indian in their family tree? If there is one, didn’t that one have two parents? That would make at least three, and on and on.

—Why do we call it American Indian DNA when it is supposed to all come from Asia? Why don’t we call it Mongolian, East Asian or Siberian DNA?

—Why are we exclusively focused on thousands of years ago rather than the periods of world history more important and better known to the present, like classical antiquity, the Middle Ages and Age of Exploration

—Is there any American Indian DNA that flowed across the Atlantic Ocean instead of coming from the shores of the Pacific Ocean? Did all inputs spread by land routes in a gradual starlike pattern of diffusion?

—Is it to be labeled European admixture if Icelanders left a colony in Duck Trap Harbor, Maine, in the eleventh century, or Mycenaeans built a harbor at Poverty Point in Archaic Indian Period Louisiana? That term is typically reserved for events after 1492. Should you describe those populations as American Indians? Part or admixed American Indians? What is to distinguish them from part or admixed American Indians of today? How do we know if admixture was pre-1492 or post? Nothing in the naked DNA signature can tell the difference. It all depends on the assumptions of history and anthropology.

In our experience, if any of your European or African or Asian male ancestors were settled in North America before 1790, you have some degree of American Indian DNA, possibly a significant amount. Young males on the developing frontier had to marry someone and they very often married Indian women. Family lore abounds in these stories, in European as well as African American contexts. Many genealogists follow their paper trails back to the seventeenth century. Forensic matches can trace the Native American contribution better than uniparental or whole-genome testing.

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  Comments: 2

  1. Thank you for the brilliant and spot-on article, Dr. Yates. You always have something enlightening to share. Wado!

  2. Very interesting. As an amateur genealogist of many years, I have very little experience with DNA testing. I have done two Y-DNA samples and one autosomal test. As far as I am aware, there are no stories in my family of Indian ancestry, nor any documentation of such. But I am interested in all aspects of DNA testing and hope to someday have a working knowledge of it!!

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