by John Allred
Past DNA Project Manager

Disclaimer:  This article first published 2012 in AFO Newsletter #92.  Since then, the science of using DNA for Genealogical/Ethnic Research has improved, advanced and become more popular than ever imagined.  If you have questions about using DNA to find a Native American ancestor, please contact current Allred DNA Project Managers Mike Arnett or Mike Kidd or visit the Allred DNA Project at    

Judging from the messages appearing on Facebook over the past few months, there seems to be a great deal of interest in the possibility that the Allreds have Native American (Indian) ancestry. Indian ancestry, often based upon family stories which may or may not be true, can be validated by appropriate documentation if that is available. For example, has a database which contains an index to the Indian census rolls from 1885-1940. In addition to a paper trail, we have a relatively new tool to examine our ancestral past – DNA analysis. And preliminary results are in from this new tool!  So far, there have been 74 men who have had analysis of their Y-chromosome DNA in the Allred project on Family Tree DNA: none of them have Indian ancestry in their direct line!

This result is not surprising because the DNA in the Y-chromosome is passed from father to son (with no input from the mother) as is our family name of Allred. The family name of Allred has been traced back to England to a time period of the 1500s - and there were no Indians in 16th century England! It is true that there are men who have the Allred Ychromosome genes but do not have the Allred name and there are other men who have the Allred name
but not the common Allred Y-chromosome genes. In both cases, where the name and the genetic profile do not match, the reason is due either to a name change, an adoption or an illegitimate child somewhere along the line. Even so, the few Allred men who do not have the common Allred Ychromosome DNA profile are all of European, not Native American, descent.

Very limited data show the same result for the mother’s of Allred men who have been tested. Of the 74 men in the Allred DNA project whose Ychromosome DNA was tested, seven had the additional test of mitochondrial DNA. Analysis of DNA in mitochondria (1) provides a way to follow the female line - mother to daughter to daughter, etc.
None of the mitochondrial DNA from the seven mothers shows any Indian ancestry in their direct line.

How does DNA analysis tell us our heritage?

How can we be so sure that Allreds do not have Indian ancestry in their direct line? To answer that question, we need to review some of the basics of DNA analysis. DNA analysis can give us a wealth of information on a number of different levels. First, it can give us information over a very long time period which provides an understanding of our genetic relationship to people who lived tens of thousands of years ago when humans were hunters / gatherers. Second, it can give us information of relationships that have occurred in our personal family history more recently but still going back 500, 1000 or more years ago. And finally, DNA analysis can give us information on our recent family history going back from the present for three or four (and maybe five) generations. Each of these time periods rely on different types of DNA analysis.

Regardless of which level, DNA analysis is useful for genealogical research because of copying mistakes, also called mutations. For example, consider the Y-chromosome which only males have; the Y-chromosome is passed from father to son2 with no genetic input from the mother. That means that a son will inherit a Y-chromosome having the exact same DNA structure as that of his father – and grandfather and great grandfather, etc. – regardless of who the mother was. In fact, the Y-chromosome of a male child would have the same DNA composition as all of his male ancestors if mistakes did not occur copying of the Y-chromosome DNA during the reproductive process. But mistakes (mutations) do occur during that copying.

The DNA “alphabet” contains only four “letters” abbreviated A, G, C, and T. It is the sequence of these four “letters”, called “bases” which determine our genetic heritage. One of the most common types of mutations is the
substitution of one base for another. For example, the original DNA may contain the base “A” at a specific site. A mistake may be made during DNA copying in which the base “G” is substituted for “A”. This is called a mutation and if it occurs during the reproductive process, the resultant child (and all of that child’s descendants) will have DNA with a “G” at that specific site rather than an “A.”

If that

mutation occurs on any of the chromosomes other than the sex chromosomes, it may have no noticeable effect or it could affect eye color, hair color, the shape of the mouth or any of thousands of factors determined by our DNA. If that mutation occurs during copying of the Y-chromosome in the reproductive process, it will not affect his physical characteristics but all of his male descendents will carry DNA with a “G” at the DNA site where his ancestors had an “A”.

Now suppose that the mutation just described happened tens of thousands of years ago. All of the male descendents of that man (and by now there are no doubt hundreds of thousands if not millions of those descendents) would have a “G” on the specific site of the Y-chromosome where everyone else would have an “A”. Now suppose that during DNA analysis of your Y-chromosome, a “G” was found at that specific site instead of an “A”. That would mean, without a doubt, that you and everyone else with that same base substitution (mutation) are descendents, through an unbroken line of males, of that man who unknowingly first experienced that mutation so many thousands of years ago. You are a member of a large number of men who have a common ancestor, to which scientists have given the name “Haplogroup”.

If you go to website DNA results graph page ( you will find that almost all Allreds are shown to be in the Haplogroup R1b1. Family Tree DNA lists our primary Y-chromosome Haplogroup as R1b1a2. We are far from alone – the R1b1 family of Haplogroups is the most common in Europe accounting for more than 40% of the population. The R1b1 Haplogroup accounts for up to 80% of the population in Northern France, Western England and Ireland. This is consistent with the very strong evidence that our family came to America from Lancashire in Western England (3).

In contrast, Y-chromosome mutations in Native American men show that they belong to either Haplogroup C3b or Q1a3a. These groups have been shown (4) to have migrated from Siberia across a land bridge to present day Alaska some 15,000 years ago during the last ice age. From there, some came overland to what are now Canada and the United States while others likely went by boat along the Pacific Ocean to Central and South America.

The point of all this is that no Allred male who’s DNA has been analyzed has mutations that would put them into either of the two Native American Haplogroups.  Rather all of them had mutations which showed that they were in one of the Haplogroups occupying Europe several thousand years ago. This shows that no Allred male found so far has Native American ancestry in his direct line from the time of modern DNA testing to tens of thousands of years ago!

What about females? Could they have Indian ancestry? This question can be answered by analysis of a form of DNA that is passed only through the female line. This form is the DNA found in mitochondria which is passed from mother to children of both sexes but can be passed to future generations only through the egg of the female (5).

This DNA is also subject to mistakes during copying and such mutations have led to the classification of mitochondrial Haplogroups just like the Y-chromosome Haplogroups described above. Mitochondrial Haplogroups of mothers of Allred men who have had the analysis shows H, I4, J, K, N, T2 and V. Native American mitochondrial Haplogroups are A, B, C, D, and X. Thus, with the small number of Allred men’s mitochondrial DNA analyzed so far, there is no overlapping of Haplogroups. This means that the mothers of these men did not have Native American ancestry within their direct female line.

Y-chromosome and mitochondrial DNA analysis does not say “NO Indian ancestry” for any Allred!

Notice that the results of both Y-chromosome and mitochondrial DNA analysis described above are limited to conclusions about ancestry in the direct line because these two types of DNA are passed only through the male and female line directly. Any of us could have Indian ancestry indirectly that would not be detected by these types of analysis. To illustrate, suppose that you are an Allred man whose grandfather married an Indian woman. Analysis of your Y-chromosome DNA would not show that your grandmother was an Indian because you, your father and your grandfather would have the Allred Ychromosome DNA with no input from your mother or grandmother, whether Indian or not. Your mitochondrial DNA analysis would not show it because your mitochondrial DNA would reflect that of your mother (that is, the woman who married your father) and not your Indian grandmother.  Again, Y-chromosome and mitochondrial DNA analyses are useful only for following the direct line of males and females, respectively, but are not useful for finding ancestors who are not in your direct line.

A different type of DNA analysis can be used to show recent Indian ancestry not in your direct line.

There is a DNA test that can be used for finding ancestral relationships over the past few generations, using DNA that is passed with essentially equal input from both father and mother because it uses all of your DNA, not just that on the Y-chromosome or in mitochondria. This test is called “autosomal” DNA analysis. The test is expensive (currently $289 for Family Finder at Family Tree and is most useful for up to three or four past generations. It could tell you whether any of your parents, grandparents, great grandparents and, with less accuracy, great, great grandparents, were Native American. The reason that it is less useful the further back you go is autosomal DNA gets diluted each generation as shown by the following chart. That is, only about half of the total DNA composition is determined by each parent.

Generation Number DNA from each
2 Parents 2 50%
3 Grandparents 4 25%
4 g-Grandparents 8 12.5%
5 gg-Grandparents 16 6.25%
6 ggg-Grandparents 32 3.12%

Suppose that your great Grandfather married an Indian woman. Using autosomal DNA analysis to find DNA markers specific to Native Americans would be quite possible since 12.5% of her DNA composition is represented in your DNA. At that level, analysts should be able to find her DNA markers within your DNA, establishing your Indian ancestry. Now suppose that it was your great, great Grandfather or even your great, great, great Grandfather who married an Indian woman. Finding her DNA markers within your DNA would get progressively harder because only about 6.25% or 3.12%, respectively, of her DNA composition is represented in your DNA (see chart).

If you suspect Indian ancestry, what should you do?  The first thing that I would do is to check out the paper trail as best I could to find out if there is documentation of Indian ancestry. Whether you next use DNA analysis depends on the circumstances. If paper documentation leads you to believe that you have Indian ancestry, either male or female, within the past four or five generations, you might want to use autosomal DNA analysis (Family Finder on Family Tree DNA) to confirm it or, if the evidence is strong, you may want to just believe it, save your money and not do a DNA analysis at all. Similarly, if the stories or a paper trail indicate the Indian ancestor was farther back than your great, great, grandparent, save your money because Family Finder will be of no help.

If family stories indicate that a male ancestor (no matter how far back) named Allred was an Indian, it is extremely unlikely to be true but a test as simple and inexpensive as a 12 marker Y-chromosome DNA analysis would easily prove it one way or the other.  If the results show that you are in the R1b1a2, you do not have a male Indian ancestor!

Finally, if family stories indicate that your Allred ancestor married an Indian woman back in the 1700s in North Carolina, there is no way to use DNA testing to find out if it is true! Your only real hope of finding the truth would be to find paper documentation and that will likely be very difficult.  So it may be that this family story may have to remain just that - an unconfirmed family legend.

(1)  Mitochondria are very small particles found in almost all human cells, including the egg. When an egg is fertilized and develops, the mitochondria found within that egg are copied and copies are passed along into daughter cells. Thus the DNA in mitochondria is passed from mother to children of both sexes but only the female can pass it on.

(2)  Most of our DNA is in chromosomes found in the nucleus of almost every cell. Humans have 46 chromosomes which occur as 23 pairs. One pair is called the “sex chromosomes.” Females have two nearly identical sex chromosomes, labeled XX while males have two non-identical sex chromosomes labeled XY. During the reproductive process, the egg from the female contains a copy of the DNA of one of the X chromosomes while sperm from the male
has a copy of either the DNA in either the X or Y chromosome. If the sperm carrying the X chromosome is successful in fertilizing the egg, the resulting embryo will have two X chromosomes (XX) and will be female. But if the sperm carrying the Y chromosome is successful instead, the resulting embryo will have an X and Y chromosome and will be male.

A more detailed explanation of the Y-chromosome and its use for genealogical research has appeared in this Newsletter: “On the Trail of Allred Ancestry - How Can DNA analysis help?” AFO Newsletter, Issue number 88, Summer 2011, pages 1-7.

(3)  Our ancestral journey did not start in England, of course. Scientists have gathered very substantial evidence that we humans – Homo sapiens – originated in Eastern Africa some 150,000 years ago.  Haplogroups can be considered on some level as a small migratory group led originally by a single patriarch. As these groups left Africa and stayed together over a long period, perhaps thousands of years, there were additional mutations which were unique to that group. By looking for these mutations in populations around the world, scientists have been able to reconstruct the movement of populations. In the case of our ancestors, the evidence indicates that our migratory group left Africa for Eastern Europe about 40,000 years ago and moved to Southwestern Europe (present day Spain) some 25,000 years ago. Some stayed in that region (notably the Spanish Basques) while others migrated north at the end of the last ice age about 10,000 years ago.  An excellent video describing this origin and migration will be found at:


(5)  Mitochondria are very small particles found in almost all human cells, including the egg. When an egg is fertilized and develops, the mitochondria found within that egg are copied and copies are passed along into daughter cells. Thus the DNA in mitochondria is passed from mother to children of both sexes but only the female can pass it on. 

Most of the Allred and Indian stories are not documented.  DNA has also proved that, at least in the early lines, there is no match.