Mexican Women’s Mitochondrial DNA Primarily Native American

Amy Tilden

 Mitatwe’eptes (aka Amy Tilden) – Nez Perce – circa 1910

In the paper, “Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins,” Kumar et al provide a piece of information I find extremely interesting.

“For mtDNA variation, some studies have measured Native American, European and African contributions to Mexican and Mexican American populations, revealing 85 to 90% of mtDNA lineages are of Native American origin, with the remainder having European (5-7%) or African ancestry (3-5%). Thus the observed frequency of Native American mtDNA in Mexican/Mexican Americans is higher than was expected on the basis of autosomal estimates of Native American admixture for these populations i.e. ~ 30-46%. The difference is indicative of directional mating involving preferentially immigrant men and Native American women. This type of genetic asymmetry has been observed in other populations, including Brazilian individuals of African ancestry, as the analysis of sex specific and autosomal markers has revealed evidence for substantial European admixture that was mediated mostly through men. In our 384 completely sequenced Mexican American mitochondrial genomes, 12 (3.1%) are of African ancestry belonging to haplogroups L0a1a’3’, L2a1, L3b, L3d and U6a7; 52 (13.6%) belong to European haplogroups HV, JT, U1, U4, U5; and K and the majority (320, 83.3%) are of Native American ancestry.”

If you have Mexican ancestry or your direct matrilineal line, meaning your mother’s mother’s mother’s line, on up the direct maternal line, please test your mitochondrial DNA, here, and join the American Indian project at Family Tree DNA.



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79 thoughts on “Mexican Women’s Mitochondrial DNA Primarily Native American

      • No, men arriving from Spain were NOT allowed to bring any woman over that they were not married to. If they were bachelors and could not find a daughter of another Spanish compadre they took Native wives. They had no other choice. Men were only allowed to bring their legal wives and children. My father is Costa Rican and his mother was very fair with Blue eyes. Her haplo is A2j !!! They really had no idea.

      • thats not entirely accurate. the fur trade in the 1600s in canada saw a huge boom in indigenous and european mixing. so much so that theres even a term for the indigenous women: “country wives”.

  1. Not surprising. I suspect most Hispanic-American populations would show a similar pattern. A Cuban-American friend of mine tested 95% European, 4% Native American, yet has the mtDNA haplogroup A2d1, which is Native American. Most Caribbean and Central American countries experienced similar early Spanish male immigration. (or French in Haiti and English in the BWI to a lesser extent) I’m not as familiar with South American immigration patterns.

    • Not even close. Mexico has a very high Native American component, but the Carribean Hispanics have a LOT of African mtdna as well. In Dominican Republic the African is 4 to 5 times higher than other Hispanic countries. As for Cuba, it goes without saying that they are largely a mulatto country similar to the Dominican Republic where the Native component is usually in the low single digits

  2. What an interesting article! I live in Northwest Oregon, I am quite familiar with the Confederated Tribes of the Nez Perce. They must have done some migration of their own, years ago, would be my guess. It is amazing how ‘tribes’ of peoples, moved about early on. Although my 9% Spanish is from Spain, most of the matches are tied with my Jewish side so far, a few in Spain and the others in South America. Some of them show they descend from relatives who lived in various parts of Russia. That is a lot of traveling! 🙂

    • Through my maternal Grandmother we are said to be descended from the Nez Perce. In doing my Genealogy, I have been able to trace my maternal grandmothers line but one. We suspect her to be our NA source. My mother, her eldest sister and myself have taken DNA tests. It shows Iberian, Southeast Asian, and the America’s colored in for heritage in my Aunt and myself. On Gedmatch our NA shows up. My daughter-in-law is 16% NA via her father who is Mexican. She has the Iberian, NA, East Asian, Southeast Asian and Broadly East Asian & NA on 23andme. Her America’s are also colored in showing NA Heritage. On Gedmatch her NA shows up as well. On WeGene/en, She shows as Spaniard and Maya while my mom shows as Hispanic. My Grandmother’s 1/2 sister told my Grandmother’s eldest daughter, Edna, the one who took a DNA test for me, that Grandma’s NA belonged to the tribe Twisted Hair was from. Grandma told me that they fought with the Sioux when Custer was killed. I am trying to track down a descendant of our source who might still carry her maternal DNA so I can hopefully have them tested.

  3. It was my impression that Native Americans were adverse to dna testing because of religious reasons. Wonder how they got a representative # of testers? Just yesterday, I received an email from a Native American whose tree I had viewed at In her tree it indicated a marriage between brother and sister. I thought she had a made a mistake, but she indicated that was not unusual at the time. Tribal differences, she did not indicate. I guess this would be considered “compounding” and wonder how this would factor in.

    • As the linked paper explains, the sample group was Mexican American from the San Antonio (Texas) Family Heart Study, and apparently did not include any self-identifying Native American.

      • This is probably because the US does not recognize Mexican tribes hence most Mexicans do not report as native. My mother belongs to halotype B as do most natives from Mexico. America Indians are halotype A and came from the Bering strait. B is now coming to light that we came across the oceans during ancient times with primarily Mongol ancestry. My family does carry the purple birthmark. Many northern Mexico tribes mixed with southern tribes. Linguistically its shown we have similar ancestry with the Zuni, Hopi tribes, also in beliefs. Its all very interesting. My mother & I went to the Hopi lands and it was quite enlightening some elders said my mom looked and talked the same way they said she was a distant auntie. When I told them she was Mexican they said oh yeah, tribes used to steal each others children all the time. My moms mother was Huichol from Zacatecas.

        • 50% of newborns in Mexico are born with the Mongolian birthmark. This is an official government statistic by the Instituto Mexicano de Seguro Social and I apologize for not having the source handy.

      • As far as Native Americans being averse to DNA testing, it has to do with fear that the government will further reduce tribal rights due to limitations in DNA testing. For example: for Sons if only the maternal line is Native, there is a possibility the mother’s Native American DNA may not show on a DNA analysis in comparison to his sisters. I think many people overlook the fact that the younger generation of Native Americans which includes so call Mexicans indigenous to the southwest US & northern Mexico. This Indigenous Native American population has grown up in a different era using a tremendous amount of technology compared to our elders. I see young native women getting their masters in genetics and they fully understand that Mexican, Latino, Latinx, Hispanic, etc are labels that have been assigned to us as a larger whole in order to erase our own intricate tribal cultural identities that are so different between the various regions of the US. Why is it that Native Americans are the only people expected to remain frozen in time without adaptation? Of course because it nullifies cognitive dissonance for the larger in control society! My family is the so called Mexicanized Indians. We are categorized this by the US government in 1905 during the formal US Census of Indian Peoples, with the explanation that the people of the area spoke both their own language and Spanish. Actually the used government in most cases used this logic to deny that “Mexican” people are Native Americans. The argument is, the people of the Southwest: California, Arizona, New Mexico, Colorado, Texas, etc speaking Spanish are to be labeled as: Mexican – Race “White” in accordance. I am lucky in that my own family history on the Spanish side is documented going back to 1410 Espana (Spain). On the Indian side of the family it was noted that multiple marriages were common. Life is precarious when cultures class. I am aware of a Native American custom of husbands marrying a brother’s wife should he die to ensure his brothers family is properly cared for, this is the first type of situation that came to mind when you spoke on the topic. I have never heard of my Native American side marrying within the family. Actually it is absolute taboo in our culture. We are a matrilineal people for us the males leave their own family to build a family with his wife community. Also, the Spanish side of the family is the side that I was surprised to see had married second cousins. I was told this practice was done in order to prevent mixing blood with the Native Americans.

  4. Roberta, this is very interesting and akin to one/some of the threads on FTDNA Forum. Will you post this link there?

  5. Diana Sotela, Interesting item, but you misunderstood Israel P’s question / comment which draws the historical distinction between invading men in English North Am who brought the women with them, in contrast to Nueva Espana, where the invaders utterly destroyed existing cultures and enslaved the native men, leaving themselves virtually unlimited access to the surviving women. Malinche is the representative iconic image of the fate of indigenous women and by implication, of indigenous males.

    • La Malinche is a truly fascinating historical figure. As mistress to Hernan Cortes, she bore him a son, Martin, the first mestizo of New Spain who had both a son and a daughter. The pattern was set.

      • Not only la malinche. One daughter of Moctezuma, a princess, was pregnant by Cortez when she was still a teenager (in all she had 5 legit husbands, all dying one after the other!), but Cortez abused of her, and her descendants bear the name of Moctezuma; some descendants living in Spain since centuries ago, they don’t look at all indian anymore.

      • Actually the first Mestizo was a female, but as history has it, her birth was not considered historically significant and her brothers birth is the one recognized as the birth of the first mestizo.

  6. Kumar’s work is great. We reported similar findings for Mexico in a scientific poster at the ASHG Conference in 2008 in Philadelphia. We never got to write an actual paper though. The sample size was nearly 3000 mtDNAs. In 2012, we published a paper in PLoS One on Panamanians mtDNA (sample size = 1500). The frequency of Native mtDNA lineages was similar to that of Kumar and his Mexican sample.

  7. I have written a few articles relating to this issue and Puerto Ricans. A few years back, Puerto Rican scientist, Dr. Juan Martinez Cruzado, conducted a National Science Foundation sponsored mitochondrial DNA survey of Puerto Ricans on the island. It so happens that 61% of all Puerto Ricans have indigenous mitochondrial DNA. Here is a link to Dr. Martinez Cruzado’s own account of the study:

  8. Does anyone know of a tribe that were yaki? Spelling is prob different? They had later joined up with the Cherokee.



    • Henry, I always felt that we had Native American blood. I am a Mexican American from Texas. I had my DNA tested because while my older brother, sister and I were dark skinned, my younger brother and sister were very light skinned, blonde and blue eyed. My wife is from New Mexico and her Jimenez side have the Native American features. The women are beautiful. Any way, our oldest daughter is dark skinned like me and our two younger childeren were born light skinned, blonde and blue eyed like my brother and sister. my DNA showed that my DNA was 40% Native American, 25% Spanish, various nationalities from around the Medeterrean and the remainder was Jewish, African, Russian, Finnish. I am curious to find out about my Native American ancestry but don’t know where to start. Do you have any suggestions? Any assistance is appreciated.

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  11. This is also because many Native Americans in the states closer to Mexico, started claiming to be Mexican-Amaerican so their children would not be taken wawy and sent to boarding schools. They immersed themselves into the Mexican American culture and their children grew up thinking they were Mexican American, Also, when Tejas was taken by the US the tirbes who resided there were not all Native American, some had to be Mexican Indegenious tribes.

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  14. Umm it’s true a large amount are native american including myself which is pretty awesome. My whole family was shocked by that one. We did a dna test and learned our haplogroup is only carried by 11% of natives in both North and South America. Most mexicans carry at least a quarter native ancestry. Mexico has the largest groups of Natives in both North and South America about 15 million while the USA has about 5 million that is double the size. So why should this surprise anyone? This study was pretty accurate.

    • There so much more natives there than here because of the genocide that took place since the beginning. And we are still dwindling in numbers. Just saying.

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  16. When the US took the west,the government started to put native americans in reservations, many of this native americans came from the east cost but they did not want to be in a reservation,so they said that they were mexicans that’s one of the reason that in New Mexico many Mexicans started to say that they were Spaniards so they wont be confused by native americans

    • Northern New Mexicans are decendents of Spaniards with a small amount of native american. We are not native Americans claiming to be mexicans to stay in this country. We have been in this area for centuries.

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  22. Mexican Mestizos (except in the deep southern part of Mexico) are by far predominantly European. Many also have West African ancestry. I think people may mistake this to mean “Mexican means Indian”, which it most certainly does not.

    • If they are ”Mestizos”, it means ”part-white/Spanish and part Native American”. If they are ”part Native American”, which near 90% are, then they are Native American because percentages, no matter how small, do not cancel out ancestry. The fact that they are white, or black (”Zambo” = black and native), doesn’t stop them being Native as well. Not all national Mexicans are Native American, no, but the culture of Mexico is Native American in character as well as Spanish so ”Mexican” does pretty much mean Native American, at least in part.

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  24. i was born in zacatecas mexico my family roots have been traced back with DNA back to the 1600 s in spain and sardinia or the westren mediteraniam also same german origin found in visigoth spain

  25. I I am a Yaque on my father side and Spanish on my mother side. My father died last month March 14, 2016 and he was 95 years old and I believe the last of his tribe on his side they were from Sonora Mexico. This is my email

  26. I have a question, when someone gets a Genetic test and shows 46 % Native American with 23% Iberian Pen. this correlates with our Mexican lineage as grandmother is from Mexico, how can they distinguish that the Native American or a percentage of it is “American Indian” arguing that they are not even half Mexican?

    • Many (most) Mexican people are mixed Native. In your case, you’re about half, which correlated to one parent or parts of both parents. There is no “Mexican” category since Mexican people will generally be a mixture of both European and Native American.

      • yes that’s what I stressed to my family member (cousin whom we share same grandmother via both our mothers) stating to her “With the large percentage of Iberian and Native American DNA that correlates your Mexican heritage right their. No DNA test is going to say Mexican as it is a multi ethnic country just like America” the argument is that she is American Indian on her dads side out weighing her Mexican heritage? I’m confused? genetically American and Native Indian are different?

  27. I was born in Northwestern Mexico. 23andme assigned me to haplogroup L1b1a. I am trying to find out more info about it.

  28. Very interesting.However the DNA studies recently done in Mexico showed that non Amerindian DNA was is more dominant than
    Previously believed.
    To put it in a nutshell those from the central and southern Mexican states tend to be 60%
    Amerindian or more on average.
    Those from the Northern states and certain pockets of Jalisco and Zacatecas tend to have
    60% non Amerindian DNA or more.
    My roots are from northern Mexico
    Several of my cousins and I had out DNA
    Tested and we were all found to have 25
    to 35 % Amerindian DNA.
    Most of our DNA was from Europe (Spain
    Greece ,France Holland etc…)
    Also European Jew, North Africasnd more.
    What escapes most people’s knowledge is that
    that for many decades there were more non
    Amerindians in the Americas.
    By 1780 it is estimated that there were only 2%
    Of the Amerindian population left from the
    Population amount that existed when Columbus landed in the Americas.
    About 780,000.
    It took many years for the Amerindian Nations
    population to rebound.

  29. Hi Roberta, I was thinking about this post, and was curious what analyses have been done in the U.S. You note, “We don’t see anything like that in the US or Canada.” It seems that an analysis of 23andme results (and now LivingDNA) should indicate the % of testers whose autosomal DNA indicate possible Native American ancestry have native Y haplogroups and native mitochondrial haplogroups. If that hasn’t been done, it seems like the kind of collaborative project that is begging to be done…

  30. Fascinating! I recently had my DNA tested through CRI Genetics. All of my grandparents are of Hispanic/ Mexican heritage. My maternal grandmother, her parents, and grandparents were all born in Mexico. While my maternal grandparents were both light skinned, grandma’s older generations had very indigenous looking features. OTOH, my grandfather’s father, grandfather, etc could pass for white (light skinned, tall, green eyes, more European looking) and their surname (Olivares) comes from Spain. And one of the grandmothers in this branch was rumored to have been French.

    So I was surprised when my test came back with over 70% Peruvian ancestry and the next highest ancestry percentage was only 9.9% Mexican! With the rest being tiny percentage random “mutt markers” from basically all over. My maternal haplogroup is B2. Other surprises included a few stray Finnish and British genetic markers that nobody has any idea where they would have come from. Interestingly, my blood type is A+, which I have read was basically nonexistent in Native American populations prior to European contact, BUT is very prevalent in Scandinavian populations.

    So, I’m a bit confused. Is there anything that can be inferred from this combination of information about other possible research leads or where all that Peruvian ancestry might have come from, or am I reading too much into things? Thanks!

    • Lotus flower. My moms DNA Showed the same. You probably have old ancient blood. My moms family are huichol and gparents born in Chalchuites Zacatecas. I couldn’t understand where the Peruvian came from but I started researching and found old Migration patterns. On the west coast of Mexico some natives do not match the indigenous tribes in that area of mexico. Historians suspect that tribes from Peru migrated up into Mexico. They show as have the same cultural dress and language as peru. I should have saved the links, I could have been reading from Spanish sites or English, but check it out. Then throw in the mix of the red heads in Peruvian ancient culture, were they Vikings? Just did my ancestry DNA. 56% native 16% Europe 13% Iberian , sprinkling of Africa which I suspect is the Spanish part, but interesting a trace of finland/no Russia. I am a very dark native American and have always been proud of my indigenous roots. DNA just confirmed it. And confirmed Zacatecas region. fathers side is mixed I suspect more where my Spanish comes from.

      • wow. ancestry just upped my ancestry 61% native; 20% spain; 6% france; 3% basque;2% Portugal and sprinklings of 1%.

    • Lotus Flower, I’m trying to find the parents/grandparents/great grandparents of our adopted daughter. She was abandoned in a public place soon after birth. We’ve found a 2nd cousin who has a good family tree for working with. This 2nd cousin has said she’s quite tall at about 5′ 10-11″ and her gm was 6′. This cousin says the tallness in the family comes from a gt gp who was from France. Interesting. Our wonderful daughter has a common “Mexican” DNA result. At about 60% European and 32% NA. She connects with people in Portugal and Poland.

      Our daughter is considered tall for the average Mexican American at about 5′ 5″1/2. She recently had a baby boy who from birth was over the 99% for height and weight and remains so to this day. At 8mos, he is now in a 1 yr old size. His Dad is only about 5’10” and height doesn’t run his family. His Dad is actually short and Mom is average for having northern European ancestry.

      This second cousin of hers say the French ancestor had the name of Michelle or close to that. Since you have a French ancestor I was wondering if perhaps French people immigrated to Mexico (southern) in the 1800’s or so? Our daughters other “Mexican” lines came from Jalisco, Mexico to CA. It’s just a thought.


  31. My Dad’s DNA showed 57% Iberia / Southwestern Europe, 30% Native Mexico, 6% Ireland, 4% West Africa, 2% North Africa, 1% other. That 30% is probably a lot of our great-great grandmas since most Spanish immigrants were single men, often without much money (soldiers, tradesmen, clergy, etc..) couldn’t afford to marry/bring a wife, so married the Indian or Mixed women in Mexico. I don’t know how the heck Irish got into the mix…

    • The Irish were Catholic, just like Mexico, and immigrated to the USA, and were persecuted by the English protestant settlers, and crossed over to Mexico during the US-Mexican war in the 1850s.

  32. I have 3 out of 4 grandparents are Native. My Dad being Q-M902, My Maternal line B2a2, My Dad’s mother B2f. I am descendant from early settlers of New Mexico who came in 1598 and again in 1693. Both my Dad and his mother are from Mexico. My results are 43% Iberian Peninsula, 30 % Native, 8% British Isles, 3% North African and 3% Akiskani Jew. I also have a ggreat-grandfather who is Irish.

  33. Hello
    My results from Ancestry were 16% Native American. The Native American comes from my father’s side of the family. The family lived in Arizona, Texas and Mexico. Where do I start to determine the origin? My father is no longer living and none of the generations back in his line are living. All I have are cousins or distant cousins living. I am trying to work my tree for Mexican American descendants. Is there a website to find more Mexican records? Thank you.

  34. I just tested myself for my Maternal DNA marker on my mothers side. It came out as B2g2 and it’s telling me that Yaqui’s have this dna marker & Mexicans. Not much research on this DNA Marker. Anyone else have this DNA Marker ?

  35. So my Mother is Native American from Mexico, my question is, which DNA test are you recommending for this study, I see different ones, with different prices..

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