Clovis People Are Native Americans, and from Asia, not Europe

In a paper published in Nature today, titled “The genome of a Late Pleistocene human from a Clovis burial site in western Montana,” by Rasmussen et al, the authors conclude that the DNA of a Clovis child is ancestral to Native Americans.  Said another way, this Clovis child was a descendant, along with Native people today, of the original migrants from Asia who crossed the Bering Strait.

This paper, over 50 pages including supplemental material, is behind a paywall but it is very worthwhile for anyone who is specifically interested in either Native American or ancient burials.  This paper is full of graphics and extremely interesting for a number of reasons.

First, it marks what I hope is perhaps a spirit of cooperation between genetic research and several Native tribes.

Second, it utilized new techniques to provide details about the individual and who in world populations today they most resemble.

Third, it utilized full genome sequencing and the analysis is extremely thorough.

Let’s talk about these findings in more detail, concentrating on information provided within the paper.

The Clovis are defined as the oldest widespread complex in North America dating fromClovis point about 13,000 to 12,600 calendar years before present.  The Clovis culture is often characterized by the distinctive Clovis style projectile point.  Until this paper, the origins and genetic legacy of the Clovis people have been debated.

These remains were recovered from the only known Clovis site that is both archaeological and funerary, the Anzick site, on private land in western Montana.  Therefore, the NAGPRA Act does not apply to these remains, but the authors of the paper were very careful to work with a number of Native American tribes in the region in the process of the scientific research.  Sarah L. Anzick, a geneticist and one of the authors of the paper, is a member of the Anzick family whose land the remains were found upon.  The tribes did not object to the research but have requested to rebury the bones.

The bones found were those of a male infant child and were located directly below the Clovis materials and covered in red ochre.  They have been dated  to about 12,707-12,556 years of age and are the oldest North or South American remains to be genetically sequenced.

All 4 types of DNA were recovered from bone fragment shavings: mitochondrial, Y chromosome, autosomal and X chromosome.

Mitochondrial DNA

The mitochondrial haplogroup of the child was D4h3a, a rather rare Native American haplogroup.  Today, subgroups exist, but this D4h3a sample has none of those mutations so has been placed at the base of the D4h3a tree branch, as shown below in a grapic from the paper.  Therefore, D4h3a itself must be older than this skeleton, and they estimate the age of D4h3a to be 13,000 plus or minus 2,600 years, or older.

Clovis mtDNA

Today D4h3a is found along the Pacific coast in both North and South America (Chile, Peru, Ecuador, Bolivia, Brazil) and has been found in ancient populations.  The highest percentage of D4h3a is found at 22% of the Cayapa population in Equador.  An ancient sample has been found in British Columbia, along with current members of the Metlakatla First Nation Community near Prince Rupert, BC.

Much younger remains have been found in Tierra del Fuego in South America, dating from 100-400 years ago and from the Klunk Mound cemetery site in West-Central Illinois dating from 1800 years ago.

It’s sister branch, D4h3b consists of only one D4h3 lineage found in Eastern China.

Y Chromosomal DNA

The Y chromosome was determined to be haplogroup Q-L54.  Haplogroup Q and subgroup Q-L54 originated in Asia and two Q-L54 descendants predominate in the Americas: Q-M3 which has been observed exclusively in Native-Americans and Northeastern Siberians and Q-L54.

The tree researchers constructed is shown below.

Clovis Y

They estimate the divergence between haplogroups Q-L54 and Q-M3, the two major haplogroup Q Native lines, to be about 16,900 years ago, or from between 13,000 – 19,700.

The researchers shared with us the methodology they used to determine when their most common recent ancestor (MCRA) lived.

“The modern samples have accumulated an average of 48.7 transversions [basic mutations] since their MCRA lived and we observed 12 in Anzick.  We infer an average of approximately 36.7 (48.7-12) transversions to have accumulated in the past 12.6 thousands years and therefore estimate the divergence time of Q-M3 and Q-L54 to be approximately 16.8 thousands years (12.6ky x 48.7/36.7).”

Autosomal

They termed their autosomal analysis “genome-wide genetic affinity.”  They compared the Anzick individual with 52 Native populations for which known European and African genetic segments have been “masked,” or excluded.  This analysis showed that the Anzick individual showed a closer affinity to all 52 Native American populations than to any extant or ancient Eurasian population using several different, and some innovative and new, analysis techniques.

Surprisingly, the Anzick infant showed less shared genetic history with 7 northern Native American tribes from Canada and the Artic including 3 Northern Amerind-speaking groups.  Those 7 most distant groups are:  Aleutians, East Greenlanders, West Greenlanders, Chipewyan, Algonquin, Cree and Ojibwa.

They were closer to 44 Native populations from Central and South America, shown on the map below by the red dots.  In fact, South American populations all share a closer genetic affinity with the Anzick individual than they do with modern day North American Native American individuals.

Clovis autosomal cropped

The researchers proposed three migration models that might be plausible to support these findings, and utilized different types of analysis to eliminate two of the three.  The resulting analysis suggests that the split between the North and South American lines happened either before or at the time the Anzick individual lived, and the Anzick individual falls into the South American group, not the North American group.  In other words, the structural split pre-dates the Anzick child.  They conclude on this matter that “the North American and South American groups became isolated with little or no gene flow between the two groups following the death of the Anzick individual.”  This model also implies an early divergence between these two groups.

Clovis branch

In Eurasia, genetic affinity with the Anzick individual decreases with distance from the Bering Strait.

The researchers then utilized the genetic sequence of the 24,000 year old MA-1 individual from Mal’ta, Siberia, a 40,000 year old individual “Tianyuan” from China and the 4000 year old Saqqaq Palaeo-Eskimo from Greenland.

Again, the Anzick child showed a closer genetic affinity to all Native groups than to either MA-1 or the Saqqaq individual.  The Saqqaq individual is closest to the Greenland Inuit populations and the Siberian populations close to the Bering Strait.  Compared to MA-1, Anzick is closer to both East Asian and Native American populations, while MA-1 is closer to European populations.  This is consistent with earlier conclusions stating that “the Native American lineage absorbed gene flow from an East Asian lineage as well as a lineage related to the MA-1 individual.”  They also found that Anzick is closer to the Native population and the East Asian population than to the Tianyuan individual who seems equally related to a geographically wide range of Eurasian populations.  For additional information, you can see their charts in figure 5 in their supplementary data file.

I have constructed the table below to summarize who matches who, generally speaking.

who matches who

In addition, a French population was compared and only showed an affiliation with the Mal’ta individual and generically, Tianyuan who matches all Eurasians at some level.

Conclusions

The researchers concluded that the Clovis infant belonged to a meta-population from which many contemporary Native Americans are descended and is closely related to all indigenous American populations.  In essence, contemporary Native Americans are “effectively direct descendants of the people who made and used Clovis tools and buried this child,” covering it with red ochre.

Furthermore, the data refutes the possibility that Clovis originated via a European, Solutrean, migration to the Americas.

I would certainly be interested to see this same type of analysis performed on remains from the eastern Canadian or eastern seaboard United States on the earliest burials.  Pre-contact European admixture has been a hotly contested question, especially in the Hudson Bay region, for a very long time, but we have yet to see any pre-Columbus era contact burials that produce any genetic evidence of such.

Additionally, the Ohio burial suggests that perhaps the mitochondrial DNA haplogroup is or was more widespread geographically in North American than is known today.  A wider comparison to Native American DNA would be beneficial, were it possible. A quick look at various Native DNA and haplogroup projects at Family Tree DNA doesn’t show this haplogroup in locations outside of the ones discussed here.  Haplogroup Q, of course, is ubiquitous in the Native population.

National Geographic article about this revelation including photos of where the remains were found.  They can make a tuft of grass look great!

Another article can be found at Voice of America News.

Science has a bit more.

22 thoughts on “Clovis People Are Native Americans, and from Asia, not Europe

  1. Thank you so much for this thorough summary. Other items I’ve read online and in the news were obviously written by individuals without your specialized knowledge. I really learned a lot from reading this post.

  2. The match to the Central and South American people may have a connection to the migrations of the Hopi. This is outlined in the “Book of the Hopi”, by Frank Waters. This is really interesting. :)

  3. I am not so sure the solutrean connection does not exist. Actually we can not explain how they have been able to create such tools, the same as those used only in one place in the world : western Europe.
    Maybe this dna testing was not significally relevant of those population.

  4. Conflating the biology associated with this one individual with the cultural expression in tools and then concluding that all persons at the time of the Clovis tool-set culture are Asian derived is going too far with a hypothesis. If a determination as to the Solutreans as the possible originators of the Clovis tool-kit is to be made then an association between biology would better be determined from a more eastern or southeastern archaeological site. Most likely, if the two biological groups (European and Asian) met it would have been more westward in America. The Solutrean biological importance in America could well have been outweighed by their cultural presence evident in their tool-kit. This evidence does not offer exclusionary proof that there was not a minor Solutrean biological presence in the Americas which may be associated with the Clovis tool-kit and its spread into the overwhelming Asian majority.

    • There will never exist evidence that offers “exclusionary proof” of the absence of any admixture, any more than there will ever be evidence that ancient aliens never came to Earth to teach Homo Sapiens language and how to build pyramids, or that Bigfoot doesn’t exist. One can never prove absence until every last person on the face of the Earth is tested.

      • That’s quite true. It’s the problem you have with the historical sciences. But you can approach ‘certainty’ with better evidence/information. And I believe that biological evidence during that time period from a Clovis sites on the east coast or moving into Texas would better allow one to say that “Clovis people are native Americans from Asia not Europe” with a more positive degree to one’s hypothesis.

  5. I thought this paper had to do with Clovis Points and Central/South American DNA. Considering that the name Clovis is derived from Clovis, New Mexico and that most of the Anasazi descendants currently reside in Arizona and New Mexico; plus both the Hopi and Mayan claim kinship to each other then it reasonable to consider that the Clovis Points belonged to the person that was discovered in Montana.

    • I agree with you. My mitochrondrial DNA is D4h3a and my families are native to Arizona and New Mexico. I also thought the name
      , “Clovis” was pertaining to local native tribes in AZ & NM. There is nothing documented on native families linked to the same Mitochrondrial DNA D4h3a here in the southwest.

  6. I think it’s interesting how there are studies stating that the ancestors of Native Americans come from Asia, but there are some people who read the same studies and then saying that this is proof that Native Americans do not come from Asia. And that Native Americans have been in North America/South America since time immortal.
    Maybe it has come down to word games. In that case, maybe the question should be phrased as this, “where did the ancestors of the Native American ancestors come from?”
    Also, just as a pet peeve there is a difference between those who founded the country of the United States of America versus those who founded North/South America. Word games suck when they serve to confuse.

  7. Hi. I’ve recently returned from travelling and teaching in Southeast Asia. I am part woodlands Cree from my father’s side. We come from southern Ontario. What i noticed in Cambodia, where i spent several years was the how similar the looks and ways of the people there. They seemed to look a lot like Native people from North America especially the elders there. Just a thought i’d like to put out to you. Any comments? Charles.

  8. Pingback: Utilizing Ancient DNA at GedMatch | DNAeXplained – Genetic Genealogy

  9. The eyes have it! From the tip of South America to the Sammi Fins! just look at our eyes.The Asian Influence is what the evidence suggests, and just look into the eyes.

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