July 11, 2012

Reconstructing the origin of Native American populations

A new paper by Reich et al., which echoes the title of a previous one by many of the same authors on India looks at the issue of Native American origins. Nicholas Wade has some good coverage of the new research at the NY Times:
North and South America were first populated by three waves of migrants from Siberia rather than just a single migration, say researchers who have studied the whole genomes of Native Americans in South America and Canada.
I have an informed hunch that this will not be the last paper in the Reconstructing... series.

The supplementary material (pdf) is open access, and lists the data used, some of which has been taken from the literature and some of which is new. There is apparently also a new ADMIXTUREGRAPH software used in a paper which seems to parallel a little the functionality of TreeMix. I don't see a download option for this software yet; perhaps Joe Pickrell who co-authored TreeMix and is now in Harvard may chime in about the differences/applicability of the two pieces of code.

UPDATE: And here is the press release:
Two striking exceptions to this simple dispersal were also discovered. First, Central American Chibchan-speakers have ancestry from both North and South America, reflecting back-migration from South America and mixture of two widely separated strands of Native ancestry. Second, the Naukan and coastal Chukchi from north-eastern Siberia carry 'First American' DNA. Thus, Eskimo-Aleut speakers migrated back to Asia, bringing Native American genes.
Interestingly, I have detected some of this "Native American" component in the Chukchi as part of my world9 calculator.

UPDATE II: Of course, if you look at the map of the sampled populations, you'll notice one big hole: the USA. Petty identity politics contra science? Data on Native groups outside the US have been studied for years, and I doubt that the sky will fall over the heads of the new Canadian and South American groups that participated in this particular study. Hopefully, one day the big hole will be filled, although I'm not holding my breath of that happening anytime soon.

Nature (2012) doi:10.1038/nature11258

Reconstructing Native American population history

David Reich et al.

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1, 2, 3, 4, 5. One contentious issue is whether the settlement occurred by means of a single6, 7, 8 migration or multiple streams of migration from Siberia9, 10, 11, 12, 13, 14, 15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call ‘First American’. However, speakers of Eskimo–Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

Link

19 comments:

Maju said...

Hmmm, not even a hunch of Neolithic flow between North and South America. How is it even possible?! Why are Native Americans different in this than West/South Eurasians or, separately, East/SE Asians?

Are they?

In fact the lack of such post-Neolithic flows may well help by comparison to estimate IF there was any Neolithic genetic flow and how much elsewhere.

Dienekes said...

There's nothing in this paper that would either confirm or disprove gene flow at any particular time period between the descendants of the 'First Americans'.

shenandoah said...

It's unfortunate that politics is allowed to hinder science. Bryan Sykes is clearly not intimidated or afraid to state the facts:

"Professor of Human Genetics at the University of Oxford since 1997, Bryan Sykes, discussed some of his fascinating DNA research findings, including his study of American genetics. The United States' population contains a convergence of DNA from a number of continents, with interesting crossovers such as some African Americans having European genes. According to earlier research (not done by Skyes), Native Americans actually originated from Siberia, China, ***and even Europe***, but the DNA blood testing that yielded these results was done without their consent, and thus raised controversy and ire, he detailed. ***Interestingly, some people from Britain have been found to have Native American genes, he added.***

"Sykes described his work on the "Seven Daughters of Eve." Astonishingly, almost everyone in Europe has mitochondrial (maternal) DNA they inherited from one of seven actual women who lived between 10,000 and 45,000 years ago. Additionally, there are "36 maternal ancestors spread throughout the world," he noted. It's suspected that Genghis Khan also established a legacy, with his particular Y chromosome shared among some 15 million males in Asia. The Y (male) chromosome in general has been subject to more degeneration and mutation than the X (female) chromosome, and if this continues males might eventually become extinct, he warned.

"In his latest project, Sykes is doing DNA testing of suspected Yeti and Bigfoot hair samples in tandem with the University of Lausanne in Switzerland. So far, some of the samples have turned out to be from bears. If the results indicate an unknown species, he said could compare DNA sequences and place the species somewhere on the evolutionary tree, such as between chimps and humans. Recent evidence has shown that in addition to Neanderthals, there were other human-type species living concurrently with homo sapiens, and Sykes posited that Bigfoot and Yeti might be "small relic populations of these other human species."

I emphasized what was to me the most interesting points in this newsletter from a radio show on which Sykes was recently a guest; but included the rest of the message, based on its possible future relevance to the same question.

Sykes has sterling credentials, and I believe most criticisms of him by (self identified) "genetic genealogists" are rooted in politics.

Maju said...

From the abstract:

We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America.

No Mexicans migrating into Peru with maize. Actually this matter of apparent low or zero genetic flow with American Neolithic has previously been found to be the case SW USA as well, although here on archaeological grounds.

eccles said...

I do wonder whether any Fuegan populations were included in this study, especially in terms of characterising the migrations

Annie Mouse said...

I think there is a problem here distinguishing between post Columbian admixture into the Canadian and North American Amerindians, from pre-Columbian European stock, possibly aboriginals, from Western Europe.

Basically I think many North American natives have been shocked by their European ancestry and there are economic and identity consequences. Most of this is I think post-Columbian.

But from what I have seen in previous genetic studies, there is evidence that some North Eastern tribes (eg Iroquois) may have had significant European content pre Columbus. This does not have to be Vikings (although there is actual oral history for this) but just regular bidirectional population flow via Iceland. This would also explain some of the American cropping up in North West Europe.

I guess the politics of this all makes it easier to just leave the North Americans out to make the picture clearer.

andrew said...

The paper seems to largely confirm existing scholarship.

As to the blank in the USA, I think that the problem here is with the lack of availability of data and not the researchers.

The Native American population of North America was disrupted more profoundly and in more fine detail than either the Spanish-Portugese ruled parts of the Americas, or Canada which had vast swaths of land less favorable to the colonial era economy.

Overall there was 90% population loss, but locally, some groups were hit much harder. There are many examples of tribes attested by early explores vanishing without a trace in a single generation. Only a dozen or two remaining tribes have more than a thousand identified members in a nation of three hundred million current residents, and most of those tribe members are deeply integrated into the larger non-indigenous society to a much greater extent than in Latin American, Alaska or Northern Canada. The genes of rest of the survivors of European contact have introgressed into the general population and been diluted profoundly. I don't think there are any tribes in the entire U.S. (and there are surely very few, if there are any) where a majority of members have even 50% indigeneous ancestry, let alone 50% indigeneous ancestry from that tribe's linguistic and geographic region.

For example, there are essentially no intact Native American linguistic communities in or derived from any of the states in the American South with the possible exception of Florida (which was Spanish ruled until the end of the 19th century). A concentration of multiple indigeneous tribes with roots across the U.S. in reservations in places like Oklahoma also led to a pan-Native American identity that promoted in group admixture between previously endogamous tribes destroying the resolution of population genetic measures of living people with Native American ancestry to resolve pre-colonial regional distinctions at anything to the highest levels of generality.

Absent ancient DNA finds, regional patterns in North American indigenuous populations that haven't been found already are probably irretrievably lost.

Dienekes said...

As to the blank in the USA, I think that the problem here is with the lack of availability of data and not the researchers.

I'm sure the researchers would have loved to get data if they could.

The techniques used in this paper would have been applicable to individuals with mixed ancestry. As mentioned in the Nicholas Wade piece:

"The team’s samples of Native American genomes were drawn mostly from South America, with a handful from Canada. Samples from tribes in the United States could not be used because the existing ones had been collected for medical reasons and the donors had not given consent for population genetics studies, Dr. Ruiz-Linares said. Native Americans in the United States have been reluctant to participate in inquiries into their origins. The Genographic Project of the National Geographic Society wrote recently to all federally recognized tribes in the United States asking for samples, but only two agreed to give them, said Spencer Wells, the project director."

Annie Mouse said...

Yaghan are Fuegan. But I think you are thinking of those intriguingly negrito-like folk from Tierra del Fuego.

Charles Nydorf said...

Its interesting that, in the early 20th century, Franz Boas used cultural features to infer back migrations from South American to North America and from North America to Siberia.

Native New Yorker said...

Bull plucky.... how can we make sense of this when Charles C. Mann in his book titled "1491: New Revelations of the Americas Before Columbus" debunks this land bridge myth?!?!? I have a strong feeling these non-Native scientists that are so tied to this land bridge theory is because it is rooted in the their christian dogma with biblical text of the tower of Babel. Western science should really take up the interconnected relation between itself and christainity. The questions that Vine Deloria brings up in his writings would give them a good place to start this discussion.

As a First Nation person, this land bridge theory and its non-Native supports is very problematic for us. As it is used to justify the colonization of the first peoples on this because we too are then viewed as colonizers and therefore do not have rights to this land, then it became an issue of might make right.

Once agian, a response to Mann and Deloria is required!

Jason Antrosio said...

Hi, this question is for Charles Nydorf--do you have any references on the Boas statement? I'm interested in a follow-up.

Jim said...

"But from what I have seen in previous genetic studies, there is evidence that some North Eastern tribes (eg Iroquois) may have had significant European content pre Columbus"

There was a Basque cod fishery in the western Atlantic for centuries before Columbus, and quite likely Norwegians and Icelanders went out that far too. It beggars belief that none of them ever landed.

The term "Iroquois" has no solid etymology. Not only is it not an autonym, but it has no uncontroversial origin in any neighboring language, but there is one theory that says it is the Basque form of a Cree or Ojibwe gentilic, with a pretty unsavory translation, as is typical in N. America.

"Western science should really take up the interconnected relation between itself and christainity"

Native New Yorker should really acqauint himslef with the very, very vexed history between western science and Christianity. He will sound less naive and uninformed then.

"As it is used to justify the colonization of the first peoples on this because we too are then viewed as colonizers and therefore do not have rights to this land, then it became an issue of might make right. "

Since almost no one outside the perpetual blood-pit of the Middle East thinks that aboriginal land claims trump all others, this is a trivial consideration. Native nations have rosck-solid land rights recognized in treatiesd, however much they have been abrogated by bureaucratic misconduct, and these rights do not resat on anyone's perception of who is or isn't a colonizer. In the eastern part of the US many populations in place when the englsih arrived were in fact colonizers - the Cherokees are a clear example of this - but it signifies not at all when it comes to the validity of their land claims.

Maju said...

@Native New Yorker: with all due respect, Humankind has one single origin and is not in America (actually in Africa and there's LOTS of evidence supporting it). As some scientifically minded Native American put it in a documentary I saw recently can't we agree that the "always" of some Native American traditions just means "a very long time" (15-20 thousand years)?

Regardless: the land bridge was and is still there but most probably the colonization was actually by means of coastal boating.

First of all you should address the phylogeny of our lineages, which is quite unmistakably branded in our genes. That seems much more important to me than whether there was or not a land bridge (which seems quite real but less relevant than you may think - your ancestors probably boated along the coast rather than merely walked).

...

@Jim:

"There was a Basque cod fishery in the western Atlantic for centuries before Columbus".

Actually not. The first unmistakable evidence of Basques fishing at Newfoundland is from 1512. It is speculated that they were exploiting the Great Banks before Columbus (and even that Columbus may have been inspired by such knowledge of land across the Atlantic) but this is unproven as of now.

"It beggars belief that none of them ever landed".

Actually they did not establish colonies (initially) but they did land once and again to salt the cod and prepare the whale blubber. They traded with the natives but there was no actual settlement until later, being part of the process of formation of New France (the seed of today's Canada).

Native New Yorker said...

Jim, I question most of what you have to say.... the cited Iroquois (the Haudenosaunee) or Cree (the nēhiyawēwin) examples are both French words... After 12 years of school (secondary) and then another 4 years (post-secondary) where I graduated top of my department and as the valedictorian, I believe I am firmly rooted and knowledgeable of the Western perspective. While I value this education, I hold my education that I receive from my elders with a much higher esteem. Perhaps, if you also invest 16 years to study our ways, then you perhaps you may would understand where I am coming from.

I’m going to go out on a limb and say that the 16 year option is not really that realistic for you – in our ways it would probably take about half of the time meet (a somewhat easy step) and then win the trust of an elder (a most challenging step). Here’s what I like to humble suggest. Here are three great books by Vine Deloria, Jr. that may give you a peep in our world….

Spirit & Reason: The Vine Deloria, Jr., Reader

God Is Red: A Native View of Religion, 30th Anniversary Edition

Evolution, Creationism, And Other Modern Myths

If you take the time and read any of the above books, I would more than happy discuss them with you. This offer I extend offer to anyone else that reads this.

Jim said...

"Jim, I question most of what you have to say.... the cited Iroquois (the Haudenosaunee) or Cree (the nēhiyawēwin) examples are both French words"

Neither one of them can possibly be French words except as loanwords. That was my point. The etymology of "Iroquois" is not settled, and the fact that the word has a French form does not change that. I suspect that despite your education you will not be able to follow a lingusitcs discsussion, so I will leave the matter.

"Perhaps, if you also invest 16 years to study our ways, then you perhaps you may would understand where I am coming from."

I am not interested in learning someone's belief system, whether that be at Liberty College of anywherre else. Belief systems will not resolve matters of fact, the matter of fact in this case being the origin of certain populations. Your position seems to be an origin in North America, which as Maju points out above, is an assertion that Native Americans are not human. I will not accpet that racist position.

@Maju

"There was a Basque cod fishery in the western Atlantic for centuries before Columbus".
Actually not. The first unmistakable evidence of Basques fishing at Newfoundland is from 1512"

Actually cod fishermen had every reason to keep their fishing grounds secret and absolutely no reason to record them - simple busienss sense - so it unsurprising that records would be late or even non-existent.

"Actually they did not establish colonies (initially) but they did land once and again to salt the cod and prepare the whale blubber. "

Yes. Adopting one name for a local political entity doesn't require much contact at all.

Maju said...

The location may be interesting to keep secret, Jim, but business include registries and accounts and would have left charcoal on shore that can surely be dated by radiocarbon (nothing so far). And anyhow at the time the main Basque fishery was Ireland.

Also it is very likely in my humble opinion that the discovery of Newfoundland (and Atlantic Canada) was not specifically a Basque-only feat but something shared by various peoples of Western Europe from Portugal to Ireland, all of which were traditionally meeting each other on various fishing grounds and mariner adventures.

The semi-mythical mentions (by Portuguese mostly) to the Island of Bacallao (cod) are the main sources about a previous knowlege of NE America. The oldest certain written reference is from 1508 however, making a pre-Columbian knowledge still not demonstrable.

More interesting are the Irish references to Hy Brasil, which is said to have been actually discovered by Bristol sailors in the 1480s, and later "officially" by John Cabot.

It is therefore very possible that Basques just used their diverse contacts with other Atlantic Europeans to reach Newfoundland, either before or after Cabot's travels. If it was a pre-Columbian arrival (possible in the case of the Bristol sailors), then it was not for much and it may have been part of the semi-secret knowledge that the Genovese sailors Columbus and Cabot had before they set sail to become famous.

The "Basque" geography of Newfoundland includes toponyms that clearly inform of the presence of other peoples like Galicians (quasi-Portuguese), Gascons, Bretons and generic French and Spaniards.

Whatever the case the word "Iroquois" does not look Basque at all to me. The form looks "French" (ending in -ois, like Quebecois, François, etc.) The root would be Iroqu- but that's not Basque either.

andrew said...

"The techniques used in this paper would have been applicable to individuals with mixed ancestry."

Only to the extent that the source of the mixed ancestry is known and can be attributed to a particular geographic or tribal (or macro-tribal linquistic) source. Many mixed ancestry Native Americans in the U.S. can't be more specific about their origins than "North American" or Western v. Eastern U.S., many have ancestry from multiple distinct Native American sources, and the apocryphal beliefs that individuals have about the source of their Native American ancestry, if they have it is very often inaccurate. A study could probably be pretty accurate in pinning down anything particular about North American native ancestry relative to South American ancestry, but accurate distinctions at a finer level may be challenging to achieve even with cooperation.

Some of the privacy issues flow from legal rules that are closely linked to the absence of universal health care in the United States. If a disease linked gene were linked to Native American ancestry in published academic papers, it would provide a strong argument for health insurance companies to charge higher rate to people with Native American ancestry than to other people, and it is quite possible that genetic predispositions to conditions such as alcoholism could indeed be found in the Native American population.

Solís said...

Do they even show in this paper where in Asia does the First American migration came from?