December 27, 2013

Reconstructing Native American migrations

Of wider interest might be the authors' estimation of the autosomal mutation rate as 1.44x10-8 mutations/bp/generation. Of course, this might depend on the archaeological calibration used (where/when did the bottleneck in the ancestry of Native Americans occur?). It might also depend on recent evidence that Native Americans are of mixed origin and thus did not really split from CHB/JPT; only part of their ancestry did. Nonetheless, this is another fairly "low" autosomal mutation rate.

(This was previously released as a preprint to the arXiv).

PLoS Genet 9(12): e1004023. doi:10.1371/journal.pgen.1004023

Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

Simon Gravel et al.

Link

25 comments:

Amy said...

Estimate of \mu also depends on complex ascertainment of 1kG. It would be hard to argue that this estimate is unbiased.

terryt said...

There is a huge amount here that German and Eastern View will disagree with, although they will probably be alone in that view. For example Dienekes' comment:

"It might also depend on recent evidence that Native Americans are of mixed origin and thus did not really split from CHB/JPT; only part of their ancestry did".

And from the link:

"People reached the Americas by crossing Beringia during the Last Glacial Maximum, likely between 16–20 kya"

Personally I found this interesting:

"People reached the islands around 7 kya, probably from a Mesoamerican source [11]. Around 4.5 kya, a second wave of migrants probably reached the islands, likely coming from the Orinoco Delta or the Guianas in South America and speaking Arawakan languages"

I guess everybody else already knew that.

German Dziebel said...

"recent evidence that Native Americans are of mixed origin"

There's no evidence that Native Americans are of mixed origin. Let me know when you uncover any.

Mark D said...

"Clearly, our model of a single idealized pre-Columbian Native American, European, and African populations, joining to form a panmictic admixed population, is an oversimplification. African and European ancestry proportions vary along the island [16] and eastern parts of Puerto Rico, with elevated proportions of African ancestry, are underrepresented in this study."

It is clear from the sample chart in Figure 2 that the PUR sample was mostly white and not at all representative of the population of Puerto Rico. I suspect this has to do with how the samples were obtained. I pointed out many months ago that a Ukrainian professor from the University of Puerto Rico was on the 1000 Genomes Sampling Committee. Knowing university professors and the limited time they have to obtain samples, I can believe that they may have been solicited from his students, rather than scientifically obtained as professional political pollsters do. Did 1000 Genomes even match their sample to US Census figures for Puerto Rico; I doubt it. 55 samples from a college campus should not IMHO form the basis of population genetics studies.

Gary Moore said...

When you get right down to it, virtually all populations are a result of admixture, including Europeans.

There is some cultural evidence to support the theory of a migration from South America through the Caribbean. The southeastern United States shows evidence of cultural diffusion from South America, including the use of blow guns and basketry techniques that are also found in the Orincoco basin and no where else.

Controversial DNA results of the testing of the remains at the Windover site in Florida found that the populations resembled South American populations more than North American populations. This also tended to confirm the long-held suspicions of linguists that the poorly attested language of the Ais tribe of eastern Florida may have been Awakan. (BTW - This study shows the perils of ADNA research in the US: the researcher's remarks that the Windover population was unlike contemporary native populations of the US was taken out of context by the racist right element and misrepresented as supporting their claim that an extinct 'ancient white race' had preceded the current Native American population.)

Niineta said...

"People reached the Americas by crossing Berengia during the Last Glacial Maximum, likely between 16–20 kya"

The timeframe of entrance into the Americas is unknown, so whether Amerindians were in the Americas pre-LGM and were pushed southward or if they skied over the glaciers on their moccasins during the LGM, the initial inhabitation of the Americas was in the south.

It’s common knowledge that the movement in North America was from south to north. Mesoamerica/southern United States is where the populations radiated from. Due to climatic conditions, the movement would have been southward then post LGM northward. Archeology supports this. To date, South America is where the oldest archeological sites are found, followed by Mexico and the southern US.

The genetic maps show the commonality of Amerindian populations is to South America not North America. Commonality seems to be recognized in all world populations, except in the Americas. They’ve simply been too busy trying to prove the Amerindians descended from modern East Asians. It’s obvious now that they didn’t. The Kiritiana (South American Amerindians) clearly attests to that.

It took 20 years for some in the scientific community to accept the Monte Verde date. It took 15 years for the Amerindian component in West Eurasians to even be mentioned.

It took one month to accept as fact; that Amerindians are hybrids, with a high West Eurasian admixture component, in spite of the fact there has never been any scientific evidence of ancient West Eurasian admixture in Amerindian.

Gary Moore said...

"Hybrid" is perhaps too strong a term and should be reserved for inter-specific admixture such as Neanderthals with Homo sapiens or Denisovians, in my opinion.

To the extent that the Beringian population is thought to have resulted from the merger of two population streams - one moving up the east coast of Asia and another moving northeast out of Siberia, they could be said to be an admixture of ancient East Asian and Central Asia populations. There now appears to have been a great deal of movement back and forth across the Eurasian steppes. Europeans are also an admixed population, with the mtDNA contributed mainly by populations from around the Mediterranean and the Caucasus. The major Y DNA components (R1a and R1b), on the other hand, came from Central Asia. HG I is thought to have been exclusively European, but it also occurs at lower levels in central Siberia, including the Altaian region. At the male DNA level, Native Americans and Europeans are in fact closely related.

It also appears that this relationship is reflected in their languages. Some researchers have claimed a relationship between Eskimo-Aleut and Indo-European, but it looks like IE and Iroquoian is a much better match based on numerous points of similarity between words in the two language families.

Rokus said...

"It took one month to accept as fact; that Amerindians are hybrids, with a high West Eurasian admixture component, in spite of the fact there has never been any scientific evidence of ancient West Eurasian admixture in Amerindian."

Maybe if the Native American community had shown itself traditionally more cooperative with genetic testing it would have been obvious from the start that humanity originated in Tierra del Fuego? This is "logic" against Mysticism the scientific community still doesn't know anything about.

Niineta said...

Maybe if the Native American community had shown itself traditionally more cooperative with genetic testing it would have been obvious from the start that humanity originated in Tierra del Fuego?

If the armchair scientific community spent more time reading the reports instead of jumping to conclusions perhaps they would be less inclined to promote so much misinformation.

The US tribes have been extensively tested and are more likely than any other North American population to be repeatedly tested. Following is a short list excluding Mexican & Canadian tribes.

Torroni A, (1992) - 167 American Indians, Navajo (48), Hopi (1), Pima (30)
Shields (1993) – Yakima (42)
Merriwether and Ferrell (1996) – Mohawk (123)

Lorenz and Smith (1996) - Washo (38), Yokut (17), Havasupai (18), Quechan (23), Kumeyaay (16), Hopi (4), Hokan (6), Bella Coola (36), CA Uto-Aztecan (14), Chumash (21)

Scozzari (1997) – Ojibwa (33)
Huoponen (1997) – Seminole (35)
Weiss (2001) – Creek (35), Choctaw (27)
Kaestle and Smith (2001) - Paiute (98)

Malhi, (2001) – Pima (43), Sioux (45), Cheyenne/Arapaho (35) Apache (38) Navajo (64). Chippewa (28), Pawnee (5), Cherokee (37), Zuni (26), Jemez (36) Micmac (6) Kiliwa (7) Wishram (20)

B Budowle, (2002) - Apache (180), Navajo (146)
Zegura, Stephen L. (2004) - 588 Native Americans from 18 populations.
anana (12), Apache (96), Navajo (78) Cheyenne (44), Sioux (44), Pima (24), Pueblo (18), Southwest Amerind (10)

Hammer, Michael F (2005) - Apache (86), Cheyenne (29), Navajo (88), Pima (19), South Dakota-Sioux (45), South Dakota (112), Vermont (19)

Bolnick, Deborah A. (2006) - Chippewa (51), Chippewa (37), Cheyenne/Arapaho (53), Chippewa (9) Shawnee (1), Micmac (1), Kickapoo (2) Fox (1), Sioux (27), Omaha (1), Cherokee (27), Cherokee (35), Chickasaw (6), Choctaw (12), Creek (15), Seminole (3)
Malhi, Ripan Singh (2008) - San Carlos Apache (23), Jemez (13), Akimal O'ohdam -Pima (38) Tohono O'ohdam - Papago (13)

Rokus said...

"the armchair scientific community"

More impressive may be the complete list of studies e.g. the National Congress of American Indians already preventend and still seeks to prevent:

http://www.ncaiprc.org/files/Genetics%20Research%20and%20AIAN%20Communities.pdf

This reluctance to cooperate has everything to do with the claim of an exclusive American origin, which is entirely political:

In a resolution passed at the NCAI Mid-Year Meeting in 2008, the members of NCAI call on the National Geographic Society to cease the Genographic Project because of its potential threats to Indigenous peoples.

The Havasupai Tribe alleged that ASU researchers collected blood samples for a genetics study of diabetes but then instead used the samples for a migration study which suggested the tribe’s ancestors originated in Asia.

Population genetics studies can be portrayed in a way that argues that a specific tribe is not “native” to U.S. lands because their ancestors originated outside North America.

For example, during litigation, some scientists theorized that based on the Kennewick man’s “Caucasoid” features, perhaps he was not “Native American” at all and thus did not fall under the jurisdiction of NAGPRA.

But no, maybe I was wrong to suggest that cooperation rather than obstruction would have helped the case for a Tierra del Fuego origin of humanity.

terryt said...

"'Hybrid' is perhaps too strong a term and should be reserved for inter-specific admixture such as Neanderthals with Homo sapiens or Denisovians, in my opinion".

Thee xpression 'hybrid' is commonly used for crosses between different breeds within a species, which in my opinion closely correlates with different regional human varieties. I see no problem with the use of the expression.

"When you get right down to it, virtually all populations are a result of admixture, including Europeans".

Very much so, and recent research has shown even modern humans are admixed with ancient groups. Unfortuanately scientists still haven't extracted the regional populations that are the centre of various population expansions that make up the hybrid nature of modern humans. It si 'possible' that America is one of those centres of expansion but the evidence for such is totally lacking in spite of what some contributors here would have us believe.

Niineta said...

But no, maybe I was wrong to suggest that cooperation rather than obstruction would have helped the case for a Tierra del Fuego origin of humanity.

Yes, you were wrong. Kennewick man was extensively studied, first by the anthropologists from the NPS/DOI; then by anthropologists at the Smithsonian Institute after winning the court case in 2004.

Between 1998 and 2000, the federal agency responsible for the Kennewick remains, conducted a series of scientific examinations. No fewer than 18 nationally/internationally recognized scientists/scholars conducted this variety of historical and scientific examinations, analyses, tests, and studies (Table 1)
http://www.nps.gov/archeology/kennewick/index.htm

Archeologists Win Court Case - February 5, 2004
http://www.cbsnews.com/news/archeologists-win-court-case/

The Smithsonian findings were made public in October, 2012.
http://www.dailymail.co.uk/news/article-2216392/Kennewick-Man-likely-Polynesian-definitely-Native-American-scientist-says.html

Results of the six year Smithsonian study:

1) The skull was most similar to Asian coastal people whose characteristics are shared with people of Polynesian descent.
2) Isotopes in the bones indicate Kennewick Man was a hunter of marine mammals.
3) Based on the Polynesian morphology and the marine diet; the conclusion was Kennewick man was not Native American.

The only reaction to the Smithsonian study:
A Burke Museum archaeologist is raising the alarm over the Smithsonian's science
http://crosscut.com/2012/11/02/science/111236/kennewick-man-critique/

The Polynesian morphology was known since the 2000 NPS/DOI studies yet, the Kennewick man is incessantly claimed as evidence of a pre-colonization European presence in the Americas. Interesting, since the Polynesians have yet to claim they were the original colonizers of the Americas.

Niineta said...

“Reconstructing Native American population history” (2012) reiterated what was known about the Americas. Yet it clearly demonstrated the researchers’ lack of knowledge of the relationships and movement of the populations under study.

Apparently they were unaware the study would encompass at least 2 distinct and separate populations. They had to rename one population “First Americans” to enable them to report their findings.

In spite of the disbelief of some, the population relationships and population movement in the Americas has long been known from archeological and anthropological studies.

This animation shows the direction and sequence of population movements.
http://www.arcticterritory.tv/great-territory/movements-of-the-first-peoples/the-thule-people-ancestors-of-todays-inuits.htm#en_01_10_03_01

This 2008 report demonstrates the gene flow/population movement in the Americas based on genetic relationships.
http://www.dnatribes.com/dnatribes-digest-2008-10-25.pdf

There are many studies from various fields, which demonstrate the directionality of population movement in the Americas. One would think researchers would look into what is already known about the populations they are about to study and how what is known might impact on their research.

But no, they simply choose to ignore any existing data, and report on what they think fits into their existing ideas/theory. It’s garbage in, garbage out, but, I guess that's what you call scientific logic.

Craig Hullinger said...

The migration of humans into America is getting more interesting all the time. It appears to me that Native Americans in northeast North America have had extensive migration from Europe or west Asia across the Atlantic. DNA testing will eventually prove or disprove this migration. More on this blog

http://dnaamerica.blogspot.com/

Annie Mouse said...

@Niineta
"This 2008 report demonstrates the gene flow/population movement in the Americas based on genetic relationships.
http://www.dnatribes.com/dnatribes-digest-2008-10-25.pdf"

That DNA tribes tree is completely impossible and does not fit in with any of the known science.

Truth is the Y haplogroups and mitochondrial haplogroups in the Americas are a subset of "Out of Africa", as the haplogroups in "Out of Africa" are a subset of African groups. America CANNOT be the source population. The people came from elsewhere.

Having said that a lot could have happened afterwards. From what I can see the dominant visible population movements in the Americas are NOT incoming flows, but expansion from two centres, roughly corresponding with the Incas and the Maya.

It is reasonable to expect that these folk expanded out into the rest of the world. Clearly they expanded west into Asia, and the Amerindian component in northern Europeans strongly suggests they moved east also, into Europe. Clearly some Amerindian women went East as mitochondrial haplogroups have been found in north eastern Europe.

That Amerindians are a subset of an Asian population is certainty from the science. But I sincerely doubt that there was a paleolithic "No Europeans Allowed" sign on the North Eastern entry point to the Americas. Prey animals traveled east into the Americas, it is not unreasonable to assume that their human predators followed. The problem is distinguishing between substantial colonial contamination and ancient input. Personally I am satisfied with the evidence that ancient Europeans contributed to the genetics of pre-Columbian North Eastern American tribes like the Iroquois.

However I am having trouble digesting the idea that Europeans contributed to deeply South American tribes like the Karitiana. The idea that the first folk poured in from the West and the East is not the problem, that seems reasonably possible. It is just that the suggested admixture does not seem to be reflected in haplogroups. In particular European mitochondrial haplogroups are not common in South America. Although there is some weird male G2. We shall see.

Niineta said...

That DNA tribes tree is completely impossible and does not fit in with any of the known science.

Truth is the Y haplogroups and mitochondrial haplogroups in the Americas are a subset of "Out of Africa", as the haplogroups in "Out of Africa" are a subset of African groups. America CANNOT be the source population. The people came from elsewhere.

It seems that when people have what they understand “about the peopling of the Americas” challenged. They switch from what they’ve been spoon-fed;

- the Americas was recently populated 20,000 years (max.).
- Amerindians are the descendants of “modern” East Asian.
- A small group(s) of Asians entered the Americas (by land or water) “rapidly” populating the double continent from the Artic to the tip of South America.

To . . . “Now you’re saying humanity (or at least Amerindians) originated in the Americas.
They seem to have only 2 options

- Amerindians arrived recently or,
- Amerindians originated in the Americas.

It never occurs to them, the migration of humans into the Americas might be an event of great antiquity.

The DNATribes link I provided (a combination of 2 previous reports), in their earlier report they stated the “genetic relationships” we find in the Americas are the same as in other world populations which are the result of population movement, admixture and diffusion and is not consistent with a rapid population expansion. (not a direct quote).

When you are looking at North America you are seeing “recent populations” post LGM, containing the genetic signature from the southern populations who likely continued to move southward/inland as the North American populations moved northward.

It’s possible the high Denisovan admixture detected in South America and the Karitiana-upper paleolithic Siberian connection may have provided some evidence of the antiquity of humans in the Americas.

But of course, antiquity doesn’t fit with what people want to believe.

Annie Mouse said...

@Niineta

So far as I can tell the Americas were populated from the first "Out of Africa" wave. My mind is open to when they arrived, as I beleive are other folk on this blog. Certainly the dates keep moving back now that Clovis-fixated scientists have retired.

I think a Beringia hiatus is part of the story although there are some questions here. And Polynesians clearly played a role.

I remember old pictures of residual Tierra del Fuego folk who looked very Australasian to me and very different from the rest of the Americas. They certainly looked like a very ancient population wave. People with a Australasian appearance (eg Australians) branched off the coastal population superhighway 50 kya.

At the moment my personal guestimate is that the first wave out of Africa just kept going east until they could travel no further (Tierra del Fuego). What happened after that is very unclear, spurts of NE Asians and Polynesians from the west and sprinkles of paleolithic Europeans from the east seems reasonable.

A European surge happened at some stage, possible with the Gravettian/Solutrean. Later a hardy, expansionist population in Beringia mass migrated chiefly into the Americas as the water rose, the glaciers melted and the climate improved. Followed by internal population explosions dominated by Maya and Inca -like folk. Arctic folk brushing the far north later.

With the exception of the North East, the pre-colonial Americas look to me like a predominantly Asian continent.

But the truth is frequently more interesting than reasonable guesses, and I look forward to the surprises.

terryt said...

"That DNA tribes tree is completely impossible and does not fit in with any of the known science".

I disagree entirely. It can be made to fit a very likely pattern of human expansion.

"the genetic relationships' we find in the Americas are the same as in other world populations which are the result of population movement, admixture and diffusion and is not consistent with a rapid population expansion".

I would guess that very few times in human history have populations expanded instantly. We know from the study of species' introduction to new environmnets there is a variable period of population buildup before any expansion. And after an initial expansion we usually have a series of expansions within the populated region. The haploid DNA easily fits such a scenario.

"It took one month to accept as fact; that Amerindians are hybrids, with a high West Eurasian admixture component, in spite of the fact there has never been any scientific evidence of ancient West Eurasian admixture in Amerindian".

The Y- and mt-DNA has always shown Amerindians to be a hybrid between a Y-DNA Q, presumably not east Eurasian in origin, and a set of predominantly eastern mt-DNAs. I agree with Annie:

"Having said that a lot could have happened afterwards. From what I can see the dominant visible population movements in the Americas are NOT incoming flows, but expansion from two centres, roughly corresponding with the Incas and the Maya".

Tobus said...

@Niineta and Annie:
Polynesians are a very recent population, leaving Taiwan roughly 5000 years ago and spreading through the pacific... any "Polynesian" affinity seen in ancient Amerindians is really East Asian, geographically speaking.

Sweet potato genetics shows it's likely there was contact between southern Amerindians and the Polynesians on Rapa Nui (Easter Island) in the last 1,000 years or so, however AFAIK no human DNA has been shown to be exchanged... this is a long time after Kennewick Man.

fmgarzam said...


About "dominant visible population movements in the Americas" mentioned by Annie and terryt:
There seems to be two kinds of movements, say one being the originating, probably of uninterrupted flows; and later rearrangement flows. Obviously there must have been some natural disaster originated rearrangements or intermigrations.
But what I read there a displacement, groups of a higher degree of civilization sort of vanquishing or displacing other groups, usually the ones with a lower degree of civilization that had lived in nicer places to live.
That would explain the Maya and the Inca phenomena. But there must be some other cases. I, being a Mexican, can clearly quote the Aztec example, them displacing the others from a good part of the high plains.
Something was mentioned here a few weeks ago about Aztec DNA, mtDNA?, displacing others. What is now Mexico city was taken over by the Aztecs. It is well known they came from north of the city, but not how far.
I have always toyed with the question if this could be the case of a more recent Asian migration of people with a higher degree of civilization. (By that I mean a higher degree of development within the same culture or comparatively with a parallel culture not much different.) How about a different two thousand year old Asian Expansion instead of the usual twenty thousand. Them finally arriving there 600 years ago and building an incredible city, something like what one good friend, during his Tibetan phase, heard from a high-ranking monk mentioning the similarities of Srinagar, Kashmir with Xochimilco and its ancient way of life, and right close to the heart of Mexico city. Is it possible that the Aztecs were closely related to the Srinagar people and its culture?
Why they did not expand north? It is an easy one. Why leave paradise, that is what Mexico City is, an eternal spring. No extreme temperatures of north. Not much to take away from wild Chichimecas and hunters and gatherers of north. Why go to Aridamerica?
Obviously of the highly civilized (not talking behaviour) white men changed everything.
Yet there are a lot of remote places where neither the highly civilized Native American nor the white men ventured. Where people still dwell very close to how it was before 1492.


terryt said...

"That DNA tribes tree is completely impossible and does not fit in with any of the known science".

Sorry. Wrong tree. I agree that the tree Niineta linked to cannot be made to fit 'with any of the known science'.

Niineta said...

impossible and does not fit in with any of the known science".

Sorry. Wrong tree. I agree that the tree Niineta linked to cannot be made to fit 'with any of the known science'.


Yes, that tree is very strange; it's not like the tree in the previous report. I can’t imagine how the data contained in their various reports supports that.

But what I wanted to demonstrate was the genetic relationships of the populations in the graphics. I pulled the graphics out but I couldn’t link to them, so I linked to the report.

The point I was making is the population movement in North America is South to North. Which is the reverse of the commonly held belief, and the directionality of population movement does have an impact on research.

Niineta said...

I didn’t actually read the caption, before my response but,

The tree is not demonstrating the “genetic relationships” of the populations but rather the “distance” of the genetic relationships.

terryt said...

"The point I was making is the population movement in North America is South to North. Which is the reverse of the commonly held belief"

True, but it by no means follows that the entry point was in the south. A coastal expansion south and subsequent expansion inland would do it. But even an expansion overland from Beringia and subsequent depopulation of the north would also explain the expansion direction.

terryt said...

I just redisovered this paper on 'Reconciling migration models to the Americas with the variation of North American native mitogenomes'. I'm sorry but I can't remember who brought it to my attention originally:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3761611/

Those who haven't seen it will find it interesting I'm sure.