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Tomenable
12-04-17, 12:49
1) Pre-Columbian samples:


http://i.imgur.com/eInWQ6Z.png


http://i.imgur.com/PH6TG8S.png


http://i.imgur.com/3D3fNuT.png


http://i.imgur.com/lKS6xow.png


http://i.imgur.com/GJ12uOz.png


http://i.imgur.com/nzOIJxQ.png


http://i.imgur.com/ntwZnHb.png


http://i.imgur.com/REeNB4n.png


2) Modern Native Americans:


http://i.imgur.com/8WOEADO.png


http://i.imgur.com/NMJ0EYG.png


http://i.imgur.com/PeBtmnS.png


http://i.imgur.com/h1kYtxV.png


http://i.imgur.com/1LGdYlN.png

Tomenable
12-04-17, 12:50
I also found modern Mayans scoring few percent of "Malayan" admixture.

The same "Malayan" admixture was present in two Botocudos (Bot15 & 17).

Tomenable
12-04-17, 13:00
Some explanations from Davidski regarding admixtures in Eurogenes K36:


An important point to keep in mind is not to take the ancestry proportions in Eurogenes K36 too literally. If you're, say, English, and you get an Iberian score of 12% this doesn't actually mean you have recent ancestry from Spain or Portugal. What it means is that 12% of your alleles look typical of the reference samples classified as Iberian, and this figure might only indicate recent Iberian admixture if it's clearly higher than those of other English users. But it calculates deep root similarities more than real recent ancestry.

So I wonder why is Kennewick Man scoring European & African admixtures?

Tomenable
12-04-17, 13:17
Those Botocudos were Polynesians (who are a mix of Taiwanese, South-East Asian and Oceanian):

"Two ancient genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil":

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370112/

"Identification of Polynesian mtDNA in remains of Botocudo Amerindians from Brazil":

http://www.pnas.org/content/110/16/6465.full

Moreover, they were fully Polynesian (not mixed with Amerindians, Europeans, or Africans):

"Botocudo Ancient Remains from Brazil":

https://dna-explained.com/2015/07/02/botocudo-ancient-remains-from-brazil/


The second interesting aspect of the genomic sequencing is that the remains did not show any evidence of admixture with European, Native American nor African individuals. More than 97% of their genome fits exactly with the Polynesian motifs. In other words, they appear to be first generation Polynesians. They carry Polynesian mitochondrial, Y and autosomal (nuclear) DNA, exclusively.

https://dnaexplained.files.wordpress.com/2015/07/botocudo-not-admixed.png

http://www.popularmechanics.com/technology/a21796/ancient-polynesian-trade-routes-extended-for-thousands-of-miles/


Recent DNA has shown trading based out of Polynesia extended as far as South America and the Caribbean, but there have been questions to the exact timing. European traders are often thought to have led the spread of commerce across the globe, enabled by early Spanish and British explorers—but the actual story may be a bit more complex.

Also Polynesians from Easter Island have Amerindian admixture:

"Oceanian Genetics - Beginners Guide and FAQ":

http://www.anthrogenica.com/showthread.php?7766-Oceanian-Genetics-Beginners-Guide-and-FAQ


I am Polynesian however score some Native American. What does this mean?

Polynesians from Easter Island and natives of South America met and mingled long before Europeans voyaged the Pacific. One study by Erik Thorsby suggests Native Americans likely arrived on Easter Island shortly after Polynesians. Other scientists’ state Pacific currents and Polynesian mastery of the waves make it more likely that the Polynesians were the voyagers. They may have sailed to South America, swapped goods for sweet potatoes and other items—and returned to their island with South American women. It is possible those Polynesians on Easter Island traveled back west to trade with east Polynesian countries. As you can see there are many possibilities.

You may have had a Native American ancestor, but unless you score a good chunk of it on an autosomal test, it will be hard to confirm. The study by Thorsby stated that in the 27 living Easter Islanders who were tested, there was around 8% Native American in their genomes.

LeBrok
12-04-17, 17:29
Nice compilation of Amerindians DNA. The picture becomes clearer and clearer.
Unfortunate is naming Siberian admixture, if most of it comes from NE Asia, the Beringia region.


Paleo Eskimo Q1a

Q-Z780



F999906


F999919
Clovis-Anzick-1


Greenland
4kya

N America, Montana
12.5kya


Run time
14.29

Run time
18.2


S-Indian
1.1

S-Indian
-


Baloch
2.66

Baloch
0.49


Caucasian
-

Caucasian
-


NE-Euro
7.4

NE-Euro
1.51


SE-Asian
0.48

SE-Asian
1.05


Siberian
26.12

Siberian
1.17


NE-Asian
12.11

NE-Asian
0.18


Papuan
-

Papuan
0.23


American
1.38

American
88.41


Beringian
40.04

Beringian
5.25


Mediterranean
1.33

Mediterranean
0.68


SW-Asian
0.42

SW-Asian
-


San
-

San
0.17


E-African
0.33

E-African
-


Pygmy
-

Pygmy
0.09


W-African
6.62

W-African
0.76




Interesting are Botocudo, clearly Polynesians of late arrival to America and completely unmixed with older population of South America. They must have sailed around the America to the other side.

Eskimo look like fairly late arrival, and with agreement with archeology.

PaleoRevenge
17-04-17, 03:23
Some explanations from Davidski regarding admixtures in Eurogenes K36:



So I wonder why is Kennewick Man scoring European & African admixtures?


What could the results possibly mean, they must mean something other than what they show because........muhhh racism. Kennewich was a watered down Solutrean, well not exactly since his Y-haplotype was obviously Siberian, but he had a Solutrean mgh. He was relic population, a transition after the Clovis were defeated by the Siberians, an intermediate population who defeated the Clovis but in turn were defeated by purer Amerindians. A mirror to the events that occurred in the Central Asia, Turks replacing the Scythians, and the Mongols replacing the Turks.

Genetiker
17-04-17, 07:15
What could the results possibly mean, they must mean something other than what they show because........muhhh racism. Kennewich was a watered down Solutrean, well not exactly since his Y-haplotype was obviously Siberian, but he had a Solutrean mgh. He was relic population, a transition after the Clovis were defeated by the Siberians, an intermediate population who defeated the Clovis but in turn were defeated by purer Amerindians. A mirror to the events that occurred in the Central Asia, Turks replacing the Scythians, and the Mongols replacing the Turks.

You're talking nonsense.

Kennewick Man is "scoring European & African admixtures" because the results posted by Tomenable are crap.

No haplogroup X has been found in the many pre-Neolithic European mtDNA samples, which makes the probability that the X2a in Kennewick Man came from the Solutreans slim to none.

It's infuriating to me, two years after my discovery (https://genetiker.wordpress.com/2015/08/08/analyses-of-ancient-american-genomes/) of genuine European admixture in a 6,000-year-old American sample, and a month after I showed (https://genetiker.wordpress.com/2017/03/20/high-resolution-k-13-analysis-of-the-european-admixture-in-chinchorro-dna/) that admixture to come from pre-LGM or Solutrean Europeans, that instead of people spreading the news of my discovery, the most important ancient DNA discovery that has ever been made, we have people like yourself still going on about Kennewick Man, two years after analysis of his DNA showed him to be a run-of-the-mill Amerindian.

Tomenable
17-04-17, 11:22
No haplogroup X has been found in the many pre-Neolithic European mtDNA samples, which makes the probability that the X2a in Kennewick Man came from the Solutreans slim to none.

But Native American Y-DNA C2b1a1a-P39 could potentially be Solutrean. Pre-Magdalenian Europe was dominated by YDNA haplogroup C, as recent studies (e.g. Fu et al. 2016, "The Genetic History of Ice Age Europe") show.

I. Native American mtDNA includes:

1) Typically East Asian mtDNA:

A2
B2
D1
D2a
D3
D4h3a
D4e1c

2) West Eurasian (might be also ANE) mtDNA:

X2a
X2g

3) Either Ancient North Eurasian (ANE) or East Asian:

C1b
C1c
C1d
C4c

II. Native American (and Inuit) Y-DNA includes:

Q1a2a1-L54
Q1a1a-F746
C2b1a1a-P39

These Y-DNA haplogroups could be from any group, not just from Mongoloid East Asians.

Haplogroup Q1a could be from Ancient North Eurasians (who were mostly "Caucasoid").

Hg C2b1a1b-F3985 - closely related to Native American C2b1a1a-P39 - can be found among modern Europeans (samples from Germany, Slovakia, Austria, Czech Rep. and Poland). It might be Solutrean.

C1b is also typical for Australian Aborigines. Maybe C2b was from Onge-like admixture?

Tomenable
17-04-17, 11:39
No haplogroup X has been found in the many pre-Neolithic European mtDNA samples

Mind you, that no actual Solutrean samples have been published so far! We have Aurignacian, Gravettian and Magdalenian samples - but no Solutrean. What if mtDNA X existed in Solutrean Europe and after the demise of Solutrean culture it went extinct in Europe? Then it could be re-introduced into Europe with Neolithic or Steppe immigrants.

holderlin
17-04-17, 17:06
You're talking nonsense.

Kennewick Man is "scoring European & African admixtures" because the results posted by Tomenable are crap.

No haplogroup X has been found in the many pre-Neolithic European mtDNA samples, which makes the probability that the X2a in Kennewick Man came from the Solutreans slim to none.

It's infuriating to me, two years after my discovery (https://genetiker.wordpress.com/2015/08/08/analyses-of-ancient-american-genomes/) of genuine European admixture in a 6,000-year-old American sample, and a month after I showed (https://genetiker.wordpress.com/2017/03/20/high-resolution-k-13-analysis-of-the-european-admixture-in-chinchorro-dna/) that admixture to come from pre-LGM or Solutrean Europeans, that instead of people spreading the news of my discovery, the most important ancient DNA discovery that has ever been made, we have people like yourself still going on about Kennewick Man, two years after analysis of his DNA showed him to be a run-of-the-mill Amerindian.

I think most people assume that this chunk of alleles is shared ancestry among European and Siberians, probably having to do with MA-1 or Afontova Gora

holderlin
17-04-17, 17:11
Mind you, that no actual Solutrean samples have been published so far! We have Aurignacian, Gravettian and Magdalenian samples - but no Solutrean.......

Yes, conspicuously absent from the landmark paper revealing the Villabruna cluster. I'm very curious about Solutrean and I'm willing to bet we see even earlier Villabruna-like samples here. I'm only basing this on their apparent penchant for being the the best refugia, which is where we see Solutrean.

Maybe this is that Paleo-Iberian R1b that all the anti-yamnaya people have hoped for.

Genetiker
18-04-17, 03:18
But Native American Y-DNA C2b1a1a-P39 could potentially be Solutrean. Pre-Magdalenian Europe was dominated by YDNA haplogroup C, as recent studies (e.g. Fu et al. 2016, "The Genetic History of Ice Age Europe") show.

All the C in ancient European samples is C1, not C2.


Hg C2b1a1b-F3985 - closely related to Native American C2b1a1a-P39 - can be found among modern Europeans (samples from Germany, Slovakia, Austria, Czech Rep. and Poland). It might be Solutrean.

The TMRCA of C2b1a1-F3918 is 13,300 years ago, so it couldn't possibly be Solutrean.

Genetiker
18-04-17, 03:25
Mind you, that no actual Solutrean samples have been published so far! We have Aurignacian, Gravettian and Magdalenian samples - but no Solutrean.

Table R81 on pages 531 and 532 of this document (http://www.tdx.cat/bitstream/handle/10803/795/05.TESIS_EFD_RESULTADOS.pdf) includes two mtDNA samples, 2NE and 3NE, that are said to be from a Solutrean layer in the Caves of Nerja, near the southern Mediterranean coast of Spain. Only parts of HVR-I were sequenced.

2NE was assigned to haplogroup J*. It has the mutation 16126C, one of three that defines JT. It lacks 16294T, one of the mutations that defines T.

3NE wasn't assigned to a haplogroup. It has the mutation 16192T, which is one of the two that defines U5, but it lacks 16270T, the other of the two.

One would like to have the complete mitochondrial genomes for those samples before concluding that some Solutreans were J.

Genetiker
18-04-17, 03:36
I think most people assume that this chunk of alleles is shared ancestry among European and Siberians, probably having to do with MA-1 or Afontova Gora

Then "most people" are wrong.

If the Chinchorro sample just had the Mal'ta-related DNA found in all Amerindians, then:



It would be located around pure Amerindians in PCA plots. It isn't. Instead it's shifted (https://genetiker.wordpress.com/2017/03/14/principal-component-analysis-confirms-european-admixture-in-chinchorro-dna/) far away from them, in the direction of Caucasoids, and more specifically, Europeans.
It would be modeled as only having ancestry from pure Amerindians in qpAdm analyses. It isn't. Instead it's modeled (https://genetiker.wordpress.com/2017/03/14/qpadm-analysis-confirms-european-admixture-in-chinchorro-dna/) as having around 45% ancestry from various Caucasoid, including European, populations.
It would only have Amerindian components in admixture analyses. It doesn't. Instead, 30–40% of its DNA is made up (https://genetiker.wordpress.com/2017/03/20/high-resolution-k-13-analysis-of-the-european-admixture-in-chinchorro-dna/) of non-Amerindian, mostly Caucasoid components.



In my high-resolution K = 9 (https://genetiker.wordpress.com/2017/03/19/high-resolution-k-9-analysis-of-the-european-admixture-in-chinchorro-dna/) and K = 13 (https://genetiker.wordpress.com/2017/03/20/high-resolution-k-13-analysis-of-the-european-admixture-in-chinchorro-dna/) admixture analyses, the Chinchorro sample has a significant amount of the light blue component, which is completely absent in the Mal'ta and Afontova Gora samples, which means that the European admixture can't possibly be from those Siberian populations, or from any genetically similar population. The light blue component is, however, found in the pre-LGM European samples.

In my high-resolution K = 13 (https://genetiker.wordpress.com/2017/03/20/high-resolution-k-13-analysis-of-the-european-admixture-in-chinchorro-dna/) analysis, the medium blue component is completely absent in the Chinchorro sample. The Mal'ta and Afontova Gora samples are made up mostly of that component, which again means that the European admixture can't possibly be from those Siberian populations, or from any genetically similar population. Instead of the medium blue component, the Chinchorro sample has a significant amount of the dark blue component. The pre-LGM European samples also have significant amounts of the dark blue component, and an absence of the medium blue component.

holderlin
18-04-17, 07:50
Then "most people" are wrong.

If the Chinchorro sample just had the Mal'ta-related DNA found in all Amerindians, then:



It would be located around pure Amerindians in PCA plots. It isn't. Instead it's shifted (https://genetiker.wordpress.com/2017/03/14/principal-component-analysis-confirms-european-admixture-in-chinchorro-dna/) far away from them, in the direction of Caucasoids, and more specifically, Europeans.
It would be modeled as only having ancestry from pure Amerindians in qpAdm analyses. It isn't. Instead it's modeled (https://genetiker.wordpress.com/2017/03/14/qpadm-analysis-confirms-european-admixture-in-chinchorro-dna/) as having around 45% ancestry from various Caucasoid, including European, populations.
It would only have Amerindian components in admixture analyses. It doesn't. Instead, 30–40% of its DNA is made up (https://genetiker.wordpress.com/2017/03/20/high-resolution-k-13-analysis-of-the-european-admixture-in-chinchorro-dna/) of non-Amerindian, mostly Caucasoid components.



In my high-resolution K = 9 (https://genetiker.wordpress.com/2017/03/19/high-resolution-k-9-analysis-of-the-european-admixture-in-chinchorro-dna/) and K = 13 (https://genetiker.wordpress.com/2017/03/20/high-resolution-k-13-analysis-of-the-european-admixture-in-chinchorro-dna/) admixture analyses, the Chinchorro sample has a significant amount of the light blue component, which is completely absent in the Mal'ta and Afontova Gora samples, which means that the European admixture can't possibly be from those Siberian populations, or from any genetically similar population. The light blue component is, however, found in the pre-LGM European samples.

In my high-resolution K = 13 (https://genetiker.wordpress.com/2017/03/20/high-resolution-k-13-analysis-of-the-european-admixture-in-chinchorro-dna/) analysis, the medium blue component is completely absent in the Chinchorro sample. The Mal'ta and Afontova Gora samples are made up mostly of that component, which again means that the European admixture can't possibly be from those Siberian populations, or from any genetically similar population. Instead of the medium blue component, the Chinchorro sample has a significant amount of the dark blue component. The pre-LGM European samples also have significant amounts of the dark blue component, and an absence of the medium blue component.

I saw this and I didn't quite know what to make of it at the time. I appreciate the breakdown, and I see what you're saying. It's pretty amazing, especially with the legends tied to this sort of thing.

In your high res K-13 there are other Amerindians that show the same admixture, but in smaller amounts. Perhaps these are possibly from post-Columbian admixure?

The component looks like European Neolithic and South Asian, and Chinchorro's have way more than any of the other Native American samples, so the speculation that they were "europeans" or "cacausoids" based on their skulls was large in part correct. But I don't know that we can say that it came from paleo-europeans from across the Atlantic. I suppose if you add in all of the oral history about european looking people, then it surely begs the question.

Among ancient samples Goyet Q376-19 looks to have similar components.

I could buy it, tentatively, but that's just me.