My attempt at modelling of Native American Global 25 samples from Latin America.

[JerryS.]

Actually I think some New World ethnic groups who are more "stabilized" genetically in terms of ancestries can be included in G25 such as the Garifuna from Central America who are predominantly West-Central African with significant Native American ancestry from around 15-25% (the highest SSA I have seen for a Garifuna is an individual who is 90% SSA and 10% Amerindian but I am not sure if he is recently mixed with other New World Afro-diaspora group or not).

Also Miskito Amerindians from Nicaragua, Honduras who are actually almost a stabilized mix between Africans and Natives might be able to be added into G25 as well.

Or maybe groups like Jamaicans, Haitians who are predominantly African genetically can be added as well or even the Surinamese/Guianan Maroons who are literally runaway African slaves who are "almost pristine" to 100% SSA genetically.

for Native (south) American wouldn't it make more sense to use people who are actually American Indians from central and South America instead of people mostly SSA?

[Tsakhur]

for Native (south) American wouldn't it make more sense to use people who are actually American Indians from central and South America instead of people mostly SSA?

Yes indeed, but we already have quite several Amerindian samples from Central and South America including Bolivian_LaPaz, Bolivian_Cochabamba and Bolivian_Pando populations on G25. So having several New World SSA/SSA mixed groups would also be brilliant as well and we can compared them to African populations.

Still, it would be great though to have more American Indians like the Tarahumara and more Huichols and Nahuas from Mexico, Embera from Panama/Colombia, Mapuche or precolonial Amerindians from Chile, Sierra Nevada Amerindians from Colombia such as Arhuaco, Kogi (believed to be the only unconquered precolumbian civilization remaining and still persisting until today), Wiwa, Kankuamo, or from more Peruvian populations like those from Lima, Arequipa and other parts of the country besides the Quechua samples (not sure where in Peru they are from, because they have notable amounts of European admixture for Native Americans, but probably not from the isolated areas of the Andes where Natives tend to be "purer" genetically from the results I saw on Gedmatch), etc.

Actually we already have quite a few ancient and precolonial individuals from Chile such as LosRieles, Ayayema, PicaOcho, Yamana, Kaweskar and CHL_Fuego_Patagonian (don't know the tribe).

[Caius Agrippa]

Agreed. Maybe if it is New World groups who are genetically more stabilized and homogeneous in terms of their recent ancestries like Mexicans, Peruvians/Bolivians, etc, it might make more sense to include them than others who are very heterogeneous and varied such as Brazilians as you have noted.

Wait by 30% Amerindian 70% SSA, do you mean that the individual is around 70% SSA and the rest of the autosomal DNA are varying amounts of European or Amerindian, or do you mean that the sample is literally 70% African and 30% Native American without zero European? There are some Brazilians who don't have any European ancestry besides Amazonian tribes?

The first option, I meant people with 70% SSA and varied admixtures. I don't think that nowadays you can find many Brazilians with 0% European ancestry, but months ago someone posted the results of Brazilian singer Milton Nascimento and he came out 99% African. Of course many Amazonian tribes would score 99-100% Amerindian. I believe there is still a considerable quantity of Brazilians with pure or almost pure African descent in some places that experimented more recent (mid 19th century) African geneflow.

Brazil was the last country in the western hemisphere to abolish African slave trade and African slavery, some parts of Brazil were receiving slaves from Africa as late as 1850. I believe most of the African input in Brazil is rather recent (19th century, post-independence) instead of an older colonial substrate. The lives of African slaves under the Portuguese were too hard for them to let substantial progeny in Brazil, most slaves were males and they were usually not allowed to reproduce. People with very deep origins in colonial Brazil usually score higher Amerindian or are mostly Portuguese with minor SSA and Amerindian admixtures, people with very significant levels of African ancestry usually would have 19th century slave ancestors from Africa rather than being descended from multiple mixed people. If you look at the results of the Brazilians who look very SSA many score over 50% African.

[RCO]

People with strong Amerindian ancestry do match other Amerindian people just like any other relatively endogamous population, so it's not easy to differentiate from South/Central/North America because they descend from the same small population. I have seen the Family Finder-FTDNA of some Brazilian-Amerindian and they match several other people from the Americas in good pieces of cM and X chrom.

[Tsakhur]

People with strong Amerindian ancestry do match other Amerindian people just like any other relatively endogamous population, so it's not easy to differentiate from South/Central/North America because they descend from the same small population. I have seen the Family Finder-FTDNA of some Brazilian-Amerindian and they match several other people from the Americas in good pieces of cM and X chrom.

Hmm which is strange. Do you think there was more genetic diversity among precolonial Amerindians than today?

Actually I noticed that the North American G25 samples such as Amerindian_North, Chipewyan, Cree and Tlingit seem to really required an Athabaskan proxy in order to achieve good distance fits while its not need for Natives from Mexico down to Southern Cone. So I think North American Natives might be the exception as they seem to have recent Siberian gene flow.

Furthermore, I notice the Euro admixture in some Amerindian individuals or averages can varied depending on what ancient Amerindian proxies are utilized:

For example, this Nahua (an Amerindian ethnicity from Mexico) individual seem to fluctuate from 1.4 to 2.6% European which is strange to me...

In the first model I run for the Nahua in the OP: Around 2.6% Euro

Target: Nahua
Distance: 1.2075% / 0.01207522
51.8 USA_Island_Chumash_SanCruz
16.4 Karitiana
13.4 CAN_400BP
11.8 USA_Spirit_Cave_11000BP
4.0 BLZ_MayahakCabPek_9300BP
2.4 Spanish_Soria
0.2 Spanish_Extremadura

But in the second model I did for the Nahua individuals: now its around 1.6% Euro. I wonder if there is a factor behind this fluctuation in European ancestry?

Target: Nahua
Distance: 1.3143% / 0.01314285
53.8 USA_Island_Chumash_SanCruz
22.0 USA_Spirit_Cave_11000BP
12.6 BRA_Sumidouro_10100BP
6.8 CAN_400BP
3.2 BLZ_MayahakCabPek_9300BP
1.6 Spanish_Soria

[Slips]

Isn't the Santa Cruz sample modern?

[Tsakhur]

Isn't the Santa Cruz sample modern?

Nope, it is medieval: (it is labelled as USA_Chumash_SanCruz)

http://open-genomes.org/analysis/PCA...ree_scaled.pdf

[Slips]

Well, medieval is still much younger than 9000+ BP

[Angoliga]

Understanding that there's a lot of variation within these regions, which G25 samples would however be deemed as best proxies for these pre-Columbian meta-populations:

• Mesoamerican
• Andean
• Patagonian
• Amazonian
• Antillean
• North-Amerindian

For any recommendations, could you provide ADMIXTURE analysis to back recommended proxies?


I was thinking of using modern Surui for Amazonian, and DOM_southeast_Ceramic for Antillean based on this paper (Fernandes et al., 2020 [Fig. 2]):

 

...if the 2 afmd are passible, what would be best suited for Mesoamerican, Andean, Patagonian and North-Amerindian?

[Tsakhur]

Understanding that there's a lot of variation within these regions, which G25 samples would however be deemed as best proxies for these pre-Columbian meta-populations:

• Mesoamerican
• Andean
• Patagonian
• Amazonian
• Antillean
• North-Amerindian

For any recommendations, could you provide ADMIXTURE analysis to back recommended proxies?


I was thinking of using modern Surui for Amazonian, and DOM_southeast_Ceramic for Antillean based on this paper (Fernandes et al., 2020 [Fig. 2]):

 

...if the 2 afmd are passible, what would be best suited for Mesoamerican, Andean, Patagonian and North-Amerindian?

Well here are some ADMIXTURE analyses to back them but it's in these two papers though:

First paper:
Here is the ADMIXTURE analysis. https://www.ncbi.nlm.nih.gov/core/lw...ms614608f2.jpg

Second paper:

The ADMIXTURE analysis is in this supplementary data page 103: http://www.cbs.dtu.dk/public/nativea...ab3884_SOM.pdf

The thing is that in G25, almost all of the Amerindian samples (except Northern Natives who have recent Siberian ancestry) are so genetically closed together as in they seem to lack genetic diversity (not sure if it is due to genetic drift and isolation that causes this), even if they lived so faraway like say Mexico and Argentina.

Quoting RCO in the above post here:

People with strong Amerindian ancestry do match other Amerindian people just like any other relatively endogamous population, so it's not easy to differentiate from South/Central/North America because they descend from the same small population. I have seen the Family Finder-FTDNA of some Brazilian-Amerindian and they match several other people from the Americas in good pieces of cM and X chrom.

For example, let say I tried to model the Pima, a Native American tribe from Southwest USA/Northern Mexico (they are considered Southwestern rather than Mesoamerican) using the following components: Northern Amerindian: represented by Athabaskan_1100BP, Southwest USA: Island Chumash San Cruz as a proxy, Mesoamerican which I used MayahabCabPek_9300BP, Antillean which is also DOM_Ceramic, Surui for Amazonian, Rio_UnCallane_1800BP and CHL_Fuego_Patagonian which are utilized as representatives of the Andean and Patagonian components, I will get his model:

Target: Pima
Distance: 1.3666% / 0.01366603
47.6 USA_Island_Chumash_SanCruz
24.2 PER_RioUncallane_1800BP
12.8 Surui
10.0 USA_AK_Athabaskan_1100BP
3.0 CHL_Fuego_Patagonian
1.6 Onge
0.8 Spanish_Andalucia

I also added Onge because I heard there are some Andamanese/Australo-Melanesian affinities among some Native Americans and looks like the Pima show minor signal of this affinity.

Have you noticed that the Mesoamerican component (MayahabCabPek) doesn't show up and that it shows Pima being almost 1/4 Andean-derived, 13% Amazonian, 10% North Amerindian and 3% Patagonian?

If I decided to remove the Southwest USA component (Island Chumash San Cruz), this is what I get:

Target: Pima
Distance: 1.6005% / 0.01600498
50.4 PER_RioUncallane_1800BP
24.6 DOM_southeast_Ceramic
13.4 USA_AK_Athabaskan_1100BP
4.4 Surui
3.8 CHL_Fuego_Patagonian
2.2 Onge
1.0 Spanish_Andalucia
0.2 Papuan

Noticed how the Pima now score at least 50% Andean admixture, almost 1/4 Antillean, 13% Northern Amerindian, the Amazonian also decreased to around 4% from approx 13% and 4% Patagonian. Meanwhile the Onge also increase to 2%.

Or let say if I decided to remove Antillean, Amazonian, Andean and Patagonian components from the source, this is what I get for the Pima:

Target: Pima
Distance: 1.5609% / 0.01560901
74.2 USA_Island_Chumash_SanCruz
21.4 BLZ_MayahakCabPek_9300BP
2.6 USA_AK_Athabaskan_1100BP
1.0 Onge
0.8 Spanish_Andalucia

Noticed how the Mesoamerican component (MayahabCabPek) suddenly shows up at 21% when before this, it doesn't appear in the previous runs at all? And observed how the Northern Amerindian component (Athabaskan) greatly reduced to only 2.6%.

What I want to demonstrate is that there seem to be a lot of overlaps between the different Amerindian components likely due to the fact that they descended from a small population/genetic bottleneck as what RCO suggested. Therefore it could be hard to determine how much North Amerindian, Central Amerindian, South Amerindian a Native American sample might have if the percentage of each component utilized can easily fluctuates based on the number of inputs you put in.

Anyway I can try to recommend the populations you can used for each Native categories

North Amerindian= Amerindian_North, Chipewyan, USA_AK_Athabaskan_1100BP, CAN_400BP, Can_6000BP
Southwestern=all the Chumash samples (USA_Island_Chumash, USA_Mainland Chumash), USA_Santa_Catalina_Island, USA_Francisco_May
Mesoamerican= Mixe, Nahua, Huichol, BLZ_MayahabCabPek_9300BP, BLZ_SakiTzul_7400BP
Antillean= DOM_Southeast_Ceramic, BHS_Taino, HTI_Ceramic, BHS_Ceramic, etc.
Amazonian = Karitiana, Surui, Piapoco
Andean= PER_RioUnCallane_1800BP, PER_Laramate_900BP, PER_Lauricocha, PER_Cuncaicha, ARG_Aconcagua_500BP
Patagonian=ARG_Fuego_Patagonian, CHL_Fuego_Patagonian, CHL_Kaweskar_1000BP, CHL_Yamana_1000BP