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View Full Version : My attempt at modelling of Native American Global 25 samples from Latin America.



Tsakhur
08-28-2020, 12:09 PM
It will be mainly about Mesoamerican, Amazonian, Andean and Southern Cone Native American groups. I will do Northern Amerindian groups in another post. These are the averages btw, not individual samples.

Warning: the post will be very long, please have a patience looking at the results and give your opinions.

Notes:
-The CAN_400BP is an individual Native American sample from Canada.
-Spirit_Cave individual is the oldest mummy in North America while Anzick is a Paleo-Indian infant sample from Montana, USA.
-The Great Andamanese is utilized as a proxy to determine the Negrito affinity in some Amerindians (some Natives such as Amazonian tribes were founded to have Onge/Melanesian-like affinity).
-MayahakCabPek is a 9300 year old Neolithic sample from Belize.
-LapoDoSanto is an Early Neolithic sample from Brazil (almost Ice-Age)
-Karitiana is utilize to represent Amazonian ancestry.
-Andean components are represented by Aconcagua_500BP (before present) from precolonial Argentina, RioUncallane and Lauricocha from ancient Peru.
-LosRieles are archaic (10900 years before present) samples from Central Chile
-Ayayema is from Late Neolithic Patagonia in Chile- utilized as proxy for Patagonian-related ancestry
-ArroyoSeco2 is a Neolithic sample from near Tres Arroyos in Argentina- maybe can represent Pampean affinity.

Here are some Mesoamerican tribes (from Northern to Southern Mexico)


The average result of the Pima tribe from SW USA/Northern Mexico (uncertain whether the samples are from US or Mexico) . Only 0.2% Iberian admixture. But keep in mind that these are the average, individual samples might varied in European admixture. 1% Negrito (Great Andamanese)-related affinity. Its interesting how the Pima seem to be able to modelled as a mix of Southwest US Amerindian (Chumash)+Northern Native (Can_400BP+Spirit_Cave)+Central American (MayahakCabPek), Amazonian (Karitiana) and Late Stone Age/Mesolithic Brazilian (Sumidouro). Also traceable amounts of 0.2% Papuan/Oceanic.

Target: Pima
Distance: 1.3060% / 0.01306024
51.2 USA_Island_Chumash_SanCruz
12.8 Karitiana
12.4 CAN_400BP
10.6 BLZ_MayahakCabPek_9300BP
8.0 BRA_Sumidouro_10100BP
3.6 USA_Spirit_Cave_11000BP
1.0 IND_Great_Andamanese_100BP
0.2 Papuan
0.2 Spanish_Soria


The average result of Pericues (only three individuals in G25), the precolonial Native American inhabitants of Baja California, Mexico who have been extinct since the 19th century: autosomally mostly Southwest US Native (Chumash) followed by Early Neolithic Brazilian (LapaDoSanto), prominent proportions of Central American (MayahakCabPek) and Northern Amerind (Spirit_Cave+CAN_400BP). The hilarious aspect is that they seem to also possessed 3.4% European admixture but I am unsure if it this "Euro" is actually ANE/archaic West Eurasian ancestry or actual Iberian admixture. Also miniscule Negrito and Papuan/Oceanic which could be noise or some type of unknown gene flow from South Asia/Melanesia.

Target: MEX_Pericues
Distance: 1.4762% / 0.01476179
53.8 USA_Island_Chumash_SanCruz
14.0 BRA_LapaDoSanto_9600BP
13.2 BLZ_MayahakCabPek_9300BP
11.2 USA_Spirit_Cave_11000BP
3.6 CAN_400BP
3.4 Spanish_Extremadura
0.4 IND_Great_Andamanese_100BP
0.4 Papuan

Here is a Huichol individual (unfortunately only 1 sample in G25): Seems very genetically unique compared to most Amerindians in the region; having Spirit_Cave ancestry as the main component, also small amounts of Anzick and completely lack Southwest USA (Chumash) admixture. Zero European and 1% Negrito (Great Andamanese)-like affinity.

Target: Huichol
Distance: 1.3742% / 0.01374182
44.2 USA_Spirit_Cave_11000BP
38.6 BRA_LapaDoSanto_9600BP
8.6 CAN_400BP
7.6 USA_Anzick
1.0 IND_Great_Andamanese_100BP

Here is also a Nahua individual (like the Huichol, only one sample in G25) from Central Mexico: also mostly Southwest US (Chumash) with Northern Amerindian (CAN_400BP+Spirit_Cave)+Amazonian (Karitiana) and some Central American (MayahakCabPek) ancestry. Its weird how this Nahua, has lower Central American admixture than the Pima, who are located much further north. Also approximately 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

Here is the average Mixe from Central-Southern Mexico: a mix of Southwest USA (Chumash)+Early Neolithic Brazilian (LapaDoSanto)+Northern Amerindian (CAN_400BP+Spirit_Cave)+Central American (MayahakCabPek) and Amazonian (Karitiana) ancestry. Zero Iberian/European admixture.

Target: Mixe
Distance: 1.8627% / 0.01862704
22.0 USA_Island_Chumash_SanCruz
19.2 BRA_LapaDoSanto_9600BP
19.2 USA_Spirit_Cave_11000BP
15.0 BLZ_MayahakCabPek_9300BP
14.2 Karitiana
10.4 CAN_400BP

The average Mixtec from Southern Mexico has similar autosomal profile to the Mixe, but much higher Early Neolithic Brazilian (LapaDoSanto) and much lower Amazonian (Karitiana) which is odd. Possesss 4% European and traceable Papuan/Oceanic but could be noise.

Target: Mixtec
Distance: 1.1135% / 0.01113511
33.6 USA_Island_Chumash_SanCruz
32.6 BRA_LapaDoSanto_9600BP
20.2 USA_Spirit_Cave_11000BP
6.6 Karitiana
2.4 CAN_400BP
2.2 Spanish_Soria
1.8 Spanish_Extremadura
0.6 Papuan

The average Zapotec result from Southern Mexico: higher Neolithic Brazilian but lower Southwest US Native, notable amount of Central American, low Amazonian and minor Mesolithic Brazilian and Northern Amerindian. Also around 3.6% European and 1% Negrito-related admixture.

Target: Zapotec
Distance: 1.2985% / 0.01298486
29.8 BRA_LapaDoSanto_9600BP
22.8 USA_Island_Chumash_SanCruz
21.8 USA_Spirit_Cave_11000BP
13.6 BLZ_MayahakCabPek_9300BP
4.8 Karitiana
3.6 Spanish_Extremadura
1.6 BRA_Sumidouro_10100BP
1.0 CAN_400BP
1.0 IND_Great_Andamanese_100BP

The average Mayan result from Guatemala: similar case to Pima and Nahua in being dominated by the Southwest US Native (Chumash) and Amazonian (Karitiana) but much lower Northern Amerindian (Spirit_Cave+barely traceable CAN_400BP). What's peculiar is that the Central American (MayahakCabPek) is very low when one would expected it to be the main ancestral component of the Mayans. Also noteworthy proportions of Mesolithic Brazilian (Sumidouro) and some Early Neolithic Brazilian (LapoDoSanto). Anyway, has around 4.2% European.

Target: Mayan
Distance: 0.8963% / 0.00896288
37.0 USA_Island_Chumash_SanCruz
20.2 Karitiana
14.2 USA_Spirit_Cave_11000BP
10.4 BLZ_MayahakCabPek_9300BP
10.2 BRA_Sumidouro_10100BP
4.2 Spanish_Extremadura
3.6 BRA_LapaDoSanto_9600BP
0.2 CAN_400BP


Next, I will post Caribbean and Northern South American/Amazonian Natives.


A Taino individual from pre-Hispanic Puerto Rico (once again, only one sample in G25 unfortunately): seem to be mostly Amazonian with significant Central American, lower Southwest US Native and Northern Amerindian. Also demonstrates negligible amounts of African which could be noise or some archaic unknown admixture.

Target: BHS_Taino
Distance: 1.6415% / 0.01641507
61.6 Karitiana
20.0 BLZ_MayahakCabPek_9300BP
10.6 USA_Island_Chumash_SanCruz
7.2 USA_Anzick
0.6 Esan_Nigeria

Precolonial Native Americans from Puerto Rico during Ceramic Age (don't know their ethnicity/tribe but is possibly the ancestors of the Carib and Taino): Mostly Amazonian with significant Central American, Early Neolithic Brazilian, smaller amounts of Southwest US Native and minor Mesolithic Brazilian. Also traceable African which could be noise or some unknown archaic admixture.

Target: BHS_Ceramic
Distance: 0.6930% / 0.00692971
48.8 Karitiana
26.0 BLZ_MayahakCabPek_9300BP
15.2 BRA_LapaDoSanto_9600BP
8.0 USA_Island_Chumash_SanCruz
1.4 BRA_Sumidouro_10100BP
0.4 Esan_Nigeria
0.2 USA_Spirit_Cave_11000BP

Precolonial Amerindians from Dominican Republic during Ceramic Age (probably the ancestors of the Carib and Taino): slightly more Amazonian than the Puerto Rican Ceramic (BHS_Ceramic) individuals, lower Central American, Early Neolithic Brazilian, but higher Northern Amerindian and even lower Southwest US Native ancestry. Negligible amount of Mesolithic Brazilian, African and Papuan/Oceanic (the latter two is possibly some archaic admixture or unknown link with Melanesia).

Target: DOM_southeast_Ceramic
Distance: 0.8535% / 0.00853495
51.6 Karitiana
19.8 BLZ_MayahakCabPek_9300BP
13.8 BRA_LapaDoSanto_9600BP
9.4 USA_Spirit_Cave_11000BP
3.6 USA_Island_Chumash_SanCruz
1.0 BRA_Sumidouro_10100BP
0.6 Esan_Nigeria
0.2 Papuan

Piapoco Amerindians from the Amazon area of Colombia: genetically almost identical to the Taino individual but possessed Northern Amerindian and lower Southwest US Native unlike the latter. Also miniscule African affinity which again, could be just archaic admixture or noise.

Target: Piapoco
Distance: 1.0566% / 0.01056626
62.8 Karitiana
20.4 BLZ_MayahakCabPek_9300BP
11.0 USA_Spirit_Cave_11000BP
5.4 USA_Island_Chumash_SanCruz
0.4 Esan_Nigeria

Lonely Yukpa sample (only one individual in G25) from Northern South America (don't know whether it is from Colombia or Venezuela): predominantly Amazonian but very substantial Southwest US Native-related admixture and low Central American. The individual shows negligible signals of Papuan which would be noise or archaic link with Oceania. 0.4% Euro which could be authentic Iberian admixture or just noise.

Target: Yukpa
Distance: 1.7506% / 0.01750582
63.6 Karitiana
29.0 USA_Island_Chumash_SanCruz
6.4 BLZ_MayahakCabPek_9300BP
0.6 Papuan
0.4 Spanish_Extremadura

Average Surui from Brazil's Amazon: pure Amazonian (literally 100% identical to the Karitiana).

Target: Surui
Distance: 1.9183% / 0.01918270
100.0 Karitiana

The average result of the Cachi/Chachi, a Native American rainforest dwelling tribe from Northern coast of Ecuador: a mix of Andean (RioUncallane+Aconcagua)+Amazonian (Karitiana)+Mesolithic Brazilian (Sumidouro)+Pampean (ArroyoSeco) and minor Central American (MayahakCabPek) ancestries. Have 4.2% Euro and almost negligible African (which could be noise, archaic admix or actual ancestry if there were African runaway slaves in Ecuador) and Papuan.

Target: Cachi
Distance: 0.7122% / 0.00712170
44.2 PER_RioUncallane_1800BP
22.8 Karitiana
8.2 ARG_Aconcagua_500BP
8.2 ARG_ArroyoSeco2_7700BP
7.8 BRA_Sumidouro_10100BP
4.2 Spanish_Extremadura
3.8 BLZ_MayahakCabPek_9300BP
0.6 Esan_Nigeria
0.2 Papuan


In the next section, it will be Andean Native Americans.


The average Quechua result from Peru: mostly Andean (Aconcagua+RioUncallane+Lauricocha) with Amazonian, Southwest US Native-related ancestry. Has 9.6% European which is one of the highest among the Latin American Native samples in G25. Negligible African which could be from slave ancestry or come from the Iberian admixture (Spaniards has very tiny SSA/North African-like affinity) and Papuan (could be noise or some archaic admixture/link).

Target: Quechua
Distance: 0.7741% / 0.00774056
29.6 ARG_Aconcagua_500BP
20.0 Karitiana
16.0 PER_RioUncallane_1800BP
14.4 USA_Island_Chumash_SanCruz
9.8 PER_Lauricocha_8600BP
5.0 Spanish_Extremadura
4.6 Spanish_Soria
0.4 Esan_Nigeria
0.2 Papuan

Average result of three Bolivians from La Paz (could be Aymara): predominantly Andean (RioUncallane+Aconcagua) with notable amounts of Pampean (ArroyoSeco). Around 2.6% Euro and negligible Amazonian (surprising because the Quechua from Peru shows good proportions of Amazonian-like admixture).

Target: Bolivian_LaPaz
Distance: 1.2349% / 0.01234893
54.4 PER_RioUncallane_1800BP
30.0 ARG_Aconcagua_500BP
12.4 ARG_ArroyoSeco2_7700BP
2.6 Spanish_Extremadura
0.6 Karitiana

Lonely Bolivian result from Cochabamba (could be Aymara or Quechua, don't know): a mix of Andean, significant Amazonian and Mesolithic Brazilian. Also negligible African (possibly actual slave ancestry or comes from Iberian admixture) and Papuan (archaic admix/ancient link with Oceania).

Target: Bolivian_Cochabamba
Distance: 1.5733% / 0.01573301
56.8 PER_RioUncallane_1800BP
21.2 Karitiana
12.8 BRA_Sumidouro_10100BP
7.8 Spanish_Extremadura
0.8 Esan_Nigeria
0.6 Papuan

Average result of Bolivians from Pando (not sure the ethnicity), the Amazonian far north region of the country: Almost purely Andean with some Northern Amerindian (Spirit_Cave). Its really weird how these samples despite being from the Amazon, doesn't show any Karitiana admixture. Maybe they are recent migrants to the region from the Andes. Approximately 11% Euro which is the highest among the Latin American Native G25 samples. 0.8% African which could come from Iberian ancestry (since Spaniards already have minor SSA/North African-like affinity) or actual slave admixture.

Target: Bolivian_Pando
Distance: 0.9458% / 0.00945823
46.4 ARG_Aconcagua_500BP
37.6 PER_RioUncallane_1800BP
10.8 Spanish_Extremadura
4.4 USA_Spirit_Cave_11000BP
0.8 Esan_Nigeria

Aymara individual (only one sample in G25); not sure if it is from Southern Peru/Bolivia or Northern Chile: a mix of Andean+Araucanian (LosRieles)+Pampean (ArroyoSeco), has lower Amazonian than the average Quechua result and minor Central American. 0.6% Euro and no African.

Target: Aymara
Distance: 1.4232% / 0.01423195
37.0 PER_RioUncallane_1800BP
19.0 CHL_LosRieles_10900BP
18.2 ARG_Aconcagua_500BP
17.8 Karitiana
5.2 ARG_ArroyoSeco2_7700BP
2.2 BLZ_MayahakCabPek_9300BP
0.6 Spanish_Soria


The average Colla result from Andean region of Northwest Argentina: mostly Andean with notable Patagonian (Ayayema), much lower Amazonian than Quechua and Aymara, minor Mesolithic Brazilian and Southwest US Native. Has almost 4% Euro and almost zero African (could be noise or some spilling from Iberian admixture).

Target: Colla
Distance: 1.0504% / 0.01050414
46.0 ARG_Aconcagua_500BP
23.0 PER_RioUncallane_1800BP
10.6 CHL_Ayayema_5100BP
9.4 Karitiana
3.8 BRA_Sumidouro_10100BP
3.8 Spanish_Soria
3.2 USA_Island_Chumash_SanCruz
0.2 Esan_Nigeria


In the last section, here are Native Americans from the Pampas and Patagonia.


The average result of Wichi tribe from Northern Argentina: a hybrid of Amazonian, Andean (Aconcagua+Lauricocha+RioUncallane) and Patagonian (Ayayema) ancestries. No Euro or African. Its peculiar how there is zero Pampean (ArroyoSeco) despite being from the Pampas region.

Target: Wichi
Distance: 1.0896% / 0.01089573
37.2 Karitiana
25.2 ARG_Aconcagua_500BP
14.6 PER_Lauricocha_8600BP
13.8 CHL_Ayayema_5100BP
9.2 PER_RioUncallane_1800BP

The average of two Kaweskar individuals from Chilean Patagonia: a hybrid of Northern Amerindian (Spirit_Cave+Anzick)+Andean (RioUncallane+Aconcagua)+Amazonian and minor Pampean (ArroyoSeco), Patagonian (Ayayema), Mesolithic Brazilian. Very strange how they hardly score Patagonian (Ayayema) ancestry. Traceable Negrito and Papuan which is noise level or archaic admixture/link to Oceania/South Asia.

Target: CHL_Kaweskar_1000BP
Distance: 1.2860% / 0.01286022
29.2 USA_Spirit_Cave_11000BP
28.0 PER_RioUncallane_1800BP
18.0 Karitiana
9.2 ARG_Aconcagua_500BP
9.0 USA_Anzick
2.8 ARG_ArroyoSeco2_7700BP
1.4 CHL_Ayayema_5100BP
1.2 BRA_Sumidouro_10100BP
0.6 IND_Great_Andamanese_100BP
0.6 Papuan

The average result of two Yamana/Yaghans from Chilean Patagonia: a mixture of Andean+Northern Native (Anzick+Spirit_Cave)+Central American+Southwest US Native. Also no Patagonian ancestry which is strange. 0.2% African which could be noise or some archaic affinity.

Target: CHL_Yamana_1000BP
Distance: 1.3191% / 0.01319138
53.2 PER_RioUncallane_1800BP
14.6 USA_Anzick
11.4 USA_Spirit_Cave_11000BP
10.2 BLZ_MayahakCabPek_9300BP
9.4 USA_Island_Chumash_SanCruz
1.0 ARG_Aconcagua_500BP
0.2 Esan_Nigeria

Average result of two unknown individuals (don't know the tribal affiliation) from Chilean Patagonia: a mix of Pampean (ArroyoSeco)+Andean+Araucanian (LosRieles)+low Northern Amerindian. 1.6% Negrito and minor African and European which could be noise or archaic admixture/affinity to South Asia.

Target: CHL_Fuego_Patagonian
Distance: 2.3256% / 0.02325648
34.0 ARG_ArroyoSeco2_7700BP
32.8 ARG_Aconcagua_500BP
22.8 CHL_LosRieles_10900BP
6.2 USA_Spirit_Cave_11000BP
2.2 CAN_400BP
1.6 IND_Great_Andamanese_100BP
0.2 Esan_Nigeria
0.2 Spanish_Extremadura

Lastly, the average result of four unknown individuals (don't know their ethnic or tribal affiliation) from the southernmost tip of Argentina: a peculiar mixture of Andean (RioUnCallane)+Central American (MayahakCabPek)+Neolithic Brazilian (LapaDoSanto)+Patagonian (Ayayema)+Amazonian and minor Northern Native (CAN_400BP) ancestry. Also minor signals of African and Papuan but very likely just noise. Very strange how the Patagonian ancestry is lower than the Andean, Central American and Neolithic Brazilian. Also noise levels of African and Papuan which could be noise or archaic affinity.

Target: ARG_Fuego_Patagonian
Distance: 1.1085% / 0.01108481
32.2 PER_RioUncallane_1800BP
21.0 BLZ_MayahakCabPek_9300BP
16.4 BRA_LapaDoSanto_9600BP
13.4 CHL_Ayayema_5100BP
9.4 Karitiana
3.8 BRA_Sumidouro_10100BP
3.4 CAN_400BP
0.2 Esan_Nigeria
0.2 Papuan


Thoughts?? Sorry for the very long post but please take a patience inspecting them.

Tsakhur
08-28-2020, 05:58 PM
Thoughts please?

Atlas
08-28-2020, 06:26 PM
I would like to say something meaningful to properly convey how impressed I am that you've compiled such a group, but I fear my knowledge of these tools is woefully inadequate.
But from what I can see, well done :)! I don't think I've ever come across pre-colonial NA samples before, and you have a string of them with your own summaries. As someone with very minor ancestry from Northern Amerindians, I eagerly await your next post on these and hope for the eastern coast in particular. Concerning your Bolivian samples from Pando, I'm uncertain that the 0.8% African would be from their 11% Iberian heritage, because that might mean (ignoring random recombination) that the "100%" Iberian sample would be ~7% African. Do Iberians really have that much African heritage on average?

Caius Agrippa
08-30-2020, 02:21 PM
I'm interested to see how Amerindians from Brazilian Coast like Tupis and Tamoios would score, I wonder if there are surprises on our way. I'm seeing many Brazilians from São Paulo, Minas Gerais, Rio de Janeiro and Bahia scoring very minor Southeast Asian (~1%) in multiple calculators and I wonder if it's some kind of admixture present in the Native Americans from this region, some type of Asian admixture Portuguese colonists who populated these regions picked in Asia, influence from Southeast African slaves (who might have had Asian admixture, Brazil received many slaves from East Africa) or just noise.

Regarding modern Native Americans, I think it's very hard to find any tribes without any European and/or African admixture around the New World. Probably only Amazonians and some Andeans maintain a more ''pure'' Native American profile. Natives from USA are mainly mixed and some individuals in significant amounts, I even heard of mostly European individuals with 1/8, 1/16 and even 1/32 or 1/64 Amerindian ancestry identifying as Native Americans in USA.

drobbah
08-30-2020, 03:49 PM
Why aren't there any New World colonial samples on G25? I always wanted to run them on G25 and see the genetic makeup of latino groups especially the countries that have a significant presence of people of West/Central African descent like the DR,Puerto Rico,Colombia and Brazil.

Tsakhur
08-30-2020, 05:35 PM
Why aren't there any New World colonial samples on G25? I always wanted to run them on G25 and see the genetic makeup of latino groups especially the countries that have a significant presence of people of West/Central African descent like the DR,Puerto Rico,Colombia and Brazil.

Ya, I don't know why David didn't include them in his spreadsheet either.

Vadim (who created MDLP) and Dienekes (who created Dodecad) have some New World populations in their gedmatch calculators, I guess some user here will have to request David to upload those Latin American or Caribbean groups from Vadim and Dienekes into G25.

Or maybe we will have to ask some Latino or New World mixed race users here on Anthrogenica to do G25 tests and then request for David to include them into his spreadsheet.

Caius Agrippa
08-30-2020, 09:14 PM
Why aren't there any New World colonial samples on G25? I always wanted to run them on G25 and see the genetic makeup of latino groups especially the countries that have a significant presence of people of West/Central African descent like the DR,Puerto Rico,Colombia and Brazil.

In my opinion including such groups isn't really very informative for G25 purposes and I don't know if a tool developed to measure ancient ancestry in Old World populations is the best tool to capture more recent geneflow in admixed New World populations. Moreover, the average ancestries in Latin America don't mean most people in a given country will score like the average, apart from more homogeneous countries like Mexico and Bolivia. Mexican average is like 45% European, 50% Amerindian and 5% African and most Mexicans indeed score like that. Cuban average is like 70% European, 25% African, 5% Amerindian, but most Cubans don't score like that, most are either heavily European or heavily African, the average means nothing here.

If you look at Brazilian samples from GEDmatch calculators you will see that they are heavily skewed towards Europe, Brazilian sample in MDLP and puntDNAL is basically a Portuguese with 6% more West African and 5-7% Amerindian. But it doesn't mean most Brazilians are over 80% European, a significant portion is, but there are many more Brazilians with very high African and Amerindian components, I've seen many Brazilians scoring around 30% Amerindian, 70% SSA and even ''perfect'' triracials with equal proportions of the three. One must be very careful while selecting samples in extremely heterogeneous countries like Brazil.

JerryS.
08-31-2020, 02:45 AM
Ya, I don't know why David didn't include them in his spreadsheet either.

Vadim (who created MDLP) and Dienekes (who created Dodecad) have some New World populations in their gedmatch calculators, I guess some user here will have to request David to upload those Latin American or Caribbean groups from Vadim and Dienekes into G25.

Or maybe we will have to ask some Latino or New World mixed race users here on Anthrogenica to do G25 tests and then request for David to include them into his spreadsheet.

I saw this and had to chuckle as I have read that there is some friction between those mentioned based on how they come up with population sample groups. In other words, I don't think that's going to happen.

Tsakhur
08-31-2020, 06:44 AM
In my opinion including such groups isn't really very informative for G25 purposes and I don't know if a tool developed to measure ancient ancestry in Old World populations is the best tool to capture more recent geneflow in admixed New World populations. Moreover, the average ancestries in Latin America don't mean most people in a given country will score like the average, apart from more homogeneous countries like Mexico and Bolivia. Mexican average is like 45% European, 50% Amerindian and 5% African and most Mexicans indeed score like that. Cuban average is like 70% European, 25% African, 5% Amerindian, but most Cubans don't score like that, most are either heavily European or heavily African, the average means nothing here.

If you look at Brazilian samples from GEDmatch calculators you will see that they are heavily skewed towards Europe, Brazilian sample in MDLP and puntDNAL is basically a Portuguese with 6% more West African and 5-7% Amerindian. But it doesn't mean most Brazilians are over 80% European, a significant portion is, but there are many more Brazilians with very high African and Amerindian components, I've seen many Brazilians scoring around 30% Amerindian, 70% SSA and even ''perfect'' triracials with equal proportions of the three. One must be very careful while selecting samples in extremely heterogeneous countries like Brazil.

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?

Tsakhur
08-31-2020, 06:48 AM
Why aren't there any New World colonial samples on G25? I always wanted to run them on G25 and see the genetic makeup of latino groups especially the countries that have a significant presence of people of West/Central African descent like the DR,Puerto Rico,Colombia and Brazil.

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.

JerryS.
08-31-2020, 07:28 AM
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
08-31-2020, 07:46 AM
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
08-31-2020, 12:01 PM
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
08-31-2020, 05:22 PM
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
09-02-2020, 07:42 PM
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
09-16-2020, 07:24 AM
Isn't the Santa Cruz sample modern?

Tsakhur
09-16-2020, 09:03 AM
Isn't the Santa Cruz sample modern?

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

http://open-genomes.org/analysis/PCA/clustering/Eurogenes_Global25_tree_scaled.pdf

Slips
09-19-2020, 07:42 AM
Well, medieval is still much younger than 9000+ BP

Angoliga
11-02-2020, 10:43 PM
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 (https://www.biorxiv.org/content/10.1101/2020.06.01.126730v1.full.pdf) (Fernandes et al., 2020 [Fig. 2]):

https://i.imgur.com/NThnDqs.png


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

Tsakhur
11-06-2020, 04:08 PM
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 (https://www.biorxiv.org/content/10.1101/2020.06.01.126730v1.full.pdf) (Fernandes et al., 2020 [Fig. 2]):

https://i.imgur.com/NThnDqs.png


...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: (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156478/)
Here is the ADMIXTURE analysis. https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image% 20to%20zoom&p=PMC3&id=4156478_nihms614608f2.jpg

Second paper:
(https://science.sciencemag.org/content/349/6250/aab3884)
The ADMIXTURE analysis is in this supplementary data page 103: http://www.cbs.dtu.dk/public/nativeamerican/aab3884_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

pgbk87
11-21-2020, 02:08 PM
Thoughts please?

Awesome stuff man! I am from Belize, and though I am predominantly West African in deep ancestry, I have NW European, Carib/Arawak and Maya ancestry.

I find it hard to believe that BLZ_MayahakCabPek_9300BP is more present in the Caribbean than in Guatemala or Mexico. This is groundbreaking if, it is indeed true. Do you have any information on BLZ_MayahakCabPek_9300BP?

In recorded times, there has been evidence of Arawakan-Maipuran speakers being exiled to northern Central America in 1797 (Proto-Mayan region). However, there has only been speculation of the opposite ever actually happening.

AppalachianGumbo
12-01-2020, 08:05 PM
I'm interested to see how Amerindians from Brazilian Coast like Tupis and Tamoios would score, I wonder if there are surprises on our way. I'm seeing many Brazilians from São Paulo, Minas Gerais, Rio de Janeiro and Bahia scoring very minor Southeast Asian (~1%) in multiple calculators and I wonder if it's some kind of admixture present in the Native Americans from this region, some type of Asian admixture Portuguese colonists who populated these regions picked in Asia, influence from Southeast African slaves (who might have had Asian admixture, Brazil received many slaves from East Africa) or just noise.

Regarding modern Native Americans, I think it's very hard to find any tribes without any European and/or African admixture around the New World. Probably only Amazonians and some Andeans maintain a more ''pure'' Native American profile. Natives from USA are mainly mixed and some individuals in significant amounts, I even heard of mostly European individuals with 1/8, 1/16 and even 1/32 or 1/64 Amerindian ancestry identifying as Native Americans in USA.

You have to be careful with this. In the US, Indigenous identify by tribe or nation. This of course is excluding people who claim Indian blood myth stories, undocumented and no DNA results to show otherwise. People who actually identify, is a political identification to Alaskan Native or American Indian. They are enrolled with a recognized US Federal tribe stemming from treaties between the federal government and tribes.. While some may not be primarily American Indian or "Native American" by race, they have recognition tribally because they meet certain criteria to be a member of that tribe/nation set by the tribe. In the US, IF someone said they are 1/32 Creek or 1/4 Navajo, it is by lineage of documented tribal blood quantified from Indian rolls/census, not actual racial fractions. Many American Indians are also Inter-tribal, even if they are mostly Indigenous. In the US, a person can only register with ONE nation or tribe. Canada Status Indians also have differing politics on what is Aboriginal in a political setting. I will also note, most American Indians don't talk about fractions of tribal blood or how much. If you belong to the nation, you are part of that nation.