AMERINDIAN SIDEBAR: SouthEast Asian in Afro-Diasporans in the Americas

Published By King Genome on 23andMe online community forum, May 6, 2014 at 6:30 PM 
I want to explore the unknown Southeast Asian (SEA)vs. East Asian/Central Siberian showing up particularly at in African-Diasporans, notably those with Native American roots due to the colonization of the “New World.” This unusuality seems to be most prevalent on’s autosomal test but can be expressed as such on other personal genome services. My inquiry is inspired by the latest relative to test at from my family branch with confirmed Native American (NA) ancestry (mt-haplo B2) in part from Northeast USA; this relative scores 3.9% SEA but there is NO Native American or East Asian components. In comparison, my relative’s aunt from this line shows 6% SEA + 1.6% NA + 0.1% East Asian-Yakut, and her son registers 2.1% SEA + 1.7% NA. Another cousin with roots in Colonial Virginia has 2% SEA +0.1% NA. For control, my sister and I match the 8% NA cousin on the X-chromosome. My sister and I share a SEA segment, and I share a NA segment with my first cousin -- we all share B2 grandparents. I’m almost certain some of our SEA is of a North Amerindian nature because of the mt-haplogroup B2 and the fact that my relative’s aunt has East Asian-Yakut nestled between a SEA and NA segment. 

According to’s autosomal test, which looks at ancestry from at least 500 years ago, the "Southeast Asian" cluster description reads: “Located at the South of China, Southeastern Asia extends from Burma to Indonesia. Modern humans arrived in Southeastern Asia as early as 50,000 years ago, using a migration route along the coast of India. Today, SEA is comprised of many ethnic groups. Here are the reference populations for this cluster: Phillippines; Vietnam; Cambodian; Indonesia; Thailand; Cambodia; Laos; Burma, and Malaysia. 

Yet most experts unanimously agree it is difficult determine the nature of this SEA because of lack of Native Americans samples. In fact, Lucas Martin of DNA Tribes says, “Native American ancestry from tribes not sampled in our SNP database (such as northeastern U.S. and eastern Canadian tribes) can be expressed in region and population components from other parts of the Americas and in some cases Asia,” including Karitiana Brazil, Miao China, Hazara Pakistan, Thailand, Daur China, Mongol Mongolia and Cambodian. Interestingly all of us who also took the DNA Tribes SNP analysis show some Cambodian and Thailand affinities in addition to Native American. For the same reasoning experts are equally hesitant to call this Southeast Asian a Malagasy heritage; some African-Diasporans in the Americas could be descended from Malagasy slaves brought to the New World. Mr. Lucas offers, “Based on available STR data, the population of Madagascar is genetically related to: (1) Southern Africans (including Mozambiquans and Bantu speaking South Africans); (2) Horn of African populations; (3) Malay Archipelago populations; and (4) Polynesians. Based on available SNP data, Oceanian and Southeast Asian ancestral components are expressed for Polynesian populations. However, Oceanian percentages (expressed without Southeast Asian percentages) might reflect other ancestry (such as Native American ancestry from tribes not yet sampled in our SNP database).” 

A DNA Tribes study of genetic evidence of multiple waves of migrations to the Americas says SEA is in fact highest in such NA populations as Colombia (2.4%), Karitiana (2.1%), but also Surui Brazil (0.4%) and Pima Mexico (0.3%). “These small components might express traces of ancestral links with Asia for the Paleo-Indian, Paleo-Eskimo, and/or Proto-Inuit (Thule) migrations to the Americas, according to the report. To this extent, we can reason Afro-Diasporans in the Americas with heritage from Meso-, Central- & South-Amerindian populations might have inherited SEA markers from those population sources. Further, the referenced the report supports the notion of SEA and Oceania components in North Amerindian tribes, which I believe is the source of my referenced indigenous ancestry, more specifically Lenni Lenapi, an Algonquin speaking people, in re: “Asia-Pacific Island components are also identified for some North American populations. These include Malay Archipelago and Polynesian components, both related to maritime cultures of the Pacific Ocean. These populations include Coast Salish of British Columbia (11.6% Polynesian and 8.1% Malay Archipelago), Dogrib of Northwest Canada (11.9% Malay Archipelago), and Inupiat of Alaska (9.0% Polynesian). Similar Pacific Ocean components are also found in Koryak (11.6% Malay Archipelago) and Chukchi (9.9% Malay Archipelago) populations of Far Eastern Siberia. Asia-Pacific Island components are concentrated near Beringia and Northwest North America and not found in other studied populations. This suggests these components might have accompanied maritime related Paleo-Eskimo and/or Thule (Proto-Inuit) expansions in contact with early populations near the Pacific Rim of East Asia.” 

FTDNA's new myOrigins autosomal test description of SEA cluster, aptly titled “East Asian Coastal Islands,” provides an interesting historical context of SEA population migratory routes: “The great rice cultures from Shanghai south to the islands of Indonesia are the center of East Asian Coastal Islands. This cluster belongs to the Burmans, Thai, Khmer, and Vietnamese, who live in the bottomlands of mainland Southeast Asia. They have moved south, east, and west out of Taiwan and into Oceania, Madagascar, and even as far as Easter Island. This cluster may also be found along the edges of South Asia, and north among the peoples of the Yellow River Plain because of the migrations of the Han Chinese.” 

The truth is most African-Diaporans with roots in Colonial Americas come from varied ethnic and genetic experiences. This means there is a chance some Southeast Asian components might be real, or the result of a Native-Asian cohabitation from a post-Columbus event. I will explore two such possible scenarios [paraphrasing/quoting from Wikipedia]: 

Filipinos are from an ethnic group which migrated to Southeast Asia during the Holocene period and evolved into the Austronesian people, a group of Malayo-Polynesian-speaking people including those from Indonesia, the Philippines, Malaysia, Malagasy, the non-Han Chinese Taiwanese Aboriginals. Since the 1500‘s they were forced to migrate to Americas via Manila Galleons, which were Spanish trading ships that sailed once or twice per year across the Pacific Ocean between Manila in Spanish East Indies (present day-Philippines), and Acapulco, New Spain (present-day Mexico). In Louisiana there was the Saint Malo settlement founded by Africans but established sometime between 1763 and 1812 by Filipinos who deserted from Spanish ships during the Manila Galleon Trade. "These Filipinos settled in the marshlands of Louisiana where no Spaniards could reach them…However, women rarely lived in the St. Malo and those who did have families had them live in New Orleans or in other localities because of isolation and harsh conditions of the settlement. … Since there were no Filipino women, the Manilamen often courted and married Cajun women, Indians, and others." This means there were many opportunities for these Filipinos to leave their SEA genetic footprints in African-American, NA and European populations, and which might be expressed today in our genomes. 

Another possible source of this SEA could be from Madagascar, where the population is a mixture of Austronesian/SEA Asian + East African/Bantu. "Malagasy slaves were once taken to Brazil and the US during Trans-Atlantic Slave trade, but their number and the number of their descendants in these countries is unknown," despite some studies reporting as little as 3000 to the US. "Another population, estimated to be around 7,000, of Afro-Peruvians live in Morropón (Piura), a city in northern Peru, are all of Malagasy descent." However the general consensus is most of these descendants don't even know that they have this background. For comparison purposes here is an example of a Malagasy profile: 
East Asian & Native American (70%) 
-- Southeast Asian (68%) 
-- East Asian-Chinese (0.7%) 
-- Native American (0.1%) 
--Nonspecific East Asian & Native American (1.5%) 
South Asian (0.7%) 
Sub Saharan African (26%) 
-- West African (16%) 
-- Central/South African (%) 
-- East African (1%) 
-- Nonspecific Sub Saharan African (4%) 
-- European (0.3%) 
-- Southern European/Iberian (0.1%) 
Oceania (0.1%) 
With the Malagasy profile, we can see how some African-Diasporans in the Americas might inherit sizable SEA DNA from such a population. However what is not being seen in African-Diasporans with Amerindian admixture is the Chinese affinity as demonstrated in the Malagasy person. Instead most of us will show small East Asian-Yakut or East Asian-Mongolia, but this could be a problem with the algorithm assigning East Asian due to a lack of both Native American, SEA and Malagasy samples. 

But does all of this translate into genetic testing companies’ proprietary algorithms reading Native American alleles as SEA in African-Diasporans from the Americas? Or if these segments are real SEA, is it from a ancient or recent (last 500 years) event, in which case we could randomly inherit all SEA segments and no NA ones? Is the Sub Saharan African and European mix in most of these individuals is making East Asian and Central Siberian “appear” as SEA? … What is your opinion?


  1. Hi . I think I am making a bit of sence to it . With my 23andme it did not list any direct south American amerindean ...except the fact that my family can directly link members in our family who are Amerindean .Even a second cousin that 23and me found ( who our grandmothers would be sisters ) stated that with her she has no Asian ( I do which is chinese ) but instead of listing her as having Amerindean it lists her as having asian ancestry .What my mother said they learned in school is that many came from the barin straight.On route to South American

    1. What is important in helping determine the source if the profile is pulling in Native American accompanied with the East Asian/SEA. I think if someone is only pulling in East Asian (without NA in the profile), the East Asian/SEA may be from a different source other than Native American. Also considering the post, a person have a mixed multitude of ancestors and sifting that out.

  2. As someone who's of part Native American descent, and has a wee bit of SEA on 23andme, I found this an excellent read.

  3. I am African American whose maternal ancestors came mostly from Arkansas. My sister and I, who are full sisters, uploaded our raw DNA from our DNA results to Wegene. Wegene said both our mitochondrial Haplogroup was N8 with a mutation of 10398. I researched that Haplogroup it is found in China. My mother's great grandmother was born around 1860 in Arkansas. My mother's grandmother was said to have asian eyes. A nephew and my brother also have asian eyes. Our Wegene DNA results say we have small traces of Lahu Chinese. Mine is .20, my sister's is .42. My sister also has SEA DNA. She has between 1 and 2 percent Cambodian and Thai DNA. My Ancestry DNA results show I have 6% Africa SE Bantu. My sister has <1% Africa SE Bantu and <1% East Asia. We always thought we had NA DNA, but I only see NA on Gedmatch and Myheritage gives me .80% Inuit/Eskimo. My sister had <1% Mayan on Wegene. I am wondering if our Haplogroup N8 is from Madagascar? What is your opinion.

  4. Very good and interesting read.