Botocudo ancient DNA sample uploaded on GEDmatch

Felix Immanuel, a software professional at Hewlett-Packard based out of Canberra, Australia who has a Bachelor of Engineering in Computer Science and a Master of Science in Forensic Computing and Cyber Security from University of South Australia, has been uploading a bunch of ancient DNA to  The most recent uploads were samples taken from skulls of two extinct Botocudo (Brazil) men.  I blogged about it in December 2014.

At that time, they hypothesized a few ways how the Polynesian motif could have made it into the genome of these now extinct Botocudo tribe.  But recently in Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil (, they talk about the hypotheses again and how they came to the conclusion that these samples are definitely Polynesian.

One thing that was consistently repeated, was how the skulls analyzed had no detectable Native American ancestry.  They say, “[w]e find that the genomic ancestry is Polynesian, with no detectible Native American component.”   That “all the genetic data point towards two individuals with Polynesian ancestry and no detectable Native American ancestry.” And they continued again saying that a “clustering analyses suggest that they have no detectable Native American ancestry and share the same components as the Polynesian population.”

The two male individual samples used, known as Bot15 and Bot17, presented a combination of mitochondrial DNA (mtDNA) variants common in present day Oceanian populations.

They pointed out a few hypotheses that was mentioned in the other paper, and that “the 1862-1864 AD Peru-Polynesia slave trade can be excluded, given that the 14C calibrated dates for the skulls predate the beginning of this trade.”  Because these skulls have been radiocarbon dated, the dates that they came up for Bot15 was 1479 – 1708 AD and 1730 – 1804 AD, and for Bot17 was 1496 – 1842 AD.  So the fact that the Peru-Polynesia slave trade occurred after the death of these people excluded the hypothesis that Polynesians were brought over during that slave trade.

Also, the Madagascar-Brazil slave trade hypothesis has been excluded due to the recent genomic data that demonstrated that the Malagasy ancestors admixed with African populations prior to the slave trade, and no such ancestry is detected in the Botocudo sample.  Madagascar was peopled by Southeast Asian and not Polynesian populations.

And finally, trade involving Euroamerican ships in the Pacific only began after 1760 AD.  By 1760 AD, both Bot15 and Bot17 were already deceased with a probability of 0.92 and 0.81, respectively, making this scenario unlikely.

These two samples analyzed had no Native American component detected.  Felix was able to extract SNPs from the raw data to come up with C-PH3092, and  C-Z31878, which are Melanesian in origin and the C haplogroup is common in eastern Polynesia.  The mtDNA haplogroups were B4a1a1a and B4a1a1.  B4a1a1a is pretty common throughout Polynesia especially in eastern Polynesia.  And most importantly these samples are a match only to eastern Polynesians.  There is no doubt that these particular samples are Polynesians.  Question is, how did they get there?  Did they manage to produce offspring with the local Botocudo groups like the Crenaques, Nac-Nuc, Minia-Jirunas, Gutcraques, Nac-Reques, Pancas, Manhangiréns or Incutcrás?  Or did they have offspring but they never survived?  Were these samples that were found the actual people who traveled directly from Polynesia?  Or did they arrive as a group and intermarried within their own group of Polynesians but later were found among the other Botocudo people?   And why travel thousands of miles over mountains and crossing rivers, possibly going through or bypassing the Pantanal that borders Bolivia and Brazil and continue to head towards the east?

We have other evidence like the kumara [sweet potato] or ‘uala [Hawaiian word for sweet potato] that originated from South America, and not to mention our many oral traditions of all the famous travelers who went abroad to Kahiki [foreign lands; Tahiti] and towards ka hikina [the east] where the rising of the sun is.  Travelers like Kuali’i, Hema, Kaha’i, Wahieloa, Laka and Luanu’u. Now DNA is showing the scientific community what we have known based on our oral traditions.

Now that Felix uploaded both of these samples up on, we see that both of the samples matches a few of us [both admixed and non-admixed] Hawaiians (including my mother), Maori, and a Cook Island Maori.  No surprise that eastern Polynesians are a match, given how they lack genetic diversity much more than the older western Polynesians. But it may also suggest, if not confirm, that it was specifically part of the expansion of eastern Polynesians.  But was there another expansion that late in the 1600s?  Another not so surprising thing about these matches is that there may be small segment matches, but when utilizing GEDmatch’s graph when comparing ONE TO ONE, we can still see small segments of full identical region for a few of these matches.

Kit # F999964
mtDNA – B4a1a1
Y DNA – C-Z31878 (C1b2 [2015])

Kit # F999963
MtDNA – B4a1a1a
Y DNA – C-PH3092 (C1b2 [2015])

You can check out Felix’s blog for other ancient DNA uploaded.

Also the supplemental information can be accessed here.


1. Y haplogroup C Botocudo sample is carbon-dated to 1419-1477 AD – Ray Banks


28 thoughts on “Botocudo ancient DNA sample uploaded on GEDmatch

  1. What is strange is that I matched with those two samples. And I am a mainly European person. However it appears I have some African, Amerindian, and Polynesian and Melanesian as well. The trick now is to find out why.


    • Hi Cheryl,
      I didn’t see you come up as a match on the ONE TO MANY for F999963 nor F999964. Unless you are using another name? I know of the people who are matching those two kits, but do not recognize your name.


    • Hi Laura,

      Would you mind sharing your GEDmatch kit #? Or you can email it to me if you want. Because you said you joined today, your ONE TO MANY (I assume) isn’t ready yet?



  2. Hello, I did the Archaic on DNA today and so got to Googling because this one is new to me. I knew I was admix and know some of it and have a nice database built for compare so did the two Id’s at 200/1 and got matches. I then looked in my Genomemate and I have three matches on this I have a Clovis here and two more that I also tested at those settings and they both match. I know a good bit of history on both of them back to the 1600 so would love to learn more. I don’t mind sharing my id online as sharing is the only way we find anything and I think I recognize this name from the Gedmatch group. I have some thoughts on the endogamous groups that these two may are descended from. I have only checked my Chromosome 5 match because it is the only one that showed up in Bot15 and Bot17 so I thought that was a good start and am interested in learning more about the division of the two since I assume it is two archaic subjects that were tested. Glad to help in anyway possible. M610654


    • I noticed that those two kits are no longer available for a ONE TO MANY match. But running your kit number against both kits showed no matches. I also saw your ONE TO MANY, also no known Polynesians on your matches. I did see Bonnie Schrack on there.


  3. I saw a 19th century picture of a group of Botocudos. They look like Polynesians to me. Some wonder how they got across the Andes, but why would they have to go that way, when they just could have followed the coast north across Central America, then down to where they settled in SE Brazil?
    America seems to have been visited and/or settled by many different groups over the millennia. For instance, there are the bones, also found in Brazil, of people, who may be from the Australian Aborigines. It is thought that some of their blood and possibly their culture exists in the people of Teirra del Fuego.


    • So what isn’t mentioned in this blog post is an update on this whole thing. Turns out a museum in NZ loaned 2 skulls, one Moriori & one Maori to the museum in Rio. Not sure what “loan” supposed to mean, but that’s what happened. And according to the archive files in the museum in NZ, it was dated at the same time the museum in Rio acquired the skulls. People in another Facebook group (International Society on Genetic Genealogy) wanted something more official rather than reading the letter from the repatriator for that particular museum. So mystery solved. I knew it wasn’t an “ancient” skull only because modern Polynesians came up as a genetic match to the skulls, my family included.


      • Hello! I recently joined GEDmatch and I am fascinated by the things I’m discovering. However, I am kind of intrigued by the results of the Archaich Matches. I am both of African and European ancestry but the results do not show any African match. How is that possible?


      • Hi Deb,

        Interesting you said you have African but show no African? Unless your non-admixed African ancestor was from generations ago? Usually that should show up if that one sole person was your 2x great-grandparent. Anything beyond a 3x great-grandparent, then it gets to be more random and you just may not have inherited any of those markers/SNPs that indicate that particular ancestry.


  4. Hello!
    I’m also new to GEDmatch and discovered tonight that I have two matches on my archaic DNA with the Bot 15 & 17 remains. I’m amazed and delighted and want to know how Polynesian ancestry came to me! Does this mean that one of my more recent ancestors (within the past 500 years) was from one of the Pacific Islands? I also have the match with a Clovis sample and as I’d expect links with Sweden, the UK and Germany. When I’ve run the other break-downs, it gave me a percentage of north African (which I think is likely the trace ‘Iberian peninsula’ that gave me). Seems I have Italian too, from Sardinia specifically. My own genealogy hasn’t revealed any of the trace regions so far, but there are quite a few gaps in my pedigree. I’m really fascinated as to how I might have Polynesian ancestry!


    • If you used the ARCHAIC DNA MATCHING tool, the threshold is lowered to a very low 0.5cM. So a lot of people will match these ancient DNA samples. Normally when you get DNA tested, the tresholds are set around 5cM – 7cM and either 500SNPs to 700SNPs. At, it’s defaulted to 500SNPs & I think 5cM in your ONE TO MANY.

      You need to do a ONE TO ONE with your kit and the Botocudo skulls (and Clovis too) at the default setting, which is 500SNPs & 7cM. 700SNPs is also acceptable too.


      • Thanks Kalani 🙂 I ran the one-to-one test with Bot 15 and 17 and got a negative result. I’m still intrigued as MDLP picks up a trace of 1.17 Polynesian, MDLP WORLD also gives me 1.11 Melanesian, while Harrapa world gives me 0.38 Papuan. If this is the result of ancient DNA, I would be curious to know how it comes into a European genome like mine, all the other ancestry is what I’d expect to find, so this little tiny bit of Polynesian makes me wonder if there was some genetic exchange with the ancestors of the Pacific Islanders and perhaps more nearby central Asian peoples? If there’s any articles about this, would love to know!


  5. yes, other people, those who have strictly European ancestry (and can be from Europe) will also get small percentages of various categories that do not even relate to them. I’ve seen Sub-Saharan African come up for Asians, and vice versa. The ancestry portions are not accurate for some, and depending on how many categories there are, the more there are, the more likely it’ll be inaccurate. If it’s more general, like Africa, Europe, Asia, then the more likely it’ll be more accurate.

    So to give you an idea, a pure Polynesian person at MDLP World will get 24% – 35%. I have a friend whose parents are from the Maluku area of Indonesia, near New Guinea and he gets 39% Melanesia. At Harappa World, pure Polynesians will get 19% – 33%. My mother is 85% Hawaiian, so she gets 20.78% Melanesia MDLP World and 18.33% Papuan Harappa. Her sister gets 21.92% Melanesia MDLP World and 19.44% Papuan Harappa World. For me and my two brothers, we get:

    Kalani – 13.38% Melanesian; 10.85% Papuan
    Kaimi – 18.47% Melanesian; 16.37% Papuan
    Travis – 11.53% Melanesian; 10.53% Papuan
    We all have different fathers and Kaimi’s father is half Hawaiian and half Filipino. My father was Filipino, so that may have increased the Oceania/Papuan/Melanesian slightly.


  6. There is a comparative on the internet about the language Kaingang or Xokleng (here in the south of Santa Catarina also they were called of Botocudo) and Polynesian languages. There are many similar words. The Botocudos of the north of Brazil and south are of the group Gê. He did a DNA test and the result states that I have 1% Oceania, 0.58% NA and 0.61% Siberia.
    My great grandmother was a descendant of NA.
    Sorry for the bad english spoken I only speak Spanish and Portuguese.
    Mow the site:


    • Obrigado Mauri! Conheço SC, eu fui lá em 2012. Eu me lembro essa palavra (grupo) Kaingag. Mas vc fez um teste de DNA com uma outra empresa? É normal q pessoas com muito East Asian tem um pouco de Oceania e vice-versa. Obrigado pelo link!


      • Eu fiz com a FTDNA, mas os resultados gerados com Gedmatch batem certo com minha ancestralidade. Na minha árvore até a sétima geração tenho 57,81% alemão, português 10,94%, 3,12% luxemburgues, 1,56% belga, 25% italiano e 1,56% indígena. No meu Gedmatch (Eurogenes, MDLP, Word9 e PuntDNAL) a porcentagem é similar a isso, acrescentando oriente médio e sul da Ásia (Índia). Gostaria de saber se tenho algum parentesco com Kaingang, Xokleng ou Guarani. Existem outros mapeamentos genéticos para Kaingang, Xokleng ou Guarani igual foi feito com os 2 crânios botocudos? Quero comparar para ver se possuem muito DNA da Oceania. Se os grupos Gês de Santa Catarina possuem parentesco com o grupo Gê da Minas Gerais ou Bahia, então a probabilidade deles possuírem muito DNA da Oceania é grande. Muito obrigado por responder.


  7. Com sua porcentagem de indígena, não existe com FTDNA (New World)? Ou tem de East Asian? Eu lembro quando cheguei em Florianópolis eu falei pra meu amigo q tem bolivianos como em SP, e ele me falou q não são bolivianos (indígenas) mas indígenas dessa área. Eu não sabia q eles existem em SC.


  8. Parece que se tem uma herença indígena, é precisa sim. Se não tem como eu, não é precisa. kkkkk Diz q eu tenho 1% – 2%, de vez em quando (depende do calculador) menos de 1%.


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