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 GEDmatch.com.  The most recent uploads were samples taken from skulls of two extinct Botocudo (Brazil) men.  I blogged about it in December 2014.

https://hawaiiandna.wordpress.com/2014/12/12/polynesian-mtdna-in-botocudo-of-brazil/

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 (http://www.ncbi.nlm.nih.gov/pubmed/25455029), 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 GEDmatch.com, 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.

Bot17,Brazil,0.4ky1
Kit # F999964
mtDNA – B4a1a1
Y DNA – C-Z31878 (C1b2 [2015])

Bot15,Brazil,0.4ky
Kit # F999963
MtDNA – B4a1a1a
Y DNA – C-PH3092 (C1b2 [2015])

You can check out Felix’s blog for other ancient DNA uploaded. http://www.fi.id.au/

Also the supplemental information can be accessed here.

Footnotes

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

Polynesia category – Ancestry.com (part 2)

Last December I blogged an entry entitled Polynesia Category – Ancestry.com.  It was about their new Pacific Islander category and how I noticed Filipinos had been coming up with that category as well.  I have been noticing other people of mainly Southeast Asian ancestry having small percentages of Polynesia in their ancestry composition.

A Taiwanese aboriginal would have about the same amount as Filipinos, ranging around 25% – 29%.  A friend that I know whose mother is a Taiwanese aboriginal and he got DNA tested came up with 13% Polynesia and 37% Asia East.  That is nearly identical to what half Filipinos would get.  A Taiwanese person who has Fujian ties centuries ago and is not a Taiwanese aboriginal showed up having 8% Polynesia and 92% Asia East.  Another friend whose mother is from the Moluccas (Indonesia) and tested himself came up with 19% Melanesia, 12% Polynesia and 17% Asia East.  I have had three Chinese people who got tested with Ancestry.com and told me that they also had Polynesia show up within the 10% – 11% range.

All of these are the results of picking up that Southeast Asian component that exists for these people including Polynesians, of which makes up about 80% of their genome.  A few weeks ago I spoke to Ross E. Curtis, Ph.D., a computational biologist, specializing in genetics and visual analytics, and has been with Ancestry.com since 2012.  I informed him of the small sampling size that they had, just 18 samples (see Polynesia Category – Ancestry.com) and the problem that provided.  He was not too familiar with the details behind, mentioned a colleague that helped to put that category together but was unable to provide any real insight into that specific category.  So whatever I am learning about this comes from actual testees and especially those who are not of Polynesian ancestry.

My mother finally did test with Ancestry.com back in March when I made an emergency trip to Wai’anae, O’ahu, Hawai’i and had my mother retake that test since it got rejected.  I had predicted that she would basically show up as 80% Polynesia and 20% European, but this is her actual results.Screen Shot 2015-06-30 at 7.33.11 AM

 

It is as almost that Ancestry tends to give us the lowest possible amount of European.  I got 8% while my mother got 11%.  And just as it did with FTDNA’s myOrigins, it gave my mother a bit more  Scandinavian.  Actually with myOrigins my mother gets 19% while I show 11% Scandinavia.

We will probably see more people of Southeast Asian origin come up with the Pacific Islander/Polynesia/Melanesia category as a proxy for Southeast Asian as more get tested.

No surprise however when I looked at her matches, a lot of close 2nd – 3rd cousin matches.

Screen Shot 2015-06-30 at 3.45.00 PM Screen Shot 2015-06-30 at 3.45.11 PM

 

My mother has three 1st – 2nd cousin matches, Extremely High confidence.  But for the 2nd – 3rd cousin range, she has sixty-seven matches, Extremely High confidence and a total of two-hundred sixty-seven matches for 3rd – 4th cousins, all Extremely High confidence as well.  Others not familiar with Polynesian endogamy, or endogamy in general insisted that these close matches have to be actual close matches.

I managed to match two of my mother’s 2nd – 3rd cousin matches on GEDmatch.com.  Assuming that the matches are listed in order of closest to the least closest, these are how the two matches up with my mother.

The 7th 2nd – 3rd cousin match:
510cM – total shared
26.9cM – largest segment

The 40th 2nd – 3rd cousin match (out of 67):
331.9cM – total shared
22.2cM – largest segment

These are one of the few larger segment matches that she has while most rarely go up to 15cM.  Something common with endogamous groups.  Only uploading to GEDmatch can it be clear if the 2nd – 3rd cousin matches are real 2nd – 3rd cousin matches, or an endogamous ones that has numerous segments rarely going higher than 15cM for the largest segment.  Other than that, any Polynesian testing at Ancestry cannot assume that the 1st – 2nd or 2nd – 3rd cousin matches are actually that close as estimated.