One thing you can always count on in the infant science of population genetics… whatever you think you know, for sure, for a fact…well….you don’t. So don’t say too much, too strongly or you’ll wind up having to decide if you’d like catsup with your crow! Well, not literally, of course. It’s an exciting adventure that we’re on together and it just keeps getting better and better. And the times…they are a changin’.
We have some very interesting news to report. Fortunately, or unfortunately – the news weaves a new, but extremely interesting, mystery.
Ancient Mitochondrial DNA
Back in 2013, a paper, Identification of Polynesian mtdNA haplogroups in remains of Botocudo Amerindians from Brazil, was published that identified both Native American and Polynesian haplogroups in a group of 14 skeletal remains of Botocudo Indians from Brazil whose remains arrived at a Museum in August of 1890 and who, the scientists felt, died in the second half of the 19th century.
Twelve of their mitochondrial haplogroups were the traditional Native haplogroup of C1.
However, two of the skulls carried Polynesian haplogroups, downstream of haplogroup B, specifically B4a1a1a and B4a1a1, that compare to contemporary individuals from Polynesian, Solomon Island and Fijian populations. These haplotypes had not been found in Native people or previous remains.
Those haplogroups include what is known as the Polynesian motif and are found in Indonesian populations and also in Madagascar, according to the paper, but the time to the most common recent ancestor for that motif was calculated at 9,300 years plus or minus 2000 years. This suggests that the motif arose after the Asian people who would become the Native Americans had already entered North and South America through Beringia, assuming there were no later migration waves.
The paper discusses several possible scenarios as to how a Polynesian haplotype found its way to central Brazil among a now extinct Native people. Of course, the two options are either pre-Columbian (pre-1500) contact or post-Columbian contact which would infer from the 1500s to current and suggests that the founders who carried the Polynesian motif were perhaps either slaves or sailors.
In the first half of the 1800s, the Botocudo Indians had been pacified and worked side by side with African slaves on plantations.
Beyond that, without full genome sequencing there was no more that could be determined from the remains at that time. We know they carried a Polynesian motif, were found among Native American remains and at some point in history, intermingled with the Native people because of where they were found. Initial contact could have been 9,000 years ago or 200. There was no way to tell. They did have some exact HVR1 and HVR2 matches, so they could have been “current,” but I’ve also seen HVR1 and HVR2 matches that reach back to a common ancestor thousands of years ago…so an HVR1/HVR2 match is nothing you can take to the bank, certainly not in this case.
Full Genome Sequencing and Y DNA
This week, one on my subscribers, Kalani, mentioned that Felix Immanuel had uploaded another two kits to GedMatch of ancient remains. Those two kits are indeed two of the Botocudo remains – the two with the Polynesian mitochondrial motif which have now been fully sequenced. A corresponding paper has been published as well, “Two ancient genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil” by Malaspinas et al with supplemental information here.
There are two revelations which are absolutely fascinating in this paper and citizen scientist’s subsequent work.
First, their Y haplogroups are C-P3092 and C-Z31878, both equivalent to C-B477 which identifies former haplogroup C1b2. The Y haplogroups aren’t identified in the paper, but Felix identified them in the raw data files that are available (for those of you who are gluttons for punishment) at the google drive links in Felix’s article Two Ancient DNA from indigenous Botocudos of Brazil.
I’ve never seen haplogroup C1b2 as Native American, but I wanted to be sure I hadn’t missed a bus, so I contacted Ray Banks who is one of the administrators for the main haplogroup C project at Family Tree DNA and also is the coordinator for the haplogroup C portion of the ISOGG tree.
You can see the position of C1b2, C-B477 in yellow on the ISOGG (2015) tree relative to the position of C-P39 in blue, the Native American SNP shown several branches below, both as branches of haplogroup C.
The branch above is the Polynesian (B477) branch and below, the Native American (P39) branch of haplogroup C.
In addition to confirming the haplogroup that Felix identified, when Ray downloaded the BAM files and analyzed the contents, he found that both samples were also positive for M38 and M208, which moves them downstream two branches from C1b2 (B477).
Furthermore, one of the samples had a mutation at Z32295 which Ray has included as a new branch of the C tree, shown below.
Ray indicated that the second sample had a “no read” at Z32295, so we don’t know if he carried this mutation. Ray mentions that both men are negative for many of the B459 equivalents, which would move them down one more branch. He also mentioned that about half of the Y DNA sites are missing, meaning they had no calls in the sequence read. This is common in ancient DNA results. It would be very interesting to have a Big Y or equivalent test on contemporary individuals with this haplogroup from the Pacific Island region.
Ray notes that all Pacific Islanders may be downstream of Z33295.
The second interesting aspect of the genomic sequencing is that the remains did not show any evidence of admixture with European, Native American nor African individuals. More than 97% of their genome fits exactly with the Polynesian motifs. In other words, they appear to be first generation Polynesians. They carry Polynesian mitochondrial, Y and autosomal (nuclear) DNA, exclusively.
In total, 25 Botocudo remains have been analyzed and of those, two have Polynesian ancestry and those two, BOT15 and BOT17, have exclusively Polynesian ancestry as indicated in the graphic above from the paper.
When did they live? Accelerator mass spectrometry radiocarbon dating with marine correction gives us dates of 1479-1708 AD and 1730-1804 for specimen BOT15 and 1496-1842 for BOT17.
The paper goes on to discuss four possible scenarios for how this situation occurred and the pros and cons of each.
The Polynesian Peru Slave Trade
This occurred between 1862-1864 and can be ruled out because the dates for the skulls predate this trade period, significantly.
The Madagascar-Brazil Slave Trade
The researchers state that Madagascar is known to have been peopled by Southeast Asians and not by Polynesians. Another factor excluding this option is that it’s known that the Malagasy ancestors admixed with African populations prior to the slave trade. No such ancestry was detected in the samples, so these individuals were not brought as a result of the Madagascar-Brazil slave trade – contrary to what has been erroneously inferred and concluded.
Voyaging on European Ships as Crew, Passengers or StowAways
Trade on Euroamerican ships in the Pacific only began after 1760 AD and by 1760, Bot15 and Bot17 were already deceased with a probability of .92 and .81, respectively, making this scenario unlikely, but not entirely impossible.
Polynesian ancestors originated from East Asia and migrated eastwards, interacting with New Guineans before colonizing the Pacific. These people did colonize the Pacific, as unlikely as it seems, traveling thousands of miles, reaching New Zealand, Hawaii and Easter Island between 1200 and 1300 AD. Clearly they did not reach Brazil in this timeframe, at least not as related to these skeletal remains, but that does not preclude a later voyage.
Of the four options, the first two appear to be firmly eliminated which leaves only the second two options.
One of the puzzling aspects of this analysis it the “pure” Polynesian genome, eliminating admixture which precludes earlier arrival.
The second puzzling aspect is how the individuals, and there were at least two, came to find themselves in Minas Gerais, Brazil, and why we have not found this type of DNA on the more likely western coastal areas of South America.
Regardless of how they arrived, they did, and now we know at least a little more of their story.
At GedMatch, it’s interesting to view the results of the one-to-one matching.
Both kits have several matches. At 5cM and 500 SNPs, kit F999963 has 86 matches. Of those, the mitochondrial haplogroup distribution is overwhelmingly haplogroup B, specifically B4a1a1 with a couple of interesting haplogroup Ms.
Y haplogroups are primarily C2, C3 and O. C3 and O are found exclusively in Asia – meaning they are not Native.
Kit F999963 matches a couple of people at over 30cM with a generation match estimate just under 5 generations. Clearly, this isn’t possible given that this person had died by about 1760, according to the paper, which is 255 years or about 8.5-10 generations ago, but it says something about the staying power of DNA segments and probably about endogamy and a very limited gene pool as well. All matches over 15cM are shown below.
Kit F999964 matches 97 people, many who are different people that kit F999963 matched. So these ancient Polynesian people, F999963 and F999964 don’t appear to be immediate relatives.
Again, a lot of haplogroup B mitochondrial DNA, but less haplogroup C Y DNA and no haplogroup O individuals.
Kit F999964 doesn’t match anyone quite as closely as kit F999963 did in terms of total cM, but the largest segment is 12cM, so the generational estimate is still at 4.6, All matches over 15cM are shown below.
Who are these individuals that these ancient kits are matching? Many of these individuals know each other because they are of Hawaiian or Polynesian heritage and have already been working together. Several of the Hawaiian folks are upwards of 80%, one at 94% and one believed to be 100% Hawaiian. Some of these matches are to Maori, a Polynesian people from New Zealand, with one believed to be 100% Maori in addition to several admixed Maori. So obviously, these ancient remains are matching contemporary people with Polynesian ancestry.
The Unasked Question
Sooner or later, we as a community are going to have to face the question of exactly what is Native or aboriginal. In this case, because we do have the definitive autosomal full genome testing that eliminates admixture, these two individuals are clearly NOT Native. Without full genomic testing, we would have never known.
But what if they had arrived 200 years earlier, around 1500 AD, one way or another, possibly on an early European ship, and had intermixed with the Native people for 10 generations? What if they carried a Polynesian mitochondrial (or Y) DNA motif, but they were nearly entirely Native, or so much Native that the Polynesian could no longer be found autosomally? Are they Native? Is their mitochondrial or Y DNA now also considered to be Native? Or is it still Polynesian? Is it Polynesian if it’s found in the Cook Islands or on Hawaii and Native if found in South America? How would we differentiate?
What if they arrived, not in 1500 AD, but about the year 500 AD, or 1000 BCE or 2000 BCE or 3000 BCE – after the Native people from Asia arrived but unquestionably before European contact? Does that make a difference in how we classify their DNA?
We don’t have to answer this yet today, but something tells me that we will, sooner or later…and we might want to start pondering the question.
I want to thank all of the people involved whose individual work makes this type of comparative analysis possible. After all, the power of genetic genealogy, contemporary or ancient, is in collaboration. Without sharing, we have nothing. We learn nothing. We make no progress.
In addition to the various scientists and papers already noted, special thanks to Felix Immanual for preparing and uploading the ancient files. This is no small task and the files often take a month of prep each. Thanks to Kalani for bringing this to my attention. Thanks to Ray Banks for his untiring work with haplogroup C and for maintaining his haplogroup webpage with specifics about where the various subgroups are found. Thanks to ISOGG’s volunteers for the haplotree. Thanks to GedMatch for providing this wonderful platform and tools. Thanks to everyone who uploads their DNA, and that of their relatives and works on specific types of projects – like Hawaiian and Maori. Thanks to my haplogroup C-P39 co-administrators, Dr. David Pike and Marie Rundquist, for their contributions to this discussion and for working together on the Native American Haplogroup C-P39 Project. It’s important to have other people who are passionate about the same subjects to bounce things off of and to work with. This is the perfect example of the power of collaboration!