Determining half-relationships with Polynesians

I recently got my cousin’s results to compare to my mother and my brothers.  This cousin’s father was my mother’s half-brother George, so a half-first cousin relationship.

Prior to making contact with my mother’s relatives I was thinking of having these cousins tested as a means to figure out who my mother’s biological father really was.  But a couple of months ago when I did make contact with these long lost relatives it was revealed that my mother’s biological father was Joseph Kaapuiki Akana, the man whom I doubted was my mother’s father based on his name (Akana is of Chinese origin) and the fact that my mother remembers her father being pure Hawaiian and her DNA composition does not support Chinese ancestry.  I thought that maybe testing these half-cousins would determine if their grandfather was my mother’s biological father.  But it is more complicated than I realized.

Like my mother’s father Joseph Kaapuiki Akana, George’s father was also Hawaiian.  George and my mother shared the same Hawaiian mother.

This is what the ISOGG Wiki Autosomal DNA Statistics page says about how much should be shared between a half-aunt and also to half-cousins.

Screen Shot 2015-12-29 at 7.17.17 PM

Combining with Blaine Bettinger’s Shared cM Project, the total shared for a half-aunt would range from 540cM to 1348cM, averaging 892cM.  The average is around the amount indicated by the ISOGG Wiki page.

For a half-first cousin, Blaine Bettinger’s Shared cM Project says it would range from 262cM to 1194cM, averaging 458cM.  Again, that average is what is indicated on the ISOGG Wiki page.

This is how GEDmatch.com compares my half-cousin to us.

Screen Shot 2015-12-29 at 7.33.09 PMIt is obviously on the high end, for a half-aunt while half-first cousin, not that extreme.  But we are talking of one example only.  There are more half-cousins that I could have test and probably will in the future.  And all of these cousins have had a grandfather that was Hawaiian, so I would expect their amounts to be high.

Comparing to non-endogamous groups, I compare my paternal aunt to her nephews and nieces and a great-nephew and great-niece on GEDmatch.

Screen Shot 2015-12-29 at 7.45.46 PM

My cousin Terri may share the lowest total among the 1st cousins but it does not seem that significantly different from the average 1700cM.  It is interesting to see that her largest segment is 104.7cM.  When I look at my half-first cousin and how much she shares with her half-aunt (my mother), the total is 1412.8cM, and largest segment is 103.3cM.  That figure can be misleading.  I have more cousins on my father’s side that I have yet to test and there may be other cousins who share less or more with our aunt than the cousins that have already tested.

If I take my aunt out of the equation, this is how the cousins compare to each other.

Screen Shot 2015-12-29 at 7.50.04 PM

A couple of my paternal 1st cousins share much less with each other than my half-cousin does with me and my brothers.

It will be awhile before I can get an ample amount of Polynesians who have close relatives tested to fully make a comparison.  Initially I wanted to see if testing half-cousins would help determine if my mother’s siblings were half or full siblings and when I was not certain that Joseph Kaapuiki Akana was her biological father.

It is clear now that any type of half-relationship is difficult to determine if the other parent is also Polynesian, and in our case Hawaiian.  My grandmother married 3 different Hawaiian men and so far from what I know, they have ties to geographically different places.

The endogamous nature just makes it hard to determine the relationship even if it is a close relationship.  It does not have to be a distant 3rd cousin and beyond to appear as a closer relationship.  Even with cousins (half or full) and half-siblings, they seem to appear on the higher end of the relationship, possibly giving a false prediction if the true relationship was not known.

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Comparing Western and Eastern Polynesians

In my last blog entry “Tiny Segments from the Same Common Ancestors“, I began comparing Western Polynesians (Samoans & Tongans), and Eastern Polynesians (Maori and Hawaiians), and compared them to each other in order to show how the tiny segments appeared like missing teeth on the chromosome browser.  Now I will show how people compare to each other based on total centimorgans and their longest block (FTDNA).

First I compare Tongans and Samoans to each other.  Both Samoans and Tongans are Western Polynesians and are the most diverse.   Polynesian settlement began in the west in the Tonga/Samoa/Fiji area.  I mentioned this in a previous entry “Loss of heterozygosity – from Western Polynesia to Eastern Polynesia.”

T = Tongan
S = Samoan
– = no match

I colored it to make it easier to see or compare Tongans to Tongans in light green, and Samoans to Samoans in light blue.  The ones not colored are comparing Samoans to Tongans.  The top number is the total shared in centimorgans, while the bottom number is the longest block (largest segment).  The average totals seem to be between the upper 200s to mid-300s. The lower numbers (in the hundreds) is due to the fact that the person is admixed.  In other words, they are not pure Samoan/Tongan, and usually have some European ancestry.

WestPoly

Comparing Tongans to themselves:
TOTAL
lowest –  117cM (part Tongan)
highest – 340cM
average – 258cM

LONGEST BLOCK
lowest – 5.79cM
highest – 10.51cM
average – 8.54cM

Comparing Samoans to themselves:
TOTAL
lowest – 165cM (part Samoan)
highest – 366cM
average – 271cM

LONGEST BLOCK
lowest – 5.66cM
highest – 16.54cM
average – 9.20cM

Comparing Tongans to Samoans:
TOTAL
lowest –  143cM
highest – 321cM
average – 248cM

LONGEST BLOCK
lowest – 5.79cM
highest – 11.07cM
average – 7.81cM

This is what it looks like when I compare those same Tongans and Samoans to Hawaiians and Maoris who are Eastern Polynesians.

H = Hawaiian
M = Maori
T = Tongan
S = Samoan
? = unable to determine if a match
– = no match

In this graph, I again colored it for easy comparison.  Hawaiian vs. Tongans in light brown, Hawaiians vs. Samoans in golden yellow, Maoris vs. Tongans in pink, and Maoris vs. Samoans in light green.

West-EastPoly

Most of the Eastern Polynesians are admixed except for two Hawaiians and one Maori.  But those that are admixed are still more than 75% Polynesian which still keeps the totals fairly high as you can clearly see it still above one hundred with the exception of one Hawaiian who is admixed to the Tongan that is admixed.  In fact, that admixed Tongan only shares with one Hawaiian and one Maori, both less than 100cM.  Yet their longest block still falls within the range.

Comparing Hawaiians to Tongans:
TOTAL
lowest – 72cM
highest – 341cM
average – 199cM

LONGEST BLOCK
lowest – 5.34cM
highest – 12.12cM
average – 7.94cM

Comparing Hawaiians to Samoans:
TOTAL
lowest –  135cM
highest – 314cM
average – 213cM

LONGEST BLOCK
lowest – 5.09cM
highest – 11.50cM
average -7.57cM

Comparing Maoris to Tongans:
TOTAL
lowest –  68cM
highest – 240cM
average – 202cM

LONGEST BLOCK
lowest – 5.31cM
highest – 10.94cM
average – 7.87cM
Comparing Maoris to Samoans:

TOTAL
lowest –  147cM
highest – 278cM
average – 229cM

LONGEST BLOCK
lowest – 5.28cM
highest – 10.94cM
average -7.81cM

When looking at the average, it seems to be consistent as far as comparing Eastern Polynesians to any Western Polynesian.  However that changes drastically when comparing Eastern Polynesians to themselves.

H = Hawaiian
M = Maori
? = unable to determine if a match
– = no match

I colored Hawaiians in light blue and Maoris in light green when comparing to themselves.  The non-colored portion is when they one group is compared to the other.

EastPoly

Comparing Hawaiians to Hawaiians:
TOTAL
lowest –  225cM
highest – 780cM
average – 463cM

LONGEST BLOCK
lowest – 8.45cM
highest – 23.58cM
average -14.90cM

Comparing Maoris to Maoris:
TOTAL
lowest –  581cM
highest – 694cM
average – 641cM

LONGEST BLOCK
lowest – 12.51cM
highest – 19.98cM
average -16.66cM

Comparing Maoris to Hawaiians:
TOTAL
lowest –  291cM
highest – 773cM
average – 514cM

LONGEST BLOCK
lowest – 8.98cM
highest – 29.68cM
average -16.20cM

So to recap, showing just the average total shared and the average longest block size:Screen Shot 2015-04-20 at 4.45.54 PM

Although I used only 3 Maoris compared to 8 Hawaiians, it was based on the top matches to my mother.  There were a few more Maoris but I did not have access to their data and that would have allowed more “?” in the charts.  But as we can see, the Western Polynesians tend to have lower totals since they are more diverse unlike the Eastern Polynesians.  More admixed Polynesians will result in lower totals, but the longest block is not that much difference from those not admixed.

In the future I will probably attempt to look at admixed Polynesians and compare them to show the average longest block sizes compared to those not admixed.

Tiny segments from the same common ancestors

Disclaimer: This post demonstrates the use of 1+cM when comparing specific groups of people in order to see patterns of multiple descent from a few ancestors.  It should not be used to validate connections with matches, particularly in this example where connections are beyond a genealogical time frame reaching at least up to 500 years.

Recently I have been comparing both western Polynesian (Tongan and Samoan) and eastern Polynesian (Hawaiian and Maori) matches.  I compared western Polynesians among themselves, and  did the same thing with eastern Polynesians comparing them among themselves.  Then I compared the two groups to each other.

To those who are not familiar with Polynesian origins and/or are new to reading my blog, I will recap.  The ancestors of Polynesians originated from the Melanesia area and thrived there for thousands of years. Thousands of years later a group of “Austronesians” originating from Southeast Asia moved into the area, intermingled briefly and continued to move into western Polynesia where Polynesian culture was born.  At least a couple of thousand of years would pass before they would continue to expand further eastward.  As Polynesians moved from west to east, their genome became less diverse due to repeated founder’s effects and bottle necking.

oceania

I analyzed my mother’s results and compared her to a Hawaiian (orange), and a Maori (blue) below.  The Hawaiian is her top match, sharing a total of 693.60cM, longest block 15.52cM, consisting of 158 segments.  The Maori is her 4th top match sharing a total of 517.90cM, longest block 18.08cM, consisting of 119 segments.  FTDNA counts all the tiny segments as low as 1cM once the criteria of a match is met, which is why the number of segments is high.

tinyseg-mom

With the default at 5+cM I did not see anything unusual other than ordinary small segment matches.  But when I reduced the setting down to 1+cM (above), you can see a lot of tiny segments resembling a comb.  The slightly bigger gaps are just the missing teeth of a comb.  Some of these patterns begin to appear at 3+cM, although most do not appear until you reduce it down to 1+cM.  In my mother’s example above I show only chromosomes 1 – 20 since there were no segments that looked like a comb on the other chromosomes.

Then I looked at a Maori woman’s results (below) and compared hers to other Maoris and one Hawaiian.  She also shows the missing teeth at 1+cM, but only in a few areas.  Some areas have the comb pattern while other areas seem random.  The random segments could be IBS (Identical by State) or IBD (Identical by Descent).  Polynesians lack genetic diversity, particularly eastern Polynesians more than western Polynesians, so the random looking segments could be both IBS and IBD segments.

tinyseg-mary

Then I looked at two Tongan men and compared them to other Tongans and Samoans.  With Tongans & Samoans there seem to be more randomness.  A few of the tiniest segments may be close to each other, but nothing resembling too much like my mother’s results, a definite comb-pattern.  Take the purple and green colors for example for this one Tongan man below.  Notice how on some chromosomes they seem to be closer together while on others it just looks random.  Again, these are only using the bare minimum 1+cM.

tinyseg-peni

The other Tongan example.

tinyseg-keni

As you can see, it is hard to look for patterns that resembles a comb, and instead you see random colors all over the chromosomes.  What was interesting to see was how little X these Tongans had.  Unlike with the Maoris and Hawaiians, many of them shared multiple segments with each other.

But what does all of this mean?  These are very small island populations.  They have had repeated emigration from these small islands that resulted in a series of founder’s population.  There there was also bottle necking that occurred a few times.  All of these combined would leave only a few closely related ancestors to populate and repopulate new areas every time.

So the multiple, very small segments that represents a comb with missing teeth is the result of people descending from just a few ancestors who contributed that particular segment, but was inherited from multiple lines going back to the same ancestor over and over again.

Below is an image where I compare my mother with two Samoans (yellow & green) and three Tongans (orange, blue & purple).  There seems to be more randomness, however, there are a few of those comb patterns.

tiny-mom&western

Notice how the X chromosome is much more full, unlike what we saw when comparing the western Polynesians (Tongans & Samoans) among themselves. The yellow color belongs to a Samoan woman. The fact that women have 2 X chromosomes may be the reason why there is a long match versus using two Tongan men whose matches included two women in their examples above.  But these are Polynesians, so you would expect more of a match on the X.  My observance of matches for the past 2 years was limited to only my mother being compared to others, which means I have seen a lot of X matches for her, and the same for myself and my brother.

From what I am noticing so far is that these patterns look like what is mentioned in research papers about Polynesian genome and the loss of heterozygosity going from west to east.  The last place in Polynesia to be settled was in the east, ending at the extreme points of the Polynesian triangle, namely Rapa Nui (Easter Island) in the south east, Aotearoa (New Zealand) to the south west, and the Hawaiian islands in the north.  This explains why my mother and the Maori woman have less random looking tiny segments compared to the Tongans and Samoans.  And if we compare western and eastern Polynesians to each other, we may see some randomness but not as much as we would see with western Polynesians alone.  Other types of Polynesians getting DNA tested would help to exhibit any other additional patterns that I cannot currently see with the majority of Hawaiians and Maoris getting tested.

Loss of heterozygosity – from Western Polynesia to Eastern Polynesia

Genetic research on Polynesians will frequently mention the loss of heterozygosity.  This is more noticeable when comparing eastern Polynesians to western Polynesians.

oceania

Map outlining migratory paths of Austronesian speaking populations, including estimated dates. Adapted from Bellwood et al., (2011) “Are ‘Cultures’ Inherited? Multidisciplinary Perspectives on the Origins and Migrations of Austronesian-Speaking Peoples Prior to 1000 BC.” [doi: 10.137/journal.pone.0035026.g001

Polynesian populations are relatively homogenous both phenotypically and genetically. Over a span of 3,200 years they moved throughout the Pacific, and unlike in Europe and other large continents, they did not mix with other populations due to isolation.  These small founder populations have experienced several bottleneck effects, which further caused this loss of heterozygosity ending with the settlement of eastern Polynesia.  Polynesians’ lack of genetic diversity is less evident in western  Polynesia where initial settlement began.  Hawai’i, New Zealand and Easter Island are considered to be eastern Polynesia, and these places were the last places of Polynesia to be settled.

Recently I have been able to look at the autosomal matches among Samoans and Tongans of western Polynesia.  Previously, I have been only studying Hawaiian matches and noticed that top matches were both Hawaiians and Maori people.  Looking at Samoans and Tongans was very interesting as I now could compare the two different regions.

My mother is 80% Hawaiian, while I am 40%.  And as admixed as I am, I still get 1st – 3rd cousin predictions on Family Tree DNA (FTDNA), while on 23andme I get 2nd cousin and 3rd to distant cousin predictions.  The centimorgan totals that I show with my matches reach as high as 369cM on FTDNA, and 161cM on 23andme.  For my mother, 693cM on FTDNA and 376cM on 23andme.  I see the same happening with Maoris, ranging between 300cM – 700cM (FTDNA) for the top 20 people.  And for a non-admixed Hawaiian, their top matches are in the 600 – 700cM range.   An admixed Polynesian would logically have lower totals. But even an admixed person can still have a fairly high amount of totals shared, as when I am comparing myself being less than half Hawaiian.

When comparing two Tongans, the highest that they shared was 335cM.   A Samoan compared to another Samoan was 366cM.  And both of these Tongans and Samoans had their remaining top matches in the range of 100cM to 200cM.  Many of their matches are the same Hawaiians and Maori that match each other at a much higher total.  It is amazing to see these autosomal matches and how diverse the western Polynesians are, or rather how Hawaiians and Maoris are not as diverse.  And even if it is an admixed Hawaiian or Maori, the matches to each other are still pretty high, and as high as what non-admixed western Polynesians would have to each other.

When comparing the longest block (largest segment) with Tongans and Samoans, they seem to rarely get close to 15cM, averaging around 10cM.  Anything more than that could indicate a possible closer relationship or perhaps a specific common geographic origin.  The Hawaiians and Maoris usually range between 10cM – 15cM for the largest segment, but can go as high as 28cM which is usually in admixed Hawaiians and Maoris compared to each other.  In other words, all Polynesians in general will have high totals exceeding 100cM, but whose largest segment rarely exceeding 10cM.

I look forward to more western Polynesians getting tested so we can see if there is any pattern to specific islands in their own island group, something I have been trying to do with Hawaiians with the few haplogroups that there are for Polynesians.  What also needs to be analyzed are people from Tahiti and the Marquesas being that they were key dispersal points for eastern Polynesians.  I managed to only see the results of one admixed Tahitian woman and her match totals are identical to mine when comparing totals.  I am curious to find out what non-admixed Tahitians will show, if it is more identical to eastern Polynesians, or to western Polynesians.

Small segments on the X; male vs. female

Kitty Cooper put out a blog post where she entitled it What Can the X Chromosome Tell Us About the Importance of Small Segments? by Kathy Johnson.   Kathy Johnson had gone through the males in her project and began analyzing and compared to females, determining how much of the females were producing false positives vs. the men.  Because not many men would get a lot of X-matches.  This seems to be an ongoing investigation with various people blogging about the validity of phasing, or rather how effective if not necessarily is it to weed out any false positive matches. It seems to be based on FamilyTreeDNA’s X-matches where they include many tiny segments as little as 1cM.  And the more substantial matches with 10cM or more tends to reduce the actual X-matches significantly, which would be due to the lack of phasing.  You can read more about it on Kitty’s blog, although most of the discussion about evaluating all of these matches took place outside of the blog and on Facebook’s “International Society of Genetic Genealogy” page.

That made me curious, because others have expressed how some men had little to no X-matches.  This was not my situation at all , and went through my list of 9 pages on FTDNA and counted 47 X-matches out of the total 89 matches that I have.  I noticed that one of them was actually an X match on my father’s side of matches, a Filipino.  I knew that was wrong.  So when I looked at it, no X match showed up in the chromosome browser until I reduced the threshold down to 1+cM where I saw a 1.9cM, a false match.

Aside from one woman mislabeled as a male in my matches, I actually have 20 men and 26 females as X-matches, not counting that Filipino false match.  That’s half of my matches.  My mother has 93 X-matches out of her 159 matches, so not that much more than me.  Could that indicate that my mother’s X-matches are more, or less of false matches?  It’s an interesting idea to see how men can have less false matches but we are looking at Polynesian matches which just adds something else to it.

I know that I do have a lot of my matches below 5cM on the X chromosome, so I used dnagedcom.com’s ADSA (autosomal DNA segment analyzer) to at least look at my ICW (in common with) matches on the X, but I had increased the threshold to 700SNPs and 10cM.

Screen Shot 2014-12-20 at 12.30.11 PM

I was thinking that not only would it be easier to use this tool by instantly seeing my X-matches above a specific threshold, but it would also compare me with others with whom we share the same segments, therefore decreasing the chances of false matches.  But taking into consideration that we are referring to Polynesians.  How would that affect it really?

I cannot determine from comparing my own to my mother’s X-matches if they would be false matches or not. Our problem, lack of documentation, lack of genetic diversity and the unpredictability of the X chromosome itself just to mention a few.

I have recently begun testing my first cousins on my non-Hawaiian side in order to take a closer look at the X chromosome and how that is passed on knowing the X path, that is how it is passed on unrecombined from father to daughter versus mother to children.  I also felt that knowing how it is passed on, it would be easier to distinguish which part of the chromosome was inherited from my grandfather versus my grandmother.  And not until I begin testing relatives from each of my grandparents’ side, I will not be able to fully distinguish all of them with the rest of the other 22 pairs of chromosomes.

Having said that, I cannot see how these X-matches, at least among Polynesians would be consist of a lot of false segments or not.  Especially when there are long segments with the more distant people, e.g., Maoris or Samoans and Tongans, of which I do have X matches with.  But the Samoans and Tongans are not included in the ICW due to the fact that I increased the threshold to exclude anything below 10cM.

I also used Gedmatch’s ONE TO MANY to get all my matches, sorted them by the largest segment on the X and just looked at how many were above 10cM.  There were only 20.

Screen Shot 2014-12-20 at 8.21.57 PM

I did the same for my brother, he got 17 above 10cM.  I also looked at other Polynesian men just to compare and the numbers varied, usually not exceeding 20 with 10cM minimum threshold.  It is still all interesting although it is hard to decipher how much of it is true for Polynesians.  Hopefully as more Polynesians get tested, we will start to notice more differences, or confirm that we just all have a high amount of X-matches.

Polynesia Category – AncestryDNA.com

Earlier this year I tested with Ancestry.com (or AncestryDNA.com) since I’ve been noticing non-Polynesians coming up with this new category.  This is way after the fact the research does not specify a Polynesia component, but rather a Melanesian and Asian or East Asian or Southeast Asian component.  I have seen other Asians, specifically Filipinos coming up with decent amount of this Polynesia category, as well as those of European descent coming up with small traces of Polynesia.

Under their Polynesia category, it mentions the sampling size was 18, and that one of the samples showed 11% Scandinavian.  A larger sampling size would yield better results especially in this case where one of the 18 samples had some European admixture.  This was enough to cause those with Scandinavian ancestry to come up with small traces of Polynesia, and in return cause people to wonder how they could have ever had such ancestry in their lineage to a point where some people create possible scenarios how they could have inherited this less than 0.1% Polynesia.

Screen Shot 2014-12-15 at 9.07.24 AM

 

Their Polynesia category was one of those categories where they had the least amount of samples.

Screen Shot 2014-12-15 at 9.42.16 AM

After receiving my results, as I suspected due to the fact that I am half Filipino, my percentage of the Polynesia category was pretty inflated.  It showed that I had 57% Polynesia versus 34% Asia East.  Knowing that my mother is 80% Hawaiian, and that my father was pure Filipino, I figured the amount of Asia that I showed 34% was missing 16% that was thrown into the Polynesia category.  That would in turn leave me with 41% Polynesia.  My mother is 20% European, and according to Ancestry I am 8% Europe, which seems to be about right.  The other DNA companies I tested at showed more than 10% Europe.  But adding the 41% plus the 8% comes out about right, 49%.

Recently I had a cousin on my father’s side of the family test, and she got her results.  She too is half Filipino, while her other half is completely Europe.  I expected her to show some Polynesia but I did not even guess how much that would be.  I was surprised to see 16% Polynesia for her, which is the same amount I had deducted from my own.  In fact, she shows 33% Asia while I show 34% Asia, and more specifically we both share 31% Asia East.  So they both are consistent.

Screen Shot 2014-12-15 at 9.03.53 AM

Although my mother was given an AncestryDNA kit, she has yet to take it.  But I can easily guess that she will easily show 20% Europe and 80% Polynesia.  Any other person who is Polynesian but admixed with some other Asian it may include part of their Asian component into Polynesia.  Maybe the fact that we are Filipinos and they have ancestral ties is why some of it is classified as such.  I did have another paternal cousin tested, she is half Filipino and half Japanese so not sure what type of results that will yield with the Polynesia category.  Will it be the same and show her as 16% Polynesia?  Or will it give her more due to her Japanese ancestry, or is that different enough to not be classified under the Polynesia category?

To find out more about AncestryDNA’s ethnicity/ancestry categories, you can read through their Ethnicity Estimate White Paper.

Polynesian mtDNA in Botocudo of Brazil

Back in mid-September Roberta Estes had a blog entry Native American Mitochondrial Haplogroups.  It’s basically a list of mitochondrial haplogroups that exists among Native Americans.  But what caught my eye was the Polynesian motif – B4a1a1.  She wrote, “B4a1a1 – found in skeletal remains of the now extinct Botocudos (Aimores) Indians of Brazil, thought to perhaps have arrived from Polynesia via the slave trade.  This haplogroup is found in 20% of the mtDNA of Madagascar. Goncalves 2013” and “B4a1a1a – found in skeletal remains of the now extinct Botocudos (Aimores) Indians of Brazil, thought to perhaps have arrived from Polynesia via the slave trade.  This haplogroup is found in 20% of the mtDNA of Madagascar. Goncalves 2013.”   And although there is the actual research out there, it started with an article back in April 2013 titled, “DNA study links indigenous Brazilians to Polynesians.”  Although the article’s title itself only mentions a link, it can be confusing to the reader and can be misleading once you begin reading through it.

The article quoted Lisa Matisoo-Smith, a molecular anthropologist at the University of Otago in Dunedin, New Zealand where she said, “But to call that haplogroup Polynesian is a bit of a misnomer,”  since the haplogroup is known to be in populations as far west as in Madagascar.  The actual research can be found here, Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil. It basically says that “Here we report the identification of mitochondrial sequences belonging to haplogroups characteristic of Polynesians in DNA extracted from ancient skulls of the now extinct Botocudo Indians from Brazil.”   She does not seem to have been referring to the actual Polynesian motif but the fact that the research cited the mutations that is defined as the Polynesian motif.

The paper questions how did the presence of a Polynesian mtDNA show up in the gene pool of an extinct Brazilian Amerindian group who lived in the interior of Brazil?  There are specific mutations occurring on the mitochondrial which identifies it as the Polynesian motif,  and considering the evolutionary history of the Polynesian motif which is associated with the Austronesian expansion and the settling of Polynesia being much more recent than the peopling of the Americas.  Why hypothesizing how the introduction of the Polynesian motif could have entered into South America, the article says in part, “….considering an ancient Paleoamerican origin of the Botocudo haplotypes, we should expect new ‘private’ mutations to have appeared.  On the other hand, because we did not sequence the whole mtDNA, we cannot rule out the existence of such variations in the coding region.”

What is interesting to note is that is it not certain that these two skulls that they have analyzed were actual Polynesians or not. That is due to the fact that there was never a full sequencing test done on those two skulls that came up with the mutations that indicate the Polynesian motif.  Instead, only HVR1, HVR2 and typed specific mutations on the coding region were sequenced.  The findings mention specifically:  6719C, 15746G, 14022G and 12239T. These specific mutations on the coding region not only exists in my own mtDNA results (B4a1a1a3, now known as B4a1a1c) but so does a friend of mine who is identified as having the Malagasy motif. The paper already mentioned how these two skulls could have come back with such a haplogroup is possibly through the slave trade, originally from Madagascar.  And there were trips originating from Madagascar that eventually took these slaves into Brazil.

So the real question is were these two skulls the result of that recent slave trade originating from Madagascar, or did somehow a very few handful of Polynesians made their way all the way to Brazil?  The Botocudos lived in the interior portion of the state of Minas Gerais, so very far from the Pacific Ocean.

Lisa Matisoo-Smith  said it best, that to call that haplogroup Polynesian is a bit of a misnomer, particularly because we know it also exists in the Philippines and the subgroup – B4a1a1b (Malagasy motif) is in Madagascar.  Until a full sequencing test is done, there still may be some debate as to whether or not Polynesians have gone that far into the interior of South America, or that these skulls were the descendants of Malagasy brought over during the slave trade.