Ancestry updates their ethnicity yet again

As of November 13, 2019, everyone’s AncestryDNA results were updated.  Back in late October, only a few people have been getting the new update and all new testees.  Now we are all on the same page.

They did several changes which include increasing the number of genetic communities for various populations, increasing the size of their reference samples, renaming of categories and adding in a few new categories such as Guam, Samoa and Tonga.

We are going to concentrate on Samoa and Tonga, which they attempted to split off from the rest of Polynesia.

When AncestryDNA created the Polynesia category back in December 2013, it only consisted of 18 Polynesian samples which included at least one (or possibly more) of the samples that have distant European ancestry.  They updated their category and rolled out the new update to everyone back on September 12, 2018 with an additional 40 more samples increasing to a total of 58 for Polynesia.

In June and December 2018, I had the opportunity to speak to David Turissini, Ph.D who is a population geneticist at AncestryDNA.  I expressed my concerns with him regarding more specific categories among Polynesians.  Basically splitting eastern from western Polynesia.  I also explained why I thought that would be much better for us particularly for matching as we all tend to match each other at a very closely predicted relationship.  And that I thought the low number of reference samples could possibly affect the way we get our results.

He told me that I already understood how Polynesians lack genetic diversity so increasing the number of samples would not make any difference.  But then I pointed out how it was not that difficult for me to distinguish a western Polynesian (Samoan, Tongan, Tokelau, Tuvalu) versus an eastern Polynesian (Maori, Tahitian, Cook Island Maori, Hawaiian, Marquesan, Rapa Nui).

Despite all that was said, I was surprised to see how they increased the number of reference samples for Polynesia along with adding in Samoa and Tonga.

New categories & increase of samples for Polynesia

You can read more about it here:

https://www.ancestry.com/cs/dna-help/ethnicity/estimates

So their reference samples of 16,638 has increased by 23,379 samples to a total of 40,017.  Of that amount, they added 130 more samples to the Polynesia category and creating Samoa with 73 and Tonga with 97 samples.

While I have not noticed a lot of Tongan results yet, I have seen several Samoans.  Most of the ethnicity results I have seen are either Hawaiians or Maoris.  For the most part, eastern Polynesians are getting either Samoa and/or Tonga in the range of 1% – 4%.  For Samoans, I’ve seen about 60% – 70% Samoa and the rest Tonga.  A few Cook Island Maoris seem to have a higher percentage of Samoa compared to other eastern Polynesians but that may be due to the fact that they have ties to Aitutaki or its neighboring islands versus Rarotonga.  Or maybe Cook Island Maoris just have a higher percentage because of another group of people that settled earlier and/or it could be due to the original people who just so happened were genetically more like Samoans.

This whole classification, while it cannot be accurate as it is nothing but an estimate, really makes it interesting and gives us a bit more of an insight as to the settling of Polynesia.  Of course we can also see this as more people are getting Y-DNA tested and mtDNA and we slowly learn more about these different migration patterns which no surprise, confirms our oral histories.

My results have changed throughout time since I tested with AncestryDNA back in January 2014.  The biggest breakthrough came last year as they actually created the Philippines category which correctly allocated my Filipino side from Polynesia, therefore decreasing my amount.

But what does my tree look like compared to my current DNA results?

 

With the latest update it made my color scheme more difficult to accomplish but in the tree I do point out the foreigners.  While my father was born in Lahaina, Maui, Hawai’i, both of his parents were from the Visayas region in the Philippines.  For my maternal grandmother’s mother – Rose Holbron, her paternal grandfather was from Hull, England while her maternal grandfather was from Queens, New York, U.S.A.  And for my maternal grandmother’s father – Frank Kanae, he had distant American ties.  His great-grandfather Isaac Lewis Kanae was the son of Captain Isaiah Lewis.  I still have not pinpointed his origin yet.  And Isaiah Lewis’ father-in-law Oliver Holmes arrived in the Hawaiian Islands in 1793 from Plymouth, Massachusetts.  At the time Oliver Holmes left Plymouth, there were only 15 states in the U.S.A.

So what I did was place their ethnicities under a continental level and compared it to my DNA results, which all adds fairly nicely, taking in random inheritance.  My mother gets 17% European compared to her sister who gets exactly 15% which is consistent with the genealogy.  And in turn my mother gave not one but both of my brothers about half of her European – 8% and 9% for them while I ended up with the higher percentage – 11% which appears as about 11% – 12% at different testing companies.

And while I show 2% Samoa, my mother ended up with 1% of both Samoa and Tonga.

 

For my cousin who is not admixed, it was interesting to see, despite the erroneous genetic communities that would come up, how hers changed.  Because we match other Polynesians at a very closely predicted relationship, and the fact that my cousin is not admixed, she matches a lot of part Polynesian people who fall into a specific genetic community among others of whom she also matches.  So she ends up with the same genetic community.

 

 

With this latest update, they finally got rid of the Native American category for both my cousin and my mother.  But now with Samoa and Tonga, it is no surprise that they would give us a small percentage of that.  And having gone through several of these 1% – 2% categories of Samoa and Tonga, they all seem to range the same – 1% – 4%.  Interestingly for my mother, her range for Tonga was 1% – 3% while her Samoa was 1% – 4%.  But the way it ended up was both 1%.

I have also been witnessing those who previously had small amounts of Polynesia now being reclassified as Samoa, Tonga or Guam.  Usually, these are people with either Melanesia or some other Southeast Asian from various parts of Indonesia.  I would be really interested in seeing more results who have ties to that area.

So while I was told the number of increase of samples would not do anything, it obviously did quite a bit.  If only they would have renamed the Polynesia category by specifying Eastern Polynesia.  They should also do the same renaming their genetic community.  It would make more sense as we know that both Samoa and Tonga is part of Polynesia and of course, their map for Polynesia would include Samoa and Tonga within that area.  I would have expected western Polynesia as I mentioned to them versus eastern Polynesia, but they really got very specific.  And in the end result, Samoans will see that they are about 30% Tongan and probably the same for Tongans where they will see a smaller percentage of Samoa.  These people do get about 0% – 1% Polynesia in their results.

We will just have to wait to see what the future updates would bring.

Previous entries about AncestryDNA’s Polynesia category:

https://hawaiiandna.wordpress.com/2014/12/15/polynesia-category-ancestrydna-com/

https://hawaiiandna.wordpress.com/2015/06/30/polynesia-category-ancestry-com-part-2/

Largest Segment – Is it the best way to gauge the closeness of relationship?

In my earlier blog posts I have mentioned how significant the largest segment size is when determining a true 2nd to 3rd cousin relationship.  Polynesians can have a total shared amount that can easily exceed 100cM.   These totals tend to over-estimate the predicted relationships.

From the ISOGG Wiki’s page, you can see that the average for 2nd cousins once removed (2C1R) is 106cM while 2nd cousins are averaging around 212.50cM.

So we tend to get a lot of these 2nd – 3rd cousin matches, depending on the company you tested with.  This is why the largest segment size has become important.  Blaine Bettinger has a post entitled The Shared cM Project – Longest Shared Segment where people had submitted their longest segment size based on their known relationships.  You can compare 2nd and 3rd cousins there and see what the average is for the longest segment size for specific relationships.

A quick look at the type of numbers just by looking at my own ONE TO MANY from GEDmatch.com.

My cousin Allen who is a 2C1R to me (his maternal grandmother & my mother are 1st cousins) has a large segment of 35.9cM.  You can see more comparisons of the largest segment for 2nd to 3rd cousins from Blaine’s Shared cM Project but I also have been keeping my own numbers from my known relatives.

Only one of those 2nd cousins shared a large segment of 21.8cM, pretty small, and then it gets even lower as you go more distant.  But normally 2nd cousins will share a rather large segment, which is why more than 20cM has always been advocated and also among the Ashkenazi Jewish community.  In fact, I thought they used 25cM, but I could be wrong.  I even mentioned 30cM would be good.

But is it a requirement?  Absolutely not.  However, if you cannot find a connection, or the same geographical origin i.e. New Zealand or Hawaii, then that would be a strong indicator that you are not as closely related as it was predicted.

I have been noticing how I do have a few Hawaiians whose largest segment is more than 30cM but have not been able to find a connection.  I also notice that these matches will not have the same geographical origins as I do.  So could it be that these large segments remain in our population for many generations?

Here’s an example of how it actually has remained for centuries by comparing my Hawaiian mother and a Maori.

Taking my mother’s ONE TO MANY matches, I sorted them by the largest segment size.  I indicated the known relatives in blue and the unknown in red.  My mother has a Hawaiian match as 44.6cM for the largest segment.  I still have not been able to find a connection, although one of that match’s branch goes back to the area of a few of my ancestors.  But even for us, that was more than 3 generations ago from my mother.  Another at 39.9cM, not sure if that person is a Hawaiian or Maori.  And there is a Maori match with the largest segment of 25.9cM.   At FTDNA, there is a Maori match whose largest segment is 23cM.

Here is the largest segment sized match with a couple of Hawaiians from MyHeritage.

37.2cM and 33.6cM.  They have pretty good trees but their ancestry goes back to totally different islands from my own ancestors.  And I saw in their trees the origins of the different islands is further back while the more recent ones were born in Honolulu where some of my more recent ancestors were born.  I did trace many of my ancestors’ descendants who remained in Honolulu but none are those connect to these matches.

Here is a Maori match from MyHeritage.

Notice that the largest segment is 34.2cM.  The highest I’ve seen with a Maori.  How can a large segment last that long after many centuries?

And while the focus here is utilizing the largest segment to get a more accurately find a true 2nd to 3rd cousin match, we know how in one generation a large segment can quickly be reduced.

Comparing with the largest segment that my mother shares with her 1/2 3C.  This is how they connect.  I outlined in yellow all testees in this particular comparison.

The largest segment that my mother & her 1/2 3C share is 49.6cM (FTDNA indicated 52cM) according to GEDmatch.  But that particular segment was not inherited entirely by my mother’s sister and seemed to have been broken up thanks to recombination and turned into a 10.7cM and a 25.1cM segment.

My mother’s deceased brother seemed to have received that same segment or maybe even slightly larger.  And while he is not alive to test, his son did, and he shares 50.2cM with this 1/2 3C of our parents, or our 1/2 3C1R.

This is what the comparisons look like.

My younger brother got nearly the entire segment as my mother got it but I got a very small portion of it, just 14.3cM.  That’s a huge difference from 49cM.  Had my mother nor my younger brother got tested, I would not have been able to find this good match and would have concentrated on matches with large segments more than 20cM or even 30cM.  My older brother got DNA tested however he does not share any of this same matching segment.  In fact, he shares 0cM on this particular chromosome.

This 1/2 3C was key in finding my mother’s biological parents.  At the time I did not know how we were related but I did concentrate on this match because of the large segment size.

So how do we really filter all of these matches?  By solely concentrating on the largest segment?  You should definitely not spend too much time on large segments that are less than 20cM and whose shared total is way over 200cM.  With those particular matches, if you compare trees and notice no common geographic area, that would be a big indicator that it is a distant match.

Remember that with a 2nd cousin you would share a pair of great-grandparents.  With a 3rd cousin you would share a pair of 2x great-grandparents.  By that generation or even a generation further back or two if you find that you do not share the same geographic location, then the match is a distant match.  The same applies for large segments greater than 30cM.  If no common geographic location, then it is probably a distant match.

MyHeritage Ethnicities

As of May 30, 2017, MyHeritage finally released their Ethnicity Estimate (beta) to those who uploaded their raw data.  So far this service is still free.  Not sure if they will discontinue that service.  Currently their tests are at a reduced price of $79.

 

Not only does MyHeritage (MH) have an Oceanian category but they included Polynesian along with Melanesian and Papuan.

 

Last year and probably the year before that, they reached out to people who had a tree at MH whose 4 grandparents were listed in a given geographic area confirming ties to that particular place or country.  And while they seem to have obtained more than Ancestry’s 18 Polynesian samples, they did not take into consideration that these people may be admixed.

A lot of admixed Polynesians who did test with MH are reporting to have lost a lot of their European while simultaneously having an increased percentage of Polynesian.  There seems to be about 10% difference.

Here are my mother, my maternal aunt and my own results.

My mother and her sister are 85% Hawaiian while 15% is of European background.  My mother gets about 17% European at the varying DNA testing companies.

Several Polynesians have shared their Ancestry results with me.  Comparing it to MH it seems that the numerous samples that they used for the Polynesian category included some admixed Polynesians of European heritage.  I have been hearing the same situation for those with admixed Native American background reporting 20% to 30% more Native American while reducing the amount of European.

What is interesting about MH is that they did have other populations not covered by the other testing companies.  They separated the Melanesian and Papuan, commonly grouped together and labeled as “Oceanian” by other companies or at GEDmatch, and provided a separate Polynesian category.  They did something similar for the Asia group.

MH has specific groups within the Southeast Asia area, such as Filipino, Cambodian, Vietnamese, Thai, Malaysian and Indonesian.  While the thinking is that if you come from that particular background which they tested, you should score perfectly with that group.  This may not apply for some either due to the limited number of samples and/or where they got their samples from, such as taking samples from one specific area.  I have only seen a few Filipinos’ results where they score 100% Filipino/Indonesian/Malaysian.  A couple of Chinese people received majority Chinese and Vietnamese and a smaller percentage of Filipino/Indonesian/Malaysian.

My guess is that this breakdown of the various Southeast Asian groups helps separate Polynesians (and Micronesians) who also have some Southeast Asian background.  At Ancestry, Chinese people were reporting about 10% Polynesia, Vietnamese as high as 15% and Filipinos around 32%.  Ancestry has no Southeast Asian category, so those of Southeast Asian background will get some of the East Asian, or what Ancestry has as “Asia East” along with a small percentage of Polynesia.

Aside from MH engulfing the European for admixed Polynesians, it seems fairly accurate at least for me being that I am half Filipino and 43% Hawaiian and about 12% European background.  I am going to assume that the West Asian below is part of my European background while the South Asian is part of my Filipino backgroundc

East Asian category for Polynesians

My mother told me today that she received from the First District Circuit Court that handled her adoption, the non-indentifying form, which is where it lists her biological parents’ ancestries.  They indicated that both parents are Hawaiian and Chinese.  I find that to be an error since my mother had her DNA tested at 3 companies.  Maybe that was based on an assumption or the biological parents may not have known too much about their ancestries.

At the age of 5, she met her biological father and described him as a “pure Hawaiian.”  This made sense since she gets the following percentages from each company.

 

So this meant that one parent was just Hawaiian while the other parent was admixed with some European.  Based on all the companies she has tested with and analysis [from Dr. McDonald], my mother gets the following averages.

European = 16%
Oceanian = 25%
East Asian = 55%

Those are based on 23andme, FTDNA’s old Population Finder and Dr. McDonald’s analysis.  FTDNA’s current myOrigin lumped their former Oceania category under Southeast Asia, or the more broader East Asian category.  AncestryDNA however created a Pacific Islander category with the subgroups Polynesia & Melanesia and between myOrigins and Ancestry, the average total is 83%.

In reality, the East Asia category is just one of two components that make up the genome of Polynesians.  The other is Melanesian/Papuan (Oceania).  For Polynesians, autosomally they are 79% East Asian and 21% Melanesian¹.

In Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study they applied ADMIXTURE on genome-wide SNP data to finely estimate the degree of admixture in Native Hawaiians.  They found that with Native Hawaiians, “an average of 32% and 68% of their genomes to be derived from Melanesian and Asian origins, respectively”.  But that “[r]ecently, Kayser et al. surveyed the nuclear genome with 377 microsatellite markers in 47 Pacific Islanders and identified 79% Asian and 21% Melanesian proportions of ancestry for Polynesians.”

So while other studies revealed that Polynesian genome consist of 79% Asian and 21% Melanesian components, the study with Hawaiians averaged 32% Melanesian and 68% East Asian².  The higher amount of Melanesian could be attributed to the repeated bottleneck effects throughout the centuries specifically for eastern Polynesians, i.e. French Polynesians, Rapa Nui, Cook Island Maoris, Maoris from New Zealand and Hawaiians.

My mother averages 25% Oceanian and 55% East Asian.  The two combined equals 80%.  25% (Oceanian) is 31% of the entire Polynesian (80%) percentage.

Just over a year ago I was going through my mother’s matches on GEDmatch and began running their kits through various admixture tools to see their totals of Oceania versus East Asia.  I wanted to see if they fell within the 27% to 32% Melanesian/Papuan/Oceanian.

This is only a partial list.  There are more lines on the bottom but I am just showing the first several.  I use various calculator admixture tools at GEDmatch that had the specific Oceania/Papuan/Melanesian category.  Dodecad World9 uses “Australian” instead. I created a column that totaled the average.  And the columns to the right of that shows those who tested at other companies and their Oceania percentages.  What is not shown in the list is the proportion of East Asian that would prove it does fall within the 27% – 32% Oceania.

The first row (in red) belongs to my mother, followed by my averages and then my brother’s.  The following lines in bold are for those at least 95% Polynesian.  I took the lowest and the highest percentages of Oceanian to see if it falls within the range consistent with the research.  Since these admixture calculators did not have just a single East Asia category alone, I listed the other categories that are known to split off from the East Asia category.

Eurogenes K9b
Oceania = 17.74%
Southeast Asian = 48.87%
Northeast Asian = 13.32%
Native American = 1.55%

Adding the Southeast Asian, Northeast Asian and Native American categories total 63.74%.  17.74% Oceanian makes up 27.8% of the total (East Asian compiled categories) of the Polynesian genome.  Consistent with the research.  Looking at the highest percentage.

MDLP World
Melanesian = 20.78%
East Asian = 56.31%
Artic Amerind = 1.65%
Mesoamerica = 0.13%

There was an Indian category showing 3.74%, but I did not add that in.  Adding it, changed the overall percentage to 33%, but leaving it out made it 35.7% of the Polynesian portion. For the others listed on that list, they also picked up a small 1 – 3% of the Indian category, and leaving it out made their average 30%.  If I look at the average column for all the admixture calculators for my mother, it comes out to 30%.

But what happens when there is a higher percentage of East Asian?  In my case, it is higher because my father was Filipino. My portion could easily be verified simply by removing 50% (my father’s contribution) from my average total of 85% East Asian giving me 35% East Asian that would be my Hawaiian/Polynesian side.  My average (GEDmatch) showed 32%.

There are many Hawaiians admixed with Chinese, Japanese, Filipino or Korean, being that they were all immigrant groups to the Hawaiian islands.  Are you able to tell if they have an Asian admixture?  Can it be distinguished from the East Asian that is part of the Polynesian genome?  This is something I have been seeing more now particularly with adoptees.

Any excess East Asian percentage  compared to the Oceanian percentage [79% to 21%], would indicate that the person is admixed with some other Asian ancestry.  Since my mother’s genome does not indicate any more East Asian than what it should for Polynesians, it is clear that she does not have any additional Asian ancestry.

Footnotes

1. Genome-Wide Analysis indicates More Asian than Melanesian Ancestry of Polynesians
2. Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study

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

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.

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.

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.

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:

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.

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.

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.

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.

The other Tongan example.

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.

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.

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.

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.

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.

 

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

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.

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.

Presentation on Polynesian DNA

I made a presentation to help other Polynesians understand DNA and what some of the research mentions about Polynesians, and what I’ve already covered in my blog about matches, endogamy, and the misleading close matches that we get.

Polynesian DNA Presentation