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.

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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.

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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

Polynesia category – Ancestry.com (part 2)

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

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

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

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

 

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

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

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

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

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

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

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

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