Determining half-relationships with Polynesians – Part II

In my last entry I demonstrated the difficulties of determining the half-relationships after receiving the DNA results of my half-first cousin.   Within an endogamous group, that could be even more difficult as we see larger amounts of DNA shared.

While the ISOGG Wiki Autosomal DNA Statistic page can list the average amount of centimorgans shared,  Blaine Bettinger’s The Shared cM Project  demonstrated that the minimum and maximum amounts shared can vary.  This becomes more evident as the distance of relationship increases.

Within an endogamous group it makes sense that having more than one pair of common ancestors may increase that amount.  The same would apply if you descend from the same common ancestor multiple times.  Both would produce higher amounts shared.

A few months ago I got the results of my aunt believed to be a full-sister of my mother.  My aunt suspected that her father was not her biological father.  And she was right.  But she was not the only one who knew of this, but the rest of the family, particularly the ones of my generations believed that this Aunt’s father was her biological father and did not suspect otherwise.

From my mother’s Family Finder (autosomal) match list at FTDNA:

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The top is my mother’s sister while the one right below it belongs to my half-1st cousin whose father George was mentioned in the last entry – Determining half-relationships with Polynesians.

Initially I was confused by the total amount since I knew it was more than what I shared with two of my half-brothers.  This is how two of my half-brothers compare to me and to each other.

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So my mother and her sister did share a bit on the high-end for half-siblings, but low end for full-siblings.  These are the predicted averages shared for siblings vs. half-siblings.

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The next step was to take a look at the X chromosome.  For half-sisters who had the same father, they would share an entire X chromosome based on how the X is inherited.  To my surprise, it looked like someone took a razor blade and sliced out some pieces of the image.

 

5+cM setting

5+cM setting

 

1+cM

1+cM

For half-sisters they share a lot compared to what I saw when comparing my half-brothers to each and to me.  Also, I decided to include both the default 5+cM setting and the 1+cM.  With my brothers, we hardly get anything when I lower it to 1+cM.  But with my mother and aunt, you can see a difference although chromosomes 4 and 18 are more likely to be IBS, but given the situation (endogamy, small communities, & isolation) it just may be IBD from a very long time ago.

So the X was not helping me one bit since I thought maybe they were areas on the chromosome that could not be read – no calls.

I immediately uploaded to GEDmatch for further analysis.  No surprise that when I looked at the X, it was the same exact thing.   Knowing that it wouldn’t be helpful, I turned to the other 22 pairs of chromosomes.

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What you would be looking for in full-siblings are full-identical regions (FIR) which are the green sections on the bar graph.  Here is an example of my 1st cousins, a brother and sister.

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About 25% will be fully identical.  You can read more about how much full versus half-identical regions siblings would share at ISOGG’s Wiki – Fully Identical Region page.

This is what my mother and aunt showed.

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There are only small chunks of  FIR rather than long segments of it that you would see in full-siblings.  So this confirms a half-sibling relationship.

The randomness of autosomal DNA

Now that Ancestry is able to show how many centimorgans and number of segments are shown, I was comparing my top two closest matches.  They are listed as “lkauhi” and “Frank”.  They are under the 2nd cousin category predicted in the 2nd – 3rd cousin range.

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Prior to my mother getting DNA tested, I had no idea exactly how close they would really be.   Now that my mother got DNA tested and I figured out who my mother’s biological parents were, I was able to construct a diagram.  “lkauhi” is on my grandfather’s side while Frank is on my grandmother’s side.

How Frank & “lkauhi” are related to me.

My mother Judy is a 2nd cousin to “lkauhi”.  That makes me and “lkauhi” 2nd cousins once removed.  While Frank and I are 2nd cousins, because his mother and my mother are 1st cousins.

Here is how much Frank and I share and how much “lkauhi” and I share.

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224 centimorgans is what “lkauhi” and I share

And although my mother shares 439cM with Frank while sharing 430cM with “lkauhi” (not shown in any diagram), the amount shared seems pretty high for a 2nd cousin.  However, we are talking about Hawaiians whose ancestors have gone through repeated founder’s effect which resulted in our high shared amounts.  She in return managed to pass unto me more of her father’s DNA so that when compared with “lkauhi” we end up sharing more compared to Frank who is in my generation and on my grandmother’s side of the family.  Unfortunately my grandparents are not alive to get them DNA tested for a true comparison.

Also, both of these people have not transferred over to GEDmatch so I am unable to get a better comparison.  This reminds me of what my cousins said about how much I look a lot like our uncle, and that both my mother and I really look like my grandfather Joseph Kaapuiki.  Maybe it is something genetic?  If my mother shared a lot with “lkauhi”, it could be because we inherited more from Elena Kauhi, my mother’s paternal grandmother.

The good thing about all of this is that it confirms that Joseph Akana fka Joseph Kaapuiki was my mother Judy’s biological father, since Joseph’s mother was Elena Kauhi.  And “lkauhi’s paternal grandfather Johnathan Kauhi was a brother to Elena Kauhi.

Both of these closest matches are from each of my maternal grandparents’ side.  Frank is from my grandmother Rose Kanae’s side while “lkauhi” is from my grandfather Joseph Kaapuiki’s mother Elena Kauhi’s side.

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.

Runs of Homozygosity – Are your parents related?

On Gedmatch there is a tool where you can run your raw data and it can determine if your parents are related by looking for strands of homozygous DNA.  Better known as “runs of homozygosity”, or ROH,  are regions of the genome that are identical because you inherited an identical copy from each parent which would indicate that there was a common ancestor.  This will create a run of homozygous variants.  ROH

ROH are informative.  The longer runs obviously tells us that there was intermarriage while short runs of ROH have the potential of informing of population history, i.e., populations that have gone through a bottleneck followed by a period of intense inbreeding that will result in long runs of ROH.  Then as time passes these long runs become to look like patches throughout an individual’s genome, showing both homozygous and heterozygous regions.

The sporadic placement of these long ROH on various chromosomes are consistent with bottleneck populations.  In Razib Khan’s blog he has an entry about how not all homozygosity is created the same.  He refers to a paper that mentions how when looking at various world populations, there was obviously a difference.  In certain areas, these long ROH was attested to cultural patterns of inbreeding, as well as small population size.  Short and medium ROH are results of bottleneck, and smaller effective population while long ROH is due to effective population size which occurs during inbreeding.

So looking at how this would affect Polynesians, I started analyzing all of this and predicting what I would see.  Since Polynesians lack genetic diversity, but knowing that eastern Polynesians (Hawaiians and Maoris to name just a couple) are less diverse than western Polynesians (Samoans and Tongans), due to the migration patterns of ancient Polynesians from west to east, I would probably see less ROH, depending on the island population, with western Polynesians versus eastern Polynesians.

I tried this tool months ago a few times but it looked like it was not working properly or the results just was not easily understandable.  I tried it again and now they break it down by each chromosome showing you how much and where these runs occur, using the minimum criteria of 7 centimorgans.

Analyzing my own mother’s results seemed to have a decent amount of ROH, specified below by total shared, largest segment and on which specific chromosomes these were found.  The largest segment was 13.9cM, the estimated number of generations to the MRCA (most recent common ancestor) is 4.1.

ROH-mom01

ROH-mom02

My mother showed that she has at least 5 chromosomes that showed ROH, the largest segment being 13.9cM, the smallest segment 7.5cM.  Another Hawaiian showed 6 chromosomes, largest segment 22.4cM, and a total of 8 segments, 3 of those segments are on one chromosome.

After going through my mother’s matches (from her ONE TO MANY) and looking at Hawaiians, Maoris of New Zealand, Samoans and a half Tongan, I definitely saw a pattern.  A couple of Maoris that did show ROH showed 2 to 3 chromosomes that had ROH, with the largest segment as large as 16.6cM, and as small as 7.1cM.  I was only able to find one Samoan woman out of the 5 known Samoan matches to my mother that had at least 2 chromosomes that showed ROH.  Her largest segment however was only 8.8cM.

This seems consistent with the research as well as the known history of the populating of Polynesia.  Hawaiians have gone through a recent bottleneck at the end of the 19th century and have recovered from that.  So it is no surprise that Hawaiians and Maoris would show more ROH than Samoans or Tongans.  More so with a population expansion after a bottleneck effect we do see how Hawaiians not only show more of ROH but it also appears to be sporadic throughout with both short and long ROH, as in one Hawaiian’s example he has 3 segments of long ROH that were on one chromosome.

Not all endogamy is the same

Kitty Cooper’s recent blog post “using Ashkenazi Jewish DNA to find family” talks about how to look for key signs when it comes to finding a true connection to your matches.  I recently blogged about the problems with Polynesian matches and endogamy, just as Ashkenazi Jews will encounter.  I had two different blog entries.  One was “ADSA and Triangulation” where triangulation is used to possibly figure out if you and two other matches can help each other figuring out your common ancestor.  And “Endogamy and Multiple Smaller Segments” where I discovered the actual problem with Polynesian DNA and finding matches.

In Kitty’s entry, she did give tips for finding real AJ matches. Whenever people talk about endogamy, they always bring up AJ as the most prominent group, but the fact is any endogamous group will have its own peculiarity.  I noticed that with Colonial families they have to have what they refer to as “sticky segments”, or segments on a chromosome that basically lingers on for awhile, generation after generation.  I have seen how these segments can begin and end at exactly the same start/end points, which is very interesting.

AJ come from a founding population that started with a small number of people.  Many other endogamous groups started in the same fashion for the most part, particularly colonial families.  With colonial families and Acadians of French Canada, you can see the constant intermarrying within families generation after generation.

DNA Research says that Polynesians slowly moved eastward creating these series of founder effects.  By the time they reached central eastern Polynesia, they were getting genetically less diverse.  They thrived for centuries developing their culture, and then more emigration occurred to the farthest parts of the Polynesian triangle.  The Maori (New Zealand), Hawaiians and Rapa Nui people (Easter Island) are expected to be a subset of the genetic variability in eastern Polynesia, which in turn is expected to be a subset from western Polynesia, which itself is a subset of Melanesia.  A series of founder effects is what lead to this low genetic diversity.

Whenever people talk about endogamy and use AJ as an example when it comes to calculating relationships, or even reading what Kitty Cooper wrote for tips in working with AJ DNA, I keep reminding people that not all endogamous groups are the same, such as the case with Polynesian DNA.  So as Polynesians moved from the west towards the east, and then finally to the most farthest corners of the Polynesian triangle, where Hawaii is at its vertex angle, New Zealand and Easter Island at its base angles, genetic diversity diminishes.

Bottleneck is another feature enhancing the degree of endogamy with Polynesians.  There may have been several bottleneck effects that took place among various island group of Polynesia.  For Hawaii, the last known bottleneck occurred in the late 19th century.  When Captain Cook, a British arrived in the Hawaiian islands in 1778, he estimated the population to be around 300,000.  Scholars will mention anywhere from 800,000 to nearly a million in the islands at the time of European contact.  The 1890 Hawaiian Kingdom census counted 40,622 aboriginal Hawaiians.  The 2000 US Census had counted 401,000 Native Hawaiians.  So the current Kanaka (Native Hawaiian) population comes from the 40,622 that existed 124 years ago.

When thinking about the lack of genetic diversity given the entire history, it should not be surprising that, as in my case being Hawaiian, that not only will I have many close matches with other Hawaiians, but with other Polynesians too.  More specifically what we have been seeing, is a close genetic relationship with the Maoris.  That is understandable since both of our groups were the last places to be colonized by Polynesians.

So what does that mean for Polynesians working on their DNA matches?  It is okay to read about other methods that endogamous groups use to find their matches, but be aware that we have much closer matches unlike other groups.  If you are on FTDNA, you will find a lot of 1st – 3rd and 2nd – 3rd cousin matches.  I get 3 pages of 2nd – 3rd cousin matches while my mother has about a page and a half of 1st – 2nd cousins, just over two pages of 1st – 3rd cousin and five pages of 2nd – 3rd cousin matches.  At 23andme, I get 2nd cousins, and 2nd – 3rd cousins and two pages of 2nd – 4th cousins.  This is what to be expected, and again a true closer relationship will be distinguishable by looking at the number of segments.  We may share a lot when it comes to total centimorgans in order to get 2nd – 3rd cousins, but a real 2nd to 3rd cousin match should not have as many segments and these multiple segments will average anywhere between 8cM – 15cM.  This means that the match is endogamous.

When doing triangulations you will see that with your matches there is a fair amount of shared segments with other people of whom will share that matching segment.  With non-endogamous groups, you need to first verify that both of your matches are sharing that same segment with each other in order to determine that you all have a common ancestor.  For Polynesians, this is often the case, and probably descended multiple times from that same ancestor.  That may seem significant and on the right path for finding a connection however its extremely low genetic diversity coupled with the fact that many records did not exist until recently usually produces no results.

Lack of Genetic Diversity

I keep telling people that when it comes to Polynesian DNA,  we lack genetic diversity.  People erroneously use “pedigree collapse”, or the more blunt “inbred” when referring to endogamous groups.  But both terms are not specific to our type of DNA situation, and research supports what Polynesians have gone through with their migratory patterns over the past few thousand years.

From oral tradition, we know that Tahiti, at one point in time was the center of religion.  From Taputapuatea, a sacred marae on Ra’iatea (old name was Havai’i) was where Polynesians from other island countries came and they worshiped.  They did this for a few centuries, while they started emigrating to the far parts of the pacific ocean, to as far south east to Rapa Nui (Easter Island), to the south west to Aotearoa (New Zealand) and north as far as the Hawaiian islands.  These three points define the Polynesian triangle and for the most part islands within these zones are known to be Polynesian.

Around 1200 A.D. is when migration ceased among these groups.  It would not be until about 500 years later when Europeans would travel within the Pacific, people such as Captain Cook who noticed that as far and isolated these islands are, that the people had similar cultures and languages.  DNA confirms that.  When Captain Cook arrived in the Hawaiian islands in 1778, he estimated a population of 300,000.  Other historians say that he under-estimated the number of Hawaiians based on what he could see from his ship, and did not take into consideration the inhabitants inland.  So they say it was about 800,000 to one million Hawaiians in 1778.  The 1890 Hawaiian Kingdom Census counted 40,622 aboriginal Hawaiians.  The 2000 US census counted about 460,000 Native Hawaiians.  The current Hawaiian population came out of the 40,000 Hawaiians from 1890, which was the last bottle neck occurrence.

Now that Polynesians are getting DNA tested, we come up as 1st, 2nd or 3rd cousins for the most part, usually sharing more than 50cM, sometimes as high as 500cM and with multiple segments, which they say is consistent with an endogamous group.  In particular are the high shared percentages among Maoris of New Zealand and Kanaka (Maoli) of Hawai’i.  But given the history of migration it is understandable why eastern Polynesians would be much more genetically similar to each other compared to the older, western Polynesians.  As Polynesians migrated further east, they became genetically closer.