Endogamy and multiple smaller segments

The past several months after nearly a year of getting into genetic genealogy I finally started to study a bit more about my endogamous matches rather than ignore them for a long time and discouraging other Polynesians to not look into their matches. I learned how to figure out a true match or what could be a true match versus an endogamous one, which would make the relationship much more distant even beyond a genealogical time frame. Analyzing DNA matches in an endogamous group is already a challenge, but unlike other endogamous groups, dealing with Polynesian endogamy means lack of genetic diversity which translates to a large amount of shared centimorgans, smaller largest segment and multiple segments producing relationships significantly much closer than what we really are which could be very distant (over more than 5 centuries) for many of our matches. I have been noticing an average of 8cM – 15cM for the largest segment even though the total can be anywhere from 100cM – 200cM.  From FamilyTreeDNA my mother gets up to four pages of matches totaling from as low as 178.42cM to 693.60cM.  On GedMatch, the totals are different, not counting the first three listed which are her children.  From the fourth one on down is where the real puzzling matches are. The diagram below is sorted by the total shared.  And with these matches the threshold is different.  It is defaulted at 5cM, 500SNPs.

My mother's top matches based by total shared.

My mother’s top matches based by total shared.

When I sort it by the largest segment, 50.2cM is the highest, then there are a lot averaging somewhere between 10cM – 15cM (not all are shown in graph below) yet with high totals.

My mother's top matches sorted by the largest matching segment.

My mother’s top matches sorted by the largest matching segment.

The large total shared having the largest segment averaging 10cM – 15cM is expected in endogamy but for Polynesians, since we come from multiple common ancestors over centuries, even for different island nations who can claim descent to a specific person or persons such as  Mauikisikisi, or Maui-tiki-tiki (Hawaiian: Mauiki’iki’i),  or ‘Aikanaka/Kaitangata, Hema, Kaha’i/Tafa’i/Tafaki, Wahieloa/Vahieroa, and Laka/Rata, it is no surprise that our totals are still high, probably higher than the other endogamous groups such as Ashkenazi Jews, or Quakers, etc.

Sorted by predicted generation.

Sorted by predicted generation.

Below is a diagram from FamilyTreeDNA and I wanted to show by choosing 5 Maoris, comparing them to my mother.  I chose them because Hawaiians like myself and my mother have a much more distant relationship with the Maoris, given that Maoris and Hawaiians as with other Polynesians have been separated and isolated some time in the 13th century.  It was up until that time where they regularly gathered at the sacred religious spot at Taputapuatea located on the island of Ra’iatea in the Tahitian islands.  Then that stopped suddenly, and there was no more interaction among the different island nations. FamilyTreeDNA has a different criteria but because of this, it seems to work for us Polynesians  only because bringing down the threshold (usually to 3+cM, not necessarily 1+cM) it allows you to see the segments which are usually closer to the much larger ones but have small missing matched segments.

5 Maori matches

5 Maori matches

To the far left is the number of segments, and I filled in to the right the total number of segments plus the largest matching segment for each person.  I also reduced the threshold to show how in endogamous populations, what was once a compound matching segment was broken up just slightly.  This may work well for Polynesians but may or may not apply to other endogamous groups.  I definitely would discourage others from non-endogamous groups to do this. The breakup can be a bit more obvious in places like on the beginning of Chromosome 10 (purple), or chromosome 16 (yellow) as well as on the X chromosome (orange). To further illustrate, I took just chromosome 16 of the last person on that list (yellow) where a Maori woman shared a total of 468.97cM, but the largest segment is only 12.80cM.  That means there are many other small segments that totaled the 468.97cM.

Analyzing chromosome 16

Analyzing chromosome 16

Looking carefully at chromosome 16, you can see what I mean by the break up.  The first matching segment consisting of 5.31cM runs from 1074819 – 3561270.  Then there’s a break, then continues with 3989366 – 6372359, then another break.  It continues again from 6690251 – 8317168.  So if we look in between the breaks, we have the following.

3561270 – 3989366

6372359 – 6690251

On the graph it looks very close, just a small break.  What it looks like is that this once was a long segment that got broken up but due to intermarrying time and time again within a small population, the breaks were not only small but the reduction of the actual match over time was a slower one. This is what it looks like at the default 5+cM setting, and then the image after that I had set it at 10+cM.

5cM setting with the 5 Maori matches

5cM setting with the 5 Maori matches

10+cM setting with the 5 Maoris

10+cM setting with the 5 Maoris

I recently had my mother’s half-1st cousin Sam get DNA tested.  Sam’s father and my maternal grandmother were half-siblings.  Getting this cousin tested would verify if my mother was the biological daughter of the woman in question, although by the time Sam took the test, my mother admitted to remembering as a 5 year old being told by her mother that she was adopted.  Either that or she just was in denial for the past 25 years as I did the research on her mother, and only now decided to come clean about it.  But Sam’s results came back last week and this is how it showed up on FamilyTreeDNA. Screen Shot 2014-09-20 at 9.49.33 AM   You can see that the largest segment/longest block is only 13.34cM even though predicted 1st – 2nd cousins with a total of 501.35cM.  A half first cousin would share about 425cM, or 6.25%.  GedMatch shows a different total, the largest segment being 14cM, still the average as I mentioned that I am seeing. Below is what it looks like on GedMatch. Screen Shot 2014-09-20 at 9.50.39 AM The total is 216cM, and on 24 segments.  I previously mentioned the number of segments as a clue with Polynesian endogamy, not only are the segments not very large but the number of segments are numerous.  In this case, 24 of them.  To compare, I have a 1st cousin once removed named Andrew on my non-Hawaiian side, but he is also Hawaiian.  We share 380cM, largest segment 42.7cM on 18 segments.  Another first cousin Leroy, (non-Hawaiian) is also a 1st cousin once removed to Andrew.  They share 439cM, 71cM is the largest segment and also 18 segments.  The difference in the number of segments is obvious where endogamy produces more segments.

Comparing my cousins and what my mom has with Sam, and her two highest matches on GedMatch.  One of those matches is my friend’s father, and the other is a Maori man who says my mother is his top match on GedMatch.

Andrew & me – 1st cousins once removed:
Total shared – 380cM
Largest segment – 42.7cM
Number of segments – 18

Andrew & Leroy – 1st cousins once removed:
Total shared – 439cM
Largest segment – 71cM
Number of segments – 18

Leroy & me – 1st cousins:
Total shared – 754cM Largest segment – 80.5cM
Number of segments 30

My mother & Sam – half 1st cousins (but not biological since my mother was adopted):
Total shared – 216cM
Largest segment – 14cM
Number of segments – 24

My mother & my friend’s father:
Total shared – 300.5cM
Largest segment – 20.4cM
Number of segments – 30

My mother & Maori man:
Total shared – 140.7cM
Largest segment – 16.3cM
Number of segments – 16

And although the number of segments for first and second cousins as well as the total shared may vary from person to person, the first 3 examples comparing myself and my cousins are the average expected for a first cousin and a first cousin once removed relationship.  But it is also clear that in the case of the Maori man who is from New Zealand and whose ancestors have been there since the beginning of their time, just as my mother and our ancestors have been in the Hawaiian islands since the first people arrived in Hawai’i about 1,500 years ago, the number of segments will help in figuring out, depending on how distant the relationship is, if it is a true relationship or an endogamous one where the actual connection is much further and/or is through multiple common ancestors. So the size of the largest segment is an indicator within endogamous groups if the relationship is closer or not.  Anything near 20cM or below it compared to a huge amount for the total shared indicates that the relationship is much further back.  That can easily be determined by the amount of segments.  The more segments you have, the more times you share common ancestors with your match. Had I not known this up until last week, I would have easily assumed that my mother and Sam are actually half first cousins.  But this actually shows, based on the number of segments and definitely by the small size of the largest segment that they are not closely related at all.


One thought on “Endogamy and multiple smaller segments

  1. Pingback: Not all endogamy is the same | Hawaiian DNA

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