Pili kūpuna

Pili kūpuna.  A term much more fitting than “endogamous” which the dictionary defines as, “the custom of marrying only within the limits of a local community, clan or tribe.”

From a Hawaiian perspective: pili ma nā kūpuna. Adhering by way of forebears.  Basically what it translates to is a relation to the ancestors; that is, more distant relationship which belonged to the granparentsʻ generation or before.  Based on two words, pili and kupuna.


Screen Shot 2014-12-02 at 2.09.33 PMThere is an ʻolelo noʻeau (proverb) that says: he ʻohana kiko moa.  “Family that hatches like chickens.”  It was an expression used to mock those who mated with no regard to relationship.  In ancient times, intermarriage was encouraged among the high chiefs, not for the commoners.

This emphasizes the fact that Hawaiians were not necessarily intermarrying on purpose, as it was strictly reserved for the chiefs.  More so after the arrival of the missionaries in 1820 and since then even the chiefs stopped intermarrying, followed by an influx of immigrants from various parts of the world such as the U.S.A., Europe and Asia.  And although we are aware of who are relatives are, and the fact that we do not necessarily intermarry our own known close relatives, we can still come up as a close cousin match.  Which is why endogamy is not really an accurate term, since it was not really the custom.  I cannot speak for other Polynesians, but definitely not among Hawaiians who have been isolated for at least 500 years.  And we are still closely related on a genetic level to Maoris of New Zealand and other Polynesians.

Pili kupuna definitely fits as to how Polynesians relate to each other, culturally and of course genetically.


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.



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 Maoris (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.

GedMatch’s Full Matching Base Pairs

Kitty Cooper had a blog entry – “When is a DNA segment match a real match? IBD or IBS or IBC?” that discussed a problem when it comes to matches, some of these are not true matches due to the fact that when we share a matching segment with someone of a common ancestor, it is based on half identical regions.  We basically get a set of alleles from each parent but genome testing looks for stretches of DNA, however it cannot figure out whether it came from your father or mother.  This is what can cause problems with matches because they may not be a true match.  More about this can be found here:

When doing a ONE TO ONE comparison on GedMatch.com, you have the option to show a graphical bar for each chromosome that is color coded and it can show where on a chromosome you match half of the base pairs, or have a full match.  Usually the full matches are seen when being compared to siblings.  Parts of it will be green, the other yellow, and also red.  When compared to an identical twin, it will be all green.

Screen Shot 2014-11-06 at 5.51.43 PM

This is what it looks like when comparing my kit to my half-brother’s.  Below are only a few of the chromosomes where we match, but you can see where the blue is under the yellow.  Blue indicates that the segments are at least 7cM and the yellow indicates that it is a half match base pair.

Screen Shot 2014-11-06 at 6.57.56 PM


Since Polynesian are super endogamous, resulting from successive founding populations and bottle necking events, it is not unusual to see full matching base pairs in green.  Below is what it looks like when comparing my mother to my friend’s father.


I am only showing four of the chromosomes, the chromsomes that had the most full base pair matches.

We are not close relatives, but my mother does share a lot with him.  These are the segments shared between my friend’s father and my mother.  Only chromosomes 1 and 3 show no green segments.  All the others do have green segments.


What this means is that both pairs of each chromosomes are matching.  So my mother’s parents and my friend’s paternal grandparents were all related.  When doing a ONE TO ONE comparison, it is usually easier to compare without the graphs, unless you are looking for something specific, like with identical twins or full versus half-siblings. In the case of endogamy however, it may or may not be useful, depending on what you are looking for.  If you are simply looking for a match, then it is not needed.  I wrote in a previous blog entry about multiple small segments as a key for endogamy, using a graph may give a better insight with how much you may be related to someone, or rather how many times you may descend from common ancestors.

Although I have not made an in-depth comparison yet, but from what I can tell it seems that the majority of the green bars indicating a full base pair match is more noticeable when comparing my mother with other Hawaiians.  I compared all the known Maori matches who share more totals with my mother versus Hawaiians who do not share as much, and from what I can see is that they do show a few tiny green segments.  The most obvious is that the less admixed the Polynesian,  the easier it is to see more green segments.  This makes logical sense and of course the amount of green would be more indicative of ties to a specific geographic area, or rather indicate that people have remained in a specific geographic area for a longer amount of time.  This too should be obvious by the multiple number of segments.

So to summarize, the full base pairs (green) means that there are multiple lines of relationship, more specifically to the parents of the matches if the amount of green segments are large or nearly matches the blue bar indicating matching segments great than 7cM.  While the multiple segments would indicate descending from a common ancestor multiple times.

ADSA and triangulation

For a very long time I have been avoiding triangulation with my mother’s matches for the simple fact that we lack documentation and how closely related we appear to be due to the lack of genetic diversity shared among Polynesian people.

I decided to once again try to make sense out of some of this by using dnagedcom.com’s Autosomal DNA Segment Analyzer, commonly known as ADSA.

A few months ago at one of our DNA Interest Group meetings we had Don Worth who developed this tool do a presentation.  He mentioned how those of Ashkenazi Jews or any endogamous group should increase the threshold to at least 10cM, in order to minimize the processing time.  At that time I still didn’t comprehend the reasoning and thought that it really wouldn’t matter.

Looking at just chromosome 11, this is what my mother’s results look like when I do not adjust the settings.


As you can see there are a lot of matches.  I knew that majority of Polynesians’ matches averages around 10cM with the largest segment.  When I increased it to 10cM, I get the following for the same chromosome.


So now it is reduced, I get less than what I would normally get, but there was a reason why I thought that increasing the threshold to 10cM for endogamous groups did not make sense to me before.   Although this is probably unique to Polynesians only compared to other endogamous groups, but the largest segment is not necessarily indicative of a closer match

The match with 13.76cM is a Maori while the others are Hawaiian.  There are two other people on that list at 12.35cM, a brother and sister who is actually much more distantly related to my mother (according to FTDNA) than the Maori person is.  That brother and sister’s father had a paternal grandmother that was Hawaiian, while their mother is Samoan.  The smaller total amount shared compared to others that share way more, is probably due to the semi-distant Hawaiian ancestress, or via their Samoan mother of whom is western Polynesian. Western Polynesians are older than eastern Polynesians, and eastern Polynesians are closer related to each other.  In other words, western Polynesians are much more diverse than eastern Polynesians.

There are other admixed Hawaiians of whom are not that close of a match to my mother, while there can be Maoris who are closer matches both having either large or small longest block/largest segment more than 10cM.  Therefore, increasing the threshold could possibly get rid of a lot of the Hawaiians of whom should be closer to my mother than the Maoris.  It seems to really matter too if the Polynesian is admixed or not.  Obviously the less admixed, the closer the relationship will show as far as the total shared is concerned.

Here is a look at the X chromosome with the minimum threshold increased to 10cM.  When I initially ran this with the default settings, the X results produced a very long list of matches.  Increasing it only managed to take out a few.


Triangulation will still be a challenge for us.  The only thing that may be helpful is understanding that more multiple segments means the more interrelated you are, whether you come from multiple common ancestors or come from the same common ancestors multiple times.  The smaller the segments, the more distant the common ancestor(s) is/are.

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.

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.