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.

New 5th Cousin connection helps map out chromosome!

HOW WE CONNECT

Now that I had figured out who my mother’s biological parents were it has become easier to find connections.  (You can read about it here: https://hawaiiandna.wordpress.com/2015/08/01/finding-a-dna-connection-despite-endogamy/)

While there is one branch where I find a lot of relatives on my great-grandmother Rose Holbron’s side, I am slowly finding distant connections on my great-grandfather Frank Kanae’s side.  Frank Kanae was Rose Holbron’s husband.

Earlier this week I received an email from a woman named Raychelle who saw me and my numerous kits of family members that I manage on GEDmatch.com as a match to her.  I began the normal response, almost ready to dismiss her since many of these matches appear to be close when in reality we are usually distant, and for others, much more distant.  And from what I could see, it wasn’t such a huge amount.  At GEDmatch, Raychelle and my mother shares 62.9cM total, with a large segment of 10.7cM.  So at least a 4th cousin level.

After I told her that she could find me on Ancestry (since she uploaded to GEDmatch via Ancestry) and look at my HOLBRON family tree, she found out that we have the LEWIS connection.

She is a 5th cousin to my mother, and a 5th cousin once removed (5C1R) to me.  I come from Isaac Lewis who was known as Isaac Lewis Kanae or Isaac Kanae Lewis, and also known by the Hawaiianized version – Aikake Lui.  While Raychelle comes from John George Lewis, and his Hawaiianized name was Keo Lui.  My assumption is that Keo was short for Keoki (George).  Keo could also be short for Keoni (John) and then there was the catholic version – Ioane for John.

But what was interesting is that she had this genealogy and I had updated mine from this to reflect what a couple of people have been researching.

According to the information that has been circulating at various sites on the internet, Isaac’s father – Captain Isaiah Lewis was the son of Captain Ezra Lewis.  And John G. Lewis was the son of Captain John Lewis, who was Captain Ezra Lewis’ son but through a different wife.  I listed them as spouse #1 and spouse #2 because different sites and people will switch the spouses showing Isaac as the son of one spouse, and another will show Isaac as the son of the other spouse, and vice versa for John G. Lewis.

Click to see larger image
So the question is, were Isaac and John full brothers, or (maternal) half-brothers?  And if they were (maternal) half-brothers, were their fathers paternal half-brothers?

While all of this information going back that far is based solely on people creating these trees without further documentation, for now I am only going by what was documented.  The trees habitually say that Polly was known as Sarah Pauline “Polly” Holmes.  While I can understand that Polly could be a diminutive for Paula and Mary, I’m not so sure that these are the same person, especially since a lot of the information lists this Sarah Pauline “Polly” Holmes having been born in Massachusetts and died there,  and that her husband Captain Isaac Lewis from Massachusetts too.

What we know for a fact according to testimonies from people who lived during the time of Polly Holmes and her father Oliver Holmes.

screen-shot-2016-12-02-at-12-32-31-pm

I am still in the process of confirming and documenting all of these ancestors, so for now I am considering Raychelle and I 5C1R, and that her 3x great-grandfather John George Lewis (Keo Lui) and my 4x great-grandfather Isaac Lewis Kanae (Aikake Lui) were full-brothers.

 

SHARED DNA SEGMENTS & CHROMOSOME MAPPING

I compared Raychelle to all of the relatives to see which segments we all had in common.  Any common segments or segments that multiple relatives share would indicate that segment was inherited from a common ancestor.  In this case, Polly Holmes and her husband Isaiah Lewis.

And while autosomal DNA inherited from our common ancestor can remain in our genome for about 5 – 6 generations, there are some cases where it can span several generations and for some as we have seen, in larger segments. These larger segments tend to be passed on within generations entirely intact and having not recombined.

With endogamy, that may confuse things as it isn’t guaranteed that the shared segment came from that same common ancestor.  Especially for Polynesians where we share many small segments.  And these multiple segments may not be in common with other relatives, or rather these segments may not overlap as what I am about to demonstrate.  So when looking to map out these segments, and at the 4x great-grandparent level, if the segments are really small, that may be suspect to being segments randomly inherited.  It may or may not be from the common ancestor, or may come from the same common ancestor multiple times through their different descendants.

I first compared my brother Kaimi and Raychelle and looked for the chromosomes that should match my mom.  Kaimi and I have different fathers, so I decided to use his to compare because his father is also Hawaiian.

I use Kaimi’s unphased and phased data to be sure that if there are extra segments that does not match our mother, then the presumption is that the segment came from Kaimi’s father.  These were the results.

screen-shot-2016-12-23-at-2-08-35-pm

You can easily see how with the phased data the size of the segment is somewhat smaller if it doesn’t remain the same or disappear altogether.

The real work comes in when I compare Raychelle to my mom’s brother’s son Chris, her half-brother’s daughter Lena and her maternal half-sister Aunty Stella.  The detailed specification of their relationship is to help you understand how they are related and know what is to be expected as far as sharing DNA with different relationships go.

What I did first was compare Raychelle to all of those family members mentioned and then see which of those matching segments actually matches up with what my mother matches.  Here’s a diagram of how we are related and descend from Isaiah Lewis and Polly Holmes.

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I’ll start first with Chris, the son of my mother’s brother Joseph.

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While there were other segments that Raychelle shared with Chris, I am only comparing overlapping segments that are shared with my mom.  There are 3 chromosomes where they share overlapping segments.  Ch 6, 7 and 20.

With Aunty Stella, there were segments on different chromosomes, sometimes on the same chromosome but in different parts of the chromosome that did not overlap.

screen-shot-2016-12-04-at-7-45-56-am

Only one overlapping segment which is on ch 7.

Then with Lena, the daughter of my mom’s half-brother George.

Lena also shared different segments and different chromosomes with Raychelle that my mom does not have, except for ch 7.

So what is consistent with all of them is that a segment on chromosome 7 is shared with Raychelle.

The diagram above  shows how everyone matches each other, with the last one again showing my mom with Raychelle and that consistent block of segment.

So the fact that we all shared an overlapping segment in common with each other indicates that particular segment was inherited from our common ancestor.  In this case, both Isaiah LEWIS and Polly HOLMES.  But how do we figure out if that segment came from Isaiah vs. Polly?  Remember that there was a discrepancy that Polly’s two husbands – Isaiah LEWIS and John LEWIS were paternal half-brothers according to some other genealogy and that Isaac LEWIS KANAE was Isaiah’s son, while John George LEWIS was John LEWIS’ son.  Both Isaac and John had the same mother – Polly HOLMES.

The best way to distinguish that inherited segment being inherited from Isaiah LEWIS or Polly HOLMES is to test members of each of those families.  That would be distant relatives of whom we cannot find a connection to just yet.  Instead, I used another method.

Since my mother tested at 23andme, they have the ability to show the ancestry broken down by each chromosome. This is what my mother’s 7th chromosome looks like.

 

screen-shot-2016-12-03-at-7-36-33-pm

23andme identifies portions of the Hawaiian segments of the chromosome as a combination of East Asian & Native American, and Oceanian.  I simplified it by just indicating Hawaiian.  Both of my mother’s parents were Hawaiian, but her mother Rose KANAE also had European ancestry.  Which is why in that diagram one chromosome is labeled as the paternal chromosome, the other as the maternal.

My mother’s maternal grandmother was Rose HOLBRON.  Rose’s paternal grandfather John HALBORN was from Hull, England, and her maternal grandfather William LUDLUM was an American whaler from Jamaica, Queens, New York.  Rose HOLBRON’s grandmothers were Hawaiian (Kanaka).

But it is Rose KANAE’S father – Frank KANAE whose paternal grandmother Mary LEWIS KANAE’s father was Isaac LEWIS KANAE.  Isaac’s father was Captain Isaiah LEWIS.  Isaac’s mother Polly HOLMES was the daughter of Oliver Holmes of Kingston, Plymouth, Massachusetts and Mahi, daughter of the chief Kalanihooulumokuikekai of Ko’olau.  My assumption was that the European portion from Rose KANAE’s father is too far back.  In other words, the European portion of that chromosome that my mother inherited from her mother could have only come from John HALBORN or William LUDLUM, or a combination of both.

There are a few factors that could make a segment remain in tact for several generations:
1) The length of the chromosome.
2) How many cross-over events there were for that particular chromosome.
3) Location on the chromosome (some areas are more SNP dense than others).
4) The possibility of having fewer cross-over events or none at all (we see this happening as well).
This segment seems to match nicely ranging from 7.1cM (my mom) to 9.1cM (Aunty Stella) with all the relatives.

So when I visually compare the section of chromosome 7 that matches up with the shared overlapping segment for all of us, this is where they line up.


If you have read my other posts, you would have read that multiple segments for Polynesians can remain for awhile given that we come from a few common ancestors multiple times.  This paritcular segment had to have come via Polly HOLMES’ mother – Mahi who got it from her parents Kalanihooulumokuikekai and his wife.  And since Raychelle is also a descendant of Polly HOLMES and Isaiah LEWIS, this portion of chromosome 7 did not come from my HOLBRON side.

While my family members used for comparison descend from Isaac LEWIS KANAE’s daughter Mary LEWIS KANAE, there are other descendants through Mary’s sister Papanaha LEWIS KANAE who got DNA tested.  But only one of them was a match to Raychelle.

screen-shot-2016-12-04-at-4-00-56-pm

This cousin shares an overlapping segment of 8cM on chromosome #7.  But when I compared that relative to my mother, they did not share that particular overlapping segment, although all my other close relatives did share that overlapping segment with this cousin.  After looking into it further, I found out that my mother seemed to have inherited a smaller section of that overlapping segment compared to other family members, and her matching criteria just did not qualify as a match according to GEDmatch.com where all of this analysis was done.  After all, she shares the least out of all the relatives only 7.1cM of this segment and Aunty Stella shares 9.1cM.  And while she gave me and my brother Kaimi this segment, my brother Travis did not inherit this segment.  Which means this portion of chromosome 7 for him was from our grandfather, not our grandmother Rose KANAE.

But that is what is complicated about mapping out segments for Polynesians. These segments could be from any of these lines going back to the same common ancestor multiple times. That means that Raychelle could just so happen match all of us via my maternal grandmother Rose KANAE’s mother’s side, or my great-grandfather Frank KANAE’s mother’s side, or John KANAE’s father’s side, and so forth.  It could also be just by chance, that we share the segment with any other of her Hawaiian ancestors.

Since many Polynesians share multiple small segments and as small as 7cM, as well as having these segments line up very close to each other if not right next to each other, it makes chromosome mapping very difficult to do.  For example, I mentioned one of Papanaha LEWIS KANAE’s descendants share that same overlapping segment on chromosome 7 with the rest of us, while the other descendants  share multiple non-overlapping segments.  I cannot easily assign them to our common ancestor – Isaac LEWIS KANAE, or presume that all of these multiple segments came from our common ancestor.

Since Polly HOLMES is 6 generations away from my mom and all of her descendants share this same overlapping segment, it is safe to presume that this segment came from Polly HOLMES’ mother – Mahi.  And now I can assign at least this small portion to Mahi.

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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.

Screen Shot 2016-05-03 at 5.47.08 PM

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.

Determining half-relationships with Polynesians

I recently got my cousin’s results to compare to my mother and my brothers.  This cousin’s father was my mother’s half-brother George, so a half-first cousin relationship.

Prior to making contact with my mother’s relatives I was thinking of having these cousins tested as a means to figure out who my mother’s biological father really was.  But a couple of months ago when I did make contact with these long lost relatives it was revealed that my mother’s biological father was Joseph Kaapuiki Akana, the man whom I doubted was my mother’s father based on his name (Akana is of Chinese origin) and the fact that my mother remembers her father being pure Hawaiian and her DNA composition does not support Chinese ancestry.  I thought that maybe testing these half-cousins would determine if their grandfather was my mother’s biological father.  But it is more complicated than I realized.

Like my mother’s father Joseph Kaapuiki Akana, George’s father was also Hawaiian.  George and my mother shared the same Hawaiian mother.

This is what the ISOGG Wiki Autosomal DNA Statistics page says about how much should be shared between a half-aunt and also to half-cousins.

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Combining with Blaine Bettinger’s Shared cM Project, the total shared for a half-aunt would range from 540cM to 1348cM, averaging 892cM.  The average is around the amount indicated by the ISOGG Wiki page.

For a half-first cousin, Blaine Bettinger’s Shared cM Project says it would range from 262cM to 1194cM, averaging 458cM.  Again, that average is what is indicated on the ISOGG Wiki page.

This is how GEDmatch.com compares my half-cousin to us.

Screen Shot 2015-12-29 at 7.33.09 PMIt is obviously on the high end, for a half-aunt while half-first cousin, not that extreme.  But we are talking of one example only.  There are more half-cousins that I could have test and probably will in the future.  And all of these cousins have had a grandfather that was Hawaiian, so I would expect their amounts to be high.

Comparing to non-endogamous groups, I compare my paternal aunt to her nephews and nieces and a great-nephew and great-niece on GEDmatch.

Screen Shot 2015-12-29 at 7.45.46 PM

My cousin Terri may share the lowest total among the 1st cousins but it does not seem that significantly different from the average 1700cM.  It is interesting to see that her largest segment is 104.7cM.  When I look at my half-first cousin and how much she shares with her half-aunt (my mother), the total is 1412.8cM, and largest segment is 103.3cM.  That figure can be misleading.  I have more cousins on my father’s side that I have yet to test and there may be other cousins who share less or more with our aunt than the cousins that have already tested.

If I take my aunt out of the equation, this is how the cousins compare to each other.

Screen Shot 2015-12-29 at 7.50.04 PM

A couple of my paternal 1st cousins share much less with each other than my half-cousin does with me and my brothers.

It will be awhile before I can get an ample amount of Polynesians who have close relatives tested to fully make a comparison.  Initially I wanted to see if testing half-cousins would help determine if my mother’s siblings were half or full siblings and when I was not certain that Joseph Kaapuiki Akana was her biological father.

It is clear now that any type of half-relationship is difficult to determine if the other parent is also Polynesian, and in our case Hawaiian.  My grandmother married 3 different Hawaiian men and so far from what I know, they have ties to geographically different places.

The endogamous nature just makes it hard to determine the relationship even if it is a close relationship.  It does not have to be a distant 3rd cousin and beyond to appear as a closer relationship.  Even with cousins (half or full) and half-siblings, they seem to appear on the higher end of the relationship, possibly giving a false prediction if the true relationship was not known.

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.

Screen Shot 2015-07-13 at 3.25.31 PM

 

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

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.

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.

oceania

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.

Screen Shot 2014-12-20 at 12.30.11 PM

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.

Screen Shot 2014-12-20 at 8.21.57 PM

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.

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.

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:
http://dna-footprints.com/203/the-abcs-of-dna-ibd-vs-ibs/
http://dna-explained.com/2012/09/03/matches-family-ibd-vs-population-ibs/

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.

mom-lawrence-GREEN-compare

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.

mom-lawrence-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.

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.