Finding a DNA connection despite endogamy

MISLEADING CLOSE MATCHES

Shortly after getting my DNA results back in May 2013, I learned that majority of my DNA predicted connections are an endogamous connection.  That means a predicted connection that appears to be much closer than it really is.  Being Polynesian (Hawaiian), I am a result of generations of constant bottlenecking and founder’s effect that have occurred through the centuries.  This effect is much more pronounced among eastern Polynesians like Maoris and Hawaiians whose homeland were the last places in Polynesia to be settled.

Since my mother was adopted and both of her parents were Hawaiian, I knew it was going to be a bigger challenge.  Like other Polynesians, documentation for genealogical purpose was limited and it was not until 1860 when King Kamehameha IV passed an act to regulate names did surnames begin appearing for Hawaiians.  Even right after that, surnames appearing within families were inconsistent and it varied between families, generations (some starting it later than others) and also islands.

At FTDNA, my mother’s matches can have a total shared cM way above 300 (5 pages of those), while her longest block [largest segment] size tends to stay under 20cM.  These are the matches from her 1st page.

FTDNA’s requirements for a match allows the tiniest segments to be included once the criteria of the longest block has been met.  But in an endogamous population, specifically Polynesians, they tend to report the number of segments to be well over a hundred.

23andme is slightly different.  At the default, the matches are sorted by relationship which is shown on the left column, while on the right column is sorted by percentage.

This is how GEDmatch.com shows the matches.

I expected the matches at Ancestry to be not as close as they were predicted for the same reason seen with FTDNA, 23andme and GEDmatch.

1) Several matches totaled above 100cM.
2) The largest segment usually does not exceed 20cM.
3) Matches are usually Hawaiians who do not match each other at the same amounts, and Maoris of whom we share a distant connection from 800 years ago.

As I looked at the Ancestry matches and compared the predicted 2nd – 3rd, or 3rd – 4th cousin predictions and how they appeared on GEDmatch, I noticed that they would fall in a large range of  187cM – 304cM for the total autosomal shared.

At the time I was trying to compare this close relative, Ancestry did not have the option to see how much you share, unlike now where they list the total amount of centimorgans you share and the number of segments.  But still no chromosome browser to do a full comparison.  Being able to see the largest segment would be key in determining a true close or distant 2nd or even 3rd cousin relationship.

So there are four matches in the 1st – 2nd cousin range (Extremely High) but I could not determine if they just appear to be close, or were true 1st to 2nd cousin matches.  Given the pattern with the other companies and GEDmatch,  I ignored Ancestry for over a year, until earlier this month when I reached out to my mother’s best match at FTDNA.

DETERMINING THE BEST MATCHES FOR TRIANGULATION

My mother’s best match belongs to a woman who tested at FTDNA.  They share 266.94cM (122.9cM GEDmatch) total, and the largest segment is 50cM.  A largest segment size of 50cM is a very good indicator that the relationship was not too distant.  I guessed somewhere around a 2nd to 3rd cousin.

Last year she shared her tree with me that goes back to her ancestress named Theresa Manner, the daughter of a Swiss man and a Hawaiian woman named Kama’u.  This match’s paternal grandmother and paternal grandfather were both Hawaiian.  Kama’u was an ancestress on the paternal grandfather’s side.

Back in January I began focusing on Theresa Manner’s husband’s line, especially since his family lived in the area where my mother was born.  Not to mention I had nothing else for Theresa Manner except her parents’ names, and Kama’u was the only Hawaiian that I saw in that line.

My match asked me if I thought there was a possibility that it was her paternal grandmother’s side versus her paternal grandfather’s side.  Her paternal grandmother was also part Portuguese, but since we were not getting matches with Portuguese people I excluded the paternal grandmother’s side.  Although this match and my mother share 2 segments on the X chromosome, the largest segment 10.2cM while the other 8.8cM,  I knew it had to be distant given the unpredictability of the X particularly for Polynesians.  So I ignored it and continued to focus on the paternal grandfather’s side.

At Ancestry, my mother’s closest match belongs to a man and is the first match at the top of the diagram above.  But this match’s tree did not have any names in common with any of the other top matches that we get.  No matter how many conversations I have had with this closest match at Ancestry, although all prior to my mother revealing to me in August 2014 that she was adopted, I still was unable to find any close connection.  Given the endogamous history and the fact that we just lack genetic diversity, it seemed more of a validation that the match was not as close as it appeared to be.

 ANCESTRY RESULTS TO HELP NARROW DOWN SPECIFIC ANCESTORS

I also focused on my mother’s ancestry, which points to two basic ancestries.   East Asian and European.  Her Polynesian portion is usually represented by the East Asian and Oceanian categories combined.  Some companies such as FTDNA’s “myOrigins¹” have lumped Oceanian under their East Asia category which previously their “Population Finder” separated them.  23andme also separates the two categories while AncestryDNA recently created a category called Pacific Islander (Polynesia).  Below are the results from those companies including analysis from Dr. Doug McDonald².  For simplification I combined the Oceanian with East Asian.

AVERAGE
81.72% = East Asian/Oceanian
17.32% = European

This next diagram shows 23andme’s chromosome view.  My mother’s X chromosome was just East Asian/Oceanian in origin.  Dr. Doug McDonald also had a chromosome view and he too found that it was only of East Asian.

Knowing the X inheritance pattern, plus the amount of European percentage that my mother has, I tried to calculate who would have been the most likely European  ancestor that married a Hawaiian.  If not European, then of European descent. So I had a few clues that helped me determine how to figure out who that was.

1) My mother recalls meeting her biological father at the age of 5, and claims that he was pure Hawaiian.
2) Our mtDNA haplogroup is B4a1a1a3³, a subclade of the Polynesian motif B4a1a1, indicating our direct maternal line as Hawaiian.
3) The odd percentages is probably the result of more than one ancestor being of European and Hawaiian ancestries.

Given those details, I constructed this diagram which would be the likely scenario of how my mother got her European and Hawaiian ancestries.

 

I thought that looking for her European ancestors would be easier to trace given the few early European (or American of European descent) arrivals in the Hawaiian Kingdom.  Unlike with Hawaiians whose DNA results produce closer predicted relationships than they really are.

I calculated both 18 years per generation in that diagram and 25 years for each generation.  The 25 year estimate took me to 1868 from my mother’s birth year of 1943, and back to a 50% European/Hawaiian person in that diagram.  Theresa Manner was born in 1866, so now I was confident that this could be very useful in tracing my earliest Hawaiian/European-descent ancestor.

Comparing this diagram to Theresa Manner and knowing that the estimates of the dates were very close, I realized that I did not go back far enough.  Although the predicted 50cM largest segment for a 2nd to 3rd cousin was good, it was best to be sure to go even further.

TRIANGULATION & FURTHER RESEARCH

My match at FTDNA also revealed that her father’s Y-DNA results showed a European haplogroup rather than a haplogroup indicating Polynesian origins of which her father has a direct male Hawaiian line.  Given this new information and not knowing where this NPE (non-paternal event) could have occurred, either with her father or her grandfather, or even further back,  I immediately excluded this line.  This was the same line I was previously looking into back in January, focusing on Theresa’s husband and their children and her husband’s siblings and their children.  Although still, that would not tell me for sure if that was my mother’s paternal or maternal side.

I realized how I was ignoring Theresa Manner, whose father was a Swiss and he married a Hawaiian woman named Kama’u.  I asked my match if  Theresa Manner had any other siblings.  Previously my match only shared Theresa’s parents, and Theresa’s husband and their children.  Again, because of the 50cM largest segment prediction, assuming it was pretty close, that I did not have to go back further.  But I knew that Theresa Manner was an important clue since she was half European (Swiss father) and half Hawaiian and was born in 1866.  That fit into the year I predicted from the diagram that I created in order to come up with the estimated 1868 birth for a male ancestor that was 50% Hawaiian and 50% European.  I was told that Theresa not only had 3 other siblings, but also 2 half-siblings.  They were Robert Holbron and Mereana (Mary Ann) Holbron.  Kama’u was previously married to John Holbron from England.

I thought that name Robert Holbron seemed familiar.  Since several of our top matches at Ancestry had public trees, I went back there to look and saw that the very top match of whom I have had correspondence with last year listed in his tree Robert Holbron and his wife Annie Ludlum as his ancestors.  This match is in the predicted range of 1st – 2nd cousins, although as mentioned previously, it may or may not have been a true 1st – 2nd cousin relationship.  But the fact that both of these matches had Kama’u in their line and of whom was probably the one responsible for passing on that large 50cM segment, I knew I found my ancestors.

With this new information things fell into place.  I referred to the diagram I created and it seemed that Robert was the more likely candidate to fit into what I had constructed as my possible ancestors.  But to be sure, I looked into his sister’s descendants first.  Mereana Holbron married an Irish man, lived in Ireland and in Hawaii.  But Robert appeared to fit the pattern I mapped out more than his sister, although his wife Annie had a surname of Ludlum, which indicated that she was an admixed Hawaiian unlike in my diagram.  But even with her being half, I knew that her mother was Hawaiian based on the fact that if Annie were my ancestor, her mother would have passed on my B4a1a1a3 directly to Annie and down to females.  And that matched up with my diagram.  My match’s tree at Ancestry listed Annie’s parents as William Ludlum and Ehu, which confirmed that Annie was half Hawaiian and of half European descent.  Later, I would find that both Robert and Annie’s estimated year of birth fit the diagram and predicted year of birth only off by 13 years.

While going through several of the old Hawaiian newspapers I found an article with a photo of Mrs. Annie Holbron celebrating her 100th birthday.

Annie Ludlum

SPECIFIC BRANCH NARROWED DOWN

I continued looking into Robert and Annie’s children and grandchildren.  I focused on their oldest daughter Rose Holbron and her husband Frank Kanae, and who our top match at Ancestry descends from.  And although I made sure I covered many of the collateral branches, I still used as a guide the diagram I created to guide me into which branch it could be.  And it took me to Rose & Frank’s 3 daughters.

While looking for their descendants and who they married, one of them had a photo uploaded into their tree on Ancestry,  and I saw the striking resemblance not only to my mother but also to my sister. I found information on her husband and children and she had one child born just a month before my mother was born.  So it seemed unlikely that this was my mother’s biological mother.  This is on the assumption that my mother’s birth date on her “legal birth certificate” is her actual birth date.  I could only assume that it may have been one of the other two sisters who was my mother’s biological mother based on the fact this woman looked like both my mother and sister.

I definitely found the right family for my mother’s maternal side.  It would be only a matter of time before I find out if the woman whose photo I found was my mother’s biological mother, or her mother’s sister.

EVALUATING ALL CLUES

My mother’s legal birth certificate left questionable details since I began researching 26 years ago. It was because it did not indicate that it was an adoption, unlike my own birth certificate which clearly states that it is an adoption. What was known and is clearly indicated on my mother’s birth certificate.

• Birth was not a hospital or institution but at a residence – 1301 Liliha St. (Honolulu)
• A midwife was present, attested to witnessing the birth of Julia Kawewehi Scott [adoptive mother].
• Usual residence of mother was 440 N. King St,  which was the permanent residence of both parents.

I spent several years looking into the address where my mother was born. I even tried to track down people who lived at the same address hoping to find someone who was alive at the time my mother was born and may know something about her birth mother.

Now that I have found the branch that we come from, again I continued to look into Rose Holbron and Frank Kanae’s daughters.  I already found one with a photo who resembles my mother and sister.  Another daughter I found was married several times, and had children from possibly more than just her own husbands, but this is based on surnames.  Her name was Rose Kanae, and her first husband was surnamed Kalei.  Her second husband was Joseph Akana, which can be a semi-common name.  A lot of Akanas, but not all are related to each other from what I saw with their last known ancestor to some of the Akanas that I found.  That surname comes from a Chinese who either became a Hawaiian citizen or just Hawaiianized his name.  That surname caught my attention and made me think about it for a bit, but given that I had done a lot of genealogy I know and do remember seeing that name and reading about that surname in other Hawaiian genealogy forums.  Then after Joseph Akana, Rose married a third time.  All of those husbands gave her children.

I was surprised to find in the city directory of 1947, that Joseph Akana lived at 1301 Liliha Street.  This was the same exact address where my mother was born.  So either this woman got pregnant from another man and Joseph Akana divorced her, or her sister got pregnant and gave birth at their residence.

At the same time I found the photo of the woman who could be my mother’s biological mother, my mother called to tell me that she received her non-identifying form from the First Circuit Court in Kapolei, O’ahu, Hawai’i.  This form just gives adoptees little information into their background and every state and court has their own way of determining what will be revealed.  For Hawaii, it is the ancestry.

When I received a copy of it, it indicated that my mother’s mother was Hawaiian and Chinese while her father was Chinese Hawaiian.  However, DNA does not support that.

Non-Identifying Form – letter form

But given the non-ID form indicating Chinese, although incorrect, this was pointing to Joseph Akana and Rose Kanae as the parents listed.  Joseph Akana’s surname was the only clue that made me believe he was not the biological father.  I had even suspected that there may have been a question of paternity with Joseph Akana and what may have caused my mother to get adopted, hence Joseph divorcing and my grandmother remarrying.

I was also told that back then, no matter which state, particularly for unwed mothers, if the biological mother knew who was going to adopt the child, she might take on the identity of that woman and check into the hospital as that person.  The woman who adopted my mother – Julia Kawewehi was Hawaiian and Chinese.  So I assumed this is what happened unless Rose Kanae really did not know her ancestry.  The DNA evidence indicates a near perfect 70% East Asian to 30% Oceanian component consistent of Polynesians⁴.  Whereas those who have some Asian ancestry in addition to Polynesian, the percentage of East Asian to Oceanian would be much more significant than 70%.  Therefore either the parents listed in the adoption files really are not her parents or they were just wrong with the ancestries of the parents.

THE FOREIGN ANCESTORS

After getting more details on my maternal grandmother Rose Kanae’s branches, I was able to see exactly all of the foreign men who married Hawaiian women in her line.

1) Oliver Holmes, (later Hawaiianized to Oliva Homa) an American who arrived on the island of O’ahu in the Sandwich Isles on October 8, 1793 on board the Margaret, who was in service of the chief Kalanikupule.  After Kalanikupule’s death in the Battle of Nu’uanu, Holmes married Mahi, the daughter of the high chief of Ko’olau⁵ whose name was Kalaniulumokuikekai⁶.  After Kalanikupule was defeated by King Kamehameha, along with Mahi’s father Kalaniulumokuikekai, Oliver and others were taken by Kamehameha and became advisors for the King.  In 1810 after King Kamehameha united all the islands, Oliver became the 3rd Governor of O’ahu.  Governor Homa, as he was called, remained in Honolulu and had one son and five daughters.  One of the daughters – Hannah Holmes married Captain William Heath Davis Sr, and their son William Heath Davis, Jr. ended up in California in San Francisco and was also one of the original founders of New Town San Diego⁷. Oliver’s other daughter Polly married Captain Isaiah Lewis and it was said that she traveled with him to the northwest coast.  Oliver had three other daughters, all of whom married captains of ships coming into the Hawaiian islands.

2) Captain Isaiah Lewis, an American and son-in-law of Oliver Holmes.  He commanded the Panther, and acquired sandalwood in Hawaii and sold it in Canton, China.  He married Polly Holmes, the daughter of Oliver Holmes & Mahi.

3) William Ludlum, an American whaler from Jamaica, Queens, New York who became a citizen of the Hawaiian Kingdom on August 7, 1850.  He married a Hawaiian woman named Ehu on January 24, 1850 in Mapulehu, Molokai.  He ran a hotel & was a Commission Agent.

4) John Holbron [John Halborn/Holborn], originally from Hull, England arrived in the 1840s.  He married a Hawaiian woman named Kama’u and became a citizen of the Hawaiian Kingdom on November 24, 1845.  He was a merchant.

After knowing for sure who these foreigners were, I was able to re-design that diagram and came up with new percentages of each ancestor.
EA/Ocean = East Asian/Oceanian

The light blue represents the male, the pink the female, and the bottom is my mother of which is calculated 14% European and 85% East Asian/Oceanian.  My mother’s results fall into that range of 14% – 19.81% European and 80.18% – 85% East Asian/Oceanian.

MISLEADING X MATCH

While my match at FTDNA did share 2  X segments with my mother (via her father of whom both of his parents were Hawaiian), the fact that I ignored it because of how unpredictable the X is lead me on the right path.  The largest segment size is 10.2cM  and the other is 8.8cM.  I have seen how a significant amount of X my mother shares with other Polynesians (i.e. Samoans, Tongans & Maoris) can be so distant.

While it can be useful in excluding certain branches, this is obviously not the case for endogamous groups, particularly not for Polynesians.  Had I focused on the X path, I would not have made the connection at all.  But it is not surprising that this male shares a distant X match with my mother on his mother’s side yet not have a recent tie to my mother on his maternal side, at least not that I have figured out just yet.

CONFIRMATION OF BIOLOGICAL PARENTS

My friend Charles Ano who have helped me with genealogy searches in the past decided to look up birth announcements in the newspaper around the time that my mother was born based on all of this information that I found.

Birth Announcement – Honolulu Advertiser – Sept 28, 1943

It listed her original name – Joyce Awapuhiokala (Akana).  I did not want to reveal this to my mother just yet since I completed the last step of accessing her adoption records just the other week.  I wanted my mother to receive copies of the actual adoption files and see for herself who they listed as her parents and her original name.

Eventually my mother found out that I knew of her original name, and after I got a chance to speak to her about it, she told me that she already knew she was born Joyce  and that she was related to the Akana family, and also had a Hawaiian name, but she did not know what that name was.  She was about 9 years old when she found out about all of this.

I did tell her that I remember her mentioning the surname – Akana.  And I knew that when I found Joseph Akana, there was something about that name that seemed familiar but could not remember exactly.  I later realized it was last year after almost giving up on DNA and before resorting to accessing her adoption files via the court, I had turned to the 1940 census, just three years before she was born and looked for the place where she was born.  It was at that time I asked her about the family names, people who lived at that address where she was born to see if it seemed familiar. None did, but it was at that time when she asked, “what about Akana?”  I never asked her much more about it, but remember she did comment about how she heard that was her family.  Unfortunately, I forgot about this important clue.

CONTACTING COUSINS – BIOLOGICAL FATHER CONFIRMED

Now knowing my mother’s original name, I decided to seek out my cousins, children of my mother’s siblings.  I already saw names of some of them based on the obituaries I found of my mother’s siblings.  I first contacted a woman whose surname matched my mother’s brother and with whom I already had contact with because at the beginning of accessing my mother’s adoption files I simultaneously tried to get my original birth certificate since my adoption was done at another court.  My adoption was a technical issue.  The mother that I speak of is my biological mother.  It turned out that this contact is a granddaughter of my mother’s brother.  After sharing with her who my mother is, what name she was born, who her parents are and identifying the other siblings based on what I found in the obituaries, she notified both her grandfather and a sister living on another island.  I sent photos of us and she shared it with her great-aunt and grandfather.  She remarked at the strong resemblance of my mother and her great-aunt.

At the same time, I found another cousin on Facebook, contacted our mutual friend and that friend revealed how this cousin probably knew my mother.  Turns out that this cousin and my mother have known each other for the past 6 years.  This cousin also told my mother at first meeting her 6 years ago that she reminded her of his aunt.  This was the same person that the other woman commented of how my mother looked like her great-aunt.

In a few days after having other cousins contacting me, they revealed the entire story of how our grandmother Rose Kanae married three times, and with her husband Joseph Akana she had four children.  A daughter who carried the surname KALEI which was the surname of Rose’s first husband.  Another daughter and of whom is the only sister to my mother that is alive, the one who we are told my mother looks like.  Then a brother and finally my mother.  Then with the last husband, Rose had two sons.  The youngest is alive and whose granddaughter I first contacted.

Only the sister that is still alive and one of the younger half-brothers were the only two children that were not given up for adoption.  The other seven children were all given up for adoption.  The older ones knew of my mother’s existence.  But what they knew was that they had a sister named Joyce Akana who was given up for adoption by a Filipino family.  My mother’s adoptive father was Filipino.

Then it was revealed to me how Joseph Akana really was my mother’s father, but Akana is a surname he took on later in life and was the surname of his paternal aunt’s husband.  His original name was Joseph Napua Kaapuiki and was a pure Hawaiian man just as my mother remembered.  And Joseph did frequent the area and since my mother grew up right by where she was born, it is no surprise that she actually did encounter her father.

And as difficult as this was given the situation with Polynesians and endogamy, it can still be done.  It would just mean that every match, especially when it comes to geographic location should be scrutinized in order to determine a really close match or not.

I was there on November 1, 2015 when my mother and her sister Stella got to meet each other.

My mother Judy on the left, with Aunty Stella on the right.

This blog entry was edited after new evidence confirmed my mother’s paternity and after she was reunited with her sister.  In May 2016 my mother received her adoption files which listed her biological parents as Joseph Akana and Rose Kanae, listing my mother’s name as Joyce Awapuhiokala Akana aka Joyce Awapuhiokala Kanae.

 

Footnotes

1. MyOrigins v1 May 2014 – April 2017.  MyOrigins v2 separated the Oceanian from the East Asian and currently Oceanian falls under the broader Central/South Asia category.
2. Dr. Doug McDonald developed a the Biogeographical Analysis software and was contracted with Family Tree DNA to write the underlying code for their Population Finder ethnicity software.
3. Phylotree build 17 currently is B4a1a1c.
4. Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study shows that autosomal results for Native Hawaiians consist of 68% Southeast Asian and 32% Melanesian components.
5. Day, A. Grove. (1984) History Makers of Hawaii. Honolulu: Mutual Publishing of Honolulu. pp. 53.
6. Honolulu Star-Bulletin – Monday, June 20, 1960: Tales About Hawaii – Oliver Holmes Founds a First Family.
7. William Health Davis, Jr.

Botocudo ancient DNA sample uploaded on GEDmatch

Felix Immanuel, a software professional at Hewlett-Packard based out of Canberra, Australia who has a Bachelor of Engineering in Computer Science and a Master of Science in Forensic Computing and Cyber Security from University of South Australia, has been uploading a bunch of ancient DNA to GEDmatch.com.  The most recent uploads were samples taken from skulls of two extinct Botocudo (Brazil) men.  I blogged about it in December 2014.

https://hawaiiandna.wordpress.com/2014/12/12/polynesian-mtdna-in-botocudo-of-brazil/

At that time, they hypothesized a few ways how the Polynesian motif could have made it into the genome of these now extinct Botocudo tribe.  But recently in Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil (http://www.ncbi.nlm.nih.gov/pubmed/25455029), they talk about the hypotheses again and how they came to the conclusion that these samples are definitely Polynesian.

One thing that was consistently repeated, was how the skulls analyzed had no detectable Native American ancestry.  They say, “[w]e find that the genomic ancestry is Polynesian, with no detectible Native American component.”   That “all the genetic data point towards two individuals with Polynesian ancestry and no detectable Native American ancestry.” And they continued again saying that a “clustering analyses suggest that they have no detectable Native American ancestry and share the same components as the Polynesian population.”

The two male individual samples used, known as Bot15 and Bot17, presented a combination of mitochondrial DNA (mtDNA) variants common in present day Oceanian populations.

They pointed out a few hypotheses that was mentioned in the other paper, and that “the 1862-1864 AD Peru-Polynesia slave trade can be excluded, given that the ¹⁴C calibrated dates for the skulls predate the beginning of this trade.”  Because these skulls have been radiocarbon dated, the dates that they came up for Bot15 was 1479 – 1708 AD and 1730 – 1804 AD, and for Bot17 was 1496 – 1842 AD.  So the fact that the Peru-Polynesia slave trade occurred after the death of these people excluded the hypothesis that Polynesians were brought over during that slave trade.

Also, the Madagascar-Brazil slave trade hypothesis has been excluded due to the recent genomic data that demonstrated that the Malagasy ancestors admixed with African populations prior to the slave trade, and no such ancestry is detected in the Botocudo sample.  Madagascar was peopled by Southeast Asian and not Polynesian populations.

And finally, trade involving Euroamerican ships in the Pacific only began after 1760 AD.  By 1760 AD, both Bot15 and Bot17 were already deceased with a probability of 0.92 and 0.81, respectively, making this scenario unlikely.

These two samples analyzed had no Native American component detected.  Felix was able to extract SNPs from the raw data to come up with C-PH3092, and  C-Z31878, which are Melanesian in origin and the C haplogroup is common in eastern Polynesia.  The mtDNA haplogroups were B4a1a1a and B4a1a1.  B4a1a1a is pretty common throughout Polynesia especially in eastern Polynesia.  And most importantly these samples are a match only to eastern Polynesians.  There is no doubt that these particular samples are Polynesians.  Question is, how did they get there?  Did they manage to produce offspring with the local Botocudo groups like the Crenaques, Nac-Nuc, Minia-Jirunas, Gutcraques, Nac-Reques, Pancas, Manhangiréns or Incutcrás?  Or did they have offspring but they never survived?  Were these samples that were found the actual people who traveled directly from Polynesia?  Or did they arrive as a group and intermarried within their own group of Polynesians but later were found among the other Botocudo people?   And why travel thousands of miles over mountains and crossing rivers, possibly going through or bypassing the Pantanal that borders Bolivia and Brazil and continue to head towards the east?

We have other evidence like the kumara [sweet potato] or ‘uala [Hawaiian word for sweet potato] that originated from South America, and not to mention our many oral traditions of all the famous travelers who went abroad to Kahiki [foreign lands; Tahiti] and towards ka hikina [the east] where the rising of the sun is.  Travelers like Kuali’i, Hema, Kaha’i, Wahieloa, Laka and Luanu’u. Now DNA is showing the scientific community what we have known based on our oral traditions.

Now that Felix uploaded both of these samples up on GEDmatch.com, we see that both of the samples matches a few of us [both admixed and non-admixed] Hawaiians (including my mother), Maori, and a Cook Island Maori.  No surprise that eastern Polynesians are a match, given how they lack genetic diversity much more than the older western Polynesians. But it may also suggest, if not confirm, that it was specifically part of the expansion of eastern Polynesians.  But was there another expansion that late in the 1600s?  Another not so surprising thing about these matches is that there may be small segment matches, but when utilizing GEDmatch’s graph when comparing ONE TO ONE, we can still see small segments of full identical region for a few of these matches.

Bot17,Brazil,0.4ky¹
Kit # F999964
mtDNA – B4a1a1
Y DNA – C-Z31878 (C1b2 [2015])

Bot15,Brazil,0.4ky
Kit # F999963
MtDNA – B4a1a1a
Y DNA – C-PH3092 (C1b2 [2015])

You can check out Felix’s blog for other ancient DNA uploaded. http://www.fi.id.au/

Also the supplemental information can be accessed here.

Footnotes

1. Y haplogroup C Botocudo sample is carbon-dated to 1419-1477 AD – Ray Banks

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.

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.

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.

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.

Polynesia Category – AncestryDNA.com

Earlier this year I tested with Ancestry.com (or AncestryDNA.com) since I’ve been noticing non-Polynesians coming up with this new category.  This is way after the fact the research does not specify a Polynesia component, but rather a Melanesian and Asian or East Asian or Southeast Asian component.  I have seen other Asians, specifically Filipinos coming up with decent amount of this Polynesia category, as well as those of European descent coming up with small traces of Polynesia.

Under their Polynesia category, it mentions the sampling size was 18, and that one of the samples showed 11% Scandinavian.  A larger sampling size would yield better results especially in this case where one of the 18 samples had some European admixture.  This was enough to cause those with Scandinavian ancestry to come up with small traces of Polynesia, and in return cause people to wonder how they could have ever had such ancestry in their lineage to a point where some people create possible scenarios how they could have inherited this less than 0.1% Polynesia.

 

Their Polynesia category was one of those categories where they had the least amount of samples.

After receiving my results, as I suspected due to the fact that I am half Filipino, my percentage of the Polynesia category was pretty inflated.  It showed that I had 57% Polynesia versus 34% Asia East.  Knowing that my mother is 80% Hawaiian, and that my father was pure Filipino, I figured the amount of Asia that I showed 34% was missing 16% that was thrown into the Polynesia category.  That would in turn leave me with 41% Polynesia.  My mother is 20% European, and according to Ancestry I am 8% Europe, which seems to be about right.  The other DNA companies I tested at showed more than 10% Europe.  But adding the 41% plus the 8% comes out about right, 49%.

Recently I had a cousin on my father’s side of the family test, and she got her results.  She too is half Filipino, while her other half is completely Europe.  I expected her to show some Polynesia but I did not even guess how much that would be.  I was surprised to see 16% Polynesia for her, which is the same amount I had deducted from my own.  In fact, she shows 33% Asia while I show 34% Asia, and more specifically we both share 31% Asia East.  So they both are consistent.

Although my mother was given an AncestryDNA kit, she has yet to take it.  But I can easily guess that she will easily show 20% Europe and 80% Polynesia.  Any other person who is Polynesian but admixed with some other Asian it may include part of their Asian component into Polynesia.  Maybe the fact that we are Filipinos and they have ancestral ties is why some of it is classified as such.  I did have another paternal cousin tested, she is half Filipino and half Japanese so not sure what type of results that will yield with the Polynesia category.  Will it be the same and show her as 16% Polynesia?  Or will it give her more due to her Japanese ancestry, or is that different enough to not be classified under the Polynesia category?

To find out more about AncestryDNA’s ethnicity/ancestry categories, you can read through their Ethnicity Estimate White Paper.

Polynesian mtDNA in Botocudo of Brazil

Back in mid-September Roberta Estes had a blog entry Native American Mitochondrial Haplogroups.  It’s basically a list of mitochondrial haplogroups that exists among Native Americans.  But what caught my eye was the Polynesian motif – B4a1a1.  She wrote, “B4a1a1 – found in skeletal remains of the now extinct Botocudos (Aimores) Indians of Brazil, thought to perhaps have arrived from Polynesia via the slave trade.  This haplogroup is found in 20% of the mtDNA of Madagascar. Goncalves 2013” and “B4a1a1a – found in skeletal remains of the now extinct Botocudos (Aimores) Indians of Brazil, thought to perhaps have arrived from Polynesia via the slave trade.  This haplogroup is found in 20% of the mtDNA of Madagascar. Goncalves 2013.”   And although there is the actual research out there, it started with an article back in April 2013 titled, “DNA study links indigenous Brazilians to Polynesians.”  Although the article’s title itself only mentions a link, it can be confusing to the reader and can be misleading once you begin reading through it.

The article quoted Lisa Matisoo-Smith, a molecular anthropologist at the University of Otago in Dunedin, New Zealand where she said, “But to call that haplogroup Polynesian is a bit of a misnomer,”  since the haplogroup is known to be in populations as far west as in Madagascar.  The actual research can be found here, Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil. It basically says that “Here we report the identification of mitochondrial sequences belonging to haplogroups characteristic of Polynesians in DNA extracted from ancient skulls of the now extinct Botocudo Indians from Brazil.”   She does not seem to have been referring to the actual Polynesian motif but the fact that the research cited the mutations that is defined as the Polynesian motif.

The paper questions how did the presence of a Polynesian mtDNA show up in the gene pool of an extinct Brazilian Amerindian group who lived in the interior of Brazil?  There are specific mutations occurring on the mitochondrial which identifies it as the Polynesian motif,  and considering the evolutionary history of the Polynesian motif which is associated with the Austronesian expansion and the settling of Polynesia being much more recent than the peopling of the Americas.  Why hypothesizing how the introduction of the Polynesian motif could have entered into South America, the article says in part, “….considering an ancient Paleoamerican origin of the Botocudo haplotypes, we should expect new ‘private’ mutations to have appeared.  On the other hand, because we did not sequence the whole mtDNA, we cannot rule out the existence of such variations in the coding region.”

What is interesting to note is that is it not certain that these two skulls that they have analyzed were actual Polynesians or not. That is due to the fact that there was never a full sequencing test done on those two skulls that came up with the mutations that indicate the Polynesian motif.  Instead, only HVR1, HVR2 and typed specific mutations on the coding region were sequenced.  The findings mention specifically:  6719C, 15746G, 14022G and 12239T. These specific mutations on the coding region not only exists in my own mtDNA results (B4a1a1a3, now known as B4a1a1c) but so does a friend of mine who is identified as having the Malagasy motif. The paper already mentioned how these two skulls could have come back with such a haplogroup is possibly through the slave trade, originally from Madagascar.  And there were trips originating from Madagascar that eventually took these slaves into Brazil.

So the real question is were these two skulls the result of that recent slave trade originating from Madagascar, or did somehow a very few handful of Polynesians made their way all the way to Brazil?  The Botocudos lived in the interior portion of the state of Minas Gerais, so very far from the Pacific Ocean.

Lisa Matisoo-Smith  said it best, that to call that haplogroup Polynesian is a bit of a misnomer, particularly because we know it also exists in the Philippines and the subgroup – B4a1a1b (Malagasy motif) is in Madagascar.  Until a full sequencing test is done, there still may be some debate as to whether or not Polynesians have gone that far into the interior of South America, or that these skulls were the descendants of Malagasy brought over during the slave trade.

Presentation on Polynesian DNA

I made a presentation to help other Polynesians understand DNA and what some of the research mentions about Polynesians, and what I’ve already covered in my blog about matches, endogamy, and the misleading close matches that we get.

Polynesian DNA Presentation

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.

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.

 

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.