Ethnicity Testing and Results

I have written repeatedly about ethnicity results as part of the autosomal test offerings of the major DNA testing companies, but I still receive lots of questions about which ethnicity test is best, which is the most accurate, etc.  Take a look at “Ethnicity Percentages – Second Generation Report Card” for a detailed analysis and comparison.

First, let’s clarify which testing companies we are talking about.  They are:

Let’s make this answer unmistakable.

  1. Some of the companies are somewhat better than others relative to ethnicity – but not a lot.
  2. These tests are reasonably reliable when it comes to a continent level test – meaning African, European, Asian and sometimes, Native American.
  3. These tests are great at detecting ancestry over 25% – but if you know who your grandparents are – you already have that information.
  4. The usefulness of these tests for accurately providing ethnicity information diminishes as the percentage of that minority admixture declines.  Said another way – as your percentage of a particular ethnicity decreases, so does the testing companies’ ability to find it.
  5. Intra-continental results, meaning within Europe, for example, are speculative, at best.  Do not expect them to align with your known genealogy.  They likely won’t – and if they do at one vendor – they won’t at others.  Which one is “right”?  Who knows – maybe all of them when you consider population movement, migration and assimilation.
  6. As the vendors add to and improve their data bases, reference populations and analysis tools, your results change. I discussed how vendors determine your ethnicity percentages in the article, “Determining Ethnicity Percentages.”
  7. Sometimes unexpected results, especially continent level results, are a factor of ancient population mixing and migrations, not recent admixture – and it’s impossible to tell the difference. For example, the Celts, from the Germanic area of Europe also settled in the British Isles. Attila the Hun and his army, from Asia, invaded and settled in what is today, Germany, as well as other parts of Eastern Europe.
  8. Ethnicity tests are unreliable in consistently detecting minority admixture. Minority in this context means a small amount, generally less than 5%.  It does not refer to any specific ethnicity. Having said that, there are very few reference data base entries for Native American populations.  Most are from from Canada and South America.

In the context of ethnicity, what does unreliable mean?

Unreliable means that the results are not consistent and often not reproducible across platforms, especially in terms of minority admixture.  For example, a German/Hungarian family member shows Native American admixture at low percentages, around 3%, at some, but not all, vendors.  His European family history does not reflect Native heritage and in fact, precludes it.  However, his results likely reflect Native American from a common underlying ancestral population, the Yamnaya, between the Asian people who settled Hungary and parts of Germany and also contributed to the Native American population.

Unreliable can also mean that different vendors, measuring different parts of your DNA, can assign results to different regions.  For example, if you carry Celtic ancestry, would you be surprised to see Germanic results and think they are “wrong?”  Speaking of Celts, they didn’t just stay put in one region within Europe either.  And who were the Celts and where did they ‘come from’ before they were Celts.  All of this current and ancient admixture is carried in your DNA.  Teasing it out and the meaning it carries is the challenge.

Unreliable may also mean that the tests often do not reflect what is “known” in terms of family history.  I put the word “known” in quotes here, because oral history does not constitute “known” and it’s certainly not proof.  For the most part, documented genealogy does constitute “known” but you can never “know” about an undocumented adoption, also referred to as a “nonparental event” or NPE.  Yes, that’s when one or both parents are not who you think they are based on traditional information.  With the advent of DNA testing, NPEs can, in some instances, be discovered.

So, the end result is that you receive very interesting information about your genetic history that often does not correlate with what you expected – and you are left scratching your head.

However, in some cases, if you’re looking for something specific – like a small amount of Native American or African ancestry, you, indeed, can confirm it through your DNA – and can confirm your family history.  One thing is for sure, if you don’t test, you will never know.

Minority Admixture

Let’s take a look at how ethnicity estimates work relative to minority admixture.

In terms of minority admixture, I’m referring to admixture that is several generations back in your tree.  It’s often revealed in oral history, but unproven, and people turn to genetic genealogy to prove those stories.

In my case, I have several documented Native American lines and a few that are not documented.  All of these results are too far back in time, the 1600s and 1700s, to realistically be “found” in autosomal admixture tests consistently.  I also have a small amount of African admixture.  I know which line this comes from, but I don’t know which ancestor, exactly.  I have worked through these small percentages systematically and documented the process in the series titled, “The Autosomal Me.”  This is not an easy or quick process – and if quick and easy is the type of answer you’re seeking – then working further, beyond what the testing companies give you, with small amounts of admixture, is probably not for you.

Let’s look at what you can expect in terms of inheritance admixture.  You receive 50% of your DNA from each parent, and so forth, until eventually you receive very little DNA (or none) from your ancestors from many generations back in your tree.

Ethnicity DNA table

Let’s put this in perspective.  The first US census was taken in 1790, so your ancestors born in 1770 should be included in the 1790 census, probably as a child, and in following censuses as an adult.  You carry less than 1% of this ancestor’s DNA.

The first detailed census listing all family members was taken in 1850, so most of your ancestors that contributed more than 1% of your DNA would be found on that or subsequent detailed census forms.

These are often not the “mysterious” ancestors that we seek.  These ancestors, whose DNA we receive in amounts over 1%, are the ones we can more easily track through traditional means.

The reason the column of DNA percentages is labeled “approximate” is because, other than your parents, you don’t receive exactly half of your ancestor’s DNA.  DNA is not divided exactly in half and passed on to subsequence generations, except for what you receive from your parents.  Therefore, you can have more or less of any one ancestor’s individual DNA that would be predicted by the chart, above.  Eventually, as you continue to move further out in your tree, you may carry none of a specific ancestor’s DNA or it is in such small pieces that it is not detected by autosomal DNA testing.

The Vendors

At least two of the three major vendors have made changes of some sort this year in their calculations or underlying data bases.  Generally, they don’t tell us, and we discover the change by noticing a difference when we look at our results.

Historically, Ancestry has been the worst, with widely diverging estimates, especially within continents.  However, their current version is picking up both my Native and African.  However, with their history of inconsistency and wildly inaccurate results, it’s hard to have much confidence, even when the current results seem more reasonable and in line with other vendors.  I’ve adopted a reserved “wait and see” position with Ancestry relative to ethnicity.

Family Tree DNA’s Family Finder product is in the middle with consistent results, but they don’t report less than 1% admixture which is often where those distant ancestors’ minority ethnicity would be found, if at all.  However, Family Tree DNA does provide Y and mitochondrial mapping comparisons, and ethnicity comparisons to your matches that are not provided by other vendors.

Ethnicity DNA matches

In this view, you can see the matching ethnicity percentages for those whom you match autosomally.

23andMe is currently best in terms of minority ethnicity detection, in part, because they report amounts less than 1%, have a speculative view, which is preferred by most genetic genealogists and because they paint your ethnicity on your chromosomes, shown below.  You can see that both chromosome 1 and 2 show Native segments.

Ethnicity 23andMe chromosome

So, looking at minority admixture only – let’s take a look at today’s vendor results as compared to the same vendors in May 2014.

Ethnicity 2014-2015 compare

The Rest of the Story

Keep in mind, we’re only discussing ethnicity here – and there is a lot more to autosomal DNA testing than ethnicity – for example – matching to cousins, tools, such as a chromosome browser (or lack thereof), trees, ease of use and ability to contact your matches.  Please see “Autosomal DNA 2015 – Which Test is the Best?”  Unless ethnicity is absolutely the ONLY reason you are DNA testing, then you need to consider the rest of the story.

And speaking of the rest of the story, National Geographic has been pretty much omitted from this discussion because they have just announced a new upgrade, “Geno 2.0: Next Generation,” to their offering, which promises to be a better biogeographical tool.  I hope so – as National Geographic is in a unique position to evaluate populations with their focus on sample collection from what is left of unique and sometimes isolated populations.  We don’t have much information on the new product yet, and of course, no results because the new test won’t be released until in September, 2015.  So the jury is out on this one.  Stay tuned.

GedMatch – Not A Vendor, But a Great Toolbox

Finally, most people who are interested in ethnicity test at one (or all) of the companies, utilize the rest of the tools offered by that company, then download their results to www.gedmatch.com, a donation based site, and make use of the numerous contributed admixture tools there.

Ethnicity GedMatch

GedMatch offers lots of options and several tools that provide a wide range of focus.  For example, some tools are specifically written for European, African, Asian or even comparison against ancient DNA results.

Ethnicity ancient admixture

Conclusion

So what is the net-net of this discussion?

  1. There is a lot more to autosomal DNA testing than just ethnicity – so take everything into consideration.
  2. Ethnicity determination is still an infant and emerging field – with all vendors making relatively regular updates and changes. You cannot take minority results to the bank without additional and confirming research, often outside of genetic genealogy. However, mitochondrial or Y DNA testing, available only through Family Tree DNA, can positively confirm Native or minority ancestry in the lines available for testing. You can create a DNA Pedigree Chart to help identify or eliminate Native lines.
  3. If the ancestors you seek are more than a few generations removed, you may not carry enough of their ethnic DNA to be identified.
  4. Your “100% Cherokee” ancestor was likely already admixed – and so their descendants may carry even less Native DNA than anticipated.
  5. You cannot prove a negative using autosomal DNA (but you can with both Y and mitochondrial DNA). In other words, a negative autosomal ethnicity result alone, meaning no Native heritage, does NOT mean your ancestors were not Native. It MIGHT mean they weren’t Native. It also might mean that they were either very admixed or the Native ancestry is too far back in your tree to be found with today’s technology. Again, mitochondrial and Y DNA testing provide confirmed ancestry identification for the lines they represent. Y is the male paternal (surname) line and mitochondrial is the matrilineal line of both males and females – the mother’s, mother’s, mother’s line, on up the tree until you run out of mothers.
  6. It is very unlikely that you will be able to find your tribe, although it is occasionally possible. If a company says they can do this, take that claim with a very big grain of salt. Your internal neon warning sign should be flashing about now.
  7. If you’re considering purchasing an ethnicity test from a company other than the four I mentioned – well, just don’t.  Many use very obsolete technology and oversell what they can reliably provide.  They don’t have any better reference populations available to them than the major companies and Nat Geo, and let’s just say there are ways to “suggest” people are Native when they aren’t. Here are two examples of accidental ways people think they are Native or related – so just imagine what kind of damage could be done by a company that was intentionally providing “marginal” or misleading information to people who don’t have the experience to know that because they “match” someone who has a Native ancestor doesn’t mean they share that same Native ancestor – or any connection to that tribe. So, stay with the known companies if you’re going to engage in ethnicity testing. We may not like everything about the products offered by these companies, but we know and understand them.

My Recommendation

By all means, test.

Test with all three companies, 23andMe, Family Tree DNA and Ancestry – then download your results from either Family Tree DNA or Ancestry (who test more markers than 23andMe) to GedMatch and utilize their ethnicity tools.  When I’m looking for minority admixture, I tend to look for consistent trends – not just at results from any one vendor or source.

If you have already tested at Ancestry, or you tested at 23andMe on the V3 chip, prior to December 2013, you can download your raw data file to Family Tree DNA and pay just $39.  Family Tree DNA will process your raw data within a couple days and you will then see your myOrigins ethnicity results as interpreted by their software.  Of course, that’s in addition to having access to Family Tree DNA‘s other autosomal features, functions and tools.  The transfer price of $39 is significantly less expensive than retesting.

Just understand that what you receive from these companies in terms of ethnicity is reflective of both contemporary and ancient admixture – from all of your ancestral lines.  This field is in its infancy – your results will change from time to time as we learn – and the only part of ethnicity that is cast in concrete is probably your majority ancestry which you can likely discern by looking in the mirror.  The rest – well – it’s a mystery and an adventure.  Welcome aboard to the miraculous mysterious journey of you, as viewed through the DNA of your ancestors!

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

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Anzick (12,707-12,556), Ancient One, 52 Ancestors #42

anzick burial location

His name is Anzick, named for the family land, above, where his remains were found, and he is 12,500 years old, or more precisely, born between 12,707 and 12,556 years before the present.  Unfortunately, my genealogy software is not prepared for a birth year with that many digits.  That’s because, until just recently, we had no way to know that we were related to anyone of that age….but now….everything has changed ….thanks to DNA.

Actually, Anzick himself is not my direct ancestor.  We know that definitively, because Anzick was a child when he died, in present day Montana.

anzick on us map

Anzick was loved and cherished, because he was smeared with red ochre before he was buried in a cave, where he would be found more than 12,000 years later, in 1968, just beneath a layer of approximately 100 Clovis stone tools, shown below.  I’m sure his parents then, just as parents today, stood and cried as the laid their son to rest….never suspecting just how important their son would be some 12,500 years later.

anzick clovis tools

From 1968 until 2013, the Anzick family looked after Anzick’s bones, and in 2013, Anzick’s DNA was analyzed.

DNA analysis of Anzick provided us with his mitochondrial haplogroup,  D4h3a, a known Native American grouping, and his Y haplogroup was Q-L54, another known Native American haplogroup.  Haplogroup Q-L54 itself is estimated to be about 16,900 years old, so this finding is certainly within the expected range.  I’m not related to Anzick through Y or mitochondrial DNA.

Utilizing the admixture tools at GedMatch, we can see that Anzick shows most closely with Native American and Arctic with a bit of east Siberian.  This all makes sense.

Anzick MDLP K23b

Full genome sequencing was performed on Anzick, and from that data, it was discovered that Anzick was related to Native Americans, closely related to Mexican, Central and South Americans, and not closely related to Europeans or Africans.  This was an important discovery, because it in essence disproves the Solutrean hypothesis that Clovis predecessors emigrated from Southwest Europe during the last glacial maximum, about 20,000 years ago.

anzick matches

The distribution of these matches was a bit surprising, in that I would have expected the closest matches to be from North America, in particular, near to where Anzick was found, but his closest matches are south of the US border.  Although, in all fairness, few people in Native tribes in the US have DNA tested and many are admixed.

This match distribution tells us a lot about population migration and distribution of the Native people after they left Asia, crossed Beringia on the land bridge, now submerged, into present day Alaska.

This map of Beriginia, from the 2008 paper by Tamm et all, shows the migration of Native people into (and back from) the new world.

beringia map

Anzick’s ancestors crossed Beringia during this time, and over the next several thousand years, found their way to Montana.  Some of Anzick’s relatives found their way to Mexico, Central and South America.  The two groups may have split when Anzick’s family group headed east instead of south, possibly following the edges of glaciers, while the south-moving group followed the coastline.

Recently, from Anzick’s full genome data, another citizen scientist extracted the DNA locations that the testing companies use for autosomal DNA results, created an Anzick file, and uploaded the file to the public autosomal matching site, GedMatch.  This allowed everyone to see if they matched Anzick.  We expected no, or few, matches, because after all, Anzick was more than 12,000 years old and all of his DNA would have washed out long ago due to the 50% replacement in every generation….right?  Wrong!!!

What a surprise to discover fairly large segments of DNA matching Anzick in living people, and we’ve spent the past couple of weeks analyzing and discussing just how this has happened and why.  In spite of some technical glitches in terms of just how much individual people carry of the same DNA Anzick carried, one thing is for sure, the GedMatch matches confirm, in spades, the findings of the scientists who wrote the recent paper that describes the Anzick burial and excavation, the subsequent DNA processing and results.

For people who carry known Native heritage, matches, especially relatively large matches to Anzick, confirm not only their Native heritage, but his too.

For people who suspect Native heritage, but can’t yet prove it, an Anzick match provides what amounts to a clue – and it may be a very important clue.

In my case, I have proven Native heritage through the Micmac who intermarried with the Acadians in the 1600s in Nova Scotia.  Given that Anzick’s people were clearly on a west to east movement, from Beringia to wherever they eventually wound up, one might wonder if the Micmac were descended from or otherwise related to Anzick’s people.  Clearly, based on the genetic affinity map, the answer is yes, but not as closely related to Anzick as Mexican, Central and South Americans.

After several attempts utilizing various files, thresholds and factors that produced varying levels of matching to Anzick, one thing is clear – there is a match on several chromosomes.  Someplace, sometime in the past, Anzick and I shared a common ancestor – and it was likely on this continent, or Beringia, since the current school of thought is that all Native people entered the New World through this avenue.  The school of thought is not united in an opinion about whether there was a single migration event, or multiple migrations to the new word.  Regardless, the people came from the same base population in far northeast Asia and intermingled after arriving here if they were in the same location with other immigrants.

In other words, there probably wasn’t much DNA to pass around.  In addition, it’s unlikely that the founding population was a large group – probably just a few people – so in very short order their DNA would be all the same, being passed around and around until they met a new population, which wouldn’t happen until the Europeans arrived on the east side of the continent in the 1400s.  The tribes least admixed today are found south of the US border, not in the US.  So it makes sense that today the least admixed people would match Anzick the most closely – because they carry the most common DNA, which is still the same DNA that was being passed around and around back then.

Many of us with Native ancestors do carry bits and pieces of the same DNA as Anzick.  Anzick can’t be our ancestor, but he is certainly our cousin, about 500 generations ago, using a 25 year generation, so roughly our 500th cousin.  I had to laugh at someone this week, an adoptee who said, “Great, I can’t find my parents but now I have a 12,500 year old cousin.”  Yep, you do!  The ironies of life, and of genealogy, never fail to amaze me.

Utilizing the most conservative matching routine possible, on a phased kit, meaning one that combines the DNA shared by my mother and myself, and only that DNA, we show the following segment matches with Anzick.

Chr Start Location End Location Centimorgans (cM) SNPs
2 218855489 220351363 2.4 253
4 1957991 3571907 2.5 209
17 53111755 56643678 3.4 293
19 46226843 48568731 2.2 250
21 35367409 36761280 3.7 215

Being less conservative produces many more matches, some of which are questionable as to whether they are simply convergence, so I haven’t utilized the less restrictive match thresholds.

Of those matches above, the one on chromosomes 17 matches to a known Micmac segment from my Acadian lines and the match on chromosome 2 also matches an Acadian line, but I share so many common ancestors with this person that I can’t tell which family line the DNA comes from.

There are also Anzick autosomal matches on my father’s side.  My Native ancestry on his side reaches back to colonial America, in either Virginia or North Carolina, or both, and is unproven as to the precise ancestor and/or tribe, so I can’t correlate the Anzick DNA with proven Native DNA on that side.  Neither can I associate it with a particular family, as most of the Anzick matches aren’t to areas on my chromosome that I’ve mapped positively to a specific ancestor.

Running a special utility at GedMatch that compared Anzick’s X chromosome to mine, I find that we share a startlingly large X segment.  Sometimes, the X chromosome is passed for generations intact.

Interestingly enough, the segment 100,479,869-103,154,989 matches a segment from my mother exactly, but the large 6cM segment does not match my mother, so I’ve inherited that piece of my X from my father’s line.

Chr Start Location End Location Centimorgans (cM) SNPs
X 100479869 103154989 1.4 114
X 109322285 113215103 6.0 123

This tells me immediately that this segment comes from one of the pink or blue lines on the fan chart below that my father inherited from his mother, Ollie Bolton, since men don’t inherit an X chromosome from their father.  Utilizing the X pedigree chart reduces the possible lines of inheritance quite a bit, and is very suggestive of some of those unknown wives.

olliex

It’s rather amazing, if you think about it, that anyone today matches Anzick, or that we can map any of our ancestral DNA that both we and Anzick carry to a specific ancestor.

Indeed, we do live in exciting times.

Honoring Anzick

On a rainy Saturday in June, 2014, on a sagebrush hillside in Montana, in Native parlance, our “grandfather,” Anzick was reburied, bringing his journey full circle.  Sarah Anzick, a molecular biologist, the daughter of the family that owns the land where the bones were found, and who did part of the genetic discovery work on Anzick, returns the box with his bones for reburial.

anzick bones

More than 50 people, including scientists, members of the Anzick family and representatives of six Native American tribes, gathered for the nearly two-hour reburial ceremony. Tribe members said prayers, sang songs, played drums and rang bells to honor the ancient child. The bones were placed in the grave and sprinkled with red ocher, just like when his parents buried him some 12,500 years before.

Participants at the reburial ceremony filled in the grave with handfuls, then shovelfuls of dirt and covered it with stones. A stick tied with feathers marks Anzick’s final resting place.

Sarah Anzick tells us that, “At that point, it stopped raining. The clouds opened up and the sun came out. It was an amazing day.”

I wish I could have been there.  I would have, had I known.  After all, he is part of me, and I of him.

anzick grave'

Welcome to the family, Anzick, and thank you, thank you oh so much, for your priceless, unparalleled gift!!!

tobacco

If you want to read about the Anzick matching journey of DNA discovery, here are the articles I’ve written in the past two weeks.  It has been quite a roller coaster ride, but I’m honored and privileged to be doing this research.  And it’s all thanks to an ancient child named Anzick.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Finding Native American Ethnic Results in Germanic People

I’m often asked about the significance of small percentages of autosomal DNA in results.  Specifically, the small percentages are often of Native American or results that would suggest Native admixture.  One of the first questions I always ask is whether or not the individual has Germanic or eastern European admixture.

Why?

Take a look at this map of the Invasion of the Roman Empire.  See the Huns and their path?

Hun map

It’s no wonder we’re so admixed.

Here’s a map of the Hunnic empire at its peak under Attila between the years 420-469.

Hun emplire

But that wasn’t the end of the Asian invasions.  The Magyars, who settled in Hungary arrived from Asia as well, in the 800s and 900s, as shown on this map from LaSalle University.

magyar map

Since both the Hungarians and some Germanic people descend from Asian populations, as do Native Americans, albeit thousands of years apart, it’s not unrealistic to expect that, as populations, they share a genetic connection.

Therefore, when people who carry heritage from this region of the world show small amounts of Native or Asian origin, I’m not surprised.  However, for Americans, trying to sort out their Native ethnic heritage, this is most unhelpful.

Let’s take a look at the perfect example candidate.  This man is exactly half Hungarian and half German.  Let’s see what his DNA results say, relative to any Asian or Native heritage, utilizing the testing companies and the free admixture tools at www.gedmatch.com.

He has not tested at Ancestry, but at Family Tree DNA, his myOrigins report 96% European, 4% Middle Eastern.  At 23andMe in speculative view, he shows 99.7 European and .2 sub-saharan African.

Moving to the admixture tools at GedMatch, MDLP is not recommended for Asian or Native ancestry, so I have excluded that tool.

Eurogenes K13 is the most recently updated admixture tool, so let’s take a look at that one first.

Eurogenes K13

 JK Eurogenes K13 v2

Eurogenes K13 showed 7% West Asian, which makes perfect sense considering his heritage, but it might be counted as “Native” in other circumstances, although I would certainly be very skeptical about counting it as such.

However, East Asian, Siberian and Amerindian would all be amalgamated into the Native American category, for a combined percentage of 1.31.

jk eurogenes k13 chart

However, selecting the “admixture proportions by chromosome” view shows something a bit different.  The cumulative percentages, by chromosome equate to 10.10%.  Some researchers mistakenly add this amount and use that as their percentage of Native ancestry.  This is not the case, because those are the portions of 100% of each individual chromosome, and the total would need to be divided by 22 to obtain the average value across all chromosomes.  The total is irrelevant, and the average may not reflect how the developer determines the amount of admixture because chromosomes are not the same size nor carry the same number of SNPs.  Questions relative to the functional underpinnings of each tool should be addressed to the developers.

Dodecad

I understand that there is a newer version of Dodecad, but that it has not been submitted to GedMatch for inclusion, per a discussion with GedMatch.  I can’t tell which of the Dodecad versions on GedMatch is the most current, so I ran the results utilizing both v3 and 12b.

jk dodecad v3

jk dodecad v3 chart

I hope v3 is not the most current, because it does not include any Native American category or pseudocategory – although there is a smattering of Northeast Asian at .27% and Southwest Asian at 1%.

Dodecad 12b below

jk dodecad 12b

The 12b version does show .52% Siberian and 2.6% Southwest Asian, although I’m not at all sure the Southwest Asian should be included.

HarappaWorld

jk harappaworld

jk harappaworld chart

Harappaworld shows .09 Siberian, .27% American (Native American), .23% Beringian and 1.8% Southwest Asian, although I would not include Southwest Asian in the Native calculation.

In Summary

Neither Family Tree DNA nor 23andMe find Native ancestry in our German/Hungarian tester, but all 3 of the admixture tools at Gedmatch find either small amounts of Native or Asian ancestry that could certainly be interpreted as Native, such as Siberian or Beringian.

Does this mean this German/Hungarian man has Native American ancestry?  Of course not, but it does probably mean that the Native population and his ancestral populations did share some genes from the same gene pool thousands of years ago.

While you might think this is improbable, or impossible, consider for a minute that every person outside of Africa today carries some percentage of Neanderthal DNA, and all Europeans also carry Denisovan DNA.  Our DNA does indeed have staying power over the millennia, especially once an entire population or group of people is involved.  We’ve recently seen this same type of scenarios in the full genome sequencing of a 24,000 year old Siberian male skeleton.

Our German/Hungarian man carries 2.4% Neanderthal DNA according to 23andMe and 2.7% according to the Genographic Project, which also reports that he carries 3.9% Denisovan.  The European average is about 2% for Neanderthal.

The net-net of this is that minority admixture is not always what it seems to be, especially when utilizing autosomal DNA to detect small amounts of Native American admixture.  The big picture needs to be taken into consideration.  Caution is advised.

When searching for Native admixture, when possible, both Y DNA and mitochondrial DNA give specific answers for specific pedigree lines relative to ancestry.  Of course, to utilize Y or mtDNA, the tester must descend from the Native ancestor either directly paternally to test the male Y chromosome, or directly matrilineally to test the mitochondrial line.  You can read about this type of testing, and how it works, in my article, Proving Native American Ancestry Using DNA.  You can also read about other ways to prove Native ancestry using autosomal DNA, including how to unravel which pedigree line the Native ancestry descends from, utilizing admixture tools, in the article, “The Autosomal Me.”

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Ethnicity Percentages – Second Generation Report Card

Recently, Family Tree DNA introduced their new ethnicity tool, myOrigins as part of their autosomal Family Finder product.  This means that all of the major players in this arena using chip based technology (except for the Genographic project) have now updated their tools.  Both 23andMe and Ancestry introduced updated versions of their tools in the fall of 2013.  In essence, this is the second generation of these biogeographical or ethnicity products.  So lets take a look and see how the vendors are doing.

In a recent article, I discussed the process for determining ethnicity percentages using biogeographical ancestry, or BGA, tools.  The process is pretty much the same, regardless of which vendor’s results you are looking at.  The variant is, of course, the underlying population data base, it’s quality and quantity, and the way the vendors choose to construct and name their regions.

I’ve been comparing my own known and proven genealogy pedigree breakdown to the vendors results for some time now.  Let’s see how the new versions stack up to a known pedigree.

The paper, “Revealing American Indian and Minority Heritage using Y-line, Mitochondrial, Autosomal and X Chromosomal Testing Data Combined with Pedigree Analysis” was published in the Fall 2010 issue of JoGG, Vol. 6 issue 1.

The pedigree analysis portion of this document begins about page 8.  My ancestral breakdown is as follows:

Geography Pedigree Percent
Germany 23.8041
British Isles 22.6104
Holland 14.5511
European by DNA 6.8362
France 6.6113
Switzerland 0.7813
Native American 0.2933
Turkish 0.0031

This leaves about 25% unknown.

Let’s look at each vendor’s results one by one.

23andMe

23andme v2

My results using the speculative comparison mode at 23andMe are shown in a chart, below.

23andMe Category 23andMe Percentage
British and Irish 39.2
French/German 15.6
Scandinavian 7.9
Nonspecific North European 27.9
Italian 0.5
Nonspecific South European 1.6
Eastern European 1.8
Nonspecific European 4.9
Native American 0.3
Nonspecific East Asian/Native American 0.1
Middle East/North Africa 0.1

At 23andMe, if you have questions about what exact population makes up each category, just click on the arrow beside the category when you hover over it.

For example, I wasn’t sure exactly what comprises Eastern European, so I clicked.

23andme eastern europe

The first thing I see is sample size and where the samples come from, public data bases or the 23andMe data base.  Their samples, across all categories, are most prevalently from their own data base.  A rough add shows about 14,000 samples in total.

Clicking on “show details” provides me with the following information about the specific locations of included populations.

23andme pop

Using this information, and reorganizing my results a bit, the chart below shows the comparison between my pedigree chart and the 23andMe results.  In cases where the vendor’s categories spanned several of mine, I have added mine together to match the vendor category.  A perfect example is shown in row 1, below, where I added France, Holland, Germany and Switzerland together to equal the 23andMe French and German category.  Checking their reference populations shows that all 4 of these countries are included in their French and German group.

Geography Pedigree Percent 23andMe %
Germany, Holland, Switzerland & France 45.7451 15.6
France 6.6113 (above) Combined
Germany 23.8014 (above) Combined
Holland 14.5511 (above) Combined
Switzerland 0.7813 (above) Combined
British Isles 22.6104 39.2
Native American 0.2933 0.4 (Native/East Asian)
Turkish 0.0031 0.1 (Middle East/North Africa)
Scandinavian 7.9
Italian 0.5
South European 1.6
East European 1.8
European by DNA 6.8362 4.9 (nonspecific European)
Unknown 25 27.9 (North European)

I can also change to the Chromosome view to see the results mapped onto my chromosomes.

23andme chromosome view

The 23andMe Reference Population

According to the 23andMe customer care pages, “Ancestry Composition uses 31 reference populations, based on public reference datasets as well as a significant number of 23andMe members with known ancestry. The public reference datasets we’ve drawn from include the Human Genome Diversity ProjectHapMap, and the 1000 Genomes project. For these datasets as well as the data from 23andMe, we perform filtering to ensure accuracy.

Populations are selected for Ancestry Composition by studying the cluster plots of the reference individuals, choosing candidate populations that appear to cluster together, and then evaluating whether we can distinguish the groups in practice. The population labels refer to genetically similar groups, rather than nationalities.”

Additional detailed information about Ancestry Composition is available here.

Ancestry.com

ancestry v2

Ancestry is a bit more difficult to categorize, because their map regions are vastly overlapping.  For example, the west Europe category is shown above, and the Scandinavian is shown below.

ancestry scandinavia

Both categories cover the Netherlands, Germany and part of the UK.

My Ancestry percentages are:

Ancestry Category Ancestry Percentage
North Africa 1
America <1
East Asia <1
West Europe 79
Scandinavia 10
Great Britain 4
Ireland 2
Italy/Greece 2

Below, my pedigree percentages as compared to Ancestry’s categories, with category adjustments.

Geography Pedigree Percent Ancestry %
West European 52.584 (combined from below) 79
Germany 23.8041 Combined
Holland 14.5511 Combined
European by DNA 6.8362 Combined
France 6.6113 Combined
Switzerland 0.7813 Combined
British Isles 22.6104 6
Native American 0.2933 ~1 incl East Asian
Turkish 0.0031 1 (North Africa)
Unknown 25
Italy/Greece 2
Scandinavian 10

Ancestry’s European populations and regions are so broadly overlapping that almost any interpretation is possible.  For example, the Netherlands could be included in several categories – and based up on the history of the country, that’s probably legitimate.

At Ancestry, clicking on a region, then scrolling down will provide additional information about that region of the world, both their population and history.

The Ancestry Reference Population

Just below your ethnicity map is a section titled “Get the Most Out of Your Ethnicity Estimate.”  It’s worth clicking, reading and watching the video.  Ancestry states that they utilized about 3000 reference samples, pared from 4245 samples taken from people whose ethnicity seems to be entirely from that specific location in the world.

ancestry populations

You can read more in their white paper about ethnicity prediction.

Family Tree DNA’s myOrigins

I wrote about the release of my Origins recently, so I won’t repeat the information about reference populations and such found in that article.

myorigins v2

Family Tree DNA shows matches by region.  Clicking on the major regions, European and Middle Eastern, shown above, display the clusters within regions.  In addition, your Family Finder matches that match your ethnicity are shown in highest match order in the bottom left corner of your match page.

Clicking on a particular cluster, such as Trans-Ural Peneplain, highlights that cluster on the map and then shows a description in the lower left hand corner of the page.

myorigins trans-ural

Family Tree DNA shows my ethnicity results as follows.

Family Tree DNA Category Family Tree DNA Percentage
European Coastal Plain 68
European Northlands 12
Trans-Ural Peneplain 11
European Coastal Islands 7
Anatolia and Caucus 3

Below, my pedigree results reorganized a bit and compared to Family Tree DNA’s categories.

Geography Pedigree Percent Family Tree DNA %
European Coastal Plain 45.7478 68
Germany 23.8041 Combined above
Holland 14.5511 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
British Isles 22.6104 7 (Coastal Islands)
Turkish 0.0031 3 (Anatolia and Caucus)
European by DNA 6.8362
Native American 0.2933
Unknown 25
Trans-Ural Peneplain 11
European Northlands 12

Third Party Admixture Tools

www.GedMatch.com is kind enough to include 4 different admixture utilities, contributed by different developers, in their toolbox.  Remember, GedMatch is a free, meaning a contribution site – so if you utilize and enjoy their tools – please contribute.

On their main page, after signing in and transferring your raw data files from either 23andMe, Family Tree DNA or Ancestry, you will see your list of options.  Among them is “admixture.”  Click there.

gedmatch admixture

Of the 4 tools shown, MDLP is not recommended for populations outside of Europe, such as Asian, African or Native American, so I’ve skipped that one entirely.

gedmatch admix utilities

I selected Admixture Proportions for the part of this exercise that includes the pie chart.

The next option is Eurogenes K13 Admixture Proportions.  My results are shown below.

Eurogenes K13

Eurogenes K13

Of course, there is no guide in terms of label definition, so we’re guessing a bit.

Geography Pedigree Percent Eurogenes K13%
North Atlantic 75.19 44.16
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 2.74 combined East Asian, Siberian, Amerindian and South Asian
Turkish 0.0031 1.78 Red Sea
Unknown 25
Baltic 24.36
West Med 14.78
West Asian 6.85
Oceanian 0.86

Dodecad K12b

Next is Dodecad K12b

According to John at GedMatch, there is a more current version of Dodecad, but the developer has opted not to contribute the current or future versions.

Dodecad K12b

By the way, in case you’re wondering, Gedrosia is an area along the Indian Ocean – I had to look it up!

Geography Pedigree Percent Dodecad K12b
North European 75.19 43.50
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 3.02 Siberian, South Asia, SW Asia, East Asia
Turkish 0.0031 10.93 Caucus
Gedrosia 7.75
Northwest African 1.22
Atlantic Med 33.56
Unknown 25

Third is Harappaworld.

Harappaworld

harappaworld

Baloch is an area in the Iranian plateau.

Geography Pedigree Percent Harappaworld %
Northeast Euro 75.19 46.58
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 2.81 SE Asia, Siberia, NE Asian, American, Beringian
Turkish 0.0031 10.27
Unknown 25
S Indian 0.21
Baloch 9.05
Papuan 0.38
Mediterranean 28.71

The wide variety found in these results makes me curious about how my European results would be categorized using the MDLP tool, understanding that it will not pick up Native, Asian or African.

MDLP K12

mdlp k12

The Celto-Germanic category is very close to my mainland European total – but of course, many Germanic people settled in the British Isles.

Second Generation Report Card

Many of these tools picked up my Native American heritage, along with the African.  Yes, these are very small amounts, but I do have several proven lines.  By proven, I mean both by paper trail (Acadian church and other records) and genetics, meaning Yline and mtDNA.  There is no arguing with that combination.  I also have other Native lines that are less well proven.  So I’m very glad to see the improvements in that area.

Recent developments in historical research and my mitochondrial DNA matches show that my most distant maternal ancestral line in Germany have some type of a Scandinavian connection.  How did this happen, and when?  I just don’t know yet – but looking at the map below, which are my mtDNA full sequence matches, the pattern is clear.

mitomatches

Could the gene flow have potentially gone the other direction – from Germany to Scandinavia?  Yes, it’s possible.  But my relatively consistent Scandinavian ethnicity at around 10% seems unlikely if that were the case.

Actually, there is a second possibility for additional Scandinavian heritage and that’s my heavy Frisian heritage.  In fact, most of my Dutch ancestors in Frisia were either on or very near the coast on the northernmost part of Holland and many were merchants.

I also have additional autosomal matches with people from Scandinavia – not huge matches – but matches just the same – all unexplained.  The most notable of which, and the first I might add, is with my friend, Marja.

It’s extremely difficult to determine how distant the ancestry is that these tests are picking up.  It could be anyplace from a generation ago to hundreds of generations ago.  It all depends on how the DNA was passed, how isolated the population was, who tested today and which data bases are being utilized for comparison purposes along with their size and accuracy.  In most cases, even though the vendors are being quite transparent, we still don’t know exactly who the population is that we match, or how representative it is of the entire population of that region.  In some cases, when contributed data is being used, like testers at 23andMe, we don’t know if they understood or answered the questions about their ancestry correctly – and 23andMe is basing ethnicity results on their cumulative answers.  In other words, we can’t see beneath the blanket – and even if we could – I don’t know that we’d understand how to interpret the components.

So Where Am I With This?

I knew already, through confirmed paper sources that most of my ancestry is in the European heartland – Germany, Holland, France as well as in the British Isles.  Most of the companies and tools confirm this one way or another.  That’s not a surprise.  My 35 years of genealogical research has given me an extremely strong pedigree baseline that is invaluable for comparing vendor ethnicity results.

The Scandinavian results were somewhat of a surprise – especially at the level in which they are found.  If this is accurate, and I tend to believe it is present at some level, then it must be a combined effect of many ancestors, because I have no missing or unknown ancestors in the first 5 generations and only 11 of 64 missing or without a surname in generation 6.  Those missing ancestors in generation 6 only contribute about 1.5% of my DNA each, assuming they contribute an average of 50% of their DNA to offspring in each subsequent generation.

Clearly, to reach 10%, nearly all of my missing ancestors, in the US and Germany, England and the Netherlands would have to be 100% Scandinavian – or, alternately, I have quite a bit scattered around in many ancestors, which is a more likely scenario.  Still, I’m having a difficult time with that 10% number in any scenario, but I will accept that there is some Scandinavian heritage one way or another.  Finding it, however, genealogically is quite another matter.

However, I’m at a total loss as to the genesis of the South European and Mediterranean.  This must be quite ancient.  There are only two known possible ancestors from these regions and they are many generations back in time – and both are only inferred with clearly enough room to be disproven.  One is a possible Jewish family who went to France from Spain in 1492 and the other is possibly a Roman soldier whose descendants are found within a few miles of a Roman fort site today in Lancashire.  Neither of these ancestors could have contributed enough DNA to influence the outcome to the levels shown, so the South European/Mediterranean is either incorrect, or very deep ancestry.

The Eastern European makes more sense, given my amount of German heritage.  The Germans are well known to be admixed with the Magyars and Huns, so while I can’t track it or prove it, it also doesn’t surprise me one bit given the history of the people and regions where my ancestors are found.

What’s the Net-Net of This?

This is interesting, very interesting.  There are tips and clues buried here, especially when all of the various tools, including autosomal matching, Y and mtDNA, are utilized together for a larger picture.  Alone, none of these tools are as powerful as they are combined.

I look forward to the day when the reference populations are in the tens of thousands, not hundreds.  All of the tools will be far more accurate as the data base is built, refined and utilized.

Until then, I’ll continue to follow each release and watch for more tips and clues – and will compare the various tools.  For example, I’m very pleased to see Family Tree DNA’s new ethnicity matching tool incorporated into myOrigins.

I’ve taken the basic approach that my proven pedigree chart is the most accurate, by far, followed by the general consensus of the combined results of all of the vendors.  It’s particularly relevant when vendors who don’t use the same reference populations arrive at the same or similar results.  For example, 23andMe uses primarily their own clients and Nat Geo of course, although I did not include them above because they haven’t released a new tool recently, uses their own population sample results.

National Geographic’s Geno2

Nat Geo took a bit of a different approach and it’s more difficult to compare to the others.  They showed my ethnicity as 43% North European, 36% Mediterranean and 18% Southwest Asian.

nat geo results

While this initially looks very skewed, they then compared me to my two closest populations, genetically, which were the British and the Germans, which is absolutely correct, according to my pedigree chart.  Both of these populations are within a few percent of my exact same ethnicity profile, shown below.

Nat geo british 2

The description makes a lot of sense too.  “The dominant 49% European component likely reflects the earliest settlers in Europe, hunter-gatherers who arrived there more than 35,000 years ago.  The 44% Mediterranean and the 17% Southwest Asian percentages arrived later, with the spread of agriculture from the Fertile Crescent in the middle East, over the past 10,000 years.  As these early farmers moved into Europe, they spread their genetic patterns as well.”

nat geo german

So while individually, and compared to my pedigree chart, these results appear questionable, especially the Mediterranean and Southwest Asian portions, in the context of the populations I know I descend from and most resemble, the results make perfect sense when compared to my closest matching populations.  Those populations themselves include a significant amount of both Mediterranean and Southwest Asian.  Looking at this, I feel a lot better about the accuracy of my results.  Sometimes, perspective makes a world of difference.

It’s A Wrap

Just because we can’t exactly map the ethnicity results to our pedigree charts today doesn’t mean the results are entirely incorrect.  It doesn’t mean they are entirely correct, either.  The results may, in some cases, be showing where population groups descend from, not where our specific ancestors are found more recently.  The more ancestors we have from a particular region, the more that region’s profile will show up in our own personal results.  This explains why Mediterranean shows up, for example, from long ago but our one Native ancestor from 7 or 8 generations ago doesn’t.  In my case, it would be because I have many British/German/Dutch lines that combine to show the ancient Mediterranean ancestry of these groups – where I have many fewer Native ancestors.

Vendors may be picking up deep ancestry that we can’t possible know about today – population migration.  It’s not like our ancestors left a guidebook of their travels for us – at least – not outside of our DNA – and we, as a community, are still learning exactly how to read that!  We are, after all, participants on the pioneering, leading edge of science.

Having said that, I’ll personally feel a lot better about these kinds of results when the underlying technology, data bases and different vendors’ tools mature to the point where there the differences between their results are minor.

For today, these are extremely interesting tools, just don’t try to overanalyze the results, especially if you’re looking for minority admixture.  And if you don’t like your results, try a different vendor or tool, you’ll get an entirely new set to ponder!

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2013 Family Tree DNA Conference Day 2

ISOGG Meeting

The International Society of Genetic Genealogy always meets at 8 AM on Sunday morning.  I personally think that 8AM meeting should be illegal, but then I generally work till 2 or 3 AM (it’s 1:51 AM now), so 8 is the middle of my night.

Katherine Borges, the Director speaks about current and future activities, and Alice Fairhurst spoke about the many updates to the Y tree that have happened and those coming as well.  It has been a huge challenge to her group to keep things even remotely current and they deserve a huge round of virtual applause from all of us for the Y tree and their efforts.

Bennett opened the second day after the ISOGG meeting.

“The fact that you are here is a testament to citizen science” and that we are pushing or sometimes pulling academia along to where we are.

Bennett told the story of the beginning of Family Tree DNA.  “Fourteen years ago when the hair that I have wasn’t grey,” he began, “I was unemployed and tried to reorganize my wife’s kitchen and she sent me away to do genealogy.”  Smart woman, and thankfully for us, he went.  But he had a roadblock.  He felt there was a possibility that he could use the Y chromosome to solve the roadblock.  Bennett called the author of one of the two papers published at that time, Michael Hammer.  He called Michael Hammer on Sunday morning at his home, but Michael was running out the door to the airport.  He declined Bennett’s request, told him that’s not what universities do, and that he didn’t know of anyplace a Y test could be commercially be done.  Bennett, having run out of persuasive arguments, started mumbling about “us little people providing money for universities.”  Michael said to him, “Someone should start a company to do that because I get phone calls from crazy genealogists like you all the time.”  Let’s just say Bennett was no longer unemployed and the rest, as they say, is history.  With that, Bennett introduced one of our favorite speakers, Dr. Michael Hammer from the Hammer Lab at the University of Arizona.

Bennett day 2 intro

Session 1 – Michael Hammer – Origins of R-M269 Diversity in Europe

Michael has been at all of the conferences.  He says he doesn’t think we’re crazy.  I personally think we’ve confirmed it for him, several times over, so he KNOWS we’re crazy.  But it obviously has rubbed off on him, because today, he had a real shocker for us.

I want to preface this by saying that I was frantically taking notes and photos, and I may have missed something.  He will have his slides posted and they will be available through a link on the GAP page at FTDNA by the end of the week, according to Elliott.

Michael started by saying that he is really exciting opportunity to begin breaking family groups up with SNPs which are coming faster than we can type them.

Michael rolled out the Y tree for R and the new tree looks like a vellum scroll.

Hammer scroll

Today, he is going to focus on the basic branches of the Y tree because the history of R is held there.

The first anatomically modern humans migrated from Africa about 45,000 years ago.

After last glacial maximum 17,000 years ago, there was a significant expansion into Europe.

Neolithic farmers arrived from the near east beginning 10,000 years ago.

Farmers had an advantage over hunter gatherers in terms of population density.  People moved into Northwestern Europe about 5,000 years ago.

What did the various expansions contribute to the population today?

Previous studies indicate that haplogroup R has a Paleolithic origin, but 2 recent studies agree that this haplogroup has a more recent origin in Europe – the Neolithic but disagree about the timing of the expansion.

The first study, Joblin’s study in 2010, argued that geographic diversity is explained by single Near East source via Anaotolia.

It conclude that the Y of Mesololithic hunger-gatherers were nearly replaced by those of incoming farmers.

In the most recent study by Busby in 2012 is the largest study and concludes that there is no diversity in the mapping of R SNP markers so they could not date lineage and expansion.  They did find that most basic structure of R tree did come from the near east.  They looked at P311 as marker for expansion into Europe, wherever it was.  Here is a summary page of Neolithic Europe that includes these studies.

Hammer says that in his opinion, he thought that if P311 is so frequent and widespread in Europe it must have been there a long time.  However, it appears that he and most everyone else, was wrong.

The hypothesis to be tested is if P311 originated prior to the Neolithic wave, it would predict higher diversity it the near east, closer to the origins of agriculture.  If P311 originated after the expansion, would be able to see it migrate across Europe and it would have had to replace an existing population.

Because we now have sequences the DNA of about 40 ancient DNA specimens, Michael turned to the ancient DNA literature.  There were 4 primary locations with skeletal remains.  There were caves in France, Spain, Germany and then there’s Otzi, found in the Alps.

hammer ancient y

All of these remains are between 6000-7000 years old, so prior to the agricultural expansion into Europe.

In France, the study of 22 remains produced, 20 that were G2a and 2 that were I2a.

In Spain, 5 G2a and 1 E1b.

In Germany, 1I G2a and 2 F*.

Otzi is haplogroup G2a2b.

There was absolutely 0, no, haplogroup R of any flavor.

In modern samples, of 172 samples, 94 are R1b.

To evaluate this, he is dropping back to the backbone of haplogroup R.

hammer backbone

This evidence supports a recent spread of haplogroup R lineages in western Europe about 5K years ago.  This also supports evidence that P311 moved into Europe after the Neolithic agricultural transition and nearly displaced the previously existing western European Neolithic Y, which appears to be G2a.

This same pattern does not extrapolate to mitochondrial DNA where there is continuity.

What conferred advantage to these post Neolithic men?  What was that advantage?

Dr. Hammer then grouped the major subgroups of haplogroup R-P3111 and found the following clusters.

  • U106 is clustered in Germany
  • L21 clustered in the British Isles
  • U152 has an Alps epicenter

hammer post neolithic epicenters

This suggests multiple centers of re-expansion for subgroups of haplogroup R, a stepwise process leading to different pockets of subhaplogroup density.

Archaeological studies produce patterns similar to the hap epicenters.

What kind of model is going on for this expansion?

Ancestral origin of haplogroup R is in the near east, with U106, P312 and L21 which are then found in 3 European locations.

This research also suggests thatG2a is the Neolithic version of R1b – it was the most commonly found haplogroup before the R invasion.

To make things even more interesting, the base tree that includes R has also been shifted, dramatically.

Haplogroup K has been significantly revised and is the parent of haplogroups P, R and Q.

It has been broken into 4 major branches from several individual lineages – widely shifted clades.

hammer hap k

Haps R and Q are the only groups that are not restricted to Oceana and Southeast Asia.

Rapid splitting of lineages in Southeast Asia to P, R and Q, the last two of which then appear in western Europe.

hammer r and q in europe

R then, populated Europe in the last 4000 years.

How did these Asians get to Europe and why?

Asian R1b overtook Neolithic G2a about 4000 years ago in Europe which means that R1b, after migrating from Africa, went to Asia as haplogroup K and then divided into P, Q and R before R and Q returned westward and entered Europe.  If you are shaking your head right about now and saying “huh?”…so were we.

Hammer hap r dist

Here is Dr. Hammer’s revised map of haplogroup dispersion.

hammer haplogroup dispersion map

Moving away from the base tree and looking at more recent SNPs, Dr. Hammer started talking about some of the findings from the advanced SNP testing done through the Nat Geo project and some of what it looks like and what it is telling us.

For example, the R1bs of the British Isles.

There are many clades under L 21.  For example, there is something going on in Scotland with one particular SNP (CTS11722?) as it comprises one third of the population in Scotland, but very rare in Ireland, England and Wales.

New Geno 2.0 SNP data is being utilized to learn more about these downstream SNPs and what they had to say about the populations in certain geographies.

For example, there are 32 new SNPs under M222 which will help at a genealogical level.

These SNPs must have arisen in the past couple thousand years.

Michael wants to work with people who have significant numbers of individuals who can’t be broken out with STRs any further and would like to test the group to break down further with SNPs.  The Big Y is one option but so is Nat Geo and traditional SNP testing, depending on the circumstance.

G2a is currently 4-5% of the population in Europe today and R is more than 40%.

Therefore, P312 split in western Eurasia and very rapidly came to dominate Europe

Session 2 – Dr. Marja Pirttivaara – Bridging Social Media and DNA

Dr. Pirttivaara has her PhD in Physics and is passionate about genetic genealogy, history and maps.  She is an administrator for DNA projects related to Finland and haplogroup N1c1, found in Finland, of course.

marja

Finland has the population of Minnesota and is the size of New Mexico.

There are 3750 Finland project members and of them 614 are haplogroup N1c1.

Combining the N1c1 and the Uralic map, we find a correlation between the distribution of the two.

Turku, the old capital, was full or foreigners, in Medieval times which is today reflected in the far reaching DNA matches to Finnish people.

Some of the interest in Finland’s DNA comes from migration which occurred to the United States.

Facebook and other social media has changed the rules of communication and allows the people from wide geographies to collaborate.  The administrator’s role has also changed on social media as opposed to just a FTDNA project admin.  Now, the administrator becomes a negotiator and a moderator as well as the DNA “expert.”

Marja has done an excellent job of motivating her project members.  They are very active within the project but also on Facebook, comparing notes, posting historical information and more.

Session 3 – Jason Wang – Engineering Roadmap and IT Update

Jason is the Chief Technology Officer at Family Tree DNA and recently joined with the Arpeggi merger and has a MS in Computer Engineering.

Regarding the Gene by Gene/FTDNA partnership, “The sum of the parts is greater than the whole.”  He notes that they have added people since last year in addition to the Arpeggi acquisition.

Jason introduced Elliott Greenspan, who, to most of us, needed no introduction at all.

Elliott began manually scoring mitochondrial DNA tests at age 15.  He joined FTDNA in 2006 officially.

Year in review and What’s Coming

4 times the data processed in the past year.

Uploads run 10 times faster.  With 23andMe and Ancestry autosomal uploads, processing will start in about 5 minutes, and matches will start then.

FTDNA reinvented Family Finder with the goal of making the user experience easier and more modern.   They added photos, profiles and the new comparison bars along with an advanced section and added push to chromosome browser.

Focus on users uploading the family tree.  Tools don’t matter if the data isn’t there.  In order to utilize the genealogy aspect, the genealogy info needs to be there.   Will be enhancing the GEDCOM viewer.  New GEDCOMs replace old GEDCOMs so as you update yours, upload it again.

They are now adding a SNP request form so that you can request a SNP not currently available.  This is not to be confused with ordering an existing SNP.

They currently utilize build 14 for mitochondrial DNA.  They are skipping build 15 entirely and moving forward with 16.

They added steps to the full sequence matches so that you can see your step-wise mutations and decide whether and if you are related in a genealogical timeframe.

New Y tree will be released shortly as a result of the Geno 2.0 testing.  Some of the SNPs have mutated as much as 7 times, and what does that mean in terms of the tree and in terms of genealogical usefulness.  This tree has taken much longer to produce than they expected due to these types of issues which had to be revised individually.

New 2014 tree has 6200 SNPS and 1000 branches.

  • Commitment to take genetic genealogy to the next level
  • Y draft tree
  • Constant updates to official tree
  • Commitment to accurate science

If a single sample comes back as positive for a SNP, they will put it on the tree and will constantly update this.

If 3 or 4 people have the same SNP that are not related it will go directly to the tree.  This is the reason for the new SNP request form.

Part of the reason that the tree has taken so long is that not every SNP is public and it has been a huge problem.

When they find a new SNP, where does it go on the tree?  When one SNP is found or a SNP fails, they have run over 6000 individual SNPs on Nat Geo samples to vet to verify the accuracy of the placement.  For example, if a new SNP is found in a particular location, or one is found not to be equivalent that was believe to be so previously, they will then test other samples to see where the SNP actually belongs.

X Matching

Matching differential is huge in early testing.  One child may inherit as little as 20% of the X and another 90%.  Some first cousins carry none.

X matching will be an advanced feature and will have their own chromosome browser.

End of the year – January 1.  Happy New Year!!!

Population Finder

It’s definitely in need of an upgrade and have assigned one person full time to this product.

There are a few contention points that can be explained through standard history.

It’s going to get a new look as well and will be easily upgradeable in the future.

They cannot utilize the National Geographic data because it’s private to Nat Geo.

Bennett – “Committed to an engineering team of any size it takes to get it done.  New things will be rolling out in first and second quarter of next year.”  Then Bennett kind of sighed and said “I can’t believe I just said that.”

Session 4 – Dr. Connie Bormans – Laboratory Update

The Gene by Gene lab, which of course processes all of the FTDNA samples is now a regulated lab which allows them to offer certain regulated medical tests.

  • CLIA
  • CAP
  • AABB
  • NYSDOH

Between these various accreditations, they are inspected and accredited once yearly.

Working to decrease turn-around time.

SNP request pipeline is an online form and is in place to request a new SNP be added to their testing menu.

Raised the bar for all of their tests even though genetic genealogy isn’t medical testing because it’s good for customers and increases quality and throughput.

New customer support software and new procedures to triage customer requests.

Implement new scoring software that can score twice as many tests in half the time.  This decreases turn-around time to the customer as well.

New projects include improved method of mtDNA analysis, new lab techniques and equipment and there are also new products in development.

Ancient DNA (meaning DNA from deceased people) is being considered as an offering if there is enough demand.

Session 5 – Maurice Gleeson – Back to Our Past, Ireland

Maurice Gleeson coordinated a world class genealogy event in Dublin, Ireland Oct. 18-20, 2013.  Family Tree DNA and ISOGG volunteers attended to educate attendees about genetic genealogy and DNA. It was a great success and the DNA kits from the conference were checked in last week and are in process now.  Hopefully this will help people with Irish ancestry.

12% of the Americans have Irish ancestry, but a show of hands here was nearly 100% – so maybe Irish descendants carry the crazy genealogist gene!

They developed a website titled Genetic Genealogy Ireland 2013.  Their target audience was twofold, genetic genealogy in general and also the Irish people.  They posted things periodically to keep people interested.  They also created a Facebook page.  They announced free (sponsored) DNA tests and the traffic increased a great deal.  Today ISOGG has a free DNA wiki page too.  They also had a prize draw sponsored by the Ireland DNA and mtdna projects. Maurice said that the sessions and the booth proximity were quite symbiotic because when y ou came out of the DNA session, the booth was right there.

2000-5000 people passed by the booth

500 people in the booth

Sold 99 kits – 119 tests

45 took Y 37 marker tests

56 FF, 20 male, 36 female

18 mito tests

They passed out a lot of educational material the first two days.  It appeared that the attendees were thinking about things and they came back the last day which is when half of the kits were sold, literally up until they threatened to turn the lights out on them.

They have uploaded all of the lectures to a YouTube channel and they have had over 2000 views.  Of all of the presentation, which looked to be a list of maybe 10-15, the autosomal DNA lecture has received 25% of the total hits for all of the videos.

This is a wonderful resource, so be sure to watch these videos and publicize them in your projects.

Session 6 – Brad Larkin – Introducing Surname DNA Journal

Brad Larkin is the FTDNA video link to the “how to appropriately” scrape for a DNA test.  That’s his minute or two of fame!  I knew he looked familiar.

Brad began a peer reviewed genetic genealogy journal in order to help people get their project stories published.  It’s free, open access, web based and the author retains the copyright..  www.surnamedna.com

Conceived in 2012, the first article was published in January 2013.  Three papers published to date.

Encourage administrators to write and publish their research.  This helps the publication withstand the test of time.

Most other journals are not free, except for JOGG which is now inactive.  Author fees typically are $1320 (PLOS) to $5000 (Nature) and some also have subscription or reader fees.

Peer review is important.  It is a critical review, a keen eye and an encouraging tone.  This insures that the information is evidence based, correct and replicable.

Session 7 – mtdna Roundtable – Roberta Estes and Marie Rundquist

This roundtable was a much smaller group than yesterday’s Y DNA and SNP session, but much more productive for the attendees since we could give individual attention to each person.  We discussed how to effectively use mtdna results and what they really mean.  And you just never know what you’re going to discover.  Marie was using one of her ancestors whose mtDNA was not the haplogroup expected and when she mentioned the name, I realized that Marie and I share yet another ancestral line.  WooHoo!!

Q&A

FTDNA kits can now be tested for the Nat Geo test without having to submit a new sample.

After the new Y tree is defined, FTDNA will offer another version of the Deep Clade test.

Illumina chip, most of the time, does not cover STRs because it measures DNA in very small fragments.  As they work with the Big Y chip, if the STRs are there, then they will be reported.

80% of FTDNA orders are from the US.

Microalleles from the Houston lab are being added to results as produced, but they do not have the data from the older tests at the University of Arizona.

Holiday sale starts now, runs through December 31 and includes a restaurant.com $100 gift card for anyone who purchases any test or combination of tests that includes Family Finder.

That’s it folks.  We took a few more photos with our friends and left looking forward to next year’s conference.  Below, left to right in rear, Marja Pirttivaara, Marie Rundquist and David Pike.  Front row, left to right, me and Bennett Greenspan.

Goodbyes

See y’all next year!!!

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Determining Ethnicity Percentages

Recently, as a comment to one of my blog postings, someone asked how the testing companies can reach so far back in time and tell you about your ancestors.  Great question.

The tests that reliably reach the furthest back, of course, are the direct line Y-Line and mitochondrial DNA tests, but the commenter was really asking about the ethnicity predictions.  Those tests are known as BGA, or biogeographical ancestry tests, but most people just think of them or refer to them as the ethnicity tests.

Currently, Family Tree DNA, 23andMe and Ancestry.com all provide this function as a part of their autosomal product along with the Genographic 2.0 test.  In addition, third party tools available at www.gedmatch.com don’t provide testing, but allow you to expand what you can learn with their admixture tools if you upload your raw data files to their site.  I wrote about how to use these ethnicity tools in “The Autosomal Me” series.  I’ve also written about how accurate ethnicity predictions from testing companies are, or aren’t, here, here and here.

But today, I’d like to just briefly review the 3 steps in ethnicity prediction, and how those steps are accomplished.  It’s simple, really, in concept, but like everything else, the devil is in the details.devil

There are three fundamental steps.

  • Creation of the underlying population data base.
  • Individual DNA extraction.
  • Comparison to the underlying population data base.

Step 1:  Creation of the underlying population data base.

Don’t we wish this was as simple as it sounds.  It isn’t.  In fact, this step is the underpinnings of the accuracy of the ethnicity predictions.  The old GIGO (garbage in, garbage out) concept applies here.

How do researchers today obtain samples of what ancestral populations looked like, genetically?  Of course, the evident answer is through burials, but burials are not only few and far between, the DNA often does not amplify, or isn’t obtainable at all, and when it is, we really don’t have any way to know if we have a representative sample of the indigenous population (at that point in time) or a group of travelers passing through.  So, by and large, with few exceptions, ancient DNA isn’t a readily available option.

The second way to obtain this type of information is to sample current populations, preferably ones in isolated regions, not prone to in-movement, like small villages in mountain valleys, for example, that have been stable “forever.”  This is the approach the National Geographic Society takes and a good part of what the Genograpic Geno 2.0 project funding does.  Indigenous populations are in most cases our most reliable link to the past.  These resources, combined with what we know about population movement and history are very telling.  In fact, National Geographic included over 75,000 AIMs (Ancestrally Informative Markers) on the Geno 2.0 chip when it was released.

The third way to obtain this type of information is by inference.  Both Ancestry.com and 23andMe do some of this.  Ancestry released its V2 ethnicity updates this week, and as a part of that update, they included a white paper available to DNA participants.  In that paper, Ancestry discusses their process for utilizing contributed pedigree charts and states that, aside from immigrant locations, such as the United States and Canada, a common location for 4 grandparents is sufficient information to include that individuals DNA as “native” to that location.  Ancestry used 3000 samples in their new ethnicity predictions to cover 26 geographic locations.  That’s only 115 samples, on average, per location to represent all of that population.  That’s pretty slim pickins.  Their most highly represented area is Eastern Europe with 432 samples and the least represented is Mali with 16.  The regions they cover are shown below.

ancestry v2 8

Survey Monkey, a widely utilized web survey company, in their FAQ about Survey Size For Accuracy provides guidelines for obtaining a representative sample.  Take a look.  No matter which calculations you use relative to acceptable Margin of Error and Confidence Level, Ancestry’s sample size is extremely light.

23andMe states in their FAQ that their ethnicity prediction, called Ancestry Composition covers 22 reference populations and that they utilize public reference datasets in addition to their clients’ with known ancestry.

23andMe asks geographic ancestry questions of their customers in the “where are you from” survey, then incorporates the results of individuals with all 4 grandparents from a particular country.  One of the ways they utilize this data is to show you where on your chromosomes you match people whose 4 grandparents are from the same country.  In their tutorial, they do caution that just because a grandparent was born in a particular location doesn’t necessarily mean that they were originally from that location.  This is particularly true in the past few generations, since the industrial revolution.  However, it may still be a useful tool, when taken with the requisite grain of salt.

23andme 4 grandparents

The third way of creating the underlying population data base is to utilize academically published information or information otherwise available.  For example, the Human Genome Diversity Project (HGDP) information which represents 1050 individuals from 52 world populations is available for scrutiny.  Ancestry, in their paper, states that they utilized the HGDP data in addition to their own customer database as well as the Sorenson data, which they recently purchased.

Academically published articles are available as well.  Family Tree DNA utilizes 52 different populations in their reference data base.  They utilize published academic papers and the specific list is provided in their FAQ.

As you can see, there are different approaches and tools.  Depending on which of these tools are utilized, the underlying data base may look dramatically different, and the information held in the underlying data base will assuredly affect the results.

Step 2:  Your Individual DNA Extraction

This is actually the easy part – where you send your swab or spit off to the lab and have it processed.  All three of the main players utilize chip technology today.  For example, 23andMe focuses on and therefore utilizes medical SNPs, where Family Tree DNA actively avoids anything that reports medical information, and does not utilize those SNPs.

In Ancestry’s white paper, they provide an excellent graphic of how, at the molecular level, your DNA begins to provide information about the geographic location of your ancestors.  At each DNA location, or address, you have two alleles, one from each parent.  These alleles can have one of 4 values, or nucleotides, at each location, represented by the abbreviations T, A, C and G, short for Thymine, Adenine, Cytosine and Guanine.  Based on their values, and how frequently those values are found in comparison populations, we begin to fine correlations in geography, which takes us to the next step.

ancestry allele snps

Step 3:  Comparison to Underlying Population Data Base

Now that we have the two individual components in our recipe for ethnicity, a population reference set and your DNA results, we need to combine them.

After DNA extraction, your individual results are compared to the underlying data base.  Of course, the accuracy will depend on the quality, diversity, coverage and quantity of the underlying data base, and it will also depend on how many markers are being utilized or compared.

For example, Family Tree DNA utilizes about 295,000 out of 710,000 autosomal SNPs tested for ethnicity prediction.  Ancestry’s V1 product utilized about 30,000, but that has increased now to about 300,000 in the 2.0 version.

When comparing your alleles to the underlying data set one by one, patterns emerge, and it’s the patterns that are important.  To begin with, T, A, C and G are not absent entirely in any population, so looking at the results, it then becomes a statistics game.  This means that, as Ancestry’s graphic, above, shows, it becomes a matter of relativity (pardon the pun), and a matter of percentages.

For example, if the A allele above is shown is high frequencies in Eastern Europe, but in lower frequencies elsewhere, that’s good data, but may not by itself be relevant.  However if an entire segment of locations, like a street of DNA addresses, are found in high percentages in Eastern Europe, then that begins to be a pattern.  If you have several streets in the city of You that are from Eastern Europe, then that suggests strongly that some of your ancestors were from that region.

To show this in more detailed format, I’m shifting to the third party tool, GedMatch and one of their admixture tools.  I utilized this when writing the series, “The Autosomal Me” and in Part 2, “The Ancestor’s Speak,” I showed this example segment of DNA.

On the graph below, which is my chromosome painting of one a small part of one of my chromosomes on the top, and my mother’s showing the exact same segment on the bottom, the various types of ethnicity are colored, or painted.

The grid shows location, or address, 120 on the chromosome and each tick mark is another number, so 121, 122, etc.   It’s numbered so we can keep track of where we are on the chromosome.

You can readily see that both of us have a primary ethnicity of North European, shown by the teal.  This means that for this entire segment, the results are that our alleles are found in the highest frequencies in that region.

Gedmatch me mom

However, notice the South Asian, East Asian, Caucus, and North Amerindian. The important part to notice here, other than I didn’t inherit much of that segment at 123-127 from her, except for a small part of East Asian, is that these minority ethnicities tend to nest together.  Of course, this makes sense if you think about it.  Native Americans would carry Asian DNA, because that is where their ancestors lived.  By the same token, so would Germans and Polish people, given the history of invasion by the Mongols. Well, now, that’s kind of a monkey-wrench isn’t it???

This illustrates why the results may sometimes be confusing as well as how difficult it is to “identify” an ethnicity.  Furthermore, small segments such as this are often “not reported” by the testing companies because they fall under the “noise” threshold of between about 5 and 7cM, depending on the company, unless there are a lot of them and together they add up to be substantial.

In Summary

In an ideal world, we would have one resource that combines all of these tools.  Of course, these companies are “for profit,” except for National Geographic, and they are not going to be sharing their resources anytime soon.

I think it’s clear that the underlying data bases need to be expanded substantially.  The reliability of utilizing contributed pedigrees as representative of a population indigenous to an area is also questionable, especially pedigrees that only reach back two generations.

All of these tools are still in their infancy.  Both Ancestry and Family Tree DNA’s ethnicity tools are labeled as Beta.  There is useful information to be gleaned, but don’t take the results too seriously.  Look at them more as establishing a pattern.  If you want to take a deeper dive by utilizing your raw data and downloading it to GedMatch, you can certainly do so. The Autosomal Me series shows you how.

Just keep in mind that with ethnicity predictions, with all of the vendors, as is particularly evident when comparing results from multiple vendors, “your mileage may vary.”  Now you know why!

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Ethnicity Results – True or Not?

I can’t even begin to tell you how many questions I receive that go something like this:

“I received my ethnicity results from XYZ.  I’m confused.  The results don’t seem to align with my research and I don’t know what to make of them?”

In the above question, the vendors who are currently offering these types of results among their autosomal tests are Family Tree DNA, 23andMe and Ancestry along with National Geographic who is a nonprofit.  Of those four, by far, Ancestry is the worst at results matching reality and who I receive the most complaints and comments about.  I wrote an article about Ancestry’s results and Judy Russell recently wrote an article about their new updated results as did Debbie Kennett.  My Ancestry results have not been updated yet, so I can’t comment personally.

Let’s take a look at the results from the four players and my own analysis.

Some years back, I did a pedigree analysis of my genealogy in an attempt to make sense of autosomal results from other companies.

The paper, “Revealing American Indian and Minority Heritage using Y-line, Mitochondrial, Autosomal and X Chromosomal Testing Data Combined with Pedigree Analysis” was published in the Fall 2010 issue of JoGG, Vol. 6 issue 1.

The pedigree analysis portion of this document begins about page 8.  My ancestral breakdown is as follows:

Geography Percent
Germany 23.8041
British Isles 22.6104
Holland 14.5511
European by DNA 6.8362
France 6.6113
Switzerland .7813
Native American .2933
Turkish .0031

This leaves about 25% unknown.  However, this looks nothing like the 80% British Isles and the 12% Scandinavian at Ancestry.

Here are my current ethnicity results from the three major testing companies plus Genographic.

Ancestry

80% British Isles

12% Scandinavian

8% Uncertain

Family Tree DNA

75% Western Europe

25% Europe – Romanian, Russian, Tuscan, Finnish

23andMe (Standard Estimate)

99.2% European

0.5% East Asian and Native American

0.3% Unassigned

Genographic 2.0

Northern European – 43%

Mediterranean – 36%

Southwest Asian – 18%

Why Don’t The Results Match?

Why don’t the results match either my work or each other?

1. The first answer I always think of when asked this question is that perhaps some of the genealogy is incorrect.  That is certainly a possibility via either poor genealogy research or undocumented adoptions.  However, as time has marched forward, I’ve proven that I’m descended from most of these lines through either Y-line, mitochondrial DNA or autosomal matches.  This confirms my genealogy research.  For example, Acadians were originally French and I definitely descend from Acadian lines.

2. The second answer is time.  The vendors may well be using different measures of time, meaning more recent versus deep ancestry.  Geno 2.0 looks back the furthest.  Their information says that “your percentages reflect both recent influences and ancient genetic patterns in your DNA due to migrations as groups from different regions mixed over thousands of years.  Your ancestors also mixed with ancient, now extinct hominid cousins like Neanderthals in Europe and the Middle East of the Denisovans in Asia.”

It’s difficult to determine which of the matching populations are more recent and which are less recent.  By way of example, many Germans and others in eastern Europe are descendants of Genghis Khan’s Mongols who invaded portions of Europe in the 13th century.  So, do we recognize and count their DNA when found as “German,” “Polish,” “Russian,” or “Asian?”  The map below shows the invasions of Genghis Khan.  Based on this, Germans who descend from Genghis’s Mongols could match Koreans on those segments of DNA. Both of those people would probably find that confusing.

genghis khan map

3. The third answer is the reference populations.  Here is what National Geographic has to say: “Modern day indigenous populations around the world carry particular blends of these regions. We compared your DNA results to the reference populations we currently have in our database and estimated which of these were most similar to you in terms of the genetic markers you carry. This doesn’t necessarily mean that you belong to these groups or are directly from these regions, but that these groups were a similar genetic match and can be used as a guide to help determine why you have a certain result. Remember, this is a mixture of both recent (past six generations) and ancient patterns established over thousands of years, so you may see surprising regional percentages.”

Each of the vendors has compiled their own list of reference populations from published material, and in the case of National Geographic, as yet unpublished material as well.

If you read the fine print, some of these results that at first glance appear to not match actually do, or could.  For example, Southwest Asia (Geno 2.0) could be Russia (Family Tree DNA) or at least pointing to the same genetic base.

This video map of Europe through the ages from 1000AD to present will show the ever changing country boundaries and will quickly explain why coming up with labels for ethnicity is so difficult.  I mean, what exactly does “France” or “Germany” mean, and when?

4. The fourth answer is focus.  Each of these organizations comes to us as a consumer with a particular focus.  Of them, one and only one must make their way on their own merits alone.  That one is Family Tree DNA.  Unlike the Genographic Project, Family Tree DNA doesn’t have a large nonprofit behind them.  Unlike 23andMe, they are not subsidized by the medical community and venture capital.  And unlike Ancestry.com, Family Tree DNA is not interested in selling you a subscription.  In fact, the DNA market could dry up and go away for any of those three, meaning 23andMe, National Geographic and Ancestry, and their business would simply continue with their other products.  To them, DNA testing is only a blip on a spreadsheet.  Not true for Family Tree DNA.  Their business IS genetic genealogy and DNA testing.  So of all these vendors, they can least afford to have upset clients and are therefore the most likely to be the most vigilant about the accuracy of their testing, the quality of the tools and results provided to customers.

My Opinion

So what is my personal opinion on all of this?

I think these ethnicity results are very interesting.  I think in some way all of them are probably correct, excluding Ancestry.  I have absolutely no confidence in Ancestry’s results based on their track record and historylack of tools, lack of transparency and frustratingly poor quality.

I think that as more academic papers are published and we learn more about these reference populations and where their genes are found in various populations, all of these organizations will have an opportunity to “tighten up” their results.  If you’ll notice, both Ancestry and Family Tree DNA still include the words “beta.”  The vendors know that these results are not the end all and be all in the ethnicity world.

Am I upset with these vendors?  Aside from Ancestry who has to know they have a significant problem and has yet to admit to or fix it, no, I’m not.  Frustrated, as a consumer, yes, because like all genealogists, I want it NOW please and thank you!!!

Without these kinds of baby steps, we will never as a community crawl, walk, or run.  I dream of the day when we will be able to be tested, obtain our results, and along with that, maybe a list of ancestors we descend from and where their ancestors originated as well.  So, in essence, current genealogy (today Y-line and mtdna), older genealogy (autosomal lines) and population genetics (ethnicity of each line).

So what should we as consumers do today?  Personally, I think we should file this information away in the “that’s interesting” folder and use it when and where it benefits us.  I think we should look at it as a display of possibilities.  We should not over-interpret these results.

There is perhaps one area of exception, and that is when dealing with majority ethnic groups.  By this, I mean African, Asian, Native American and European.  For those groups, this type of ethnicity breakdown, the presence or absence of a particular group is more correct than incorrect, generally.  Very small amounts of any admixture are difficult to discern for any vendor.  For an example of that, look at my Native percentages and some of those are proven lines.  For the individual who wants more information, and more detail into the possibilities, I wrote about how to use the raw autosomal data outside of the vendors tools, at GedMatch, to sort out minority admixture in The Autosomal Me series.

Perhaps the Genographic Project page sums it up best with their statement that, “If you have a very mixed background, the pattern can get complicated quickly!”  Not only is that true, it can be complicated by any and probably all of the factors above.  When you think about it, it’s rather amazing that we can tell as much as we can.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Autosomal DNA, Ancient Ancestors, Ethnicity and the Dandelion

 dandelion 1

Understanding our own ancient DNA is a little different than contemporary DNA that we use for genealogy, but it’s a continuum between the two with a very long umbilical cord between them, then, and now.  And just when you think you’re about to understand autosomal DNA transmission and how it works, the subject of ancient DNA comes up.  This is particularly perplexing when all you wanted in the first place was a simple answer to the question, “who am I and who were my ancestors?”  Well, as you’re probably figured out by now, there is no simple answer.

Inheritance

In a nutshell – we know that every generation gets divided by 50% when we’re talking about autosomal DNA transmission.

So you inherit 50% of the DNA of each of your parents.  They inherited 50% of the DNA of each of their parents, so you inherit ABOUT 25% of the DNA of each of your grandparents.

Did you see that word, about?  It’s important, because while you do inherit exactly 50% of the DNA of each parent, you don’t inherit exactly 25% of the DNA of each grandparent.  You can inherit a little less or a little more from either grandparent as your parents 50% that you’re going to receive is in the mixer.

This is also true for the 12.5% of each of your great-grandparents, and the 6.25% of each of your great-great-grandparents, and so forth, on up the line.

The chart below shows the percentages that you share from each generation.

Relationship to You Approximate % Of Their DNA You Share
Parents Exactly 50%
Grandparents 25
Great-grandparents 12.5
Great-great-grandparents 6.25
Great-great-great-grandparents 3.125
Great-great-great-great-grandparents 1.5625

Ethnicity

So, here’s the question posed by people trying to understand their ethnicity.

If I have 3% Melanesian (or Middle Eastern, Indo-Tibetan or fill-in-the-blank ethnicity), doesn’t that mean that one of my great-great-great-grandparents was Melanesian?

There are really two answers to this question.  (I can hear you groaning!!!)

If the amount is 25% (for example) and not very small amounts, then the answer would be yes, that is very likely what this is telling you.  Or maybe it’s telling you that you have two different great-grandparents who have 12.5 each – but those relatives are fairly close in time due to the amount of DNA that came from that region.  See, that was easy.

However, the answer changes when we’re down in the very small percentages, below 5%, often in the 1 and 2% range.  This answer isn’t nearly as straightforward.

The Dandelion – Your Ancestor

The answer is the dandelion.

dandelion 2

The dandelion is one of your ancestors who lived in the Middle East, let’s say, 20,000 years ago, maybe 30,000 years ago.  In case you’re counting generations, that is 800 to 1200 generations ago.  The percentage of DNA you would carry from a single ancestor who lived 20,000 years ago, assuming you only descended from that ancestor 1 time, is infinitesimally small.  There are more zeroes following that decimal point than I have patience to type.  Let’s call that ancestor Xenia and let’s say she is a female.

However, you did inherit DNA from many of your ancestors who lived 20,000 years ago, thousands of them, because all of them, through their descendants, make up the DNA you carry today.  So infinitesimally small or not, you do carry some of the DNA of some of those ancestors.  It’s just broken into extremely small pieces today and their individual contributions to you may be extremely small.  You don’t carry any DNA from some of them, actually, probably most of them, due to the recombination event, dividing their DNA in half, happening 800 times, give or take.

Now, given that your ancestors’ DNA is divided in every generation by approximately half, and we know there are about 3 billion base pairs on all of your chromosomes combined, this means that by generation 32 or 33, on average, you carry 1 segment from this ancestor.  By generation 45, you carry, on average, .00017 segments of this ancestor’s DNA.  And for those math aficionados among us, this is the mathematical notation for how much of our ancestor’s DNA we carry after 800 generations: 4.4991E-232.

But, we also know that this dividing in half, on the average, doesn’t always work exactly that way in reality, because some of those ancestors from 20,000 years ago did in fact pass their DNA to you, despite the infinitesimal odds against that happening.  Some of their DNA was passed intact generation after generation, to you, and you carry it today.  The DNA contributed by any one ancestor from 800 generations ago is probably limited to one or two locations, or bases, but still, it’s there, and it’s the combined DNA of those ancient ancestors that make us who we are today.

The autosomal DNA of any specific ancestor from long ago is probably too small and fragmented to recognize as “theirs” and attribute to them.  Of course, the beauty of Y DNA and mitochondrial is that it is passed in tact for all of those generations.  But for autosomal DNA and genealogy, we need hundreds of thousands of DNA pieces in a row from a particular ancestor to be recognizable as “theirs.”  When we measure DNA for genealogy, what we are measuring is both centiMorgans, a measure of distance between chromosome positions (length) and the number of contiguous SNP (Single Nucleotide Polymorphism) base locations that match (quantity).  The values from these calculations tells us how closely we are related to people, because remember, DNA is divided in each generation so there is a mathematically predictable amount we will share with specific relatives.

Here is an example from a Family Finder comparison table showing both centiMorgans and matching SNPs with a second cousin.

family finder table

The matching threshold for genealogical significance is either 5 or 7 cM depending on which of the major companies you are using.  At Family Tree DNA, if you match above the threshold, then you can view down to 1cM, which is the case above.  Another match criteria is the number of SNPs, or locations, matching contiguously.  Anything below about 500-800 is considered to be a population match, not a genealogical match, unless you also have a significant number of genealogical matches at higher cMs and segments with this person.

OK, where is all of this going?

Dispersion

Think of your ancestor 20,000 years ago as the dandelion.  Now, blow.

dandelion 3

Xenia lived in the Middle East.  Where might her descendants land, over time, with every new generation?  In Europe?  In Asia?  In India?  In America via the Native Americans through Asia?  In North Africa?  Where?

So let’s say that groups of descendants settle across the globe.  Let’s say that her mitochondrial haplogroup is X.  Yes, haplogroup X is found both in Europe and in Asia and in the Native Americans, so this is actually a good example.  So Xenia carried mitochondrial haplogroup X and we know for sure via mitochondrial DNA testing that indeed, Xenia’s seeds were scattered to all of the winds.  The only place we haven’t found Xenia’s children is in Subsaharan Africa and the Australian archipelago, at least not yet.

Ok, so now that we know where her children and their children went, let’s go back to ancient DNA.

Predictive DNA

The way ethnicity is determined is by studying the frequency with which a specific allele or group of alleles is found in any particular population.  Two “pure” examples come to mind.

The first example is the Duffy Null allele that is only found in the Subsaharan African populations.  Currently this marker is found in about 68% of American blacks and in 88-100% of African blacks.  If you have the Duffy Null allele, you have African heritage.  Of course, you don’t know which line or which ancestor it came from, or how far back in time, but it assures you that you do in fact have African heritage.  It could have been from an ancestor long ago.  It could have been very recent.  This is one of the factors considered when determining percentage of ethnicity.

A second example is the STR marker known as D9S919 which is present in about 30% of the Native American people.  The value of 9 at this marker is not known to be present in any other ethnic group, so this mutation occurred after the Native people migrated across Beringia into the Americas, but long enough ago to be present in many descendants.  There is also no other known marker that is only found only among Native Americans, although I expect as we move into full genome sequencing we will discover more.  You can test this marker individually at Family Tree DNA, which is the only lab that offers this test.  If you have the value of 9 at this marker, it confirms Native heritage, but if you don’t carry 9, it does NOT disprove Native heritage.  After all, many Native people don’t carry it.  Again, you don’t know how long ago this marker was introduced into your ancestry.

These two examples are very unique because the markers are found only in certain groups.  Generally, with the rest of the DNA values, they are found in different amounts, or frequencies, in different parts of the world and ethnic groups.

So, if you’re trying to determine the ethnicity of an individual, you’re going to compile a huge data base of percentages of DNA values found of Ancestrally Informative Markers (AIMs) in different parts of the world.

So, you would compare the participant’s values against your data base and you will come up with those regions or ethnicities that are present most often in your comparison.  This is exactly what the products and services that provide you with your ethnicity percentages do – and how accurate the results are depend highly on the data base itself, the amount of data, and the quality of data.  Dare I mention Ancestry’s issue that they’ve had since they first began offering their autosomal product over a year ago where everyone seems to have Scandinavian ancestry?  Ancestry doesn’t share with us their sources, so as a community we have no idea how they have come up with these numbers.

You can easily compare your autosomal results in nauseating detail at both 23andMe and Family Tree DNA by testing with both companies, or by testing with either 23andMe or Ancestry and transferring your autosomal results to Family Tree DNA.  All 3 of these companies will give you a somewhat different result, but they should be in the same ballpark.  You can also then download your raw data file from any of those vendors and upload it to www.gedmatch.com where you can then do ethnicity comparisons using a variety of tools.  These tools, an example shown below, will have much more variance and detail than the vendor’s tools or results.  And because of that, they tend to be more confusing as well.

gedmatch example

Many people with small amounts of minority admixture are disappointed with the results through the vendors, especially if their Native American admixture doesn’t show.  I wrote extensively about this in my series, The Autosomal Me, so I won’t rehash it here, but using the GedMatch tools is very enlightening, as you can see above with my results.  And do I really have Indo-Tibetan and Indo-Iranian ancestors?

Where’s Xenia?

Back to Xenia and her descendants.  Let’s say that Xenia’s descendants settled in four primary locations.  One is in the Middle East – they never left home.  One is in Asia and from there, to the Americans to become the Native Americans and lastly, to Europe.  Now let’s say there is a pocket of them in the Altai region of Asia and a pocket in France.  The Altai is the ancestral home of the Native Americans and could explain the Indo-Tibet result, above.  We’ll call that Central Asia.  And France is where my Acadian ancestors were from.  Hmmm….this is getting confusing.  To make matters even more confusing, I might well descend from both groups, who originally descended from Xenia.

Let’s say that I do in fact carry small segments of Xenia’s DNA.  Now let’s say that this same DNA is found in a group of people in Central Asia, maybe in Tibet, it’s published in an obscure journal someplace, and it finds its way into a data base.  Voila – there you go – I now have a match in Central Asia in a place called Indo-Tibet.  But do I really?

Does this mean that my ancestor was from Central Asia?  Not necessarily.  And if so, maybe not recently, but the people from that location for some reason share some of the DNA that I carry.  The question of course is why, how and when?

What this really means to you is a matter of degrees.  If you have a few matches from obscure regions, along with very small percentages, it is likely a result of the dandelion’s dispersion.  If you have a lot of matches, meaning a high percentage hit rate, from a particular region, pay attention, it probably has some genealogical significance.

It’s no wonder people are confused by this!  Now, just think how many dandelions you have.  In 15 generations, you have 32,768 ancestors.  In fact, this is how we know for sure that we all descend from the same ancestor multiple times.  Our number of ancestors quickly exceeds the world population.  In 30 (25 years) generations, in about the year 1263, we reach about 1 billion ancestors.  In 1750, there were 791 million people on Earth, in 1600, 580 million, in 1500, 458 million and in 1000, 310 million.

Ancestors - Years

We know that we very likely descend several times from a much smaller group of ancestors from isolated local populations.  However, just looking at the 32,000+ ancestors in 15 generations, it’s still an entire dandelion field!!!

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The Autosomal Me – The Holy Grail – Identifying Native Genealogy Lines

holy grail

Sangreal – the Holy Grail.  We are finally here, Part 9 and the final article in our series.  The entire purpose of The Autosomal Me series has been to use our DNA and the clues it holds to identify minority admixture, in this case, Native American, and by identifying those Native segments, and building chromosomal clusters, to identify the family lines that contributed that Native admixture.  Articles 1-8 in the series set the stage, explained the process and walked us through the preparatory steps.  In this last article, we apply all of the ingredients, fasten the lid, shake and see what we come up with.  Let’s take a minute and look at the steps that got us to this point.

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.”  Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works.  Part two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.

Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.

In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering.   We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7, “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments” took a deeper dive and focused on the two chromosomes with proven Native heritage and began by comparing those chromosome segments using the 4 GedMatch admixture tools.

Part 8, “The Autosomal Me – Extracting Data Segments and Clustering,” we  extract all of the Native and Blended Asian segments in all 22 chromosomes, but only used chromosomes 1 and 2 for illustration purposes.  We then clustered the resulting data to look for trends, grouping clusters by either the Strong Native criteria or the Blended Asian criteria.

In this final segment, Part 9, we will be applying the chromosomal information we’ve gathered to our matches and determine which of our lines are the most likely to have Native Ancestry.  This, of course, has been the goal all along.  So, drum roll…..here we go.

In Part 8, we ended by entering the start and stop locations of both Strong Native and Blended Asian clusters into a table to facilitate easy data entry into the chromosome match spreadsheet downloaded from either 23andMe or Family Tree DNA.  If you downloaded it previously, you might want to download it again if you haven’t modified it, or download new matches since you last downloaded the spreadsheet and add them to the master copy.

My goal is to determine which matches and clusters indicate Native ancestry, and how to correlate those matches to lineage.  In other words, which family lines in my family were Native or carry Native heritage someplace.

The good news is that my mother’s line has proven Native heritage, so we can use her line as proof of concept.  My father’s family has so many unidentified wives, marginalized families and family secrets that the Native line could be almost any of them, or all of them!  Let’s see how that tree shakes out.

Finding Matches

So let’s look at a quick example of how this would work.  Let’s say I have a match, John, on chromosome 4 in an area where my mother has no Native admixture, but I do.  Therefore, since John does not match my mother, then the match came from my father and if we can identify other people who also match both John and I in that same region on that chromosome, they too have Native ancestry.  Let’s say that we all also share a common ancestor.  It stands to reason at that point, that the common ancestor between us indicates the Native line, because we all match on the Native segment and have the same ancestor.  Obviously, this would help immensely in identifying Native families and at least giving pointers in which direction to look.  This is a “best case’ example.  Some situations, especially where both parents contribute Native heritage to the same chromosome, won’t be this straightforward.

Based on our findings, the maximum range and minimum (least common denominator or “In Common” range is as follows for the strongest Native segments on chromosomes 1 and 2.

  Chromosome 1 Chromosome 2
Largest   Range 162,500,000   – 180,000,000 79,000,000   – 105,000,000
Smallest   Range 165,658,091   – 171,000,000 90,000,000   – 103,145,425

At GedMatch

At GedMatch, I used a comparison tool to see who matched me on chromosome 1.  Only 2 people outside of immediate family members matched, and both from Family Tree DNA.  Both matched me on the critical Native segments between about 165-180mg.  I was excited.  I went to Family Tree DNA and checked to see if these two people also matched my mother, which would confirm the Native connection, but neither did, indicating of course that these two people matched me on my father’s side.  That too is valuable information, but it didn’t help identify any common Native heritage with my mother on chromosome 1.  It did, however, eliminate them as possibilities which is valuable information as well.

DNAGedcom

I used a new tool, DNAGedcom, compliments of Rob Warthen who has created a website, DNA Tools, at www.dnagedcom.com.  This wonderful tool allows you to download all of your autosomal matches at Family Tree DNA and 23andMe along with their chromosomal segment matches.  Since my mother’s DNA has only been tested at Family Tree DNA, I’m limiting the download to those results for now, because what I need is to find the people who match both she and I on the critical segments of chromosome 1 or 2.

Working with the Download Spreadsheet

It was disappointing to discover that my mother and I had no common matches that fell into this range on chromosome 1, but chromosome 2 was another matter.  Please note that I have redacted match surnames for privacy.

step 9 table 1

The spreadsheet above shows the comparison of my matches (pink) and Mother’s (white).  The Native segment of chromosome 2 where I match Mother is shaded mustard.  I shaded the chromosome segments that fell into the “common match” range in green.  Of those matches, there is only one person who matches both Mother and I, Emma.  The next step, of course, is to contact Emma and see if we can discover our common ancestor, because whoever it is, that is the Native line.  As you might imagine, I am chomping at the bit.

There are no segments of chromosome 2 that are unquestionably isolated to my father’s line.

Kicking it up a Notch

Are you wondering about now how something that started out looking so simple got so complex?  Well, I am too, you’re not alone.  But we’ve come this far, so let’s go that final leg in this journey.  My mom always used to say there was no point in doing something at all if you weren’t going to do it right.  Sigh….OK Mom.

The easiest way to facilitate a chromosome by chromosome comparison with all of your matches and your Strong Native and Blended Asian segments is to enter all of these segment groups into the match spreadsheet.  If you’re groaning and your eyes glaze over right after you do one big ole eye roll, I understand.

But let’s take a look at how this helps us.

On the excerpt from my spreadsheet below, for a segment of chromosome 5, I have labeled the people and how they match to me.  The ones labeled “Mom” in the last column are labeled that way because these people match both Mom and I.  The ones labeled “Dad” are labeled that way because I know that person is related on my father’s side.

Using the information from the tables created in Step 8, I entered the beginning and end of all matching segment clusters into my spreadsheet.  You can see these entries on lines 7, 8, 22, 23 and 24.  You then proceed to colorize your matches based on the entry for either Mom or Dad – in other words the blue row or the purple row, line 7, 22 or 24.  In this example, actually, line 5 Rex, based on the coloration, should have been half blue and half purple, but we’ll discuss his case in a minute.

The you can then sort either by match name or by chromosome to view data in both ways.  Let’s look at an example of how this works.

Legend:

  • White Rows:  Mother’s matches.  When Mother and I both match an individual, you’ll see the same matches for me in pink.  This double match indicates that the match is to Mother’s side and not Father’s side.
  • Pink Rows:  My matches.
  • Purple “Mom” labels in last column:  The individual matches both me and Mom.  This is a genetic match.
  • Teal “Dad” labels in last column: Genealogically proven to be from my father’s side.  This is a genealogical, not a genetic label, since I don’t have Dad’s DNA and can only infer these genetically when they don’t also match Mother.
  • Dark Pink Rows labeled “Me Amerind Only” are Strong Native or Blended Asian segments from Chromosome Table that I have entered.  My segments must come from one of my parents, so I’ve either colored them purple, if the match is someone who matches Mother and I both, or teal, if they don’t match both Mom and I, so by inference they come from my father’s line.
  • Dark Purple Rows labeled “Mom Amerind Only” are Mom’s segments from the Chromosome Table.
  • Dark Teal Rows labeled “Dad Amerind Only” are inferred segments belonging to my father based on the fact that Mother and I don’t share them.

Inferred Relationships

This is a good place to talk for just a minute about inferred relationships in this context.  Inference gets somewhat tenuous or weak.  The inferred matches on my father’s side began with the Native segments in the admix tools.  Some inferences are very strong, where Mother has no Native at all in that region.  For example, Mom has European and I have Native American.  No question, this had to come from my father.  But other cases are much less straightforward.

In many cases, categorization may be the issue.  Mom has West Asian for example and I have Siberian or Beringian.  Is this a categorization issue or is this a real genetic difference, meaning that my Siberian/Beringian is actually Native and came from my father’s side?

Other cases of confusion arise from segment misreads, etc.  I’ve actually intentionally included a situation like this below, so we can discuss it.  Like all things, some amount of common sense has to enter the picture, and known relationships will also weigh heavily in the equation.  How known family members match on other chromosome segments is important too.  Do you see a pattern or is this match a one-time occurrence?  Patterns are important.

Keep in mind that these entries only reflect STRONG Asian or Native signals, not all signals.  So even if Mother doesn’t have a strong signal, it doesn’t mean that she doesn’t have ANY signal in that region.  In some cases, start and stop segments for Mom and Dad overlapped due to very long segments on some matches.  In this case, we have to rely on the fact that we do have Mother’s actual DNA and assume that if they aren’t also a match to Mother, that what we are seeing is actually Dad’s lines, although this may not in actuality always be true.  Why?  Because we are dealing with segments below the matching threshold limit at both Family Tree DNA and 23andMe, and both of my parents carry Native heritage.  We can also have crossed a transitional boundary where the DNA that is being matched switches from Mom’s side to Dad’s side.

Ugh, you say, now that’s getting messy.  Yes, it is, and it has complicated this process immensely.

The Nitty-Gritty Data Itself

step 9 table 2

Taking a look at this portion of chromosome 5, we have lots going on in this cluster.  Most segments will just be boring pink and white (meaning no Native), but this segment is very busy.  Mom and I match on a small segment from 52,000,000 to 53,000,000.  Indeed, this is a very short segment when compared to the entire chromosome, but it is strongly Native.  We both also match Rex, our known cousin.  I’ve noted him with yellow in the table. Please note that Mom’s white matches are never shaded.  I am focused on determining where my own segments originate, so coloring Mother’s too was only confusing.  Yes, I did try it.

You can see that Mother actually shares all or any part of her segment with only me and Rex.  This simplifies matters, actually.  However, also note that I carry a larger segment in this region than does Mother, so either we have a categorization issue, a misread, or my father also contributed.  So, a conundrum.  This very probably implies that my father also carried Native DNA in this region.

Let’s see what Rex’s DNA looks like on this same segment of chromosome 5, from 52-53 using Eurogenes.  In the graph below, my chromosome is the top bar, Rex’s the middle and the bottom bar shows common DNA with the black nonmatching.  Yellow is Native American, red is South Asian, putty is Siberian, lime green is Mediterranean, teal is North Europe, orange is Caucus.

Step 9 item 3

This same comparison is shown to Mother’s DNA (top row) below.

step 9 item 4

It’s interesting that while Mother doesn’t have a lot of yellow (Native), she does have it throughout the same segment where Rex’s occurs, from about 52 through 53.5.

Does this actually point to a Native ancestor in the common line between Rex, Mom and I, which is the Swiss/German Johann Michael Miller line which does include an unidentified wife stateside, or does this simply indicate a common ancient population long ago in Asia?  It’s hard to say and is deserving of more research.  I feel that it is most likely Native because of the actual yellow, Native segment. If this was an Asian/European artifact, it would be much less likely to carry the actual yellow segment.

Is Rex also genealogically related to my father?  As I’ve worked through this process with all of my chromosomes and matches, I’ve really come to question if one of my father’s dead ends is also an ancestral line of my mother’s.

The key to making sense of these results is clusters.

Clusters vs Singleton Outliers

The work we’ve already done, especially in Step 8, clusters the actual DNA matching segments.  We’ve now entered that information into the spreadsheet and colored the segments of those who match.  What’s next?

The key is to look for people with clusters.  Many matches will have one segment, of say, 10 that match, colored.  Unless this is part of a large chromosome cluster, it’s probably simply an outlier.  Part of a large chromosome cluster would be like the large Strong Native segments on chromosome 1 or 2, for example.  How do we tell if this is a valid match or just an outlier?

Sort the spreadsheet by match name.  Take a look at all of the segments.

The example we’ll use is that of my cousin, Rex.  If you recall, he matches both me and Mother, is a known first cousin twice removed to me, (genetically equal to a second cousin), and is descended from the Miller line.

In this example, I also colored Mother’s segments because I wanted to see which segments that I did not receive from her were also Native. You can see that there are many segments where we all match and several of those are Native.  These also match to other Miller descendants as well, so are strongly indicative of a Native connection someplace in our common line.

If we were only to see one Native segment, we would simply disregard this as an outlier situation.  But that’s not the case.  We see a cluster of matches on various segments, we match other cousins from the same line on these segments, and reverting back to the original comparison admixture tools verifies these matches are Native for Rex, Mom and me.

step 9 item 5

Hmmmm…..what is Dad’s blue segment color doing in there?  Remember I said that we are only dealing with strong match segments?  Well, Mom didn’t have a strong segment at that location and so we inferred that Dad did.  But we know positively that this match does come from Mother’s side.  I also mentioned that I’ve come to wonder if my Mom and Dad share a common line.  It’s the Miller line that’s in question.  One of Johann Michael Miller’s children, Lodowick, moved from Pennsylvania to Augusta County, Virginia in the 1700s and his line became Appalachian, winding up in many of the same counties as my father’s family.  I’m going to treat this as simply an anomaly for now, but it actually could be, in this case, an small indication that these lines might be related.  It also might be a weak “Mom” match, or irrelevant.  I see other “double entries” like this in other Miller cousins as well.

What is the pink row on chromosome 12?  When I grouped the Strong Native and Asian Clusters, sometimes I had a strong grouping, and Mom had some.  The way I determined Dad’s inferred share was to subtract what Mom had in those segments from mine.  In a few cases, Mom didn’t have enough segments to be considered a cluster but she had enough to prevent Dad from being considered a cluster either, so those are simply pink, me with no segment coloring for Mom or Dad.

Let’s say I carry Strong Native/Mixed Asian at the following 8 locations:

10, 12, 14, 16, 18, 20, 22, 24

This meets the criteria for 8 of 15 ethno-geographic locations (in the admix tools) within a 2.5 cM distance of each other, so this cluster would be included in the Mixed Asian for me.  It could also be a Strong Native cluster if it was found in 3 of 4 individual tools.  Regardless of how, it has been included.

Let’s now say that Mom carries Native/Mixed Asian at 10, 12 and 14, but not elsewhere in this cluster.

Mom’s 3 does not qualify her for the 8/15 and it only leaves Dad with 5 inferred segments, which disqualifies him too.  So in this case, my cluster would be listed, but not attributable directly to either parent.

What this really says is that both of my parents carry some Native/Blended Asian on this segment and we have to use other tools to extrapolate anything further.  The logic steps are the same as for Dad’s blue segment.  We’re going to treat that as an outlier.  If I really need to know, I can go back to the actual admixture tools and see whether Mom or Dad really match me strongly on which segments and how we compare to Rex as well.  In this case, it’s obvious that this is a match to my Mother’s side, so I’m leaving well enough alone.

Let’s see what the matches reveal.

Matches

Referring back to the Nitty Gritty Data spreadsheet, Mom’s match to Phyllis on row 15 confirms an Acadian line.  This is the known line of Mother’s Native ancestry.  This makes sense and they match on Native segments on several other chromosomes as well.  In fact, many of my and Mother’s matches have Acadian ancestry.

My match to row 19, Joy, is a known cousin on my father’s side with common Campbell ancestry.  This line is short however, because our common ancestor, believed to be Charles Campbell died before 1825 in Hawkins County, TN.  He was probably born before 1750, given that his sons were born about 1770 and 1772.  Joy and I descend from those 2 sons.  Charles wife and parents are unknown, as is his wife.

My match to row 20, inferred through my father’s side, is to a Sizemore, a line with genetically proven Native ancestry.  Of course, this needs more research, but it may be a large hint.  I also match with several other people who carry Sizemore ancestors.  This line appears to have originated near the NC/VA border.

I wanted to mention rows 4 and 17.  Using our rules for the spreadsheet, if I match someone and they don’t also match Mother on this segment, I have inferred them to be through my father.  These are two instances that this is probably incorrect.  I do match these people through Mother, but Mother didn’t carry a strong signal on this segment, so it automatically became inferred to Dad.  Remember, I’m only recording the Strong Native or the Blended Asian segments, not all segments.  However, I left the inferred teal so that you can see what kinds of judgment calls you’ll have to make.  This also illustrates that while Mom’s genetic matches are solid, Dad’s inferred matches are less so and sometimes require interpretation.  The proper thing to do in this instance would be to refer back to the original admixture tools themselves for clarification.

Let’s see what that shows.

step 9 item 6

Using HarrappaWorld, the most pronounced segment is at about 52.  Teal is American.  You can see that Mother has only a very small trace between 53 and 54, almost negligible.  Mother’s admixture at location 52 is two segments of purple, brown and cinnamon which translate to Southwest Asian (lt purple), Mediterranean (dk purple), Caucasian (brown) and Balock (cinnamon), from Pakistan.

Checking Dodecad shows pretty much the same thing, except Mother’s background there is South Asian, which could be the same thing as Caucus and Pakistan, just different categorizations.

In this case, it looks like the admixture is not a categorization issue, but likely did come from my father.  Each segment will really be a case by case call, with only the strongest segments across all tools being the most reliable.

It’s times like this that we have to remember that we have two halves of each chromosome and they carry vastly different information from each of our parents.  Determining which is which is not always easy.  If in doubt, disregard that segment.

Raw Numbers

So, what, really did I figure out after all of this?

First, let’s look at some numbers.

I was working with a total of 292 people who had at least one chromosomal segment that matched me with a Strong Native or Blended Asian segment.  Of those, 59 also matched Mom’s DNA.  Of those, 18 had segments that matched only Mom.  This means that some of them had segments that also matched my father.  Keep in mind, again, that we are only using “strong matches” which involves inferring Dad’s segments and that referring back to the original tools can always clarify the situation.  There seems to be some specific areas that are hotspots for Native ancestry where it appears that both of my parents passed Native ancestry to me.

Many of my and my mother’s 59 matches have Acadian ancestry which is not surprising as the Acadians intermarried heavily with the Native population as well as within their own ethnic group.

Several also have Miller Ancestry.  My Miller ancestor is Johann Michael Miller (1692-1771) who immigrated in the colonial period and settled on the Pennsylvania frontier.  His son, Philip Jacob Miller’s (1726-1799) wife was a woman named Magdalena whose last name has been rumored for years to be Rochette, but no trace of a Rochette family has ever been found in the county where they lived, region or Brethren church history…and it’s not for lack of looking.  Several matches point to Native Ancestry in this line.  This also begs the question of whether this is really Native or whether it is really the Asian heritage of the German people.  Further analysis, referring back to the admixture tools, suggests that this is actually Native. It’s also interesting that absolutely none of Mother’s other German or Dutch lines show this type of ancestry.

There is no suggestion of Native ancestry in any of her other lines.  Mother’s results are relatively clean.  Dad’s are anything but.

Dad’s Messy Matches

My father’s side of the family, however, is another story.

I have 233 matches that don’t also match my mother.  There can be some technical issues related to no-calls and such, but by and large, those would not represent many.  So we need to accept that most of my matches are from my Father’s side originating in colonial America.  This line is much “messier” than my mother’s, genealogically speaking.

Of those 233 matches, only 25 can be definitely assigned to my father.  By definitely assigned, I mean the people are my cousins or there is an absolutely solid genealogical match, not a distant match.  Why am I not counting distant matches in this total?  We all know by virtue of the AncestryDNA saga that just because we match family lines and DNA does NOT mean that the DNA match is the genealogical line we think it is.  If you would like to read all about this, please refer to the details in CeCe Moore’s blog where she discussed this phenomenon.  The relevant discussion begins just after the third photo in this article where she shows that 3 of 10 matches at Ancestry where they “identify” the common DNA ancestor are incorrect.  Of course, they never SAY that the common ancestor is the DNA match, but it’s surely inferred by the DNA match and the “leaf” connecting these 2 people to a common ancestor.  It’s only evident to someone who has tested at least one parent and is savvy enough to realize that the individual whose ancestor on Mom’s side that they have highlighted, isn’t a match to Mom too.  Oops.  Mega-oops!!!

However, because we are dealing in our project, on Dad’s side, with inferences, we’re treading on some of the same ground.  Also, because we are dealing with only “strong clustered” segments, not all Native or Asian segments and because it appears that my parents both have Native ancestry.  To make matters worse, they may both have Algonquian, Iroquoian or both.

I have also discovered during this process that several of my matches are actually related to both of my parents.  I told you this got complex.

Of the people who don’t match Mother, 32 of them have chromosomal matches only to my father, so those would be considered reliable matches, as would the closest ones of the 25 that can be identified genealogically as matching Dad.  Many of these 25 are cousins I specifically asked to test, and those people’s results have been indispensable in this process.

In fact, it’s through my close circle of cousins that we have been able to eliminate several lines as having Native ancestry, because it doesn’t’ show as strong and they don’t have it either.

Many of these lines group together when looking at a specific chromosome.  There is line after line and cousin after cousin with highlighted data.

Dad’s Native Ancestors

So what has this told me?  This information strongly suggests that the following lines on my father’s side carry Native heritage.  Note the word “carry.”  All we can say at this point is that it’s in the soup – and we can utilize current matches at our testing company and at GedMatch, genealogy research and future matches to further narrow the branches of the tree.  Many of these families are intermarried and I have tried to group them by marriage group.  Obviously, eventually, their descendants all intermarried because they are all my ancestors on my father’s side.  But multiple matches to other people who carry the Native markers but aren’t related to my other lines are what define these as lines carrying Native heritage someplace.

  • Campbell – Hawkins County, Tn around 1800, missing wife and parents, married into the Dodson family
  • Dodson – Hawkins County, Tn, Virginia – written record of Lazarus Dodson camping with the Cherokee – missing wife, married into the Campbell and Estes family
  • Claxton/Clarkson – Russell Co., Va, Claiborne and Hancock Co., Tn – In NC associated with the known Native Hatcher family.  Possibly a son-in-law.  Missing family entirely.
  • Cook – Russell Co., Va. – daughter married Claxton/Clarkson – missing wives
  • Harrold, Harrell, Herrell – Hancock Co., Tn., Wilkes Co., NC – missing wives
  • McDowell – Hancock Co. Tn, Wilkes Co., NC, Augusta Co., Va – married into the Harrell family, missing wife
  • McNeil, McNiel – Wilkes Co., NC – missing wives, married into the Vannoy family
  • Vannoy – Wilkes County – some wives unaccounted for pre-1800
  • Crumley – Greene County, Tn., Lee Co., Va. – oral history of Native wife, married into the Vannoy family
  • Brown – Greene County, Tn, Montgomery Co., Va – married into the Crumley family, missing wives

While this looks like a long list, the list of families that don’t have any Native ancestry represented is much longer and effectively serves to eliminate all of those lines.  While I don’t have “THE” answer, I certainly know where to focus my research.  Maybe there isn’t the one answer.  Maybe there are multiple answers, in multiple lines.

The Take Away

Is this complex?  Yes!  Is it a lot of work?  You bet it is!  Is everything cast in concrete?  Never!  You can see that by the differences we’ve found in data interpretation, not to mention issues like no-calls (areas that for some reason in the test don’t read) and cross overs where your inheritance switches from your mom’s side to your dad’s side.  Is there any other way to do this?  No, not if your minority admixture is down in that weedy area around 1%.

Is it worth it?  You’ll have to decide.  It guess it depends on how desperately you want to know.

Part of the reason this is difficult is because we are missing tools in critical locations.  It’s an intensively laborious manual process.  In essence, using various tools, one has to figure out the locations of the Native and Asian chromosome segments and then use that information to infer Native matches by a double match (genetic match at DNA company plus match with Strong Native/Blended Asian segment) with the right parent.  It becomes even more complex if neither parent is available for testing, but it is doable although I would think the reliability could drop dramatically.

Tidbits and Trivia

I’ve picked up a number of little interesting tidbits during this process.  These may or may not be helpful to you.  Just kind of file them away until needed:)

  • Matches at testing companies come and go….and sometimes just go.  At Family Tree DNA, I have some matches that must be trembling on the threshold that come and go periodically.  Now you see them, now you don’t.  I lost matches moving from the Affy chip to the Illumina chip and lost additional matches between Build 36 and 37.  Some reappeared, some haven’t.
  • The start and stop boundaries changed for some matches between build 36 and build 37.  I did not go back and readjust, as most of these, in the larger scheme of things, were minor.  Just understand that you are looking for  patterns here that indicate Native heritage, not exact measurements.  This process is a tool, and unfortunately, not a magic wand:)
  • The centromere locations change between builds.  If you have matches near or crossing the middle of the chromosome, called the centromere, there may be breaks in that region.  I enter the centromere start and stop locations in my spreadsheet so that if I notice something odd going on in that region, the centromere addresses are right there to alert me that I’m dealing with that “odd” region.  You can find the centromere addresses in the FAQ at Family Tree DNA for their current build.
  • At 23andMe, when you reach the magic 1000 matches threshold, you start losing matches and the matching criteria is elevated so that you can stay under 1000 matches.  For people with colonial American or Jewish heritage, in other words those with high numbers of matches, this is a problem.
  • Watch for matches that are related to both sides of your family.  If your family lived in colonial America, you’re going to have a lot of matches and many are probably related to each other in ways you aren’t aware of.
  • If your parents are related to each other, this process might simply be too complex and intertwined to provide enough granular data to be useful.
  • Endogamous groups are impossible to sort through as to where, meaning which ancestor, the DNA came from.  This is because the original group founders’ DNA is just getting passed around and around, with little or no new DNA being introduced.  The effect of this on downstream generations relative to genetic genealogy is that matches appear to be more closely related than they are because of the amount of matching DNA they carry.  For my Brethren and my Acadian groups of people, I just list them by the group name, since, as the saying goes, “if you’re related to one Acadian, you’re related to all Acadians.”
  • If you’re going to follow this procedure, save one spreadsheet copy with the Strong Native only and then a second one with both the Strong Native and Blended Asian.  I’m undecided truthfully whether the Mixed Asian adds enough resolution for the extra work it generates.
  • When in question, refer back to the original tools.  The answer will always be found there.
  • Unfortunately, tools change.  You may want to take screen shots.  During this process, FTDNA went from build 36 to 37, match thresholds changed, 23andMe introduced a new user interface (which I find much less intuitive) and GedMatch has made significant changes.  The net-net of this is when you decide to undertake this project, commit to it and do it, start to finish.  Doing this little by little makes you vulnerable to changes that may make your data incompatible midstream – and you may not even realize it.
  • This entire process is intensively manual.  My spreadsheet is over 5500 rows long.  I won’t be doing it again…although I will update my spreadsheet with new matches from time to time.  The hard work is already done.
  • This same technique applies to any minority ancestry, not just Native, although that’s what I’ve been hunting for and one of the most common inquiries I receive.
  • I am hopeful that in the not too distant future many of these steps and processes will be automated by the group of bright developers that contribute to GedMatch or via other tools like DNAGedcom. HINT – HINT!!!

I would like to follow this same process to identify the source of my African heritage, but I’m thinking I’ll wait for the tools to become automated.  The great irony is that it’s very likely in the same lines as my Native ancestors.

If You Want to Test

What does it take to do this for yourself using the tools we have today, as discussed?

If your parents are living, the best gift you can give yourself is to test them, now, while you still can.  My mother has been gone for several years, but her DNA archived at Family Tree DNA was still viable.  This is not always the case.  I was fortunate.  Her DNA is one of the best gifts she gave me.  Not just by inheritance, but by having hers tested.  I thank her every single day, for both!  I could not have written this article without her DNA results.  The gift that keeps on giving.

If you don’t have a parent to test, you can test several other family members who will provide some information, but clearly won’t carry the same amounts of common DNA with you as your parents.  These would include your aunts and uncles, your parents’ siblings and what I’ve referred to as your close cousin circle.  Attempt to test at least someone from each line.  Yes, it gets expensive, but as one of my cousins said, as she took her third or 4th DNA test.  “It’s only money.  This is about family.”

You can also test your own siblings as well to obtain more information that you can use to match up to your family lines. Remember, you only receive half of your parents DNA, and your siblings will received some DNA from your parents that you didn’t.

I don’t have any other siblings to test, but I have tested cousins from several lines which have proven invaluable when trying to discern the sources of certain segments. For example, one of these Native segments fell on a common segment with my cousin Joy.  Therefore, I know it’s from the Campbell line, and because I have the Campbell paternal Y-DNA which is European, I know immediately the Native admixture would have had to be from a wife.

Much of this puzzle is deductive, but we now have the tools, albeit manual, to do this type of work that was previously impossible.  I am somewhat disappointed that I can’t pinpoint the exact family lines, yet, but hopefully as more people test and more matches provide genealogical information, this will improve.

If you want to play in this arena, you need to test at either Family Tree DNA, 23andMe, or both.  Right now, the most cost effective way to achieve this is to purchase a $99 kit from 23andMe, test there, then download your results from 23andMe and upload them to Family Tree DNA for $99.  That way, you are fishing in both pools.  Be aware that less than half of the people who test at either company download results to GedMatch, so your primary match locations are with the testing companies.  GedMatch is auxiliary, but critical for this analysis.  And the newest tool, DNAGedcom is a Godsend.

Also note that transferring your result to Family Tree DNA is NOT the same thing as actually testing there.  Why does this matter?  If you want a future test at Family Tree DNA, who is the premiere genetic genealogy testing company, offering the most variety and “deepest” commercial tests, they archive your DNA for 25 years, but if you transfer results, they don’t have your DNA to archive, so no future products can be ordered.  All I can say is thank Heavens Mom’s DNA was there.

Ancestry.com doesn’t provide any tools such as the chromosome browser or even the basic information of matching segments.  All you get is a little leaf that says you’re related, but the questions of which segment or how are not answerable today at Ancestry and as CeCe’s experience proved, its unreliable.  It’s  possible that you share the same surnames and ancestor, but your genetic connection is not through that family line.  Without tools, there is no way to tell.  Ancestry released raw data files a few weeks ago and very recently, GedMatch has implemented the ability to upload them so that Ancestry participants can now utilize the additional tools at GedMatch.

Although this has been an extraordinarily long and detailed process, I can’t tell you how happy I am to have developed this new technique to add to my toolbox.  My Native and African ancestors have been most elusive.  There are no records, they didn’t write and probably didn’t even speak English, certainly not initially.  The only clues to their existence, prior to DNA, were scant references and family lore.  The only prayer of actually identifying them is though these small segments of our DNA – yep – down in the weeds.  Are there false starts perhaps, and challenges and maybe a few snakes down there?  Yes, for sure, but so is the DNA of your ancestors.

Happy gardening and rooting around in the weeds.  Just think of it as searching for the very best buried treasure!  It’s down there, just waiting to be found.  Keep digging!

I hope you’ve enjoyed this series and that it leads you to your own personal genealogical treasure trove!

treasure chest

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

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Genealogy Services

Genealogy Research

The Autosomal Me – Extracting Data Segments and Clustering

This is Part 8 of a multi-part series, “The Autosomal Me.”

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.”  Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works.  Part two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.  Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.  In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering.   We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7, “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments”, took a deeper dive and focused on the two chromosomes with proven Native heritage and began by comparing those chromosome segments using the 4 GedMatch admixture tools.

In this segment, Part 8, we’ll be extracting all of the Native and Blended Asian segments on all 22 chromosomes, but I’ll only be using chromosomes 1 and 2 for illustration purposes.  We will then be clustering the resulting data to look for trends.  If you’re following along and using this methodology, you’ll be extracting the Native segment start and stop locations from all 22 chromosomes.

I apologize in advance for the length of this article, but there was just no good place to break it into pieces.

So, let’s get started.  As a reminder, we are using the admixture tools at www.gedmatch.com.

I experimented with several types of extractions to see which ones best reflected the results found by both 23andMe and Dr. McDonald and confirmed by the start and stop segments in the highly Native segments of chromosomes 1 and 2 in Part 7 of this series.  We verified that all 4 tools accurately reflected and corroborated the segments listed as Native, so now we’re going to apply that same methodology to the rest of our chromosomal data.

Initially, I tried to use the information from chromosomes 1 and 2 to extract the Native chromosomes using only the “best” tool, but when I looked at all 4 tools, I quickly realized that there was no single “best” choice.  A couple of crucial points came to light.

  • Some of the geographic colors are almost impossible to tell apart.
  • None of the tools are universally best.
  • When looking at all 4 tools, generally a “best 3 out of 4” approach allowed for one of the tools to be wrong, to perhaps reference a slightly different data base that called the segment differently or for the colors to be indistinguishable.  In other words, if three called a segment Native and one did not, it’s Native and conversely, if less than 3 call it Native, in this comparison, it’s not.

Unfortunately, this created an awful lot of work.  This is probably the best example of where automation tools could and would make a huge difference in this process.

I did two separate extracts.  The first one is what I refer to as the “Strong Native” extract and the second is the “Blended Asian.”  In part, I did these separately as a check and balance to be sure that my first extraction was accurate.

In the first extract, I selected only one category, the one best fitted to “Native American” for each tool.  I used the following categories for each admixture tool:

  • MDLP – Amerind
  • Eurogenes – North Amerindian
  • Dodecad – NE Asian
  • Harrappaworld – American

I completed this process for every chromosome, but I’m only showing the first two chromosomes in this article.

By way of example, using the first tool, MDLP, North Amerind looks black, but is actually very dark grey.  It is, fortunately, distinctive.

On the chromosome painting below, my results for the first part of chromosome 1 are shown in the first band, and mother’s for the same segment are shown as the second band.  The bottom band represents common segments and the black is non-matching segments, meaning those I obtained from my father.  Sometimes this third band can help you determine what you are really seeing in terms of colors and blending, but it’s not always useful.  In this case, trying to spot a small amount of dark gray against black is almost impossible, so not terribly helpful.  But if you were looking for red, that would be another story.  As you move through this process, remember, it’s not exact and utilizing best 3 of 4 will help you recover from any major errors.

You can see that my grey segments show up from about 12-13 and then again at about 14.5.  Sometimes it’s difficult to know how to count something.  For example, my Native at 14.5 – it’s actually more like 14.25 -14.5, but I chose not to divide further than half mb segments.  As long as you are consistent in whatever methodology you select, it will work out.

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Please note that when reading these charts, that the small hash mark is the indicator for the measure.  In other words, the small hash mark above 10M means that is the 10M location.  It’s obvious here, but on some charts, the hash mark and the location legend look to be 1-off.  Again, as long as you’re consistent, it really doesn’t matter.

Mother’s Native segments are more pronounced and obvious.  They range from about 8-14.  Using the actual tools, you would record this and then continue scrolling to the right until you reach the end of the chromosome.  On chromosomes 1 and 2, I found the strong Native segments for the four admixture tools, as shown below.

The boxed numbers show the areas that were found “in common” between 23andMe, Dr. McDonald and the admixture tools, as determined in Part 7 of this series.  Highlighted segments show segments where at least 3 of 4 admixture tools reported Native heritage.  As you can see, there were clearly additional Native segments not reported by 23andme and Dr. McDonald.

Strong Native Chromosomal Detail Table

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Because we have both my and mother’s results, we can infer my father’s contribution.  Clearly, some of his will wind up being some amount of “noise” and some IBS segments, but not all, by any means, and this is the only way to get a “read” on Dad.  This is one form of phasing data.  Phasing refers to various methodologies of figuring out which DNA comes from what source, meaning which parental line.

While the strongest Native segments are the ones individually most likely to indicate Native American ancestry, that really isn’t the whole story.  I discovered that many of these Native segments are actually embedded in other segments that are indicative of Native heritage too.  In other words, it’s not a line in the sand, yes or no, but more of a sliding scale.

On the chromosome painting below, this one using Eurogenes, with my results shown above and mother’s below, you can see two excellent examples.  Regions relevant to Native ancestry include:

  • Red – South Asian
  • Brown – Southwest Asian
  • Yellow – North Amerindian and      Arctic
  • Putty – Siberian
  • Emerald – East Asian

You can see that while mine is almost universally yellow, or Native, with a little Siberian (putty) mixed in for good measure between 169-170, a hint of East Asian (emerald) plus a little Asian (red), mother’s isn’t.  In fact, hers is a mixture of Native American and South Asian (red), with more red than yellow,  Siberian (putty) and a large segment of East Asian (emerald green).

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While her yellow Native segments alone would be staggered across this entire segment in 7 different pieces, when taken together as a whole, the “blended Asian” segment reaches entirely across the screen with the exception of 1 mb between 161.5-162.5, roughly.

The following Blended Asian Chromosomal Detail Table shows all of the blended Asian segments using all four of the admixture tools for chromosomes 1 and 2.

It’s clear that these regions are not solely “Native American” but reach back in time genetically into Asia, particularly Northeast Asia.

Again, the boxed numbers show the “in common” segments between all tools and the yellow highlighted segments are common between at least three of the four admixture tools.

Please note that there were some issues distinguishing colors, as follows:

  • For the MDLP comparison, Mesoamerican and Paleo Siberian are both putty colored and indistinguishable on the chart.  Also, the apple green for Arctic Amerind is very similar to the Austronesian.
  • When using Dodecad, Southeast Asian (light green) and South Asian (apple green) are nearly impossible to distinguish from each other on the graphs.
  • When using HarappaWorld, the apple green for Siberian was very similar to the light forest green for Papua New Guinea and was very difficult to distinguish.  The South Asian putty appears often with the other Native markers, and I considered including this group, but it too was difficult to distinguish from other regions so in the end, I opted not to include this category.
  • If you are colorblind – get help as this is impossible otherwise.

Blended Asian Chromosomal Detail Table

On the blended Asian Chromosome Detail Table, I added yellow highlighting where the same segments show in other Asian geographies that showed in the Strong Native table.  In each column, the Strong Native category is the last one at the bottom of the list.

The blue highlighting shows other common segments found that were not included in the Strong Native segments.  For a Strong Native yellow segment to be highlighted, it had to be present in 3 of 4 tools, or 75%.  In the Blended Asian group, there are a total of 15 categories between the 4 admixture tools, so for a segment to be shaded blue, it must be found in at least 8 of the categories, so just over half.  There are many segments that are found in several categories across the tools.  For example, segment 192-193 on chromosome 1 is found five times.  This isn’t to say you should discount this segment, only that it isn’t one of the strongest, most universal.  Surprisingly, there really weren’t too many that were close to the cutoff.  Several, but not a majority, were in the 4 or 5 range, only one was at 7.

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Clustering

The third step in data extraction is to look at all of the data together.  In this step, we are removing the geographic boundaries of Siberian, N. Amerindian, etc. and combining all of our data.  I have only combined the data within columns, not between columns, so we can get a feel for which tool or tools performed best or maybe not so well.  Each chromosome in each column has its data ordered numerically, and yes, this is a manual cut and paste process.  Sorry.  I warned you, this is an very manually intensive process.

After I put each column in numerical order, I arranged them so that the numbers were approximately in a line, or a row, with each other.  For example, in the first group below, you can clearly see that the first cluster of results is found using all 4 tools.  When looked at individually, only the blue results were noted as common (at least 8 of 15 for blue), but when viewed as a cluster, you can see between the tools that the cluster itself runs from about 7.5, with a small break from 8-9, and then to about 14.5.  As you would expect the beginning and end points of the cluster trail off and are not uniform between tools, but the main part of the cluster is found in all the tools.  This introduces the question of how to measure a cluster.  In this case, there is a clean break using all tools between 8 and 9, but that is only 1 mb, rather difficult to measure accurately.  You could record this as two distinct clusters but since it’s very closely adjacent the rest of the cluster, I’m inclined to include this as one large cluster and use the starting and ending segments for the cluster as a whole, in other words, the cluster runs from 7.5 through 14.5.  The alternate, or more conservative methodology would be to use the “in common” numbers, but in this case, that would be only 10-11.5 and I think you would miss a great deal of useful data.  So, for clusters, I’m recording the full extent of the cluster.  In some cases, you may need to exercise a judgment call.

Let’s look at the second group of numbers, beginning with 18.5 in Harrappaworld.  This grouping runs though about 28.  Eurogenes found some blended Asian between 27-28.5 as well in two of the geographies, but over all, of the 15 tools, we don’t see much.  This could be a result of a number of things.  I could have had problems with the colors, there may be only a very small amount and it may be categorized as something else with the other tools.  I would not consider this a cluster, and using our best 3 or 4 methodology eliminates this cluster from consideration.  This also holds true for 43-43.5.

However, the next cluster, from 55.5 to 58 is found in the Strong Native comparison, indicated by the yellow highlighting and is found using all 4 tools.  This is definitely a cluster.

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I’ve synthesized the cluster information into a list.  From the clusters above, I’ve created a list that I will be using in the next segment for data input into my spreadsheet of matches.  The blended segments below that include Strong Native segments are shown with yellow.

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Using the GedMatch admixture applications, we’ve isolated the strongest Native and the Blended Asian segments and clusters in preparation for identifying specific Native family lines within our group of matches.

This process shows that, for the most part, the Strong Native segments picked up the strongest signals, about half of the segments that will be useful in determining Native admixture, although it does miss some.

When we use the clustering technique to view our results across all the admixture tools, we see a somewhat different picture emerge, adding several Blended Asian clusters.

In Part 9 of this series, we will use the highlighted Strong Native segments and the Blended Asian clusters, both of which suggest Native chromosomal “hotspots” to begin our comparison to our genetic matches for genealogical relevance.  In other words, using this information, we will determine which genealogical lines carry Native ancestry.

Part 9 may be somewhat delayed.  The good news is that Family Tree DNA is finishing work on their Build 36 to Build 37 conversion.  The bad news is that it fell right in the middle of writing this series.  When they finish Build 37, I’ll finish Part 9 of this series.  In the mean time, you can be extracting your minority segments using the tools and techniques that we have covered in Parts 1-8.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research