23andMe Patents Technology for Designer Babies

I try very hard to stay away from politics, religion and ethical discussions.  My Hoosier farmer Dad used to say opinions about those topics are like a certain body part, everyone has one and they all stink.

Today, however, I’m going to violate my own rule because willingly or not, by own DNA has been drug into this arena – without my direct knowledge – and so has yours if you have tested with 23andMe.

23andMe has patented the technology for making designer babies, but has stated that they don’t intend to use it.  If you’re scratching your head about now, so was I.  scratching head

This Fox News article explains about 23andMe’s patent application and recent approval.

They also report that 23andMe claims they have no plan to implement this system, confirmed by a quote from 23andMe.  If you’re thinking that makes no sense at all, you’re not alone.  Kind of reminds me of an alcoholic purchasing alcohol but claiming they have no intention of drinking it, a pedophile purchasing kiddie porn and claiming they have no intention of viewing it, a burglar caught with burglary tools and claiming they aren’t going to use them or maybe in a less sinister vein, a cat chasing a mouse and claiming they have no intention of catching it.  Yeah, right.

An article in Genetics in Medicine elaborates further.  This article explains how the designer baby process takes place.

“Taken out of “patentese,” what 23andMe is claiming is a method by which prospective donors of ova and/or sperm may be selected so as to increase the likelihood of producing a human baby with characteristics desired by the prospective parents, the selection being based on a computerized comparison of the genotypic data of the egg provider with that of the sperm provider.”

Clearly, very few people would have an issue with this technology if it were utilized to only deselect mixtures which would produce children with serious genetic diseases for at-risk couples.  However, utilizing this technique to produce designer children based on the whim of their parents could be another matter altogether, and to many people, crosses the murky line of what is and is not appropriate or acceptable, for whatever reason.  It’s not my intention here to debate the ethics of this technology or technique.  I can’t help but think, however, of the Chinese today who have a “one child policy,” only allowing one child per family which has led to sex selection in an attempt for families to assure that one child is a male.  Worse yet, I’m reminded of Hitler’s horrific genocide, the Holocaust, based on, in part, physical traits.

What does 23andMe themselves have to say about this?  On their May 28th 2012 blog, they announced their Parkinson’s patent.  In that announcement they stated that they “have a research arm with more than 20 scientists dedicated to making meaningful discoveries that will improve the lives of all of us.”

On October 1, 2013, their blog announced their second patent, the “designer baby” patent and states the following:

“Last week, 23andMe was awarded a patent for which we applied more than five years ago, and which relates to one of the tools we offer individuals as part of their genetic exploration. The tool — Family Traits Inheritance Calculator — offers an engaging way for you and your partner to see what kind of traits your child might inherit from you. The Family Trait Inheritance Calculator has also been part of our service since 2009 and is used by our customers as a fun way to look at such things as what eye color their child might have or if their child will be able to perceive bitter taste or be lactose intolerant. The tool offers people an enjoyable way to dip their toes into genetics.”

Here’s a look at 23andMe’s Family Inheritance Calculator.  The categories reported are bitter taste perception, lactose intolerance, earwax, eye color, muscle performance and alcohol flush reaction.  Certainly, this looks innocuous enough.

Utilizing a screen shot from two family members, the first column displays the child’s genes, the second, one parent’s, and the final column predicts the resulting outcome of that trait in the child.  In this case, the child has brown eyes, wet earwax, doesn’t run and has no alcohol flush reaction.

23andMefamilytraits

So if you’ve been dangling your toes in the water and thought you were just having fun, well, there might be something much more sinister under the water, depending on your perspective and your toes, well, they might just be bait.

The final paragraph in the Genetics in Medicine article sums this situation up quite well.

“What makes this case even more surprising is the fact that 23andMe is no stranger to controversy regarding its patenting activities. In the days following its May 2012 announcement on the company blog that it was to be granted a US patent for a test for propensity to develop Parkinson disease, the blog was filled with reactions of upset customers, the providers of the genetic and phenotypic data which constitutes 23andMe’s biobank. Since 23andMe is a commercial entity, clearly intended to bring profit to its investors at some stage at least, its attempts to seek patents are not surprising. Moreover, such attempts are not inherently problematic. However, for a company that invites audience participation, and so needs customers and their goodwill to maintain and expand its most valuable asset, i.e., its biobank, it is surprising that, following the uproar that greeted the announcement of its Parkinson disease patent, 23andMe has pursued this patent with no apparent public discussion. For instance, do the consumers who have also allowed 23andMe to use their genotypic data for the research conducted by the company agree with the use of their information for the purpose of developing a method for gamete donor selection? Public trust is central to the continuing success of human genetics research in general and biobank-based research in particular. We urge maximal transparency by all engaged in human genetics research.”

Customers are the Biobank

Herein lies the problem.  I’m one of those consumers and I had no idea whatsoever that this research was underway.  That makes it clandestine at worst and certainly not transparent at best.  My DNA, along with all of their other clients who constitute their “biobank” was used for this research which has now been patented in the form of “designer baby” technology.  I’m not going to say publicly whether I’m in favor of or opposed to designer babies, per se, but I’m going to say that I’m extremely uncomfortable discovering that this is what was being done with my DNA.  I’m not happy – really not happy.

When I purchased my DNA test at 23andMe, it was for genealogy, although I have clearly benefitted from the health traits aspects too.  I have been a willing participant in several surveys, including the ones about Parkinsons.  My mother had Parkinsons, at least we think she did, as Parkinsons is a diagnosis by excluding other possible diseases.  In other words, there is no test for Parkinson’s disease itself.  My thoughts of course when I’ve taken these surveys about diseases, traits and such is that the research would be utilized in identifying genetic sources and then perhaps treatments or drugs to cure those diseases.  I fully expected the treatments to be patented, but I did not expect the genetic aspects, or the genes themselves, to be patented.

In all fairness, I did give consent and I knew that their primary focus is and was medical research.  However, I didn’t expect they would utilize my DNA for this.  I trusted and had confidence in them.  Now I don’t.

Consenting for What?

Here’s a link to their consent form.  The first paragraph says “23andMe aims to make and support scientific discoveries and publish those discoveries in scientific journals.”  Hey, I’m good with that.  In fact, I applaud it.  A patent is not a scientific journal article.

Looking further, under item 5, under Benefits, it says, “23andMe may develop intellectual property, including but not limited to patents, copyrights and trademarks, and/or commercialize products or services, directly or indirectly, based on the results of this study, and in such cases you will not receive any compensation.”  I don’t quite understand how that is a benefit to me, at least not directly.  But it does say the word, patent.  It’s just that, well, I expected the patents to be related to disease cures, like cancer and Parkinsons and things like that, not designer babies.  Designer babies clearly have been a priority for them, and they have been working very quietly, too quietly, on this for a long time.  The patent was applied for in 2008.  Discussion about their Parkinsons research is all over their website, but not a peep about their designer baby research.  Why is that?

Recently, the Supreme Court struck down a similar patent on the Breast Cancer Genes.  This patent is different in that it doesn’t directly patent the genes themselves, but the gamete selection technique, as best I can tell.

Customer Options

What can I, as a consumer, do?  I’m very uncomfortable now with 23andMe and their priorities.  I feel that we as consumers, their customers, have been betrayed.  I feel that they have compromised their own integrity by focusing on designer babies for the wealthy who want to select eye color instead of on disease cures for the masses, which is what I expected would be done with my DNA.  I’m wondering what other things they are working on that I will find equally as objectionable.

This isn’t a debate about the ethics of designer babies, but a discussion about how my, and your, DNA is being utilized.

What can I do?  I still want the genealogy matching services, but I no longer want to participate in their medical research.  According to the consent form, customers do have an option to withdraw.  Here is what that says:

“Your alternative is not to participate in the 23andWe research study…If you choose not to give consent for 23andWe research, your Genetic & Self-Reported Information may still be used for other purposes, as described in our Privacy Statement.

At any time, you may choose to withdraw all or some of your Genetic & Self-Reported Information from 23andWe research by changing your consent status within the 23andMe “Settings” page or by sending a request to the Human Protections Administrator at hpa@23andme.com.  You will still be allowed full access to the Personal Genome Service®, but 23andMe will prevent the requested information from being used in new 23andWe research occurring after 30 days from receipt of your request. Any research on your data that has been performed or published prior to this date will not be reversed, undone, or withdrawn. Your Genetic & Self-Reported Information may still be used for other purposes as described in the 23andMe Privacy Statement.

Choosing not to give consent or withdrawing from 23andWe will not affect your access to your Genetic Information or to the Personal Genome Service®.

You may also discontinue participation by closing your Personal Genome Service® account, as described in the Terms of Service. Requests for account closure must be made in writing to 23andMe’s business address or via Customer Care.”

Hmm, it says that even if I withdraw, they can still use some information.   I did as they suggested, and consulted the Privacy Statement.  I’m not a lawyer, but this paragraph seems to suggest that regardless, they can use at least some of my information anyway.

They state: If you do not give your consent to participate in 23andWe Research, 23andMe may still use your Genetic and Self-Reported Information for purposes such as quality control or other R&D activities. Genetic and Self-Reported Information used for such purposes may be included in Aggregated Genetic and Self-Reported Information disclosed to third-party research partners who will not publish the information in a peer-reviewed scientific journal. Research partners may include commercial or non-profit organizations that conduct or support scientific/medical research or conduct or support the development of drugs or devices to diagnose, predict, or treat health conditions.”

So, the net-net of this seems to be that my only recourse if I really don’t want my DNA utilized is to close my account entirely – and even then, I’m not at all sure that they don’t retain my information and utilize it.  Maybe Judy Russell or Blaine Bettinger could provide a better legal review.

What I’m Doing

Let me tell you what I am going to do.

1.  I’m going to change my settings to prevent my DNA from being utilized in further research, and I’m not going to answer any more surveys until I feel much better about what 23andMe is doing, if ever.  In fact, I was going to show you how to do this too, if you’re interested.  However, after logging into 23andMe, the “settings” page is not in evidence since their last page reorganization, nor can it be found by searching, and neither is the “gear” that used to be the gateway to settings, so I will be e-mailing their Human Projects Administrator at hpa@23andMe.com.  This settings page required to withdraw should be obvious.

Edit – Update – The Settings Option is a dropdown from your name after you sign into 23andMe.  Then click on Privacy/Consent.

23andme settings

2.  Furthermore, I will no longer be recommending that people test at 23andMe without a very strong caveat and a link to this posting.

3.  I’ve removed their link from my blog sidebar.  Poof – gone.

What Do You Think?

I invite your input?  What do you think?  How do you feel?  What are you going to do?

______________________________________________________________

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

Why DNA Test?

puzzle pieces

Sometimes I receive a question that just stops me in my tracks.  This past week, when a very experienced genealogist ask me “Why do you guys DNA test anyway?,” I was so dumbstruck as to be almost speechless.  Well, almost, but not quite, and I recovered quickly.

I did manage to stifle the urge to say “because we can,” but there would have been some truth in that statement.

For me, DNA testing is just a fact of life, ingrained into every molecule of my being, so I had to think a bit before answering.

Why do we do this anyway???

  1. Because we can!  Ok, I just had to say it, to get it out of my system.  But in reality, it’s true, because you don’t know what you don’t know.  And it’s low hanging fruit.  For between $49 and $99, at Family Tree DNA you can take a multitude of tests, but primarily  Y DNA, mitochondrial DNA and autosomal.  And with that, you can find out what it is that you don’t know.  The story of “Finding Anne Marie” is the perfect example. In fact, it has been turned into a book.
  2. We test to discover if we are related paternally (Y-DNA) to others of the same or similar surnames.  This also means that we can eliminate researching any lines that you don’t match.  So we do it so we can stop barking up the wrong tree, and hopefully, bark up the right one.  This article about Triangulation for Y DNA talks about surname matching.  This paternal Y test was one of the first and is still probably the primary DNA genealogy test done today.
  3. We can test relationship theories.  For example, let’s say that we don’t know who the father of our ancestor is, but there are 4 male candidates, all brothers, in the county at the time our ancestor was born.  Certainly, being rabid genealogists, we’ve already done the genealogy work, like check tax records, census schedules, church records and anything local, but now we need big guns because those resources didn’t reveal parentage.   This story about the Perez family in Guam and in Hawaii illustrates this beautifully and uses both Y DNA in combination with autosomal.  In the case of the 4 brothers above, we can search for their wives surnames in our matches and see if we can identify which couple by using the wive’s lines’ DNA.
  4. We test to find out about our ancient ancestry.  What “clan” or haplogroup did we come from?  There are a number of tests we can take to discover if we are Native American, for example, or African.  Some tests, like the autosomal tests, look back only a few generations, so they are broad, not deep, and some, like the Y and mitochondrial tests are very deep, going back hundreds of generations, but not broad at all, focusing like a laser beam on only that one specific direct line.  This article about “Proving Native American Ancestry Using DNA” tells about the various kinds of tests and how they can help with genealogy.
  5. We test to create a DNA pedigree chart that parallels and integrates with our genealogy pedigree chart.  Every ancestor and their DNA has an ancient story to tell that would be silenced without DNA.  In essence, we recover ancestry otherwise lost to us. How else would you ever find out that you descend from Vikings or Niall of the 9 Hostages?
  6. We test to better understand our genesis.  For example, we want to map our chromosomes to know which one came from which ancestor.  Ok, maybe number 6 only applies to geeky genealogists – but there appear to be a lot of us out there.  Kitty Cooper’s new mapping tool is quite popular.
  7. We test to find our family.  Just today, I “met” a cousin I match autosomally  and we discovered that we have some of the same “coureur du bois” stories in our Acadian families.  The difference is that she knew what they were, and I didn’t.  Click – that’s the sound of a puzzle piece falling into place.
  8. Some people test to prove paternity, or find biological parents or siblings.  Over the past couple of years, several great adoption tools and groups have been formed as we’ve learned to work more effectively with autosomal DNA.
  9. We test because it’s fun.  It adds another dimension and several more tools to the addiction we love, genealogy.
  10. Some test to discover more about their health traits.  For some, this health information is just a side benefit, but you never know when that health information will have a profound influence on your life.
  11. Some people want to participate in scientific research.  This is probably not a primary reason to test, but it does motivate a lot of people and this is one field where an individual can still actively participate and make a difference, sometimes a huge difference.
  12. Some people, like Lenny Trujillo, want to leave a legacy and what a legacy he has left.  This is one of the most common reasons people order the Personalized DNA Reports.  In some cases, their DNA line ends with them, but in others, it’s a way of leaving information for future generations.  Many people have these reports bound and give them as family-wide gifts.
  13. We test because we want to find the location in Europe, or wherever “the old country” is for our family, that our immigrant ancestors came from.  The Speaks family is a great example.  The American group had tested and confirmed the DNA of the original immigrant, but we didn’t know where the Speaks family came from, although we believed they immigrated from England.  Another Speaks family member, from Australia, tested, and matched the American group.  The difference was that our Australian cousin knew exactly where his English ancestor was from.  Through DNA testing, we found the home of our Speaks family in Gisburn, Lancashire, England.  You can read about it in “The Speak Family – 3 Continents and a Dash of Luck.”
  14. We want to prove or disprove our oral history.  In many cases, that history includes some type of minority admixture.  By minority, I mean not our primary ethnicity.  In the series, “The Autosomal Me,” I described in agonizing detail how to use tiny bits of DNA to do just that, and to identify which family lines contributed that minority admixture.  In my case, both Native and African.  Native had always been a part of our family’s oral history, but the African was initially a surprise.
  15. We test because we’re curious about where we came from, who we are related to, what they know about our ancestors that we might not.  As I’ve said before, “It’s About the Journey.”  Inquiring minds want to know…..

And it all starts with a DNA test!

______________________________________________________________

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!!!

???????????????????????????????????????????????????????????????????????

______________________________________________________________

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

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

______________________________________________________________

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

The Autosomal Me – DNA Analysis – Splitting Up

DNA Analysis purchased 1-24-2013

This is Part 6 of a multi-part series.

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 this segment, Part 6, “DNA Analysis – Splitting Up” we’re going to focus on specific aspects of those tools and begin our analysis of our minority ancestry.

Analysis.  Sounds like I’m climbing on the shrink’s couch.  But I’m not, I’m saving all my dollars for DNA kits!  Besides, I don’t want to stop!  This analysis, we’ll do by putting several pieces of data together and sorting the wheat from the chaff.  And yes, we’ll be splitting up…well…splitting our DNA up into pieces contributed by our father and mother.

Let’s start with looking at the DNA segments that mother and I share that are Native.

According to Doug McDonald, we have significant Native matches on chromosomes 1 and 2, with third party tools confirm that finding.  Unfortunately, the only company where Mom’s DNA resides is Family Tree DNA whose test did not reveal the Native ancestry.  23andMe did confirm Native segments in my DNA in those locations.

I’ve used several third party tools at GedMatch to see where Mom and I both have Native heritage, where she has it and I don’t, and equally as important, where I have it and she doesn’t?  What is that so important?  Simple, it means my father had Native heritage too, and tells me on which chromosomes his Native DNA is located  This could, when matching people in the future, on particular segments, help to isolate who our common Native ancestor was, or at least which line.  That is the ultimate goal we are working towards with this entire process.

In this case, to identify my father’s Native lines, if Mom and I neither or both have Native markers at a particular chromosome location, the values are irrelevant, because the Native lineage came from mother.  I did notice in a few cases that I had more than mother, and of course, in that situation, it means that my father contributed some too, or my mother had a misread in that region or a categorization issue exists.  For that reason, I am looking for patterns, not single instances.  We’ll discuss using patterns in a future segment.

Using the MDLP chromosome mapping tool, as MDLP appears to be the most comprehensive, I created a spreadsheet using my results as a base.  I then added mother’s values in the spaces where I had no values, and then I highlighted my results in the locations where mother had no value.  The essence of this is that the red, bold, underscore values mean Mom had a Native result here, but I didn’t receive it.  A yellow highlighted cell means I got the entire amount from my father, because my mother has no percentage showing.  In other cases, of course, it’s possible that both mother and father contributed Native ancestry on some adjacent chromosome segments.  The MDLP mapping tool with my additions is shown below for chromosomes one through eight.  Chromosomes 9-22 are similar, but the chart is too big to display as a whole.  This provides an example of how to do this analysis with your own results.

MDLP Chromosome Map Table

The results were very interesting.

My two primary regions, North-East-Europe and Atlantic-Mediterranean-Neolithic, were represented on every chromosome for both my mother and myself.  No surprises there.  The other regions would be considered minority admixture.

In 2 categories, North-European-Mesolithic and East Siberian, only my father contributed genetic material on some chromosomes and there were no chromosomes where my mother alone contributed.

In 1 category, Melanesia, only my mother contributed genetic material on some chromosomes and there were no chromosomes where my father alone contributed.

In all other categories, both parents contributed on some chromosomes where the other didn’t.  This is important, because it will allow me to associate a match with a particular segment of a chromosome on a particular parent’s side with Native ancestry.

In the minority categories for Native American, Mesoamerican, Arctic-Amerind, South America Amerind and North Amerind, grouped together, both parents contributed on some chromosomes where the other didn’t, and in two categories, on 3 chromosomes, I carry more than my mother, indicating an additional contribution from my father.

This is a repeated occurrence, with Native ancestry for my parents and I combined showing on a total of 42 chromosome locations across 4 geographic/ethnic categories, and in at least three cases, both parents contributed.

In the African categories, South African, Sub-Saharan and Pygmy, I had contributions from both parents on a combined total of 18 chromosome segments.  The African admixture, in total, was less than the Native, and they are assuredly below 5% combined.  If they were present at higher levels, I wouldn’t need to go through these genetic gyrations to prove or disprove the heritage and which parent contributed, because it would be evident in the testing results of all companies.

In our next segment, Step 7, we will be further scrutinizing Chromosomes 1 and 2 for additional information about Native heritage and assigning specific Native segments that I carry on various chromosomes  to either my mother or father’s lineage.

______________________________________________________________

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

Personal Genetics – Coming out of the Closet – Ostriches, Eagles and Fear

Ostrich

While most of the people subscribing to this blog are here because of genetic genealogy, genetic genealogy is only one piece of the picture of the future of personal genetics.  Ironically, it’s genetic genealogy that gave low cost genetics a push into the mainstream, some 7 or 8 years before 23andMe, the first personal health genetics company, launched in 2006.

This week, the magazine, ieee Spectrum, of all places, has an absolutely wonderful article, The Gene Machine and Me, about the future of personal genetics.  Many of these types of articles are sensationalized and full of what I call “fear-mongering,” but this one is not only excellently written, it’s accurate and interesting – a triple hitter home run as far as I’m concerned.

I’d like to talk for just a minute or two about the high points in this article, about this emerging technology, what it means to us and about fear.  I’ll be sharing my personal journey down this path.

For those who would like to know how next-generation technology works – by the way – that’s the chip technology employed by Family Tree DNA for the Family Finder product, 23andMe for all of their testing and the National Geographic Geno 2.0 project – this article has a very educational description that is understandable by regular air-breathing humans.  The next-next generation sequencing, discussed here and offered shortly by Ion Torrent, will certainly revolutionize personal genetics much as the Illlumina genotyping chip technology has today.

The benefit of full genomic and exome sequencing, the new technology on the horizon for consumers, is in the information it will tell us about ourselves.  And I’m not referring to genealogy here, although that assuredly will be a big beneficiary of this new world of personal genetics.  For genealogists, there is mention of soon-to-be capabilities of sequencing from one single molecule of DNA.  For those of us with hair brushes and toothbrushes that we’ve been jealously guarding for years now, waiting for the technology to improve to the point where we can obtain the DNA of our dearly departed loved ones, this is going to be our ticket.  As excited as I am about that, that’s not the potential I’m talking about.  I’m talking about information about our own bodies and the potential future foretold in those genes.  Notice the word potential.

The information in our genes is seldom a death sentence.  In rare cases, it is, such as Huntington’s Disease.  If this disease runs in your family, you already know it and testing should be done in conjunction with genetic and/or medical counseling.  For these people, DNA testing will either confirm that they carry that gene, or relieve their mind that they do not.

For the vast majority of us, the information held in our genes it much less dire.  In fact, it’s a good news message, as it will provide us ample warning, an opportunity, to do something differently with our lives to prevent what might otherwise occur.  So it’s not a death sentence, more of a life sentence.  For me, it was an epiphany.  Yes, I took positive action and made dramatic life changes as a result of my DNA test results.  In essence, this is my “coming out” story.

I was one of the first people to order the new 23andMe test when it was first offered, mostly for the genealogy aspect, but as you know, it includes health traits and information.  When I received the results of that test a few years ago, in black and white, where I could not possibly ignore them, the reports indicated that I was at elevated risk for certain conditions.  Those conditions were certainly beginning to manifest themselves in my life.  I was on medication for two of them.  My weight, at the time, was certainly a contributing factor to the development of those conditions.  My sister had died near the age I am now as a result of those conditions.  She looked like me, was built like me, was heavy like me, and very probably carried those exact same genetic risk factors.  Our grandfather died of the same thing about the same age.  Our father had it too, but he died in a car accident – caused by a coronary episode, at age 61.  Seeing this, in black and white, and knowing my family history, I decided to do something to prevent that future, or at least to delay or mitigate it as much as possible.

I lost over 100 pounds and yes, for almost 5 years now, I’ve maintained that weight loss, well except for a pesky 10 or 15 pounds that I fight with regularly.  But still, the 100 pound loss is far more important than the 10-15 pounds I battle with.  I am off of all medication related to those and related conditions.  I’ve changed what and how I eat, and a benefit I really didn’t anticipate is how much better I feel.  You have no idea how much I hate these old pictures of me when I was heavy.  This was taken at National Geographic Headquarters in Washington DC, in 2005, at our DNA Conference.

Me Nat Geo 2005

This next photo is me at one of our Lost Colony archaeology digs about five years later wearing one of my favorite t-shirts that says “Well Behaved Women Seldom Make History.”  All of the genealogists should be laughing about now.  No one wants well-behaved women because you can’t find them in the records.  If my clothes look a bit large, that’s because they are, but that t-shirt was too small before the weight loss.  I could never have done the physical work on those digs, or survived the heat, before losing the weight and going from a size 22 to a 12 in the photo below.  These kinds of activities were all unforeseen benefits of the weight loss.  My sister’s untimely death was not wasted on me, but served as a warning bell, well, more of an unrelenting siren actually, when I saw those DNA results.

???????????????????????????????

I also took my 23andMe results, at least some of them, the ones related to the conditions I was dealing with, to my physician.  I really had to think long and hard about this.  So now, let’s talk about the fear part of the equation.

Fear of genetic results falls pretty much into two categories.  We’ll call these the Ostriches and the Eagles.

My brother was an Ostrich.  Yep, he was, head right in the sand.  He had cancer, his wife had cancer, twice, his daughter, in her 30s, had cancer, yet their decision when offered free DNA testing was to decline – because they didn’t want to know.  Fear of the information itself, fear of knowing, perhaps spurred because of a sense of fate – nothing we can do about it so why know about it.  He also refused to discuss it, so I really can’t tell you why, and he died, of cancer, last year, so that opportunity is past.  Personally, I think knowing about a genetic proclivity would equate to more vigilant monitoring.  And knowing the proclivity didn’t exist would set one’s mind at ease.  I would think you would be a winner either way, but my thinking and his were obviously quite different.

The other group are the Eagles.  They are vigilant and acutely aware of the fact that health based discrimination does exist.  It has been worse in the past than it is now.  This is the reason I had to think long and hard about taking any of my results to my physician.  Once in your medical record, it’s permanent.

Today, GINA, the Genetics Information Nondiscrimination Act, goes a long way to protecting people, especially in an employment situation, but it does not cover everything.

Anyone who has ever tried to obtain health care insurance individually or through a small business knows all too painfully about pre-existing condition exclusions.  Well, the good news is that ObamaCare, love it or hate it, levels that playing field for the “rest of us,” those who either were denied or had to make life and employment decisions based on whether or not they had insurance coverage through a group where discrimination related to pre-existing conditions didn’t exist.

The other good news is that you don’t have to take any of your DNA test results to your doctor.  It’s entirely up to you.  You can test anonymously, using an alias, if you’re really paranoid.  Your results through personal genetic testing are yours and for no one else to see unless you disclose them.

Lastly, let’s talk realistically about the types of insurance that still discriminate – which would be life insurance, extended care insurance, etc.  They are in the business of odds-making.  They are betting you will live and you are betting you will die sooner than later.  As you age, the odds shift, cause let’s face it, eventually, you will die – and they will have to pay out.  Now the only way they can make money is if you pay more premiums during your life than they have to pay out in the end, or they make the premiums so expensive you stop paying, letting the policy lapse, before you die, so they never have to pay.  Of course, if they think the odds are stacked too far in your favor, they simply won’t insure you.  So, if you or your family members have Huntington’s Disease, you’re not likely to be able to get life insurance outside of a group policy, with or without a genetic test.  In fact, there is a questionnaire about your family history when you apply for individual life insurance.

I bought individual life insurance about 10 years ago.  They sent a nurse to the house to draw my blood.  They wanted chain of custody, to know the blood sample was mine, which is not the case with personal DNA testing.  I had to provide ID.  If the insurance company wanted to run a DNA test, prohibitively expensive then, but not in the next few years, they certainly could do so.  Let’s just say it plain and simple – everyone has pre-existing genetic proclivities to something – no one is immune.  These results are not generally black or white either, but expressed as a range.  For example, 4.2 European women out of 100 will develop Restless Leg Syndrome in thier lifetime.  My risk is 5.2, so slightly elevated above the average.  I’m only “above average” in 5 areas, and below average in most.  And the insurance companies are still going to be in the odds-making business – they can’t deny everyone or they won’t have any business – and they will use this new tool as soon as it becomes economically viable.  There is no escaping it.

So yes, the Eagles are right to watch vigilantly – but for now – how much you share and with whom is entirely in your control, so you don’t need to be an Ostrich either.  There is a great deal of good that can come from personal genetic testing, in addition to genetic genealogy.  Knowledge is power.

So now, if you haven’t already, read this great article, The Gene Machine and Me!!!

______________________________________________________________

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

The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools

This is Part 5 of a series.

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 this segment, Part 5, we’re going to look at various third party tools and what they can do for our search for minority admixture.  We will use the download files from either 23andMe and Family Tree DNA and utilize third party tools to analyze the raw data.  We’ll see how third party developers put those puzzle pieces together, if the results are consistent and what they tell us.

The Weeds

When dealing with testing companies, particularly any individual source (as opposed to multiple testing company results, as I have done), minority admixture, especially less than 1% may not be successfully recognized.  One percent equates to between 6 and 7 generations or about to the 1800 threshold in time.  However the history of both African and Native admixture in colonial America goes back another 200 years to the Jamestown era.

The social history in the US means that there are many people looking for this admixed heritage as long ago as 1609 when Jamestown was established and the first European/Native marriages took place (although there were “blonde Indians” reported by Jamestown settlers).  In round numbers, that’s about 400 years or between 13 and 16 generations.  Of course, a minority ancestor drops below the 1% threshold between 7 and 8 generations (with the first generation being the person tested) and by the time you get to the 12th generation, you’re at .048%.  At this level, Bennett Greenspan says we’re “rooting around in the weeds,” and he’s right.

However, rooting around in the weeds for those dreaded IBS (Identical by State) segments in genealogy is exactly what we need when looking for small amounts of minority admixture.  What’s an IBS segment you ask?  It’s a segment that is typically too small to be counted as an IBD, or identical by descent, segment.  IBS means that you’re from a common population if you match someone with a very small segment, not necessarily that you share a common ancestor within the past several generations.  But how to you tell if a small segment is IBS or IBD?

There is no absolute line in the sand, but often segments smaller than 7cM (centimorgans) or 700 SNPS (some say 5cM and 500 SNPs) fall into the IBS category.  This has caused some researchers to discard all segments of this size because they can’t tell the difference.  That’s unfortunate, because clearly some of these segments are IBD and the IBS segments can be useful too.

When looking for minority admixture in two people, both of them having these small segments in the same location can provide meaningful information, and can confirm minority heritage.  Said another way, if two people have less than 1% Native heritage, both share a common ancestor, and both carry part of their “less than 1%” on the same segment….one might say it’s not likely to be coincidence.  Identifying the common segments of your common ancestor can lead to identifying the specific family line those segments came from, especially if you match others as well.  This is in essence what Minority Admixture Mapping, or MAP, does.  It uses these techniques to look for patterns in these small fragmented pieces that, when taken together, indicate minority heritage.  Having said that, some IBS segments will indeed, be simply that, because you share the same base population, but some will be IBD, or more current in time.  With the MAP technique, we’re sorting through ways to utilize these small segments, whether they are IBS or IBD.

Using the tools, MDLP, Eurogenes, Dodecad and HarrappaWorld at GedMatch allows us to “root around in the weeds,” to quote Bennett, and find those all-important small IBS/IBD segments that connect us to a particular ethnicity and ultimately, to other relatives who carry these same segments in the same locations.

In general, using these this type of DNA is called BGA, or Biogeographical Ancestry where we use SNPs of autosomal DNA called AIMs, Ancestry Informative Markers.  A SNP is a Single Nucleotide Polymorphism, or a mutation that happened in one specific location on a gene.  AIMs are generally SNPs, not clusters of markers, found at different frequencies in different populations.  We combine all we know about them scientifically with information about population frequencies and then draw inferences about where our ancestors came from based on that information.  So a SNP that is useful in determining ancestry is called an AIM.

These SNPs, or AIMs, are the foundation for these BGA tools that we will be using to sort through small segments of minority admixture.  So this is a building block process.  Scientists identify SNPs found in different populations at different frequencies and identify them as such, then scientists and genetic genealogists create BGA tools that use and combine SNPs/AIMs to suggest populations and ethnicities for those who carry them.  Using these tools, majority ancestry is easy to discern.  We’re going to use those tools to look at groups of SNPs/AIMs clustered in small, fragmented IBS or IBD segments to do Minority Admixture Mapping (MAP) to confirm our minority admixture and to identify our minority admixed lines, families and perhaps even (in time) our original minority ancestor.

I bet you thought I couldn’t fit all of those acronyms in one paragraph, but I did:)  It is a bit like alphabet soup, but when you understand that this is a building process, it’s much easier to grasp as a whole.

Having at least one parents DNA makes this process much easier, because you can immediately tell if your other parent, by inferrence or process of elimination, has contributed any of the minority ancestry, or if it’s all on one side of the tree.  Of course, that’s assuming your parents aren’t related to each other.  There’s a test for that too at GedMatch.  If you don’t have one parent available, you can “make do” with aunts, uncles and cousins, but it’s a much more tedious process.

Third Party Tools

To use any of these BGA tools, you’ll need to download your results from either 23andMe, Family Tree DNA or National Geographic.  Currently at GedMatch, the only supported formats are 23andMe or Family Tree DNA, because the National Geographic test is so new.  I used my Family Finder (Illumina Build 36) raw data file.

To download your results from 23andMe, sign on to your account, then click on this link and it will take you to the area to download your results.

https://www.23andme.com/you/explorer/

Save the file and do not open it as the act of opening it sometimes causes corruption and you will have a hard time uploading the file.  If the upload fails, download a new copy and start over.  If you have an older copy on your computer, it’s always a good idea to use a fresh copy to incorporate any changes made by the vendor since your last file download.

To download your results from Family Tree DNA, sign on to your personal page, click on the Family Finder tab and then on “Download Raw Data.”  As I write this, Family Tree DNA is in the midst of a conversion from Build 36 to Build 37 for their autosomal files (in order to facilitate the integration of 23andMe results), so you may need to be a bit patient while this process completes.  Files may not be available for download at some points.  You certainly don’t want to mix comparisons, meaning using one build 36 and one build 37 file for comparison.

If you’re following this process yourself with your own data, please read all the way through this posting before starting your own processing.

Now, let’s look at the third party tools.

Stanford University

This tool is available at Stanford University.  Scientists have collaborated to provide this service and I think it’s quite interesting.  This tool is not compatible with any browser except Chrome and it requires a download of your autosomal data in a .txt file.  If it can’t load your file, the loading task simply never completes.  For me, that meant it wasn’t a .txt file I was trying to load.

http://esquilax.stanford.edu/

Load your file and choose Ancestry, then Paintings, then Hap Map 3 (experimental), then Paint my Chromosomes.

weeds 1

Their legend, above, translates to the regions, below.

ASW – African ancestry in Southwest USA

CHD – Chinese in Metropolitan Denver, Colorado

GIH – Gujarati Indians in Houston, Texas

LWK – Luhya in Webuye, Kenya

MEX – Mexican Ancestry in Los Angeles

TSI – Toscani in Italia

weeds2

Unfortunately, this isn’t terribly useful.  Hap Map 3 utilizes additional regions, including Utah, but this tool doesn’t seem to be mapping them, so my closest match region is Italy, which is midleading since none of my family was from Italy.  Hap Map 2 is also an option which does include the Utah population, but it’s not as up to date otherwise as Hap Map 3.

David Pike has figured out how to tweak these settings some.  You can read about it at this link:  https://www.23andme.com/you/community/thread/8062/.  David’s posting on June 20th shows what he did.  However, compared to the other tools available, I find this a poor choice and did not spend a lot of time trying to work with it.

However, a second feature that they provide is fun.

Stanford provides a Neanderthal tool that’s a little different than the Nat Geo or 23andMe ones.  Click on Explore, Neanderthal, Look Up Exercise.  Then enter your primary ethnicity and click on Look Up Exercise again.

Of a possible 84 Neanderthal alleles, I have 9, partially displayed below.

weeds3

GedMatch

www.Gedmatch.com is a complimentary (voluntary contribution) site created by two genetic genealogists that includes several autosomal analysis tools.  One of the areas of this site is “Admix Tools.”  On that page one finds several private or proprietary tools, some written by genetic genealogists, some by researchers, and all free.  Let’s take a look at each one and their results.  If you want to see any of the results more closely than the photos here allow, you can run each of the comparisons using kit F6656 (mine) as the first kit and kit F9141 (my mother) as the second kit.

Each of these tools offers the same functionality, as follows.

weeds 4

We will be utilizing 4 of these functions for each tool.

  • Admixture Proportions
  • Admixture Proportions by Chromosome
  • Chromosome Painting
  • Paint Differences between 2 kits, 1 chromosome

We select from the tools as follows:

weeds 5

Let’s take a look at what the tools provide.

MDLP World 22

The MDLP software is sponsored by two genetic genealogists.  You can read more about the project at http://magnusducatus.blogspot.com/ and http://magnusducatus.blogspot.com/2012/09/behind-curtains-mdlp-world-22-showcase.html.

weeds 6

MDLP shows several populations.  I was interested to see if my mother also shared the African percentage.  Interestingly, mother does have a South African segment, but it’s .12, so less than mine.  Therefore, I would have obtained part of my African heritage from my father.  She also has three different categories of Native American heritage, compared to my one.  She carried a total of 1.92% and I carry .58%.  Otherwise, our results are very similar.

weeds 7

The next feature is ethnicity mapping by chromosome.  While the display is too large to see well it’s interesting to note that indeed, both Native American and African were detected on several chromosomes, not just on chromosomes 1 and 2 as reported by 23andMe and Dr. McDonald.  Note that DeCode Genetics showed “East Asian” admixture on several chromosomes.

weeds 8

Here’s a portion of the above chart that you can actually see.  The highlighted blue regions are your major ethnic regions.

weeds 9

Another feature is chromosome painting, shown below.  This shows the first part of my chromosomes 1 and 2 painted by ethnic/regional breakdown.  The legend for each tool is different and above their graph.

weeds 10

weeds 11

These tools also provide the ability to compare one chromosome between two people.  On the graph below, my chromosome 1 is on the top, and my mother’s is second, with the third band being our common painting.  The black represents non-shared regions, meaning those contributed to me by my father.  Unfortunately, North American Native American is dark grey, sometimes difficult to distinguish from black.

weeds 12

The graph below shows that while I do share a large piece of Chromosome 1’s Native region (about 160-180mb) with my mother, there are also segments, 169-170 for example, where I have Native genes that she does not, indicating Native heritage in this location from my father’s side.

weeds 13

Eurogenes K9

Eurogenes was created by another genetic genealogist.  You can read more about it at http://bga101.blogspot.com.au/2012/04/eurogenes-admixture-utilities-at.html.

weeds 14

Eurogenes calls me primarily North European with .67 Native American and no African in the percentages above, but below, on the individual chromosomes, some African does show, although not on as many chromosomes as MDLP.

weeds 15

In the charts above and below, you can see that Eurogenes detected small amounts of African along with Native American.

weeds 16

weeds 17

Notice that at about 10mb on chromosome 1, on the graph below in the top band, that the North American Indian (yellow) and the South Asian (red) are imbedded with each other.  These appear again together at the beginning of chromosome 2, shown as the second band.  This hints at how and why it’s sometimes so difficult to determine and filter Native American from Asian.  There is no line in the sand, there is a continuum between populations, the only differentiator being 10,000 to 15,000 years spent apart in which time, they, hopefully, developed enough differentiating mutations that we can tell them apart.

weeds 18

On the chart below, the top band shows the chromosome painting of my chromosome, and the second band shows the chromosome 1 Native American segment (about 160-180 mb) of my mother with the third band showing both matching and non-matching regions, painted black.  Looking at the segment of chromosome 1, in the graph below, characerized as Native, we can see in mine, top row, that this is categorized as Native American (yellow), but some of the same regions below, in Moms are categorized as South Asian (red), causing a technical non-match, when in reality, It’s likely a categorization issue, not a genetic mismatch.  In future analysis, we’ll be using two methods of comparison, one called “Strong Native” that only matches Native to Native and another, the “Blended Asian” method that allows for grouping of similar ancestral types that together likely indicate a Native heritage.

weeds 19

Dodecad V3

Dodecad was created by an anthropologist.  You can read more about it at http://dodecad.blogspot.com/ and http://dodecad.blogspot.com/2011/06/design-of-dodecad-v3.html.

weeds 20

Dodecad, unfortunately, does not subdivide into Native American, so the Native will show here as some form of Asian.  Northwest Africa shows in the percentages above, but more detailed African heritage shows in the chromosome detail below in regions not shown above.

weeds 21

weeds 22

weeds 23

weeds 24

Above, my chromosome painting for the first part of chromosomes 1 and 2.

Below, the comparison showing the Native segments from about 160-180mb.   My Native segment (top) compared to mother’s (middle) with the comparison of the two on the bottom for chromosome 1.

weeds 25

HarappaWorld

HarappaWorld divides results into fewer population groups and is focused on Asia.  You can read more about it at http://www.harappadna.org/2012/05/diy-harappaworld/.

weeds 26

In HarrappaWorld, Beringian and American appear to be equivalent to Native American.  Like Dodecad and Eurogenes, African does not show in the total percentages, but does on the individual chromosome analysis, although in smaller percentages with this application.

weeds 27

weeds 28

weeds 29

Chromosome painting of my chromosomes 1 and 2 are shown below.

weeds 30

The graphs below show the Native region comparison of chromosome 1 between me, top row, mother, middle row, and the third graph showing the common areas, with black representing areas where there is no match.

weeds 31

For each of these tools and their results, we’ll do further analysis in a future segment of this series.

Tools Summary

Now that we’ve looked at these individual tools,  and building on the Test Results Chart created in Parts 3 and 4, let’s compare and see what information these tools add.

Test Results Chart Including Third Party Tools

Test/Company European Asian Native African Unknown
Pedigree Analysis

75%

0

~1%

0

24%

Testing Companies
Family Tree   DNA – Original

100%[1]

0

0

0

deCodeme

92%

5%

Inferred[2]

3%

deCodeme –   X

91%

6%

Inferred

3%

Dr.   McDonald

97-99%

1-3%

0.5%

0

23andMe –   Original

99%

1%

Inferred[3]

0

0

23andMe –   2012 – Standard

99.2%[4]

0

.5%

0

.3%

23andMe –   2012 – Conservative

98.7%[5]

0

.3%

0

1%

23andMe –   2012 – Speculative

99.3%[6]

0

.5%

0

.2%

Family Tree   DNA – 2012

100%[7]

Geno 2.0

79%[8]

18%

0

0

0

Ancestry

92%[9]

0

0

0

8%

Third Party Tools
MDLP

86.68%

12.55%

.58%

.17%

0

Eurogenes

94.83%

4.5%

.67%

0

0

Dodecad

85.47%

13.43%

Inferred

1.09%

0

HarrappaWorld

86.56%

12.80%

.65%

0

0

Of the various chromosomes, the breakdown is as follows. Dodecad does not break the categories in a comparable fashion to these other 3 tools, so their results are omitted in the following chart.  Please note that how geographies are categorized can make a significant difference.

Minority by Chromosome Chart

Tool/Chr MDLP Native Eurogenes Native Harrappa Native MDLP African Eurogenes African Harrappa African
1 Y Y Y N N N
2 Y Y Y Y Y N
3 N N N Y Y N
4 Y N Y N N N
5 N N N N N N
6 Y Y Y Y N N
7 N N Y N N N
8 Y Y Y Y N Y
9 Y N N Y N N
10 Y N N Y N N
11 Y N Y Y N N
12 Y N Y N N N
13 Y N Y N N N
14 Y Y Y Y N N
15 Y N N N N Y
16 Y Y Y Y N N
17 Y Y Y N N N
18 N N N N N N
19 Y Y Y Y N N
20 Y Y Y Y N N
21 Y N Y N N N
22 N N N Y Y N

From these various tools, it’s obvious that I do have some Native admixture, probably about 1%, and it’s from both parents.  I also have some African, but it looks to be an even smaller proportion that Native American.

Join me for Part 6 of this series, where we look at how to analyze and use this information.


[1] 71.5% western European, 28.4% Northeastern European

[2] Inferred that Asian is actually Native in an American with no history of Asian ancestry.

[3] No category, inferred.

[4] 78.6% Northern European, 1.8% Southern European, 18.7% Nonspecific European

[5] 54.6% Northern European, .3% Southern European, 43% Nonspecific European

[6] 91.7% Northern European, 3% Southern European, 3.3% Nonspecific European

[7] 75.18% West Europe (French and Orcadian), 24.82 Europe (Romanian, Russian, Tuscan and Finnish).  Note that my mother’s results are almost identical except the Finnish is missing from hers.

[8] 43% North Europe and 36% Mediterranean

[9] 80% British, 12% Scandinavian

______________________________________________________________

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

The Autosomal Me – Testing Company Results

This is Part 4 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 2 gave an example of the power of fragmented chromosomal mapping and the raw beauty of the results.  Part 3, “The Autosomal Me – Who Am I?,” discussed how to use our pedigree charts to gauge expected results and how autosomal results are grouped into population buckets.  We also named this technique, Minority Admixture Mapping, or MAP for short.

In this segment, Part 4, let’s take a look at what the testing company autosomal results look like.  The results are presented in timeline order, with the oldest results first and the latest, and presumably most accurate results, last.

23andMe Version 1

23andMe was the first company to offer this type of testing affordably.  They initially only offered 3 population groups, and one inferred that Asian was actually Native American.  Of course, that wasn’t a valid assumption for everyone, but it was the best that could be done under the circumstances.  This was my ethnicity results display at 23andMe until December 2012 went their updated version was released.

Autosomal test 1

DeCode Genetics

DeCode Genetics initially offered autosomal tests for ancestry.  Unfortunately, under the pressure of financial issues, they stepped away from the genetic genealogy marketspace and have since been sold.

Their test showed the following ethnic breakdown, picking up both my Native and African heritage:

autosomal test 2

I particularly like these results because the X chromosome is included, and seeing Native on the X chromosome, which has a unique inheritance path is a very important piece of data.

Family Tree DNA Version 1

Family Tree DNA’s first version of their Family Finder product produced results stating that I am 100% European, split between western and northern, shown below (minus the map.)

autosomal test 3

Dr. Doug McDonald

Doug McDonald, a retired physical chemistry professor, compiles contributed raw data and compares the raw data locations with both reference populations and the contributor results.  This is not a commercial endeavor but a private research project which has been ongoing for years.  His analysis of my raw data results from 23andMe and Family Tree DNA showed that they are primarily European.  His first analysis was without Middle Eastern populations and the results showed European except for a total of about 3% East Asian, Oceana and American.   However, in a second run including the Pakistan and Middle Eastern populations, the results now showed 88% European, about 1% Oceanic and American and the balance Middle Eastern and Pakistani.

A small amount of Middle Eastern heritage is not unexpected since I do have confirmed Turkish ancestors.

Dr. McDonald indicated that this was slightly more, 1-2%, than most Europeans, and that I was generally planted firmly in the middle of the “English” area in his data.  His results showed no African.

Standard deviation (statistical noise) is about 1%.  He can achieve these low deviation numbers by using such a large number of markers (536,904 to be exact)[1] for his comparison.  I am grateful to Dr. McDonald for his contribution, not only to me, but to this field.

The graph below shows that my primary ancestry falls in the English/French region.

autosomal test 4

The second graph maps these results on my chromosomes. The American, bright green, is found on chromosomes 1 and 2, and the X chromosome shows South Asian.

autosomal test 5

Doug indicates that the Native American is found at about the .5% level.  Interestingly, on my mother’s graphs and charts (below), the Native segments are nearly identical, but my first grey South Asian segment on my X is Mideast on her chart.

autosomal test 6

It’s also interesting to note that my Native American on chromosome 2 is larger than my mother’s which may well reflect Native heritage on my father’s side.  Ironically, the oral history of Native ancestry was on my father’s side, not my mothers.

Doug’s analysis has been updated several times over the years and these results are the most current.  The vendors have made upgrades too.  In 2012, both 23andMe and Family Tree DNA underwent upgrades to their ethnicity software and the Genographic Project version 2.0 test was released.

23andMe 2012 Updated Version

The new 23andMe software offers different confidence levels.

The standard estimate, or confidence level, shows that I have about .5% Native American.  This is consistent with Dr. McDonald’s findings.

autosomal test 7

A second view is available which paints the chromosomes.  A split view is also available if one of your parents has been tested at 23andMe as well.  That is not an option for me.

autosomal test 8

The conservative estimate, below, shows less Native at .2%.

autosomal test 9

The speculative level below shows the Native back to .5% but adjusts the European regions significantly.

autosomal test 10

Although 23andMe does not provide participants with the start and stop locations, through alternative means, meaning a very smart friend, Rebekah Canada, who is a Java programmer, start and stop locations can be discerned.

CeCe Moore documented Rebekah’s technique for those who will be following along with their own results through this process.

In a future segment of this series, we’ll look at alternative ways to discern Native segments.  Thanks to Rebekah’s technique, I can tell you that 23andMe shows my Native segments as follows:

Chromosome 1 – 165,658,091 to 175,711,116

Chromosome 2 – 86,316,174 to103,145,426

23andMe also provides a Neanderthal percentage.  What fun!!!

autosomal test 11

Family Tree DNA Updated 2012 Version

My mother was deceased before chip based autosomal testing was available, but I ordered the Family Finder test for her as soon as it was available.  Thankfully her DNA was stored at Family Tree DNA and was still viable.

autosomal test 12

Mother’s original results are shown above and her most recent results are shown below.  Her results shifted within Europe and her margin of error doubled.

autosomal test 13

My current results from Family Tree DNA’s updated software are shown below.

 autosomal test 14

National Geographic Genographic 2.0

I was very surprised to see my National Geographic results.  They were very unexpected, in particular the high percentages of Mediterranean and Southwest Asian, totaling 54%.

autosomal test 15

It made more sense when I read the information.  It’s true, reading is fundamental.

autosomal test 16

These results are, in essence, more anthropological in nature.

autosomal test 17

autosomal test 18

Of course, one of the fun parts of the Genographic results are the Neanderthal and Denisovan percentages.

autosomal test 19

These are somewhat different than the 23andMe results, although if you add the Neanderthal and Denisovan values together, the resultant 2.2% is very close to 23andMe’s 2.5%.

Ancestry.com

In 2012, Ancestry introduced an autosomal DNA test as well.  What it provides is very limited, with limited tools, but it does provide percentages of ethnicity in addition to matches.  Recently, Ancestry announced that the percentages may change over time.  They have been severely beaten within the genetic genealogy community for quality issues with this product, including percentages of ethnicity that are highly erroneous.  Their stated time reference is 500 years ago.

Recently this new page was added before you can see your detailed results.

autosomal test 20

Ancestry shows my heritage as only British and Scandinavian.

autosomal test 21

Ironically, Ancestry has mapped the birth locations of my ancestors in Europe on the map above, based on my family tree submitted.  Interesting that Germany doesn’t show in Ancestry’s ethnicity list but many of my family lines originated in Germany and Holland, and none in Scandinavia.

Testing Provider Summary

Where do we stand now?

A summary of the various test results is shown below compared to my pedigree analysis.

Test Results Chart

autosomal test 22

I have included Dr. McDonald’s analysis here, not because he’s a testing provider in the sense of the testing companies, but because his offering was available in this timeframe, and because he worked with Family Tree DNA to develop their Population Finder code.

You can see that the results are relatively consistent between testing companies.  There is certainly no question about majority ancestry, but the minority admixture which hovers someplace near 1%, give or take 5% in either direction, is much less consistent and not always reported.  If I were to have tested with only one company and taken the results as gospel, I could certainly have been left believing that I had no Native or African admixture.  For many people, it’s this small amount of minority admixture that they are seeking.  So in answer to the question of which testing company is “best,” the answer is, if you’re looking for trace amounts of anything, the compendium of all the testing companies (minus Ancestry) would provide the best set of results.  We will be using the match information as well in the next sections, so certainly nothing has been “wasted” testing with multiple companies, again, except Ancestry.  I am hopeful that Ancestry will in the future release our raw data (which they have promised to do) in a useable format, fix their misleading ethnicity results and add chromosome painting tools so that we can fully utilize our data.

In Part 5 of the series, we’ll take a look at third party tools and how they can continue to refine and add to our knowledge of our admixture.


1.  Genealogy-DNA Rootsweb posting by Doug McDonald on 7-26-09 and personal correspondence.

2.  71.5% western European, 28.4% Northeastern European

3.  Inferred that Asian is actually Native in an American with no history of Asian ancestry.

4.  No category, inferred.

5.  78.6% Northern European, 1.8% Southern European, 18.7% Nonspecific European

6.  54.6% Northern European, .3% Southern European, 43% Nonspecific European

7.  91.7% Northern European, 3% Southern European, 3.3% Nonspecific European

8.  75.18% West Europe (French and Orcadian), 24.82 Europe (Romanian, Russian, Tuscan and Finnish).  Note that my mother’s results are almost identical except the Finnish is missing from hers.

9.  43% North Europe and 36% Mediterranean

10.  80% British, 12% Scandinavian

______________________________________________________________

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

Thick Hair, Small Boobs, Shovel Shaped Teeth and More

Yep, there’s a gene for these traits, and more.  The same gene, named EDAR (short for Ectodysplasin receptor EDARV370A), it turns out, also confers more sweat glands and distinctive teeth and is found in the majority of East Asian people.

This is one of the results of the National Geographic’s Genographic project.  This mutation found at location rs3827760 on chromosome 2 occurred about 35,000 years ago.  It apparently has conferred some advantage to its carriers, because it is found in the majority of Asian people today.  We don’t exactly know why that happened, but maybe ancient male Asians preferred thick haired, small boobed and sweaty women.  Or maybe those women survived when women with more body fat (yes, boobs are fat, sorry guys) and who could sweat less perished.

This New York Times article discusses the experiments performed to verify that this gene in fact does confer those traits.  The scientific article itself is available in the journal, Cell although it’s behind a paywall.

Want to know if you carry this trait?  If you’ve tested with either Family Tree DNA or 23andMe, you’re in luck.

Download your raw results file and open the file using any tool.  Generally, a spreadsheet or Notepad will be your preferred methods.  Then using the search function of the tool you’ve selected (ctl+f for Notepad or Excel’s find function) search for rs3827760.  You will see two letters comprised of either T, A, C or G.  If you have a G shown for either letter at this location, then you carry this particular mutation.

If you carry this mutation, you’ve probably already headed for the mirror.  You’ll know already if you have small breasts, if you’re a female, believe me.  You may never have thought about thick hair shafts, which isn’t to be confused with lots of hair.  And your level of sweatiness is just what it is.  I’ve never even considered that there were different sweatiness levels.  But what about Asian teeth?  Well, that trait is called sinodonty and here’s a nice wiki article and another nice article, with examples, here.  If your teeth are shovel shaped, meaning the backs of your upper 4 teeth are shaped like a spoon as opposed to straight, then you have this trait.

Asian teeth

So are you wondering what this might have to do with genetic genealogy?  Well, if you carry this gene, then you obtained it from some Asian ancestor.  If you’re in America and not of Asian ancestry, then there are pretty much only two routes.  One would be Native American ancestry and the second would be the population or invasion of Europe by Asian groups, such as the Mongol Hordes and the Huns.  Your genealogy will have to be your guide as to which source contributed this gene to your ancestors, and ultimately to you.

Oh yes, and one last thing, this mutation isn’t the only one involved in at least some of these traits, specifically the teeth.  I don’t carry the G and I do have some of the Asian teeth characteristics.  I don’t have thick hair shafts which makes sense since EDAR is primarily associated with this trait.  And, well, I’m just not discussing the boobs and sweaty traits (and my husband is utterly forbidden to comment)…..TMI:)

______________________________________________________________

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

The Autosomal Me – Unraveling Minority Admixture

haystack

You’re invited to come along with me on a journey.  It’s an epic event, a journey into the deepest recesses of our cells, into the smallest pieces of our DNA, into the part previously thought to be useless because it’s so tiny.  It’s the journey to find minority admixture.  Minority in this case means small amounts of admixture.  In my personal situation, this means both Native American and African.

People who have larger amounts of admixture don’t necessarily have to do this, although it can still provide useful information.  If your autosomal percentages are uniformly recognized and reported by most or all of the testing companies, meaning over 1%, you probably know which of your relatives contributed your minority heritage and you don’t need to look for that proverbial needle in a haystack.  Not everyone is that fortunate.  I’m not.  I know of Native heritage through my mother’s Acadian ancestors, but the ones in my father’s side have consistently eluded identification.  It’s there, but where?  It’s haystack time for me!

This past year or two, genetic genealogy has been hallmarked by advances in autosomal DNA and the supporting technologies using tools like 23andMe and Family Tree DNA’s Family Finder tests.  In order to figure out how people are related to you, what level of cousins they are, and which genealogical line they come from, we’ve been using independent tools like phasing, where you compare your DNA to that of your parents or other close known relatives to see who gave you which pieces, or segments, of DNA.  Then, when someone matches you on that segment, you can tell which side of yoru family it came from, and sometimes which genealogical line it came from.  This sets the stage for one day being able to have this conversation with someone:

“Hi John, I see that we are 117th cousins and we have a match at location 17,387,426 on chromosome 3.”  Beth

“Hi Beth, why yes, we are indeed cousins, but we’re actually 115th cousins, 11 times removed instead of 117th cousins.  Our match is through Attilla the Hun’s 37th concubine.”  John

Ok, so maybe I’m dreaming a bit…but this conversation is not just a possibility, it’s a certainty 10 years from now, but perhaps with less dramatic cousinships:)

To date, the rule of thumb for finding ancestors has been that small matches should be disregarded because they are probably identical by state (IBS), not identical by descent (IBD), meaning not useful genealogically.

What’s IBS you ask?  It’s a segment that is typically too small to be counted as an IBD, or identical by descent, segment.  This means that you and the person you match on this small segment descend from a common population, not necessarily that you share a common ancestor within the past several generations.  Genealgoically relevant segments are recognizable because they are larger.  To understand why and how this works, refer to my article, “Autosomal Results, the Basics.”

There is no absolute line in the sand, but generally segments smaller than 7cM (centimorgans) or 700 SNPs (some say 5cM and 500 SNPs) fall into this category.  Dr. Tim Janzen, the genealogical “father of phasing” discards all matches in his spreadsheets less than 3.5cM.  That’s because he’s looking for positive genealogical matches and does not want the data to be cluttered up by possible IBS matches.

However, when you have small amounts of minority ancestry, it stands to reason that these small tidbits could be very useful in identifying which of your genealogical lines produced these small amounts of admixture.  If you can identify which lines provided this minority admixture, then you’re well on the way to identifying which ancestor contributed the minority admixture.

When looking for minority admixture in two related people, finding these small segments in the same location should provide meaningful information and confirm minority heritage.  Said another way, if you both have less than 1% Native heritage, both share a common ancestor, and both carry your less than 1% on the same segment….one might say it’s not likely to be coincidence, especially if there is a pattern across multiple chromosomes/segments.  Identifying the common segments of your common ancestor can lead to identifying the specific family line, especially if you match others as well.  In essence, this is the genetic equivalent of “surround and conquer.”

Let me give a very short example here.

Let’s say I match my mother on part of chromosome 1 that is Native.

Then let’s say I match her first cousin (my first cousin once removed) on mother’s mother’s side on a smaller piece of that same segment.  This immediately tells me that this particular bit of Native heritage is not from mother’s father’s side.

autosomal Hill

Another match to a more distant Hill cousin further defines the path of Native ancestry,  showing that the Native heritage came through mother’s grandfather’s mother’s line.  You can see how we track this ancestry and whittle down the possible sources.

So, I’ve set out to test this minority ancestry tracking theory.  Because we are dealing with such small segments of DNA, “rooting around in the weeds,” as Bennett Greenspan so aptly put it, and have no mechanized tools, this journey is long, tiresome and tedious.  It’s also thrilling.

As with all experiments, I have wondered many times if I was wasting my time.  I’ve completed steps and then redone them a different way when I realized there was a better or more revealing method.  More than once.  That comes with the territory.

I debated about how to share this new technique.  In the past, I would have published this as an academic paper, but with the delays surrounding the publication of JoGG, and the fact that the last paper through JoGG took 18 months to get out the door, much of this information would be stale by then.  I thought about publishing as an e-book as well, but I finally settled on my blog.  I feel that I can reach more people in a much more timely fashion this way.  I also really like the blog because I can write in a more relaxed fashion than I could in any other venue and it gives you the opportunity to interact as well.

I also don’t know what to call this new methodology.  I have just been referring to it as the weeds method, but that’s not very scientific.  I considered the APM technique – Ancestry Population Mapping.  Sounds too nonspecific.  The PTM – Personal Torture Method – nah – puts people off even if it is true.  MAT – Minority Ancestry Tracking – that’s a possibility but isn’t very specific.  Fragmented Chromosome Mapping, FCM, has possibilities.  So, I’m open to suggestions.  If at the end of this series, it’s still the weeds method….well, then weeds it is.

Over the next few weeks, I’ll be writing about this journey, my discoveries, and sharing techniques with step by step instructions so that you can use the same tools.  Join me for the multi-part series, “The Autosomal Me.”

______________________________________________________________

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