Native American Haplogroups Q, C and the Big Y Test

Sicangu man c 1900I’m writing this to provide an update about Native American paternal research, and to ask for your help and support, but first, let me tell you why.  It’s a very exciting time.

If you don’t want the details, but you know you want to help now….and we have to pay for these tests by the end of the day December 1 to take advantage of the sale price…you can click below to help fund the Big Y testing for Native American haplogroups Q and C.  Both projects need approximately $990.  Everything contributed goes directly to testing.

To donate to the American Indian project, in memory of someone, a family member perhaps, or maybe in honor of an ancestor, or anonymously, click this link:

https://www.familytreedna.com/group-general-fund-contribution.aspx?g=AIP

In order to donate to haplogroup C-P39 project, please click this link:

http://www.familytreedna.com/group-general-fund-contribution.aspx?g=Y-DNAC-P39

Now for the story…

As many of you know, haplogroup Q and C are the two Native American male haplogroups.  To date, every individual with direct paternal Native American ancestors descends from a subgroup of either haplogroup Q or C, Q being by far the most prevalent.  Both of these haplogroups are also found to some extent in Asia and Europe, but there are distinct and specific lineages found in the Americas that represent only Native Americans.  These subgroups are not found in either Europe or Asia.

In December, 2010, we found the first SNP (single nucleotide polymorphism) marker that separated the European and the Native American subclades of haplogroup Q.  Since that time, additional markers have been found through the Walk the Y program and other research.

How did this happen?  A collaborative research approach between individual testers and project administrators.  In this case, Lenny Trujillo was a member of the haplogroup Q project and he agreed to take the WTY (Walk the Y) test, which indeed, discovered a very unique SNP marker that defines Native American haplogroup Q, as opposed to European haplogroup Q.

Much has changed in three years.  The WTY test which was focused solely on research is entirely obsolete, being replaced by a new much more powerful test called the Big Y, and at a reduced cost.  The Big Y sequences a much larger portion of the Y chromosome, which will allow us to discover even more markers.

Why is this important?  Because today, in haplogroups Q and C, we are learning through standard STR (short tandem repeat) surname marker tests who is related to whom, and how distantly, but it’s not enough.  For example, we have a group of haplogroup Q men in Canada who match each other, but then another group with a different SNP marker that is located in the Southwest, Mexico, and then in the North Carolina/Virginia border area.  Oh yes, and one more from Charleston, SC.  Most Native American men who carry haplogroup C are found in Northeastern Canada….but then there is one in the Southwest. What do these people have in common?  Is their relationship “old” or relative new?  Do they perhaps share a common historical language group?  We don’t know, and we’d like to.  In order to do that, we need to further refine their genetic relationship.  Hence, the new tool, the Big Y.

The Big Y sequences almost all of the Y chromosome – over 10 million base pairs and nearly 25,000 known SNPs.  But the good news is that the Big Y, like its predecessor, the WTY, has the ability to find new SNPs.  And they are being found by the buckets – so fast that the haplogroup trees can’t even keep up.  For example, the haplogroup project page still lists most Native people as Q1a3a, but in reality many new SNPs have been discovered.  The official haplogroup tree is still under construction, but you can see an updated version on the front page of the haplogroup Q project.

That’s the good news – that the Big Y represents a huge research opportunity for us to make major discoveries that may well divide the Native groups in the Haplogroup C and Q projects into either language groups, or maybe, if we are lucky, into tribal “confederacies,” for lack of a better word.  I hate to use the word tribes, because the definition of a tribe has changed so much.  What we would like to be able to do it to tell someone from their test results that they are Iroquoian, for example, or Athabascan, or Siouian.  This has been our overarching goal for years, and now we’re actually getting close.  That potential rests with the Big Y.

The bad news is that the test costs $495, and that’s the sale price good only through Dec. 1., and we need funding.  In the haplogroup Q project, we do have a few people who are testing.  Everyone who did the WTY has been sent a $50 coupon to apply towards the Big Y test.  I hope everyone who did do the WTY will indeed order the Big Y as well.  If not, then the coupon can be donated to us, as project administrators, to apply towards the Big Y test of someone else in the group who is testing.  If you’re not going to test, please donate your coupon.

In haplogroup Q, we have two additional men who we desperately want to take the Big Y test, and 2 in haplogroup C as well.  We’re asking for two things.  First, for unused $50 coupons and second, for contributions against the $495 price.  We’d certainly welcome large contributions, or a sponsor for an entire test, but we’d also welcome $5, $10, $25 or whatever you’d like to contribute.  Every little bit helps.

To donate to the American Indian project and to help fund this critical research, click this link:

https://www.familytreedna.com/group-general-fund-contribution.aspx?g=AIP

In order to donate to haplogroup C-P39 project for this research, please click this link:

http://www.familytreedna.com/group-general-fund-contribution.aspx?g=Y-DNAC-P39

Thank you everyone, in advance, for your help.  We can’t do this without you.  This is what collaborative citizen science is all about.  Of course, we’ll report findings as we receive them and can process the information.

Thanksgiving Conundrum

First ThanksgivingFirst Thanksgiving at Plymouth Bay (1621) by Jennie A. Brownscombe (1914)

Justin Petrone, like me, is a mixed race person with Native American ancestry, although unlike me, initially, he never thought of himself in those terms.  I’ve always known and since I was a child, self-identified myself in that way.  Like me, Justin has spent years searching for his elusive ancestors, more often than not, hidden in the mists of time with only suggestions of who their ancestors are by words on tax lists and census records like “free person of color.”

Most of the time, Native people were transparent, until they became at least “civilized” enough to be counted on the census, or taxed or they did something else to bring them into the white man’s realm.  More recently, Justin and others like us have been able to confirm, or deny, that heritage via DNA testing.  So even if we don’t know exactly who our ancestor is, we are positive THAT our Native heritage is real.  In some cases, through DNA testing we can learn which of our ancestral lines is Native.

Most of us who grew up knowing we were mixed blood Native learned years ago that if our ancestors’ tribe survived at all, meaning it was not annihilated by warfare or disease, they don’t accept us.  We are not one of “them” and there is no welcome home party.  We don’t have the blood quantum necessary to be a tribal member, and therefore, to them, we don’t exist either.  Not at all, we’re persona non grata.  Yep, you’re “Indian” right up until your admixture level crosses over that magic political line, whatever that is in whichever tribe, and then you’re not Indian at all – don’t exist.  All of your Indianness just evaporates that day I guess.  Apparently, it’s only in our blood, in our genes and in our hearts that we remain Native after that, because the European culture originally tried to kill off the Native people and the “official” Native people today don’t want any more “members” than they already have clamoring to divide a limited size pie.  So we don’t exist.

For many, being denied and relegated to “wannabe” status by “our own people” is devastating, especially for those who really don’t want any part of the financial pie.  Many simply want to belong, to understand the culture and their heritage – to have an educational avenue to recover in some small way that which was stripped and taken from their ancestors so violently.  To have this cultural travesty being perpetrated a second time by the very people who mixed blood descendants feel are their cousins, “their own people,” by being rejected, mocked, and turned away as “not good enough, not Indian enough” is an unexpected emotional blow, a very cold slap in the face and the faces of our Native ancestors.

After all, the tribal members today are the ones who survived comparatively intact, while the descendants of non-tribal member Indians were the ones often most tragically victimized….the ones where the systematic de-Indianization worked.  Logic would suggest that those who survived “as Indians” would welcome the descendants of those who did not and in vindication for what was done to their Indian brethren, would want to share the lost culture with their descendants, to resurrect the Indian in the descendant, and to insure that the cultural heritage continues into posterity.  But that’s not how it works, in the real political world.

I think of this as we approach Thanksgiving every year.  I think of what was taken from our people, my ancestors, and ultimately from me and my children.  I think of the sanitized, feel-good stories we were told as we cut and pasted Indians and Pilgrims in grade school as children.  I think of the heritage we don’t have, what we don’t know, what is lost forever.

I think of how the culture of denial today has played into exactly what those original Europeans wanted – to strip the Indians of their life, often in order to obtain their land, and if they couldn’t kill all of them, then to strip them of their religion, their language and their culture.  There is more than one way to kill an Indian.  The government had an official plan for how to do just that….and now the official Tribes are helping them complete the act by denying that heritage to their descendants.  Soon, in another generation or two, there will be fewer and fewer, and then no official Indians, as they continue to marry outside of the tribes and the blood quantum drops.  Ultimately, the government will have won….by the very hands and rules of the Tribes themselves based on their own blood quantum level required for tribal membership, unless, of course, the tribes change their rules.  In that lies the ultimate irony.

It’s terribly unfortunate that a middle ground can’t be found, where descendants can be “affiliated” with ancestral tribes, not full benefit-receiving members.  In that way, they could be educated in the traditional way, regain and celebrate their culture and heritage.  I would think it would be politically beneficial to the tribes too, because in sheer terms of numbers, there are a whole lot more of “us” non-tribal member descendants than official tribal members.  I would think the tribes would see the benefit in having the large contingent of “us” firmly on their “side” of any political argument, not having been flatly rejected and turned away.  There is tremendous power in numbers.  Just saying….

I try not to feel righteously indignant, but as Thanksgiving approaches and I see the storybook pictures of the Pilgrims and the Indians, and knowing what happened, and continues to happen, I can’t help but feel some level of sadness, anger and sometimes, outrage, at the way the systematic annihilation of the Indian people has been whitewashed and the way their descendants are treated today.  This was what motivated me to begin the Native Heritage Project and the Native Names Project to document the names of the Indian people buried in reams and reams of records.  This is in addition to various DNA projects to find and document those elusive Native ancestors.

And then, there’s Justin.  Poor Justin.  Justin has known for some time that he was a Native descendant.  He has been searching for that connection, exactly which one of his ancestors was the Native person – not easy to discern in colonial America.  So often, Indian heritage was very well hidden due to the various insidious forms of discrimination that were inflicted upon these people and their families well into the 1900s.  Justin and I have exchanged e-mails, back and forth, as he has shared finds and I’ve shared information from the Native Names Project.

But then, Justin found it…and “it” wasn’t at all what he expected.  In addition to being descended from Native people, Justin is also descended from one of the most notorious Indian killers in American history.

“In 1637, in the service of the Massachusetts Bay Colony, Captain John Underhill led an attack, together with Mohegan Indians, on the Pequot fortified village near modern Mystic, Connecticut. They set fire to the village, killing any who attempted to flee. About 400 Pequots died in what came to be called the Mystic Massacre. But Captain Underhill’s soldier of fortune Indian killing was only just beginning. In the service of New Netherland, he slaughtered between 500 and 700 individuals thought to be of the Siwanoy and Wechquaesgeek groups of the Wappinger Confederacy. And in 1644, he cleared Fort Massapequa right here on Long Island, killing about 120 Indians. According to historical accounts, after the Natives were dead and stacked up, Underhill and his men sat down and ate their breakfast.”

So what does Justin do with this horrible event that occurred just 16 years after that first celebration of Thanksgiving?  I mean, most of us have developed this life-long love affair with our Native ancestors, even if we don’t know who they were, exactly.  They were victims, betrayed by European promises, and we have spent untold hundreds, probably thousands or tens of thousands of hours and dollars trying to resurrect them in some small way from the nameless oblivion of history.  Part of who we are is defined by who they were.  We love our ancestors, all of them.  Many of us feel an obligation to do what we can to right the wrongs done to our ancestors in any way possible, even if the only thing we can do is identify them, maybe recover their name or something about them to give them a voice, a definition, a tangible memory to record for posterity.  It’s something, better than nothing, and it defines them as more than an almost anonymous disappearing footnote in history where the European’s put them and the Native tribes of today condemn them to stay.

But never, never do we expect to find an Indian killer, and not only that, a no-excuses, non-penitent repeat offender….so desensitized to human death that he and his cronies sat by the bodies of those families, including women and children, systematically, genocidally murdered and ate breakfast, probably covered in their blood.

In my family story, I know who the good guys are, and the bad guys.  I know who to love and who to hate, who to root for and who were the oppressors. And I’m not descended from really “bad guys,” at least not Indian Killer type bad guys.  I’ve got a few other colorful people, some slave owners, a couple bigamists, a wife-murderer and a moonshiner…but not people who systematically, unemotionally, slaughtered entire tribes of people.  And in those tribes of people were Justin’s ancestors too.  So now, what does Justin do with this?  Who does he love and who does he hate?  How does he come to terms with this, that he carries the genes and ancestry of both?  Do they fight within him from time to time?  Who is Justin?

Happy Thanksgiving.

Now What? – 23andMe and the FDA

I’m sure everyone reading this knows by now that 23andMe has been ordered to stop marketing their DNA test until they comply with previous FDA requirements.  I wrote about this earlierForbes and several others have weighed in too.  The Forbes article is particularly interesting because it is written by Matthew Herper who has covered the FDA for 13 years, so has significant perspective.

Since that time, a firestorm of questions, comments and emotions have been forthcoming, from all directions.  As consumers, we feel trapped, caught in the middle of a battle, along with our DNA and results.  And sadly, it looks like the battle didn’t have to occur, had 23andMe not ignored the FDA for months after promising results it never delivered.   I want to make a couple of comments, then talk about what we, as consumers, can do to prepare for the worst case.

But before I do that, I want to make it very clear that I don’t expect that the worst case scenario will happen.  What would that be?  23andMe going out of business.  I don’t think that will happen.  Even though they, according to the FDA letter, have been negligent in taking care of business and meeting their commitments, they have bright minds and deep pockets….and 15 days to make some sort of conciliatory peace with the FDA.  Now I’m not a psychic, but I’m betting that 23andMe headquarters is very busily figuring out all of the things they need to do to put this ugly public chapter behind them.  Of course, I could be wrong.  This could be the death knell for 23andMe.  But I don’t think so, unless they cannot prove the accuracy of their product or they continue to ignore the FDA and fail to meet commitments.

Most of the questions and concerns voiced today by consumers revolve around what will happen to results they already have on the 23andMe website.

There is no reason to think that the results would be removed as long as the website is functional.  And their website is their link with the world, so as long as there is 23andMe, there will be a website.

However, the unthinkable has happened before, and 23andMe appears to have been somewhat negligent, so, just in case, what can we do?

1. Print your health results for future reference

On your personal page at 23andMe, select the “Health Overview” option which will then display your elevated risks in each of 4 option categories..

23andMe FDA1

For each of the 4 sections, Health Risks, Inherited Conditions, Traits and Drug Response, there is a blue link at the bottom that says “see all 122 risk reports,” for example.  Click on the “see all” link and then simply print the results in each of the 4 categories.  If you want to preserve any of the more detailed information in any of the categories, you’ll have to use screen shots.

2. Download your raw data file

Regardless of what you do, or don’t, do with these results, they are yours.  After downloading your file, you can simply save the results for later, you can upload them to donation based www.gedmatch.com (when GedMatch is again accepting files, currently estimated to be Dec.1) or you can transfer your file to Family Tree DNA to add your results to their data base and avail yourself of their matches and tools.  Right now, the transfer price for either 23andMe or Ancestry files is only $49, which is significantly less than taking a new test at $99 (although the $99 test currently comes with a $100 restaurant.com giftcard.)  This gives you the ability to find new matches with people who haven’t tested at 23andMe.

23andme fda2

To download your raw data file at 23andMe, sign on to your account, then click on your name in the upper right hand corner of the screen, then on “Browse Raw Data,” then on “Download” in the upper right hand corner of the screen.  You’ll then be prompted for your password again and the answer to your secret question.  Default will be set to download all data.  Leave it that way.  You’ll then be asked if you want to open the file or save it.  Save it.  On a Windows PC, if you don’t direct otherwise, it will be saved in the Downloads directory with a file name where the word “genome_” preceeds the name of the person who tested.  Mine is “genome_Roberta_Estes_Full_20131125XXXXXX.

Word of Warning…..

In the past month, 3 of the 5 files I’ve downloaded from 23andMe have been incomplete.  I’ve been working with 23andMe for three very frustrating weeks now via e-mail to try to figure out why they are incomplete.  So far, I have no answers and I’ve asked if these incomplete files have affected my (and my families) results posted at 23andMe.  To date, I’m still getting their standard reply about not being responsible for third party upload sites, which of course is not the question I asked, at all.

A normal 23andMe file will have about 950,000 rows on a spreadsheet, each one representing a single location tested.  23andMe confirmed this number last week.  For example, I have 991,000 plus change and my niece has 960,000 plus change.  All 3 of the incomplete files have only 574,515 lines each, exactly.  And yes, all of them are build 37, and no, they did not test at the same time.  I even downloaded them a second, third and fourth time, from different locations using different computers, etc.  The files are simply massively incomplete.

These incomplete files cannot be uploaded and utilized by other tools (www.gedmatch.com) or firms, including Family Tree DNA because 40% of the data is missing.

Given this experience, the FDA’s concerns about accuracy have certainly given me pause to reflect….

You can get a good idea as to whether your file is complete or not by the zipped file size when it downloads.  The zipped size of the incomplete files is around 5K (4901 to be exact) and the zipped size of the correct files is about 8K (8262 and 8013K to be exact).

Good luck getting help if your file is incomplete.  In order to contact the 23andMe customer service department, you have to jump through hoops, stand on your head, pat your stomach and rub your foot at the same time while chewing gum and blowing bubbles.  Ok, tiny exaggeration.  You really only have to click on “help” then use the “what’s your question” function, and then at the end of that exercize when you don’t receive the answer you need, you can submit a question to them via a form….but not until you go through that process.  They’ll get back with you in about a week with a canned reply and then you can begin the back and forth dialogue, with 2-3 day intervals between each e-mail.

3. Contact your matches

If you haven’t contacted all of your matches already, now would be a wonderful time to send invitations.  I send a message with each one that includes my e-mail address.  Unfortunately, you are forced to utilize the in-house messaging system at 23andMe, so unless you’ve exchanged e-mail addresses with your matches, if the 23andMe system goes away, you have no way to contact anyone ever again.

4. Send your e-mail address to all of the people who have already accepted match requests

Obviously, this is for the same reason.  Otherwise, your ability to communicate with your matches will disappear if the website does.  Personally I far prefer e-mail rather than the messaging system anyway, so this is not a wasted opportunity.

I want to say, again, that I don’t believe that anything horrible will happen to 23andMe.  I don’t want to be an alarmist.  They have deep pockets and lots of lawyers.  They may get a slap on the hand, but in the long run, I think they’ll be around in one form or another, assuming, of course, that they can prove their results are accurate.  I do have to ask myself why 23andMe has been unable to do this in 5 years.  Was it just not a priority, corporate arrogance, or is there a real problem lurking?  However, as for my data and results, better safe than sorry, and we should  probably be taking these steps anyway.  I’m glad I downloaded the data files for my family, because it has exposed a problem that I otherwise wouldn’t have known existed.  Hopefully, I’ll still have time to get it resolved.

FDA Orders 23andMe to Discontinue Testing

23andme logo

Never, ever, mess with the big guns.

The FDA has issued a cease and desist letter to 23andMe and ordered the firm to stop selling their DNA tests based on concerns of accuracy, failure to comply with FDA requirements and the fact that they are providing “specific health recommendations” to their clients.

Here is the actual letter.

“The Food and Drug Administration (FDA) is sending you this letter because you are marketing the 23andMe Saliva Collection Kit and Personal Genome Service (PGS) without marketing clearance or approval in violation of the Federal Food, Drug and Cosmetic Act.

Therefore, 23andMe must immediately discontinue marketing the PGS until such time as it receives FDA marketing authorization for the device.”

Normally, the DTC (direct to consumer) test concerns voiced are about people misinterpreting their results, or being frightened by them, without the involvement of a physician.  In other words, the move until now has been to force you to visit a doctor to obtain a prescription for this type of test.  Of course, the underlying assumption is that the physician will then be available and have expertise in all of the areas that the test covers.  That, of course, would mean another follow-up visit, and if all you really wanted was the genealogically relevant results, this would in effect kill that part of their business.  In fact, it would probably kill the business entirely, at least under the current marketing model.

The FDA says that the product that 23andMe sells is a medical device, especially since it involves important medical information such as the detection of the BRCA-related breast cancer gene and sensitivity to the blood-thinner, warfarin.

Again from the FDA to 23andMe letter:

“Some of the uses for which PGS is intended are particularly concerning, such as assessments for BRCA-related genetic risk and drug responses (e.g., warfarin sensitivity, clopidogrel response, and 5-fluorouracil toxicity) because of the potential health consequences that could result from false positive or false negative assessments for high-risk indications such as these.”

The FDA wants 23andMe to show that these tests are accurate.  They are concerned, for example, that the BRCA test provided by 23andMe might provide either a false positive or, even worse, a false negative.  A false positive would, of course, provide an individual with a great deal of angst, but they would certainly immediately visit a physician who would prescribe industry-standard follow-up testing where the “false positive” would be caught.  A false negative, on the other hand, might mask a deadly situation, delaying detection until too late.

The FDA states that they have been working with 23and Me who has failed to provide the necessary proof.  From the looks of this letter, and understanding there are two sides to every story, it looks like 23and Me has not taken the FDA seriously.

“As part of our interactions with you, including more than 14 face-to-face and teleconference meetings, hundreds of email exchanges, and dozens of written communications, we provided you with specific feedback on study protocols and clinical and analytical validation requirements, discussed potential classifications and regulatory pathways (including reasonable submission timelines), provided statistical advice, and discussed potential risk mitigation strategies. As discussed above, FDA is concerned about the public health consequences of inaccurate results from the PGS device; the main purpose of compliance with FDA’s regulatory requirements is to ensure that the tests work.

However, even after these many interactions with 23andMe, we still do not have any assurance that the firm has analytically or clinically validated the PGS for its intended uses, which have expanded from the uses that the firm identified in its submissions. In your letter dated January 9, 2013, you stated that the firm is “completing the additional analytical and clinical validations for the tests that have been submitted” and is “planning extensive labeling studies that will take several months to complete.” Thus, months after you submitted your 510(k)s and more than 5 years after you began marketing, you still had not completed some of the studies and had not even started other studies necessary to support a marketing submission for the PGS. It is now eleven months later, and you have yet to provide FDA with any new information about these tests.  You have not worked with us toward de novo classification, did not provide the additional information we requested necessary to complete review of your 510(k)s, and FDA has not received any communication from 23andMe since May. Instead, we have become aware that you have initiated new marketing campaigns, including television commercials that, together with an increasing list of indications, show that you plan to expand the PGS’s uses and consumer base without obtaining marketing authorization from FDA.”

I do believe the FDA has their undivided attention now.

“Therefore, 23andMe must immediately discontinue marketing the PGS until such time as it receives FDA marketing authorization for the device.”

23andMe has 15 days to reply and if they don’t, it could get even uglier.

“Please notify this office in writing within fifteen (15) working days from the date you receive this letter of the specific actions you have taken to address all issues noted above. Include documentation of the corrective actions you have taken. If your actions will occur over time, please include a timetable for implementation of those actions. If corrective actions cannot be completed within 15 working days, state the reason for the delay and the time within which the actions will be completed. Failure to take adequate corrective action may result in regulatory action being initiated by the Food and Drug Administration without further notice. These actions include, but are not limited to, seizure, injunction, and civil money penalties.”

Yep, never mess with the big guns.

In 2010, five different companies, including 23andMe, were served with warning letters when Pathway Genomics announced it would sell its DNA testing product at Walgreen, a plan that never came to fruition after the warning letter.  However, this is the first letter of this type to be served on a genomics testing company.

What’s next?  We just don’t know.  23andMe has yet to comment, but it looks from this letter like they have limited choices at the moment.

Stay tuned for the next episode of the Wild West in DTC Testing.

Watson, Crick and Spotted Dick

dna 1953

In September, 2013, my husband, Jim, and I visited the British Isles.  This trip was planned around various aspects of genealogy and family history – all of which pertain to and were enabled by DNA.  I’m going to be sharing portions with you over the next several weeks.  These stories will all include DNA, but I’m also going to share other photos with you.  The culture, so different from ours, is critically important to understanding our ancestors and these areas are simply beautiful.  I’d like to share the entire experience, not just the DNA piece.  So I’m inviting you along on my day in London.  Come on….we’ll have fun!

I didn’t plan my trip to England with Watson and Crick’s DNA model in mind – that part just kind of evolved, a positive mutation, so to speak.

Jim and I traveled with a family group that indeed did make this trip as a result of DNA – but that is another story for another article, several, in fact.  In any case, we weren’t really in charge of where we were staying in London – the tour company took care of fanthat – supposedly.  That is a long and sorry saga which I’ll spare you.  Let’s just say we weren’t staying at the hotel where we were SUPPOSED to have reservations and the one where we were staying didn’t have air conditioning.  It was “broken.”  It should have been an aha moment when they handed me a fan when we checked in.  At least they did that much.  It was very hot.

Suffice it to say, we were close to Hyde Park and Kensington Gardens in London.  The idea was that we could take a walk in the park if we wanted to.  Flowers often grace every nook and cranny in Europe and the thought of walking and viewing was quite enticing to me.  Here is a rose garden in front of a private home near Hyde Park. Just lovely.

London rose garden

The London subway is a bit overwhelming, but it really a good transportation system once you get used to it.  You can get places far more quickly by subway than by car on the surface streets.

london subway

Still, you stand a high probability of getting lost, at least initially, and it’s pretty intimidating.  So we opted to walk when we could.  Plus, you get to see a lot more of the area that way.  After all, it’s not always the destination.  Sometimes, it’s about the journey.

Before we left for London, I searched for the location of the double helix model created by Watson and Crick in 1953 when they discovered DNA.  I found that it is in the British Science Museum.

After arrival in London, looking at the map, I discovered that the Science Museum was just on the other side of Hyde Park.  I asked and was told that it’s about a 10 minute walk.  Have I mentioned never to believe a British person about distances???  It must be genetic – they seem to have a distance judgment impairment gene!

Jim and I set out to walk to the Museum because it seemed like a much better option than three different subway transfers.  And after all, it was only 10 minutes away and only drizzling.

Me hyde park

We cut across the park and enjoyed the walk and found the museums, further away than we thought, of course.  We discovered we were walking on the Princess Diana Memorial walkway, and only after we got home and looked at the photo did I realize that Kensington Palace is behind me.

British parks and gardens are really quite remarkable.  There are a lot of them and they have beautiful statues and flowers. This statue is of Prince Albert.

prince albert

Half an hour or 45 minutes later, we arrived at the Science Museum.  It’s quite large, and we asked where the DNA exhibit was located, received directions, and off we went.  We were pleased to see that they had an entire exhibit area devoted not to DNA but to what makes people unique.  Of course DNA had a prominent position in that exhibit.

dna book

The “books of genes” shown above and below is actually the top back of a seat in the museum exhibit.

dna seat

But we were unable to find the Watson/Crick model.  We asked a second time and the guard told us that it was downstairs “by the autos.”  We had just come through that area and we didn’t quite believe it would be there, but since it wasn’t where we were, we went to look.  Sure enough, in with the 1950s cars and the earliest computers, in a display case but not near anything else similar, we found the double helix model with only a small display description.  In fact, we had walked right past it earlier and didn’t notice it because where it is located and how it is displayed is so nondescript.

dna sign

OLYMPUS DIGITAL CAMERA

The helix model itself is kind of difficult to see because it’s small and kind of thin and in the middle of a case with glass on all sides.  Jim is trying to get a good picture, but that is almost impossible between its position and the glass and lighting.

Crick Watson Jim

The model is constructed using clamps.

Crick Watson closeup

It’s actually difficult to see because the aluminum templates, shown below (wiki photo) are on a flat plane so they are being photographed sideways.

DNA model leaves

I was thrilled to see the model, but saddened that it has been relegated to the section of “vintage cars” when it was the discovery that fueled many of the life-changing medical discoveries of the past few years and nearly everything in the exhibit we had just seen about what makes people unique.  If not DNA, then what?

The Crick/Watson double helix model should be the crown jewel of these types of exhibits, not relegated to a place in the footnotes of the 1950s.

The model itself is elegant in that its simplicity belies the complexity of DNA.  Yet, that complexity is comprised of simplest of elements combined in the simplest of manners.  It’s hard to believe sometimes that we are looking at the recipe for reproduction, for all of life itself.

Here are Crick and Watson with the model.

crick watson with model

Of course, we walked back to our hotel, but we took a bit of a different route, past both sets of palace gates (below) and up some side streets.

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

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

Glory be, we also found a Starbucks!!  We discovered a beautiful old church on Kensington High Street and slipped into the courtyard which is also the cemetery.

church high kensington

It’s hard to believe that just a few feet away on the other side of the fence the London traffic and hustle and bustle are in full force.

OLYMPUS DIGITAL CAMERA

This courtyard is a tiny haven of tranquility. Of course, I had to look at the stones to see if there were any familiar names.  After all, some of my ancestors were here – however, they weren’t wealthy enough to have stones in churchyards.

Some things have no equivalent here.

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

Humps, in case you are wondering, are speed bumps.  The even more interesting sign was the one that had a picture of two humps, side by side, on the same sign.

We passed this lovely pub that is just so quintessentially English and so beautiful.  Surely looks inviting doesn’t it.  Want to have an ale???

OLYMPUS DIGITAL CAMERA

That evening, we met up with my cousins from New Zealand (more about that later) in The Swan Pub, a very quaint and very English old coaching pub across from Hyde Park, and had an English dinner of what else, fish and chips.

But that wasn’t the end of the adventures.  Nosiree….there was what we term as  “adventure eating” left to be done.  There was Spotted Dick on the dessert menu.  Yes, we did, we had to order that and try some.  Here’s Jim getting ready to try Spotted Dick.  Looks kind of apprehensive doesn’t he.  I must admit, it was very, very good.

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

I hope you’ve enjoyed coming along with me on my day in London visiting Watson, Crick and Spotted Dick.

Native American Gene Flow – Europe?, Asia and the Americas

Pre-release information from the paper, “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans” which included results and analysis of DNA sequencing of 24,000 year old skeletal remains of a 4 year old Siberian boy caused quite a stir.  Unfortunately, it was also misconstrued and incorrectly extrapolated in some articles.  Some people misunderstood, either unintentionally or intentionally, and suggested that people with haplogroups U and R are Native American.  That is not what either the prerelease or the paper itself says.  Not only is that information and interpretation incorrect, the paper itself with the detailed information wasn’t published until November 20th, in Nature.

The paper is currently behind a paywall, so I’m going to discuss parts of it here, along with some additional information from other sources.  To help with geography, the following google map shows the following locations: A=the Altai Republic, in Russia, B=Mal’ta, the location of the 24,000 year old skeletal remains and C=Lake Baikal, the region from where the Native American population originated in Asia.

native flow map

Nature did publish an article preview.  That information is in bold, italics and I will be commenting in nonbold, nonitalics.

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1, 2, 3, there is no consensus with regard to which specific Old World populations they are closest to4, 5, 6, 7, 8. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date.

Within the paper, the authors also compare the MA-1 sequence to that of another 40,000 year old individual from Tianyuan Cave, China whose genome has been partially sequenced.  This Chinese individual has been shown to be ancestral to both modern-day Asians and Native Americans.  This comparison was particularly useful, because it showed that MA-1 is not closely related to the Tianyuan Cave individual, and is more closely related to Native Americans.  This means that MA-1’s line and Tianyuan Cave’s line had not yet met and admixed into the population that would become the Native Americans.  That occurred sometime later than 24,000 years ago and probably before crossing Beringia into North America sometime between about 18,000 and 20,000 years ago.

The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10, 11, 12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages5.

The paper goes on to say that MA-1 is a member of mitochondrial (maternal) haplogroup U, very near the base of that haplogroup, but without affiliation to any known subclade, implying either that the subclade is rare or extinct in modern populations.  In other words, this particular line of haplogroup U has NOT been found in any population, anyplace.  According to the landmark paper,  “A ‘‘Copernican’’ Reassessment of the Human Mitochondrial DNA Tree from its Root,” by Behar et al, 2012, haplogroup U itself was born about 46,500 years ago (plus or minus 3.200 years) and today has 9 major subclades (plus haplogroup K) and about 300 branching clades from those 9 subclades, excluding haplogroup K.

The map below, from the supplemental material included with the paper shows the distribution of haplogroup U, the black dots showing locations of haplogroup U comparison DNA.

Native flow Hap U map

In a recent paper, “Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity” by Brandt et al (including the National Geographic Consortium) released in October 2013, the authors report that in the 198 ancient DNA samples collected from 25 German sites and compared to almost 68,000 current results, all of the ancient Hunter-Gatherer cultural results were haplogroup U, U4, U5 and U8.  No other haplogroups were represented.  In addition, those haplogroups disappeared from the region entirely with the advent of farming, shown on the chart below.

Native flow Brandt map

So, if someone who carries haplogroup U wants to say that they are distantly related to MA-1 who lived 24,000 years ago who was also related to their common ancestor who lived sometime prior to that, between 24,000 and 50,000 years ago, probably someplace between the Middle East where U was born, Mal’ta, Siberia and Western Europe, they would be correct.  They are also distantly related to every other person in the world who carries haplogroup U, and many much more closely that MA-1 whose mitochondrial DNA line is either rare as chicken’s teeth (i.e. never found) or has gone extinct.

Let me be very clear about this, there is no evidence, none, that mitochondrial haplogroup U is found in the Native American population today that is NOT a result of post-contact admixture.  In other words, in the burials that have been DNA tested, there is not one example in either North or South America of a burial carrying mitochondrial haplogroup U, or for that matter, male Y haplogroup R.  Native American haplogroups found in the Americas remain subsets of mitochondrial haplogroups A, B, C, D and X and Y DNA haplogroups C and Q.  Mitochondrial haplogroup M has potentially been found in one Canadian burial.  No other haplogroups have been found.  Until pre-contact remains are found with base haplogroups other than the ones listed above, no one can ethically claim that other haplogroups are of Native American origin.  Finding any haplogroup in a contemporary Native population does not mean that it was originally Native, or that it should be counted as such.  Admixture and adoption have been commonplace since Europeans first set foot on the soil of the Americas. 

Now let’s talk about the Y DNA of MA-1.

The authors state that MA-1’s results are found very near the base of haplogroup R.  They note that the sister lineage of haplogroup R, haplogroup Q, is the most common haplogroup in Native Americans and that the closest Eurasian Q results to Native Americans come from the Altai region.

The testing of the MA-1 Y chromosome was much more extensive than the typical STR genealogy tests taken by consumers today.  MA-1’s Y chromosome was sequenced at 5.8 million base pairs at a coverage of 1.5X.

The resulting haplotree is shown below, again from the supplementary material.

Native flow R tree

 native flow r tree text

The current haplogroup distribution range for haplogroup R is shown below, again with comparison points as black dots.

Native flow R map

The current distribution range for Eurasian haplogroup Q is shown on the map below.  Haplogroup Q is the most common haplogroup in Native Americans.

Native flow Q map

Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2, 13.

Kennewick Man is probably the most famous of the skeletal remains that don’t neatly fit into their preconceived box.  Kennewick man was discovered on the bank of the Columbia River in Kennewick, Washington in 1996 and is believed to be from 7300 to 7600 years old.  His anatomical features were quite different from today’s Native Americans and his relationship to ancient people is unknown.  An initial evaluation and a 2010 reevaluation of Kennewick Man let to the conclusion by Doug Owsley, a forensic anthropologist, that Kennewick Man most closely resembles the Ainu people of Japan who themselves are a bit of an enigma, appearing much more Caucasoid than Asian.  Unfortunately, DNA sequencing of Kennewick Man originally was ussuccessful and now, due to ongoing legal issues, more technologically advanced DNA testing has not been allowed.  Nova sponsored a facial reconstruction of Kennewick Man which you can see here.

Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago14, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

In addition to the sequencing they set forth above, the authors compared the phenotype information obtainable from MA-1 to the Tyrolean Iceman, typically called Otzi.  You can see Otzi’s facial reconstruction along with more information here.  This is particularly interesting in light of the pigmentation change from darker skin in Africa to lighter skin in Eurasia, and the question of when this appearance change occurred.  MA-1 shows a genetic affinity with the contemporary people of northern Europe, the population today with the highest frequency of light pigmentation phenotypes.  The authors compared the DNA of MA-1 with a set of 124 SNPs identified in 2001 by Cerquira as informative on skin, hair and eye pigmentation color, although they also caution that this method has limited prediction accuracy.  Given that, they say that MA-1 had dark hair, skin and eyes, but they were not able to sequence the full set of SNPs.  MA-1 also had the SNP value associated with a high risk of male pattern baldness, a trait seldom found in Native American people and was not lactose tolerant, a trait found in western Eurasians.  MA-1 also does not carry the mutation associated with hair thickness and shovel shaped incisors in Asians.

The chart below from the supplemental material shows the comparison with MA-1 and the Tyrolean Iceman.

Native flow Otzi table

The Tarim Mummies, found in the Tarim Basin in present-day Xinjiang, China are another example of remains that seem out of place.  The earliest Tarim mummies, found at Qäwrighul and dated to 1800 BCE, are of a Europoid physical type whose closest affiliation is to the Bronze Age populations of southern Siberia, Kazakhstan, Central Asia, and the Lower Volga.

The cemetery at Yanbulaq contained 29 mummies which date from 1100–500 BCE, 21 of which are Mongoloid—the earliest Mongoloid mummies found in the Tarim Basin—and eight of which are of the same Europoid physical type found at Qäwrighul.

Notable mummies are the tall, red-haired “Chärchän man” or the “Ur-David” (1000 BCE); his son (1000 BCE), a small 1-year-old baby with brown hair protruding from under a red and blue felt cap, with two stones positioned over its eyes; the “Hami Mummy” (c. 1400–800 BCE), a “red-headed beauty” found in Qizilchoqa; and the “Witches of Subeshi” (4th or 3rd century BCE), who wore 2-foot-long (0.61 m) black felt conical hats with a flat brim. Also found at Subeshi was a man with traces of a surgical operation on his neck; the incision is sewn up with sutures made of horsehair.

Their costumes, and especially textiles, may indicate a common origin with Indo-European neolithic clothing techniques or a common low-level textile technology. Chärchän man wore a red twill tunic and tartan leggings. Textile expert Elizabeth Wayland Barber, who examined the tartan-style cloth, discusses similarities between it and fragments recovered from salt mines associated with the Hallstatt culture.

DNA testing revealed that the maternal lineages were predominantly East Eurasian haplogroup C with smaller numbers of H and K, while the paternal lines were all R1a1a. The geographic location of where this admixing took place is unknown, although south Siberia is likely.  You can view some photographs of the mummies here.

In closing, the authors of the MA-1 paper state that the study has four important implications.

First, we find evidence that contemporary Native Americans and western Eurasians shareancestry through gene flow from a Siberian Upper  Palaeolithic population into First Americans.

Second, our findings may provide an explanation for the presence of mtDNA haplogroup X in Native Americans, which is related to western Eurasians but not found in east Asian populations.

Third, such an easterly presence in Asia of a population related to contemporary western Eurasians provides a possibility that non-east Asian cranial characteristics of the First Americans derived from the Old World via migration through Beringia, rather than by a trans-Atlantic voyage from Iberia as proposed by the Solutrean hypothesis.

Fourth, the presence of an ancient western Eurasian genomic signature in the Baikal area before and after the LGM suggests that parts of south-central Siberia were occupied by humans throughout the coldest stages of the last ice age.

The times, they are a changin’.

Dr. Michael Hammer’s presentation at the 9th Annual International Conference on Genetic Genealogy may shed some light on all of this seeming confusing and somewhat conflicting information.

The graphic below shows the Y haplogroup base tree as documented by van Oven.

Native flow basic Y

You can see, in the lower right corner, that Y haplogroup K (not to be confused with mtDNA haplogroup K discussed in conjunction with mtDNA haplogroup U) was the parent of haplogroup P which is the parent of both haplogroups Q and R.

It has always been believed that haplogroup R made its way into Europe before the arrival of Neolithic farmers about 10,000 years ago.  However, that conclusion has been called into question, also by the use of Ancient DNA results.  You can view additional information about Hammer’s presentation here, but in a nutshell, he said that there is no early evidence in burials, at all, for haplogroup R being in Europe at an early age.  In about 40 burials from several location, haplogroup R has never been found.  If it were present, especially in the numbers expected given that it represents more than half of the haplogroups of the men of Europe today, it should be represented in these burials, but it is not.  Hammer concludes that evidence supports a recent spread of haplogroup R into Europe about 5000 years ago.  Where was haplogroup R before spreading into Europe?  In Asia.

Native flow hammer dist

It appears that haplogroup K diversified in Southeast Asian, giving birth to haplogroups P, Q and R. Dr. Hammer said that this new information, combined with new cluster information and newly discovered SNP information over the past two years requires that haplogroup K be significantly revised.  Between the revision of haplogroup K, the parent of both haplogroup R, previously believed to be European, and haplogroup Q, known to be Asian, European and Native, we may be in for a paradigm shift in terms of what we know about ancient migrations and who is whom.  This path for haplogroup R into Europe really shouldn’t be surprising.  It’s the exact same distribution as haplogroup Q, except haplogroup Q is much less frequently found in Europe than haplogroup R.

What Can We Say About MA-1?

In essence, we can’t label MA-1 as paternally European because of Y haplogroup R which now looks to have had an Asian genesis and was not known to have been in Europe 24,000 years ago, only arriving about 5,000 years ago.  We can’t label haplogroup R as Native American, because it has never been found in a pre-Columbian New World burial.

We can say that mitochondrial haplogroup U is found in Europe in Hunter-Gatherer groups six thousand years ago (R  was not) but we really don’t know if haplogroup U was in Europe 24,000 years ago.  We cannot label haplogroup U as Native because it has never been found in a pre-Columbian New World burial.

We can determine that MA-1 did have ancestors who eventually became European due to autosomal analysis, but we don’t know that those people lived in what is now Europe 24,000 years ago.  So the migration might have been into Europe, not out of Europe.  MA-1, his ancestors and descendants, may have lived in Asia and subsequently settled in Europe or lived someplace inbetween.  We can determine that MA-1’s line of people eventually admixed with people from East Asia, probably in Siberia, and became today’s First People of North and South America.

We can say that MA-1 appears to have been about 30% what is today Western Eurasian and that he is closely related to modern day Native Americans, but not eastern Asians.  The authors estimate that between 14% and 38% of Native American ancestry comes from MA-1’s ancient population.

Whoever thought we could learn so much from a 4 year old?

For anyone seriously interested in Native American population genetics, “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans” is a must read.

It’s been a great month for ancient DNA.  Additional recent articles which pertain to this topic include:

http://www.nytimes.com/2013/11/21/science/two-surprises-in-dna-of-boy-found-buried-in-siberia.html?src=me&ref=general&_r=0

http://www.sciencedaily.com/releases/2013/11/131120143631.htm

http://dienekes.blogspot.com/2013/11/ancient-dna-from-upper-paleolithic-lake.html

http://blogs.discovermagazine.com/gnxp/2013/11/long-first-age-mankind/#.Uo0eOcSkrIU

http://cruwys.blogspot.com/2013/11/day-1-at-royal-societys-2013-ancient.html

http://cruwys.blogspot.co.uk/2013/11/day-2-at-royal-societys-2013-ancient.html

http://www.sciencedaily.com/releases/2013/11/131118081251.htm

Be Still my H(e)art…

You’re not going to believe this.  I’m not sure I believe it.

Remember, I closed my article on the Younger family yesterday by saying that I was hopeful that I might solve the mystery of who Marcus Younger’s wife, Susanna, was?  Well, I said that, but I had no real expectation that it would really happen, not after one already huge breakthrough.  I began working through cousin Larry’s matches, sending e-mails, and within six hours or so, I had several replies, one of which was this:

“Hello my name is Andrea. Thank you for sending me this email. I am new to genealogy and have a large interest in my family history. Younger is not a known surname for me, although Hart is. My oldest known Hart ancestor is Anthony Hart born in Oct 1755 in King and Queen, Virginia. He was my 5th great grandfather. He lived in Halifax Virginia in 1840 with his children and grandchildren. How is the surname Hart related to Younger?”

Oh Andrea, let me tell you.  You have made my day, my decade, my 30 years, and yes, indeed, this is the second jackpot hit in two days in the same family line.  I shoulda bought a lottery ticket but I think I’d rather have this:)

It has always been speculated that Marcus Younger’s wife, Susanna, was a Hart.  In fact, it was speculated that she was the possible sister of that one and the same Anthony Hart in Halifax County, Virginia, based on this tax record from King and Queen County, Va. just before Marcus Younger moved to Halifax County.  Robert Hart is believed to be Anthony’s father, but that is unproven.

1785

Alterations of land in King and Queen County

Proprietor’s Name                     QT Land                     of whom had

Anthony Hart                               190a                         Robert Hart

Anthony Hart                                94a                          Marcus Younger

There are a couple of other records in which they appear together too.

Unfortunately, King and Queen County is a burned county.

Now, we have a couple of pretzel twists that need to be considered.  In Larry’s line, Marcus’s son John married Lucy Hart who is mentioned in Anthony Hart’s Revolutionary War pension application in 1832.  So Larry could be expected to match Andrea regardless of who Marcus’s wife was.

However, I don’t descend from the same line as Larry and Andrea matches me as well.  I descend from Marcus through his daughter, Mary, sister to John who married Lucy Hart.  So, I should NOT match Andrea unless I too carry some Hart DNA.  But I do, in two distinct places where I also match Larry.  On the chromosome browser below, Andrea is orange, I am blue and we are being compared to Larry.  You can see that we all 3 match on the same segments on chromosomes 1 and 8.

younger hart 1

Additionally, Andrea matches other cousins descended from my Younger line.

Furthermore, Andrea and David (from the previous article whose pedigree proved that Marcus and Thomas Younger are related) both match Lawson, but they don’t match each other.  This makes perfect sense.  David descends from Thomas Younger, who has no known Hart connection.  So David matches Larry because of the Younger line and Andrea matches Larry because of the Hart line.

You can see in the chromosome browser view below that indeed, both Andrea, orange, and David, blue match Larry, but in no location do they match each other in addition to matching Larry.  No place does their DNA show one under the other, overlapping, when compared to Larry.

younger hart 2

Turning now to the spreadsheet where I can see all of the people who match both Larry and David together, I want to know who else Andrea matches.

First, I confirmed that Andrea does not match anyone else from the Alexander Younger line through sons Thomas and James, and she does not.  If she had, that would put a very big fly in the ointment and would prevent any conclusion about Marcus’s wife.  But since she doesn’t, that obstacle is removed.

Andrea does match the following people on several segments:

  • Me
  • Loujean, our newly found adoptee cousin whose closest autosomal match is Larry
  • Larry
  • Buster, my cousin, who also descends through Marcus’s daughter, Mary

We are all four descended from the Marcus line and she doesn’t match anyone who descends from the Thomas or Alexander lines, which makes perfect sense since Anthony Hart looks to be the probable brother of Marcus Younger’s wife, Susannah, based on the historical records and some relationship is now confirmed by the DNA.

Am I ready to call this a positive match yet and Susannah a Hart?  Technically, I probably could, but I’m rather conservative and I’m just not quite ready to give an unconditional thumbs up.  To make myself feel entirely warm and fuzzy, I’d love to see another Hart match for me or my cousins not descended through John’s line. I’d also love to be able to reconstruct the Hart family back in Queen and King and Essex Counties and have some additional paper document to go along with the results.  That would certainly be easier to accomplish were the Queen and King records not burned.  This family lived on the border between the two and had records in both counties.

Truly, I’m left speechless about my good fortune this weekend.  I’m happy dancing a hole in the floor.

happy dance 2

But I’m also left wondering how many other answers are really there, in the DNA of the people we match and I just haven’t worked with the matches effectively.  Maybe those walls are just waiting to fall….waiting for me to notice them.  Maybe yours are too.