Native American Haplogroups Q, C and the Big Y Test

Posted on November 30, 2013 by Roberta Estes

I’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.

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.

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Thanksgiving Conundrum

Posted on November 28, 2013 by Roberta Estes

First 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.

______________________________________________________________

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Now What? – 23andMe and the FDA

Posted on November 26, 2013 by Roberta Estes

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 earlier. Forbes 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..

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.

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.

______________________________________________________________

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FDA Orders 23andMe to Discontinue Testing

Posted on November 25, 2013 by Roberta Estes

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.

______________________________________________________________

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Watson, Crick and Spotted Dick

Posted on November 24, 2013 by Roberta Estes

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 that – 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.

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.

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.

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.

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.

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

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.

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.

The model is constructed using clamps.

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.

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.

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.

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.

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???

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.

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

Posted on November 22, 2013 by Roberta Estes

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 20^th, 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.

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 Asians^{1, 2, 3}, there is no consensus with regard to which specific Old World populations they are closest to^{4, 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-gatherers^{10, 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.

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.

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.

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

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

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 Asians^{2, 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.

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 9^th 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.

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.

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

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Be Still my H(e)art…

Posted on November 18, 2013 by Roberta Estes

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.

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.

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.

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.

Update: Please note that as of August 2019, this connection is still not proven. Still hoping!

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Proving Men Whose Y-Lines Don’t Match Are Related

Posted on November 17, 2013 by Roberta Estes

The old “Younger Store” in Halifax County, Virginia

BINGO – BINGO

Yes, I’m shouting. This is a 30 year BINGO – a wall that DNA just tore down!!! WOOHOO

Good thing you can’t see my happy dance. I wouldn’t care right this moment, but I’m POSITIVE I’d be embarrassed later.

Ok, so taking deep breath here – here’s the story.

The Younger Men

I descend from Marcus Younger of Halifax County, Virginia, through his daughter Mary who married George Estes in 1786. Marcus was born probably somewhat before 1740 in either Essex County, Virginia. Our first positive record of him is in 1780 when he gave to the Revolutionary War cause “1 gallon, 2 quarts and 1/2 pint brandy.” We don’t know who Marcus’s wife was, but she may have been a Hart or a Ferguson. Marcus moved to Halifax County, Virginia shortly after the war and subsequently died there in 1815 with a will listing his children. There were also subsequent chancery suits relating to his estate, thankfully, that reveal a great amount of information about his children and their lives. Marcus had only one son, John, born in 1760. Mary was probably his second child as her husband, George Estes, was born in 1761.

Also living in close proximity to Marcus Younger in Essex County, near the border with Queen and King, was Thomas Younger who was significantly older than Marcus, but was not his father. Thomas appears in deeds in Essex County, Virginia in the 1740s, but was in King and Queen County in 1752. Thomas moved to Halifax County by 1765 when he is found on a tax list and died there in 1791, with a will that was witnessed by both Marcus Younger and Marcus’s son John. This alone suggests strongly that Marcus was not the son of Thomas because heirs generally did not witness wills unless they were nuncupative wills taken orally just before the person died, and Thomas’s was not. Furthermore, there were chancery suits following both Thomas and Marcus’s deaths that tell us exactly who their heirs were. This will-witnessing also suggests an extremely close relationship between Thomas Younger and Marcus Younger. But what, exactly, was that relationship?

Thomas’s parents were Alexander Younger and Rebecca Mills. Alexander died in Essex County in 1727, with a will. He had three sons, Thomas, above, James who married a Nash and is well accounted for, and a John who died between 1725 and 1727 when Alexander’s estate is settled. Almost nothing is known about John. In addition, there were 5 sisters, only two of which are even somewhat accounted for beyond 1732 or as adults. This indeed may be a very important clue to the Marcus puzzle.

Who’s Your Daddy?

Descendants of Thomas Younger and of Marcus Younger both took the Y DNA test some years ago, and we were absolutely stunned to discover that their Y DNA did not match. We have two descendants of John, only son of Marcus, and they do match each other, but no other Youngers.

The several descendants of Thomas Younger match each other and also the descendants of Alexander’s other son, James. So Marcus seems to be related to the family, carries the surname, but does not share a direct paternal ancestor on his father’s side.

Our candidates for his parents are quite limited.

Barring a totally unknown Younger person, we have the following candidates.

John Younger, son of Alexander, brother to Thomas – but that would also mean that John was not the biological son of Alexander but did share a mother since Marcus’s descendants autosomally match this line today. Since Alexander’s estate paid to register the death of John, that implies that John was not yet married at the time of his death and responsible for himself. This pretty much eliminates John.

The other alternative is that Marcus is the illegitimate child of one of Alexander’s daughters. His daughters were named Ann, Mary, Janet, Susannah and Elizabeth. Unfortunately, three of those names are repeated in Marcus’s daughters, but it could effectively eliminate Janet and Ann, unless Marcus had a child with that name that died young and he did not reuse the name as so many people did at that time. As it turns out, Ann and Janet married about 1732, but we have no information on the other 3 daughters other than they were minors at their father’s death in 1727 and Thomas was appointed their legal guardian in 1732.

This scenario, that Marcus was the child of one of Alexander’s daughters would fit what we do know about this family both genetically and genealogically.

The DNA Jackpot

This brings us to today. And what a day it is. Until now, none of the descendants of Marcus Younger autosomally matched the descendants of Thomas Younger, at least not that we could prove.

I manage the kit of one of the descendants of John Younger, Marcus’s son, we’ll call him Larry.

I received a query from someone about matching Larry autosomally. I sent the note that I always do, with some basic genealogy info. What I received back was a pedigree chart screen shot from the match, who we’ll call David, that included Thomas Younger as his ancestor. He descended from Thomas via a daughter.

Once again, I was stunned, because here was the link we had sought for so many years…a genetic bond between Thomas and Marcus.

Of course, the first thing I did was to ask about other lines as well through which Larry and David might be related. There were none.

Then I turned to DNA. On the Family Tree DNA match list, Larry matches me and Larry matches David, but David is not on my match list. This could well be because we don’t have any segment matches above the match threshold of approximately 7.7cM at Family Tree DNA, but since we both match Larry, I could look at Larry’s matches and then drop the comparison level to below the matching threshold to see all of our common matches between the three of us.

Here are our default 5cM matches.

I am orange. David is blue. Larry is who we are being compared against.

Dropping the cM level to 1 shows us that golden nugget we have searched for so diligently.

Look at chromosome 1. All 3 of us match on a small segment of DNA. That DNA is Younger DNA. And that little orange and blue segment proves that indeed, Marcus and Thomas were related.

This also means that there will be others who fall into this “too small to be a match but hugely relevant small segment” scenario. In order to take a look, I triangulated all of the matches for my cousin Larry and David, and there were a total of 15 individuals.

But here’s the amazing part.

There are 16 people in total, including Larry and David who match.

I compared them in the chromosome browser, and downloaded all of them. I then sorted them by chromosome and start/end segment. Here is that oh so beautiful “proof” match on chromosome 1.

There are a total of 191 individual segments across all chromosomes where these people match Larry.

Of those 191 segments, there are also 94 segments on which one or more of us also match each other. Those are shaded green above for chromosome 1.

Of those 94 segments, only 8 were large enough to be above the matching threshold. That means that there were a total of 86 segments that were below the matching threshold but that were useful genealogically. On chromosome 1 above, only Larry and I would have been over that threshold, and we were already shown as matches.

Looking at those 8 large segment matches, some were between known relatives on both sides, like me and Larry on chromosome 1, but until there was someone who connected the dots and matched someone on both sides, like David, on a segment large enough to be counted as a match, the connection wasn’t there and the other matches weren’t meaningful to the question and answer of whether Marcus and Thomas were related.

David matches Larry on a large enough segment to be counted as a match on chromosomes 4 and 10, neither of which is a match to me in that location.

The golden “proof” egg, in this case, for the three of us, was hidden in a very small segment on chromosome 1 that would otherwise have gone entirely unnoticed and unreported because it was not over the match threshold.

What’s next, you ask? I’m sending e-mails to all 15 people, of course, asking how they connect to the Younger family. Maybe, just maybe, I’ll be doubly lucky today and one of them will descend from one of the unknown wives families. We have a couple of those surnames that are theorized but unproven. That would be like hitting the lottery twice in one day!

This story already has a most wonderful PS. The genealogy Gods are at work.

As soon as I finished composing this article, I had an e-mail from a match to Larry. This lady is actually his closest match, but was not in the triangulation group I had been working with. She told me that she is an adoptee and that she was seeking information. On the off chance that she might fit into the group I had been working with, I downloaded her segments too and added it to the spreadsheet. Not only does she fit in the group, she also matches me as well and other proven Younger descendants. not on chromosome 1, but on 3 other common locations.

She matches Larry most closely, so she likely descends from John Younger’s line through Larry’s ancestor. I sent this woman some photos of the Younger descendants in my line, and she replied saying this is the first actual biological family line she has ever found. She started actively looking in 1994 when she applied for her redacted adoption information and received a razored out paper that was full of holes and looked like Swiss cheese. I can only imagine how she must have felt.

So, of course, I did what any other insanely addicted genealogist would have done. I stayed up half the night, literally, putting together all of my “notes” in some semblance of order so she can see her family line, photos of my trip to fine the Marcus Younger cemetery, etc. I asked her how she feels, and she said she is very excited and it’s also a tad bit scarry. Yes, I imagine so…knowing you’re related to a crazy genealogist. But you know, I bet she’s doing her happy dance too.

Note: Photo of Younger Store taken by Brownie Mackie in 2002 in Halifax County, Va.

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Genographic Consortium Publications

Posted on November 15, 2013 by Roberta Estes

During the Family Tree DNA Conference, Dr. Miguel Vilar, the Scientific Data Manager for the Explorer Programs was kind enough to give us an update on the Genographic project. One of the things that he mentioned was that no overarching paper had been written about the completed Geno 1.0 phase of the project, although that has been discussed. He did say that a total of 42 papers have been written by the Genographic Consortium as the result of the Genographic project, to date, and that there are several more in the pipeline.

As follow-up to that comment, Dr. Vilar was kind enough to provide a list of the papers along with a short description of the findings in each one. Thank you to both Dr. Vilar and National Geographic for sharing.

Personally, I take a great deal of pleasure and satisfaction in knowing that I was (and am) in a cumulative way a small part of this amazing, ongoing project. For anyone who has not yet, but would like to participate in testing, the Genographic 2.0 project is ongoing.

The Genographic Consortium has published 42 scientific papers, and other manuscripts are in advanced stages of preparation. Below are the titles and references plus short descriptions of the major findings, compliments of Dr. Vilar.

2007

1. Behar, D. M., Rosset, S., Blue-Smith, J., Balanovsky, O., Tzur, S., Comas, D., Mitchell, R. J., Quintana-Murci, L., Tyler-Smith, C., Wells, R. S., and The Genographic Consortium. 2007. The Genographic Project public participation mitochondrial DNA database. PLoS Genetics 3: 1083-1095.

This paper establishes Genographic’s database as the new standard mtDNA data repository and reports a new “Nearest Neighbor” statistical method for improved haplogroup classification, presenting learned experience from the public part of the project. It also makes publicly available a portion of the Genographic database, a process that will continue throughout project duration. This technical paper has been crucial in establishing the project’s importance in the scientific community.

2008

2. Gan, R. J., Pan, S. L., Mustavich, L. F., Qin, Z. D., Cai, X. Y., Qian, J., Liu, C. W., Peng, J. H., Li, S. L., Xu, J. S., Jin, L., Li, H., and The Genographic Consortium. 2008. Pinghua population as an exception of Han Chinese’s coherent genetic structure. Journal of Human Genetics 53: 303-313.

The Han Chinese are the largest ethnic group in the world with more than 1.3 billion people, comprising 19 percent of the world population. Chinese is the language spoken by this ethnic group, which can be classified into 10 major dialects. This paper focuses on studying the genetic structure of the people speaking one of these dialects, the Pinghua people. When the genetic structure of Pinghua people was compared to the rest of the Han Chinese populations, it was observed that Pinghua populations did not directly descend from Han Chinese, who originated in the north, but from other southern populations. Thus, from a genetic point of view, the Pinghua populations represent an exception to the rest of Han Chinese populations. These results can be explained if ancestral populations of Pinghua people were not replaced by Han Chinese population, but if they assimilated the Han Chinese language and culture.

3. Zalloua, P. A., Xue, Y., Khalife, J., Makhoul, N., Debiane, L., Platt, D. E., Royyuru, A. K., Herrera, R. J., Soria Hernanz, D. F., Blue-Smith, J., Wells, R. S., Comas, D., Bertranpetit, J., Tyler-Smith, C., and The Genographic Consortium. 2008. Y-chromosomal diversity in Lebanon is structured by recent historical events. American Journal of Human Genetics 82: 873-882.

Lebanon is a small country in the Middle East inhabited by almost 4 million people from a wide variety of ethnicities and religions. The results of this paper indicate that male genetic variation within Lebanon is strongly structured by religion. This unusual situation can be accounted for by two major known historical migrations into Lebanon. The Islamic expansion from the Arabian Peninsula beginning in the 7th century introduced genetic lineages typical of the Arabian peninsula into Lebanese Muslims, while the crusader activity in the 11th-13th centuries introduced Western European lineages into Lebanese Christians.

4. Behar, D. M., Villems, R., Soodyall, H., Blue-Smith, J., Pereira, L., Metspalu, E., Scozzari, R., Makkan, H., Tzur, S., Comas, D., Bertranpetit, J., Quintana-Murci, L., Tyler-Smith, C., Wells, R. S., Rosset, S., and The Genographic Consortium. 2008. The dawn of human matrilineal diversity. American Journal of Human Genetics 82: 1130-1140.

African genetic diversity is unlike that found anywhere else in the world. This paper seeks to make sense of some of the most fundamental questions surrounding our earliest ancestors on the continent. Where specifically did we originate in Africa? Was it from a single group or the result of many? When do we first see African lineages appear outside of Africa? About 350 novel mitochondrial whole-genome sequences were included — doubling the existing published dataset — and the paper presented a new tree of African mtDNA diversity, reporting many novel African lineages for the first time. This paper provides an age estimate for the earliest split of humans in East Africa as one group headed south and was subsequently isolated. It explains that all humans came from a single population that split into two groups, shows that more than 99 percent of all living humans descend from one of these two groups, and suggests historical reasons for why genetic mixture did not exist between these ancient populations. It also presents evidence for the emergence of these early lineages into the Middle East and the origins of the two major non-African groups, M and N, respectively. The paper received considerable media attention — approximately 275 articles — including substantial pieces in the Economist and on CNN/BBC online.

5. Behar, D. M., Blue-Smith, J., Soria-Hernanz, D. F., Tzur, S., Hadid, Y., Bormans, C., Moen, A., Tyler-Smith, C., Quintana-Murci, L., Wells, R. S., and The Genographic Consortium. 2008. A novel 154-bp deletion in the human mitochondrial DNA control region in healthy
individuals. Human Mutation 29: 1387-1391.

This paper describes a novel deletion of 154 base pairs within the control region of the human mitochondrial genome that was originally identified in an anonymous Japanese public participant. It was demonstrated that this deletion is a heritable character since it was transmitted from the participant’s mother to her two sons. This is the first time that such a large deletion located in this specific portion of the control region has been observed to not have negative effects in the health of the carriers. The identification of this large heritable deletion in healthy individuals challenges the current view of the control region as playing a crucial role in the replication and regulation of the mitochondrial genome. It is anticipated that this finding will lead to further research on the reported samples in an attempt to increase our understanding of the role of specific sequences within the control region for mtDNA replication. Finally, this paper illustrates the importance of creating a large database of human genetic variation in order to discover rare genetic variants that otherwise would remain unidentified. The discovery of such rare mtDNA haplotypes will be important to identifying the relative power of adaptive and non-adaptive forces acting on the evolution of the mtDNA genome.

6. Parida, L., Melé, M., Calafell, F., Bertranpetit, J., and The Genographic Consortium. 2008. Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns. Journal of Computational Biology 15: 1133-1153.

Traditionally the nonrecombinant, maternally inherited (mtDNA) and paternally inherited (Y chromosome) genomes have been widely used for phylogenetic and evolutionary studies in humans. However, these two genomes only represent 1 percent of the total genetic variation within an individual, and sampling just these two loci is inadequate to reconstruct with any precision the time-depth and pattern of human evolution. The scope of this paper is to elaborate on a mathematical algorithm that includes recombination patterns among human populations. This approach will allow us to use the rest of the recombining genome to reconstruct more accurately the patterns of human migration.

7. Rossett, S., Wells, R. S., Soria-Hernanz, D. F., Tyler-Smith, C., Royyuru, A. K., Behar, D. M., and The Genographic Consortium. 2008. Maximum-likelihood estimation of site-specific mutation rates in human mitochondrial DNA from partial phylogenetic classification. Genetics 180: 1511-1524.

This paper presents novel algorithms to estimate how frequently each base pair of the hypervariable region of the mtDNA changes. Implementations of these algorithms will help to better investigate functionality in the mtDNA and improve current classification of mtDNA haplogroups.

8. Zalloua, P. A., Platt, D. E., El Sibai, M., Khalife, J., Makhoul, N., Haber, M., Xue, Y., Izaabel, H., Bosch, E., Adams, S. M., Arroyo, E., López-Parra, A. M., Aler, M., Picornell, A., Ramon, M., Jobling, M. A., Comas, D., Bertranpetit, J., Wells, R. S., Tyler-Smith, C., and The Genographic Consortium. 2008. Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean. American Journal of Human Genetics 83: 633-642.

The Phoenicians gave the world the alphabet and a love of the color purple, and this study shows that they left some of their genes as well. The paper shows that as many as one in 17 men in the Mediterranean basin may have a Phoenician as a direct male-line ancestor, using a novel analytical method for detecting the subtle genetic impact of historical population migrations. Its first application has been to reveal the genetic legacy of the Phoenicians, an intriguing and mysterious first-millennium B.C. trading empire. From their base in present-day Lebanon, the Phoenicians expanded by sea throughout the Mediterranean, founding colonies as far as Spain and North Africa, where their most powerful city, Carthage, was located. The world’s first “global capitalists,” the Phoenicians controlled trade throughout the Mediterranean basin for nearly a thousand years until their conquest by Rome in the 2nd century B.C. Over the ensuing centuries, much of what was known about this enigmatic people was lost or destroyed. This paper received substantial international and domestic press coverage, including an article in The New York Times.

2009

9. Parida, L., Javed, A., Melé, M., Calafell, F., Bertranpetit, J., and The Genographic Consortium. 2009. Minimizing recombinations in consensus networks for phylogeographic studies. BMC Bioinformatics 10: Article S72.

This paper implements a new mathematical model to identify recombination spots in human populations to infer ancient recombination and population-specific recombination on a portion of the X chromosome. The results support the widely accepted out-of-Africa model of human dispersal, and the recombination patterns were capable of detecting both continental and population differences. This is the first characterization of human populations based on recombination patterns.

10. El-Sibai, M., Platt, D. E., Haber, M., Xue, Y., Youhanna, S. C., Wells, R. S., Izaabel, H., Sanyoura, M. F., Harmanani, H., Ashrafian Bonab, M., Behbehani, J., Hashwa, F., Tyler-Smith, C., Zalloua, P. A., and The Genographic Consortium. 2009. Geographical structure of the Y-chromosomal genetic landscape of the Levant: A coastal-inland contrast. Annals of Human Genetics 73: 568-581.

This paper examines the male-specific phylogeography of the Levant and its surroundings. The Levant lies in the eastern Mediterranean region, south of the mountains of south Turkey and north of the Sinai Peninsula. It was found that the Levantine populations cluster together when considered against a broad Middle-East and North African background. However, within Lebanon there is a coastal-inland (east-west) pattern in the diversity and frequency of several Y haplogroups. This pattern is likely to have arisen from differential migrations, with different lineages introduced from the east and west.

2010

11. Haak, W., Balanovsky, O., Sanchez, J. J., Koshel, S., Zaporozhchenko, V., Adler, C. J., Der Sarkissian, C. S. I., Brandt, G., Schwarz, C., Nicklisch, N., Dresely, V., Fritsch, B., Balanovska, E., Villems, R., Meller, H., Alt, K. W., Cooper, A., and The Genographic Consortium. 2010. Ancient DNA from European Early Neolithic farmers reveals their Near Eastern affinities. PLoS Biology 8: Article e1000536.

The nature and speed of the Neolithic transition in Europe is a matter of continuing debate. In this paper, new genetic analyses based on ancient human remains from the earliest farming culture in Central Europe known as the Linear Pottery Culture (5,500-4,900 years ago) indicate a shared genetic maternal affinity with modern-day Near East and Anatolia, and therefore they likely came from the Middle East. However, these lineages from the earliest agriculturalists were also distinct from the current genetic lineages observed in European populations, indicating that major demographic events continued in Europe during the Neolithic. These results point out the importance of using ancient DNA to better understand past demographic events.

12. Melé, M., Javed, A., Pybus, M., Calafell, F., Parida, L., Bertranpetit, J., and The Genographic Consortium. 2010. A new method to reconstruct recombination events at a genomic scale. PLoS Computational Biology 6: Article e1001010.

A chromosomal recombination event creates a junction between two parental sequences. These recombinant sequences are transmitted to subsequent generations, and recombination is one of the main forces molding human genetic diversity. However, the information about genetic relationships among populations given by these events is usually overlooked due to the analytical difficulty of identifying the history of recombination events. This paper validates and calibrates the IRiS software for inferring the history of recombination events, allowing the creation of novel recombinational “markers” known as recotypes, which can be analyzed in a similar way to standard mutational markers.

13. Qin, Z., Yang, Y., Kang, L., Yan, S., Cho, K., Cai, X., Lu, Y., Zheng, H., Zhu, D., Fei, D., Li, S., Jin, L., Li, H., and The Genographic Consortium. 2010. A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the Last Glacial Maximum. American Journal of Physical Anthropology 143: 555-569.

The Tibetan Plateau was long considered one of the last areas to be populated by modern humans. Recent archaeological, linguistic and genetic findings have challenged this view. In this paper, maternal lineages of 562 individuals from nine different regions within Tibet have been analyzed to further investigate the timing and routes of entry of humans into the plateau. The maternal diversity in Tibet primarily reflects northern East Asian ancestry, likely reflecting a population expansion from this region into the plateau prior to the Last Glacial Maximum (LGM) ~18,000 years ago. In addition, the highest diversity was concentrated in the southern part of the plateau, indicating that this region probably acted as a population refugium during the LGM and the source of a post-LGM expansion within the plateau.

14. Zhadanov, S. I., Dulik, M. C., Markley, M., Jennings, G. W., Gaieski, J. B., Elias, G., Schurr, T. G., and The Genographic Project Consortium. 2010. Genetic heritage and native identity of the Seaconke Wampanoag tribe of Massachusetts. American Journal of Physical Anthropology 142: 579-589.

The biological ancestry of the Seaconke Wampanoag tribe, a group of Native American clans in southern Massachusetts, reflects the genetic consequences of epidemics and conflicts during the 16^th century that decimated their population, reducing them from an estimated 12,000 individuals at the beginning of the century to less than 400 at the end. The majority of the paternal and maternal lineages in present-day Seaconke Wampanoag, however, belong to West Eurasian and African lineages, revealing the extensive interactions with people from different ancestries that settled the region during the past four centuries.

2011

15. Adler, C. J., Haak, W., Donlon, D., Cooper, A., and The Genographic Consortium. 2011. Survival and recovery of DNA from ancient teeth and bones. Journal of Archaeological Science 38: 956-964.

The recovery of genetic material from ancient human remains depends on the sampling methods used as well as the environment where the human material was preserved. The results presented in this study quantify the damage caused to ancient DNA by various methods of sampling teeth and bones. The negative impact is minimized if very low drill speeds are used during DNA extraction, increasing both the quantity and quality of material recovered. In addition, the mtDNA content of tooth cementum was five times higher than other commonly used methods, making this component the best place to sample ancient DNA. These conclusions will help to guide future sampling of DNA from ancient material.

16. Haber, M., Platt, D. E., Badro, D. A., Xue, Y., El-Sibai, M., Ashrafian Bonab, M., Youhanna, S. C., Saade, S., Soria-Hernanz, D. F., Royyuru, A., Wells, R. S., Tyler-Smith, C., Zalloua, P. A., and The Genographic Consortium. 2011. Influences of history, geography, and religion on genetic structure: The Maronites in Lebanon. European Journal of Human Genetics 19: 334-340.

Cultural patterns frequently leave genetic traces. The aim of this study was to explore the genetic signature of the establishment of religious communities in a region where some of the most influential world religions originated, using the Y chromosome as an informative male-lineage marker. The analysis shows that the religions in Lebanon were adopted within already distinguishable communities. Differentiation appears to have begun before the establishment of Islam and Christianity, dating to the Phoenician period, and isolation continued during the period of Persian domination. Religious affiliation served to reinforce the genetic signatures of pre-existing population differentiation.

17. Martínez-Cruz, B., Ziegle, J., Sanz, P., Sotelo, G., Anglada, R., Plaza, S., Comas, D., and The Genographic Consortium. 2011. Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes. Investigative Genetics 2: Article 13.

This paper presents a robust and accurate Y-chromosome multiplex assay that can genotype in a single reaction 121 markers distinguishing most of the haplogroups and subhaplogroups observed in European populations. The assay was >99 percent accurate in assigning haplogroups, minimizing sample handling errors that can occur with several independent TaqMan reactions.

18. Jota, M. S., Lacerda, D. R., Sandoval, J. R., Vieira, P. P. R., Santos-Lopes, S. S., Bisso-Machado, R., Paixão-Cortes, V. R., Revollo, S., Paz-y-Miño, C., Fujita, R., Salzano, F. M., Bonatto, S. L., Bortolini, M. C., Tyler-Smith, C., Santos, F. R., and The Genographic Consortium. 2011. A new subhaplogroup of Native American Y-chromosomes from the Andes. American Journal of Physical Anthropology (published online Sept. 13, 2011.)

Almost all Y chromosomes in South America fall into a single haplogroup, Q1a3a. This paper presents a new single nucleotide polymorphism (SNP) in the Q1a3a lineage that is specific to Andean populations, allowing more accurate inferences of the population history of this region. This novel marker is estimated to be ~5,000 years old, consistent with an ancient settlement of the Andean highlands.

19. Yan, S., Wang, C. C., Li, H., Li, S. L., Jin, L., and The Genographic Consortium. 2011. An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4. European Journal of Human Genetics 19: 1013-1015.

Y-chromosome Haplogroup O is the dominant Y-chromosome lineage in East Asians, carried by more than a quarter of all males on the world. This study revises the haplogroup O phylogeny, using several recently discovered markers. The newly generated tree for this haplogroup will lead to a more detailed understanding of the population history of East Asia.

20. Yang, K., Zheng, H., Qin, Z., Lu, Y., Farina, S. E., Li, S., Jin, L., Li, D., Li, H., and The Genographic Consortium. 2011. Positive selection on mitochondrial M7 lineages among the Gelong people in Hainan. Journal of Human Genetics 56: 253-256.

The Gelong people migrated in the last 1,000 years from Guizhou province in southern China to Hainan island (the hottest province in China). The genetic structure of the Gelong people showed a clearly sex-biased pattern of admixture with the indigenous Hainan population (Hlai people), with 30.7 percent of the maternal lineages being of Hainan origin in contrast to 4.9 percent of the paternal lineages. This striking pattern is partially explained through the action of selection on the M7 Hainan autochthonous maternal lineages, leading to their expansion in the admixed population. This may be due to some selective advantage provided by the M7 lineages in the tropical Hainan climate. Future whole mtDNA genome sequencing of these M7 lineages may reveal their functional relevance and the mechanism involved in human adaptation to tropical climates.

21. Balanovsky, O., Dibirova, K., Dybo, A., Mudrak, O., Frolova, S., Pocheshkhova, E., Haber, M., Platt, D., Schurr, T., Haak, W., Kuznetsova, M., Radzhabov, M., Balaganskaya, O., Druzhinina, E., Zakharova, T., Soria Hernanz, D. F., Zalloua, P., Koshel, S., Ruhlen, M., Renfrew, C., Wells, R. S., Tyler-Smith, C., Balanovska, E., and The Genographic Consortium. 2011. Parallel evolution of genes and languages in the Caucasus region. Molecular Biology and Evolution 28: 2905-2920.

The Caucasus region harbors some of the highest linguistic diversity on Earth, leading to the moniker “The Mountain of Languages.” To investigate the forces that may have molded Caucasian linguistic patterns, the Genographic team studied Y-chromosome variation in 1,525 men from 14 populations in the Caucasus. The Y-chromosome lineages found in the Caucasus originated in the Near East and were introduced to the Caucasus in the late Upper Paleolithic or early Neolithic periods. This initial settlement was followed by a high degree of population isolation due to the mountainous terrain. Comparisons between the genetic and linguistic trees showed a striking correspondence between the topology and divergence times for the two, revealing a parallel evolution of genes and languages in the Caucasus in the past few millennia. This high degree of correspondence between genetic and linguistic patterns has not been seen in other regions of the world.

22. Gaieski, J. B., Owings, A. C., Vilar, M. G., Dulik, M. C., Gaieski, D. F., Gittelman, R. M., Lindo, J., Gau, L., Schurr, T. G., and The Genographic Consortium. 2011. Genetic ancestry and indigenous heritage in a Native American descendant community in Bermuda. American Journal of Physical Anthropology 146: 392-405.

Bermuda is an isolated group of islands in the middle of the Atlantic settled during the 17^th century by Western Europeans along with African and Native American slaves. The pattern of Y-chromosome and mitochondrial DNA diversity was studied in 111 members of a “native” community on St. David’s Island. Two-thirds of the paternal lineages are of European origin, while two-thirds of the mitochondrial DNA lineages are African. In contrast to other English-speaking communities in the Americas, however, the majority of St. David’s maternal lineages appear to derive from central and southern Africa, regions that historically were controlled by Portuguese slave traders. It is likely that the English settlers of Bermuda obtained slaves from these Portuguese sources. Despite genealogical records and oral traditions indicating significant arrivals of Native Americans as labor force, the proportion of Native American lineages was less than 2 percent on both the paternal and maternal sides. This study gives new insights into the complex history of colonization and migration in the Caribbean.

23. Cai, X., Qin, Z., Wen, B., Xu, S., Wang, Y., Lu, Y., Wei, L., Wang, C., Li, S., Huang, X., Jin, L., Li, H., and The Genographic Consortium. 2011. Human Migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes. PLoS ONE 6: e24282. doi:10.1371/journal.pone.0024282

The number and timing of the initial migrations to East Asia remain unresolved. This paper studied the Y-chromosome diversity in Mon-Khmer (MK)- and Hmong-Mien (HM)-speaking populations who are believed to be the source populations of other East Asians. The pattern of diversity for the O3a3b-M7 and O3a3c1-M117 lineages among MK, HM and other East Asian populations suggests an early unidirectional diffusion from Southeast Asia northward into East Asia around the time of the Last Glacial Maximum (~18,000 years ago). The ancestral population sizes of these first colonizers are believed to have gone through drastic reductions due to the barriers imposed by the geographic conditions (mountains and jungle) and the colder climate at the time of the migration. This “serial bottleneck” effect has left a distinctive genetic pattern in the present-day populations of East Asia, revealing their past demographic history.

24. Melé, M., Javed, A., Pybus, M., Zalloua, P., Haber, M., Comas, D., Netea, M. G., Balanovsky, O., Balanovska, E., Jin, L., Yang, Y., Pitchappan, R. M., Arunkumar, G., Parida, L., Calafell, F., Bertranpetit, J., and The Genographic Consortium. 2011. Recombination gives a new insight in the effective population size and the history of the Old World human populations. Molecular Biology and Evolution (published online Sept. 1, 2011.) doi:10.1093/molbev/msr213

The IRiS method (described in paper 12) was used to assess the patterns of recombination on the X chromosome in 30 populations from Africa, Europe and Asia. The results suggest that the ancestors of non-African populations first left Africa in a single coastal migration across the Bad-el-Mandeb strait rather than through the Sinai Peninsula. The method allowed the team to estimate that sub-Saharan ancestral population sizes were four times greater than those in populations outside of Africa, while Indian ancestral sizes were the greatest among Eurasians. These results suggest that Indian populations played a major role in the expansions of modern humans to the rest of the world.

25. Javed, A., Melé, M., Pybus, M., Zalloua, P., Haber, M., Comas, D., Netea, M. G., Balanovsky, O., Balanovska, E., Jin, l., Yang, Y., Arunkumar, G., Pitchappan, R., Bertranpetit, J., Calafell, F., Parida, L., and The Genographic Consortium. 2011. Recombination networks as genetic markers in a human variation study of the Old World. Human Genetics (first published online Oct. 18, 2011.)

An expanded analysis of the recombination dataset published in abbreviated form in paper 24, analyzing three additional populations. The conclusions outlined in paper 24 are bolstered through the more thorough presentation of the results.

2012

26. Behar DM, Harmant C, Manry J, van Oven M, Haak W, Martinez-Cruz B, Salaberria J, Oyharçabal B, Bauduer F, Comas D, Quintana-Murci L; Genographic Consortium. 2012. The Basque paradigm: genetic evidence of a maternal continuity in the Franco-Cantabrian region since pre-Neolithic times. American Journal of Human Genetics 9;90(3):486-93.

This study focus on the maternal genetic diversity of Basques, the last European population to have kept a pre-Indo European language, to increase knowledge of the origins of the Basque people and, more generally, on the role of the Franco-Cantabrian refuge in the post-glacial repopulation of Europe. The maternal ancestry of 908 Basque and non-Basque individuals from the Great Basque Country and adjacent regions were studied plus 420 complete mtDNA genomes within haplogroup H. The results identified six mtDNAhaplogroups autochthonous to the Franco-Cantabrian region and, more specifically, to Basque-speaking populations. Further, expansion of these haplogroups were estimated at ~4,000 ybp with a separation from the general European gene pool to have happened ~8,000 ybp predating the Indo-European arrival to the region. Thus, the results clearly support the hypothesis of a partial genetic continuity of contemporary Basques with the indigenous Paleolithic settlers of their homeland.

27. Martínez-Cruz B, Harmant C, Platt DE, Haak W, Manry J, Ramos-Luis E, Soria-Hernanz DF, Bauduer F, Salaberria J, Oyharçabal B, Quintana-Murci L, Comas D; the Genographic Consortium. Evidence of pre-Roman tribal genetic structure in Basques from uniparentally inherited markers. Molecular Biology and Evolution (published online March 12, 2012) doi: 10.1093/molbev/mss091.

Basques have received considerable attention from anthropologists, geneticists and linguists during the last century due to the singularity of their language and to other cultural and biological characteristics. Despite the multidisciplinary efforts performed to address the questions of the origin, uniqueness and heterogeneity of Basques, the genetic studies performed up to now have suffered from a weak study-design where populations are not analyzed in an adequate geographic and population context. To address the former questions and to overcome these design limitations, uniparental genomes (Y chromosome and mitochondrial DNA) of ~900 individuals from 18 populations were analyzed, including those where Basque is currently spoken and surrounding populations where Basque might have been spoken in historical times. Results situate Basques within the western European genetic landscape, although with less external influences than other Iberians and French populations. In addition, the genetic heterogeneity and structure observed in the Basque region results from pre-Roman tribal structure related to geography and is linked to the increased complexity of emerging societies during the Bronze Age. The rough overlap of tribal and current dialect limits supports the notion that the environmental diversity in the region has played a recurrent role in cultural differentiation and ethnogenesis at different time periods.

28. Kang, L., Lu, Y., Wang, C., Hu, K., Chen, F., Liu, K., Li, S., Jin, L., Li, H., and The Genographic Consortium. 2012. Y-chromosome O3 Haplogroup diversity in Sino-Tibetan populations reveals two migration routes into the Eastern Himalayas. Annals of Human Genetics 76: 92–99.

This paper further explores the question of how Himalayas was populated by studying the genetic diversity of the paternal lineages of two ethnic groups from the eastern Himalayas: the Luoba and Deng. These two Sino-Tibetan speaking groups exhibited a distinct genetic composition indicating different genetic origins. The paternal diversity of the Louba people indicates past gene flow from Tibetans as well as from western and north Eurasian people. In contrast, Deng exhibited lineages similar to most of Sino-Tibetans from the east. The overall lowest diversity observed in the eastern Himalayas suggests that this area was the end point of two migratory routes of Sino-Tibetans from north China around 2,000-3,000 years ago. These date estimates also agrees with the historical records.

29. Lu, Y., Wang, C., Qin, Z., Wen, B., Farina, S. E., Jin, L., Li, H., and The Genographic Consortium. 2012. Mitochondrial origin of the matrilocal Mosuo people in China. Mitochondrial DNA 23: 13–19

The Mosuo people currently live around the Lugu Lake on the border of the Yunan and Sichuan provinces of China and they are the last matrilocal population in the main land of the country. To investigate the maternal history of this ethnic group, partial genetic sequences of the mitochondria (a maternally inherited genome) were studied among Mosuo people and other larger surrounding ethnic groups. Groups with matrilocal traditions are expected to exhibited a lower mitochondrial genetic diversity because the movement of these genomes are reduced since woman remain within families after marriage. However, the results presented here did not reflect these expectations indicating that Mouso may have started practicing matrilocality long time ago, at least after the Paleolithic Age. In contrast to previous studies that showed a clear relationship between Mouso and Naxi people based on just mtDNA haplogroup frequencies, the network analyses presented here indicated clear clusters of individual sequences between Mouso and Pumi lineages. The genetic resemblance between these two group are concordant with other evidences from cultural and language studies. These results indicate that simply comparing haplogroups frequencies among ethnic groups may lead to erroneous conclusions and analyses comparing mtDNA sequences are better suitable for exploring genetic relationship among ethnic groups.

30. Haber M, Platt DE, Ashrafian Bonab M, Youhanna SC, Soria-Hernanz DF, Martínez-Cruz B, Douaihy B, Ghassibe-Sabbagh M, Rafatpanah H, Ghanbari M, Whale J, Balanovsky O, Wells RS, Comas D, Tyler-Smith C, Zalloua PA; The Genographic Consortium. 2012. Afghanistan’s Ethnic Groups Share a Y-Chromosomal Heritage Structured by Historical Events. PLoS ONE 7(3): e34288. doi:10.1371/journal.pone.0034288

This study focus on how Afghanistan’s ethnic groups relate to each others and with other populations from neighboring countries. The results presented indicated that major genetic differences among Afghanistan’s ethnic groups are relatively recent. The different modern ethnic groups share a genetic heritage probably formed during the Neolithic in the founding of the early farming communities. However, differentiation among the ethnic groups likely started during the Bronze Age driven by the establishment of the first civilizations. Later migrations and invasions to the region, gave the Afghans a unique genetic diversity in Central Asia.

31. Schurr, T. G., Dulik, M. C., Owings, A. C., Zhadanov, S. I., Gaieski, J. B., Vilar, M. G., Ramos, J., Moss, M. B., Natkong, F. and The Genographic Consortium. 2012. Clan, language, and migration history has shaped genetic diversity in Haida and Tlingit populations from Southeast Alaska. American Journal of Physical Anthropology. (published online May 1, 2012) doi: 10.1002/ajpa.22068.

This manuscript gives new insights about the genetics of the linguistically distinctive Haida and Tlingit tribes of Southeast Alaska. More espcifically, this paper study the role that Southeast Alaska may have played in the early colonization of the Americas; the genetic relationships of Haida and Tlingit to other indigenous groups in Alaska and Canada; the relationship between linguistic and genetic data for populations assigned to the Na-Dene linguistic family; the possible influence of matrilineal clan structure on patterns of genetic variation in Haida and Tlingit populations; and the impact of European entry into the region on the genetic diversity of these indigenous communities. The analysis indicates that, while sharing a ‘northern’ genetic profile, the Haida and the Tlingit are genetically distinctive from each other. In addition, Tlingit groups themselves differ across their geographic range, in part due to interactions of Tlingit tribes with Athapaskan and Eyak groups to the north. The data also reveal a strong influence of maternal clan identity on mtDNA variation in these groups, as well as the significant influence of non-native males on Y-chromosome diversity. These results yield new details about the histories of the Haida and Tlingit tribes in this region.

32. Dulik, M. C., Owings, A. C., Zhadanov, S. I., Gaieski, J. B., Vilar, M. G., Schurr, T. G., and The Genographic Consortium. 2012. Y-chromosome analysis of native North Americans reveals new paternal lineages and genetic differentiation between Eskimo-Aleut and Dene speaking populations. Accepted for publication in April in PNAS.

The genetic origins of the linguistically diverse Native Americans and when they reached the Americas are questions that have been explored during the last several decades. This study provides new information to these questions by increasing the number of populations sampled and the genetic resolution used in the analyses Here, it is tested whether there is any correlation between genetic diversity from paternally inherited Y-chromosomes and native populations speaking the two distinctive linguistic families: Eskimo-Aleut and Na-Dene. The results indicate that the Y chromosome genetic diversity among the first Native American was greater than previously shown in other publications. In addition, the Eskimo-Aleut and Na-Dene speaking populations showed clear genetic differences between then. The disparities in language, culture and genetic diversity between these two populations likely reflect the outcome of two migrations that happened after the initial settlement of people into the Americas.

33. Martinez-Cruz B, Ioana M, Calafell F, Arauna LR, Sanz P, Ionescu R, Boengiu S, Kalaydjieva L, Pamjav H, Makukh H, Plantiga T, van der Meer JWM, Comas D, Netea M, The Genographic Consortium. 2012. Y-chromosome analysis in individuals bearing the Basarab name of the first dynasty of Wallachian kings. PLoS ONE 7(7): e41803

The most famous Transylvanian prince is Vlad III from the Basarab royal dynasty, also commonly known as Dracula. The ethnic origins of the Basarab is intensively debated among historians and it is unclear of whether they are descendants of the Cuman people (an admixed Turkic people that reached Romania from the East in the 11^th century) or of Vlach people (local Romanians). This paper investigated the Y chromosome of 29 Romanian men carrying the surname Basarab and in order to identify their genetic origin the data was compared with four Romanian and other surrounding populations. Different Y-chromosome haplogroups were found within the individuals bearing the Basarab name, indicating that not all these individuals can be direct biological descendants of the Basarab dynasty. In addition, all these haplogroups are common in Romania and other Central and Eastern European populations. The Basarab group exhibited closer genetic distances with other Romanian populations. These results together with the absence of Eastern Asian paternal lineages in the Basarab men can be interpreted as a lack of evidence for a Cuman origin of this royal dynasty, although it cannot be positively ruled out. As a final conclusion, it seems that the Basarab dynasty was successful in spreading its name beyond the spread of its genes.

34. Rebala K, Martínez-Cruz B, Tönjes A, Kovacs P, Stumvoll M, Lindner I, Büttner A, Wichmann H-E, Siváková D, Soták M, Quintana-Murci L, Szczerkowska Z, Comas D, The Genographic Consortium. 2012. Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements. European Journal of Human Genetics 21(4): 415-422

One of the most outstanding phenomena in the Y-chromosomal diversity in Europe concerns the sharp genetic border identified between the ethnically /linguistically defined Slavic (from Poland) and German populations (from Germany). The Polish paternal lineages also reveal great degree of homogeneity in spite of a relatively large geographic area seized by the Polish state. Two main explanations have been proposed to explain the phenomena: (i) Massive human resettlements during and shortly after the World War II, and (ii) an early medieval Slavic migrations that displayed previous genetic heterogeneity. In order to answer these questions, 1,156 individuals from several Slavic and German populations were analyzed, including Polish pre-war regional populations and an autochthonous Slavic population from Germany. This study demonstrates for the first time that the Polish paternal lineages were unevenly distributed within the country before the forced resettlements of millions of people during and shortly after the WWII. Finally, the coalescence analyses support hypothesis that the early medieval Slavic expansion in Europe was a demographic event rather than solely a linguistic spread of the Slavic language.

35. Arunkumar G, Soria-Hernanz DF, Kavitha VJ, Arun VS, Syama A, Ashokan KS, Gandhirajan KT, Vijayakumar K, Narayanan M, Jayalakshmi M, Ziegle JS, Royyuru AK, Parida L, Wells RS, Renfrew C, Schurr TG, Smith CT, Platt DE, Pitchappan R; Genographic Consortium. 2012. Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system. PLoS ONE. 7(11): e50269

Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system. This study investigates the origin of the caste system by genotyping 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) populations from the Dravidian-speaking Tamil Nadu state in the southernmost part of India. 81% of Y chromosome were autochthonous Indian haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10-30 Kya). Results show a strong evidence for genetic structure, and coalescent analyses suggest that the stratification was established 4-6 thousand years ago, with little admixture took place during the last several millennia. The overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation are best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.

2013

36. Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, Ghassibe-Sabbagh M, Johnsrud B, Khazen G, Matisoo-Smith E, Soria-Hernanz DF, Wells RS, Tyler-Smith C, Platt DE, Zalloua PA, The Genographic Consortium. 2013. Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of Modern Middle Eastern populations with European and African populations. PLoS ONE 8(1):e54616

The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. In addition, post LGM expansions into the region and subsequent population movements have created a striking genetic mosaic in the region. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated. Lebanon’s mtDNA showed a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by Y-haplogroups J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe, as indicated by the mtDNA data. Lastly, while each population shows evidence of historic expansions that now define the Middle East, Africa, and Europe, most Middle Eastern populations show distinctive mtDNA and Y-haplogroup characteristics that suggest long standing settlements with relatively little impact from other populations.

37. Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, Koshel S, Zaporozhchenko V, Gronenborn D, Moiseyev V, Kolpakov E, Shumkin V, Alt KW, Balanovska E, Cooper A, Haak W, The Genographic Consortium. 2013. Ancient DNA reveals prehistoric gene-flow from Siberia in the complex human population history of North East Europe. PLoS Genetics 9(2): e1003296

Archaeological, anthropological, and genetic research of Northeastern European populations have revealed a series of influences from Western and Eastern Eurasia. While genetic data from modern-day populations is commonly used to make inferences about origins and past migrations, ancient DNA provides a powerful tool by giving a snapshot of the past genetic diversity. This study generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three Mesolithic and the Early Metal Age (7,500 and 3,500 years ago) sites in northwest Russia. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroup U (U2e, U4, U5a), commonly observed in hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested genetic influx from central/eastern Siberia. This genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami suggests a strong influence of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrated how ancient DNA can improve our understanding of human population movements across Eurasia.

38. Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Jane Adler C, Richards SM, Sarkissian CD, Ganslmeier R, Friederich S, Dresely V, van Oven M, Kenyon R, Van der Hoek MB, Korlach J, Luong K, Ho SY, Quintana-Murci L, Behar DM, Meller H, Alt KW, Cooper A, The Genographic Consortium. 2013. Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nature Communications 4:1764

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. This project investigated maternal population history of modern Europeans by sequencing 39 complete haplogroup H mitochondrial genomes from ancient remains; and comparing this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Results revealed that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from later pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Newly dated haplogroup H genomes enabled the reconstruction of the evolutionary history of the haplogroup, and revealed a mutation rate 45% higher than previous estimates.

39. Elhaik E, Greenspan E, Staats S, Krahn T, Tyler-Smith C, Xue Y, Tofanelli S, Francalacci P, Cucca F, Pagani L, Jin L, Li H, Schurr TG, Greenspan B, Spencer Wells R, The Genographic Consortium. 2013. The GenoChip: a new tool for genetic anthropology. Genome Biology & Evolution 5(5): 1021-1031

The Genographic Project is an international effort aimed at charting human migratory history. The first phase of the project was focused on haploid DNA markers (Y-chromosome and mtDNA), while the current phase focuses on markers from across the entire genome using the newly created GenoChip. GenoChip was designed to enable higher resolution research into outstanding questions in genetic anthropology. It includes ancestry informative markers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and it was designed to identify all known Y-chromosome and mtDNA haplogroups. The chip was also carefully vetted to avoid inclusion of medically relevant markers. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays. Although all arrays yielded similarly shaped FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. In summary, the GenoChip is a dedicated genotyping platform for genetic anthropology. With an unprecedented number of approximately 12,000 Y-chromosomal and approximately 3,300 mtDNA SNPs and over 130,000 autosomal and X-chromosomal SNPs with no health, medical, or phenotypic relevance, the GenoChip is a useful tool for genetic anthropology and human population genetics.

40. Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, Sanz P, Yang-Yao D, Manry J, Ciani G, Luiselli D, Quintana-Murci L, Comas D, Pettener D; The Genographic Consortium. 2013. Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata. PLoS ONE 8(5): e65441

Italy played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia, shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern, this project analyzed the haploid markers in ∼900 individuals from across the Italian peninsula, Sardinia and Sicily. Results show a sex-biased pattern, indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West-South East Y-chromosome structure appeared through continental Italy, likely a result of historical and demographic events. In contrast, mitochondrial (maternal) diversity is distributed homogeneously in accordance with older pre-historic events, as was the presence of an Italian Refugium during the last glacial period in Europe.

41. Sandoval JR, Lacerda DR, Jota MS, Salazar-Granara A, Vieira PP, Acosta O, Cuellar C, Revollo S, Fujita R, Santos FR, The Genographic Consortium. 2013. The genetic history of indigenous populations of the Peruvian and Bolivian Altiplano: the legacy of the Uros. PLoS ONE 8(9): e73006

Since pre-Columbian times, different cultures established themselves around the Titicaca and Poopo Lakes. Yet by the time of Spanish colonization, the Inca Empire and the Aymara and Quechua languages were dominant in the region. This study focused on the pre-Columbian history of the Altiplano populations, particularly the Uros, which claim to be directly descend from the first settlers of the Andes. Results indicate that the Uros populations stand out among others in the Altiplano, while appearing more closely related to the Aymara and Quechua from Lake Titicaca and surrounding regions, than to the Amazon Arawaks. Moreover, the Uros populations from Peru and Bolivia are genetically differentiated from each other, indicating a high heterogeneity in this ethnic group. Lastly, the results support the distinctive ancestry for the Uros populations of Peru and Bolivia, likely derived from ancient Andean lineages, but further complicated by a partial replacement during more recent farming expansion, and the establishment of complex civilizations in the Andes, such as the Inca.

42. Brandt G, Haak W, Adler CJ, Roth C, Szécsényi-Nagy A, Karimnia S, Möller-Rieker S, Meller H, Ganslmeier R, Friederich S, Dresley V, Nicklish N, Pickrell JK, Siroko F, Reich D, Cooper A, Alt KW, The Genographic Consortium 2013. Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity. Science 342, no.6155: 257-261.

Genographic project scientists, in collaboration with archeologists from Germany, successfully sequenced and analyzed DNA from 364 individuals that lived in Central Europe between 5,500 and 1,500 BC. What they found was that the shift in the frequency of DNA lineages closely matched the changes and appearances of new Central European cultures across time. In other words, the people who lived in Central Europe 7,000 years ago had different DNA lineages than those that lived there 5,000 years ago, and again different to those that lived 3,500 years ago. Central Europe was dynamic place during the Bronze age, and the genetic composition of the people that lived there demonstrates that. Ultimately, Central Europe is a melting pot of genetic lineages from different prehistoric cultures that lived there at different periods of time, each new one partially replacing the one before it.

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Gene by Gene Genomics Research Center Lab Tour

Posted on November 14, 2013 by Roberta Estes

Both before and after the 9th Annual Family Tree DNA International Conference for Genetic Genealogy this past weekend, Max Blankfeld and Bennett Greenspan were gracious enough to allow interested administrators to visit and tour their labs. I’ve toured other DNA labs, but their lab has very cool leading edge equipment. It was a wonderful treat to see it in action.

What I didn’t have was my “good” camera, so I’m sharing my iPhone photos.

I went on the last tour available and there were only a few of us, so it an excellent opportunity to see things up close and personal.

This lab is much larger than I expected. Gene by Gene, in addition to doing all of the DNA processing for Family Tree DNA, DNA Traits and the National Geographic Genographic project, is doing a significant amount of processing for research institutions such as medical schools. While we were there, they were getting ready to prep to run a large order of several hundred exome samples.

But come along with me and you can see for yourself. Bennett gave the tour personally. The bad news is that you’re going to have to rely on my memory, because nothing was allowed in the lab other than our cameras. This was to prevent contamination.

There are other contamination prevention methods as well. Anyone with open toed shoes had to put on booties. Here’s my friend Lisa, who comments periodically on my blog, suiting up for the tour. Next, we were given lab coats to wear inside the facility which we then took off and left by the door, but inside the lab, as we left.

The first stop inside is where they prepare the kits for shipping to customers when an order is placed. They purchase the empty vials, prepare the formula and fill and cap the vials, all automatically.

The “capping” process is the most interesting part and caused them the most consternation in trying to figure out the best way to do this. Bennett said they worried about having a non-tethered lid that might be dropped by the customer, and contaminated, as it turns out, needlessly.

After the kits come back, all but one of the vials goes into storage, shown below, beside the lab, for future testing. This environment does not have to be specially controlled outside of a normal office environment.

The vial that gets opened for the testing undergoes a different process that begins with removing the DNA from the vial and mixing it with a chemical solution that shakes the DNA out of the cells.

This is done overnight in a shaker machine. Reminded me of a paint shaker.

Have you ever seen a custom $600,000 freezer with a robot to retrieve the frozen goods? No? Well, you’re about to. If you have ever tested with Family Tree DNA and there is any DNA left in a vial that has been opened, it’s in this freezer which took the vendor 7 weeks to assemble on site. Capacity is over 550,000 vials and it’s about half full currently.

After the DNA is shaken out of the cells, that mixture has to be handled differently. It has been barcoded during the entire process and the prepared DNA mixture is then put into storage plates which are robotically stored. This retrieval process is initiated when an order is received by the robotic software. Keep in mind that the unit holds more samples than Family Tree DNA has today, in a very regulated deep freeze environment. Depending on what this robotic arm is doing, meaning moving plates around or extracting a specific vial, it changes its own tool on the end of its arm. It knows where every vial is in the freezer. I must admit, my Mom who has been gone since 2006 has DNA there and it made me feel kind of funny to know I was visiting “her.” But my DNA is with hers, along with a whole lot of other family members, so I guess it’s just one big family reunion in there.

After the correct vial is retrieved and the DNA mixture is extracted, the liquid is put onto a “chip” for the autosomal testing. The chip itself is about an inch by maybe 3 inches and holds 12 tests.

The DNA is pipetted into the side and then it is wicked into the chip itself.

Here is a set of two chips loaded and ready to be processed. This means that at total of 24 individual samples are being sequenced. Notice the little grey square to the size of each larger grey square. That tiny grey square is where the DNA mixture it placed and it’s wicked into the larger grey square for processing. We asked how that is done and were told that the technique is part of Illumina’s trade secrets.

Gene by Gene owns several sequencing machines. I know they have at least two Sanger sequencing machines and 4 different sizes and types of Illumina sequencing machines that run chip based tests like the Geno 2, the Family Finder and now the Big Y tests, in addition to the exome and full genome tests. These machines are incredible given that they can run hundreds of tests at a time, which is also how they have dropped the test costs exponentially in the past few years. Some equipment is optimized for running many samples but more slowly and some for running fewer samples but more quickly.

After reading and being automatically scored, the DNA results are reported to the client.

At the end of the lab tour, just outside, is the Customer Service area where the Customer Service Reps work. I’ll tell you what, they had their hands full this week and weekend with their regular call load, a conference and an office full of nosey and interested project administrators.