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

Posted on October 18, 2014 by Roberta Estes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Indeed, we do live in exciting times.

Honoring Anzick

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

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

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

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

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

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

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

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Tenth Annual Family Tree DNA Conference Wrapup

Posted on October 15, 2014 by Roberta Estes

This slide, by Robert Baber, pretty well sums up our group obsession and what we focus on every year at the Family Tree DNA administrator’s conference in Houston, Texas.

Getting to Houston, this year, was a whole lot easier than getting out of Houston. They had storms yesterday and many of us spent the entire day becoming intimately familiar with the airport. Jennifer Zinck, of Ancestor Central, is still there today and doesn’t have a flight until late.

And this is how my day ended, after I finally got out of Houston and into my home airport. This isn’t at the airport, by the way. Everything was fine there, but I made the apparent error of stopping at a Starbucks on the way home. This is the parking lot outside an hour or so later. What can I say? At least I had my coffee, and AAA rocks, as did the tow truck driver and my daughter for getting out of bed to come and rescue me!!! Hmmm, I think maybe things have gone full circle. I remember when I used to go and rescue her:)

So far, today hasn’t improved any, so let’s talk about something much more pleasant…the conference itself.

Resources

One of the reasons I mentioned Jennifer Zinck, aside from the fact that she’s still stuck in the airport, is because she did a great job actually covering the conference as it happened. Since I had some time yesterday to visit with her since our gates weren’t terribly far apart, I asked her how she got that done. I took notes too, and photos, but she turned out a prodigious amount of work in a very short time. While I took a lightweight MacBook Air, she took her regular PC that she is used to typing on, and she literally transcribed as the sessions were occurring. She just added her photos later, and since she was working on a platform that she was familiar with, she could crop and make the other adjustments you never see but we perform behind the scenes before publishing a photo.

On the other hand, I struggled with a keyboard that works differently and is a different size than I’m used to as well as not being familiar with the photo tools to reduce the size of pictures, so I just took rough notes and wrote the balance later. Having familiar tools make such a difference. I think I’ll carry my laptop from now on, even though it is much heavier. Kudos to Jennifer!

I was initially going to summarize each session, but since Jen did such a good job, I’m posting her links. No need to recreate a wheel that doesn’t need to be recreated.

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy/

ISOGG, the International Society of Genetic Genealogy is not affiliated with Family Tree DNA or any testing company, but Family Tree DNA is generous enough to allow an ISOGG meeting on Sunday before the first conference session.

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-isogg-meeting/

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-sunday/

You can find my conference postings here:

http://dna-explained.com/2014/10/11/tenth-annual-family-tree-dna-conference-opening-reception/

http://dna-explained.com/2014/10/12/tenth-annual-family-tree-dna-conference-day-2/

http://dna-explained.com/2014/10/13/tenth-annual-family-tree-dna-conference-day-3/

Several people were also posting on a twitter feed as well.

https://twitter.com/search?q=%23FTDNA2014&src=tyah

Those of you where are members of the ISOGG Yahoo group for project administrators can view photos posted by Katherine Borges in that group and there are also some postings on the Facebook ISOGG group as well.

Now that you have the links for the summaries, what I’d like to do is to discuss some of the aspects I found the most interesting.

The Mix

When I attended my first conference 10 years ago, I somehow thought that for the most part, the same group of people would be at the conferences every year. Some were, and in fact, a handful of the 160+ people attending this conference have attended all 10 conferences. I know of two others for certain, but there were maybe another 3 or so who stood up when Bennett asked for everyone who had been present at all 10 conferences to stand.

Doug Mumma, the very first project administrator was with us this weekend, and still going strong. Now, if Doug and I could just figure out how we’re related…

Some of the original conference group has passed on to the other side where I’m firmly convinced that one of your rewards is that you get to see all of those dead ends of your tree. If we’re lucky, we get to meet them as well and ask all of those questions we have on this side. We remember our friends fondly, and their departure sadly, but they enriched us while they were here and their memories make us smile. I’m thinking specifically of Kenny Hedgepath and Leon Little as I write this, but there have been others as well.

The definition of a community is that people come and go, births, deaths and moves.

This year, about half of the attendees had never attended a conference before. I was very pleased to see this turn of events – because in order to survive, we do need new people who are as crazy as we are…er….I mean as dedicated as we are.

ISOGG traditionally hosts a potluck reception on Saturday evening. Lots of putting names with faces going on here.

Collaboration

I asked people about their favorite part of the conference or their favorite session. I was surprised at the number of people who said lunches and dinners. Trust me, the food wasn’t that wonderful, so I asked them to elaborate. In essence, the most valuable aspect of the conference was working with and talking to other administrators.

It’s not like we don’t talk online, but there is somehow a difference between online communications and having a group discussion, or a one-on-one discussion. Laptops were out and in use everyplace, along with iPads and other tools. It was so much fun to walk by tables and hear snippets of conversations like “the mutation at location 309.1….” and “null marker at 425” and “I ordered a kit for my great uncle…..”

I agree, as well. I had pre-arranged two dinners before arriving in order to talk with people with whom I share specific interests. At lunches, I either tried to sit with someone I specifically needed to talk to, or I tried to meet someone new.

I also asked people about their specific goals for the next year. Some people had a particular goal in mind, such as a specific brick wall that needs focus. Some, given that we are administrators, had wider-ranging project based goals, like Big Y testing certain family groups, and a surprising number had the goal of better utilizing the autosomal results.

Perhaps that’s why there were two autosomal sessions, an introduction by Jim Bartlett and then Tim Janzen’s more advanced session.

Autosomal DNA Results

Note the cool double helix light fixture behind the speakers.

Tim specifically mentioned two misconceptions which I run across constantly.

Misconception 1 – A common surname means that’s how you match. Just because you find a common surname doesn’t mean that’s your DNA match. This belief is particularly prevalent in the group of people who test at Ancestry.com.

Misconception 2 – Your common ancestor has to be within the past 6 generations. Not true, many matches can be 6-10^th cousins because there are so many descendants of those early ancestors, even as many as 15 generations back.

Tim also mentioned that endogamous relationships are a tough problem with no easy answer. Polynesians, Ashkenazi Jews, Low German Mennonites, Acadians, Amish, and island populations. Do I ever agree with him! I have Brethren, Mennonite and Acadian in the same parent’s line.

Tim has been working with the Mennonite DNA project now for many years.

Tim included a great resource slide.

Tim has graciously made his entire presentation available for download.

There are probably a dozen or so of us that are actively mapping our ancestors, and a huge backlog of people who would like to. As Tim pointed out with one of his slides, this is not an easy task nor is it for the people who simply want to receive “an answer.”

I will also add that we “mappers” are working with and actively encouraging Family Tree DNA to develop tools so that the mapping is less spreadsheet manual work and more automated, because it certainly can be.

Upload GEDCOM Files

If you haven’t already, upload your GEDCOM to Family Tree DNA. This is becoming an essential part of autosomal matching. Furthermore, Family Tree DNA will utilize this file to construct your surname list and that will help immensely determining common surnames and your common ancestor with your Family Finder matches. If you have sponsored tests for cousins, then upload a GEDCOM file for them or at least construct a basic tree on their Family Tree DNA page.

Ethics

Family Tree DNA always tries to provide a speaker about ethics, and the only speakers I’ve ever felt understood anything about what we want to do are Judy Russell and Blaine Bettinger. I was glad to see Blaine presenting this year.

The essence of Blaine’s speech is that ethics isn’t about law. Law is cut and dried. Ethics isn’t, and there are no ethics police.

Sometimes our decisions are colored necessarily by right and wrong. Sometimes those decisions are more about the difference between a better and a worse way.

As a community, we want to reduce negative press coverage and increase positive coverage. We want to be proactive, not reactive.

Blaine stresses that while informed consent is crucial, that DNA doesn’t reveal secrets that aren’t also revealed by other genealogical forms of research. DNA often reveals more recent secrets, such as adoptions and NPEs, so it’s possibly more sensitive.

Two things need to govern our behavior. First, we need to do only things that we would be comfortable seeing above the fold in the New York Times. Second, understand that we can’t make promises about topics like anonymity or about the absence of medical information, because we don’t know what we don’t know.

The SNP Tsunami

One of my concerns has been and remains the huge number of new SNPs that have been discovered over the past year or so with the Big Y by Family Tree DNA and corresponding tests from other vendors.

When I say concern, I’m thrilled about this new technology and the advances it is allowing us to make as a community to discover and define the evolution of haplogroups. My concern is that the amount of data is overwhelming. However, we are working through that, thanks to the hours and hours of volunteer work by haplogroup administrators and others.

Alice Fairhurst, who volunteers to maintain the ISOGG haplotree, mentioned that she has added over 10,000 SNPs to the Y tree this year alone, bringing the total to over 14,000. Those SNPs are fully vetted and placed. There are many more in process and yet more still being discovered. On the first page of the Y SNP tree, the list of SNP sources and other critical information, such as the criteria for a SNP to be listed, is provided.

So, if you’re waiting for that next haplotree poster, give it up because there isn’t a printing press that big, unless you want wallpaper.

These slides are from Alice’s presentation. The ISOGG tree provides an invaluable resource for not only the genetic genealogy community, but also researchers world-wide.

As one example of how the SNP tsunami has affected the Y tree, Alice provided the following summary of R-U106, one of the two major branches of haplogroup R.

From the ISOGG 2006 Y tree, this was the entire haplogroup R Y tree. You can see U106 near the bottom with 3 sub-branches. While this probably makes you chuckle today, remember that 2006 was only 8 years ago and that this tree didn’t change much for several years.

2007 was the same.

2008 shows 5 subclades and one of the subclades had 2 subclades.

2009 showed a total of 12 sub-branches and 2010 added one more.

2011 however, showed a large change. U106 in 2011 had 44 subgroups total and became too large to show on one screen shot. 2012 shows 99 subclades, if I counted accurately. The 2014 U106 tree is shown below.

There’s another slide too, but I didn’t manage to get the picture. You get the idea though…

As you can imagine, for Family Tree DNA, trying to keep up with all of the haplogroups, not just one subgroup like U106 is a gargantuan task that is constantly changing, like hourly. Their Y tree is currently the National Geographic tree, and while they would like to update it, I’m sure, the definition of “current tree” is in a constant state of flux. Literally, Mike Walsh, one of the admins in the R-L21 group uploads a new tree spreadsheet several times every day.

In order to deal attempt to deal with this, and to encourage people who don’t want to do a Big Y discovery type test, but do want to ferret out their location on their assigned portion of the tree, Family Tree DNA is reintroducing the Backbone tests.

They are starting with M222, also known as the Niall of the 9 Hostages haplogroup which is their beta for the new product and new process. You can see the provisional tree and results in the two slides they provided, below. I apologize for the quality, but it was the best I could do.

Haplogroup administrators are going to be heavily involved in this process. Family Tree DNA is putting SNP panels together that will help further define the tree and where various SNPs that have been recently discovered, and continue to be discovered, will fall on the tree.

As Big Y tests arrive, haplogroup project administrators typically assemble a spreadsheet of the SNPS and provisionally where they fall on the tree, based on the Big Y results.

What Bennett asked is for the admins to work with Family Tree DNA to assemble a testing panel based on those results. The goal is for the cost to be between $1.50 and $2 (US) for each SNP in the panel, which will reduce the one-off SNP testing and provide a much more complete and productive result at a far reduced price as compared to the current $29 or $39 per individual SNP.

If you are a haplogroup administrator, get in touch with Family Tree DNA to discuss your desired backbone panels. New panels, when it’s your turn, will take about 2 weeks to develop.

Keep in mind that the following SNPs, according to Bennett, are not optimal for panels:

Palindromic regions
Often mutating regions designated as .1, .2, etc.
SNPs in STRs

Nir Leibovich, the Chief Business Officer, also addressed the future and the Big Y to some extent in his presentation.

Utilizing the Big Y for Genealogy

In my case, during the last sale, I ordered several Big Y tests for my Estes family line because I have several genealogically documented lines from the original Estes family in Kent, England through our common ancestor, Robert Estes born in 1555 and his wife Anne Woodward. The participants also agreed to extend their markers to 111 markers as well. When the results are back, we’ll be able to compare them on a full STR marker set, and also their SNPs. Hopefully, they will match on their known SNPs and there will be some new novel variants that will be able to suffice as line marker mutations.

We need more BIG Y tests of these types of genealogically confirmed trees that have different sons’ lines from a distant common ancestor to test descendant lines. This will help immensely to determine the actual, not imputed, SNP mutation rate and allow us to extrapolate the ages of haplogroups more accurately. Of course, it also goes without saying that it helps to flesh out the trees.

I personally expect the next couple of years will be major years of discovery. Yes, the SNP tsumani has hit land, but it’s far from over.

Research and Development

David Mittleman, Chief Scientific Officer, mentioned that Family Tree DNA now has their own R&D division where they are focused on how to best analyze data. They have been collaborating with other scientists. A haplogroup G1 paper will be published shortly which states that SNP mutation rates equate to Sanger data.

FTDNA wants to get Big Y data into the public domain. They have set up consent for this to be done by uploading into NCBI. Initially they sent a survey to a few people that sampled the interest level. Those who were interested received a release document. If you are interested in allowing FTDNA to utilize your DNA for research, be it mitochondrial, Y or autosomal, please send them an e-mail stating such.

Don’t Forget About Y Genealogy Research

It’s very easy for us to get excited about the research and discovery aspect of DNA – and the new SNPs and extending haplotrees back in time as far as possible, but sometimes I get concerned that we are forgetting about the reason we began doing genetic genealogy in the first place.

Robert Baber’s presentation discussed the process of how to reconstruct a tree utilizing both genealogy and DNA results. It’s important to remember that the reason most of our participants test is to find their ancestors, not, primarily, to participate in the scientific process.

Robert has succeeded in reconstructing 110 or 111 markers of the oldest known Baber ancestor, shown above. I wrote about how to do this in my article titled, Triangulation for Y DNA.

Not only does this allow us to compare everyone with the ancestor’s DNA, it also provides us with a tool to fit individuals who don’t know specific genealogical line into the tree relatively accurately. When I say relatively, the accuracy is based on line marker mutations that have, or haven’t, happened within that particular family.

Jim illustrated how to do this as well, and his methodology is available at the link on his slide, below.

I had to laugh. I’ve often wondered what our ancestors would think of us today. Robert said that that 11 generations after Edward Baber died, he flew over church where Edward was buried and wondered what Edward would have thought about what we know and do today – cars, airplanes, DNA, radio, TV etc.. If someone looked in a crystal ball and told Edward what the future held 11 generations later, he would have thought that they were stark raving mad.

Eleven generations from my birth is roughly the year 2280. I’m betting we won’t be trying to figure out who our ancestors were through this type of DNA analysis then. This is only a tiny stepping stone to an unknown world, as different to us as our world is to Edward Baber and all of our ancestors who lived in a time where we know their names but their lives and culture are entirely foreign to ours.

Publications

When the Journal of Genetic Genealogy was active, I, along with other citizen scientists published regularly. The benefit of the journal was that it was peer reviewed and that assured some level of accuracy and because of that, credibility, and it was viewed by the scientific community as such. My co-authored works published in JOGG as well as others have been cited by experts in the academic community. It other words, it was a very valuable journal. Sadly, it has fallen by the wayside and nothing has been published since 2011. A new editor was recruited, but given their academic load, they have not stepped up to the plate. For the record, I am still hopeful for a resurrection, but in the mean time, another opportunity has become available for genetic genealogists.

Brad Larkin has founded the Surname DNA Journal, which, like JOGG, is free to both authors and subscribers. In case you weren’t aware, most academic journal’s aren’t. While this isn’t a large burden for a university, fees ranging from just over $1000 to $5000 are beyond the budget of genetic genealogists. Just think of how many DNA tests one could purchase with that money.

Brad has issued a call for papers. These papers will be peer reviewed, similarly to how they were reviewed for JOGG.

Take a look at the articles published in this past year, since the founding of Surname DNA Journal.

The History, Adoption, and Regulation of Jewish Surnames in the Russian Empire, A Reviewby Dr. Jeffrey Mark Paull and Dr Jeffrey Briskman
Preliminary Phylogenetic Analysis of Briese Family Relationships by David Briese
Differences in Autosomal DNA Characteristics between Jewish and Non-Jewish Populations by Dr. Jeffrey Mark Paull, Gaye Sherman Tannenbaum, and Dr Jeffrey Briskman
Using STRs for Intra-Family Y-DNA Comparisons: Segmenting Markers by Joe Flood, PhD
Y-DNA of the British Monarchy by Brad Larkin
The Irish Septs by David Austin Larkin
Using Y Chromosome DNA Testing to Pinpoint a Genetic Homeland in Ireland by Dr. Tyrone Bowes, PhD
Ancestral Parish Sampling in Ulster and Wexford for the Larkin DNA Project by Brad Larkin

The citizen science community needs an avenue to publish and share. Peer reviewed journals provide us with another level of credibility for our work. Sharing is clearly the lynchpin of genetic genealogy, as it is with traditional genealogy. Give some thought about what you might be able to contribute.

Brad Larkin solicited nominations prior to the conference and awarded a Genetic Genealogist of the Year award. This year’s award was dually presented to Ian Kennedy in Australia, who, unfortunately, was not present, and to CeCe Moore, who just happened to follow Brad’s presentation with her own.

Don’t Forget about Mitochondrial DNA Either

I believe that mitochondrial DNA the most underutilized DNA tool that we have, often because how to use mitochondrial DNA, and what it can tell you, is poorly understood. I wrote about this in an article titled, Mitochondrial, The Maligned DNA.

Given that I work with mitochondrial DNA daily when I’m preparing client’s Personalized DNA Reports (orderable from your personal page at Family Tree DNA or directly from my website), I know just how useful mitochondrial can be and see those examples regularly. Unfortunately, because these are client reports, I can’t write about them publicly.

CeCe Moore, however, isn’t constrained by this problem, because one of the ways she contributes to genetic genealogy is by working with the television community, in particular Genealogy Roadshow and the PBS series, Finding Your Roots. Now, I must admit, I was very surprised to see CeCe scheduled to speak about mitochondrial DNA, because the area of expertise where she is best known is autosomal DNA, especially in conjunction with adoptee research.

During the research for the production of these shows, CeCe has utilized mitochondrial DNA with multiple celebrities to provide information such as the ethnic identification of the ancestor who provided the mitochondrial DNA as Native American.

Autosomal DNA testing has a broad but shallow reach, across all of your lines, but just back a few generations. Both Y and mitochondrial DNA have a very deep reach, but only on one specific line, which makes them excellent for identifying a common ancestor on that line, as well as the ethnicity of that individual.

I have seen other cases, where researchers connected the dots between people where no paper trail existed, but a relationship between women was suspected.

CeCe mentioned that currently there are only 44,000 full sequence results in the Family Tree DNA data base and and 185K total HVR1, HVR2 and full sequence tests. Y has half a million. We need to increase the data base, which, of course increases matches and makes everyone happier. If you haven’t tested your mitochondrial DNA to the full sequence level, this would be a great time!

There are several lessons on how to utilize mitochondrial DNA at this ISOGG link.

I’m very hopeful that CeCe’s presentation will be made available as I think her examples are quite powerful and will serve to inspire people. Actually, since CeCe is in the “movie business,” perhaps a short video clip could be made available on the FTDNA website for anyone who hasn’t tested their mitochondrial DNA so they can see an example of why they should!

myOrigins

I would be fibbing to you if I told you I am happy with myOrigins. I don’t feel that it is as sensitive as other methods for picking up minority admixture, in particular, Native American, especially in small amounts. Unfortunately, those small amounts are exactly what many people are looking for.

If someone has a great-great-great-great grandparent that is Native, they carry about 1%, more or less, of the Native ancestor’s DNA today. A 4X great grandparent puts their birth year in the range of 1800-1825 – or just before the Trail of Tears. People whose colonial American families intermarried with Native families did so, generally, before the Trail of Tears. By that time, many tribes were already culturally extinct and those east of the Mississippi that weren’t extinct were fighting for their lives, both literally and figuratively.

We really need the ability to develop the most sensitive testing to report even the smallest amounts of Native DNA and map those segments to our chromosomes so that we can determine who, and what line in our family, was Native.

I know that Family Tree DNA is looking to improve their products, and I provided this feedback to them. Many people test autosomally only for their ethnicity results and I surely would love to have those people’s results available as matches in the FTDNA data base.

Razib Khan has been working with Family Tree DNA on their myOrigins product and spoke about how the myOrigins data is obtained.

Given that all humans are related, one way or another, far enough back in time, myOrigins has to be able to differentiate between groups that may not be terribly different. Furthermore, even groups that appear different today may not have been historically. His own family, from India, has no oral history of coming from the East, but the genetic data clearly indicates that they did, along with a larger group, about 1000 years ago. This may well be a result of the adage that history is written by the victors, or maybe whatever happened was simply too long ago or unremarkable to be recorded.

Razib mentioned that depending on the cluster and the reference samples, that these clusters and groups that we see on our myOrigins maps can range from 1000-10,000 years in age.

The good news is that genetics is blind to any preconceived notions. The bad news is that the software has to fit your results to the best population, even though it may not be directly a fit. Hopefully, as we have more and better reference populations, the results will improve as well.

Razib showed a PCA (principal components analysis) graph, above. These graphs chart reference populations in different quadrants. Where the different populations overlap is where they share common historic ancestors. As you can see, on this graph with these reference populations, there is a lot of overlap in some cases, and none in others.

Your personal results would then be plotted on top of the reference populations. The graph below shows me, as the white “target” on a PCA graph created by Doug McDonald.

The Changing Landscape

A topic discussed privately among the group, and primarily among the bloggers, is the changing landscape of genetic genealogy over the past year or so. In many ways I think the bloggers are the canaries in the mine.

One thing that clearly happened is that the proverbial tipping point occurred, and we’re past it. DNA someplace along the line became mainstream. Today, DNA is a household word. At gatherings, at least someone has tested, and most people have heard about DNA testing for genealogy or at least consumer based DNA testing.

The good news in all of this is that more and more people are testing. The bad news is that they are typically less informed and are often impulse purchasers. This gives us the opportunity for many more matches and to work with new people. It also means there is a steep learning curve and those new testers often know little about their genealogy. Those of us in the “public eye,” so to speak, have seen an exponential spike in questions and communications in the past several months. Unfortunately, many of the new people don’t even attempt to help themselves before asking questions.

Sometimes opportunity comes with work clothes – for them and us both.

I was talking with Spencer about this at the reception and he told me I was stealing his presentation. He didn’t seem too upset by this:)

I had to laugh, because this falls clearly into the “be careful what you wish for, you may get it” category. The Genographic project through National Geographic is clearly, very clearly, a critical component of the tipping point, and this was reflected in Spencer’s presentation. Although I covered quite a bit of Spencer’s presentation in my day 2 summary, I want to close with Spencer here. I also want to say that if you ever have the opportunity to hear Spencer speak, please do yourself the favor and be sure to take that opportunity. Not only is he brilliant, he’s interesting, likeable and very approachable. Of course, it probably doesn’t hurt that I’ve know him now for 9 years! I’ve never thought to have my picture taken with Spencer before, but this time, one of my friends did me the favor.

I have to admit, I love talking to Spencer, and listening to him. He is the adventurer through whom we all live vicariously. In the photo below, Spencer along with his crew, drove from London to Mongolia. Not sure why he is standing on the top of the Land Rover, but I’m sure he will tell us in his upcoming book about that journey,

I’m warning you all now, if I win the lottery, I’m going on the world tour that he hosts with National Geographic, and of course, you’ll all be coming with me via the blog!

Spencer talked about the consumer genomics market and where we are today.

Spencer mentioned that genetic genealogy was a cottage industry originally. It was, and it was even smaller than that, if possible. It actually was started by Bennett and his cell phone. I managed to snap a picture of Bennett this weekend on the stage looking at his cell, and I thought to myself, “this is how it all started 14 years ago.” Just look where we are today. Thank you Michael Hammer for telling Bennett that you received “lots of phone calls from crazy genealogists like you.”

So, where exactly are we today? In 2013, the industry crossed the millionth kit line. The second millionth kit was sold in early summer 2014 and the third million will be sold in 2015. No wonder we feel like a tidal wave has hit. It has.

Why now?

DNA has become part of national consciousness. Businesses advertise that “it’s in our DNA.” People are now comfortable sharing via social media like facebook and twitter. What DNA can do and show you, the secrets it can unlock is spreading by word of mouth. Spencer termed this the “viral spread threshold” and we’ve crossed that invisible line in the sand. He terms 2013 as the year of infection and based on my blog postings, subscriptions, hits, reach and the number of e-mails I receive, I would completely agree. Hold on tight for the ride!

Spencer talked about predictions for near term future and said a 5 year plan is impossible and that an 18 month plan is more realistic. He predicts that we will continue to see exponential growth over the next several years. He feels that genetic genealogy testing will be primary driver of growth because medical or health testing is subject to the clinical utility trap being experienced currently by 23andMe. The Big 4 testing companies control 99% of consumer market in US (Ancestry, 23andMe, Family Tree DNA and National Geographic.)

Spencer sees a huge international market potential that is not currently being tapped. I do agree with him, but many in European countries are hesitant, and in some places, like France, DNA testing that might expose paternity is illegal. When Europeans see DNA testing as a genealogical tool, he feels they will become more interested. Most Europeans know where their ancestral village is, or they think they do, so it doesn’t have the draw for them that it does for some of us.

Ancestry testing (aka genetic genealogy as opposed to health testing) is now a mature industry with 100% growth rate.

Spencer also mentioned that while the Genographic data base is not open access, that affiliate researchers can send Nat Geo a proposal and thereby gain research access to the data base if their proposal is approved. This extends to citizen scientists as well.

Michael Hammer

You’ll notice that Michael Hammer’s presentation, “Ancient and Modern DNA Update, How Many Ancestral Populations for Europe,” is missing from this wrapup. It was absolutely outstanding, and fascinating, which is why I’m writing a separate article about his presentation in conjunction with some additional information. So, stay tuned.

Testing, More Testing

It’s becoming quite obvious that the people who are doing the best with genetic genealogy are the ones who are testing the most family members, both close and distant. That provides them with a solid foundation for comparison and better ways to “drop matches” into the right ancestor box. For example, if someone matches you and your mother’s sister, Aunt Margaret, especially if your mother is not available to test, that’s a very important hint that your match is likely from your mother’s line.

So, in essence, while initially we would advise people to test the oldest person in a generational line, now we’ve moved to the “test everyone” mentality. Instead of a survey, now we need a census. The exception might be that the “child” does not necessarily need to be tested because both parents have tested. However, having said that, I would perhaps not make that child’s test a priority, but I would eventually test that child anyway. Why? Because that’s how we learn. Let me give you an example.

I was sitting at lunch with David Pike. were discussing autosomal DNA generational transmission and inheritance. He pulled out his iPad, passed it to me, and showed me a chromosome (not the X) that has been passed entirely intact from one generation to the next. Had the child not been tested, we would never have known that. Now, of course, if you’ll remember the 50% rule, by statistical prediction, the child should get half of the mother’s chromosome and half of the father’s, but that’s not how it worked. So, because we don’t know what we don’t know, I’m now testing everyone I can find and convince in my family. Unfortunately, my family is small.

Full genome testing is in the future, but we’re not ready yet. Several presenters mentioned full genome testing in some context. Here’s the bottom line. It’s not truly full genome testing today, only 95-96%. The technology isn’t there yet, and we’re still learning. In a couple of years, we will have the entire genome available for testing, and over time, the prices will fall. Keep in mind that most of our genome is identical to that of all humans, and the autosomal tests today have been developed in order to measure what is different and therefore useful genealogially. I don’t expect big breakthroughs due to full genome testing for genetic genealogy, although I could be wrong. You can, however, count me in, because I’m a DNA junkie. When the full genome test is below $1000, when we have comparison tools and when the coverage won’t necessitate doing a second or upgrade test a few years later, I’ll be there.

Thank you

I want to offer a heartfelt thank you to Max Blankfeld and Bennett Grenspan, founders of Family Tree DNA, shown with me in the photo below, for hosting and subsidizing the administrator’s conference – now for a decade. I look forward to seeing them, and all of the other attendees, next year.

I anticipate that this next decade will see many new discoveries resulting in tools that make our genealogy walls fall. I can’t help but wonder what the article I’ll be writing on the 20^th anniversary looking back at nearly a quarter century of genetic genealogy will say!

______________________________________________________________

Disclosure

Thank you so much.

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Ancient DNA Matching – A Cautionary Tale

Posted on September 30, 2014 by Roberta Estes

I hope that all of my readers realize that you are literally watching science hatch. We are on the leading, and sometimes bleeding edge, of this new science of genetic genealogy. Because many of these things have never been done before, we have to learn by doing and experimenting. Because I blog about this, these experiments are “in public,” so there is no option of a private “oops.” Fortunately, I’m not sensitive about these kinds of things. Plus, I think people really enjoy coming along for the ride of discovery. I mean, where else can you do that? It’s really difficult to get a ride-along on the space shuttle!

One of the best pieces of advice I ever got was from someone who was taken from my life far too early. I had made a mistake of some sort…don’t even remember what…and he gave me a card that said, “The only people who don’t make mistakes are the people who don’t try.”

This isn’t an “oops” moment. More like an “aha” moment. Or more precisely, a “huh” moment. It falls in the “Houston, we’ve got a problem” category.

So, this week’s new discovery is that there seems to be some inconsistency in the matching to the Anzick kit at GedMatch. Before I go any further, I want to say very clearly that this is in no way a criticism of anyone or any tool. Every person involved is a volunteer and we would not be making any of these steps forward, including a few backwards, without these wonderful volunteers and tools.

I have reached out to the people involved and asked for their help to unravel this mystery, and I’m sharing the story with you, partly so you can understand what is involved, and the process, partly so that you don’t inadvertently encounter the same kinds of issues and draw unrealistic or incorrect conclusions, and partly so you can help. If there has been any common theme in all of my articles in the past week or so about the ancient DNA articles, it has been that we really don’t understand what conclusions to draw yet…and we still don’t. So don’t.

Let’s introduce the players here.

The Players

Felix Chandrakumar has very graciously prepared the various ancient DNA files and uploaded them to GedMatch. Felix has written a number of DNA analysis tools as well.

John Olson is one of the two volunteers who created and does everything at Gedmatch, plus works a full time job. By the way, in case you’re not aware, this is a contribution site, meaning they depend on your financial contributions to function, purchase hardware, servers, etc. If you use this site, periodically scroll down and click on the donate button. We, as a community, would be lost without John and his partner.

David Pike is a long time genetic genealogist who I have had the pleasure of working with on a number of Native American and related topics over the years. He also has created several genetic genealogy tools to deal with autosomal DNA. David prepared the Anzick files for some private work we were doing several months ago, so he has experience with this DNA as well. Dr. Pike has a great deal of experience analyzing the endogamous population of Newfoundland, which is also admixed with Native Americans.

Marie Rundquist, also a long time genetic genealogist who specializes in both technology and Acadian history along with genetic genealogy. Acadians are proven to be admixed with Native Americans. Marie shares my deep interest and commitment to Native American study and genetics. Furthermore, Marie and I also share ancestors and co-administer several related projects. As you might imagine, Marie and I took this opportunity immediately to see if she and her mother share any of Anzick’s segments with me and my mother.

So, a big thank you to all of these people.

The Mystery

When Felix originally e-mailed me about the Anzick kit being uploaded to GedMatch, as you might imagine, I stopped doing whatever I was doing and immediately went to study Anzick and the other ancient DNA kits.

I wrote about this experience in the article, “Utilizing Ancient DNA at GedMatch.”

As part of that process, I not only ran Anzick’s kit utilizing the “one to many” option, I also compared my own kit to Anzick’s. My proven Native lines descend through my mother, so I ran her kit against Anzick’s as well, at the same thresholds, and I combined the two results to see where mother and I overlapped.

I showed these overlaps in the article, along with which genealogy lines they matched by utilizing my ancestor matching spreadsheet.

Everything was hunky dory…for then.

Day 2

The next day, I received a note from Felix that the Anzick kit may not have been fully tokenized at GedMatch previously, so I reran the Anzick “one to all” comparison and wrote about those results in the second article, “Analyzing the Native American Clovis Ancient Results.” Because it wasn’t yet fully processed originally, the second results produced more matches, not fewer.

I wasn’t worried about the one to one comparison of Anzick to my own kit, because one to one comparisons are available immediately, while one to many comparisons are not, per the GedMatch instructions.

“Once you have loaded your data, you will be able to use some features of the site within a minute or so. Additional batch processing, which usually takes a couple of days, must complete before you can use some of the tools comparing you to everyone in the data pool.”

So, everything was stlll hunky dory.

Day 3

The next day, Marie and I had a few minutes, sometime between 2 and 3AM, and no, I’m not kidding. We decided to compare results. I decided it would be quicker to run the match again at GedMatch than to sort through my Master spreadsheet, into which I had copied the results and added other information. So, I did a second download of the Anzick comparison, utilizing the exact same thresholds (200 SNPs, 2cM, and the rest left at the default,) and added them to a spreadsheet that Marie and I were passing back and forth, and sent them to Marie. I noticed that there seemed to be fewer matches, but by then it was after 3AM and I decided to follow up on that later.

Not so hunky dory…but I didn’t know it yet.

Day 4

The following day, Dr. Ann Turner (MD), also a long-time genetic genealogist, posted the following comment on the article.

“These results, finding “what appear to be contemporary matches for the Anzick child”, seemed very counter-intuitive to me, so I asked John Olson of GEDMatch to look under the hood a bit more. It turns out the ancient DNA sequence has many no-calls, which are treated as universal matches for segment analysis. Another factor which should be examined is whether some of the matching alleles are simply the variants with the highest frequency in all populations. If so, that would also lead to spurious matching segments. It may not be appropriate to apply tools developed for genetic genealogy to ancient DNA sequences like this without a more thorough examination of the underlying data.”

I had been aware of the no-calls due to the work that Dr. David Pike did back in March with the Anzick raw data files, but according to David, that shouldn’t affect the results.

Here’s what Dr. Pike, a Professor of Mathematics, had to say:

“Yes, these forensic samples have very high No-Call rates, which may give rise to more false matches than we would normally experience. Also, be aware that false matches are more prone to occur when using reduced thresholds (such as 100 SNPs and 1 cM) and unphased data. In this case I don’t think there’s any way around using low thresholds, simply because we’re looking for very small blocks of DNA (probably nobody alive today will have any large matching blocks with the Anzick child).

On the assumption that there will be a nearly constant noise ratio, meaning that most people will have about the same number of false matches with the Anzick child, those who are from the same gene pool should have an increased number of real matches. So by comparing the total amount of matching DNA, it ought to be possible to gauge people’s affinity with Anzick’s gene pool.”

Here are Felix’s comments about no-calls as well:

“Personally, no calls are fine as long as there are more SNPs matching above the threshold level because the possibility of errors occurring exactly on no-call positions for all the matches in all their matching segments is impossible.”

Courtesy of Felix, we’ll see an example of how no calls intersperse in a few minutes.

If no-calls were causing spurious matches in the Anzick kit, you’d expect to see the same for the other ancient DNA kits. I know that the Denisovan and Neanderthal kits also have many no-calls, and based on the nature of ancient DNA, I’m sure all of them do. So, if no calls are the culprit, they should be affecting matches to the other kits in the same way, and they aren’t.

Hunky-doryness is being replaced by a nonspecific nagging feeling…same one I used to get when my teenagers were up to something.

Day 5

A day or so later, Felix uploaded file F999913 to replace F999912 with the complete SNPs from all of the companies. The original 999912 kit only included the SNP locations utilized by Family Tree DNA. Felix added the SNPs utilized by 23and Me not utilized at Family Tree DNA, and the ones from Ancestry as well. This is great news for anyone who tested at those two companies, but I had utilized my kit from Family Tree DNA, so for me, there should be no difference at all.

I later asked Felix if he had changed anything else in the file, and he said that he had not. He provided extensive documentation about what he had done.

I waited until kit F999912 was deleted to be sure tokenizing was complete for F999913 and re-compared the data again. As expected, Anzick’s one to all had more matches than before, because additional people were included due to the added SNPs from 23andMe and Ancestry.

Some of Anzick’s matches are in the contemporary range, at 3.1 estimated generations, with the largest cM segment of 22.8 and total cMs of 202.8.

These relatively large matches cause Felix to question whether the sample is actually ancient, based on these relatively large segments. I addressed my feelings on this in the article, Ancient DNA Matches – What Do They Mean?

Marie and Dr. Pike, both with extensive experience with admixed populations addressed this as well. Marie commented,

“Native DNA found in the Anzick sample hasn’t changed all of that much and may still be found in modern, Native American populations, and that if people have Native American ancestry, they’ll match to it.”

Dr. Pike says:

“I agree with Marie on this… within endogamous populations, there is an increased likelihood of blocks of DNA being preserved over lengthy time frames. Moreover, even if a block of DNA gets cut up via recombination, within an endogamous population the odds of some parts of the block later reuniting in a person’s DNA are higher than otherwise. And it exaggerates the closeness of [the] relationship that gets predicted when comparing people.

I have seen something similar within the Newfoundland & Labrador Family Finder Project, whereby lots of people are sharing small blocks of DNA, likely as a result of DNA from the early colonists still circulating among the modern gene pool.

As an anecdotal example, I have a semi-distant relative (with ancestry from Newfoundland) at 23andMe who shares 3 blocks of DNA with my father, 2 with my mother and 5 five me. As you can imagine, the relative is predicted to be a closer cousin to me than she is to either of my parents!

It doesn’t take an endogamous or isolated population to see this effect.

It can also happen in families involving cousin marriages too, although that would be more pronounced and not quite the same thing as we’re discussing with respect to ancient DNA.”

This addition of other companies SNPs should not affect my matches with Anzick because my kits are both from FTDNA and won’t utilize the added SNPs.

However, I ran my and my mother’s matches again, and we had a significantly different outcome than either of the previous times.

I utilized the same threshold for all downloads and those are the only values I changed – 200 SNPs and 2cM, leaving the other values at default, for all Anzick comparisons to my mother and my kits.

I am not hunky-dory anymore.

The Heartburn

These matches, which should be the same in all three downloads, produced significantly different results.

Here are the number of matches at the same threshold comparing me and Mom to the Anzick file:

Me and Anzick

original download 999912 – 47 matches
second download 999912 – 21 matches
999913 – 35 matches

Mom and Anzick

original download 999912 – 63
second download 999912 – 37
999913 – 36

And no, the 36 /35 that mom and I have for 999913 are not all the same.

Kit Number	Matches Between Me, Mother and Anzick
#1-F999912 original download	19
#2-F999912 second download	6
#3-F999913	11

Of those various downloads, the following grid shows which ones matched each other.

	#1 to #2	#2 to #3	#1 to #3	All 3
# of Matches	6	2	3	2

So, comparing the first download to the last download, of the 19 original matches, we lost 16 matches. In the third download, we gained 8 matches and only 3 remained as common matches. So of 30 total matches between my mother, myself and Anzick, in two downloads that should have been exactly the same, only 3 matches held, or 10%.

Obviously, something is wrong, but what, and where? At that point, I asked Marie to download her and her mother’s results again too, and she experienced the same issue.

Clearly a problem exists someplace. That’s the question I asked Felix, John and David to help answer.

I realize that this spreadsheet it very long, and I apologize, but I think this issue is much easier to see visually. I’ve compiled the matches by color and shade to make looking at them relatively easy.

My matches to the Anzick kit are in shades of pink – the first match download being the lightest and the last one to kit F999913 being the darkest. Mother is green, same shading scheme.

The three columns to the right show the matching segments for each download – shaded in green. You can easily see which ones line up, meaning which ones match consistently across all three downloads. There aren’t many. They should all match.

Obviously this led to many questions that I asked of the various players involved.

My first thought was that perhaps a matching algorithm change occurred in GedMatch, but John assured me that he had made no changes.

Next question was whether or not Felix changed something other than adding the 23andMe and Ancestry SNPs. He had not.

Felix was kind enough to explain about bunching and to do some analysis on the files.

“When you have low thresholds, make sure you don’t allow errors. For example, at 200 SNPs, the default ‘Mismatch Evaluation window’ and in GEDMatch is same as SNP threshold and ‘Mismatch-Bunching limit’ is half of mismatch evaluation window. So, at 200 cM, you are allowing 1 error every 100 SNPs apart from no-calls.

I did some analysis on your phased mother’s kit, PF6656M1 so that at least we know that it is an IBD for one generation. The spreadsheet (below) are segments I found at 2 cM/200 SNPs threshold without allowing any errors.”

Kit PF6656M1 is one single kit created by phasing my data against my mother’s so that we don’t have to run both kits. I had not utilized the phased kit previously, so I was interested in his results.

The results above confirm chromosome matches, 2, 17, 19 and 21, but introduce a new match on chromosome 4. This match was present in the original download, but not in the second or third download, so once again, we have disparate data, except the thresholds Felix used were at a different level.

One of the more interesting things that Felix included is the no-call match information, the three columns to the right. I want to show what the no-calls look like. There are not huge segments that are blank and are being called as matches because they are no-calls, when they shouldn’t be. No calls are scattered like salt and pepper. In fact, no calls happen in every kit and they are called as matches so they don’t in fact disrupt a valid match string, potentially making it too small to be considered a match. Of course, ancient DNA has more no-calls that contemporary DNA kits.

Below are the first few match positions from chromosome 2 where mother, Anzick and I have a confirmed match across all downloads. The genotype shows you that both kits match.

For consistency, I ran the same kits that Felix ran, PF6656M1 and F999913, with the original thresholds I had used, and found the following:

Chr	Start Location	End Location	Centimorgans (cM)	SNPs
1	31358221	33567640	2.0	261
2	218855489	220351363	2.4	253
4	1957991	3571907	2.5	209
5	2340730	2982499	2.3	200
17	53111755	56643678	3.4	293
19	46226843	48568731	2.2	250
21	35367409	36761280	3.7	215

This introduces chromosomes 1 and 5, not shown above. The chromosome 1 match was shown in the first and second download, but not the third, and the chromosome 5 match was shown in the first download only, but not the second or third.

Can you see me beating my head against the wall yet??

In a fit of apparent insanity, I decided to try, once again, an individual download of Anzick compared to my mother and to me, but not utilizing the phased kit – the original F6656 and F9141, and at the original thresholds, for consistency. I wanted to see if the matches were the same now as they were a day or so ago. They should be exact. This first one is mine.

What you should see are two identical downloads. I have color coded the rows so you can see easily – and what you should see are candy-cane stripes – one red and one white for every match location.

That’s not what we’re seeing. The kits are the same, the match parameters are the same, but the results are not. Once again, the downloads don’t match.

I did another match on mother and Anzick, and her results were consistent between the first and second match to kit F999913.

The begs the next question. Have mother’s results always been consistent, suggesting a problem with my kit?

I sorted all of her downloads, and no, they are not consistent, except for the first and second download matches to kit F999913, shown above. The inconsistencies show up in both mother and my kits, although not in the same locations. Recall also that Marie had the same issue.

In Summary

Something is wrong, someplace. I know that sounds intuitively obvious – NOW. But it wasn’t initially and I wouldn’t even have suspected a problem without running the second and third downloads, quite unintentionally. Most people never do that, because once you’ve done the match, you have no reason to ever match to that particular person again. Given that, you’ll never know if a problem exists.

So, the only Anzick GedMatch matches I have any confidence in at all, at this point, are the few that are consistent between all of the downloads, and I didn’t add the fourth download into the mix. I don’t’ see any point because I’ve pretty much concluded that until we determine where the issue resides, that I won’t have confidence in the results.

The next question that comes to mind, and that I can’t answer, is whether or not this issue is present in contemporary matching kits – or if this is somehow an ancient DNA problem – although I don’t know quite how that could be – since matching is matching.

I haven’t saved any matches that I’ve run to other people in spreadsheets, so I can’t go back and see if a GedMatch match today produces the exact same results as a previous match.

Clearly there is no diagnosis or solution in this summary. We are not yet hunky dory.

What You Can Do

Run your Anzick and ancient DNA matches multiple times, at the same exact thresholds, on different days, to see if your results are consistent or inconsistent. Same kit, same thresholds, the results should be identical.
If you have some saved GedMatch matches with contemporary people, and you are positive of the match thresholds used, please run them again to see if the results are identical. They should be.
No drawing of or jumping to conclusions, please, especially about ancient DNA:) It’s a journey and we are fellow pilgrims!

If your results are not consistent, please document the problem and let the appropriate person know. I don’t want to overwhelm John at GedMatch but I’m concerned at this point that the problem may not be isolated to ancient DNA matching since the issue seems to extend to Marie’s results as well.

If your results, especially to Anzick, from previous matches to now are consistent, that’s worth knowing too. Please add a comment to that effect.

Thoughts and ideas are welcome.

______________________________________________________________

Disclosure

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Legacy Tree Genealogists for genealogy research

Ancient DNA Matches – What Do They Mean?

Posted on September 25, 2014 by Roberta Estes

The good news is that my three articles about the Anzick and other ancient DNA of the past few days have generated a lot of interest.

The bad news is that it has generated hundreds of e-mails every day – and I can’t possibly answer them all personally. So, if you’ve written me and I don’t reply, I apologize and I hope you’ll understand. Many of the questions I’ve received are similar in nature and I’m going to answer them in this article. In essence, people who have matches want to know what they mean.

Q – I had a match at GedMatch to <fill in the blank ancient DNA sample name> and I want to know if this is valid.

A – Generally, when someone asks if an autosomal match is “valid,” what they really mean is whether or not this is a genealogically relevant match or if it’s what is typically referred to as IBS, or identical by state. Genealogically relevant samples are referred to as IBD, or identical by descent. I wrote about that in this article with a full explanation and examples, but let me do a brief recap here.

In genealogy terms, IBD is typically used to mean matches over a particular threshold that can be or are GENEALOGICALLY RELEVANT. Those last two words are the clue here. In other words, we can match them with an ancestor with some genealogy work and triangulation. If the segment is large, and by that I mean significantly over the threshold of 700 SNPs and 7cM, even if we can’t identify the common ancestor with another person, the segment is presumed to be IBD simply because of the math involved with the breakdown of segment into pieces. In other words, a large segment match generally means a relatively recent ancestor and a smaller segment means a more distant ancestor. You can readily see this breakdown on this ISOGG page detailing autosomal DNA transmission and breakdown.

Unfortunately, often smaller segments, or ones determined to be IBS are considered to be useless, but they aren’t, as I’ve demonstrated several times when utilizing them for matching to distant ancestors. That aside, there are two kinds of IBS segments.

One kind of IBS segment is where you do indeed share a common ancestor, but the segment is small and you can’t necessarily connect it to the ancestor. These are known as population matches and are interpreted to mean your common ancestor comes from a common population with the other person, back in time, but you can’t find the common ancestor. By population, we could mean something like Amish, Jewish or Native American, or a country like Germany or the Netherlands.

In the cases where I’ve utilized segments significantly under 7cM to triangulate ancestors, those segments would have been considered IBS until I mapped them to an ancestor, and then they suddenly fell into the IBD category.

As you can see, the definitions are a bit fluid and are really defined by the genealogy involved.

The second kind of IBS is where you really DON’T share an ancestor, but your DNA and your matches DNA has managed to mutate to a common state by convergence, or, where your Mom’s and Dad’s DNA combined form a pseudo match, where you match someone on a segment run long enough to be considered a match at a low level. I discussed how this works, with examples, in this article. Look at example four, “a false match.”

So, in a nutshell, if you know who your common ancestor is on a segment match with someone, you are IBD, identical by descent. If you don’t know who your common ancestor is, and the segment is below the normal threshold, then you are generally considered to be IBS – although that may or may not always be true. There is no way to know if you are truly IBS by population or IBS by convergence, with the possible exception of phased data.

Data phasing is when you can compare your autosomal DNA with one or both parents to determine which half you obtained from whom. If you are a match by convergence where your DNA run matches that of someone else because the combination of your parents DNA happens to match their segment, phasing will show that clearly. Here’s an example for only one location utilizing only my mother’s data phased with mine. My father is deceased and we have to infer his results based on my mother’s and my own. In other words, mine minus the part I inherited from my mother = my father’s DNA.

My Result	My Result	Mother’s Result	Mother’s Result	Father’s Inferred Result	Father’s Inferred Result
T	A	T	G	A

In this example of just one location, you can see that I carry a T and an A in that location. My mother carries a T and a G, so I obviously inherited the T from her because I don’t have a G. Therefore, my father had to have carried at least an A, but we can’t discern his second value.

This example utilized only one location. Your autosomal data file will hold between 500,000 and 700,000 location, depending on the vendor you tested with and the version level.

You can phase your DNA with that of your parent(s) at GedMatch. However, if both of your parents are living, an easier test would be to see if either of your parents match the individual in question. If neither of your parents match them, then your match is a result of convergence or a data read error.

So, this long conversation about IBD and IBS is to reach this conclusion.

All of the ancient specimens are just that, ancient, so by definition, you cannot find a genealogy match to them, so they are not IBD. Best case, they are IBS by population. Worse case, IBS by convergence. You may or may not be able to tell the difference. The reason, in my example earlier this week, that I utilized my mother’s DNA and only looked at locations where we both matched the ancient specimens was because I knew those matches were not by convergence – they were in fact IBS by population because my mother and I both matched Anzick.

Q – What does this ancient match mean to me?

A – Doggone if I know. No, I’m serious. Let’s look at a couple possibilities, but they all have to do with the research you have, or have not, done.

If you’ve done what I’ve done, and you’ve mapped your DNA segments to specific ancestors, then you can compare your ancient matching segments to your ancestral spreadsheet map, especially if you can tell unquestionably which side the ancestral DNA matches. In my case, shown above, the Clovis Anzik matched my mother and me on the same segment and we both matched Cousin Herbie. We know unquestionably who our common ancestor is with cousin Herbie – so we know, in our family line, which line this segment of DNA shared with Anzick descends through.

If you’re not doing ancestor mapping, then I guess the Anzick match would come in the category of, “well, isn’t that interesting.” For some, this is a spiritual connection to the past, a genetic epiphany. For other, it’s “so what.”

Maybe this is a good reason to start ancestor mapping! This article tells you how to get started.

Q – Does my match to Anzick mean he is my ancestor?

A – No, it means that you and Anzick share common ancestry someplace back in time, perhaps tens of thousands of years ago.

Q – I match the Anzick sample. Does this prove that I have Native American heritage?

A – No, and it depends. Don’t you just hate answers like this?

No, this match alone does not prove Native American heritage, especially not at IBS levels. In fact, many people who don’t have Native heritage match small segments? How can this be? Well, refer to the IBS by convergence discussion above. In addition, Anzick child came from an Asian population when his ancestors migrated, crossing from Asia via Beringia. That Eurasian population also settled part of Europe – so you could be matching on very small segments from a common population in Eurasia long ago. In a paper just last year, this was discussed when Siberian ancient DNA was shown to be related to both Native Americans and Europeans.

In some cases, a match to Anzick on a segment already attributed to a Native line can confirm or help to confirm that attribution. In my case, I found the Anzick match on segments in the Lore family who descend from the Acadians who were admixed with the Micmac. I have several Anzick match segments that fit that criteria.

A match to Anzick alone doesn’t prove anything, except that you match Anzick, which in and of itself is pretty cool.

Q – I’m European with no ancestors from America, and I match Anzick too. How can that be?

A – That’s really quite amazing isn’t it. Just this week in Nature, a new article was published discussing the three “tribes” that settled or founded the European populations. This, combined with the Siberian ancient DNA results that connect the dots between an ancient population that contributed to both Europeans and Native Americans explains a lot.

If you think about it, this isn’t a lot different than the discovery that all Europeans carry some small amount of Neanderthal and Denisovan DNA.

Well, guess what….so does Anzick.

Here are his matches to the Altai Neanderthal.

Chr	Start Location	End Location	Centimorgans (cM)	SNPs
2	241484216	242399416	1.1	138
3	19333171	21041833	2.6	132
6	31655771	32889754	1.1	133

He does not match the Caucasus Neanderthal. He does, however, match the Denisovan individual on one location.

Chr	Start Location	End Location	Centimorgans (cM)	SNPs
3	19333171	20792925	2.1	107

Q – Maybe the scientists are just wrong and the burial is not 12,500 years old, maybe just 100 years old and that’s why the results are matching contemporary people.

A – I’m not an archaeologist, nor do I play one…but I have been closely involved with numerous archaeological excavations over the past decade with The Lost Colony Research Group, several of which recovered human remains. The photo below is me with Anne Poole, my co-director, sifting at one of the digs.

There are very specific protocols that are followed during and following excavation and an error of this magnitude would be almost impossible to fathom. It would require kindergarten level incompetence on the part of not one, but all professionals involved.

In the Montana Anzick case, in the paper itself, the findings and protocols are both discussed. First, the burial was discovered directly beneath the Clovis layer where more than 100 tools were found, and the Clovis layer was undisturbed, meaning that this is not a contemporary burial that was buried through the Clovis layer. Second, the DNA fragmentation that occurs as DNA degrades correlated closely to what would be expected in that type of environment at the expected age based on the Clovis layer. Third, the bones themselves were directly dated using XAD-collagen to 12,707-12,556 calendar years ago. Lastly, if the remains were younger, the skeletal remains would match most closely with Native Americans of that region, and that isn’t the case. This graphic from the paper shows that the closest matches are to South Americans, not North Americans.

This match pattern is also confirmed independently by the recent closest GedMatch matches to South Americans.

Q – How can this match from so long ago possibly be real?

A – That’s a great question and one that was terribly perplexing to Dr. Svante Paabo, the man who is responsible for producing the full genome sequence of the first, and now several more, Neanderthals. The expectation was, understanding autosomal DNA gets watered down by 50% in every generation though recombination, that ancient genomes would be long gone and not present in modern populations. Imagine Svante’s surprise when he discovered that not only isn’t true, but those ancient DNA segmetns are present in all Europeans and many Asians as well. He too agonized over the question about how this is possible, which he discussed in this great video. In fact he repeated these tests over and over in different ways because he was convinced that modern individuals could not carry Neanderthal DNA – but all those repeated tests did was to prove him right. (Paabo’s book, Neanderthal Man, In Search of Lost Genomes is an incredible read that I would highly recommend.)

What this means is that the population at one time, and probably at several different times, had to be very small. In fact, it’s very likely that many times different pockets of the human race was in great jeopardy of dying out. We know about the ones that survived. Probably many did perish leaving no descendants today. For example, no Neanderthal mitochondrial DNA has been found in any living or recent human.

In a small population, let’s say 5 males and 5 females who some how got separated from their family group and founded a new group, by necessity. In fact, this could well be a description of how the Native Americans crossed Beringia. Those 5 males and 5 females are the founding population of the new group. If they survive, all of the males will carry the men’s haplogroups – let’s say they are Q and C, and all of the descendants will carry the mitochondrial haplogroups of the females – let’s say A, B, C, D and X.

There is a very limited amount of autosomal DNA to pass around. If all of those 10 people are entirely unrelated, which is virtually impossible, there will be only 10 possible combinations of DNA to be selected from. Within a few generations, everyone will carry part of those 10 ancestor’s DNA. We all have 8 ancestors at the great-grandparent level. By the time those original settlers’ descendants had great-great-grandparents – of which each one had 16, at least 6 of those original people would be repeated twice in their tree.

There was only so much DNA to be passed around. In time, some of the segments would no longer be able to be recombined because when you look at phasing, the parents DNA was exactly the same, example below. This is what happens in endogamous populations.

My Result	My Result	Mother’s Result	Mother’s Result	Father’s Result	Father’s Result
T	T	T	T	T	T

Let’s say this group’s descendants lived without contact with other groups, for maybe 15,000 years in their new country. That same DNA is still being passed around and around because there was no source for new DNA. Mutations did occur from time to time, and those were also passed on, of course, but that was the only source of changed DNA – until they had contact with a new population.

When they had contact with a new population and admixture occurred, the normal 50% recombination/washout in every generation began – but for the previous 15,000 years, there had been no 50% shift because the DNA of the population was, in essence, all the same. A study about the Ashkenazi Jews that suggests they had only a founding population of about 350 people 700 years ago was released this week – explaining why Ashkenazi Jewish descendants have thousands of autosomal matches and match almost everyone else who is Ashkenazi. I hope that eventually scientists will do this same kind of study with Anzick and Native Americans.

If the “new population” we’ve been discussing was Native Americans, their males 15,000 year later would still carry haplogroups Q and C and the mitochondrial DNA would still be A, B, C, D and X. Those haplogroups, and subgroups formed from mutations that occurred in their descendants, would come to define their population group.

In some cases, today, Anzick matches people who have virtually no non-Native admixture at the same level as if they were just a few generations removed, shown on the chart below.

Since, in essence, these people still haven’t admixed with a new population group, those same ancient DNA segments are being passed around intact, which tells us how incredibly inbred this original small population must have been. This is known as a genetic bottleneck.

The admixture report below is for the first individual on the Anzick one to all Gedmatch compare at 700 SNPs and 7cM, above. In essence, this currently living non-admixed individual still hasn’t met that new population group.

If this “new population” group was Neanderthal, perhaps they lived in small groups for tens of thousands of years, until they met people exiting Africa, or Denisovans, and admixed with them.

There weren’t a lot of people anyplace on the globe, so by virtue of necessity, everyone lived in small population groups. Looking at the odds of survival, it’s amazing that any of us are here today.

But, we are, and we carry the remains, the remnants of those precious ancestors, the Denisovans, the Neanderthals and Anzick. Through their DNA, and ours, we reach back tens of thousands of years on the human migration path. Their journey is also our journey. It’s absolutely amazing and it’s no wonder people have so many questions and such a sense of enchantment. But it’s true – and only you can determine exactly what this means to you.

______________________________________________________________

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Analyzing the Native American Clovis Anzick Ancient Results

Posted on September 23, 2014 by Roberta Estes

155

This ancient DNA truly is the gift that keeps on giving.

Today, Felix Chandrakamur e-mailed me and told me that the Anzick results were not yet fully processed at Gedmatch when I performed a “compare to all.” He knows this because he knows when he uploaded the results, and after they were finished, he ran the same compare and obtained vastly different results. I am updating my original article to point to this one, so the data will be accurately reflected.

In fact, the results are utterly fascinating, take your breath away kind of fascinating. Felix wrote an article about his findings, Clovis-Anzick-1 ancient DNA have matches with living people!

While finding what appear to be contemporary matches for the Anzick child may sound ho-hum, it’s not, and when you look at the results and the message they hold for us, it’s absolutely astounding.

Felix ran his comparison with default values of 7cM. This is the threshold that is typically utilized as the line in the sand between “real” and IBS, matches – real meaning the results are and could be, if you could find your common ancestor, genealogically relevant. In this case, that clearly isn’t true.

The exception to this rule is heavily admixed groups, such as Ashkenazi Jewish people who are related to every other Askhenazi Jewish person autosomally. It seems, looking at these results, that this is the same situation we find with the 12,500 year old Anzick child and currently living people. This population had to be painfully small for a very long time and the DNA had to exist in every person within that population group for it to be passed in segments this large to people living today.

After receiving Felix’s e-mail, of course, I had to go back and run the compares again. In particular, I wanted to run the one to many, as he had.

I began at the 1cM level and noticed that I received exactly 1500 results, which seemed to me like a cutoff – not an actual number of matches. So, I upped that threshold to 2, then 3, then 4, then 5, then 6, then finally to the default of 7. It was only at 7, the IBS/IBD default, that the results were under the 1500 threshold, at 1466.

1466 current matches?????

This is absolutely amazing. The Anzick child lived about 12,500 years ago in Montana. How are 1466 matches to currently living people possible?

Many of these matches are to people from the southwest and Mexico today. They are not, for the most part, from eastern Canada.

Let’s take a look at what we found.

In the 1466 results, as Felix mentioned, the closest matches match at current “cousin” levels to Anzick. The highest 7 matches that show haplogroups are haplogroup Q1a3a. Unfortunately, with the constant renaming of the haplogroups recently, it’s difficult to interpret the haplogroup exactly, which is why we’ve gone to SNP names. Looking at some of the names and e-mails, several appear to carry Spanish surnames or be from Mexico or South America.

Of the 1466 results:

2 were Y haplogroup C
79 were Y haplogroup Q
520 carried a mitochondrial DNA haplogroup of A, B, C, D, M or X
Of the 79 haplogroup Q carriers, 52 also carried a Native mitochondrial haplogroup.
A total 549 individuals out of 1466 carried at least one Native American haplogroup, or about 37.5%. That’s amazingly high.

Of these closest matches who are Y haplogroup Q, they also all carry variant Native American mitochondrial DNA haplogroups as well, so these people may not be heavily admixed. In other words, they may be almost “pure” Native American.

In order to test this theory, I entered the number of the kit that rated the highest in terms of total cM at 160.1 with the largest segment at 14.8. You can click on the images to enlarge.

As you can see, this individual is very nearly 100% Native American.

The second individual on the list, who may be from Guatemala, also carries almost no admixture.

Of the highest 21 matches that listed any haplogroup information, all have either or both Native Y or mitochondrial DNA haplogroups.

Out of curiosity, I ran the first person on the list who had neither a Native American Y or mitochondrial haplogroup – both being European.

As you can see, below, they are still clearly heavily Native American, but clearly admixed.

I moved to the last person of the 1466 on this list whose DNA matched at a total of 7cM, who did not carry a Native haplogroup. This individual, below, is more heavily admixed.

Lastly, I ran the same admixture tool on the last person, who had a total of 7cM matching that did have a Native American mitochondrial haplogroup.

Not surprisingly, the individual with almost no non-Native admixture is much more likely to carry the ancient segments in higher percentages than the individuals who are admixed. This again strongly suggests that at one point, these segments were present in an entire group of Native people and may still be present in very high numbers in people who carry no admixture.

Out of curiosity, and assuming that these first two individuals are not known to be related to each other, I ran them against each other in a one to one comparison.

There were no matches at the default values, but by dropping them just a little, to 5cM and 500 SNPs, they match on 6 segments.

It looks like they should match on chromosome 17 at the 700 SNP/7 cM default threshold.

At 200 SNPs and 2cM, there were 67 segments. These are clearly ancient in nature and size, but matching just the same. By lowering the threshold to 100 SNPs and 1cM, they share a whopping 990 segments.

Indeed, these two men very clearly share a lot of population specific DNA from the ancient people of the New World, including that of Anzick male child who lived in Montana 12,500 years ago.

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Utilizing Ancient DNA at GedMatch

Posted on September 22, 2014 by Roberta Estes

128

Mummy of 6 month old boy found in Greenland

It has been a wonderful week for those of us following ancient DNA full genome sequencing, because now we can compare our own results to those of the ancient people found whose DNA has been fully sequenced, including one Native American.

Felix Chandrakumar has uploaded the autosomal files of five ancient DNA specimens that have been fully sequenced to GedMatch. Thanks Felix.

When news of these sequences first hit the academic presses, I was wishing for a way to compare our genomes – and now my wish has come true.

Utilizing GedMatch’s compare one to all function, I ran all of the sequences individually and found, surprisingly, that there are, in some cases, matches to contemporary people today. I dropped the cM measure to 1 for both autosomal and X.

Please note that because these are ancient DNA sequences, they will all have some segments missing and none can be expected to be entirely complete. Still, these sequences are far better than nothing.

1. Montana Anzick at GedMatch

This is the only clearly Native American sample.

http://www.y-str.org/2014/09/clovis-anzick-dna.html

F999912

9-27-2014 – Please note that kit F999912 has been replaced by kit F999913.

10-23-2014 – Please note that kit F999913 has been replaced by kit F999919.

No matches at 1cM in the compare to all. This must be because the SNP count is still at default thresholds, in light of information discovered later in this article.

Update – as it turns out, this kit was not finished processing when I did the one to one compare. After it finished, the results were vastly different. See this article for results.

2. Paleo Eskimo from Greenland at GedMatch

http://www.y-str.org/2013/12/palaeo-eskimo-2000-bc-dna.html

F999906

Thirty-nine matches with segments as large at 3.8. One group of matches appears to be a family. One of these matches is my cousin’s wife. That should lead to some interesting conversation around the table this holiday season! All of these matches, except 1, are on the X chromosome. This must be a function of these segments being passed intact for many generations.

I wrote about some unusual properties of X chromosomal inheritance and this seems to confirm that tendency in the X chromosome, or the matching thresholds are different at GedMatch for the X.

3. Altai Neanderthal at GedMatch

http://www.y-str.org/2013/08/neanderthal-dna.html

F999902

One match to what is obviously another Neaderthal entry.

4. Russian Causasus Neanderthal at GedMatch

Another contribution from the Neanderthal Genome Project.

http://www.y-str.org/2014/09/mezmaiskaya-neanderthal-dna.html

F999909

No matches.

5. Denisova at GedMatch

http://www.y-str.org/2013/08/denisova-dna.html

F999903

Two matches, one to yet another ancient entry and one to a contemporary individual on the X chromosome.

But now, for the fun part.

My Comparison

Before I start this section, I want to take a moment to remind everyone just how old these ancient segments are.

Anzick – about 12,500 years old
Paleo-Eskimo – about 4,000 years old
Altai Neanderthal – about 50,000 years old
Russian Caucasus Neanderthal – about 29,000 years old
Denisova – about 30,000 years old

In essence, the only way for these segments to survive intact to today would have been for them to enter the population of certain groups, as a whole, to be present in all of the members of that group, so that segment would no longer be divided and would be passed intact for many generation, until that group interbred with another group who did not carry that segment. This is exactly what we see in endogamous populations today, such as the Askenazi Jewish population who is believed, based on their common shared DNA, to have descended from about 350 ancestors about 700 years ago. Their descendants today number in the millions.

So, let’s see what we find.

I compared by own kit at GedMatch utilizing the one to one comparison feature, beginning with 500 SNPs and 1cM, dropping the SNP values to 400, then 300, then 200, until I obtained a match of some sort, if I obtained a match at all.

Typically in genetic genealogy, we’re looking for genealogy matches, so the default matching thresholds are set relatively high. In this case, I’m looking for deep ancestral connections, if they exist, so I was intentionally forcing the thresholds low. I’m particularly interested in the Anzick comparison, in light of my Native American and First Nations heritage.

The definition of IBS, identical by state, vs IBD, identical by descent segments varies by who is talking and in what context, but in essence, IBD means that there is a genealogy connection in the past several generations.

IBS means that the genealogy connection cannot be found and the IBS match can be a function of coming from a common population at some time in the past, or it can be a match by convergence, meaning that your DNA just happened to mutate to the same state as someone else’s. If this is the case, then you wouldn’t expect to see multiple segments matching the same person and you would expect the matching segments to be quite short. The chances of hundreds of SNPs just happening to align becomes increasingly unlikely the longer the matching SNP run.

So, having said that, here are my match results.

Anzick

I had 2 matches at 400 SNPs, several at 300 and an entire list at 200, shown below.

Chr	Start Location	End Location	Centimorgans (cM)	SNPs
1	6769350	7734985	1.7	232
1	26552555	29390880	1.9	264
1	31145273	33730360	2.7	300
1	55655110	57069976	1.9	204
1	71908934	76517614	2.8	265
1	164064635	165878596	2.8	264
1	167817718	171330902	3.3	466
1	186083870	192208998	4.2	250
2	98606363	100815734	1.4	256
2	171132725	173388331	2.0	229
2	218855489	220373983	2.5	261
3	128892631	131141396	1.7	263
3	141794591	143848459	2.5	207
4	1767539	3571907	2.7	235
4	70345811	73405268	2.5	223
5	2340730	2982499	2.3	200
5	55899022	57881001	2.3	231
5	132734528	134538202	1.9	275
5	137986213	140659207	1.7	241
6	34390761	36370969	1.8	293
8	17594903	18464321	1.9	200
8	23758017	25732105	1.7	240
8	109589884	115297391	1.9	203
9	122177526	124032492	1.6	229
10	101195132	102661955	1.2	264
10	103040561	105596277	1.3	304
10	106135611	108371247	1.5	226
12	38689229	41184500	1.6	247
13	58543514	60988948	1.6	220
13	94528801	95252127	1.0	277
14	60929984	62997711	1.8	255
14	63724184	65357663	1.7	201
14	72345879	74206753	1.7	263
15	36850933	38329491	2.7	238
16	1631282	2985328	2.5	273
16	11917282	13220406	3.7	276
16	15619825	17324720	3.1	305
16	29085336	31390250	1.3	263
16	51215026	52902771	3.4	224
17	52582669	56643678	4.7	438
19	11527683	13235913	1.7	203
19	15613137	16316773	1.2	204
19	46195917	49338412	3.3	397
20	17126434	18288231	2.1	225
21	35367409	36969215	4.1	254
21	42399499	42951171	1.6	233
22	33988022	35626259	5.0	289

In my case, I’m particularly fortunate, because my mother tested her DNA as well. By process of elimination, I can figure out which of my matches are through her, and then by inference, which are through my father or are truly IBS by convergence.

I carry Native heritage on both sides, but my mother’s is proven to specific Native ancestors where my father’s is only proven to certain lines and not yet confirmed through genealogy records to specific ancestors.

Because I had so many matches, quite to my surprise, I also compared my mother’s DNA to the Anzick sample, combined the two results and put them in a common spreadsheet, shown below. White are my matches. Pink are Mom’s matches, and the green markers are on the segments where we both match the Anzick sample, confirming that my match is indeed through mother.

We’ll work with this information more in a few minutes.

Paleo

At 200 SNP level, 2 segments.

1	26535949	27884441	1.1	258
2	127654021	128768822	1.2	228

My mother matches on 9 segments, but neither of the two above, so they are either from my father’s side or truly IBS by convergence.

Altai Neanderthal

Russian Neanderthal

Neither my mother nor I have any matches at 100SNPs and 1cM.

Denisovan

I have one match.

Chr	Start Location	End Location	Centimorgans (cM)	SNPs
4	8782230	9610959	1.2	100

My mother matches 2 segments at 100 SNPs but neither match is the same as my segment.

Matching to Ancestral Lines

I’ve been mapping my DNA to specific ancestors utilizing the genealogy information of matches and triangulation for some time. This consists of finding common ancestors with your matches. Finding one person who matches you and maps to a common ancestor on a particular segment consists of a hint. Finding two that share the same ancestral line and match you and each other on the same segment is confirmation – hence, the three of you triangulate. More than three is extra gravy:)

I have also recorded other relevant information in my matches file, like the GedMatch Native chromosomal comparisons when I wrote “The Autosomal Me” series about hunting for my Native chromosomal segments.

So, after looking at the information above, it occurred to me that I should add this ancestral match information to my matches spreadsheet, just for fun, if nothing else.

I added these matches, noted the source as GedMatch and then sorted the results, anxious to see what we might find. Would at least one of these segments fall into the proven Native segments or the matches to people who also descend from those lines?

What I found was both astonishing and confusing….and true to form to genealogy, introduced new questions.

I have extracted relevant matching groups from my spreadsheet and will discuss them and why they are relevant. You can click on any of the images to see a larger image.

This first set of matches is intensely interesting, and equally as confusing.

First, these matches are to both me and mother, so they are confirmed through my mother’s lines. In case anyone notices, yes, I did switch my mother’s line color to white and mine to pink to be consistent with my master match spreadsheet coloration.

Second, both mother and I match the Anzick line on the matches I’ve utilized as examples.

Third, both 23andMe and Dr. Doug McDonald confirmed the segments in red as Native which includes the entire Anzick segment.

Fourth, utilizing the Gedmatch admixture tools, mother and I had this range in common. I described this technique in “The Autosomal Me” series.

Fifth, these segments show up for two distinct genealogy lines that do not intersect until my grandparents, the Johann Michael Miller line AND the Acadian Lore line.

Sixth, the Acadian Lore line is the line with proven Native ancestors.

Seventh, the Miller line has no Native ancestors and only one opportunity for a Native ancestor, which is the unknown wife of Philip Jacob Miller who married about 1750 to a women rumored to be Magdalena Rochette, but research shows absolutely no source for that information, nor any Rochette family anyplace in any proximity in the same or surrounding counties to the Miller family. The Miller’s were Brethren. Furthermore, there is no oral history of a Native ancestor in this line, but there have been other hints along the way, such as the matching segments of some of the “cousins” who show as Native as well.

Eighth, this makes my head hurt, because this looks, for all the world, like Philip Jacob Miller who was living in Bedford County, PA when he married about 1750 may have married someone related to the Acadian lines who had intermarried with the Micmac. While this is certainly possible, it’s not a possibility I would ever have suspected.

Let’s see what else the matches show.

In this matching segment Mom and I both match Emma, who descends from Marie, a MicMac woman. Mom’s Anzik match is part of this same segment.

In this matching segment, Mom and I both match cousin Denny who descends from the Lore line who is Acadian and confirmed to have MicMac ancestry. Mom’s Anzik segments all fit in this range as well.

In this matching segment, cousin Herbie’s match to Mom and I falls inside the Anzick segments of both Mom and I.

More matching to the proven Miller line.

This last grouping with Mom is equally as confusing at the first. Mom and I both match cousin Denny on the Lore side, proven Acadian.

Mom and I both match the Miller side too, and the Anzik for both of us falls dead center in these matches.

There are more, several more matches, that also indicate these same families, but I’m not including them because they don’t add anything not shown in these examples. Interestingly enough, there are no pointers to other families, so this isn’t something random. Furthermore, on my father’s side, as frustrating as it is, here are no Anzick matches that correlate with proven family lines. ARGGHHHHHH……

On matches that I don’t share with mother, there is one of particular interest.

You’ll notice that the Anzik and the Paleo-Greenland samples match each other, as well as me. This is my match, and by inference, not through mother. Unfortunately, the other people in this match group don’t know their ancestors or we can’t identify a common ancestor.

Given the genetic genealogy gold standard of checking to see if your autosomal matches match each other, I went back to GedMatch to see if the Paleo-Greenland kit matched the Clovis Anzik kit on this segment, and indeed, they do, plus many more segments as well. So, at some time, in some place, the ancestors of these two people separated by thousands of miles were related to each other. Their common ancestor would have either been in Asia or in the Northern part of Canada if the Paleo people from Greenland entered from that direction.

Regardless, it’s interesting, very interesting.

What Have I Learned?

Always do experiments. You never know what you’ll find.

I’m much more closely related to the Anzick individual than I am to the others. This isn’t surprising given my Native heritage along with the endogamous culture of the Acadians.

My relationship level to these ancient people is as follows:

	Lived Years Ago	Relatedness	Comments
Montana Anzick	12,500	107.4cM at 200 SNP level	Confirmed to Lore (Acadian) and Miller, but not other lines
Greenland Paleo	4,000	2.3cM at 200 SNP level	No family line matches, does match to Anzick in one location
Altai Neanderthal	50,000	2.1cM at 200 SNP level	No family line matches
Russian Neanderthal	29,000	0
Denisovan	30,000	1.2cM at 200 SNP	No family line matches

The Lores and the Millers

Looking further at the Lore and Miller lines, there are only two options for how these matching segments could have occurred. There are too many for them all to be convergence, so we’ll have to assume that they are indeed because we shared a common population at some time and place.

The nature of how small the segments are testify that this is not a relatively recent common ancestor, but how “unrecent” is open to debate. Given that Neanderthal and Denisovan ancient segments are found in all Europeans today, it’s certainly possible for these segments to be passed intact, even after thousands of years.

The confirmations to the Lore line come through proven Lore cousins and also through other proven Acadian non-specific matches. This means that the Acadian population is highly endogamous and when I find an Acadian match, it often means that I’m related through many ancestors many times. This, of course, increases the opportunity for the DNA to be passed forward, and decreases the opportunity for it to be lost in transmission, but it also complicates the genealogy greatly and makes determining which ancestor the DNA segment came from almost impossible.

However, I think we are safe to say the segments are from the Acadian population, although my assumption would be that they are from the Native Ancestors and not the French, given the high number of Anzick matches, Anzick being proven to be Native. Having said that, that assumption may not be entirely correct.

The Miller line is relatively well documented and entirely from Germany/Switzerland, immigrating in the early 1700s, with the exception of the one unknown wife in the first generation married in the US. Further examination would have to be done to discover if any of the matches came through Johann Michael Miller’s sons other than Philip Jacob Miller, my ancestor. There are only three confirmed children, all sons. If this segment shows up in Johann Michael Miller’s line not associated with son Philip Jacob Miller, then we would confirm that indeed the segment came from Europe and not a previously unknown Native or mixed wife of Philip Jacob.

Bottom Line

So, what’s the bottom line here? I know far more than I did. The information confirms, yet again, the Acadian Native lines, but it introduces difficult questions about the Miller line. I have even more tantalizing questions for which I have no answers today, but I tell you what, I wouldn’t trade this journey along the genetic pathway with all of its unexpected bumps, rocks, slippery slopes and crevices for anything!! That’s why it’s called an adventure!

______________________________________________________________

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Big Y DNA Results Divide and Unite Haplogroup Q Native Americans

Posted on June 25, 2014 by Roberta Estes

One of my long standing goals has been to resurrect the lost heritage of the Native American people. By this I mean, primarily, for genealogists who search for and can’t find their Native ancestors. My blog, www.nativeheritageproject.com, is one of the ways that I contribute towards that end. Many times, records are buried, don’t exist at all, or don’t reflect anything about Native heritage. While documents can be somewhat evasive and frustratingly vague, the Y DNA of the male descendants is not. It’s rock solid.

The Native communities became admixed beginning with the first visits of Europeans to what would become the Americas. Native people accepted mixed race individuals as full tribal members, based on the ethnicity of the mother. Adoption also played a key role. If a female, the mother, was an adopted white child, the mother was considered to be fully Native, as was her child, regardless of the ethnicity of the father.

Therefore, some people who test their DNA expecting to find Native genetics do not – they instead find European or African – but that alone does not mean that their ancestors were not tribal members. It means that these individuals have to rely on non-genetic records to prove their ancestors Native heritage – or they need to test a different line – like the descendants of the mother, through all females, for example, for mitochondrial DNA.

On the other hand, some people are quite surprised when their DNA results come back as Native. Many have heard a vague story, but often, they don’t have a clue as to which genealogical line, if any, the Native ancestry originated. Native ancestry was often hidden because the laws that prevailed at the time sanctioned discrimination of many kinds against people “of color,” and if you weren’t entirely of European origin, you were “of color.” Many admixed people, as soon as they could, “became” white socially and never looked back. Not until recently, the late 20^th century, when discrimination had for the most part become a thing of the past and one could embrace their Native or African heritage without fear of legal or social reprisal.

Back in December of 2010, we found the defining SNP that divided haplogroup Q between Europeans and Native Americans. At the time, this was a huge step forward, a collaboration between testing participants, haplogroup administrators, citizen scientists and Family Tree DNA.

This allowed us to determine who was, and was not included in Native American haplogroups, but it was also the tip of the iceberg. You can see below just how much the tree has expanded and its branches have been shuffled. This is a big part of the reason for the change from haplogroup names like Q1a3 to Q-M346. For example, at one time or another the SNP M3 was associated with haplogroup names Q1a3a, Q1a3a1 and Q1a3a1a. On the ISOGG tree below, today M3 is associated with Q1a2a1a1.

The new Family Tree DNA 2014 tree is shown below for one of the Big Y participants whose terminal SNP is L568, found beneath SNP CTS1780 which is found beneath L4, which is beneath L213 which is beneath L474 which is beneath MEH2 which is beneath L232 which is, finally, beneath M242.

The introduction of the Big Y product from Family Tree DNA, which sequences a large portion of the Y chromosome, provided us with the opportunity to make huge strides in unraveling and deciphering the haplogroup Q (and C, the other male Native haplogroup in the Americas) tree. I am hopeful that in time, and with enough people taking the Big Y test, that we will one day be able to at least sort participants into language and perhaps migration groups.

In November, 2013, we asked for the public and testers to support our call for funds to be able to order several Big Y tests. The project administrators intentionally did not order tests in family groups, but attempted to scatter the tests to the far corners, so to speak, and to include at least one person from each disparate group we have in the haplogroup Q project, based on STR matches, or lack thereof, and previous SNP testing.

Thanks to the generosity of contributors, we were able to order several tests. In addition, some participants were able to order their own tests, and did. Thank you one and all.

The tests are back now, and with the new Big Y SNP matching, recently introduced by Family Tree DNA, comparisons are a LOT easier.

So, of course, I had to see what I could find by comparing the SNP results of the several gentlemen who tested.

To protect the privacy of everyone involved, I have reduced their names to initials. I have included their terminal SNP as identified at Family Tree DNA as well as any tribal, ethnic or location information we have available for their most distant paternal ancestor.

There are two individuals who believe their ancestors are from Europe, and there is a very large group of European haplogroup Q members, but I’m not convinced that the actual biological ancestors of these two gentlemen are from Europe. I have included both of these individuals as well. Let’s just say the jury is still out. As a control, I have also included a gentleman who actually lives in Poland.

Of the individuals above, SD, CT and CM are SNP matches.

CD, WJS and WBS are SNP matches with each other.

BG and ETW are also SNP matches to each other.

None of the rest of these individuals have SNP matches. (Note, you can click to enlarge the chart.)

In the table above, the Non-Matching Known SNPs are shown with the number of Shared Novel Variants. For example, SD and CT have 4 non-matching SNPS and share 161 Novel Variants and are noted as 4/161.

We can easily tell which of the known SNPs are nonmatching, because they are shown on the participants match page.

What we don’t know, and can’t tell, is how many Novel Variants these people share with each other, and how many they might share with the individuals that aren’t shown as matches.

Keep in mind that there may be individuals here that are not shown as matches to due no-calls. Only people with up to and including 4 non-matching Known SNPs are counted as matches. If you have the wrong combination of no-calls, or, aren’t in the same terminal haplogroup, you may not be shown as a match when you otherwise would be.

The other reason for my intense interest in the Novel Variants is to see if they are actually Novel, as in found only in a few people, or if they are more widespread.

I downloaded each person’s Novel Variants through the Export Utility (blue button to the right at the top of your personal page,) and combined the Novel Variants into a single spreadsheet. I colorized each person’s result rows so that they would be easy to track. I have redacted their names. The white row, below, is the individual who lives in Poland.

There are a total of 3506 Novel Variants between these men. When sorting, many clustered as you would expect. There is the Algonguian group and what I’ve taken to calling the Borderlands group. This group has someone whose ancestor was born in VA and two in SC. I have documentation for the Virginia family having descendants in SC, so that makes sense. The third group is an unusual combination of the gentleman who believes his ancestors are from Germany and the gentleman whose ancestors are found in a New Mexico Pueblo tribe, but whose ancestor was, likely, based on church records, a detribalized Plains Indian who had been kidnapped and sold.

Clusters that I felt needed some scrutiny, for one reason or another, I highlighted in yellow in the Terminal SNP column. Obviously the Polish/Pueblo matching needs some attention.

Another very interesting type of match are several where either all or nearly all of the individuals share a Novel Variant – 15 or 16 of 16 total participants. I don’t think these will remain Novel Variants very long. They clearly need to be classified as SNPs. I’m not sure about the process that Family Tree DNA will use to do this, but I’ll be finding out shortly.

Here’s an example where everyone shares this Novel Variant at location 7688075,except the gentleman who lives in Poland, the man who believes his ancestor is from Germany, and the Creek descendant.

I was very surprised at how many Novel Variants appear in all 16 results of the participants, including the gentleman who lives in Poland – represented by the white row below.

So, how were the Novel Variants distributed?

Category	# of Variants	Comments
Algonquian Group	140	This is to be expected since it’s within a specific group. Any matches that include people outside the 3 Algonquian individuals are counted in a separate category. These matches give us the ability to classify anyone who tests with these marker results as provisionally Algonquian.
Borderlands	83	This confirms that these three individuals are indeed a “group” of some sort. This also gives us the ability to classify future participants using these mutations.
All or Nearly All – 15 or 16 Participants	80	These are clearly candidates for SNPs, and, given that they are found in the Native and the European groups, they appear to predate the division of haplogroup Q.
Several Native and European, Combined	45	This may or may not include the person who lives in Poland. This group needs additional scrutiny to determine if it actually does exist in Europe, but given that there are more than 3 individuals with each of these Novel Variants, they need to be considered for SNPhood.
Pueblo/NC	1
Poland/Borderlands	2
Mexico/Algonquian	2
German/Pueblo	9	I wonder if this person is actually German.
Poland/Mexico	20	I wonder if this person’s ancestors are actually from Poland.
Algonquian, NC, Creek	1
Borderland, Mexico, Creek	1
Algonquian/Cherokee	1
All Native, no Euro	2
Algonquian, Borderlands, Mexico, NC	1
Algonquian, Mexico, Borderlands	1
Borderlands, Pueblo	1
Borderlands, Creek, NC	1
Algonquian, Cherokee, Mexico	3
Algonquian, Pueblo, Creek, Borderlands	1
Cherokee, NC	2
Algonquian, Borderlands	2
Borderlands, NC	1
Algonquian, NC	1
Polish/NC	10

Some of this distribution makes me question if these SNP mutations truly are a “once in the history of mankind” kind of thing. For example, how did the same SNP appear in the Polish person and the NC person, or the Pueblo person, and not in the rest of the Native people?

New SNPs?

So, are you sitting down?

Based on these numbers, it looks like we have at least 125 new SNP candidates for haplogroup Q. If we count the Algonquian and the Borderlands groups of matches, that number rises to about 250. This is very exciting. Far, far more than I ever expected. of these SNPS, about half will identify Native people, even Native groupings of people. This is a huge step forward, a red letter day for Native American ancestry!

SNPs and STRs

Lastly, I wanted to see how the SNP matching compared to STR matching, or if it did at all, for these men.

Only two men match each other on any STR markers. CD and WJS matched on 12 markers, but not on higher panels. The TIP calculator estimated their common ancestor at the 50^th percentile to be 17 generations, or between 425 and 510 years ago. We all know how unrealistic it is to depend on the TIP calculator, but it’s the only tool we have in situations like this.

Given that these are the only two men who do match on STR markers, albeit distantly, in a genealogical timeframe, let’s see what the estimates using the 150 years per SNP mutation comes up with. This estimate is just that, devised by the haplogroup R-U106 project administrators, and others, based on their project findings. 150 years is actually the high end of the estimate, 98 being the lower end. Of course, different haplogroups may vary and these results are very early. Just saying.

CD has 207 high quality Novel Variants. He shares 188 of those with WJS, leaving 19 unshared Novel Variants. Utilizing this number, and multiplying by 150, this suggests that, if the 150 years per SNP is anyplace close to accurate, their common ancestor lived about 2850 years ago. If you presume that both men are incurring mutations at the same rate in their independent lines, then you would divide the number of years in half, so the common ancestor would be more likely 1425 years ago. If you use 100 years instead of 150, the higher number of years is 1900 and the half number is about 950 years.

It’s fun to speculate a bit, but until a lot more study has occurred, we won’t be able to reasonably estimate SNP age or age to common ancestor from this information. Having said all of that, it’s not a long stretch from 710 years to 950 years.

It looks like STR markers are still the way to go for genealogical matching and that SNPS may help to pull together the deeper ancestry, migration patterns and perhaps define family lines. I hope the day comes soon that I can order the Big Y for lots more project members. Most of these men do have STR marker matches, and to men with both the same and different surnames. I’d love to see the Big Y results for those individuals who match more closely in time.

This is still the tip of the iceberg. There is a lot left to discover! If you or a family member have haplogroup Q results, please consider ordering the Big Y. It would make a wonderful gift and a great way to honor your ancestors!

You can also contribute to the American Indian project at this link:

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

In order to donate to the haplogroup C-P39 project which also includes Native Americans, please click this link:

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

______________________________________________________________

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Native American DNA Projects

Posted on May 26, 2014 by Roberta Estes

I’m often asked about projects that are for or include Native American DNA results. Please note that different project administrators have different criteria for admission to a project. Some require definitive proof of descent, some require no documentation at all. This is entirely left to the discretion of the project administrators. Therefore, you should NEVER assume that because you match someone in one of these projects that you have Native heritage. There are various ways to prove Native heritage using DNA which I’ve discussed in the article, “Proving Native American Ancestry Using DNA.”

Furthermore, some of these projects aren’t exclusively for Native American descendants, but you may find Native descendants or families among the project members because of the topic or where the project is focused.

Regarding haplogroup projects. Some haplogroups include both people who are and who are not Native. Check with the particular project to understand the nuances. In many cases, research through the projects is ongoing.

If you know of additional projects which should be added to this list, please let me know.

Native American, First Nations or Aboriginal DNA Projects

Acadia Metis Mothers
http://www.familytreedna.com/public/AcadiaMetisMothers/default.aspx

Algonquian East DNA Project
http://www.familytreedna.com/public/algonquian_east/default.aspx

American Indian DNA Project
http://www.familytreedna.com/public/AmericanIndian/

AmerIndian Ancestry out of Acadia Project
http://www.familytreedna.com/public/AcadianAmerIndian/

AmerIndian Mexico (Southwest US and Mexico)
http://www.familytreedna.com/public/MexicoAmerindian/

Cherokee DNA Project
http://www.familytreedna.com/public/CherokeeDNAProject/default.aspx

Mitochondrial American Indian Founder Project
http://www.familytreedna.com/public/AmerindFoundermtDNA/default.aspx

Mothers of Acadian mtDNA Project
http://www.familytreedna.com/public/mothersofacadia/default.aspx
Some Native results

Native People of Southwest Virginia
http://www.familytreedna.com/public/napeopleofswvirginia/

Piqua/Shawnee – no public website – contact admins below
cavetank@aol.com, tankerkh@uc.edu, ewest14@woh.rr.com

Robeson Co., NC American Indian (formerly Lumbee)
https://www.familytreedna.com/groups/robesonconcamericanindian/about

Tuscarora
http://www.familytreedna.com/public/Tuscarora/

Waccamaw DNA Project
http://www.familytreedna.com/public/CapefearIndians/default.aspx

Wesorts-Piscataway
http://www.familytreedna.com/public/Wesorts-Piscataway

Wiccocomico Native American DNA Project
http://www.familytreedna.com/public/wiccocomico/default.aspx

Mitochondrial DNA Haplogroup Projects

Haplogroup A Mitochondrial DNA
http://www.familytreedna.com/public/haplogroupAmtDNA/
Note – Native American DNA is a subgroup of haplogroup A. See this link for specifics.

A2 Mitochondrial DNA Project
http://www.familytreedna.com/public/mtDNA_A2
A2 is known to be Native.

A4 Mitochondrial DNA Project
http://www.familytreedna.com/public/A4-mtDNA/
Haplogroup A4 is known to be Native.

B2 Mitochondrial DNA Project
http://www.familytreedna.com/public/mt-DNA-B/
B2 is known to be Native.

Haplogroup C Mitochondrial DNA Project
http://www.familytreedna.com/public/C_Haplogroup_mtDNA
Subgroups of haplogroup C are known to be Native.

Haplogroup D Mitochondrial DNA Project
http://www.familytreedna.com/public/D/
Subgroups of haplogroup D are known to be Native.

Haplogroup X Mitochondrial DNA Project
http://www.familytreedna.com/public/x/
Subgroups of haplogroup X are known to be Native.

Haplogroup X2b4 Mitochondrial DNA Project
http://familytreedna.com/public/x2b4mtdna
X2b4 is currently being studied to determine if it is Native or has a Native component.

Y Haplogroup Projects

Y Haplogroup C
http://www.familytreedna.com/public/Chaplogroup/
Subgroups of haplogroup C are known to be Native.

Haplogroup C-P39
http://www.familytreedna.com/public/ydna_C-P39/#sthash.cKkws2cd.dpbs
This SNP defined Native Americans within haplogroup C.

American Indian Haplogroup Q1a3a1 – QM3
http://www.familytreedna.com/public/Amerind%20Y/?/publicwebsite.aspx?vgroup=Amerind+Y

Related Topics

You may find Native families listed in these projects.

Caribbean DNA Project
https://www.familytreedna.com/public/caribbeanproject

Cumberland Gap Mitochondrial DNA Project
http://www.familytreedna.com/public/Cumberlandgap-mtdna/?/publicwebsite.aspx?vgroup=Cumberlandgap-mtdna

Cumberland Gap Y DNA Project
http://www.familytreedna.com/public/CumberlandGap-YDNA

Early Chesapeake
http://www.familytreedna.com/public/Early_Chesapeake

East Carolina Roots
http://www.familytreedna.com/public/eastcarolinaroots/default.aspx

Melungeons

Click to access MelungeonsMulti-EthnicPeopleFinal.pdf

Mitochondrial DNA of the Middle Appalachians
http://www.familytreedna.com/public/mtDNA%20of%20Middle%20Appalachians/default.aspx?section=mtresults

New Mexico DNA Project
http://www.familytreedna.com/public/newmexicoDNA/

North Carolina Early 1700s
http://www.familytreedna.com/public/NorthCarolinaEarly1700s/default.aspx

Puerto Rico DNA Project
http://www.familytreedna.com/public/puertoricansurname/

Southwestern Virginia Roots
http://www.familytreedna.com/public/SWVirginia

Virginia 1600s
http://www.familytreedna.com/public/va-1600s

Voices in Time
http://www.familytreedna.com/public/voicesintime/

______________________________________________________________

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Finding Native American Ethnic Results in Germanic People

Posted on May 21, 2014 by Roberta Estes

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

Why?

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

It’s no wonder we’re so admixed.

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

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

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

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

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

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

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

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

Eurogenes K13

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

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

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

Dodecad

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

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

Dodecad 12b below

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

HarappaWorld

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

In Summary

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

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

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

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

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

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

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Bluejacket Reunion with a Tomahawk

Posted on March 19, 2014 by Roberta Estes

I want to thank Carlyle Henshaw for this wonderful article. When I asked him for permission to publish, here’s what Carlyle had to say.

“I really had fun researching that article. The three Bluejacket brothers that establish Bluejacket Crossing were George, Henry and Charles. Henry was my great great grandfather. The three brothers were grandsons of Shawnee Chief Blue Jacket, 1737-1808. He was the last principal war chief of the Shawnee Tribe of Indians. We have 15 members in our PekowiBlueJacket Project. All trace to Blue Jacket genealogically. We all descend from the three brothers via DNA. Nine of us have Family Finder. Four males have fathers who are named Bluejacket and all match each other. One is haplogroup Q and three are Q1a3a1. All in all, everyone matches up in the Blue Jacket line, genetically and genealogically. We have sixth, seventh and eighth generations from Blue Jacket represented.”

A REUNION with a TOMAHAWK

by Carlyle Hinshaw

Twin Bridges State Park — On July 1, 2001, the Shawnee Indian Blue Jacket family held its biennial reunion at this lovely place eight miles southeast of Miami, Oklahoma. The picnic was comprised of 60 relatives and other Shawnee friends and two fine Ottawa County Coon Hounds who know a Shawnee repast when they see, er, smell one! Blue Jackets from the Cherokee Nation (Cherokee Adopted Shawnee), Eastern Shawnee Tribe and Shawnee Tribe gathered to celebrate their long, illustrious history. Several excellent stories arose and are being told as time allows for the telling.

Robert Harry Withrow, Jr., of Kanab, Utah, brought a Pipe Tomahawk used by and handed down through, his family from Shawnee days in northeastern Kansas Territory during the middle 1800’s. Robert also brought along the story of the Pipe Tomahawk.

On November 30, 1831, a group of 334 Shawnees, including families of Chief John Perry, Henry and James (Jim) Blue Jacket, Peter Cornstalk and John Woolf arrived at the Shawnee Agency in Kansas after a three month “Trail of Tears” from Allen County, Ohio. Most of the adults rode horseback and the children in baggage wagons. These Wapaghkonetta and Hog Creek Shawnees had ceded (August 8, 1831) their homelands to the U. S. Government for 100,000 acres within or contiguous to, the existing Shawnee Reserve south of the Kansas (Kaw) River. The following year, 24 Shawnees of the River Huron in Michigan Territory made their trek to the new Shawnee country. In 1833, 14 more followed suit and in 1839, the total of River Huron Shawnees in the Shawnee Reserve was 38. (Louise Barry, THE BEGINNING OF THE WEST, p. 223-24, Kansas State Historical Society, Topeka, 1972).

The new Shawnee lands were however, smack dab in the middle of the great western migration. Starting with a fur party path in 1827 (Sublette’s Trace), several trails headed up in the Independence, Missouri – confluence of the Kaw and Missouri rivers area and the main trace of the Oregon California Road crossed Shawnee lands south of the Kaw. Westward Ho traffic steadily increased and reached a crescendo after the discovery of gold in California in 1849. Settlement along the various trails began and Indian lands became more and more desirable to emigrants wanting to establish roots.

Treaty of 1854

Successful in their continual efforts to displace Indians, the U. S. Government had Shawnee leaders travel to Washington DC and sign a treaty on May 10, 1854, ceding 1, 600,000 acres of their land for 200,000 within the same area. Now that was a hell of a deal for the governmental’s! Shawnee signers of the document included: Joseph Parks, Black Hoof (was he still around?), George McDougal, Silverheels, Paschal Fish, Long Tail, George Blue Jacket, Graham Rogers, Wa-wah-che-pa-e-kar (or, Black Bob), Tooly and Henry Blue Jacket. Witness’s to the signatures included Agent Benjamin F. Robinson and Interpreter Charles Blue Jacket. Each Shawnee was awarded, in severalty, 200 acres and that included Absentee Shawnees and Adopted Shawnees.

Hughmongous tracts of lands immediately became available for settlement and many new areas were incorporated, including Lawrence in 1854 and Eudora in 1857. German settlers purchased land for the latter town from Paschal Fish, who, along with John Blue Jacket, had been assistant gun and blacksmiths for the Leavenworth Agency in 1837. Quick to take advantage of this new situation, the Blue Jacket brothers, Henry, George and Charles, went into the hotel and ferry business. George and storekeeper William “Dutch Bill or Billy” Greiffenstein incorporated the town of Sebastian, six miles SE of Lawrence in the SE1/4 of the SW1/4 of Section 12 – Township 13 South – Range 20 East. The town did not survive and is not shown on modern maps. Henry died at Blue Jacket’s Crossing of the Wakarusa River on May 3, 1855, leaving his wife, Eliza, with six children and expecting a seventh. The latter was born in early 1856.

On the afternoon of May 19, 1855, the first steamboat to ply the Kansas River, the EMMA HARMON, left Kansas City en-route to Topeka and other way landings. Stopping to re-supply wood around noon the next day, they slipped into the stream again and almost immediately were hailed by an Indian wanting a tow up river for his flatboat. They stopped, made the small boat fast and proceeded west up river. The flatboat had just been made by Tooly, a Shawnee who had operated a ferry where the Delaware River, coming from the north, joined the Kaw between Lawrence and Topeka. Upon reaching the confluence of the Kaw and Wakarusa, they cast the Indian loose in his craft. Amidst cheering and waving from the passengers, the red man poled his way up the smaller stream. That Indian boat captain had to be one of two cousins, both strapping 21 year olds, Stephen S. Blue Jacket, eldest son of Henry, or William George Blue Jacket, eldest son of George! Thus began operations of Blue Jacket’s Ferry. (Kansas Historical Quarterly, V. 6, p. 17-19)

Civil War

The Free State – Slave State concept became an overriding one at this time, as anti-slavery Kansas Jayhawkers actively worked with the underground railroad bringing freedom to many and pro-slavery Missouri Bushwhackers fought to bring the freedmen back into slavery. With Lawrence as the “free state” capitol, local traffic added to the depth of Oregon California Road ruts. Kansas in fact became a free State in 1861 as the Civil War broke out.

On the night of August 21, 1863, Confederate Captain William Clarke Quantrill led 400 raiders from successes at Independence, Missouri against Union troops, toward Lawrence to punish the anti-slavery zealots of many years standing. The inhabitants of Blue Jacket’s Crossing got wind of Quantrill’s sweep across northeastern Kansas and took precautions. Eliza Silverheels, wife of David Likens Blue Jacket, had a one year old boy at the time but took it upon herself to round up the children and some older protectors, loaded them with provisions and the very youngest and sent them into the hills south of the Wakarusa.

Defending Hearth and Home

Eliza was determined to guard her home, stayed there and lay in wait for the band of guerillas prancing toward Lawrence. This great-great grandmother of Robert Harry Withrow, Jr., was armed with a Pipe Tomahawk, most assuredly obtained from her father-in-law, the Rev. Charles Blue Jacket, by now an ordained Methodist Minister.

As the raiders crossed the Wakarusa at this Shawnee enclave, one, bent on looting Eliza’s home and perhaps intent on doing bodily harm to any inhabitants, tried to enter by a window. A young, enraged Shawnee Indian woman brandishing a wicked looking Tomahawk confronted him! With great effort, Eliza gave a mighty swing of her weapon, so mighty in fact, that when the axe met the raider, her arm broke. The haft of the Tomahawk broke at the same time. The Quantrillian was not so fortunate, as the blow to his head did him in for good!

The Confederates hit Lawrence at 5 AM, killing upwards of 200 men, looting, raping and setting fire to the entire town in an atrocity of the worst kind. Quantrill later was abandoned by most of his men and killed by Union troops in Kentucky. Lawrence began recovery immediately, regardless of the heartbreak foisted upon them by those monsters.

Pipe Tomahawks

The successful defender passed the family Pipe Tomahawk on to daughter Cindarella Blue Jacket who passed it to her daughter Cindarella Florence (Mills) Brown. Mrs. Brown’s daughter, Betty June, married Robert Harry Withrow and they parented Robert, Jr., who is the current keeper of the family heirloom. The Withrow family and 90 year old grand mom, Cindarella Florence, all attended the picnic and all contributed to this story.

European and Americans developed pipe Tomahawks for the Indian trade. Made with a smoking handle and a tobacco bowl insert at the head, they served, among other things, as “badges of prestige” given to Indian leaders at treaty signings and other occasions. Giver and receiver ornately decorated most. Modern artisans reproduce them and can be acquired at less than $50.00 to $500.00. Documented historical antiquities sell for upwards of $35,000!

Robert Withrow’s Pipe Tomahawk does not have the original smoking haft, thanks to Eliza’s mighty blow, however, its origin is documented by makers marks.

The maker was a Vickers metal smith in London, England in 1833. The head was cast in the Naylor, Vickers and Company’s Sheffield foundry.

Both sides of the head have the “Bleeding Heart” symbol, which is a common decoration on the antique ones.

The Masonic emblem was probably etched by gun and black smithy, John Blue Jacket, brother of the Rev. Charles Blue Jacket, who, along with many other Shawnees, was active in that organization.

The other side is scribed with a man in the moon, which is a bit unusual. The French Moon or crescent moon was, however, a common inscription, sometimes included when the head was cast.

Robert Withrow, Jr. is a teacher of survival skills across the country, both to private and military groups. It is fitting that he continues to preserve Shawnee history and heritages.

Top L-R: Robert Withrow, Robert Withrow, Jr ., Robert John Brown
Bottom, L-R: Betty Withrow, Cindarella Brown, Saundra Davis.

The elder Withrows live in Chetopa KS, Robert and Saundra in Centralia IL and Cindarella in Centralia.

Cindarella had the good fortune to remember her grandparents. She was born in 1911 and David Likens Blue Jacket passed away on April 4, 1919 and Eliza (Silverheels) Blue Jacket on June 12, 1929. Great historical events were told directly to their daughter Cindarella (Blue Jacket) Mills and to their grand daughter Cindarella Mills. Now, at 90 years of age, the latter is still able to give us insight to our Shawnee heritage. Thank you Cindarella Florence (Mills) Brown.

Gaylord Carlyle Hinshaw
1713 Baron Dr
Norman OK 73071
405-364-4584
bjexploration@swbell.net

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Thank you so much.

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