The Autosomal Me – The Ancestors Speak

Posted on February 10, 2013 by Roberta Estes

This is Part 2 in the series, “The Autosomal Me.” Part 1 was “The Autosomal Me – UnRaveling Minority Admixture.”

Every Sunday, I write something called a Sunday Story. I’ve done this for years. I send them to my kids and I delude myself into thinking they read them. I’m really writing them for my grandkids someday and hopefully, some as yet unborn descendants I’ll have that will care about finding out about the life and times of their a-few-greats grandmother who lived along with the dinosaurs in the last half of the 1900s and first half of the 2000s. I know, I’m optimistic.

I decided that perhaps I would share this weeks Sunday story with all of you. This way, I know that at least someone will read it. Actually, aside from my husband, it’s my daughter-in-law who comments the most often. So welcome to my Sunday Story! You are all honorary cousins!

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I know that a great deal of what I do with genetics is lost on my friends and family members. That’s OK, because it’s very specialized. However, I wanted to take a little bit of time to share with you an aspect of the genetics I work with that I think is very beautiful in both a literal and a spiritual way.

The point of genetic genealogy, of course, is to learn about our ancestors, who they were and our connection to them. There are various ways to do this, but most of the time it’s through various matches to other people who share a common ancestor either recently or perhaps further back in time.

Of course, therein lies the rub – how long ago are two people related and who was their common ancestor? Some people who carry minority ancestry are at a distinct disadvantage, because the testing that provides matches and ethnicity generally relies on amounts in excess of 1%, which equates to about 6 or 7 generations. While many of us know that we carry minority ancestry, we would be hard pressed to say that our “pure” Native (or other minority) ancestor fell into that 6 or 7 generation bracket. Six or 7 generations equates to about 150-175 years before our birth, or about 1775-1800 for most of us. By then, many Native people were already admixed and many already lived outside of a traditional tribal unit. Some people carry Native heritage from multiple lines, but since it comes from multiple ancestors, it too is often quite fragmented, so it doesn’t really improve the situation much unless some of those fragments happen to fall together to make larger segments.

Therefore, we are looking for very small amounts of admixture that often don’t show on traditional tests, or if they do, it’s in miniscule amounts.

Enter chromosome painting.

Without going in to boring detail, I’ve recently been working with a new methodology of identifying these fragmented and very small segments. I am using several chromosome painting tools. I’ll be blogging soon enough about how all of this is done, but I just wanted to share with you a couple of beautiful pieces of DNA, through which our ancestors are speaking, and we can see them, in a manner of speaking.

On the graph below, which is my chromosome painting of one a small part of one of my chromosomes on the top, and my mother’s showing the exact same segment on the bottom, the various types of ethnicity are colored, or painted. You can see that both of us have a primary ethnicity of North European, shown by the teal.

The grid shows location 120 on the chromosome. Think of this number as a house number on a street. It’s numbered so we can keep track of where we are on the chromosome. For genealogy purposes, the smallest segment normally considered as relevant is 7 mb or marker segments long. Each tick mark equals one segment or address, so a segment 7 mb long would be from 120-127 which takes you right over to the legend. As you can see, the primary ethnicity has no problem reaching way beyond the contiguous 7 threshold, but the minority ethnicity would not be counted because it’s too small.

However, by the very definition of what minority ancestry is, these small segments are not only present, providing critical information, they are essential in our search and very informative. Let’s see what they are saying to us.

First, let’s talk for a minute about ancestry. There is no line in the sand very often between populations. There are generally only degrees of difference. So in the case of Native American, which is yellow on this chart, we also expect to see it “drift back in time” by being found in conjunction with Siberian (putty), South Asian (red) and East Asian (emerald green). Native Americans were not dropped from alien spaceships, they evolved over time from these other Asian populations, so we would expect to see some of their genetics in Native American people.

So let’s take a look at what we do actually see in the DNA.

The first brightly colored segment in the top band is mine. It includes Native American (yellow), South Asian (red), a big chunk of East Asian (emerald Green), a little bit from the Caucus (ginger) which is the Middle East area, and a piece of West African (light green).

There are two messages from the ancestors in this piece of DNA. First, this segment absolutely, positively does NOT come from mother. We can see this clearly because she has nothing but North European (teal) in that section of her DNA. So, this little gem came from Dad.

The second piece of information is that the ancestor who provided this DNA to Dad was very likely admixed, Native and African.

Of course, if you’re thinking ahead at this point, you’ll be asking, “Which one of your Dad’s other relatives has this same segment?” because, yes, that’s exactly how we will tell which of his lines contributed the Native ancestry. But you’re getting ahead of the story, and well, that is a story for another time. This story today, is about the direct messages of the ancestors and the beauty of our DNA itself.

Let’s look at the next segment of minority DNA. It starts about location 123. Mom’s is much more pronounced than mine and much richer. This tells us that I didn’t receive much of Mom’s. Instead I received mostly North European (teal), along with some East Asian (emerald).

Mom has almost a perfect Native segment here. By perfect, I mean we find a progression from Native back through time through all 4 categories I would expect to find. I consider this entire segment “Native” because it indicates Native heritage. You can see the emerald green (East Asian), putty (Siberian), red (South Asian) and yellow (North American Indian and Arctic) nestled together with no other minority ancestry in close proximity. This means it’s not part of a different kind of Asian segment. Remember, part of Europe was settled by the Mongol Hordes and the Huns, so we do see Asian and western Asian DNA in Europe, along with DNA from the Caucus, but we don’t see isolated segments like this, with just eastern Asian DNA and Native American. So this little beauty is the perfect Native indicator, positively, even though it is only about 4 segments long.

Now take a look at my DNA in that same region in the top row. It’s kind of hard to see the emerald green against the teal, but I only inherited the East Asian (emerald) segments from Mom. Of note, however, is that I also have an East Asian (green) segment that Mom doesn’t have. My East Asian starts about 122 where hers doesn’t begin until 123. So good old Dad contributed a bit here as well. Again, we know this because Mom only has North European at that segment.

And now of course for the kicker. Your DNA looks this same way. How boringly teal it is, or how beautifully rainbow multi-colored depends on how much minority ancestry you have, from how many different lines, and which of your parents you received it from.

I hope you can see why I’m so excited to be developing this new technique to work with highly fragmented DNA to find our ancestors. They are there, they have a voice, and they are speaking to us. All we have to do is figure out how to listen.

I am simply in awe of the beauty of this technique, literally as well as figuratively. While I certainly understand and appreciate logically that matching other people means we’re related, there is something awe-inspiring and tangible about being able to see the painted graphs and view the layers of ancestry nestled together, life forces reaching through time, protecting that DNA with its precious message for us over many generations. All this time, just waiting for us to be able to understand the most personal message from our ancestors, delivered, from them, in our genes, to each of us. This is the voice of our ancestors.

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The Autosomal Me – Unraveling Minority Admixture

Posted on February 6, 2013 by Roberta Estes

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

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

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

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

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

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

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

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

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

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

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

Let me give a very short example here.

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

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

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

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

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

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

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

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

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King Richard, Is That You???

Posted on February 4, 2013 by Roberta Estes

The newsworld is abuzz today with the news that skeletal remains found a few months ago under a parking lot in Leicester are indeed those of England’s King Richard the Third who was killed in the Battle of Bosworth Field in 1485. He was hastily buried by the Greyfriars friars, but the associated church is long gone and the location forgotten. The parking lot inadvertently covered the cemetery which included, ironically, King Richard III. He was buried without a coffin or shroud in a shallow grave. His skull is shown below, courtesty of the University of Leicester.

Of course, for the genetic genealogy community, the exciting part of this is that DNA evidence is a prime piece of the puzzle proving his identification, along with bone analysis of his known scoliosis.

The mitochondrial DNA of the remains matches that of Michael Ibsen, a Canadian cabinetmaker and direct maternal descendant of Richard’s sister, Anne of York.

Be sure to watch the video that accompanies this news article.

http://www.cnn.com/2013/02/03/world/europe/richard-iii-search-announcement/index.html?iid=article_sidebar

Debbie Kennett, a British genetic genealogy blogger has been following these developments closely and has done a wonderful writeup complete with the backstory and discovery. In addition, she has compiled a nice list of resources for those interested.

http://cruwys.blogspot.co.uk/2013/02/richard-iii-king-is-found.html

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Projects, Administrators and Expectations

Posted on February 2, 2013 by Roberta Estes

One of the reasons I wanted to start a blog was to be able to chat about genetic genealogy topics that interest people. I can tell what’s on your mind by the questions I receive. For some reason, I’ve received several questions and some complaints about projects and administrators recently, and I think a fireside chat might clarify things a lot.

A few questions arrived in my in-box this past week that I’d like to paraphrase and address. The first question is from a male and the second from a female.

Question 1 – I’m in a number of projects. One of the administrators contacted me and suggested I do some additional SNP testing. But my surname project administrator has never said anything about this. If I needed more testing, why wouldn’t my surname project administrator tell me about this? Is this legitimate?

Question 2 – I’m so upset. I tried to join the XYZ surname project and the administrator told me that I couldn’t. Why can’t they be more flexible and realize I’m related to that family? This project is listed by Family Tree DNA as one I should join, but the administrator won’t let me.

I see confusion, misunderstanding and frustration in both of these questions, for both the participants and the administrators. I’d like to talk a little bit about projects, why they are formed, administrators, participants and expectations.

Projects

There are four types of projects at Family Tree DNA.

1. Surname Projects – The earliest projects formed were surname projects. Those are based on surnames, like Estes, and typically focus on the paternal lines and the Y chromosome and only that specific surname. Herein lies the first point of confusion. Because these projects were formed to sort out male family lines of a particular surname, they are typically restricted to males who carry that surname, or sometimes males who match that surname through adoptions of some sort.

Question 2 relates to this problem. From her perspective, she “should be” allowed to join, because she is related. But from a scientific perspective, there is no benefit for a female to join a male focused project. However, from a public relations perspective, it won’t hurt to let her join. Because women’s surnames change every generations, she could theoretically join all the surname projects for all of her ancestors. None of it would benefit her for matching etc., but it won’t hurt anything either.

From an administrator’s perspective, having people in a project that can’t advance the goals of the project is simply clutter. Not only that, but we have to do something with them, categorize them somehow, or leave them ungrouped. It’s also confusing to people looking at a Y-line project to see other surnames and apparently unrelated or unconnected people. Conversely, I want people to be happy with genetic genealogy and since she is related and very interested, perhaps she can contribute something in the way of research.

If this sounds a bit like the angel and devil, one on each shoulder talking to each other…..well, that’s because it is and there is no one right answer.

There is an exception, of course, to what I just said. It seems there is always an exception to everything.

Family Finder

Recently with the Family Finder tests, more and more administrators are including people in their surname projects who are related to that family but who do not carry the surname because it’s the only way we have today of including Family Finder participants and grouping them. I have begun to do this myself as a project administrator.

The alternative to this is to begin lineage projects, such as the Johann Michael Miller Descendants project, just for descendants who have taken the Family Finder test. This is a way to know who they are, to group them so that you can work with their results. The challenge is that projects are not set up to function this way. They are set up to display Yline (males) and mitochondrial DNA results, only, or both for a kit, and in this case, the Yline and mitochondrial DNA results are both irrelevant and misleading if they are displayed as valid results. Administrators are trying to figure out the best way to deal with this.

The work-around I’ve implemented is a grouping within the surname project labeled Family Finder where those who are related but don’t carry the particular surname are grouped. I am actively recruiting descendants for these groupings as Family Finder holds great promise in finding those elusive unidentified wives, unnamed children…..but I digress.

Here’s what my Crumley project looks like. You can see that the grouping of Family Finder is entirely irrelevant to the rest of the project, but it’s the best we can do under the current project structure.

2. Haplogroup Projects – The second type of project formed was haplogroup projects. These are for both Y-line and mitochondrial. Some haplogroups have only one project, like mitochondrial haplogroup K, for example. Others, like mitochondrial haplogroup H or Y-line R have many subprojects. These projects are a function of who wants to study what – and who is willing to do the work.

Haplogroup projects, by and large, are research projects. This means that they are arranged quite differently than surname projects. Surname projects are generally arranged by family and within family, by line, when possible. Haplogroup projects aren’t concerned with surnames, but with deep ancestry and location, and they are arranged by haplogroup and sub-haplogroup.

A great deal of the progress in understanding haplogroups, their history, migration patterns and the discovery of subgroups has come from the haplogroup projects. They are very important, make no mistake. Family Tree DNA is the only place in the world where there are groups of people grouped by haplogroup in public projects. This is citizen science at it’s best.

The haplogroup Q project had made significant scientific contributions. You can see that participants are grouped by haplogroup, meaning by SNP. In some cases, administrators also group participants by the tests needed to further refine their haplogroups. When you refine your haplogroup with further testing, you also refine your personal story and contribute to science as well.

Haplogroup Q groups participants by their haplogroup, above, but when they need additional testing, they are grouped with others who need that test, below. Why do they need additional testing? That’s how we learn about haplogroups. Every additional SNP that you test positive or negative for tells us more about migrations, about where your ancestors lived and what they did. The power of this isn’t just in one test, but in many tests combined that write the story of our ancestors.

To illustrate the power of many versus one, the mapping function comes to mind. Each project administrator can enable or disable mapping. Mapping can be very useful to surname projects, but it’s crucial to haplogroup projects.

Here’s the map for all of haplogroup Q. Interesting, but all that this really tells us is that it’s pretty universal. It’s one of two Native American haplogroups, but sub-groups are found throughout Asia and Europe as well. Want to know if you’re Native? Then you’ll have to do SNP testing.

The map below shows the oldest known ancestors for those who carry SNP M25. Looking at this map tells you immediately that these people aren’t Native American. But if you live in the US and you’re looking for Native ancestry, and you don’t test to this level, you can be left with the erroneous impression that your haplogroup Q result IS Native when it isn’t.

Ah, the power of maps. Most project administrators enable maps.

The administrators of haplogroup projects are focused very differently than surname project administrators. This explains the confusion in question 1 about why the surname admin didn’t suggest SNP testing, but the haplogroup project admin did.

Administrators Are Different People

Ok, stop laughting!

This introduces a bit of a different topic and that is what motivates haplogroup administrators. I mean, let’s face it, why WOULD you volunteer for this? The answer is simple – passion combined with a smidgen of insanity!

Surname administrators are most often the family genealogist. We all know them. We probably are them. It’s what attracted us to genetic genealogy in the first place. They may or may not be terribly familiar with the science of genetics, with SNPs, and may or may not be aware of the benefits of SNP testing. They can, however, recite the details of the original immigrant who arrived in Virginia in 1683 and all their children!

Haplogroup project administrators tend to be scientists. I’m very fortunate that my co-admin on the haplogroup E1b1a project is a population geneticist. Yes, they are interested in their surname family, but they are also very focused on their ancient ancestry too – in making that connection between the two and unraveling their story. To them, haplogroup projects represent opportunities not otherwise available.

This brings us to the third and fourth kinds of projects, lineage and geographic projects, whose administrators are passionate about their project’s subject.

3. Lineage Projects – Not many of these exist today and most that do are maternal (mitochondrial) DNA lineage projects, such as the descendants of Jane Doe, but I expect as we sort through how to best address lineage with Family Finder tests, lineage projects will become more widely utilized.

4. Geographic projects, the fourth type of project, are all projects other than above. These include many special interest projects, such as the Hatteras Island project, the Cumberland Gap project, the Mothers of Acadia project, the Lumbee project, the Lost Colony project, and many more.

These projects are as different as the people who founded them. Some projects are research projects and some are what I term courtesy projects.

My Cumberland Gap Project is a courtesy project. This means I formed it to allow people from a particular region to interact and to share. There is an associated Yahoo group that is very active. I do not have to approve membership. It’s open for all

The Lost Colony projects (and there are three, Y-line, mitochondrial and Family) are research projects. This means that the membership is restricted to people with specific qualifications. I don’t do this to be mean, it’s critical to the research goals of the project. Let me illustrate. The goal of the Lost Colony Y-line project is to test people with a specific set of surnames (the Lost Colonists surnames) who are found in very early eastern North Carolina counties. The project description says this and so does the FAQ. However, 99% of the requests to join the projects say something like this: “I want to compare my results with that of the Lost Colonists.” Well, guess what folks…..we’re trying to figure out what the Lost Colonists’ DNA looks like too.

Right now, the people in the Lost Colony Y-line project are good candidates to be descended from the colonists. We’re working to find the colonist families in England to confirm. However, if I let everyone who wants to compare their DNA to these people into the project, how would we ever know who is a true colonist candidate and who is just a comparer???

People get really upset when I explain this to them. And I have to say this…I can’t resist….had they read the project background and goals in the first place….they could have saved themselves and me both some time because they would have known that they don’t qualify, and why. They can support the project in other ways if they are interested.

As a project administrator, my largest frustration by far is with people who don’t read what is available for them.

I finally set up the Lost Colony Family project as a courtesy project for everyone who wants to test and compare their results to each other. Now there is a place for the frustrated people who can’t join the Lost Colony Y-line or mitochondrial projects.

Some geographic (and surname) projects require pedigree charts and a specific genealogy to join. For example, both the Lumbee and Cherokee projects have this requirement. Of course, for a Y-line or mtDNA project, your connection must be through either the paternal line or the maternal line. We receive requests to join daily from people who are connected, but not by Y-line or mtDNA, and they are terribly frustrated and sometimes quite angry when they are told they aren’t qualified to join. It’s not a judgment, it’s the way DNA works.

Project administrators are the gatekeepers to be sure the project retains focus and stays on track, which is only fair to the people hoping to learn and gain information by being project members. Project administrators are not there to simply be difficult to random applicants. Most of us really dislike having to decline a join request, even if we do explain. We know that some people simply won’t understand and will be upset or angry with us personally. Not fun.

This begs the question of why people are trying to join projects that aren’t good fits for them anyway???

Picking the Right Project

The good news and the bad news is that Family Tree DNA tries to help people find relevant projects. Unfortunately, it’s easy to misinterpret this if you don’t understand the source of this information. Below is an example. I’ve entered my surname, Estes, and these are the “associated projects” that are shown. Many people interpret these to be “recommended” by Family Tree DNA, and they join each and every one of them. That’s not the goal, nor are all projects appropriate for everyone.

Since I’m a female, none of the Y projects are relevant to me, and neither is the Estes surname project, generally. However, a new person wouldn’t have the experience to know this, so administrators need to help educate people. I wrote about this in the article, “What Project Do I Join?”

These projects are on this list because their administrator included the surname in their project profile, meaning they are interested in attracting people, or at least some people, with that surname. However, they may not be interested in attracting all people with that surname. If your surname is Estes and your family never set foot in America, then obviously the Cumberland Gap group, focused on the convergence of states Kentucky, Tennessee and Virginia, is not likely to be of interest to you. Since it is a courtesy project, you can join if you want, but if it was a project like the Lost Colony projects, then you would need to provide some evidence that your family fits the criteria for those the project is seeking.

Ok, so now we’ve talked about the four kinds of projects and how to select the right one for you. Let’s talk a little bit about what you can expect from an administrator and what they expect from you.

Administrators

First of all, administrators are volunteers. They receive no compensation of any sort, no discounts, nothing, except they are eligible to attend the annual DNA Conference in Houston. Eligible to attend does not mean the conference is free. I don’t bring this up as a complaint, it’s just that there has been a persistent rumor that refuses to entirely die that administrators receive some percentage of sales or compensation of some sort for running projects. They don’t and never have.

Because they are volunteers, their administration and personal communication styles vary widely. Many don’t have any co-administrators so have no backup or assistance. Some are prompt at answering e-mails, some not. Genetic genealogy and projects are now more than 10 years old. People age, they die, they get distracted and some just haven’t kept up. This field moves very rapidly. If you see a project in trouble, consider offering to help. If that doesn’t work, notify Family Tree DNA.

There are published guidelines for administrators. Mostly these deal with privacy and what they can and can’t do. Most of this is intuitive, but maybe not to everyone so it is in writing.

A good project administrator:

Communicates with members, especially if contacted
Keeps the project groups current
Assists members equally and fairly
Is honest, but sensitive, especially in difficult situations like undocumented adoptions (NonParental Events)
Is courteous

Sounds kind of like the scouts doesn’t it?

Every project is different. As an administrator, every time I send group messages to large projects, my e-mail address gets blacklisted as a spammer. So I set up a Yahoo group for each of these projects, plus have provided my blog address. Every person receives this information when they join in an automated e-mail which explains explicitly how to join the Yahoo groups and subscribe to my blog. Still, last week, someone left one of these projects with the comment “no communication.” Sigh. Remember what I said about reading???

A few very poorly run projects do exist. In one case, the administrator does not use Family Tree DNA’s public website, nor a private one, and the only way you can obtain project information is by signing up with My Family. In another case, the administrator keeps the results private, much like above, but wrote a book about the surname a couple years ago. That seems to call into question the motivation for the project. These are sad and frustrating experiences for the participants.

Project admins cannot:

Charge a fee to join a project
Share or change private information (in fact, the Family Tree DNA website blocks that for admins)
Share the identity or personal information of participants without permission
Move members from one project to another
Use member information for any commercial purpose without authorization
Use member information and e-mails for spamming, etc.
Use a DNA project to advocate a personal or political agenda

Notify family tree DNA is you feel something is wrong or you have a concern. Consider offering to help if you notice a project languishing.

Project Members

We’ve talked about projects, why they are different and what you can expect from an administrator, but what do they expect from you as a participant, or potential participant?

1. Courtesy – I’ve met many lovely people through genetic genealogy, but I’ve also met my share of real dooseys. I see increasingly more “entitlement attitude” relative to projects with join criteria. In the words of one person who did not meet the criteria, “I deserve to be in this project. I have the right.” I strongly suspect that only the nice people who want to learn will have gotten this far in this article, so I won’t expound further:) For you folks, I don’t need to!

2. READ – Please, please read what is provided relative to the project goals and join criteria. Now this is a double edged sword, because it means the admin needs to be sure to provide this information and keep it current. Maybe I need to look at my project verbiage to see if it needs to be bolded, highlighted or in red!

3. Information – If information is requested, especially in a specific format, please comply as best you can. There is generally a reason for the request. Most admins don’t want to make extra work for you or themselves. Not all projects require information. I ask for a pedigree chart for everyone in my surname projects, and you would be amazed at how many people join the project and then never reply to any of my e-mails – probably about 50%. This is why some admins have gone to requiring a pedigree chart of some sort before people are allowed to join. And providing a pedigree chart does not mean sending a link to your tree at Ancestry. At Ancestry, all the admin can do is write everything down, by hand, IF they can find your line of the family in the chart. Remember, current and recent generations are “private” at Ancestry, so finding the right family line is almost impossible without additional information. I provide a mini-genealogy form for my project members that has them complete only the direct line directly back from them. Here’s the one for mitochondrial and the one for Y-line is the same except the word mother is changed to father.

Our Fireside Chat

I hope this has helped dispel some of the confusion surrounding projects, administrators, participants and expectations. This field started out to be quite simple, with only Y surname projects, but as the field has developed and evolved over the last decade, so have projects and with that has come some level of complexity. Joining the correct projects for you, your family and your DNA can be one of the most beneficial aspects of genetic genealogy, allowing you to find family and collaborate your research efforts with others.

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What is a Haplogroup?

Posted on January 24, 2013 by Roberta Estes

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Sometimes we’ve been doing genetic genealogy for so long we forget what it’s like to be new. I’m reminded, sometimes humorously, by some of the questions I receive.

When I do DNA Reports for clients, each person receives a form to complete with a few questions designed to give them the opportunity to tell me what their testing goals are and to ask any questions they might have. One woman asked, “Can you tell me about my psychogroup?”

I thought that psychogroup was particularly appropriate for a cluster of genealogists, especially genetic genealogists, but decided I had better let that one go.

Then there was the person who wanted to know about their hologroup. I wondered if I needed 3D glasses for that one.

Someone else wondered about their helpgroup. I couldn’t help but think of introducing myself, “Hello, my name is Roberta and I’m a member of haplogroup J.” Kinda gives new meaning to “what’s your sign?”

Then there was the person who though it was a Biblical reference, Holygroup and wanted to know how they connected to Biblical folks. Well, we do talk about Y-line Adam and Mitochondrial Eve, so why wouldn’t someone ask that?

My favorite, though is the person who gave this reason for leaving a haplogroup project, “not my glopo.” Hey, at least they realized that, as opposed to the person who called me a member of the KKK for suggesting that they did not belong in a particular project. I found that to be particularly humorous, given my ethnic mix, heritage and family.

But today, when my cousin asked me if a haplogroup follows the mitochondrial DNA, I decided it was time to talk about what a haplogroup is, a little history, and why we use them. And Shanen, thanks for asking!

Think of a haplogroup as an ancestral clan, a large family, like the Celts, or Vikings. These would be larger than Native American tribes, encompassing members of many tribes. There are two male Native American haplogroups that include all Native American males. There are a few more African clans, or haplogroups, but not many.

There are clans for the Y chromosome, which is of course tested by the Y DNA test at Family Tree DNA and generally follows the paternal surname up and down the tree. Y DNA is passed from father to son, only, through the Y chromosome which only males possess.

There are also clans for mitochondrial DNA, tested by the mtDNA tests at Family Tree DNA, which follows the direct maternal line up your family tree. This means your mother, her mother, her mother, etc. Woman give their mitochondrial DNA to all of their offspring, males and females, but only females pass it on.

You can see the Y-line, paternal (blue) and mitochondrial, maternal (red), lines on the pedigree chart below.

Companies like 23andMe and the Geno 2.0 project provide haplogroups for both Y-line and mitochondrial DNA, but neither of them test personal mutations that allow you to compare your mutations against those of other people for genealogical matches. The regular Y-line and mitochondrial tests at Family Tree DNA do that. In addition, both also provide your haplogroup or clan designation.

A new haplogroup is born when a very specific new mutation occurs. All descendants will carry that mutation. That mutation defines that haplogroup. So if a new haplogroup is born today, we wouldn’t know it was a haplogroup until hundreds or thousands of years later when we see that lots of people have this same mutation from a single individual. As you might imagine, many haplogroups over the ages have died out, but some have been very successful as evidenced by the fact that we are all here today! Roughly half of the European men carry Y haplogroup R and mitochondrial haplogroup H is found in nearly 50% of all Europeans – both descending, respectively, from one single person tens of thousands of years ago.

Since all of humanity, both male and female, sprang initially from Africa, the earliest haplogroups were found there. As some people moved further away and crossed into Asia and Europe, they developed unique mutations that would give rise to the European, Asian and Native American haplogroups we know today. There are 4 main groupings, African, European, Asian and Native American, but there are several subgroups within most of those main groups, except for Native Americans who only have two male haplogroups.

So in essence, haplogroups are a pedigree chart of the clans of humanity. Family Tree DNA displays a haplogroup chart with the main haplogroups shown on everyone’s personal page for Y-line DNA. They were simply named alphabetically with no connection to a word. So no, A is not A because it’s African, even though it happens to be. N is not Native American. E is not European. You get the drift. Any resemblance is purely coincidental.

Your clan, in this example, haplogroup I, is shown with an arrow. Every clan, male and female, has subclans, often known as subclades for Y DNA or subgroups for mitochondrial DNA. To see the various subgroups of I, click on the tab and voila, there they are, the subgroups of haplogroup I. Yours is the lowest one on the tree that is green, in this case I2b1a1.

Because of the dramatic new number of haplogroups recently discovered, future versions of the haplotree will be moving away from the letter based names like I2b1a1 and will only use the terminal, or lowest branch, SNP to identify a haplogroup. In this case, that would be L126 or L137 which are equivalent SNPs. So in the future this person’s haplogroup will be called I-L126 instead of I2b1a1 because L126 will never change, but the name I2b1a1 changes every time a new upstream haplogroup is discovered between the root of haplogroup I and I2b1a1 and needs to be inserted into its proper place in the tree.

As we learn more about the subgroups, each one has its own story which is somewhat different than the stories of the other subgroups. Some are evident, such as Jewish clusters, some not so much. Each clan story involves how that haplogroup came to be found where it is today. For example, haplogroup E is African, but within haplogroup E, there are two major divisions with very different stories for their clans. One group is found only in Sub-Saharan African and one is found mostly in the Middle East and the Mediterranean basin and is known colloquially as the Berber haplogroup. We’re still learning about subgroups, and with the Geno 2.0 test, the haplotree is growing exponentially.

Family Tree DNA predicts your clan, or haplogroup, with any Y-DNA test as long as you match exactly at 12 markers to someone who has been SNP tested. SNP testing is what tests for the special haplogroup defining mutations. If you don’t match, they will SNP test you for free to establish your primary haplogroup.

Many people purchase additional SNP tests to further define their Y haplogroup so that they can learn about where their ancestors were, when, and what they were doing. For example, we know that SNP M222 equates to Niall of the 9 Hostages in history. How cool is that to know!

Some years ago, Dr. Doug McDonald assembled this wonderful map of the basic haplogroups of the world. Although we’ve discovered subgroups for each haplogroup, it’s still quite valid. E3b has since been renamed E1b1b and ExE3b means haplogroup E1b1a. RxR1 means haplogroup R except R1a and R1b which have their own legend.

Mitochondrial DNA also has haplogroups, which are clans. On the drawing below, compliments of Dr. Whit Athey, it’s easier to see how the daughter clans arose, were born, and were named. Because of the naming pattern, this looks a little less like a pedigree chart and a little more like stars, planets and moons.

One difference between Y-line DNA and mitochondrial DNA clans is that although they are all currently named alphabetically, the mitochondrial clans have names. That is thanks to Dr. Bryan Sykes who wrote the book, “The Seven Daughters of Eve” published in 2001. For example, he named haplogroup H, Helena because Helena is Greek for light. He told somewhat accurate stories about each clan and although quite scientifically dated now, described the life that each clan would have lived in post-glacial Europe. This book was the first book about DNA to reach the popular reading public, and was a huge success because he humanized science and normal air-breathing humans could relate. I ordered my first mitochondrial DNA test through his company and received one page with a Sunday School gold star on the red dot for haplogroup J.

I was thrilled at the time, but times have changed a lot. Due to advances in research and new subclades being defined, thanks in large part to citizen scientists like you, I now know that I’m haplogroup J1c2f as a result of my full sequence mitochondrial DNA test.

Unlike Y-line DNA, no additional SNP test is required to fully determine your mitochondrial DNA haplogroup. When you take the full mitochondrial sequence test (mtFullSequence) at Family Tree DNA, you receive your most detailed, full haplogroup designation automatically. With the HVR1 (mtDNA) and HVR2 (mtDNAPlus) tests, you receive at least your base haplogroup. The full sequence is required to determine your full haplogroup.

To put this in perspective, think of your mitochondrial DNA as a clock face. There are a total of 16,569 locations in your mitochondrial DNA. The HVR1 test tests the number of locations from 11:55 to noon and the HVR2 test tests the number of locations between noon and 12:05PM. The full sequence test tests the rest, the balance of the 50 minutes of the hour.

Family Tree DNA is the only commercial testing company that offers the full sequence test.

As more discoveries are made for both male and female haplogroups, the subgroup names sometimes change within the clan or main haplogroup because new branches get inserted in the tree as they are discovered.

For example, from a scientific paper, here’s an early version of the haplogroup H mitochondrial phylotree which is what the haplotree is called for mitochondrial DNA.

Here’s a later version.

You wouldn’t even be able to see today’s version, because the print would have to be miniscule to fit it on the page. In Dr. Behar’s paper, “A ‘Copernican’ Reassessment of the Human Mitochondrial DNA Tree from its Root” published in April 2012, the supplemental material records haplogroup H87. Most of those subgroups have subgroups of their own, like you can see above, and those that don’t today soon will as new discoveries are made.

Now that you know what a haplogroup is, there’s a lot you can do with both mitochondrial and Y-line DNA results.

Even if you do nothing more, it’s fun to identify your clan. It’s the only way of extending our genealogy back in time beyond surnames. For me, to connect my last known maternal ancestor, Elisabetha Mehlheimer, born in or near Goppsmannbuhl, Germany around 1800 to the cave paintings in Chauvet, France created about 12,000 years ago was a magical moment, a reach across time through a tenuous umbilical strand allowing me to identify and touch my 12,000 year-old ancestor. In my wildest genealogist dreams, I never dreamed this could or would ever be possible and indeed, it wouldn’t be, were it not for the genetic genealogy tools we have today.

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Hackers and Your Genetic Secrets

Posted on January 20, 2013 by Roberta Estes

Did that title get your attention? Well, it was meant to, just like it was meant to in this NBC article titled “Scientists Demonstrate How Hackers Could Unlock Your Genetic Secrets.” Or how about this one in the New York Times, “Web Hunt for DNA Sequences Leaves Privacy Compromised?” Sensationalism sells….and so does fear. Don’t panic, the sky is not falling.

I’ve had several people forward me a variety of links to several articles about this expressing concern. Most people didn’t really understand what was going on…and since “family tree databases” were mentioned in the first paragraph, it frightened them.

This article says that the “security cracking trick relies on the availability of genetic information linked to surnames in a variety of public family-tree databases.” Well, that’s sort of true, but not exactly true. The issue is not the family tree databases, it’s the fact that the researchers in The Thousand Genomes Project, while keeping the names of those 1000 people “anonymous,” provided enough information that these scientific researchers, not hackers, were able to data mine the 1000 Genomes participants information to determine their Y-DNA marker values, then compared those haplotypes (marker values) just like we do in databases such as Ysearch and Sorenson. And yes, they likely had matches to several surnames, like most of us do.

Individuals in the 1000 Genomes Project signed a release indicating that they knew that their data was to be used publicly, although their identity would not be revealed but that researchers could not guarantee their privacy. The 1000 Genomes Project, unfortunately, posted the ages of the participants, which at the time seemed innocuous enough, and it was common knowledge within the scientific community that they all lived in Utah. With these three pieces of information, their age, their location, and from the scientists data mining, a possible surname, the scientists were then able, if the surname wasn’t something like Smith or Jones, to use publicly available Google and “white pages” types of searches to find people in that state, of that age, by that surname, and then using obituaries and such, connect them through online family trees to their more distant families. They did this with Craig Venter, for example.

This technique is nothing new to genealogists, as we’ve been finding cousins that way for years – the difference being of course that we didn’t data mine, otherwise in this case more aptly referred to as “scientific hacking,” the 1000 Genomes Project in order to find their Y-line DNA markers to determine a possible surname for them. That is the issue and the point of this article and ironically, it’s scientists who did it, then published the “how-to” manual.

Any genetic genealogist knows, especially anyone dealing with adoptees, that you can only reveal a biological surname about 30% of the time. In fact the scientists success rate was lower, 12%. But that’s actually irrelevant in the bigger context of the article. Their point was that they succeeded at all.

This is sort of like putting personal information on the internet, except your name, and then being surprised that someone could connect the dots and put the pieces together. No one would be surprised today if that were to happen. In fact, I’m sure we all have received cautions and warnings about putting too much info on Facebook because burglars were robbing homes when people were vacationing. Many people have their hometown, their high school and their birthday and year publicly available on Facebook. Now how many “security questions” does that answer right there? Combine that with your dog’s name and your mother’s maiden name and you’ve got almost all of the common ones.

Aside from the fear-mongering, I have three issues with these reports as a whole.

1. Statements like “they traced those three family tree pedigrees to find other connections between relatives and sensitive genetic data.” Whoa, stop right there. Just because you share a surname or even if you are a direct and immediate relative, that says nothing, absolutely nothing, about whether or not you inherited some genetically disposed health issue. Remember, children inherit half of their DNA from each parent. So unless they are finding identical twins or parents, one cannot infer that an entire family tree of people share frightening health traits. It’s irresponsible to suggest otherwise.

2. “For years, experts have worried that sensitive genetic data could be used to discriminate against patients, potential employees or would-be insurance customers. Such discrimination is illegal when it comes to employment or health insurance, but the law doesn’t’ cover life insurance, disability insurance or long-term care insurance. Theoretically an insurer could search through genetic records and turn you down because you have a genetic predisposition to, say, Alzheimer’s disease.”

Discrimination is an issue, and laws have been put in place to prohibit discrimination in the workplace. But insurers aren’t going to sift through genetic data like a private investigator. Suggesting this is unnecessary fear-mongering. Insurers don’t do that, they simply tell you that a blood test is a pre-requisite of obtaining insurance. I know, I bought life insurance and they sent a nurse to my house to verify my identity and take a blood sample. At that time, they were looking for diabetes, AIDs and probably a whole lot more. Today, they might be looking for genetic pre-dispositions. I don’t know, but I do know they have a direct method of obtaining that information and it’s not spending untold hours sifting through someone else’s data that likely isn’t relevant to you anyway.

3. This “research” project was inspired at Whitehead Institute, an affiliate of MIT, a publicly funded institution. When Yaniv Erlich dreamed up this new hacking technique, he said he couldn’t resist trying it, so instead of simply discovering a potential issue and privately and quietly working with the proper people to resolve the issue, he decided to exploit it publicly, obtaining, I suppose, his 15 minutes of fame. So yes, your tax dollars did indeed likely pay for some or all of this “research.”

In one of the articles, Dr. Jeffrey R. Botkin, associate vice president for research integrity at the University of Utah, which collected the genetic information of some research participants whose identities were breached, cautioned about overreacting. “Genetic data from hundreds of thousands of people have been freely available online,” he said, “yet there has not been a single report of someone being illicitly identified.” He added that “it is hard to imagine what would motivate anyone to undertake this sort of privacy attack in the real world.” But he said he had serious concerns about publishing a formula to breach subjects’ privacy. By publishing, he said, the investigators “exacerbate the very risks they are concerned about.”

Well, it’s obvious that these folks at Whitehead institute don’t live in the real world and clearly don’t have enough real scientific research to do.

So, what is the take home of all of this?

You are not at risk of having anything exposed in this incident unless you are one of the 1000 people in the 1000 Genomes Project. If you are part of the 1000 Genomes Project, and male, there is a 12% risk that they figured out your last name and using other tools, possibly who you are, along with your family. If you are related to someone in the 1000 Genomes Project, the researchers might have figured out that you are related to them. So now the risk is that they’ll do what with that information??? Guaranteed, someone will figure out the same information and much more quickly, without your DNA and without government funding if you simply stop paying your bills.

If you participate in a research project, such as the 1000 Genomes Project, where your full results are made publicly available, you sign a release, and that release indicates that your privacy may not be able to be protected. You are aware of the risks before you begin.

We, as a community, have been warned for years not to put information that might be medically informative on the internet, such as full sequence mitochondrial DNA information. Anyone who does so, does it at their own risk. The people in the 1000 Genomes Project knowingly took that risk.

If you stay within the confines of the genealogy and DTC mainstream testing companies, you are fairly well protected. Having said that, reading the consent forms of any of the companies makes it clear that your identity is never entirely protected. We’re genealogists after all. What good is genealogical testing if you can’t contact people you match?

Inferred health risks are not the issue they are being portrayed to be in these articles. Your cousins health risks are not necessarily yours. Genetic inheritance is a complex and individual event.

Insurers who can use health information to restrict or deny insurance are simply going to request a blood sample. They are not going to act like a blood hound on the scent of a rabbit and sort through tons of information for inferences. Why would they when they can obtain the information they seek, directly and much less expensively?

For those researchers involved with information made publicly available, such at the 1000 Genomes Project, this is a wake-up call that perhaps less information available publicly is better. Some information, such as ages and location should perhaps be available only to legitimate researchers, which would still have included the Whitehead Institute people, but would have taken away much of their thunder. I understand this change has already been implemented, but that doesn’t entirely mitigate the issue of genetic data mining publicly available full genomic sequence information for identity, only makes it a little more difficult and less likely to succeed.

I clearly understand why hackers want my bank account information, and why identity thieves want my personal information, but why, in the real world, not at Whitehead institute, would anyone ever spend the time and effort to do this? The motivation for these researchers was clearly to publish, but I can think of no reason other than that or simply “because they could” to spend the time doing something like this. Who would want to and for what purpose?

The sky is not falling

It’s behind a paywall, but you can access the scientific article here that started all of this hubbub.

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Transferring Results from National Geographic to Family Tree DNA

Posted on January 13, 2013 by Roberta Estes

There are several reasons why you might want to transfer your National Geographic Genographic Geno version 1.0 and 2.0 results to Family Tree DNA.

Please note these are only valid for the Geno 2.0 version, prior to the Helix tests that began in November of 2016.

If you’re not a Family Tree DNA client, there is a whole new genetic genealogy world just waiting on you, and transferring your results is free. National Geographic test version 1.0, which is no longer available, included a 12 marker Y DNA test, and version 2.0, currently available, includes extensive haplogroup (clan) information that complements the 12-111 marker tests at Family Tree DNA, as well as other information. If you haven’t yet taken the 12 marker or other Y DNA tests at Family Tree DNA, you will be offered that opportunity in order to find your matches. After transferring your results to Family Tree DNA, you will be able to order additional tests, contact your matches via e-mail and share your genealogy information. It’s an exciting time in genetic genealogy!

YDNA SNPs

If you are already a Family Tree DNA customer, then you’ll want to download your data for a different reason. The Geno 2.0 chip includes an extensive list of Y DNA SNPs that are tested, far beyond what Family Tree DNA offers, and you will want to integrate this data into your results pages at Family Tree DNA.

Mitochondrial DNA

If you have not yet tested your mitochondrial DNA, Geno 2.0 provides you with your haplogroup, your deep ancestral clan information. The markers required to define your haplogroup will transfer to Family Tree DNA. If you want, you can then order the mtDNA, mtDNAPlus or the full mitochondrial sequence test to see what personal mutations you carry, and who you match.

If you have taken any mitochondrial DNA test at Family Tree DNA, none of the Geno 2.0 information will transfer, including updated haplogroup information. The Full Mitochondrial Sequence test at Family Tree DNA is more extensive than the Geno 2.0 haplogroup only test.

Autosomal Results

The two autosomal tests, the one provided by Family Tree DNA (Family Finder) and the one included in the Geno 2.0 product are entirely different beasts. The Family Finder test provides you with a list of cousin matches with numerous matching tools and an ethnicity report.

The Geno 2.0 product also provides an ethnicity report but uses different comparison populations and markers than Family Tree DNA, so they serve different purposes, the Family Tree DNA Family Finder product being more focused towards genealogy and the National Geographic product being more focused towards anthropology or deep ancestry. I mean, let’s face it, you’re probably not going to be able to go back far enough in time to tack a pure Neanderthal or a pure Denisovan on your family tree, your favorite brother-in-law excepted:)

How to Transfer Your Results

In order to facilitate the transfer, you’ll need to set up an account at National Geographic, and you’ll need your National Geographic kit numbers. So find those before you start. If all else fails, find that lovely black box your Geno 2.0 test kit arrived in. Your participant number is on the inside of the front cover. And you thought it was just another pretty box!

You’ll also need your Family Tree DNA kit number and password for the kit you want these results to transfer into.

Go to the Genographic website at http://www.genographic.com and click on
“Check Results.” You’ll be prompted through setting up your account at National Geographic. Whether or not you want to transfer data, you need to set up your account because if you don’t, and you lose your Nat Geo kit number, you’re toast.

After you enter your kit ID and set up your account, you’ll see the main results screen. This is mine, and no, my paternal results aren’t missing…there aren’t any because as a female, I don’t carry a Y chromosome!

Now click on “Profile” in the upper right hand corner of the screen. You’ll see the profile screen below.

You’ll see your profile, along with your kit numbers. You’ll need these for the next step so you’ll want to be sure to write them down. I’ve greyed mine above, but you can see where they were. Note that if you have already transferred your Geno 1.0 results previouisly, adding that kit number here has been reported to generate an error. If so, then try again without the 1.0 kit number.

Next, click on “Expert Options” at the top right of the screen. You’ll see “Download Data” and “Transfer Data to Family Tree DNA.”

Click on “Transfer Data to Family Tree DNA.” You’re almost done!!! You will be transferred to a screen on the Family Tree DNA site.

The kit numbers that you need are the numbers are displayed in your National Geographic account settings screen that I suggested you write down – plus – of course – your Family Tree DNA kit number and password that you want your National Geographic results associated with.

Complete this and click on next. You will see an order screen that looks like you are placing an order. Don’t worry, the order is free, but you do need to complete the form. Click through the options and at the end, the free order for your transfer will be complete.

It takes about 24 hours before you can see your results on your personal page at Family Tree DNA.

Y SNPs

Currently, as of January 12, 2013, you will be able to see your terminal SNP on your Haplotree and SNP tab if your terminal SNP is one that Family Tree DNA tests for in their lab.

However, if your SNP is new on the Geno 2.0 chip, then you won’t be able to see your terminal SNP on your personal page at Family Tree DNA, yet, so be sure to make note of your terminal SNP from your National Geographic results. Some Geno 2.0 results at Family Tree DNA today show an upstream SNP, and others show no SNP at all.

This is one of those good news/bad news situations. The good news is that we are functioning on the leading, sometimes bleeding edge of science and get to play a very important role, which is exciting. The bad news is that we’re bleeding a bit right now. Family Tree DNA really can’t fix this problem until a new haplotree is in place.

The problem is that haplogroup/subgroup discoveries are being made so rapidly that the haplotree is in a bit of a state of flux….OK, a big state of flux, which will take some time to sort through. More, many more, discoveries than ever expected continue to be made as more kits are run through the process. Let’s just say we’re having some minor growing pains. But what a great problem to have. We already knew that Geno 2.0 would change the tree dramatically, but we really had no idea HOW dramatically. Now I’m wondering if we’ll even recognize it! What we thought was a tree was only a sprout. And it’s still growing!

Why I do believe, why yes, I do hear….In the Valley of the Jolly, Ho, Ho. Ho…

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Out of Eden – Retracing the Steps of Humanity

Posted on January 11, 2013 by Roberta Estes

So how long would it take a human, today, to walk the path that humanity traveled? Paul Salopek, a prize-winning journalist, (including a Pulitzer for his article about the Human Genome Diversity Project) and National Geographic fellow is going to find out, if it’s even possible.

According to Paul’s calculations, it will take him about 7 years to walk from the Garden of Eden, Herto Bouri, a village in Ethiopia’s Middle Awash valley, which has the longest and most continuous record of human evolution of any place on Earth, to the southern-most tip of South America. Paul left yesterday, January 10, 2013, so only another roughly 6 years and 364 days until his arrival. But then again, I’m thinking it’s not so much about the destination as the journey.

The map, below, released by National Geographic, documents the path Paul will take.

This same path, taken in essence by ancient humans, took 30,000 to 40,000 years, depending on the timeframe used for humans leaving Africa and arriving at the tip of South America. Of course, they didn’t have a nifty map, most of them didn’t make it, as the path then was entirely by trial and error. What Paul will accomplish in 7 years, it took ancient people between 1200 and 1600 generations to complete.

You can read more about Paul’s journey and see some great National Geographic photos at this link: http://news.yahoo.com/man-begins-7-walk-path-ancient-humans-170907164.html

Better yet, you can follow his progress at this link: http://www.outofedenwalk.com/
Click on the “follow” tab to sign up for e-mail notifications when Paul posts something interesting.

Under “The Storytelling” tab, be sure to watch the short video about Paul’s inspiration for making this epic journey.

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Decoding and Rethinking Neanderthals

Posted on January 10, 2013 by Roberta Estes

On January 9, 2013, PBS ran a wonderful documentary, Decoding Neanderthals, about Neanderthals, what we have recently discovered about them, and what it means to us as humans. There has been a lot of discussion about this topic spurred by both the 23andMe and the Geno2.0 tests that provide a percentage of Neanderthal to participants. Geno2.0 also provides a percentage of Denisovan.

Program Description:
Over 60,000 years ago, the first modern humans—people physically identical to us today—left their African homeland and entered Europe, then a bleak and inhospitable continent in the grip of the Ice Age. But when they arrived, they were not alone: the stocky, powerfully built Neanderthals had already been living there for hundreds of thousands of years. So what happened when the first modern humans encountered the Neanderthals? Did we make love or war? That question has tantalized generations of scholars and seized the popular imagination. Then, in 2010, a team led by geneticist Svante Paabo announced stunning news. Not only had they reconstructed much of the Neanderthal genome—an extraordinary technical feat that would have seemed impossible only a decade ago—but their analysis showed that “we” modern humans had interbred with Neanderthals, leaving a small but consistent signature of Neanderthal genes behind in everyone outside Africa today. In “Decoding Neanderthals,” NOVA explores the implications of this exciting discovery. In the traditional view, Neanderthals differed from “us” in behavior and capabilities as well as anatomy. But were they really mentally inferior, as inexpressive and clumsy as the cartoon caveman they inspired? NOVA explores a range of intriguing new evidence for Neanderthal self-expression and language, all pointing to the fact that we may have seriously underestimated our mysterious, long-vanished human cousins.

I’m going to share some of the highlights of the program, but this is in no way a spoiler, as the program contains lots of visual information that just can’t be conveyed by a review.

Chris Stringer from the Natural History Museum in London introduced us to the Neanderthals. It turns out that our perception of what a Neanderthal looks like is a result in large part of skeleton that was reconstructed improperly due to advanced arthritis, causing the individual to appear to walk hunched over, much like, well, our stereotypical view of a caveman. Just goes to show what bad PR can cause.

Neanderthal skeletons can be positively identified. Their facial structure is different than that of modern man, with an identifiable brow ridge and bones that push forward in the nose and mouth region, as compared to our flatter faces today.

Neanderthals lived a short life, most were dead by age 30. They were large and strong. They participated in up-close and personal hunting, using spears, which meant they had to come in close contact with their prey.

Neanderthals began living in Europe about 300,000 years ago, having exited from Africa. They evolved to fit the European, colder, climate. It had been thought up until recently that they lacked the brainpower of humans, had no spoken language, or the ability for such, no personal ornamentation, art or evidence of ritual or religion. These are the functions that make us uniquely human and separate us from the non-human world, and we fully believed that Neanderthals lacked these defining characteristics.

We have learned differently, much as a result of genetic discoveries that tell a different story of Neanderthals.

Homo sapiens left African about 40,000 years ago, and within 10,000 years, Neanderthals, who had spread throughout most of Europe and much of Asia were gone. The map below shows the locations where fossilized Neanderthal remains have been found.

The assumption has been made that Homo Sapiens were responsible for the Neanderthals demise, either by killing them off or providing too much competition for scarce resources, outnumbering them 10 to 1.

Svante Paabo, a Swedish geneticist now at the Max Planck Institute for Evolutionary Anthropology forever changed the genetic world, how we perceive Neanderthals, and paradoxically, how we think of ourselves.

Pääbo is known as one of the founders of paleogenetics, a discipline that uses the methods of genetics to study early humans and other ancient populations.

In August 2002, Paabo published findings about the “language gene”, FOXP2, which is lacking or damaged in some individuals with language disabilities. This research would prove critical, later, in the humanization of the Neanderthal.

In 2006, he announced a plan to reconstruct the entire genome of Neanderthals. In 2007, Pääbo was named one of TIME Magazine’s 100 most influential people of the year.

In February 2009, at the Annual Meeting of the American Association for the Advancement of Science (AAAS), it was announced that the Max Planck Institute for Evolutionary Anthropology had completed the first draft version of the Neanderthal genome. Over 3 billion base pairs were sequenced in collaboration with the 454 Life Sciences Corporation. This project, led by Pääbo, shed and will continue to shed new light on the recent evolutionary history of modern humans.

In March 2010, Pääbo and his coworkers published a report about the DNA analysis of a finger bone found in the Denisova Cave in Siberia; the results suggest that the bone belonged to an extinct member of the genus Homo that had not yet been recognized, the Denisova hominin.

In May 2010, Pääbo and his colleagues published a draft sequence of the Neanderthal genome in the journal Science. Below, a scientist at Max Plank extracting Neanderthal DNA.

Paabo shared in the program that many times during the Neanderthal sequencing project, he himself “despaired many times of being able to do it”, doubting that it could be done. It took a total of 4 years. The team found good candidates, 3 well-preserved female bone fragments from the Vindija Cave in Croatia.

Because of the age of the fragments, and because they had been in the ground for so long, much of the DNA recovered wasn’t Neanderthal, but that of bacterial organisms and fungus. The team developed a method to eliminate the bacteria, leaving only Neanderthal DNA. However, those genetic fragments still had to be reassembled, piece by piece, like a huge jigsaw puzzle with no picture on the box, into the Neanderthal genome.

Four long years later, the puzzle was finished. I hope the team had a very big celebratory party!

Ed Green, a scientist on Paabo’s team said that the first thing the scientists looked for was to determine whether or not Neanderthals had the FOXP2 gene for language, and if so, is it identical to the human version, or is it different. The answer was that it was identical to the language gene carried by Homo Sapiens, modern humans. This tells us not only that Neanderthals had the capabilities for language, but that this gene evolved in Africa, before Neanderthals left, 300,000 years ago.

The next question, of course, was whether or not modern humans carried any DNA that could be labeled as Neanderthal. In other words, the question of inter-species breeding arose. It was believed that this was impossible, because two different species cannot have fertile offspring. This was proven to be an inaccurate assumption relative to Neanderthal and Homo Sapiens.

Paabo’s team sequenced the DNA of 5 individuals from different parts of the world. They isolated parts of the Neanderthal DNA that were measurably different from that of modern humans. In other words, those sequences could be positively identified as Neanderthal. Compared against the DNA of the 5 contemporary individuals, only the person from Africa had none of the Neanderthal DNA.

Paabo didn’t believe the results, thought they might be an artifact of statistical error or the result of not enough data, so he had his team repeat the exercise with different people, again, and again, and again, and every time, the results came back the same. Neanderthals and humans inbred, and to the degree that there is Neanderthal DNA in every population on every continent outside of Africa today.

John Hawks, an anthropologist at the University of Wisconsin used jelly beans to illustrate Neanderthal DNA in worldwide populations today. It turns out that the Chinese have the least amount, with about 1% and the people of Tuscany have the most, with about 4%. So the mountainous areas of Europe and Italy were a hotbed of Neanderthal activity and human interbreeding.

This caused other experts to think again about the Neanderthals in what could be called a radical shift in perspective. All of a sudden, when we realized that they were part of us, they became more human to us. They could and probably did have speech, so they could and probably did other “human” things too.

Joao Zilhao, a paleolithic archaeologist at the University of Bristol, also a flintknapper, spent years reconstructing the process of making Neanderthal tools, what were once believed to be scraps of flint with sharp edges. He proved, among other things, that obtaining these “scraps” involved a complex process of very specific flintknapping strokes. This skill was far from the previously perceived unintelligent caveman, and furthermore, it likely required language instruction.

Another early technology, in use 250,000 years ago, involved a complex process to create a type of pitch to secure spearheads to spear shafts.

The Neanderthals began evolving before our very eyes.

Michael Walker, a professor of Zoology and Physical Anthropology at the University of Murcia, discovered indeed that Neanderthals likely did have ceremony and ritual, the hallmarks of religion, which involved the ability for complex thought and reasoning. Shells and bones, drilled or punched to be worn as ornaments have been identified, along with pigments believed to have been used as body paints.

We still do this today; look at the fans at any football game.

In addition, it appears that a burial may have been found in Spain, along with two panther paws. Michael mentioned them as a trophy, I thought more in terms of spiritual significance.

John Hawks discussed what the Neanderthal parts of our genome have done for humans. Many of the Neanderthal genes have no known purpose, but there is one significant exception. It’s somehow ironic that we may indeed have survived as a species in a foreign environment, colder Europe, thanks to inbreeding with the Neanderthals. Humans carry a very specific Neanderthal piece of DNA that is essential to the immune system’s ability to attack viruses and bacteria, the HLA or Human Leukocyte Antigen. Because individuals who carried HLA might well have survived when others didn’t, the HLA became naturally selected for, and therefore present in the descendant population, us, “saving lives to this day.’

As John said, we are just beginning to understand our debt to the Neanderthals. Not only that, we also are rethinking what extinction really meant. We have presumed that Neanderthals went extinct, or died out, because we could no longer find their remains in fossil evidence. Perhaps, as Mark Twain said “reports of my demise have been greatly exaggerated.”

Is the reason we could no longer find separate Neanderthals because they interbred and assimilated into the Homo Sapiens population who were probably the dominant species, outnumbering them ten to one? Was their extinction not a dying out at all, but an absorption? Perhaps that was simply the natural progression of things, or maybe they realized that their recipe for success, for long-term survival, was not to remain separate, but to become part of the larger population. In fact they do survive today in just that way, as a part of all of us outside of Africa.

Decoding Neanderthals is available to watch online at http://www.pbs.org/wgbh/nova/evolution/decoding-neanderthals.html

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Security and Privacy

Posted on January 9, 2013 by Roberta Estes

Did you really mean to say that you didn’t want to see your matches???? Have you accidentally done this?

At Family Tree DNA, you may notice that some of your matches, especially at the 12 marker or HVR1 levels, particularly if you have a lot of matches, may be marked “private” and greyed out, with no contact or other information. What does this mean and why would someone take a DNA test for genealogy, then mark their results as private?

Those are great questions and there are several answers. First, some people don’t realize that the selection they make in their “Account Settings” tab affects how their results are displayed, or not displayed, to their matches. They also don’t realize that it can suppress those matches for them as well.

You can see that for both Y-line and mitochondrial DNA, you can disable matches and e-mail notification. This means that you won’t receive match notifications for 12 marker matches, if you disable that level, nor will any of your information be shown to your matches. Furthermore, you won’t see those matches either. They will not appear on your match list. In fact, you won’t have a match list for the level you disable.

Some people only test at 12 markers, for example, so if you disable 12 marker matches, be absolutely sure that you really don’t want to be notified if you match someone with the same surname at 12 markers that did not test at a higher level. If you disable these notifications and matches, this is what your matches will see:

As you can see, your match will be able to see your surname only, how many mutations difference there is between you and them, no “most distant ancestor,” no haplogroup information and more importantly, no way to contact you. This is typically not what people mean to do, but this is the result.

In one case, a man was distraught because he had no matches, but had disabled matches at all levels of testing, so of course, none showed. He had matches, he just couldn’t see them and he didn’t notice the message that said he had disabled matching at that level. He thought that the only function he had disabled was the e-mail match messages, but that wasn’t the case. It’s all or nothing at each level. You can’t disable the messages without disabling the matches too.

There are other security options you can select as well. Some, are found under “Personal Profile” settings, others under “Account Settings,” and finally, a beneficiary designation in case something should happen to you. This is the only person that Family Tree DNA will allow to access your account. Please take a little time to click through these options so that you personalize your experience in such a way that best fits your testing goals.

Aside from your matches and project displays, the only other people who can see your information are the volunteer group administrators of the groups you join. You can control, by your selections, how much they can view. There are several items they can view, but not change, such as your e-mail address, for example. Group administrators have a set of guidelines that they must follow.

In the case of mitochondrial DNA, if you have tested at the full sequence level, the project administrators of haplogroup projects cannot see your full sequence level which is necessary to categorize your results into subgroups unless you specifically change your setting to allow them to view your mitochondrial full sequence results. This is found under “Account Settings” then “Results Display Settings.” Change the answer to yes for the appropriate projects.

The key, of course, to privacy and security is to have as much privacy as you wish, without actually hurting your chances of making genealogical connections, and contacts, which is, after all, the entire reason that you tested in the first place.

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Disclosure

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