Mitochondrial DNA Smartmatching – The Rest of the Story

Posted on June 28, 2013 by Roberta Estes

Sometimes, a match is not a match. I know, now I’ve gone and ruined your day…

One of the questions that everyone wants the answer to when looking at matches, regardless of what kind of DNA testing we’re talking about, is “how long ago?” How long ago did I share a common ancestor with my match? Seems like a pretty simple question doesn’t it?

The answer, especially with mitochondrial DNA is not terribly straightforward. A perfect example of this fell into my lap this week, and I’m sharing it with you.

Mitochondrial DNA – A Short Primer

There are three regions that are tested in mitochondrial DNA testing for genealogy. The HVR1 and HVR2 regions are tested at most testing companies, and at Family Tree DNA, the rest of the mitochondria, called the coding region, is tested as well with the full mitochondrial sequence test. This is the mitochondrial equivalent of Paul Harvey’s “the rest of the story,” and of course we all know that the real story is always in “the rest of the story” or he wouldn’t be telling us about it!

Many times, the rest of the story is critically important. In mitochondrial DNA, it’s the only way to obtain your full haplogroup designation. If you don’t want to just be haplogroup J or A or H, you can test the coding region by taking the full sequence test and find out that you’re J1c2 or A2 or H21, and discover the story that goes with that haplogroup. Guaranteed, it’s a lot more specific than the one that goes with simple J, A or H. Often it’s the difference between where your ancestor was 2000 years ago and 20,000 years ago – and they probably covered a lot of territory in 18,000 years!

Let’s take a quick look at mitochondrial DNA.

To begin with, the HVR1 and HVR2 regions are called HVR for a reason – it’s short for hypervariable. And of course, that means they vary, or mutate, a lot more rapidly, as compared to the coding region of the mitochondrial DNA.

In layman’s terms, think of a clock. No, not a digital clock, an old-fashioned alarm clock.

The entire mitochondrial DNA has 16,569 locations. The HVR1 and HVR2 regions take up the space on the clock face from 5 till until 5 after the hour. The rest is the coding region – the mitochondrial “rest of the story.” The coding region mutates much slower than the two HVR regions.

Just to be sure we’re on the same page, let’s talk for just a minute about how mitochondrial haplogroup assignments work. For a detailed discussion of haplogroup assignments and how they are done, see Bill Hurst’s discussion here.

Generally a base haplogroup can be reasonably assigned by HVR1 region testing, but not always. Sometimes they change with full sequence testing – so what you think you know may not be the end result.

My full haplogroup is J1c2f. My base haplogroup is J. I’m on the first branch of J, J1. On branch J1, I’m on the third stick, c, J1c. On the third stick J1c, I’m on the second twig, J1c2. On the second twig, J1c2, I’m leaf f, or J1c2f. Each of these branches of haplogroup J is determined by a specific mutation that happened long ago and was then passed to all of that person’s offspring, between them and me today. The question is always, how long ago?

Mutation Rates – How Long Ago is Long Ago?

While we have a tip calculator at Family Tree DNA for Y-line DNA to predict how long ago 2 Y-line matches shared a most recent common ancestor, we don’t have anything similar for mitochondrial DNA, partly because of the great variation in the mutation rates for the various regions of mitochondrial DNA. Family Tree DNA does provide guidelines for the HVR1 region, but they are so broad as to be relatively useless genealogically. For example, at the 50^th percentile, you are likely to have a common ancestor with someone whom you match exactly on the HVR1 mutations in 52 generations, or about 1300 years ago, in the year 713. Wait, I know just who that is in my family tree!

These estimates do not take into account the HVR2 or coding regions.

I did some research jointly with another researcher not long ago attempting to determine the mutation rate for those regions, and we found estimates that ranged from 500 years to several thousand years per mutation occurrence and it wasn’t always clear in the publications whether they were referring to the entire mitochondria or just certain portions. And then there are those pesky hot-spots that for some reason mutate a whole lot faster than other locations. We’re not even going there. Suffice it to say there is a wide divergence in opinion among academics, so we probably won’t be seeing any type of mito-tip calculator anytime soon.

Enter SmartMatching

Family Tree DNA does their best to make our matches useful to us and to eliminate matches that we know aren’t genealogically relevant.

For example, this week, I was working on a client’s DNA Report. Let’s call him Joe. Joe is haplogroup J1c2. I am haplogroup J1c2f. J1c2f has one additional haplogroup defining mutation, in the coding region, that J1c2 does not have.

Joe and I did not show as matches at Family Tree DNA, even though our HVR1 and HVR2 regions are exact matches. Now, for a minute, that gave me a bit of a start. In fact, I didn’t even realize that we were exact matches until I was working with his results at MitoSearch and recognized my own User ID.

I had to think for a minute about why we would not be considered matches at Family Tree DNA, and I was just about ready to submit a bug report, when I realized the answer was my extended haplogroup. This, by the way, is the picture-perfect example of why you need full sequence testing.

Family Tree DNA knows that we both tested at the full sequence level. They know that with a different haplogroup, we don’t share a common ancestor in hundreds to thousands of years, so it doesn’t matter if we match exactly on the HVR1 and HVR2 levels, we DON’T match on a haplogroup defining mutation, which, in this case, happens to be in the coding region, found only with full sequence testing. Even if we have only one mismatch at the full sequence level, if it’s a haplogroup defining marker, we are not considered matches. Said a different way, if our only difference was location 9055 and 9055 was NOT a haplogroup defining mutation, we would have been considered a match on all three levels – exact matches at the HVR1 and HVR2 levels and a 1 mutation difference at the full sequence level. So how a mutation is identified, whether it’s haplogroup defining or not, is critical.

In our case, I carry a mutation at marker 9055 in the coding region that defines haplogroup J1c2f. Joe doesn’t have this mutation, so he is not J1c2f, just J1c2. So we don’t match.

So – How Long Ago for Me and Joe?

Dr. Behar in his “Copernican Reassessment of the Mitochondrial DNA Tree,” which has become the virtual Bible of mitochondrial DNA, estimates that the J1c2f haplogroup defining mutation at location 9055 occurred about 2000 years ago, plus or minus another 3000 years, which means my ancestor who had that mutation could have lived as long ago as 5000 years.

The mutations that define haplogroup J1c2 occurred about 9800 years ago, plus or minus another 2000. So we know that Joe and I share a common ancestor about 7,800 – 11,800 years ago and our lines diverged sometime between then and 2,000 – 5,000 years ago. So, in round numbers our common ancestor lived between 2,000 and 9,800 years ago. Not much chance of identifying that person!

The ability to eliminate “near-misses” where the HVR1+HVR2 matches but the people aren’t in the same haplogroup, which is extremely common in haplogroup H, is actually a very useful feature that Family Tree DNA nicknamed SmartMatching. With over 1000 matches at the HVR1 level, more than 200 at the HVR1+HVR2 level and another 50+ at the full sequence level, Joe certainly didn’t need to have any “misleading” matches included that could have been eliminating by a logic process.

So while Joe and I match, technically, if you only look at the HVR1 and HVR2 levels, we don’t really match, and that’s not evident at MitoSearch or at Ancestry or anyplace else that does not take into consideration both full sequence AND haplogroup defining mutations. Family Tree DNA is the only company that does this.

It’s interesting to think about the fact that 2 people can match exactly at the HVR1+HVR2 levels, but the distance of the relationship can be vastly different. I also match my mother on the HVR1+HVR2 levels, exactly, and our common ancestor is her. So the distance to a common ancestor with an exact HVR1+HVR2 match can be anyplace from one generation (Mom) to thousands of years (Joe), and there is no way to tell the difference without full sequence testing and in this case, SmartMatching.

And that, my friends, is the rest of the story!

Big News! Probable Native American Haplogroup Breakthrough

Posted on June 27, 2013 by Roberta Estes

We are on the verge of another new and very exciting discovery, but we need funding to finish the research. Let me tell you about what’s going on and maybe you’ll decide to be a part of this new discovery by making a contribution.

It’s not everyday that someone gets the opportunity to make a significant contribution to scientific discovery. But you have that opportunity today.

I believe a new Native American haplogroup has been discovered. We have strong evidence, but we need to finish testing on a group of people for the final proof. People whose DNA results qualify for testing have been notified, and several are ready and willing to have their results upgraded, but don’t have the funding. I’ve funded some, and I’ve used contributed funds I’ve squirreled away from past donations, and now I’m reaching out in the hopes that together we can collaboratively make this happen.

Most of you know that I’m a long time researcher in both the genetic genealogy and Native American fields, particularly where they intersect. I’ve being involved with genetic genealogy since the beginning and am tri-racial myself, descended from multiple Native ancestors and tribes. I write the Personal DNA Reports for Family Tree DNA, own www.dnaexplain.com and write the free blogs, www.dna-explained.com and www.nativeheritageproject.com. You can verify anything in this article directly with Bennett Greenspan, the President of Family Tree DNA at bcg@familytreedna.com. In fact, Bennett is both aware and supportive of this DNA testing endeavor and has offered reduced test pricing for a short time to facilitate this discovery process.

By the way, this is not the first time this has happened. I was also involved with a similar discovery in December 2010. You can read about that discovery at this link. http://dna-explained.com/2012/09/11/lenny-trujillo-the-journey-of-you/

Ok, now that you know who I am and why I care, let me tell you about the discovery.

Discovery of a New Native American Haplogroup

To date, only 5 female Native American base haplogroups, or clans, have been discovered. A, B, C, D and X. Within these haplogroups are subgroups, and not all subgroups in each haplogroup are Native American. Some are Asian and European. In fact, in haplogroup A, which is the haplogroup being studied in this project, only subgroup A2 has been confirmed to be Native American – until now.

Recently, I was working with a client’s DNA, writing a Personal DNA Report, and I realized, based on her information and that of some of the people she matched, that a subgroup of haplogroup A4 is also very likely Native American.

For Native American history, this is a big discovery. But we need more information. We need to proof. How can we do that?

Advanced Testing

We need to test people in haplogroup A who are predicted to fall into this new Native American haplogroup at the full sequence level. Mitochondrial DNA testing falls into three levels. The highest level, the full sequence level is the one that tests the entire mitochondria and is required to obtain a full haplogroup assignment. In other words, if you don’t test the full sequence, you’ll know that you are haplogroup A, but you’ll never know if you are A2, A4 or A10 for that matter.

Of people who have tested only at the lower levels, we have identified a small group of people who we believe will test to be haplogroup A4 or a subgroup based on some specific mutations. Bennett Greenspan has offered discount testing for the upgraded test through July 5th.

Some people have been able to pay for their own upgrade, but not all, and I certainly don’t want the lack of funds to impede the discovery and proof of a new haplogroup. This is akin to raising the history of this group of Native people from the dead, from the dust where some of our history and people have been lost until now.

We need several hundred dollars in total. If everyone that we’d like to test participates, it will cost more than $2000. You can contribute directly to the haplogroup A4 mtDNA project at Family Tree DNA and the funds will be used directly for this testing. Every little bit helps – no amount is too small. You can contribute in memory of someone, anonymously, or however you wish.

http://www.familytreedna.com/group-general-fund-contribution.aspx?g=mtDNA-A4a

In a few months, we’ll let you know the outcome of this testing and what we discover, right here. I can hardly wait!

Thank you in advance for your support.

Roberta Estes

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Triangulation for Autosomal DNA

Posted on June 21, 2013 by Roberta Estes

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In our last article, Triangulation for Y DNA, we covered triangulation for the Y chromosome, how it works, and how it can help a genetic genealogist.

In this article, we’re going to cover triangulation for autosomal DNA.

Triangulation for autosomal DNA is kind of a chicken and egg thing. The goal is to associate and identify specific DNA segments to specific ancestors. The easiest way to do this, or to begin the process, is with known relatives. This gets you started identifying “family segments.” From that point, you can use the known family segments, along with some common sense tools, to identify other people that are related through those common ancestors. Through those matches with other people, you can continue to break down your DNA into more and more granular family lines. This is easiest to visualize thinking about your 4 grandparents.

Triangulation is easiest if you have parents or grandparents living, and you can test them. Yes, all of them. Their DNA will give your immediate pointers when you have matches to which side of the family you share with your matches. If you can test your 4 grandparents, you immediately know which of those 4 lines someone who matches you descends through, because they will also match one, and hopefully only one, of your 4 grandparents. However, for some of us, testing even one parents is simply not possible, so first, let’s look at some examples of triangulation without your parents DNA results.

I’m fortunate that one of my cousins has given a lot of focus to our Vannoy line. Vannoy was the surname of my great-grandmother, Elizabeth Vannoy (1846-1918) who married Lazarus Estes (1845-1919). The Vannoy line has a mystery we’ve been trying to solve for decades now called, “Who Was Elijah Vannoy’s Father?”. Elijah was Elizabeth’s grandfather. Your family probably has a similar mystery, and these tools hold the potential to answer those questions. They also have the potential to introduce more questions. But then again, isn’t that the way of genealogy? For every ancestor we find, we get two more questions.

Several of the Vannoy cousins are interested in solving this mystery as well, so they have taken the autosomal Family Finder test at Family Tree DNA.

We know how they are related, and the men have all been proven to be Vannoy via Y-line testing. By doing this, we’ve assured no undocumented adoptions, also known as NPEs (NonParental Events) in the Vannoy line.

We expect our cousins to match, and indeed they do. This is my test result showing my three cousins who match me.

In my family mystery, “Who Was Elijah Vannoy’s Father?”, there are 4 candidates, all brothers who lived in Wilkes County, NC in the late 1700s. Elijah was born in 1786. We have the wives surnames. Hickerson is our primary candidate surname, so I wanted to see everyone who matches me on my match list who also shows the Hickerson surname. I enter that surname in the “ancestral surname” box, and click on “run report.” The matches returned will all carry the Hickerson surname, which you can see by scrolling for the highlighted names. Turns out, it was only my Vannoy cousins – today – but tomorrow might be different.

Now for the triangulation tool.

I want to see if these three people share common DNA not just with me, but with each other. If we all share a common segment of DNA, then that confirms a common ancestor and attributes the DNA at that address on that chromosome to that specific ancestral family. This is the fundamental concept on which triangulation is based.

In my case, the known ancestral family is Vannoy, not Hickerson, at least not yet, so let’s look at the Vannoy cousins as compared to me.

Each of the participants results are color coded. On the page below, you can see that each matching segment of the chromosomes is colored. It turns out that all of us share a fairly large segment on Chromosome 15. So now we can attribute that segment to Elijah Vannoy, our oldest proven ancestor in that line. You can also see some areas where one or two of my cousins match my DNA, but not all of us. Those can also be attributed to Elijah Vannoy’s line since we share no other (known) common ancestors.

This cousin match is simple because the men share the same surname, but if this was 3 women with different surnames, the matching would still work. The challenge of course would be to find the common ancestor. In this case, if all 3 women had Elijah Vannoy in their tree, we could still tell that this segment of Chromosome 15 was attributed to the Vannoy family because they all matched me and matched each other as well on the same DNA segment.

Eliminating False Matches

Now let’s move to the “what ifs.” When my kids were young, I just hated sentences that started with “what if.”

What if I have a fourth match, Jane, with unknown ancestry who matches me on these segments, but does not match any of my cousins?

To determine this you would also have to look at your cousin’s matches or ask Jane if she also matches those cousins. Remember that half of your DNA is that of your mother and the other half is that of your father. You will have people that match you, and potentially on the same segments as your known relatives match you, but are not related to both you and your relatives. This means they are matching you on the other half of your DNA. In this case, if Jane didn’t match my Vannoy cousins too on that same segment of chromosome 15, then we would know that Jane’s match would be from my mother’s side.

To illustrate this point, let’s move to my results at 23andMe.

Let’s use Family Inheritance Advanced to see an example of two people who match me on the same segment, but are from opposite sides of my family. My cousins Stacy and Cheryl are from Dad’s and Mom’s side of the family, respectively. We know they don’t share common ancestry, but look, they both match me on four of the same segments.

How is this possible, you ask. Remember, I have two halves of each chromosome, one from Mom and one from Dad. It just so happens that Cheryl and Stacy both match me on the same segment, but they are actually matching two different sides of my chromosome. For this reason, these are called HIRs, or Half Identical Regions.

Now let’s prove this to the doubting Thomas’s out there.

Here is the comparison of Cheryl and Stacy directly to each other. They do have one small matching segment, 6 cM, so on the small side. But they don’t match each other on any of the segments where I match both of them.

If they did match each other and me on the same locations, it would mean that we three have common ancestry.

The fact that they match each other on one segment could also mean they have distant common ancestry, which could be from one of our common lines or a line that I don’t share with them, or it could mean they have an identical by state (IBS) segment, meaning they come from a common population someplace hundreds to thousands of years ago.

The real message here is that you can never, ever, assume. We all know about assume, and if you do, it will. In this case, assuming would have been easy if you didn’t delve into the big picture, because both of these family lines contain Millers from Ohio living in close proximity in the 1800s. However these Miller lines have been proven not to be the same lines (via Yline testing) and therefore, any assumptions would have been incorrect, despite the suggestive location and in-common names. Furthermore, cousin Stacy’s Miller line married into her line after our common ancestor, so is not blood related to me. But conclusions are easy to jump to, especially for excited or inexperienced genetic genealogists. It’s tempting even for those of us who are fairly seasoned now, but after you’ve been burned a few times, you do learn some modicum of restraint!

So, what’s next?

Color your Chromosomes

In my article, “The Autosomal Me – the Holy Grail – Identifying Native Genealogy Lines,” I described in detail the process of downloading your DNA information from either 23andMe or Family Tree DNA and then utilizing that information in a spreadsheet to look at matches – not 3 or 4 matches at a time, but chromosome by chromosome.

In my case, I was fortunate to have my mother’s DNA results at Family Tree DNA before she passed away, and I was equally as fortunate that they were still viable for the Family Finder test. Believe me, I held my breath.

Because I have her results, I can tell immediately if my matches are from her side or from my father’s side. If the person matches both Mom and me, then it’s from her side. See how easy triangulation is.

Let’s take a look at Chromosome 15 with all of those Vannoy matches on my spreadsheet and see what kind of information we can glean.

On my master spreadsheet, my Mother’s matches have been copied in and are color coded, but since none of these people match Mother, I have eliminated that aspect here to avoid unnecessary confusion.

The people identified as “Dad” mean that I know they are genealogically related on my father’s side. People who match Mother genetically are labeled Mom. There aren’t any on this segment of chromosome 15, in our example above. The blank cells in that column, by inference, match Dad’s DNA, since they don’t match Mom. When I confirm genealogically how we’re related, I’ll enter “Dad” in that column, but not until then.

I’d like to comment on information gleaned from the spreadsheet. Every DNA segment has a story to tell.

Cousin Estes

First, Cousin Estes, with yellow highlighting, is one of my closest Estes relatives. He is a third cousin on the Estes side and also descends from Lazarus Estes and Elizabeth Vannoy. He matches me on the segment from 26 (million) to 58 (million). My Vannoy group of matches, shaded green, extend from 33 to 58, so this tells me that the area from 26 to 33 where I match Cousin Estes, and not any Vannoys, is probably from an Estes ancestor, and not the Vannoy line.

Unfortunately, I don’t have any other matches on this segment, so I can’t figure out which line it comes from, just yet.

The green areas are common between me, cousin Estes and the Vannoy cousins. If we could find a Hickerson match on these same segments, we could then solve the family mystery AND attribute part of this DNA to the Hickerson line. But so far, no dice. This is why it’s important to continue to look and to reach out to people you match, especially those who don’t enter their family surnames or post a GEDCOM file. The answer may be waiting for you.

The Insanity Factor

The pink segment labeled Cousin Younger is making me insane, so let me share some insanity with you.

The Younger line descends through the Estes line, significantly upstream. The Y DNA of Marcus Younger, who had 1 son who had 1 son, does not match the expected Younger DNA line in Halifax County, Va. Cousin Younger’s only solid Y match also doesn’t match his expected family line, so we’re fish out of water on the Y-line. Two undocumented adoption cases that match each other, but no one else. Great, just great. These are the things genetic genealogy nightmares are made of.

Mary Younger, daughter of Marcus Younger, married George Estes who fought in the Revolutionary War. Their son John R. Estes married Nancy Ann Moore in Halifax County and they settled in Claiborne County, TN about 1820 where the Vannoy family is found as well, having migrated from Wilkes Co., NC. John Y. Estes, son of John R. Estes had son Lazarus Estes who married Elizabeth Vannoy. Here’s the generational progression:

Marcus Younger – wife unknown, Y DNA doesn’t match Younger line
Mary Younger married George Estes, Halifax Co., VA
John R. Estes married Nancy Ann Moore, moved to Claiborne Co, TN
John Y. Estes married Rutha Dodson
Lazarus Estes married Elizabeth Vannoy
George Estes married Ollie Bolton
My father, William Sterling Estes

And of course, there’s a monkey-wrench, so let’s throw it in. Marcus Younger’s grandson, ancestor of Cousin Younger, married a Moore woman in Halifax County, VA. We believe we know who her parents are, but we’re not positive. If they are who we believe, Y-line DNA tests say the 2 Moore families, living within sight of each other, aren’t the same Moore line….but they interact closely and my Moore line doesn’t match any Moores upstream anyplace. So, we have another unknown ingredient in the soup.

So, from me, Marcus Younger is 7 generations upstream. I should carry about 1.5% of his DNA. I was pleased to see that my Younger cousin and I matched.

However, and this is a BIG however, the Vannoy line should not be related to the Younger line. We know that both of these cousins are matching on my father’s side, not just because of the genealogy, but because neither matches my mother. But they are somehow related, as Cousin Younger is matching the Vannoy group big as life on chromosome 15. Could this be an IBS (identical by state) segment? Yes, it’s small – but I’m not comfortable relegating it to IBS because it’s genealogically “inconvenient,” at least not yet.

So, something may well be wrong, amiss or unknown in the genealogy, either in Tennessee, which is doubtful as we have that fairly solidly nailed down, especially in recent generations, or in Virginia where there is at least one known disconnect and possibly two taking into consideration the Moore monkeywrench. Still, the Vannoy family was not living in the same state as the Younger family and came from New Jersey to North Carolina, not from Virginia. Maybe the connection is in one of the unknown wives lines.

So, you can see my reason for being perplexed. One thing is sure. DNA doesn’t lie. It’s up to us to figure out the message it is conveying and which ancestor it is from.

Powerful Tools

I hope you can see what a powerful tool we have at our disposal. Of course, it can reveal who your ancestors are, along with some surprises. I don’t mind the surprises. I view them as gifts from the ancestors. It’s those crazy-making half-surprises that bother me. I swear, the ancestors have a sense of humor.

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Triangulation for Y DNA

Posted on June 18, 2013 by Roberta Estes

Based on the number of questions I’m receive about triangulation, it’s time to write an article.

There are two kinds of triangulation that we use in genetic genealogy. One type is for the Y chromosome and it’s to determine the original values of the DNA of the common ancestor. The second type of triangulation is for autosomal DNA and it’s to determine if you share a common ancestor with someone and what the DNA of that ancestor looked like.

This article is about the first type, for Y DNA.

Why would you want to use triangulation?

Sometimes in order to know if a particular line has descended from an ancestor, you need to know what that ancestor’s Y DNA marker values were.

For example, if you have an ancestor born in the 1600s, and he had two sons whose descendants tested today, each line could have 4 mutations each, or 6, which could put the matching software over the threshold – meaning they might not be reported as matches. We have this situation in one of the Estes lines that seems to be particularly prone to mutate.

Family Tree DNA has set up match thresholds. For someone to be listed as your match, they need to have no more than the following total number of mutations difference from your results.

Markers in Panel Tested	Maximum Number of Mutations Allowed
12	0 unless in a common project, then 1
25	2
37	4
67	7
111	10

So you can see that if you have a high number of mutations in the first panel or two, you might not show as a match.

But if you know what the original ancestors Y-line DNA looks like, then it’s easy to tell that they really are matches and that both lines have simply had several mutations.

It’s much more accurate to compare everyone to the original ancestor instead of trying to compare them to each other.

Let’s take a look at the Estes project by way of example.

Abraham Estes, the progenitor of the Southern Estes line was born in 1647 in Nonington, Kent, England. He immigrated to Virginia in 1683 and began begetting shortly thereafter. His wife was Barbara, and although the internet is full of family trees that say her last name is Brock, there is not one shred of evidence to support that. In any case, Abraham and Barbara had a total of 8 sons who lived and the sons had about 42 sons, so we have a good number of Estes families throughout the US today, mostly descending from Abraham. There is also a northern line founded by Abraham’s cousin, Richard Estes although they don’t have nearly as many descendants.

This chart shows the results of DNA testing through 7 different Estes lines, 6 of which are Abraham’s sons and one of which is a descendant of the Northern line.

The green row at the top is Abraham’s reconstructed DNA, and now, everyone in the project gets compared to Abraham on my spreadsheet.

It’s easy to see how this is done. For each marker, beginning with 393, we determine what the normal value is for the family. For marker 393, all lines carry a value of 13. One line, John through Elisha, shows a mutation to a value of 14 which would signal a line marker mutation for this particular line. This is quite useful, because when we see someone who carries a value of 14 at this location, especially in conjunction with any other line marker mutations that might exist in that line, like a value of 11 at marker 391, we know where to look genealogically to find the tester’s place in the family. Line marker mutations are great guideposts.

So, marker by marker, I’ve reconstructed Abraham, shown at the top in green.

Marker Frequency

You might wonder why the value of 25 at 390 is red and underscored and 12 at 391 is bolded, red and underscored.

One of the things I do for each of my family lines, and for clients who order Personalized DNA Reports, is to determine which of their markers carry rare values. In this case, the value of 25 at 390 is found in only 16% of haplogroup R1b1a2. The value of 12 at 391 is found in only 4% of the haplogroup R1b1a2 population. My threshold for rare markers is less than 25% and for very rare, 6% or less. Bold red indicates very rare, red indicates rare and the underscore is present so that people printing in black and white can see the difference

Why and how does this make a difference? In a situation where you’re trying to decide if someone really does match the Estes line, this information can be a big help.

The last kit on the chart does carry the Estes surname, but does not match the Estes line genetically. This is obvious by looking at all the yellow squares, which are mismatches to Abraham, but let’s say that this person tested at 12 markers and he matched the Estes DNA on all of our rare markers, but mismatches a couple on the more common markers. This is more likely a true Estes match than if they mismatch us on all of our rare markers. The Estes rare markers combined create a type of family genetic fingerprint. This is particularly important for adoptees.

And yes, to answer the next question, a Marker Frequency Table can be purchased separately for those who want their marker frequencies through 111 markers, but don’t want a Personalized DNA Report, by purchasing a Quick Consult. A marker frequency table looks like this but extended, of course, through all of your markers:

Now, we know what the original Abraham Estes’s DNA looked like. We also know which of our markers are unique. This can also help us when comparing to other surnames we may be related to before the advent of surnames. There is family history to be gleaned from those matches as well.

And lastly, because we also have cousin Richard’s DNA signature, we can use that information to reconstruct the common ancestor of Abraham Estes and Richard Estes, which is the grandfather of both men, Robert Estes, born 1555 in Ringwould, Kent, England. Not bad for genetic technology, reaching back more than 450 years in time and telling us what our ancestor’s DNA looked like, and all without even reaching for a shovel.

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The Warrior Gene

Posted on June 16, 2013 by Roberta Estes

In sports, business or your personal life, how you respond to stress and aggression may be in your genes, or at least partly so. Let’s take a look at a great documentary and the science behind it.

Human behavior is complex and influenced by our genes, our environment, and our circumstances. One of the most provocative and often controversial of genetic variants has been dubbed the “Warrior Gene.”

Studies have linked the “Warrior Gene” to increased risk-taking and to retaliatory behavior. Men with the “Warrior Gene” are not necessarily more aggressive, but they are more likely to respond aggressively to perceived conflict.

On December 14, 2010, National Geographic Channel’s Explorer: “Born to Rage?” documentary investigated the discovery behind a single “warrior gene” directly associated with violent behavior.

With bullying and violent crime making headlines, this controversial finding stirs up the nature-versus-nurture debate. Now, former Grammy-winning rocker, author and radio/television broadcaster Henry Rollins goes in search of carriers from diverse, sometimes violent backgrounds who agree to be tested for the genetic mutation. Who has the warrior gene? And are all violent people carriers? The results turn assumptions upside down.

A rock band front man. A bullet-scarred Harley rider. A former gang member from East L.A. Even a Buddhist monk with a far-from-peaceful past. Which one carries the gene associated with violence? An extraordinary discovery suggests that some men are born with impulsive, aggressive behavior … but it’s not always who you think.

It’s a hotly debated topic: nature versus nurture. Many experts believe our upbringing and environment are the primary influences on our behavior, but how much are we predisposed by our DNA? The discovery of a single gene variation affecting only men, which appears to play a crucial role in managing anger, argues that nature may have a far bigger influence on behavior. It’s this low-functioning, shortened gene linked to violent behavior that has become known as the “warrior gene,” and one-third of the male population has it.

One of those men, who describes himself as “fairly furious all the time” and agrees to be tested for the gene with a simple cheek swab, is Henry Rollins — a former poster boy of youthful rebellion and the American punk scene. Some of his tattoos are too provocative and socially offensive to show.

In this special Explorer episode, he dives into his own history of rage and searches out others with aggressive behavior from a range of different backgrounds. “If you can think of a stove, and the pilot light is always on, always ready to light all four burners, that is me, all the time,” he says. “I’m always ready to go there.”

Follow Rollins as he meets with former foot soldiers in one of the most violent street gangs in East Los Angeles; fighters in the ultraviolent sport of mixed martial arts, and Harley Davidson bikers. He’ll also talk to a Navy SEAL veteran and Buddhist monks whose lives weren’t always so tranquil.

After learning more about the warrior gene, many of the men believe they have it, which could offer an explanation of their past behavior. Their sentiment mimics Rollins as he says, “If I find out that I have the warrior gene, that would be interesting. If I find out I don’t, I must say, I would feel a bit of disappointment.” As the anticipation builds, be there when they receive the surprising outcome of the test.

Then, Explorer takes a look at the original study — on one family with generations of men displaying patterns of extreme physical aggression — that led Dutch geneticist Dr. Han Brunner to the revolutionary discovery of this rare genetic dysfunction. We’ll also take a look at new revelations that warrior gene carriers are significantly more likely to punish when provoked. In one study attempting to demonstrate this, subjects are given permission to administer punishment to their partner (who was secretly instructed to make a nuisance of himself), with unexpected results.

For any man questioning his inner warrior, a simple cheek swab test is available at Family Tree DNA.

So wanna know who, in the documentary, had the warrior gene? Well, hint….it wasn’t the biker…although his lady assured him he would always be her warrior. But I’m not going to tell you who does have it. All I’ll say is that you’ll be amazed at the outcome. The link to watch the video is below. Enjoy!

http://topdocumentaryfilms.com/born-rage-inside-warrior-gene/

The Science

Let’s take a look at the actual science behind this most interesting and controversial mutation.

The Warrior Gene is a variant of the gene MAO-A on the X chromosome and is one of many genes that play a part in our behavioral responses. The “Warrior Gene” variant reduces function in the MAOA gene. Because men have one copy of the X-chromosome, a variant that reduces the function of this gene has more of an influence on them. Women, having two X-chromosomes, are more likely to have at least one normally functioning gene copy, and scientists have not studied variants in women as extensively.

Recent studies have linked the Warrior Gene to increased risk-taking and aggressive behavior. Whether in sports, business, or other activities, scientists found that individuals with the Warrior Gene variant were more likely to be combative than those with the normal MAO-A gene. However, human behavior is complex and influenced by many factors, including genetics and our environment. Individuals with the Warrior Gene are not necessarily more aggressive, but according to scientific studies, are more likely to be aggressive than those without the Warrior Gene variant.

This test is available for both men and women, however, there is limited research about the Warrior Gene variant amongst females. Additional details about the Warrior Gene genetic variant of MAO-A can be found in the paper titled “A functional polymorphism in the monoamine oxidase A gene promoter” by Sabol et al, 1998.

When testing for the Warrior Gene, we are looking for an absence of MAOA (monoamine oxidase A) on the X chromosomes. Based on how many times we see the repeat of a certain pattern on the X or Xs we can tell if the MAOA is present or absent (depleted). Three repeats of the pattern indicates that the X chromosome is deficient of MAOA and therefore you have the Warrior Gene. If we see 3.5, 4 or 5 repeats of the pattern, MAOA is present and this is a normal variant of the gene on your X chromosome.

warrior 6 However, women have 2 X chromosomes where men have 1 X and 1 Y. As mentioned above, the gene is carried on the X chromosome, so women can either have it 1) not at all, 2) on only 1 X (therefore making them a carrier), or 3) on both Xs (exhibiting the trait).

Looking at results, with one X-chromosome, men with the “Warrior Gene” will show a value of 3. Other men will have normal variants: 3.5, 4, 4.5 or 5. With two X-chromosomes, women will have two results. For example, a woman might have 3 and 3, 3 and 5, or 4.5 and 5.

This first example is of a female with one copy of the normal variant and one copy of the Warrior Gene indicated by a value of 3.

In the second example, shown below, this female has the Warrior Gene trait, because she carries the Warrior Gene depletion, shown as a value of 3, on both of her chromosomes, the one contributed to her by her father and the one contributed to her by her mother. This also tells us that her father has the Warrior Gene, since he carries only the X chromosome contributed by his mother, which he gave to his daughter. It also tells us that her mother was either a carrier, if she had only the one copy she gave to her daughter, or had the Warrior Gene herself is she carried two copies.

A male’s results would have only one result listed. If he has a value of 3, he had the Warrior Gene. Any other value is NOT indicative of the Warrior Gene.

Happiness Gene in Women

In an unexpected turn of events, in August 2012, another study in the journal Progress in Neuro-Psychopharmacology & Biological Psychiatry indicates that while this gene may express as aggression in men, it may be the happiness gene in women. Even women with only one copy of the gene were shown to be happier than women who carry no copies. A study of 193 women and 152 men evaluated their happiness level and women who carried this mutation on one or both X chromosomes rated themselves as significantly happier than women who did not carry this trait. There was no difference in the male participants.

http://www.livescience.com/22789-gene-linked-to-happiness-in-women.html

Caveat

Among the many advances and discoveries of modern DNA and genetics are ‘scientific’ oddities. These genetic wonders make it into popular culture and sometimes develop a life there that far outpaces their academic worth. But they are interesting. These factoids are best used as ‘cocktail party conversation’ starters or maybe a good way to tease Uncle Leo at the family picnic. Family Tree DNA, where you can find out if you have the Warrior Gene, portrays it to their customers as just that, a novelty.

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Supreme Court Decision – Genes Can’t Be Patented

Posted on June 13, 2013 by Roberta Estes

In a victory for consumers, patients, researchers and women, the Supreme Court today returned a decision that human genes cannot be patented.

Their decision states that DNA ”is a product of nature and not patent eligible merely because it has been isolated.”

This case was a result of a suit against Myriad Genetics, a company that was granted patents for isolating two human genes, known as BRCA1 and BRCA2, both of which are well known breast cancer genes, recently brought to light by Angelina Jolie’s decision to have preventative mastectomys after both the gene and related breast cancer were found to be prevalent in her family. Shortly after that decision and surgery, Jolie’s aunt died of breast cancer.

While companies cannot patent the genes themselves, they can develop treatments and hopefully, cures, and those can be patented. Synthetic genes created are also eligible for patents. Myriad wasn’t the only company to do this. The government has issued patents to over 4000 genes to both companies and universities.

The patenting of genes made it impossible for other competing companies who could test for the gene technically to do so. In other words, it artificially created a sole supplier situation where only one company could provide the test for that gene, and therefore could set the price wherever they wanted. Jolie revealed that the cost of screening for those two genes alone was $3000, a cost prohibitive to many women. However, the actual cost of the testing is significantly less. I was wondering just how much less, then the answer arrived in my inbox.

I know that Gene by Gene, through its division, DNA Traits has the capability to offer this test and has been selling it internationally since 2012. Bennett Greenspan, president of Gene by Gene has discussed this with me privately, and how terribly it pained him not to be able to do this testing to help people within the US. Bennett shared some pretty profound thoughts about the unfair situation this created.

I was just getting ready to call Bennett, when less than 6 hours after the Supreme Court decision, I received an e-mail from Gene by Gene, which contained the answer – $995. So the actual cost to the American consumer is only about one third to one quarter of what they were being charged as a result of the patent.

Today’s Supreme Court decision is truly a victory for patients, consumers, researchers, women and all US citizens. Below is the content of the e-mail I received from Gene by Gene announcing the ability for DNATraits to sell the BRCA test in the US.

In effort to increase access to potentially lifesaving BRCA1 and BRCA2 tests, DNATraits can now offer tests for $995, a fraction of the cost of similar tests prior to the court decision

HOUSTON — Jun. 13, 2013 – Thanks to today’s U.S. Supreme Court decision opening the door to greater access to genetic medicine by American patients and their health care providers, testing for genes specifically linked to breast, ovarian and other cancers will now be more widely available and at a lower cost than ever before.

DNATraits, a division of Houston-based genomics and genetics testing company Gene By Gene, Ltd., announced today that it will offer testing for the BRCA1 and BRCA2 genes in the United States for $995. Prior to today’s unanimous Supreme Court ruling, when exorbitant licensing fees kept DNATraits and others from offering BRCA gene tests in the United States, the cost for such tests was around $4,000.

“We’re pleased to make this important testing more widely available and accessible in the United States,” said Gene By Gene President Bennett Greenspan. “Our highly automated CLIA-registered lab and efficient processes enable us to make genetic and genomic testing more affordable and accessible to more individuals, in the U.S. and worldwide. And that’s our company’s mission, in a nutshell.”

The company’s announcement about the tests, which gained national attention when actress Angelina Jolie courageously revealed in May that being a BRCA1 carrier was among the factors in her decision to have a preventive double mastectomy, comes after today’s Supreme Court ruling in “Association For Molecular Pathology v. Myriad Genetics.”

“We commend the Supreme Court for opening the door to greater technological innovation and access to genetic tools that promise to save and improve the quality of human lives in the United States,” Greenspan added. “It’s critical that as an industry we are able to continue to engage in healthy competition to drive down the costs of these tests – because as more individuals have access to and undergo them, the more information we’ll have about many serious diseases that eventually may lead to cures.”

DNATraits has processed testing for the BRCA1 and BRCA2 genes for individuals living outside the U.S. since 2012. Those genes are processed using traditional Sanger DNA sequencing, which is considered the gold standard for DNA analysis, at the company’s Genomic Research Center in Houston, a CLIA-registered lab which has processed more than 5 million discrete DNA tests from more than 700,000 individuals and organizations globally.

In addition to the BRCA gene tests, DNATraits offers a pre-natal array that covers 111 population specific diseases, as well as other not population-specific diseases, like Duchene Muscular Dystrophy.

Customer Inquiries

Individuals interested in learning more about either the BRCA1 or BRCA2 tests should ask their doctors for more information. They and their health care providers can also visit the company’s website, www.dnatraits.com, or call (713) 868-1438 for more information.

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The Autosomal Me Summary and Links

Posted on June 2, 2013 by Roberta Estes

“The Autosomal Me” is a 9 part series published between February 6, 2013 and May 31, 2013. They are a bit dated now, but the concepts are still rock solid.

Here are all of the links in one place.

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.” Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works. Part two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.

Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.

In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering. We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7, “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments” took a deeper dive and focused on the two chromosomes with proven Native heritage and began by comparing those chromosome segments using the 4 GedMatch admixture tools.

Part 8, “The Autosomal Me – Extracting Data Segments and Clustering,” we extract all of the Native and Blended Asian segments in all 22 chromosomes, but only used chromosomes 1 and 2 for illustration purposes. We then clustered the resulting data to look for trends, grouping clusters by either the Strong Native criteria or the Blended Asian criteria.

The final segment, Part 9, “The Autosomal Me – The Holy Grail – Identifying Native Genealogy Lines,” utilized all of the chromosomal information we’ve gathered in the earlier steps. We apply that information to our matches and determine which of our lines are the most likely to have Native Ancestry. This, of course, fulfills the goal of using DNA information to identify small amounts of minority admixture.

In summary, this series has been quite interesting and indeed, it did achieve the goals initially set forth. However, it was very manually intensive and took far longer than anticipated, partly due to circumstances beyond my control, like software updates and vendor changes. A second reason that it took longer than expected was due to the sheer amount of work involved in the various steps, particularly steps 8 and 9. In addition, because Minority Admixture Mapping (MAP) is developmental, I had to try several different approaches to determine which one, or ones, worked best. Despite the immense amount of work, I would describe this approach certainly as useful and successful. In fact, I don’t know how else I would have ever eliminated some genealogical lines as candidates for Native heritage and focused on others without the combination of MAP’s new techniques combined with both old and new tools provided by others.

Having said that, I would suggest that this technique, because of the intensive manual effort required, is only for the very committed genetic genealogist – the warrior, so to speak. It also will not work well with only a few matches. I would suggest that you would need at least 200 or 300 matches, preferably more, which is typical of someone with colonial American heritage. If that is you, and you are desperate to find your minority admixed lines….then this type of project may be for you. Please thoroughly read all 9 articles before beginning.

Many of the techniques in the various steps can be utilized individually, without completing the entire MAP process. For example, comparing vendor and third party results, using the GedMatch admixture tools and the chromosome comparisons for percentages of ethnicity all provide useful information in their own right, outside of the full MAP process.

Bon voyage on your journey of discovery to find “The Autosomal You”! Your ancestors are the pot of gold at the end of that rainbow.

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