X Marks the Spot

Posted on September 27, 2012 by Roberta Estes

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When using autosomal DNA, the X chromosome is a powerful tool with special inheritance properties. Many people think that mitochondrial DNA is the same as the X chromosome. It’s not.

Mitochondrial DNA is inherited maternally, only. This means that mothers give their mitochondrial DNA to all of their children, but only the females pass it on. So tracking mitochondrial DNA back up your tree, it goes to your mother, to her mother, to her mother, until you run out of direct line mothers on that branch. The mitochondrial DNA is shown by the red shading below. The Y chromosome is blue.

Mitochondrial DNA is not one of the 23 chromosomes you obtain from both of your parents.

The X chromosome is different. The X chromosome is one of the 23 pairs of chromosomes. The 23^rd pair is the pair that dictates the gender of the child. If a child has an X and a Y, it’s a male. Remember that the father contributes the Y chromosome to male children only. If the child has two X chromosomes, it’s a female.

The inheritance patterns for the X chromosome for males and females is therefore different. Men inherit only one X chromosome, from their mother, while women inherit two Xs, one from their mother and one from their father. In turn, their parents inherited their X in a specific way as well. All ancestors don’t contribute to the X chromosome.

In my paper published in the Journal of Genetic Genealogy (Vol. 6 #1) in the fall of 2010, in a paper titled Revealing American Indian and Minority Heritage Using Y-line, Mitochondrial, Autosomal and X Chromosomal Testing Data Combined with Pedigree Analysis, in addition to other types of analysis, I analyzed my X chromosome and what it told me about where some of my Native and African inheritance came from.

At that time, the only company returning ethnicity information about the X chromosome was deCode genetics. My X chromosome showed that I carried Native American heritage on the X chromosome as well as on some other chromosomes.

I’m going to share the part of this paper involving the X chromosome and how it can be used genealogically and in particular, to identify candidates who could have contributed this Native and African ancestry.

Blaine Bettinger granted me permission to use 2 charts in the paper and again for this blog. Thanks much, Blaine. He originally published them on his blog, The Genetic Genealogist, in December 2008 and January 2009 in his blogs about how to use the X chromosome for genealogy.

The first chart shown below is the male’s X chromosome inheritance chart. You can see that he only obtains his X chromosome from his mother who inherited it from both her mother and father, but only from some of her ancestors on either side.

The next chart is the female’s inheritance chart. She obtains her X from both of her parents.

Blaine color coded these, pink for females and blue for males, so I was then able to quickly use them to fill in my ancestor’s names. I know this next chart looks messy, but it’s what I did and I still refer to this regularly. I don’t’ expect you to READ this, I expect you’ll DO something like this with your own pedigree chart. So excuse the look into my messy closet:)

I numbered the slots so that I could work with them later.

The results were quite surprising. The first thing that became immediately evident is that I didn’t have to worry about a few lines. On the chart below, you can see that my mother’s German lines could be immediately eliminated, because we know they were not the source of the Native American heritage.

This leaves only three individuals on the mother’s side as candidates for Native ancestry. Those are the numbered slots between the German lines.

The people below correspond to the numbered slots above. See, I told you that you didn’t need to read the chicken scratch chart.

5 – Naby (probably short for Abigail), last name unknown but may be Curtis, born in Connecticut in about 1793.

7 – Capt. Samuel Mitchell, born probably about 1700, possibly in Kittery, Maine or possibly in Europe, mother unknown. This line is probably eliminated.

8 – Captain Mitchell’s wife, Elizabeth, last name unknown

Using the pedigree chart, we narrowed the mother’s side from 21 possible slots to 5 with one more probably eliminated. Of these, mitochondrial DNA sampling of the descendants of the two women whose last name is unknown would produce the answer to the question of maternal Native or African ancestry.

The father’s side is more complex because many of his ancestors immigrated in the colonial era. Candidates for Native ancestry are as follows:

20 – Mary, wife of John Harrold (Herrald, later Harrell), born about 1750, died in 1826 in Wilkes County, NC. She was rumored to have been Irish.

21 – Michael McDowell, born 1747 in Bedford Co., Va. – his mother is unknown. His father was a second generation immigrant who lived in Halifax and Bedford Counties in Virginia.

22 – Isabel, wife of Michael McDowell, probably born about 1750, surname unknown, located in Virginia.

27 – Elizabeth, born about 1765, wife of Andrew McKee of Virginia.

28 – Agnes Craven is the last slot on the chart, but not the last in the line. Her father was Col. Robert Craven born 1696 in Delaware and was well to do. His mother is unknown. Robert’s wife was Mary Harrison, born in Oyster Bay, New York to Isaiah Harrison and Elizabeth Wright. These lines appear to reach back to Europe but are unconfirmed, probably eliminating these lines.

30 – Phoebe McMahon, wife of Joseph Workman, born 1745 York Co., Pa, daughter of Hugh McMahon, mother unknown.

31 – Gideon Faires’ mother was Deborah, born 1734, possibly in Augusta Co., Va.

32 – Sarah McSpadden’s father was Thomas McSpadden born 1721 in Ireland, eliminating this line. Sarah’s mother was Dorothy Edmiston whose father was born in Ireland, eliminating that line. Dorothy’s mother was named Jean and was born in 1696 but nothing further is known.

33 – Martha McCamm, born before 1743, wife of Andrew Mackie of Virginia, parents unknown.

On the father’s side, we began with 13 slots, positively eliminating one and probably eliminating a second, leaving 11. Of these, 7 could be resolved on the maternal line by mitochondrial DNA testing. Taken together, this side of the pedigree chart is a much better candidate for both Native and African DNA sources. Notice all of the females who have no surnames. These are excellent places to look for Native ancestry. On my chicken scratch version, these are highlighted in yellow.

While the X chromosomal pedigree chart analysis is not the perfect scenario, the pedigree chart has 128 slots. Using the X chromosome narrows the candidates to 34 slots. Genealogy narrowed the slots to 15 and focused mitochondrial DNA testing could narrow them to 6. Further genealogy research on those ancestors could potentially eliminate them by placing them “over the pond” or by discoveries which would facilitate DNA testing.

Marja and Me

You might recall that Marja and I are also related on our X chromosome. In this case, since she is from Finland, the probabilities are exactly the opposite. It’s much less likely that our connection is on my father’s or mother’s British Isles lines, and much more probable that it’s through my mother’s German lines. The early colonial settlers tended to be from the British Isles and certainly the people filling the X chromosome slots from my father’s side appear to be, with names like McDowell, McSpadden, etc.

Mother’s Anabaptist line (Brethren) is the German grouping through my mother’s father and descends from France and Switzerland,although these particiular lines don’t appear to have become Brethren until after immigrating to America. Marja also has other matches with people from the Anabaptist project.

Those end-of-line people are:

Barbara Kobel – born 1713 probably Scholarie Co., NY
Anna Maria Deharcourt – born 1687 Muhlhofan, France, died Oley Valley, Berks Co., Pa., probable parents Jean Harcourt and wife, Susanna
Veronica – wife of Rudolph Hoch, born 1683 Basel, Switzerland, died 1728 Oley Valley, Berks Co., Pa.
Susanna Herbein – born 1698, Switzerland, father Jacob, died 1763 Oley Valley, Berks Co., Pa.
Jacob Lentz – born 1783 Wurttemburg, Germany, died 1870, Montgomery Co., Ohio
Fredericka Moselman – born 1788 Wurttemburg, Germany, died 1863 Montgomery Co., Ohio

Mother’s Dutch line is eliminated, because it’s through her father’s father. Marja and I thought that might be a possibility, but we can see from this chart that it is not. My father also has a Dutch line that was eliminated because it came from his paternal line.

Mother’s Lutheran Palatinate line, end-of-line ancestors show below, is though Mother’s maternal line.

Johann Jacob Borstler – born about 1659 Beindersheim, Bayern, Germany
Anna Stauber – born 1659, Schaeurnheim, Germany, father Johannes Stauber
Johann Peter Renner – born 1679, Mutterstadt, Bayern, Germany
Anna Catherina Schuster – born about 1679 probably in Mutterstadt, Germany
Maria Magdalena Schunck – born 1688 probably Mutterstadt, Germany, father Johann George Schunck
Johann Martin Weber – born about 1700 Mutterstadt, Germany
Rudolph Sager and wife Elizabetha – born about 1669 Ruchheim, Bayern, Germany
Rosina Barbara Lemmert – born 1669 Mutterstadt, Bayern, Germany
Anna Blancart – born 1642 Mutterstadt, possibly French
Johann George Hoertel and wife, Anna Catharina – born about 1642, Mutterstadt, Bayern, Germany
Matthaus Matthess – born 1695/1715 Rottenback, Bayern, Germany, wife unknown
Anna Gerlin – born 1697, Windischerlaibac, Bayern, Germany
Johannes Buntzman – born 1695/1720 Fulgendorf, Bayern, Germany
Barbara Mehlheimer – mitochondrial line J1c2 – born 1823 Goppsmannbuhl, Bayern, Germany, mother Elizabetha, unmarried

Note that the mitochondrial line is indeed one of the lines that contributes to the X chromsome inheritance path, but only one of many.

So Marja, it looks like we have to be related through one of my British Isles ancestors, listed in the first part of this article, or from one of Mother’s two German groups. Personally, I’m betting on the German groups, but you never know. DNA is full of surprises.

The good news is that my mother’s information is also at GedMatch, along with mine and Marja’s, so by process of elimination, we can at least figure out whether to focus on the pink or the blue side of my chart.

Today, downloading your raw results to GedMatch, combined with Blaine’s X charts above, is really the only good way of working with X chromosome matches.

I’m planning to package this article as a pdf file and send it to my X chromosome matches. You can substitute your information for mine and do the same thing. Hopefully, your matches will then understand the X chromsome, its unique inheritance properties, and will provide their X end-of-line ancestors for you as well.

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It’s Dick Hill’s Fault…

Posted on September 25, 2012 by Roberta Estes

Yes indeed – it’s Dick’s fault. What’s Dick’s fault, you ask? The fact that I haven’t had enough sleep for the past three days. That’s what’s Dick’s fault, him and his book, Finding Family: My Search for Roots and the Secrets in My DNA.

What a book it is! I know Dick Hill, and I thought I knew his story, but I didn’t. I knew pieces of his story. Just snippets. I was missing the best parts.

Dick spent his life, after college, writing for a living in a variety of professional positions, and you can tell. His writing is precise and skillful, and it draws you into the story from the first page, even if you do think you know the story line.

In my case, I had commitments during the day, so I took the book to bed intending to read to go to sleep. Sometime around 3AM, I made myself stop reading so that I could get at least a few hours sleep. Thankfully, the third night, I finished the book.

Dick’s story begins with a slip up at the doctor’s office where he discovered he was adopted. He was 18 and on his way off to college, so even though he was quite surprised, he was relatively unconcerned at that time. However, over the years, and finally with a virtual deathbed confession of his father, his interest grew. It took his father’s revelation that he had a brother to really light that spark.

As these things go, his brother was relatively easy to find. His biological father was not. In fact, he didn’t know who his father was. He knew that his father was not his mother’s husband. Are you confused yet? Well, don’t be….it’s just part of this wonderfully elusive and slippery plot. Just when you think you have it figured out, I guarantee you, you don’t!

Dick’s story is particularly close to my heart. Dick knew who his brother on his mother’s side was, but he hunted for his father for decades. I knew who my father was, or I thought I did, and I hunted for my brother for decades. Dick and I used many of the same early DNA siblingship tools to prove and disprove relationships, and eventually, the newer wide spectrum autosomal chip testing available at both 23andMe and Family Tree DNA, with very similar results. I’m not going to tell you what those results were or are….you’ll have to read the book to find out.

Let’s just suffice it to say that there were a total of about 13 different candidates to be Richard’s father, all of which Richard had to unweave from the web of intentional deception and state-sanctioned “untruths” one by one. One by one he would identify candidates and be hopeful. One by one, he would eliminate them as possibilities. More than once, he thought sure he had the answer. More than once, he was wrong. Some candidates got rejected, reconsidered, rejected, reconsidered…..does this sound repetitive? You should be on Dick’s roller coaster ride!

I was so relieved to finally reach the end of the book. Richard found his father, in an unbelievable and ironic twist of fate, and finally, I could go to sleep! This book is what we used to refer to as a barn-burner! Gets ahold of you and just won’t let you go!

Congratulations Dick on a wonderfully executed masterpiece.

Whether you are interested in genetic genealogy, adoption searches or just like a good heart-warming mystery, you’ll love this book! But consider yourself warned…..don’t think you’re going to read it to go to sleep…..

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The Malhi Molecular Anthropology and Ancient DNA Labs

Posted on September 22, 2012 by Roberta Estes

I’ve known Ripan Malhi for years now, but until this past week, I had never met him in person. Dr. Malhi attempted to extract the DNA from both a stamp, supposedly licked by my grandfather, and my father’s hair, complete with follicle. I could hardly wait those long days to determine if any DNA was present. I tried not to pester him, but I felt like the proverbial child constantly asking “are we there yet?”

Unfortunately, none of the multiple attempts were successful, but they established a relationship between Ripan and myself. Ripan and I were trying to figure out this week just how long ago that was and we think it was about 10 years. We know it was more than 7 years, since he has been at the University of Illinois since 2006 where he established the Malhi Labs, and it was significantly prior to that.

After finishing his PhD, Ripan founded a company called Trace Genetics. It was there that I first met Ripan. They specialized in ancient DNA processing. A few years later, in 2006, Ripan sold that company and established both the Malhi Ancient DNA Lab and the Malhi Molecular Anthropology Lab at the University of Illinois where he is an Associate Professor.

Ripan has a long list of publications to his credit. It won’t surprise you to discover that Native American and ancient DNA are both areas in which he specializes, and in particular, ancient Native American DNA.

The Malhi Molecular Anthropology Laboratory generates DNA variation data from different genetic systems (i.e. mitochondrial genome, Y chromosome, autosomal) to infer evolutionary history of populations and species. Currently, research in the lab is split into two independent research areas, the evolutionary history of Native Americans and evolutionary genetics of non-human primates in the areas of:

Molecular Anthropology
Ancient DNA Analysis
Evolutionary Genomics
Forensic Science
Population Genetics

Dr. Malhi was very gracious during my visit to the University of Illinois and agreed to show me both of his labs. Not only that, he came to the Native American House to get me so that I wouldn’t get lost navigating the campus and delivered me back as well. For that, I’m extremely grateful! A campus with 40,000 students isn’t a campus, it’s a city and parking is almost non-existent!

First we visited the Ancient DNA Lab. This lab is separate from the rest of the processing, and is actually in a different building altogether. Access is extremely limited and only those who need to go inside, do. I’m not one of those people.

Why such limited access? In a word, contamination, the arch-nemesis of ancient DNA processing. Ancient DNA, by definition is old, degraded and generally in short supply. The process of extracting it from whatever medium you are working with, teasing out whatever is left, without introducing any outside contamination, is tricky at best. Limiting the exposure in the room itself is the first step in a series of protocols designed to limit, prevent and then identify contamination if it exists.

The room is double air locked and pressurized so that when someone enters or exists the air is blown out and none of the surrounding air enters the lab.

The room itself can accommodate two researchers. The window is tinted yellow as the lighting is also controlled within the lab. So if these photos look yellow, it’s because they are.

You can see the DNA extraction area in this photo. Work is done inside a cubicle, again, to limit contamination. You can see the mortar and pestle used to sometimes grind the materials. Other times, such as with teeth, drills are used.

After the DNA is extracted and amplified, assuming DNA is found, and it’s not contaminated, the results are then taken to the second lab, down the street, for processing.

This is the Molecular Anthropology lab where most of the people work, since they deal only with already extracted ancient DNA or contemporary DNA.

Contemporary DNA is considered a medical hazard while the DNA is still in a body fluid of some type (saliva, blood, cheek swab), so medical precautions must be taken. In many ways, this lab looks just like a lab at a medical facility. In fact, it’s in the Medical Sciences building.

DNA is extracted from contemporary samples in this work area. After extraction, it is no longer considered a medical hazard, so from that point forward, only normal lab protocols are in force, not medical biohazard protection.

The DNA is then further processed in this area. Ripan discussed some of his current projects as we toured. He continues his work on Native American population genetics, and in particular, the migration and settlement of the Native people on this continent. Currently he collaborates with Canadian tribes and is involved with an ongoing project to analyze the remains of several hundred Native burials that have previously been discovered.

Not only does he work with Native population genetics, and remains, but he also encourages Native American students to join his programs and work in the labs. He works closely with the Native American House.

I’m hopeful that Ripan’s projects and ongoing analysis will bring some answers to questions like whether or not mitochondrial haplogroup X is found in any tribes west of the St. Lawrence Seaway (inferring that it did come from Asian, not Europe), whether haplogroup M is found in the founding Native population and whether European or African haplogroups of any description are found pre-Columbian contact in the Americas.

I want to thank Dr. Malhi for his hospitality, for making time for the tour this week, and to wish him Godspeed in his continuing research. And yes, that does mean I want him to hurry. That hasn’t changed in the past decade!

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Germain Doucet and Haplogroup C3b

Posted on September 18, 2012 by Roberta Estes

I love a good mystery, don’t you? Well, the Doucet family has one and it’s a doosey.

Marie Rundquist, the founder and administrator of the Amerindian Ancestry Out of Acadia project at Family Tree DNA has recently written a new paper about the C3b results within the project.

Marie’s paper, titled “C3b Y Chromosome DNA Test Results Point to Native American Deep Ancestry, Relatedness, Among United States and Canadian Study Participants,” tells about the project and the findings relative to haplogroup C3b. Her raw data is available within the project. The Native American people involved are the Mi’kmaq and ironically, while we have found several Mi’kmaq men who carry haplogroup C3b, we haven’t found any carrying the much more common Q1a3a.

The Acadian people were French and settled in the eastern-most region of Canada beginning in 1605 in Port Royal, Nova Scotia. They mixed freely with the Native people and intermarried. Beginning in 1710 and continuing until 1755, when they were forcibly deported, they were in conflict with the English government and refused to sign an oath of loyalty to England. The families were highly endogamous. Today, if you discover you descend from an Acadian family, you will discover that you descend from many Acadian families. I have one cousin who discovered that he and I are related 132 different ways.

The map below shows Acadia just before the Acadians were deported.

Marie’s paper shows that 6 different families with different surnames carry haplogroup C3b and all are related within 16 generations, or between 400 and 500 years. Many are, of course, related much more closely.

The Doucet family is represented by 8 different males who all tested as haplogroup C3b. They descend from various sons of Germain Doucet, born in 1641. Germain was always presumed to be the son of the French founder, Germain Doucet, born in 1595 in France, the commander of Fort Royal.

Hmmm, this is known as a fly in the ointment. Indeed, the original descendants of Germain Doucet (1595) who had tested carried haplogroups of R1b1a2, clearly European, just as we would expect. But then, there was another Doucet test and he was discovered to be haplogroup C3b.

Keith Doucet, the man who tested to be C3b, and Marie subsequently wrote about their discovery and the process they went through to find other men to confirm that DNA result in a story titled “Confirmed C3b Y DNA Results Test the Heritage of Cajun Cousin Keith Doucet.”

This of course, raises questions, none of which can be readily answered. Doesn’t every genealogy find raise at least two new questions? Well, this one raises a few more than two.

The other son of Germain Doucet (1595), Pierre tests to be R1b1a2, while “son” Germain (1641) tested to be C3b. Obviously, these man cannot both be the genetic children of Germain Doucet (1595) and unless a Native American Mi’kmaq male made their way to France sometime in the distant past, Germain (1641)’s father was not from France and was not Germain Doucet (1595).

We know that Germain Doucet (1595) arrived in Port Royal in 1632, was noted as the commander in 1640 and returned to France in 1654 after Port Royal fell to the English, leaving at least two of his 4 children who had married in Port Royal.

So what happened? Here are some possibilities.

Germain Doucet (1595) and his wife adopted an Indian child and named him Germain Doucet

One of Germain Doucet’s older daughter’s had an illegitimate child and named him Germain Doucet, in honor of her father.

Germain’s wife became pregnant by a Native man.

A Native person adopted Germain Doucet’s name out of respect. When Native people were baptized in the Catholic faith, they were given non-Native names.

So, through Marie’s project and hard work, we’ve solved one mystery and introduce yet another.

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Native and African American Houses – University of Illinois at Urbana-Champaign

Posted on September 15, 2012 by Roberta Estes

This week I was honored to speak at the University of Illinois at Urbana-Champaign. These speaking engagements were different than anything I’ve ever participated in. I’ve done quite a bit of university speaking, but generally conferences. These events were different because the students themselves from these two Houses invited me and funded my visit. To say I felt a great obligation to find a way to connect to them is an understatement.

Normally my audience consists of genealogists, and sometimes civic groups, but generally not young people ranging in age from 18 to 22 or so, plus grad students. These folks were born in the 1990s for the most part and ancient history to them is anything before cell phones. They were only about 10 years old when social networking in the form of My Space was launched, so they’ve never know a world without the internet, electronic gadgetry and social networking. I was extremely glad I had my two blogs to offer them.

I thought about how they might perceive DNA and genealogy, and I changed the presentation entirely, approaching it from a different perspective – that of personal genetics. While this new field started in 1999 as a genealogical endeavor (thank you Bennett Greenspan), it has moved far from its original genesis. Today we have a toolbox full of tools that can answer different questions for us, in various ways. For these bright young people full of potential, personal genetics will be with them their entire lives and it won’t be a frontier like it is for us, but a way of life. My presentation was entitled “The Gift of You” and it discussed genealogy of course, but deep ancestry, health, ethnicity and “cousinship” using fun examples. I also passed out candy when I got answers, which helped a lot:) Food, the most common denominator.

While all 4 sessions were sponsored by both the African American and Native American Houses, 2 sessions were held at the Bruce B. Nesbitt African American Cultural Center, 1 at the Native American House and the final presentation in a larger auditorium venue. All sessions were open to all students and the public as well, and indeed were attended by a wide variety of people with very interesting and diverse backgrounds.

I was particularly impressed with the regular luncheon, with speakers, held by the African American House, entitled “Food for the Soul.” I wish I lived close enough to attend as many of the topics are very interesting. This event was very well attended.

After each of the 4 sessions, several people stayed and discussed various aspects of genetic testing, genealogy and career paths.

I can’t even begin to express how hopeful this trip made me. These young people who attended these sessions are bright and forward thinkers. They are involved in supportive and nurturing programs through the two Houses as well as the academic curriculum at the University of Illinois. They are encouraged to reach beyond the known horizons. And yes, some of them are interested in genealogy too. I’m hopeful that there will be someone to pass that torch to someday!

I want to share with you a conversation I had with one young man who stayed after the session at the Native American House. He is mixed Caucasian, Peruvian, Chinese and Jewish, born in California, an extremely culturally diverse place. He is a graduate student in the Communications/Medical program meaning at the end of 8 long years, he comes out the other end with an MD degree and a PhD. And he is bright, very, very bright, compassionate and pleasant. I don’t know where he’s going to practice, but I want him to be my doctor!

He shared with me part of his story. Between his undergrad and graduate school, he embarked on a journey of discovery. He tracked his grandmother’s life backwards. He began at her grave in Israel, journeyed through China where they sought refuge from the holocaust, and where his grandmother’s mother died of a “female disease.” From there he went back to Germany where the family had escaped the holocaust. During this time he discovered that his mother and he both carry the BRCA1 gene which produces a hereditary breast-ovarian cancer syndrome. Another family member indeed has this disease today. His profound interest in his family history and this mutation led to a discussion about epigenetics and the ENCODE project which revealed that what was once considered to be junk DNA isn’t junk afterall. And then, the question:

“What if we could use epigenetics to turn OFF the BRCA1 gene?”

I told him, I’m way beyond my level of expertise, but the fact that this extremely talented young man is pondering this question, and has a very personal impetus to answer it is one of the most promising and hopeful events I’ve witnessed in a very long time. This truly is the gift of our ancestors, in so many unseen and unspoken ways.

The art at the beginning of this article, titled “Elevator”, by Sol Aquino, 2003 (acrylic on canvas) featured on the SACNAS brochure I picked up at the Native American House portrays this connection is a most profound way.

During these two days, I got to spend time with Rory James, the Director of the Bruce B. Nesbitt Center, and with Jamie Singson, the Director of the Native American House, and the staff and volunteer students at both facilities. I was extremely impressed with the knowledge of both of these gentlemen and their heartfelt concern for the students, their education and their futures. I know that these men and their staff will shepherd these students and provide them with ongoing opportunities to learn about their history and how it connects with their futures as they complete their more structured academic studies. I wish facilities like this had been in place when I was a student.

The attendees were extremely diverse, in terms of racial and cultural makeup, in terms of student versus community members, age, and in terms of their interests relative to personal genetics. Their stories were both amazing and inspirational.

I think that Jamie Singson summed it up perfectly at the end of the final session as we walked through the cool evening air back to the Native American House from the auditorium. People had stayed for an additional couple of hours after the presentation and a small group of about 5 of us had a very enlightening and lovely discussion. Jamie said, “What I take away from this is how much everyone wants to belong and to find the place where they fit in.”

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Lenny Trujillo: The Journey of You

Posted on September 11, 2012 by Roberta Estes

In the fall of 2010, Lenny Trujillo embarked on a journey unaware that he was going anyplace. That was the journey to discover himself, his ancestry….and what a journey it has been. Lenny was unique, very unique.

After Lenny’s results came back, he purchased a DNA Report. In the process of analyzing his DNA, I realized what an opportunity was at hand. Lenny was Native American and his Y DNA likely harbored new SNPs that would identify a new sub-haplogroup, and we needed to take a look. When I wrote Lenny and asked if he would consider a Walk the Y (WTY) test, he told me that he had retired that very day. My heart sunk, because I presumed that meant “no”, that he’d be making financial adjustments like so many retirees. But then Lenny went on to say that he wanted to proceed in order to leave a legacy for his grandchildren.

And what a legacy Lenny has to leave them. Lenny made history and advanced science. Indeed, by comparing Lenny’s DNA to another European man in haplogroup Q1a3, 7 new SNPs were discovered. I wrote a paper about this process and Lenny’s contribution. This was a red letter day for Native American ancestry, as well as for Lenny, delivered as fate would have it, Christmas week.

However, Lenny’s remarkable story doesn’t end there. That’s only the beginning. But, I’ll let Lenny tell his own story, in his own words. He wrote an article for the Los Angeles Beat which was published today. His story is so heartwarming and inspirational and the records that document his Native ancestry that Lenny has been able to find have been absolutely amazing.

Lenny also tells his story on the Family Tree DNA YouTube Channel in various segments for those who haven’t yet seen Family Tree DNA’s infomercial.

So whether you read it or watch it, or both, come along, share Lenny’s journey, and enjoy!

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Ancestry Autosomal Results are Back

Posted on September 10, 2012 by Roberta Estes

My cousin, Harold, e-mailed me and asked me to check my Ancesry results to see if I matched a certain nickname (user). I told him I’d be glad to when my results come in, sometime in October. He replied that my results are in and have been for a couple days, as I’ve been showing as a match to him. Hmmm….would have been nice if Ancestry had notified me. We’ll chalk this up to the internet troll eating the e-mail notification message. Thank you cousin Harold.

When Ancestry received my kit on August 21st, they said to expect my results in 6-8 weeks. They beat their own mark by at least 50%. It took about 3 weeks instead of 6-8. Everyone is always happy receiving something early. It’s all about setting expectations correctly, and they did.

I was excited to take a look. Sure enough, there was cousin Harold, right up at the top of the match list. Harold and I have been working on a particulary elusive genealogy problem for some time now, so both of us test everyplace we can in the hopes of cracking this tough nut. In a future blogs, we’ll talk about using genetic genealogy to do focused testing and solve very specific problems.

I only have just a few minutes this morning, so it’s a good thing that Ancestry’s user interface is easy and intuitive.

I was disappointed to see that Scandinavian show up. I know beyond any doubt that I’m not 12% Scandinavian. That’s equivalent to one great-grandparent. I did a pedigree analysis as part of a paper titled Revealing American Indian and Minority Heritage Using Y-line, Mitochondrial, Autosomal and X Chromosomal Testing Data Combined with Pedigree Analysisthat was published in the Journal of Genetic Genealogy. CeCe Moore has already reported on this false Scandinavian problem at Ancestry.

Given my time constraints this morning, I had to limit myself to a quick test drive. I have one 3rd cousin match, Harold, nineteen 4th cousins and 90 distant matches. In total 122 matches and of those, only 14 don’t have pedigree charts, although I’ve noticed that some charts are very skeletal, with only parents and maybe grandparents listed.

I couldn’t resist scrolling down the list and clicking on “review match” links for the 4th cousins. I find the “nicknames” frustrating. Some are marginally recognizable. I use my full name in mine, but others are entirely obfuscated.

I had no idea who Alyssa2309 was, but she is listed third on my 4th cousin list, so I clicked on Review Match. Much to my surprise, she is truly a cousin. My great-grandfather is her great-great-great-grandfather. I was very glad at this moment that I had taken the time to manually enter my pedigree chart information for 10 generations. Without that information, Ancestry could not have connected our common ancestors on our trees.

Ok, that’s very cool. This isn’t a brick wall line for me, but it’s still fun to find a new cousin. Maybe she has some photos that I don’t, or vice versa. Alyssa2309, I’ll be in touch, count on it! Here’s a picture of our common ancestors, Lazarus Estes (1845-1919) and Elizabeth Vannoy (1846-1918).

I continued clicking. It has now taken on an addictive quality and I’m only through about 5. Oops, I’ve hit my first “private” tree. How disappointing. I wish Ancestry had done the common surname analysis so I know whether or not to bother attempting to contact this person.

You can see, above, that Ancestry compares the charts of the two people who match and shows you the shared surnames, in this case, the very common Miller and Moore. You can then click and go to that surname on the person’s pedigree chart, or you can simply scan down the chart, displayed to the right through 10 generations. This is a very nice feature.

I finished a quick look at my nineteen 4th cousins. Of those nineteen, there are three where I can clearly identify our common ancestor, and there are two or three more that with some genealogy digging, we might well be able to connect the dots. One of those is a dead end brick wall line for me, so I’m hopeful. More than half show no common surnames.

More than ever, now I really desperately need more information and the raw data to continue with my ancestor matching project. While the Ancestry match information is a tantalizing teaser, that’s all it is. They don’t show how or where you match, how much, segment size or number of SNPs, the chromosome(s), start and stop locations, nor the raw data, of course. No chromosome matching or mapping like at both Family Tree DNA and at 23andMe. How frustrating. It’s like showing you the tip of the iceberg and refusing to provide you with the rest, although you know full well it’s there and available, because other testing companies using the same test platform provide this information. This is SO FRUSTRATING!

In essence, we have the shiny user interface (complete with erroneous population data), and the surface matching information, but no substance. Nothing under the hood. Knowing there is information there that I need and can’t have is worse than not knowing at all.

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Doug McDonald on Biogeograpical Analysis

Posted on September 9, 2012 by Roberta Estes

Dr. Doug McDonald developed what is known at BGA software, meaning Biogeographical Analysis, before either 23andMe or Family Tree DNA offered their products. In fact, Doug contracted with Family Tree DNA to write the underlying code for their Population Finder ethnicity software.

I have worked with Doug for years on several projects. He has always been very gracious with his time and resources in the genetic genealogy community, for which I am always grateful.

There has been a lot of discussion about the meaning of various descriptions of ethnicity, specifically, Orkney and Middle Eastern, in the Family Finder results. I asked Doug about this and his reply is below.

“The Family Tree DNA population database was generated before an English comparison panel became available. Hence, Orcadian had to be used. Irish is quite different from English or Orcadian.

So, to fit typical English, something more southern and eastern has to be mixed in. However, the proportion is usually fairly small, unless French fits well, which it frequently does not. Thus the program chooses some place in Eastern Europe or the Mideast, or, rarely, Pakistan or India. There is nothing “wrong” with this genetically. There is, however, something “wrong” genealogically on a genealogical time scale. Pop Finder was designed to do as well as possible on a recent time scale. That it does, but this leads to seeing, sometimes, these “strange” results.

The problem is that the people using these results from FTDNA and Ancestry are genetic genealogists and not population geneticists and at the genealogical level it seems that many people are taking their results far too literally so I was really trying to caution against this approach. If people see that they have this Middle Eastern percentage they are sometimes trying to find explanations in their recent ancestry. They think that the Middle Eastern component might represent Jewish ancestry, Native American ancestry, Moorish ancestry, etc, whereas in reality this is mostly not the case at all, if the rest is Orcadian/Irish.

Mideast won’t represent American! But it does mean something! There are several possibilities.

1) If a person is shown as mostly Orcadian and just a few percent Mideast, the Mideast probably means that they are, as mentioned above, on average from a few percent of the way from the Orknies to the Mideast. If the Mideast percentage is getting up to 15% or more then one must start considering that the Mideast is real and recent.

2) If a person is listed as mostly from somewhere in France or Spain, then the first thought for Mideast is that it is real. Small bits of African listed make it likely that there is North African.

3) People from far southern Italy (Calabria), Sicily, Malta, Greece, etc. should expect large amounts of Mideast listed along with Spanish/Italian/Tuscan. Part or all of the Mideast in these cases is usually listed as Jewish, for two reasons: these people derive from the same ancestral populations as the Jews, and large numbers of Jews moved to Sicily after the Inquisition.

Also …

4) Native American is listed as just that. It is quite uncommon for it to be listed in error … except for genuine people from Siberia and Saami. FTDNA does not mistakenly show American as Asian. “Mayan” is the usual listing for any Native American north of Panama, through all of Mexico, and east of the Rockies in the USA and Canada.

5) South Asian also sometimes appears in otherwise near-pure Europeans for the same reason as Mideastern.

6) People who are highly mixed on a continental level are generally fairly accurately represented. However, FTDNA does have a fairly high threshold for listing small components, like Native American in Europeans or Afro-(European)Americans.

For the genetic genealogist, a single “canned” report like provided by FTDNA can provide valuable clues on a continental level. For a clearer picture on a detailed level, people need more analysis from third party tests on their raw files. There are several ones out there, of varying nature.

The best place to start other than my own reports are those from Dienekes Pontikos, such as “DIYDodecad” and “Dodecad Oracle” which “cover the field” and are very accurate. Some of these are somewhat user unfriendly, however, because they require you to load programs on your computer and run them.

People often suggest that data on more populations will help with the “Mideast in Europe” problem. It would, but only for people who are of one, unadmixed, present-day European population. Otherwise it will just muddy the waters.”

I want to thank Doug for his explanation. Doug’s analysis is complementary, but you’ll need to contact him at mcdonald@scs.uiuc.edu and send your raw autosomal data files.

I noticed that at www.gedmatch.com, John Olson offers an admix page where he has included several different software tools to evaluate admixture, including five versions of Dodecad. This eliminates the need to install software on your computer. However, you do need to upload your raw autosomal data files to GedMatch in order to be able use his utilities. You can see instructions for uploading your file from either Family Tree DNA or 23andMe on the home page.

GedMatch is free, but donations are always welcome and needed. GedMatch really is a very useful tool in many ways. You can see by the commentary on their main page that they are experiencing significant issues to to high usage and desperately need a new server. You can scroll to the bottom of the main GedMatch page to donate. I just did!

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It’s Not Junk Afterall!

Posted on September 6, 2012 by Roberta Estes

You know, I hate it when people label things they don’t understand. In this case, the pieces of our genetic code that weren’t understood were labeled “junk DNA” or were referred to as “dark matter.” I’ve always disliked this immensely, because I did not for one minute believe it was junk, just because we didn’t yet understand what it did.

I personally always thought part of that junk DNA had been created especially for genealogists, and that all we had to do was to figure out how to unravel it:) At least that’s what I tell people in my presentations.

Finally, today, validation. Scientists have discovered more about our DNA, and our junk DNA isn’t junk. Eighty percent of it has a purpose as gene switches. How about that! Us genealogists knew all along that it wasn’t junk.

Take look at this very interesting article in the New York Times.

Here are the first six papers from the ENCODE project. In addition, 24 more papers are being published in Genome Research and Genome Biology. Six review articles are on the way in The Journal of Biological Chemistry and Science is publishing an article as well.

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Matches – Family (IBD) vs Population (IBS)

Posted on September 3, 2012 by Roberta Estes

Recently, I received the following query from one of our blog followers.

“Family Finder matches are based on autosomal DNA inherited from both male and female sides of the family. The FAQ indicates that we may share some autosomal DNA with cousins beyond genealogical times “as remote as 20^th cousins.” Population Finder ethnic admixture percentages are also based on autosomal DNA, but cover a range of 100 to 2000 years (up to 80 generations), according to the Population Finder FAQ. Why does the ethnic admixture calculation extend over a longer period than the Family Finder matches, since both are based on (the same?) autosomal DNA?”

This is a great question. Let’s look at autosomal DNA and how DNA works, and we’ll soon see why genealogical and anthropological (ethnic admixture) DNA overlap. And by the way, kudos for reading the FAQ!

In each generation, the child receives half of their DNA from Mom and half from Dad. As you look back in time, you can see the inheritance percentages, approximately, in the table below. Why do I say approximate? Because when the DNA of Grandma and Grandpa that Mom (or Dad) carries is being selected to be passed on to the child, there may be a little more or less of Grandma or Grandpa’s so while the child does receive exactly 50% from Mom and Dad, they don’t receive exactly 25% from each grandparent. It could be 60-40 or even just 49-51. It’s here that things begin to get complicated.

Generation	Percent of DNA carried by the current Generation
Parents	50%
Grandparents	Approximately 25%
Great-grandparents	Approximately 12.5%
GG-grandparents	Approximately 6.25%
GGG-Grandparents	Approximately 3.125%
GGGG-Grandparents	Approximately 1.5625%
GGGG-Grandparents	Approximately 0.7813%

You can see that in just 7 generations, we are below the threshold of 1%. This is why Family Tree DNA says that their ethnicity prediction is reliable through about the 5^th or 6^th generation. Beyond that, you’re at less than 1% of any one GGGG-grandparent.

Over time, the DNA from any specific ancestor, especially one from 20 generations ago is likely to “wash out”, meaning that in the next generation, the child is less and less likely to receive anything from that ancestor, and what they do receive would be in increasingly small pieces. However, that’s not always true, because we clearly do inherit our DNA from someone.

So let’s look at an example using the Family Finder Chromosome Browser from Family Tree DNA which allows you to compare the inherited pieces of DNA of multiple people.

The graphic above shows the comparison of my mother to me, shown in orange, and then to a Miller cousin, shown in blue. My mother and I share half of all of our DNA, so my orange matches her on every chromosome.

My mother and the Miller cousin, shown in blue, share a great grandparent, John David Miller. So both the Miller cousin and my mother could expect to inherit approximately 12.5% of their DNA from that Miller great-grandparent. While they wouldn’t inherit exactly the same DNA from that Miller grandparent, they would very likely inherit some of the same DNA from John David Miller. In fact, they could expect to inherit approximately 3.12% of the same DNA from him.

Looking at chromosome 5, for example, you can see that Mom and her Miller cousin share a total length of 62.18 cM (centimorgans, a unit for measuring genetic linkage, the distance between chromosome positions).

If you look at my comparison, below, with Mom and the Miller cousin, again, shown in blue, you can see that I inherited 33.13 cM of the same DNA, slightly more than half (53%) of the Miller DNA that Mom shares with her cousin.

You can also choose to view this data in a table.

Mom’s table, above, shows that the length of 62.18 cM is comprised of 14,024 individuals SNPs. For me, the same table, below, shows that my inheritance on chromosome 5 is really in 2 separate segments. The 33.13 segment contains 8100 SNPs, so more than half of the number (57%) my Mom’s carries. A second segment of 2.14 cM carries 500 SNPs for total Miller inheritage on chromosome 5 of 8600 SNPs (61%) . Why didn’t the second segment show up on the Chromosome Browser? Because I have the threshold set at 5cM, the default. In the card shuffle between Mom and Dad that decided which SNPs I received, a little segment of Mom’s other parent’s DNA got inserted in the Miller segment, so the Miller segment was no longer intact, but pieces of it are still there and one piece is large.

You can change the cM threshold, but for people who are not known to be family, 5cM is a reasonable threshold to differentiate between identical by state, IBS which means happenstance or a common root population, and identical by descent, IBD, because you share a common ancestor in a genealogical timeframe.

This Miller comparison is a good example of how SNPs are inherited and shows that while approximately 50% of the DNA from each of your ancestors gets inherited in every generation, it’s never really exactly 50%, either in length or in the number of SNPs inherited. It also shows how larger blocks of DNA are broken into smaller segments in each generation and how chunks move from being IBD to IBS over time and mutiple inheritances.

SNPs, or single nucleotide polymorphisms, are the basic unit of inheritance. We look at 4 nucleotides to determine the condition, or state of that SNP. Sometimes SNPs repeat, are in essence strung together, and these are the STRs, short tandem repeats, we are so familiar with in the Y chromosome in genetic genealogy. These are our markers and the marker values are the number of repeats at marker location 390, for example.

Most of the time, we’re just looking at one SNP location and the nucleotide held at that location. The magic of course, is when there are many of these nucleotides that are found in common as a group. A large grouping indicates a common ancestor, like we’ve seen above.

However, for population genetics, the individual nucleotides and groupings of smaller segments are very important, because just like large blocks indicate families and common genealogical ancestry, smaller blocks indicate common populations. This is how population geneticists identify populations, and how tools like Population Finder identify specific populations from which we descend. Populations, however, blend, so this is rarely cut and dried, but occasionally, it is.

The Duffy-Null allele is a great example. The Duffy Null allele is found only in African populations, and is therefore an important informative marker to determine African heritage. Currently this marker is found in about 68% of American blacks and in 88-100% of African blacks. If you have the Duffy Null allele, you have African heritage. Of course, you don’t know which line or which ancestor it came from, but it assures you that you do in fact have African Heritage This is one of the factors considered when determining percentage of ethnicity.

The relevance of the Duffy Null allele is determined by the number of other “African” markers that appear in high quantity. If there are few other African markers, then African ancestry was likely further back in time. If there are many, then African ancestry was likely more recent. These statistical calculations are how the importance of autosomal markers is determined and how percentages or estimates of ethnicity are calculated.

Most of the time, SNPs and clusters of SNPs aren’t this specific and are found in many populations in varying frequencies. It’s learning how to put this puzzle together, or rather, tease it apart, that keeps population geneticists busy.

What all of this really means is that genealogical relatedness and population relatedness aren’t really two different things, but two different ends of a continuum where genealogical relatedness is evident by a high number of cMs and contiguous SNPs that match. We saw that in the Miller example.

We know that if two people only show matches if you adjust the threshold to 1cM, for example, they are likely IBS, or only related via a population or region of the world.

However, it’s the grey area inbetween that becomes confusing. For example, trying to determine whether someone who might be a cousin really is, or not, based on very small matching DNA segments. For situations such as these, the best answer is to test more cousins to see if they may have inherited differently. I guess that’s both the bad news and the good news in autosomal genetic genealogy, there’s always hope (and clarity) if you just test more people!!!

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