The Autosomal Me – Testing Company Results

Posted on February 24, 2013 by Roberta Estes

This is Part 4 of a multi-part series, The Autosomal Me.

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 2 gave an example of the power of fragmented chromosomal mapping and the raw beauty of the results. Part 3, “The Autosomal Me – Who Am I?,” discussed how to use our pedigree charts to gauge expected results and how autosomal results are grouped into population buckets. We also named this technique, Minority Admixture Mapping, or MAP for short.

In this segment, Part 4, let’s take a look at what the testing company autosomal results look like. The results are presented in timeline order, with the oldest results first and the latest, and presumably most accurate results, last.

23andMe Version 1

23andMe was the first company to offer this type of testing affordably. They initially only offered 3 population groups, and one inferred that Asian was actually Native American. Of course, that wasn’t a valid assumption for everyone, but it was the best that could be done under the circumstances. This was my ethnicity results display at 23andMe until December 2012 went their updated version was released.

DeCode Genetics

DeCode Genetics initially offered autosomal tests for ancestry. Unfortunately, under the pressure of financial issues, they stepped away from the genetic genealogy marketspace and have since been sold.

Their test showed the following ethnic breakdown, picking up both my Native and African heritage:

I particularly like these results because the X chromosome is included, and seeing Native on the X chromosome, which has a unique inheritance path is a very important piece of data.

Family Tree DNA Version 1

Family Tree DNA’s first version of their Family Finder product produced results stating that I am 100% European, split between western and northern, shown below (minus the map.)

Dr. Doug McDonald

Doug McDonald, a retired physical chemistry professor, compiles contributed raw data and compares the raw data locations with both reference populations and the contributor results. This is not a commercial endeavor but a private research project which has been ongoing for years. His analysis of my raw data results from 23andMe and Family Tree DNA showed that they are primarily European. His first analysis was without Middle Eastern populations and the results showed European except for a total of about 3% East Asian, Oceana and American. However, in a second run including the Pakistan and Middle Eastern populations, the results now showed 88% European, about 1% Oceanic and American and the balance Middle Eastern and Pakistani.

A small amount of Middle Eastern heritage is not unexpected since I do have confirmed Turkish ancestors.

Dr. McDonald indicated that this was slightly more, 1-2%, than most Europeans, and that I was generally planted firmly in the middle of the “English” area in his data. His results showed no African.

Standard deviation (statistical noise) is about 1%. He can achieve these low deviation numbers by using such a large number of markers (536,904 to be exact)[1] for his comparison. I am grateful to Dr. McDonald for his contribution, not only to me, but to this field.

The graph below shows that my primary ancestry falls in the English/French region.

The second graph maps these results on my chromosomes. The American, bright green, is found on chromosomes 1 and 2, and the X chromosome shows South Asian.

Doug indicates that the Native American is found at about the .5% level. Interestingly, on my mother’s graphs and charts (below), the Native segments are nearly identical, but my first grey South Asian segment on my X is Mideast on her chart.

It’s also interesting to note that my Native American on chromosome 2 is larger than my mother’s which may well reflect Native heritage on my father’s side. Ironically, the oral history of Native ancestry was on my father’s side, not my mothers.

Doug’s analysis has been updated several times over the years and these results are the most current. The vendors have made upgrades too. In 2012, both 23andMe and Family Tree DNA underwent upgrades to their ethnicity software and the Genographic Project version 2.0 test was released.

23andMe 2012 Updated Version

The new 23andMe software offers different confidence levels.

The standard estimate, or confidence level, shows that I have about .5% Native American. This is consistent with Dr. McDonald’s findings.

A second view is available which paints the chromosomes. A split view is also available if one of your parents has been tested at 23andMe as well. That is not an option for me.

The conservative estimate, below, shows less Native at .2%.

The speculative level below shows the Native back to .5% but adjusts the European regions significantly.

Although 23andMe does not provide participants with the start and stop locations, through alternative means, meaning a very smart friend, Rebekah Canada, who is a Java programmer, start and stop locations can be discerned.

CeCe Moore documented Rebekah’s technique for those who will be following along with their own results through this process.

In a future segment of this series, we’ll look at alternative ways to discern Native segments. Thanks to Rebekah’s technique, I can tell you that 23andMe shows my Native segments as follows:

Chromosome 1 – 165,658,091 to 175,711,116

Chromosome 2 – 86,316,174 to103,145,426

23andMe also provides a Neanderthal percentage. What fun!!!

Family Tree DNA Updated 2012 Version

My mother was deceased before chip based autosomal testing was available, but I ordered the Family Finder test for her as soon as it was available. Thankfully her DNA was stored at Family Tree DNA and was still viable.

Mother’s original results are shown above and her most recent results are shown below. Her results shifted within Europe and her margin of error doubled.

My current results from Family Tree DNA’s updated software are shown below.

National Geographic Genographic 2.0

I was very surprised to see my National Geographic results. They were very unexpected, in particular the high percentages of Mediterranean and Southwest Asian, totaling 54%.

It made more sense when I read the information. It’s true, reading is fundamental.

These results are, in essence, more anthropological in nature.

Of course, one of the fun parts of the Genographic results are the Neanderthal and Denisovan percentages.

These are somewhat different than the 23andMe results, although if you add the Neanderthal and Denisovan values together, the resultant 2.2% is very close to 23andMe’s 2.5%.

Ancestry.com

In 2012, Ancestry introduced an autosomal DNA test as well. What it provides is very limited, with limited tools, but it does provide percentages of ethnicity in addition to matches. Recently, Ancestry announced that the percentages may change over time. They have been severely beaten within the genetic genealogy community for quality issues with this product, including percentages of ethnicity that are highly erroneous. Their stated time reference is 500 years ago.

Recently this new page was added before you can see your detailed results.

Ancestry shows my heritage as only British and Scandinavian.

Ironically, Ancestry has mapped the birth locations of my ancestors in Europe on the map above, based on my family tree submitted. Interesting that Germany doesn’t show in Ancestry’s ethnicity list but many of my family lines originated in Germany and Holland, and none in Scandinavia.

Testing Provider Summary

Where do we stand now?

A summary of the various test results is shown below compared to my pedigree analysis.

Test Results Chart

I have included Dr. McDonald’s analysis here, not because he’s a testing provider in the sense of the testing companies, but because his offering was available in this timeframe, and because he worked with Family Tree DNA to develop their Population Finder code.

You can see that the results are relatively consistent between testing companies. There is certainly no question about majority ancestry, but the minority admixture which hovers someplace near 1%, give or take 5% in either direction, is much less consistent and not always reported. If I were to have tested with only one company and taken the results as gospel, I could certainly have been left believing that I had no Native or African admixture. For many people, it’s this small amount of minority admixture that they are seeking. So in answer to the question of which testing company is “best,” the answer is, if you’re looking for trace amounts of anything, the compendium of all the testing companies (minus Ancestry) would provide the best set of results. We will be using the match information as well in the next sections, so certainly nothing has been “wasted” testing with multiple companies, again, except Ancestry. I am hopeful that Ancestry will in the future release our raw data (which they have promised to do) in a useable format, fix their misleading ethnicity results and add chromosome painting tools so that we can fully utilize our data.

In Part 5 of the series, we’ll take a look at third party tools and how they can continue to refine and add to our knowledge of our admixture.

1. Genealogy-DNA Rootsweb posting by Doug McDonald on 7-26-09 and personal correspondence.

2. 71.5% western European, 28.4% Northeastern European

3. Inferred that Asian is actually Native in an American with no history of Asian ancestry.

4. No category, inferred.

5. 78.6% Northern European, 1.8% Southern European, 18.7% Nonspecific European

6. 54.6% Northern European, .3% Southern European, 43% Nonspecific European

7. 91.7% Northern European, 3% Southern European, 3.3% Nonspecific European

8. 75.18% West Europe (French and Orcadian), 24.82 Europe (Romanian, Russian, Tuscan and Finnish). Note that my mother’s results are almost identical except the Finnish is missing from hers.

9. 43% North Europe and 36% Mediterranean

10. 80% British, 12% Scandinavian

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Thick Hair, Small Boobs, Shovel Shaped Teeth and More

Posted on February 17, 2013 by Roberta Estes

Yep, there’s a gene for these traits, and more. The same gene, named EDAR (short for Ectodysplasin receptor EDARV370A), it turns out, also confers more sweat glands and distinctive teeth and is found in the majority of East Asian people.

This is one of the results of the National Geographic’s Genographic project. This mutation found at location rs3827760 on chromosome 2 occurred about 35,000 years ago. It apparently has conferred some advantage to its carriers, because it is found in the majority of Asian people today. We don’t exactly know why that happened, but maybe ancient male Asians preferred thick haired, small boobed and sweaty women. Or maybe those women survived when women with more body fat (yes, boobs are fat, sorry guys) and who could sweat less perished.

This New York Times article discusses the experiments performed to verify that this gene in fact does confer those traits. The scientific article itself is available in the journal, Cell although it’s behind a paywall.

Want to know if you carry this trait? If you’ve tested with either Family Tree DNA or 23andMe, you’re in luck.

Download your raw results file and open the file using any tool. Generally, a spreadsheet or Notepad will be your preferred methods. Then using the search function of the tool you’ve selected (ctl+f for Notepad or Excel’s find function) search for rs3827760. You will see two letters comprised of either T, A, C or G. If you have a G shown for either letter at this location, then you carry this particular mutation.

If you carry this mutation, you’ve probably already headed for the mirror. You’ll know already if you have small breasts, if you’re a female, believe me. You may never have thought about thick hair shafts, which isn’t to be confused with lots of hair. And your level of sweatiness is just what it is. I’ve never even considered that there were different sweatiness levels. But what about Asian teeth? Well, that trait is called sinodonty and here’s a nice wiki article and another nice article, with examples, here. If your teeth are shovel shaped, meaning the backs of your upper 4 teeth are shaped like a spoon as opposed to straight, then you have this trait.

So are you wondering what this might have to do with genetic genealogy? Well, if you carry this gene, then you obtained it from some Asian ancestor. If you’re in America and not of Asian ancestry, then there are pretty much only two routes. One would be Native American ancestry and the second would be the population or invasion of Europe by Asian groups, such as the Mongol Hordes and the Huns. Your genealogy will have to be your guide as to which source contributed this gene to your ancestors, and ultimately to you.

Oh yes, and one last thing, this mutation isn’t the only one involved in at least some of these traits, specifically the teeth. I don’t carry the G and I do have some of the Asian teeth characteristics. I don’t have thick hair shafts which makes sense since EDAR is primarily associated with this trait. And, well, I’m just not discussing the boobs and sweaty traits (and my husband is utterly forbidden to comment)…..TMI:)

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The Autosomal Me – Who Am I?

Posted on February 13, 2013 by Roberta Estes

This is Part 3 of a multi-part series.

This series focuses on answering the questions of identity through autosomal testing, in particular, for minority ancestry. By minority, I mean any small, elusive amount of any type of ancestry you are seeking to discover in your heritage. In my case, that’s both Native American and African.

This segment, Part 3, focuses on using pedigree charts to gauge expected results, how autosomal ethnic groups are determined and how fragmented minority admixture mapping is different from other techniques. This leads us into Part 4 which shows the various results from different testing companies and how they differ.

Part 5 features third party analysis tools and Part 6 begins the analyses of the data that parts 3, 4 and 5 provide.

Let’s hope that with all of this information, we can answer at least part of the question: Who am I? Who am I really?

A lot of who I am has to do with who my ancestors were, where they lived, what they did, choices they made. Did they fight in the American or French Revolution? On which side? Were they Native? Were they African? Were they slaves? So, who were they?

One of the reasons I began with genetic genealogy more than a decade ago was to confirm or disprove the persistent family history of Native American heritage that I had been unable to resolve using only traditional genealogy tools. I have made inroads with that, in unexpected ways and places, because of and in addition to genetic genealogy. Genetic genealogy and traditional genealogy go hand in hand.

It’s difficult tracking down each line to perform mitochondrial or Yline DNA tests. Sometimes, it’s beyond difficult and it’s impossible. Lines die out, people refuse to test or you simply can’t find the right people. We need other tools.

Enter autosomal genetics. From the beginning, early in genetic genealogy, we had the CODIS type forensic and paternity type tests. I reviewed the results of those early tests relative to my pedigree chart in a paper I wrote, Revealing American Indian and Minority Heritage Using Y-line, Mitochondrial, Autosomal and X Chromosomal Testing Data Combined with Pedigree Analysis published in JoGG in the Fall 2010 Issue. We’ve come a long way since then.

In that article, I dissected my pedigree chart to determine how much of different types of ancestry I carried and how that compared with the testing that had been performed at that time.

Using the end of line ancestors pedigree analysis method described in the paper, which determines the percentage of ethnicity that each end-of-line ancestor contributed to me, my origins totals were as follows:

Geographic Origin Chart

(1) The ethnic heritage of several lines could probably be inferred by surname or ethnicity of marriage partner. However, I have avoided the temptation to make inferences within the United States, as the Native or African ancestry may well lie with one of these ancestors. These are in fact the perfect candidates and to eliminate them from consideration by inferring origins would be a disservice.

In broader categories, and combining those that are similar, we find:

This is a useful exercize, not just for minority admixture, but to help evaluate the results you receive from the various testing companies. For example, you might notice that there is no Scandinavian showing in my pedigree chart, which makes Ancestry’s 80% British and 12% Scandinavian suspect right off the bat. It also makes results as high as 25% Native American reported in one of the earlier tests impossible. This pedigree analysis tool helps you understand what is reasonable to expect in terms of ethnicity breakdown.

Now that we know what the majority ancestry looks like and any minority ancestry that we are aware of, let’s take a look at the various types of autosomal testing available.

Tests and Population Markers

In the paper, I reviewed the older results from companies using either CODIS or proprietary markers. These low resolution tests are out of date now (although many are still being sold) and have been replaced by the much more thorough wide spectrum tests using chip based technology, allowing hundreds of thousands of DNA locations to be tested and evaluated. Of course, the word evaluated is the loose cannon in that sentence, because the quality of the evaluation is key here. And the evaluation is dependent upon accurate and widespread data bases to compare DNA results against to determine which populations have higher and lower frequencies of specific alleles (markers) occurring in their populations.

For example, let’s compare a population in Siberia that shows 100% of a specific marker value, let’s say a value of 10 at marker location ZZZ. Now let’s compare that result to a population from Africa at that same marker location, but with a value never found in Siberia, let’s say a value of 7. Each of thousands of markers are evaluated this way, creating patterns. Now, you have a tester who doesn’t know where their ancestors are from, whose results at marker location ZZZ have a value of 10. Would you say they are more likely to have ancestry in Siberia or Africa?

This participant’s marker results for ZZZ go in the “very strongly Siberia” bucket. Of course, other markers they carry might indicate Africa, or Europe, or elsewhere, because we are a Heinz 57 mix of all of our ancestors. But this is, in essence, how our ethnicity is determined by autosomal DNA testing. Needless to say, you can be a lot more accurate with thousands of markers than with the 15 or 21 CODIS markers, or even the 300+ in some of the proprietary tests.

BGA Testing

Using autosomal results to determine ethnicity is called BGA testing, or Biogeographical Ancestry testing. It has been used for years to determine percentages of ethnicity. So, how is what I’m doing different and what makes it unique and new to genetic genealogy?

1. Traditional BGA testing deals in percentages of ethnicity, meaning generally 1% or more. Small amounts are difficult to track in the best of circumstances. When dealing with small amounts of admixture, not all tests will be able to identify the minority ethnicity in question. We’re using these tests, plus additional BGA chromosomal painting tools combined with some spreadsheet comparison techniques to cross that 1% threshold.

2. The prevailing winds in this industry have been that anything smaller than 1% was undetectable, and that any amount of admixture less than 7cM, 5cM or 3.5cM (depending on the source) was usless. While this is relatively accurate (but not always) when determining a genealogical relationship within the past few generations, it’s not true when looking beyond the accepted 6 to 7 generation threshold where the 1% ethnicity issue comes into play. At that point, we know we can’t identify the minority ancestor genealogically, so we have to identify them by their membership in a minority population group. I am using a variety of tools and techniques to reach across that threshold.

3. Instead of using these various tools to try to establish a genealogical relationship with another tester (such as we share a common great-grandfather), I am using these tools to attempt to identify which line or lines carry minority admixture. If you already know who in your family tree contributes that admixture, you don’t need this technique. If you are looking to confirm minority admixture below 1%, searching for the minority admixture contributing line, or trying to figure out which of your known ancestors contributed minority admixture, then this technique is for you.

Typically these tools have been used to track segments from known ancestors, like a Jewish grandmother, for example. These segments are large and evident. That’s not the case with small amounts of minority admixture. Using several BGA tools together helps to eliminate the possibility of one tool picking up on these small segments and another one missing it. We are bringing all of the resources from various camps together to bear on the situation. This is the ultimate form of recycling, using the shreds that were left on the cutting room floor and deemed to be usless when in actuality, they are diamonds in the rough. We’re reassembling them and looking at them from a different perspective. It’s a new kind of quilting!

A New Name

As I’ve worked through this process, it seems that Minority Admixture Mapping best suits what we are doing, so MAP it is. It makes sense and you can say it.

I still want to know who I am, so in Part 4, we begin our data analysis by looking at the autosomal ethnicity results of the various testing companies and how they compare.

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The Autosomal Me – The Ancestors Speak

Posted on February 10, 2013 by Roberta Estes

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

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

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

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

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

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

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

Enter chromosome painting.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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The Autosomal Me – Unraveling Minority Admixture

Posted on February 6, 2013 by Roberta Estes

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

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

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

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

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

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

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

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

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

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

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

Let me give a very short example here.

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

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

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

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

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

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

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

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

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King Richard, Is That You???

Posted on February 4, 2013 by Roberta Estes

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

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

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

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

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

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

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

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Projects, Administrators and Expectations

Posted on February 2, 2013 by Roberta Estes

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

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

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

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

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

Projects

There are four types of projects at Family Tree DNA.

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

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

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

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

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

Family Finder

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Administrators Are Different People

Ok, stop laughting!

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Picking the Right Project

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

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

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

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

Administrators

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

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

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

A good project administrator:

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

Sounds kind of like the scouts doesn’t it?

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

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

Project admins cannot:

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

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

Project Members

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

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

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

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

Our Fireside Chat

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

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