Demystifying Autosomal DNA Matching

Posted on January 17, 2015 by Roberta Estes

What, exactly, is an autosomal DNA match?

Answer: It’s Relative

I’m sorry, I just had to say that.

But truthfully, it is.

I know this sounds like a very basic question, and it is, but the answer sometimes isn’t as straightforward as we would like for it to be.

Plus, there are differences in quality of matches and types of matches. If you want to sigh right about now, it’s OK.

We’ve talked a lot about matching in various recent articles. I have several people who follow this blog religiously, and who would rather read this than, say, do dishes (who wouldn’t). One of our regulars recently asked me the question, “what, exactly, is a match and how do I tell?”

Darned good question and I wish someone had explained this to me so I wouldn’t have had to figure it out.

In the computer industry, where I spent many years, we have what we call flow charts or wernier diagrams which in essence are logic paths that lead to specific results or outcomes depending on the answers at different junctions.

I had a really hard time deciding whether to use the beer decision-making flow chart or the procrastinator flow chart, but the procrastinator flow chart was just one big endless loop, so I decided on the beer.

What I’m going to do is to step you through the logic path of finding and evaluating a match, determining whether it’s valid, identical by descent or chance, when possible, and how to work with your matches and what they mean.

Let me also say that while I use and prefer Family Tree DNA, these matching techniques are universal and apply to results from 23andMe as well, but not for Ancestry who gives you no browser or tools to compare your DNA to anyone else. So, you can’t compare your results at Ancestry.

Comparing DNA results is the lynchpin of genetic genealogy. You’re dead in the water without it. If you have tested at Ancestry, you can always transfer your results to Family Tree DNA, where you do have tools, and to GedMatch as well. You’re always better, in terms of genealogy, to fish in as many ponds as possible.

Before we talk about how to work with matches, for those who need to figure out how to find matches at Family Tree DNA and 23andMe, I wrote about that in the Chromosome Browser War article. This article focuses on working with matching DNA after you have found that you are a match to someone – and what those matches might mean.

Matching Thresholds

All autosomal DNA vendors have matching thresholds. People who meet or exceed those thresholds will be shown on your match list. People who do not meet the initial threshold will not be considered as a match to you, and therefore will not be on your match list.

Currently, at Family Tree DNA, their match threshold to be shown as a match is about 20cM of total matching DNA and a single segment of about 7.7cM with 500 SNPs or over. The words “about” are in there because there is some fuzziness in the rules based on certain situations.

After you meet that criteria and you are shown as a match to an individual, when you download your matching data, your matches to them on each chromosome will be shown to the 1cM and 500 SNP level

At 23andMe, the threshold is 7cMs/700 SNPs for the first segment. However, 23andMe has an upper limit of people who can match you at about 1000 matches. This can be increased by the number of people you are communicating or sharing with. However, your smallest matches will be dropped from your list when you hit your threshold. This means that it’s very likely that at least some of your matches are not showing if you have in excess of 1000 matches total. This means that your personal effective cM/SNP match threshold at 23andMe may be much higher.

Step 1 – Downloading Your Matching Segments

For this comparison, I’m starting with two fresh files from Family Tree DNA, one file of my own matches and one of my mother’s matches. My mother died before autosomal DNA testing was available, so her results are only at Family Tree DNA (and now downloaded to GedMatch,) because her DNA was archived there. Thank you Family Tree DNA, 100,000 times thank you!!!

At Family Tree DNA, the option to download all matches with segment information is on the chromosome browser tab, at the top, at the right, shown below.

If you have your parents DNA available to test and it hasn’t been tested, order a kit for them today. If either or both parents have been tested, download their results into the same spreadsheet with yours and color code them in a way you will understand.

In my case, I only have my mother’s results, and I color coded my matches pink, because I’m the daughter. However, if I had both parents, I might have colored coded Mother pink and Dad blue.

Whatever color coding you do, it’s forever in your master spreadsheet, so make a note of what it is. In my case, it’s part of the match column header. Why is it in my column header? Because I screwed up once and reversed them in a download.

Step 2 – Preparing and Sorting Your Spreadsheet

In my master DNA spreadsheet, I have the following columns,

The green cell matches are matches to me from 23andMe. My cousin, Cheryl also tested at 23andMe before autosomal testing was offered at Family Tree DNA.

The Source column, in my spreadsheet, means any source other than FTDNA. The Ignore column is an extraneous number generated at one time by downloads. I could delete that column now.

The “Side” column is which side the match is from, Mom or Dad. Mom’s I can identify easily, because I have her DNA to compare to. I don’t identify a match as Dad’s without having identified an ancestral line, because I don’t have his DNA to compare to.

And no, you can’t just assume that if it doesn’t match Mom, it’s an automatic match to Dad because you may have some IBS, identical by chance, matches.

The Common Ancestors/Comments column is just that. I include things like when I e-mailed someone, if the match is triangulated and if so, with whom, etc.

In my master spreadsheet, the first “name” column (of who tested) is deleted, but I’ve left it in the working spreadsheet (below) with my mother for illustration purposes. That way, neither of us has to remember who is pink!

Step 3 – Reviewing IBD and IBS Guidelines

If you need a refresher on, phasing, IBD, identical by descent, IBS which can mean either identical by chance or identical by population, it would be a good time to read or reread the article titled How Phasing Works and Determining IBD Versus IBS Matches.

Let’s briefly review the IBD vs IBS guidelines, because we’ll be applying them in this article.

Identical by Chance – Can be determined if an individual you match does not match to one of your parents, if parents are available. If parents are not available for matching, IBS by chance segments won’t triangulate with other known genealogical matches on a common segment.

Identical by Descent – Can be suggested if a common ancestor (or ancestral line) can be determined between any two people who are not known relatives. If the two people are known close relatives, and their DNA matches, identical by descent is proven. IBD can be proven with previously unknown family or genealogical matches when any three people descending from that same ancestor or ancestral line all match each other on the same segment of DNA. Three way matching is called triangulation.

Identical by Population – Can be determined when multiple people triangulate with you on a specific segment of DNA, but the triangulated groups are from proven different lineages and are not otherwise related. This is generally found in smaller segments from similar regions of the world. Identical by population is identical by descent, but the ancestors are so far back in time that they cannot be determined and may contribute the same DNA to multiple lineages. This is particularly evident in Jewish genealogy and other endogamous groups.

Step 4 – Determining Parental Side and IBS by Chance

The first thing to do, if you have either or both parents, is to determine whether your matches phase to your parents or are IBS by chance.

In this context, phasing means determining whether a particular match is to your father’s side of the family or to your mother’s side of the family.

Remember, at every address in your DNA, you will have two valid matches to different lines, one from your mother and one from your father. The address on your DNA consists of the chromosome number which equates to the street name, and then the start and end locations, which consists of a range of addresses on that street. Think of it as the length of your property on the street.

First, let’s look at my situation with only my mother’s DNA for comparison.

It’s easy to tell one of three things.

Do mother and I both match the person? If so, that means that DNA match is from mother’s side of the family. Mark it as such. They are green, below.
If the individual does not match me and mother, both, and only matches me, then the match is either on my father’s side or it’s IBS by chance. Those matches are blue below. Because I don’t have my father’s DNA, I can’t tell any more at this step.
Notice the matches that are Mom’s but not to me. That means that I did not receive that DNA from Mom, or I received a small part, but it’s not over the lowest matching threshold at Family Tree DNA of 1cM and 500 SNPs.

In this next scenario, you can see that mother and I both match the same individual, but not on all segments. I selected this particular match between me, my mother and Alfred because it has some “problems” to work through.

The segments shown in green above are segments that Mom carries that I don’t. This means that I didn’t receive them from mother. This also means they could be matching to Alfred legitimately, or are IBS by chance. I can’t tell anything more about them at this point, so I’ve just noted what they are. I usually mark these as “mother only” in my master spreadsheet.

The first of the two green rows above show a match but it’s a little unusual. My segment is larger than my mothers. This means that one of five things has happened.

Part of this segment is a valid match. At the end, where we don’t match, the match extends IBS by chance a bit at the end, in my case, when matching Alfred. The valid match portion would end where my mother’s segment ends, at 16,100,293
There is a read error in one of the files.
The boundary locations are fuzzy, meaning vendor calculations like ‘healing’ for no calls, etc..
I also match to my father’s line.
Recombination has occurred, especially possible in an endogamous population, reconnecting identical by population segments between me and Alfred at the end of the segment where I don’t match my mother’s segment, so from 16,100,293 to 16,250,884.

Given that this is a small segment, the most likely scenario would be the first, that this is partly valid and partly IBS by chance. I just make the note by that row.

The second green segment above isn’t an exact match, but if my segment “fits within” the boundaries of my mother’s segments, then we know I inherited the entire segment from her. Once again, my boundaries are off a bit from hers, but this time it’s the beginning. The same criteria applies as in 1-5, above.

The green segments above are where I match Alfred, but my mother does not. This means that these segments are either IBS by chance or that they will match my father. I don’t know which, so I simply label them. Given that they are all small segments, they are likely IBS by chance, but we don’t know that. If we had my father’s DNA, we would be able to phase against him, too, but we don’t.

Now, if I was to leave this discussion here, you might have the impression that all small segment matches have problems, but they don’t. In fact, here’s a much more normal “rea life” situation where mother and I are both matching to our cousin, Cheryl, Mom’s first cousin. These matches include both large and small segments. Let’s take a look and see what we can tell about our matches.

Roberta and Barbara have a total of 83 DNA matches to Cheryl.

Some matches will be where Barbara matches Cheryl and Roberta doesn’t. That’s normal, Barbara is Roberta’s mother and Roberta only inherits half of Barbara’s DNA. These rows where only Barbara, the mother, matches Cheryl are not colorized in the Start, End, cM and SNP columns, so they show as white.

Some matches will be exact matches. That too is normal. In some cases, Barbara passes all of a particular segment of DNA to Roberta. These matches are colored purple.

Some of these matches are partial matches where Roberta inherited part of the segment of DNA from Barbara. These are colored green. There are two additional columns at right where the percentage of DNA that Roberta inherited from Barbara on these segments is calculated, both for cM and SNPs.

Some of the matches are where Roberta matches Cheryl and Barbara doesn’t. Cheryl is not known to be related to Roberta on her father’s side, so assuming that statement is correct, these matches would be IBS, identical by state, meaning identical by chance and can be disregarded at legitimate matches. These are colored rust. Note that most of these are small segments, but one segment is 8.8cM and 2197 SNPs. In this case, if this segment becomes important for any reason, I would be inclined to look at the raw data file of Barbara to see if there were no calls or a problem with reads in this region that would prevent an otherwise legitimate match.

Let’s look at how these matches stack up.

	Number	Percent (rounded)	Comment
Exact Matches	26	31	100% of the DNA
Barbara Only	20	24	0% of the DNA
Partial Matches	29	35	11-98% of the actual DNA matches
Roberta Only (IBS by chance)	7	8	Not a valid match

I think it’s interesting to note that while, on the average, 50% of the DNA of any segment is passed to the child, in actuality, in this example of partial inheritance, meaning the green rows, inheritance was never actually 50%. In fact, the SNP and cM percentages inherited for the same segment varied, and the actual amounts ranged from 11-98% of the DNA of the parent being inherited by the child. The average of these events was 54.57143 (cM) and 54.21429 (SNPs) however.

On top of that, in 13 (26 rows) instances, Roberta inherited all of Barbara’s DNA in that sequence, and in 20 cases, Roberta inherited none of Barbara’s DNA in that sequence.

This illustrates that while the average of something may be 50%, none of the actual individual values may be 50% and the values themselves may include the entire range of possibilities. In this case, 11-98% were the actual percentage ranges for partial matches.

Matching Both Parents

I don’t have my father’s DNA, but I’m creating this next example as if I did.

Matches to mother are marked in green.

I have two matches where I match my father, so we can attribute those to his side, which I’ve done and marked in orange.

The third group of matches to me, at the bottom, to Julio, Anna, Cindy and George don’t match either parent, so they must be IBS by chance.

I label IBS by chance segments, but I don’t delete them because if I download again, I’ll have to go through this same analysis process if I don’t leave them in my spreadsheet

Step 5 – How Much of the DNA is a Match?

One person asked, “exactly how do I tell how much DNA is matching, especially between three people.” That’s a very valid question, especially since triangulation requires matching of three people, on the same segment, proven to a common ancestral line.

Let’s look at the match of both me and my mother to Don, Cheryl and Robin.

In this example, we know that Don, Cheryl and Robin all match me on my mother’s side, because they all three match me and my mother, both on the same segment.

How do we determine that we match on the same segment?

I have sorted this spreadsheet in order of end location, then start location, then chromosome number so that the entire spreadsheet is in chromosome order, then start location, then end location.

We can see that both mother and I match Cheryl partially on this segment of chromosome 1, but not exactly. The start location is slightly different, but the end location matches exactly.

The area where we all three match, meaning me, Mom and Cheryl, begins at 176,231,846 and ends at the common endpoint of 178,453,336

On the chart below, you can see that mother and I also both match Don, Cheryl’s brother, on part of this same segment, but not all of the same segment.

The common matching areas between me, Mom and Don begins at 176,231,846 and ends at 178,453,336.

Next, let’s look at the third person, Robin.

Mom and I both match Robin on part of this same overlapping segment as well. Note that my segment extends beyond Mom’s, but that does not invalidate the portion that does match between Robin, Mom and I.

Our common match area begins at the same location, but ends at 178,453,336, the same location as the common end area with Don and Cheryl

Step 6 – What Do Matches Mean? IBD vs IBS in Action

So, let’s look at various types of matches and what they tell us.

Looking at our matching situation above, let’s apply the various IBD/IBS rules and guidelines and see what we have

1. Are these matches identical by chance? No. How do we know?

a. Because they all match both me and a parent.

2. Are these matches identical by descent? Yes. How do we know?

a. Because we all match each other on this segment, and we know the common ancestor of Cheryl, Don, Barbara and me is Hiram Ferverda and Evaline Miller. We know that Robin descends from the same ancestral Miller line.

3. Are these matches identical by population. We don’t know, but there is no reason at this point to think so. Why?

a. Because looking at my master spreadsheet, I see no evidence that these segments are also assigned to other lineages. These individuals are also triangulated on a large number of other, much larger, segments as well.

4. Are these matches triangulated, meaning they are proven to a common ancestor? Yes. How do we know?

a. Documented genealogy of Hiram Ferverda and Evaline Miller. Don, Barbara, Cheryl and me are known family since birth.
b. Documented genealogy of Robin to the same ancestral family, even though Robin was previously unknown before DNA matching.
c. Even without the documented genealogy, Robin matches a set of two triangulation groups of people documented to the same ancestral line, which means she has to descend from that same line as well.

In our case, clearly these individuals share a common ancestor and a common ancestral line. Even though these are small segments on chromosome 1, there are much larger matching segments on other chromosomes, and the same rules still apply. The difference might be at some point smaller segments are more likely to be identical by population than larger segments. Larger segments, when available, are always safer to use to draw conclusions. Larger groups of matching individuals with known common genealogy on the same segments are also the safest way to draw conclusions.

Step 7 – Matching With No Parents

Sometimes you’re just not that lucky. Let’s say both of your parents have passed and you have no DNA from them.

That immediately eliminates phasing and the identical by chance test by comparing to your parents, so you’ll have to work with your matches, including your identical by chance segments.

A second way to “phase” part of your DNA to a side of your family is by matching with known cousins or any known family member.

In the situation above, matching to Cheryl, Don and Robin, let’s remove my mother and see what we have.

In this case, I still match to both of my first cousins, once removed, Cheryl and Don. Given that Cheryl and Don are both known cousins, since forever, I don’t feel the need for triangulation proof in this case – although the three of us are triangulated to our common ancestor. In other words, the fact that my mother does match them at the expected 1^st cousin level is proof enough in and of itself if we only had one cousin to test. We know our common ancestor is Cheryl and Don’s grandparents, who are my great-grandparents, Hiram Ferverda and Evaline Miller.

When I looked at Robin’s pedigree chart and saw that Robin descended from Philip Jacob Miller and wife Magdalena, I knew that this segment was a Miller side match, not a Ferverda match.

Therefore, matching with someone whose genealogy goes beyond the common ancestor of Cheryl, Don and me proves this line through 4 more generations. In other words, this DNA segment came through the following direct line to reach Me, Mother, Cheryl and Don.

Philip Jacob Miller and Magdalena
Daniel Miller
David Miller
John David Miller
Evaline Louise Miller who married Hiram Ferverda

Clearly, we know from the earlier chart that my mother carried this DNA too, but even if we didn’t know that, she obviously had to have carried this segment or I would not carry it today.

So, even though in this example, our parents aren’t directly available for IBS testing and elimination, we can determine that anyone who matches both me and Cheryl or me and Don will have also matched mother on that segment, so we have, in essence, phased those people by triangulation, not by direct parental matching.

Step 8 – Triangulation Groups

What else does this match group tell us?

It tells us that anyone else who matches me and any one of our triangulation group on that segment also descends from the Miller descendant clan, one way or another.

Why do they have to match me AND one of the triangulation group members on that segment? Because I have two sides to my DNA, my Mom’s side and my Dad’s side. Matching me plus another person from the triangulation group proves which side the match is on – Mom’s or Dad’s.

We were able to phase to eliminate any identical by chance segments people on Mom’s side, so we know matches to both of us are valid.

On Dad’s side, there are some IBS by chance people (or segments) thrown in for good measure because I don’t have my Dad’s DNA to eliminate them out of the starting gate. Those IBS segments will have to be removed in time by not triangulating with proven triangulated groups they should triangulate with, if they were valid matches.

When you map matches on your chromosome spreadsheet, this is what you’re doing. Over time, you will be able to tell when you receive a new match by who they match and where they fall on your spreadsheet which ancestral line they descend from.

GedMatch also includes a triangulation utility. It’s a great tool, because it produces trios of people for your top 400 matches. The results are two kits that triangulate to the third person whose kit number you are matching against.

The output, below, shows you the chromosome number followed by the two kit numbers (obscured) that triangulate at this location, and then the start and end location followed by the matching cMs. The result is triangulation groups that “slide to the right.”

In the example above, all of the triangulation matches to me above the red arrow include either Mother, my Ferverda cousins or the Miller group that we discussed in the Just One Cousin article. In other words they are all related via a common ancestor.

You can tell a great deal about triangulation groups by who is, and isn’t in them using deductive reasoning. And once you’ve figured out the key to the group, you have the key to the entire group.

In this case, Mom is a member of the first triangulation group, so I know this group is from her side and not Dad’s side. Both Ferverda cousins are there, so I know it’s Mom’s Dad’s side of the family. The Miller cousins are there, so I know it’s the Miller side of Mom’s Dad’s side of the family.

Please also note that while this entire group triangulates within itself, that the group manages to slide right and the first triangulated group of 3 in the list may not overlap the DNA of the last triangulated group of 3. In fact, because you can see the start and end points, you can tell that these two triangulated groups don’t overlap. The multiple triangulation groups all do match some portion of the group above and below them (in this case,) and as a composite group, they slide to the right. Because each group overlaps with the group above and below them, they all connect together in a genetic chain. Because there is an entire group that are triangulated together, in multiple ways, we know that it is one entire group.

This allows me to map that entire segment on my Mom’s side of my DNA, from 10,369,154 to 41,685,667 to this group because it is contiguously connected to me, triangulated and unbroken. The most distant ancestor listed will vary based upon the known genealogy of the three people being triangulated For example, part of this segment, may come from Philip Jacob Miller himself, the line’s founder,, but another part could come from his son’s wife, who is also my ancestor. Therefore, the various pieces of this group segment may eventually be attributed to different ancestors from this particular line based upon the oldest common ancestor of the three people who have triangulated.

In our example above, the second group starts where the red arrow is pointing. I have absolutely no idea which ancestor this second group comes from – except – I know it does not come from my mother’s side because her kit number isn’t there.

Neither are any of my direct line Estes or Vannoy relatives, so it’s probably not through that line either. My Bolton cousins are also missing, so we’ve probably eliminated several possible lines, 3 of 4 great grandparents, based on who is NOT in the match group. See the value of testing both close and distant cousins? In this case, the family members not only have to test, they also have to upload their results to GedMatch.

Conversely, we could quickly identify at least a base group by the presence in the triangulation groups of at least one my known cousins or people with whom I’ve identified my common ancestor. Two from the same line would be even better!!!

Endogamy

The last thing I want to show you is an example of what an endogamous group looks like when triangulated.

This segment of chromosome 9 is an Acadian matching group to my Mom – and the list doesn’t stop here – this is just the size of the screen shot. These matches continue for pages.

How do I know this group is Acadian? In part, because this group also triangulates with my known Lore cousin who also descends from the same Acadian ancestor, Antoine Lore, son of Honore Lore and Marie Lafaille. Additionally, I’ve worked with some of these people and we have confirmed Honore Lore and Marie Lafaille as our common ancestor as well. In other cases, we’ve confirmed upstream ancestors.

Unfortunately, the Acadians are so intermarried that it’s very difficult to sort through the most distant genetic ancestor because there tend to be multiple most distant ancestors in everyone’s trees. There is a saying that if you’re related to one Acadian, you’re related to all Acadians and it’s the truth. Just ask my cousin Paul who I’m related to 137 different ways.

Matches to endogamous groups tend to have very, very long lists of matches, even triangulated, which means proven, matches.

Oh, and by the way, just for the record, this lengthy group includes some of my proven Acadian matches that were trimmed, meaning removed, from my match list when Ancestry did their big purge due to their new and improved phasing. So if there was ever any doubt that we did in fact lose at least some valid matches, the proof lies right here, in the triangulation of those exact same people at GedMatch

Summary

I hope this step by step article has helped take the Greek, or maybe the geek, out of matching. Once you think of it in a step by step logical basis, it makes a lot of sense and allows you to reasonably judge the quality of your matches.

The rule of thumb has been that larger matches tend to be “legitimate” and smaller matches are often discarded en masse because they might be problematic. However, we’ve seen situations where some larger matches may not be legitimate and some smaller matches clearly are. In essence, the 50% average seldom applies exactly and rules of thumb don’t apply in individuals situations either. Your situation is unique with every match and now you have tools and guidelines to help you through the matching maze.

And hey, since we made it to the end, I think we should celebrate with that beer!!!

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Just One Cousin

Posted on January 11, 2015 by Roberta Estes

Recently, someone wrote to me and said that they thought the autosomal DNA matching between groups of family members was wonderful, but they have “just one first cousin” and feel left out. So, I decided to see what could be done with just two cousins. In this case, the two cousins are full siblings and both first cousins to my mother, Barbara. This would be the same process whether there was one or two cousins, since the two are siblings. Utilizing two cousins who are siblings just gives me the advantage of additional matching and triangulation capabilities.

This does presume that both people involved are willing to share and do a bit of comparison work on their various DNA accounts. In other words, you can’t do this by yourself without cooperation from your cousin.

Here’s the common ancestor of our testers.

Barbara, Cheryl and Don took a Family Finder autosomal DNA test at Family Tree DNA.

The DNA shared by Barbara, Cheryl and Don is from their common ancestral couple, Hiram B. Ferverda and Evaline Louise Miller.

Some of that shared DNA will be Hiram’s Ferverda DNA and some will be Evaline’s Miller DNA. The only way to differentiate between the Ferverda and Miller DNA is to test people who are only Ferverda or only Miller, descendants of people upstream of Hiram and Evaline, and if there are any common segments between the testers and those Ferverda or Miller individuals, you can then assign that DNA segment to that side of the family – Miller or Ferverda.

I’m using Barbara’s chromosome as the “match to” background, below. Cheryl, in orange, and Don, in blue, are shown as matches to Barbara. You can see that these three people share a lot of their grandparents DNA. You can also see where Don and Cheryl didn’t inherit the same DNA from their father, in some instances, like on chromosome 1 below, where Cheryl (orange) matches Barbara on a much larger part of the chromosome than Don does (blue.) But then look at chromosome 13 where Barbara and Don match on a huge segment and Cheryl, just a small portion. Don and Cheryl inherited different DNA from their parents at these locations.

The three testers’ common DNA segments on chromosome 1 are shown in the table below. I’ve colored Cheryl’s pink and her brother, Don’s, blue. You can see that Barbara matches some segments with Don that Cheryl didn’t inherit from her parents. All of the DNA Barbara matches with Cheryl on this chromosome is also matched, at least in part, in that location, with Don. The chart below, matches the graphic above, for chromosome 1 and is the “view data in a table” option on the chromosome browser as well as the leftmost “download to excel” option. The download to excel option at right downloads all of the matches for the individual, not just the ones currently showing in the chromosome browser.

When at least two known relatives have tested, we have something to compare against. In this case, we have a total of 3 people, 2 siblings and a first cousin, before we start matching outside known family. We don’t know which of their shared DNA comes from which ancestor, but we can now look for people who match Barbara and at least Cheryl OR Don which proves a common ancestor between the three individuals. Matching Barbara, Cheryl AND Don would be even better.

The gold standard for DNA matching, called triangulation, that proves a particular segment to a specific ancestor is as follows.

All (at least 2) people match you on the same segment.
Those people also match each other on the same segment.
Meaning, at least three people with a known common ancestral line must match on the same segment.

The key word here is “on the same segment”.

The next thing to do is to find out which of Barbara’s, Cheryl’s and Don’s matches are “in common with” each other. This means Barbara, Cheryl and Don all share a matching segment with these other people, but without additional analysis, we can’t determine whether they share a match on the same segment or not.

I ran Barbara “in common with” Cheryl and you can see that the first two people returned on that match list were me and Don because matches are listed in the order of the largest cM of shared data first. The “in common with” tool is the blue crossed arrows, below.

Next I ran Barbara in common with Don.

There were a total of 43 people in common with Cheryl and 49 with Don.

I downloaded the matching individuals (download link at the bottom right of the match page) and sorted them in a spreadsheet to see who matches whom. Here’s what the first part of my spreadsheet looks like (sorted in chromosome and segment order.) I colorized the rows by cousin for easier visualization.

We have 92 total matching individuals in common with Barbara and Cheryl and then Barbara and Don. A total of 19 people are listed as matching BOTH Cheryl and Don (for a total of 38 rows in the spreadsheet), so that means that there are 54 people who are in common with either Barbara and Cheryl or Barbara and Don, but not in common with all 3, Barbara AND Cheryl AND Don. This illustrates how differently siblings inherit DNA from their parents and how it affects matches another generation later.

In Common With Matches	To both Don and Cheryl	To Cheryl only or Don only, but not both
Barbara	19 (38 rows of 92)	54

Clearly, the people who match all three individuals, Barbara, Cheryl and Don are likely the closest relatives.

So let’s focus on those closest matching people. If you were utilizing only one cousin here, you would simply utilize every “in common with” match between two individuals and move forward. Because I have siblings here, and because I don’t want to deal with 72 different people, I’m using the fact that they are siblings to focus my efforts on the most closely related matches – people who match Barbara AND both siblings. You could also limit your focus by something like a common ancestral surname between all match members.

The next step is for each tester, meaning Barbara, Cheryl and Don, to compare each individual on the common match list to their DNA. This means that Barbara, Cheryl and Don all three will compare to all 18 individuals. We now have only 18 matching people, instead of 19, because I removed my own matches, since mine are a subset of Barbara’s. Checking to see how each of our testers matches each common matching person is the only way to determine that there is a three (or 4) way triangulation that will confirm a common ancestor.

There are two ways to do this at Family Tree DNA.

1. You can, 5 matches at a time, compare in the chromosome browser, then download only the matching segments to a spreadsheet for those 5 individuals. This means 4 sets of matches for each of three people.

Two cousins browser download

2. You can download Barbara, Cheryl and Don’s entire segment match list and then eliminate the matches that aren’t relevant to the discussion – meaning everyone except the 18 common matches between the three people.

The download option for the entire segment match list for the person whose kit you are looking at is shown at the top of the chromosome browser, to the right. Downloading the currently showing individuals matching segments is shown at the top of the chromosome browser, to the left.

Because we can only push 5 people at a time to the chromosome browser, in this case, it will be easier to simply download all of the matches for each of the three individuals and then put them into a common spreadsheet and sort by the names we determined match in common between all three cousins.

I downloaded all of the matches for Barbara, Cheryl and Don, colorized them and then sorted them in the spreadsheet by the name of who they matched. I then searched for the names of the 18 individuals who matched Barbara, Cheryl and Don, and copy/pasted them into a separate spreadsheet.

I could then sort the 18 matching individuals results by chromosome and start and end location.

Barbara’s DNA matches are white rows, Cheryl’s are pink and Don’s are blue.

The segments where Barbara, Don and Cheryl all match more than one other person on an overlapping area of their DNA segments are colorized green. This means that 4 or more people match on that same identical segment, the three known cousins and at least one other person.

The segments where at least Barbara and either Don or Cheryl (but not both) match at least one other person are colorized yellow. This means that least three people match on that same segment.

Since the gold standard of triangulation is 3 individuals matching on the same segment, both the yellow and green segments contain matches that fall into this category and are triangulated. All of those segments match at least two of the cousins, who match each other, plus in some cases, additional people too.

Let’s walk through one triangulation sequence.

In the green cluster, above, you can see that Barbara, Cheryl and Don all match Arthur on overlapping portions of the same segment. The overlapping portion between all 3 individuals and Arthur runs from 49,854,186 to 53,551,492. In addition, both Don and Cheryl match Tiffany on part of that same segment and Barbara matches Dean on part as well. These segments aren’t exactly the same for any of the cousins, with different amounts of matching DNA as reflected in the different cM and SNP values.

So, who is triangulated based on just this one green cluster? Barbara, Cheryl, Don and Arthur are triangulated to a common ancestor. We know that common ancestor is either the common ancestor of Cheryl, Don and Barbara – Hiram Ferverda and Evaline Miller – or upstream of that couple.

Tiffany is triangulated to both Cheryl and Don, but since Cheryl and Don are siblings, that’s irrelevant at this point – meaning we can’t tell if that match is IBS by chance or real because there is no additional match – at least not in this cluster.

In total, there are 19 green clusters (triangulated to at least 4 people) and 12 yellow clusters (triangulated to at least 3 people.)

In other words, the DNA that came from Hiram Ferverda and Evaline Miller is present in these matching people as well. The million dollar question, is, of course, which upstream ancestor did it come from? We genealogists are never satisfied, are we? Every answer just leads to more questions.

Before we begin looking at the DNA results and discussing what they mean, I want to share with you the family tree of Hiram Ferverda and Evaline Miller, because the DNA of the people who match Don, Cheryl and Barbara had to come from these people as well. This chart shows 7 generations back from Barbara, Cheryl and Don. The common ancestors of the people with whom they triangulate are likely to be within this timeframe.

The colorized ancestors above are the ancestors who contributed the X chromosome to both John Ferverda, Barbara’s father and Roscoe Ferverda, Cheryl and Don’s father.

In my working example, below, I’m utilizing the matches on chromosome 14 because chromosome 14 includes examples of a couple of interesting features.

Let’s look at the first green grouping. All three cousins match to SB and then Barbara matches also to Constance and William, our Lentz cousin on part of that overlapping segment as well. This suggests that this grouping might come from the Lentz side of the Miller tree, although we’ll see something else in a minute that might give us pause to reflect. So just hold that thought. Regardless, it does tell us that these individuals do share a common ancestor and it’s on the Miller side, not the Ferverda side.

The second green grouping is larger and includes larger segments as well, which are more reliably used, although the smaller green cluster clearly meets and exceeds the triangulation requirement of 3 matching individuals on the same segment.

This larger green cluster is actually quite interesting, because there are a total of 4 individuals, Ellen, Arthur, Eric and Tiffany who are all triangulated on this same segment with Don, Cheryl and Barbara. So, not only are they triangulated to Don, Cheryl and Barbara, but also to each other. These 7 people all share a common ancestor.

The yellow grouping shows an area where Eric matches Barbara and Don plus Arthur as well, but not Cheryl. We don’t know anything about Arthur or Eric’s genealogy, so we don’t know if this is Miller or Ferverda DNA, at least not yet. We’ll learn more about Arthur and Eric in a minute, even without their genealogy!

There are a couple of other areas on other chromosomes that are of interest too.

On this cluster on chromosome 12, we find a known Miller cousin, Rex, 2nd cousin to Barbara, Cheryl and Don. Because Rex also descends from the parents of Evaline Miller, we know that this segment shared with Rex has to be Miller DNA, not Ferverda DNA.

On this segment of chromosome 3, below, we see that Barbara, Cheryl and Don match Herbert, another known Miller cousin, plus Dee and Constance in much smaller amounts on the same segment. This tells us that this segment is descended from our common ancestor with Herbert.

Barbara, Don and Cheryl’s common ancestor with Herbert is Daniel Miller and Elizabeth Ulrich (Ullery), which makes them third cousins once removed – except – Herbert got a second dose of Miller DNA because Daniel Miller’s son, Isaac, married his first cousin who was also a Miller and shared grandparents with him. So Herbert, genetically, is closer than he would appear since he received the double dose of Miller DNA three generations upstream.

Gotta love these close knit families. The Millers were Brethren. These double doses of family DNA often carry forward by matching downstream when they might otherwise not be expected do so. That’s the upside of these endogamous groups. Now, here’s the downside.

See the segments with the words problem written to the right? Do you recognize what the problem is? You’ll notice that in the matching group we have BOTH cousin Herbert who is a Miller (and not a Lentz) and cousin William who is a Lentz (and not a Miller.)

This is a very common situation in endogamous communities.

To make matters worse, we are dealing with very small segments here, where we often see confusion. However, let’s look at the possibilities.

We do have triangulation, so one of three things has happened here.

First, the Brethren are an endogamous population that intermarried nearly exclusively within their faith. The Lentz and Miller families were both Brethren.

Here are our possibilities.

Our Lentz cousin has some Miller in one of his lines. This is entirely possible since he has a “short” pedigree chart and his families are living in the same Brethren communities as the other Lentz and Miller families.
Our Miller cousin has some Lentz in one of his lines. That is less likely, because his genealogy is pretty well fleshed out, although certainly possible because, once again, the families were living within close proximity and attending the same churches, etc.
This segment is truly a population based segment and will be found in people descending from that same base population. If this is the case, we still received it from one of our ancestors who came from that population, but since the Lentz and Miller lines may have both carried this same segment, we can’t tell who it came from. In other words, their common ancestor is further back in time than the Lentz and Miller families found in the US.

This segment cannot be IBS by chance because it does triangulate with the three cousins, Barbara, Don and Cheryl. The definition of IBS by chance shows us that chance segments would not phase (or match with) with a parent. If Don, Cheryl and Barbara all three carry this matching segment, it’s because their fathers both received it from their grandparents who were the common ancestor of Don, Cheryl and Barbara.

Neither Cheryl, Don nor Barbara can phase directly to their parents, who are deceased, so in this case, matching against first cousins is the best substitute we have. We know that common DNA between the first cousins had to come from their father’s, who were brothers. This in essence virtually phases Barbara, Don and Cheryl to their father’s on these matching segments. Not ideal, by any means, but even partial parental phasing is better than no phasing at all.

A third match, Dean, shows Miller in his family tree, but I could not connect his Miller line to the Johann Michael Miller ancestral line, from which our Miller line descends – so Dean is not a known cousin. Sometimes a common surname, even if found in the same geographic location, is not proof that the DNA connection is through that line. It’s easy to make that assumption, but it’s an assumption that is just waiting to bite you. Don’t do it!

Because of our known, proven DNA and genealogy matches to Herbert, we can attribute all of the segments where Herbert triangulates with either Barbara and Cheryl or Barbara and Don as Miller for all people involved. This means that this common DNA descends either from Daniel Miller and Elizabeth Ulrich or Daniel’s father Philip Jacob Miller and Magdalene, surname unknown.

Why have I listed two couples? Because, remember, Herbert has a double dose of Miller DNA from cousins and we don’t know which segment Barbara inherited, one from Daniel/Elizabeth or one from Philip Jacob/Magdalene (or some of each.) If the segment is from Daniel/Elizabeth, it could have come from either the Ulrich or Miller side. If it came from Daniel, then it also came from his father and mother, Philip Jacob/Magdalena and could either be Miller or Magdalena’s unknown line.

Because of our known, proven DNA and genealogy matches to Rex, we can attribute all of the segments where Rex triangulates with either Barbara and Cheryl or Barbara and Don as Miller for all people involved. Their common ancestor is John David Miller and Margaret Lentz, so their shared DNA could be either Lentz or Miller and is likely some of each.

For segments where there is no triangulation, but Barbara matches either Herbert or Rex, I still note that segment as Miller on my spreadsheet, since they are proven cousins, but I just omit the triangulation note.

For Barbara, that’s a total of 51 segments of her DNA that we can now assign to a Miller ancestral couple.

Furthermore, every segment that Barbara matches with either Cheryl or Don is now confirmed to be from her father’s side of the family, not her mother’s. While we don’t have Barbara’s parents available for testing, this is a pseudo way to phase your results to determine matches from one parents’ side of the family. For Barbara, that’s a total of 91 segments, some of them quite large. For example, roughly half of chromosome 13 matched with Don.

Just as a matter of interest, within those 91 segments that Barbara matches with either Don or Cheryl, a total of only 7 segments matched exactly between all 3 individuals in terms of start and end location, cMs and SNPs. While you might expect a number of small segments to match exactly, these weren’t all small. In fact, most weren’t small and some were quite large.

Exactly matching DNA segments between Barbara and Cheryl and Barbara and Don.

Chromosome	Matching cM	Matching SNPs
1	8.65	1189
1	7.01	1150
8	27.79	7279
10	20.78	5141
12	27.68	6046
14	2.11	700
14	49.47	9032

This means that these segments were not divided at all in a total of 5 DNA transmission events.

Hiram to John
Hiram to Roscoe
John to Barbara
Roscoe to Cheryl
Roscoe to Don

Additionally, I carry two of these exact segments as well, so those two segments survived 6 transmission events.

Clearly these segments are what we would term “sticky” because they certainly are not following the statistical average of dividing the DNA in half (by 50%) in each transmission event.

There is one more thing we can tell from matching.

Both Barbara and Cheryl match with SB on the X chromosome on the same segments.

This is particularly interesting because of the special inheritance path of the X chromosome. We know that SB must be related on Evaline Miller’s side of the family, because John and Roscoe Ferverda did not receive an X chromosome from their father. So Barbara, Cheryl and Don have to have received it from Evaline. Unfortunately, SB listed no genealogy on Family Tree DNA, but based on the X chromosome inheritance path, I can tell you that SB is either descended from John David Miller and Margaret Lentz, or from the Schaeffer, Lentz or Moselman lines colored pink or blue, below.

At this point, I made a chart of how the matches grouped with each other on each of the green clusters.

I intended to create a nice chart in Excel or Word, but with all of the various colors of ink involved, I didn’t think I could find enough color differentiation so we’ll just have to suffer with my hand-made chart. There are subtle color differences here – a different color or marker type for each of the 19 green clusters.

What I did was to look at each of the green DNA spreadsheet groupings and create a colorized chart, by group, for each grouping. So everyone in the first cluster had their X in the boxes of who they matches in the same color, say blue pen. The second group, orange marker, and so forth. That way I can see who was orange or yellow or blue and if those groups tend to cluster together.

Remember Arthur and Eric from above, whose genealogy we knew nothing about. You can see, for example, that Arthur matches in various groups with lots of people, and most often, Tiffany. Arthur and Eric also match in multiple groups that include each other and Rex, a known Miller descendant, so we can attribute both Arthur and Eric’s DNA matches to the Miller side of the tree. Keep in mind, all of these people also match with Barbara, Cheryl and Don.

Tiffany clusters with Arthur and Sarah and Eric in multiple groups and with Constance, David, Ellen, Leland and Rex in at least one other cluster. So another Miller side person.

On chromosome 14, Eric, Ellen, Arthur and Tiffany were all triangulated on the same segment with Don, Cheryl and Barbara, so we know those 7 individuals unquestionably share a common ancestor.

Let’s look at SB again, our X match. Since SB’s X connection can’t come from the Miller side, given the X inheritance path, and SB also matches with our Lentz cousin, it’s likely that SB is related through the Lentz lines.

Normally, when doing this matching relationship chart, you tend to see two distinct groupings, a mother’s side and a father’s side. In other words, there will be some groups that absolutely don’t overlap with the others. That’s not the case here.

So, by now you might be wondering what happened to the Ferverda side of the family? I was secretly hoping to find a closet Ferverda relative in this exercise, and I thought we might have, actually. Notice that Harold has no clustering at all, but he clearly matches Barbara, Cheryl and Don – but doesn’t cluster with any other Miller or Lentz cousins. Therefore, he could be from the Ferverda side of the family, but since he provided no genealogy information or surnames at Family Tree DNA, I can’t easily tell.

However, I am not entirely without recourse. I checked Harold “in common with” Barbara and discovered that he matches both Rex, our Miller cousin and William, our Lentz cousin, so even though Harold did not triangulate with William and/or Rex on any segments with both Barbara and/or Cheryl/Don, those Miller/Lentz matches certainly suggest descent from this line. I’ll be sending him an e-mail!

So, there are no Ferverda cousins represented in these matches.

I decided to check one more thing, now that I know that all of these matches are on the Miller side and that we have 3 known, proven genealogical cousins, Rex, Herbert and William. I wanted to see how many of our individuals who match Barbara, Cheryl and Don also match one of the known cousins. I selected Barbara as the base match kit to use, since we know they all matched Barbara, Cheryl and Don, and then I ran “in common with” for each one of them with Barbara, with the following results. A few did match one of the Miller or Lentz cousins, but fewer than I expected.

*However, we had a surprise. Dean matched another Miller male individual whose line is proven to descend through two children of Philip Jacob Miller and Magdalena, surname unknown. Another first cousin marriage. Another cousin discovered!

Furthermore, I noticed yet another individual, Doug, in Barbara’s match list and in common with 6 of the matches as well. Looking at Doug’s pedigree chart, not only is he a Miller descendant, he also descends from two of the Miller wives lines too. Another cousin confirmed!

But why no Ferverda matches?

Recent immigrants.

The Ferverda side of the family immediately jumps the pond to Holland, with Hiram himself being an immigrant as a young teen in the 1860s. There are few Ferverda (Fervida, Ferwerda) descendants here in the US to test, and many are Brethren or Mennonite. Few people in the Netherlands have participated in DNA testing.

The converse of that, Evaline Miller’s lines have all been in the US since the early/mid-1700s, so there are lots of descendants. Oh, the difference about a hundred years and 5 or 6 generations makes in the number of descendants who might be available to test. This situation, unfortunately, created a very lopsided chart without the division I’m used to seeing. On the other hand, thank goodness Evaline’s line and Hiram’s line are very distinct!

At this point, if you’re doing this “one cousin” exercise, you’ll need to do a few things.

1. Check each of the matching individuals to see if they have uploaded or created a pedigree chart at Family Tree DNA. If they do, their pedigree icon will be green, shown below. If so, click on the icon and search for every surname (and variant) associated with your known common lines with your cousin.

2. Check to see if these people entered a list of surnames, even if they don’t have a pedigree chart. The surnames are listed in the furthest right column. If you have entered your surnames, any that match yours will be bolded. Beware of variant spellings.

You can see above that I am the only one of the matches shown with a pedigree chart icon, shown in green, and the common surnames are bolded at right.

3. If your matches don’t have a pedigree chart, write to them and tell them you have a common ancestor and give them a list of your ancestors in your direct line. Please, PLEASE include the name on the kit that you match. Many people manage multiple kits and will ignore requests with only partial information.

4. If you have additional cousins to test, do so. I’m sure you can see how valuable additional cousins DNA would be.

5. Be sure to check your matches by “ancestral surname” to be sure that you haven’t missed any cousins who have already tested. The ancestral surname search box can be seen above the “known relationship” heading in the graphic above.

6. If you haven’t done so, enter your surnames under the “Manage Personal Information” tab under “My Account” at Family Tree DNA. Then click on the genealogy tab, then Surnames.

7. From your main personal page, of course, you can upload your Gedcom file by clicking on “My Family Tree.”

8. Run “in common with” for each of the common matches of your two cousins and look for common matching names between them. Those matching “in common with” names serve as a hint as to shared ancestry. Your answer may be hiding in your cousins’ trees!

Utilize all of these tools to help your search.

Summary

Not bad for thinking we couldn’t do anything with our DNA matches because we had “just one cousin” to work with, even though I cheated and used siblings.

What, exactly, did we manage to do?

I attributed 91 segments of Barbara’s DNA to her father’s side of the tree.
I filled in 51 segments of Barbara’s DNA to ancestral couples.
I found 5 confirmed genealogy/DNA cousins.
I found 16 people whose genealogy is unknown, but who triangulate with Barbara, Cheryl and Don. We know for sure which side of the tree these people match on – all Millers.
I can tell the X match which lines they descend from, even if they don’t know.
I can do one more very cool thing. Utilizing the Lazarus utility at GedMatch, I can now recreate at least a partial autosomal DNA file for both John and Roscoe Ferverda, the fathers of our testers. Join me in a couple days and we’ll see how that works!

This same process works between any two people who know how they are related and their common ancestor. It’s a great way to find cousins you didn’t know you had, or you didn’t know have DNA tested, and how they are related to you and each other.

Some people get very discouraged when even thinking about working with endogamous populations, or cousin marriages. One of the reasons I used this particular example is that I wanted to illustrate that while these situations are challenging from time to time, they are far from hopeless – so don’t let that deter you.

In fact, of the 5 confirmed cousins discovered during this process, some in unexpected ways, at least 3 and possibly 4 are through multiple lines. Some of these matches are probably thanks to endogamy.

Happy hunting!

______________________________________________________________

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Thank you so much.

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How Phasing Works and Determining IBD Versus IBS Matches

Posted on January 2, 2015 by Roberta Estes

Over the past few weeks there has been quite a bit of discussion surrounding phasing and matching of autosomal DNA. I’ve had several questions about what phasing is, why it might be important, and how phasing affects matching. These topics go hand in hand.

Phasing

One of the terms used in genetic genealogy is phasing. Many people don’t understand what phasing is, why it’s important, and that there are really two kinds of phasing.

The goal of phasing originally was to determine which side of our family, Mom or Dad, a piece of our DNA, and therefore a particular match, came from. As the industry has developed, phasing has taken on a slightly different meaning. Today, it’s often used generally to imply that phasing would improve our matches and therefore “should be done.”

These are really two kinds of phasing, used for two different purposes. Originally phasing was used to mean parent phasing. A second type, which I’ll call academic phasing, has wider applications. But first, let’s talk about why we need phasing at all.

Why Do We Need Phasing?

Because there is no zipper in our DNA. It would be very useful….very…if our DNA came in nice straight columns, with Mom’s on one side and Dad’s on the other. But that’s not how it works.

We carry two nucleotides in each inherited position, one from Mom and one from Dad. I discussed this in detail in this article.

Our autosomal DNA, when read, does not and cannot separate Mom’s contribution from Dad’s (except for the X chromosome in some situations, which we are not going to discuss in this article.)

In this example, Mom contributed all As and Dad contributed all Cs.

My results for these locations look like this – a mixture of Mom’s and Dad’s in no order. In other words, they are combined and I can’t tell the difference – at least not without either Mom or Dad’s data to compare against.

Ideally, if we could separate my values into Mom and Dad’s columns, like above, then we could match exactly against cousins from Mom’s side and from Dad’s side, because those cousins would also carry all As or all Cs in part or all of those locations, like in the example above.

In this case, I match both Mary and Myrtle, and Mary and Myrtle each match a respective parent.

This is the textbook case of IBD, or identical by descent.

But then, there’s Joe. I match Joe, because I carry both A and C at each of these locations. Joe, however, has alternating As and Cs. The acid test of whether I match Joe by descent (IBD) or by chance (IBS) is if Joe matches my parents.

In this case, as you can see, Joe does not match my parents. Because my matches to both Mary on my mother’s side and Myrtle on my father’s side are IBD, Joe also does NOT match Mary or Myrtle.

This is the underlying foundation of why we use triangulation and can say that if three people with a known ancestor all match each other, we can map that segment as IBD, identical by descent, from that known ancestor.

In fact, the definition of a proven ancestral “match” in genetic genealogy is when:

Two or more people match you on a particular segment
Those people also match each other on the same segment

This is true whether or not you’ve been able to identify the ancestor responsible for those shared segments.

Let’s look at how that works.

In the following example, you can see that Mary, Anne and Sue all match Mom, because they all have all As. They also match me, because I have an A and a C in each location, so they match my A, but they do not match Joe who has alternating As and Cs. So you can see that I am the only person in the group that Joe matches. This is how we know that Joe is an IBS by chance match and this particular matching segment for Joe can be eliminated as a valid match to me.

Let’s also say that I know that Anne, Sue and Mary descend from my mother’s Miller line and that Henry, Harold and Myrtle descend from my father’s Vannoy line. So, in this case, I have proven triangulation of myself, my parents and 3 other known individuals with the same genealogy lines. These segments are now considered proven to those particular ancestors or ancestral lines because there is no other way for all of us to share these segments other than sharing a common ancestor.

This is also the basis upon which we can infer that our parents carried a particular piece of DNA if we don’t have their DNA to compare – because that’s the ONLY way we could have acquired that DNA segment – through that parent.

So let’s look at this exact same situation if we don’t have either parent’s data to utilize. You can see that Mom and Dad are missing from this next example.

If three cousins all share that same segment of DNA, it HAD to come from a common ancestor, and one or the other of our parents HAD to have carried it too.

You can see that while we don’t have the benefit of our parent’s DNA in the above example, that Joe still matches me. Anne, Sue and Mary still all match each other, as do Henry, Harold and Myrtle. But Joe does not match any of the known cousins. We can therefor determine that Joe’s DNA, on this particular segment, is IBS by chance, not IBD, so not inherited from a common ancestor. Therefore, we can discard Joe as a valid match on this segment. This does NOT infer that Joe might not be a valid match on other segments, just not on this segment.

So, there are two ways to determine IBS by chance segments.

To compare your matches on that segment against both parents.
To compare your matches on that segment against proven genealogical matches from both sides of your tree.

For specifics of how to do this, also refer to the Chromosome Browser War article and for the basics, to the Ancestor Mapping article.

Now, let’s remove Joe, who doesn’t match, and see what our segment match looks like.

All of these people match me, because I carry an A and a C, one from each parent. With my parents DNA included, I can tell immediately where the matches occur.

I’m fortunate that I have my mother’s autosomal DNA. That means that I can do “poor man’s phasing” by comparing my results against at least one parent. The people who don’t match me and my mother must match me and my father or they are IBS by chance.

But even without any parents, because I know that the green people share a common Miller ancestor and the blue people share a common Vannoy ancestor, we can clearly identify that these people match, and why – and we can infer that our parents had this same DNA because there is no other way for us to obtain it.

Now let’s look at one final situation where we have Nancy who doesn’t know how her genealogy connects. Let’s say she is an adoptee.

You can see very clearly where Nancy matches me and my mother’s proven cousins. She does not match my father’s proven cousins.

I’m sure I don’t need to tell you at this point that Nancy shares a common ancestor with our Miller line. We may not know who, at this point, but by studying the genealogy of these people and others who also match, we may be able to narrow it down quite substantially.

So, in a nutshell, phasing against a parent, or both parents, determines quite accurately which side of our family tree a match comes from.

We can do that same thing in essence by finding cousins who all match on the same DNA segment and share a common ancestor. This is why testing multiple cousins is so important. Once that segment of our DNA is mapped to an ancestor or ancestral line, we know that anyone else who also matches at least two other people with that same segment also share this same genealogical line at some level.

No Parent DNA

Phasing is fine and dandy if you have the DNA of one and preferably both of your parents, but probably more than 50% of the genealogists don’t have that luxury.

In the adoptee community, they not only don’t have their parents DNA to test, they don’t have a pedigree chart so they can’t even utilize triangulation techniques with cousins or people with a shared genealogy. This is why they attempt to piggyback off of our already triangulated data to a particular ancestral line – again, based on the proven concept that if you match a group of 3 other people who have triangulated – you too inherited that DNA from a common ancestor with those people.

In the example above, Anne, Sue, Mary and I match on that DNA segment and know that our common ancestral line is that of Johann Michael Miller. Since Nancy, an adoptee, matches us, she too is descended in some fashion from the Johann Michael Miller lineage (upstream or downstream – meaning possibly a wife’s line) as well.

What about all of the matches that we have that we can’t attribute to one side or the other, or those people like adoptees who don’t have any pedigree chart or parent’s data to work with?

Obviously, they can’t utilize phasing in the typical sense. Nor can companies figure out our genealogy and apply it to our DNA results – that’s up to us – with the possible exception of a parent match.

A second type of phasing is being used to attempt to reduce the number of IBS matches by both chance and population.

Academic Phasing

In academia, in order to study populations, computer programs were written to attempt to sort through data for likenesses and differences. The goal, for genetic genealogists is to find segments that are IBD, identical by descent and eliminate others that are either IBS by chance or IBS by population.

What academic phasing programs like Beagle attempt to do is to sort through populations and determine the most likely combinations of nucleotides found, and thereby extrapolate IBD vs IBS.

These programs have inherent problems, not the least of which is that they are not created to deal with an ever increasing data base size where hundreds (if not thousands) of new records are added daily. Ancestry, when faced with the problem of a rapidly increasing data base of over half a million DNA testers who were accumulating matches in the thousands, tried to address this. Ancestry’s problem is only growing, which is one of those wonderful business problems to have. In order to attempt to reduce the number of matches and improve those matches, they created their own technology relative to phasing, which they detailed in a white paper released with their new DNA Circles feature. The jury is still out on how well they succeeded.

Inherent to all of the academic phasing programs is the challenge that the vendor (or whomever) involved must decide where to draw the line between what they consider to be useful and not useful. Ancestry did not tell us their criteria for determining the cutoff that they used in their proprietary phasing program.

However, we can determine some things based on the graph they did provide to each of the attendees during DNA Day. They gave us a “before phasing” and “after phasing” picture of our own genomes as compared with our matches. We’ve talked before about the pileup areas that Ancestry discovered based on their phasing. Please note that I’ve used my own chart in this example, but based on the charts of others at the same meeting, each person’s was quite different – so the numbers here are provided only as examples utilizing my own information.

This is my genome compared to my matches before Ancestry reduced my matches after phasing.

This is my genome compared to my matches after my pileup reduction surgery.

In this second chart, you can see, that for me, they have drawn the line at about 25 common matches as being a relevant cutoff point, out of just under 13,000 prior matches. Please note that this cutoff of about 25 is my cutoff point. Yours might be quite different – but there is no way of knowing.

This looks like locations where I had more than 25 matches, out of 13,000, were determine to be “too matchy” and therefore a pileup area. Now, given that I descend from at least four endogamous populations, the Mennonite, Brethren, Acadians and Native Americans, I would suggest that I would expect to have more than 25 matches on some of the same segments within these populations groups – especially those closer in time and with many descendants. At Family Tree DNA, where I have 770 matches, I have matches with more than 25 people with Acadian ancestry. If you extrapolate only the 25/770 number at Family Tree DNA (which is low) to 13,000 matches, I would expect to have over 400 Acadian matches at Ancestry – which might explain why I lost all of my Acadian matches at Ancestry.

It appears in my first chart that the cutoff line is drawn at about the location of this arrow – if you drew a line straight across at that location from left to right. It appears from looking at this, that I didn’t lose that many matches, but I did. I went from 12,846 to 3,350 or a reduction of about 75%. I’m not bemoaning the loss of the number of matches, because as they were, they weren’t terribly useful.

However, I did lose all of my known Acadian matches. In other words, in some cases, the matches may have gotten pruned too far. Now truthfully, at Ancestry, since we don’t have analysis tools, this really doesn’t matter much to me.

I’m only using this example because it’s the only concrete example that we have today of academic phasing applied to a commercial data base and the effects of utilizing academic phasing and applying it commercially to prune our matches. In my case, I found it extremely interesting to see the large pileup area and I would just love to see where that maps to on my chromosome spreadsheet, and if there is anything remarkable about it. Is it my Acadian matches, or is it truly an amalgamation of miscellaneous matches from Europe (or someplace else) with no story to tell? I’m fine with either answer, but I can’t now and will never be able to know.

In any event, this type of phasing is used in essence to prune our trees universally by determining which matches are more legitimate and which are less so.

To date, Ancestry is the only vendor to implement this type of phasing.

Felix Immanuel discusses phased data, IBS and endogamous societies in his article, “Why phasing DNA is bad for valid and close matches.”

Phasing Summary

There are two types of phasing. The first, which is phasing to parents and known family data is achievable by genetic genealogists. We have been utilizing a form of “poor man’s” phasing for a long time now where we compare known matches to one or both of parents and selectively remove matches that match us but not either parent. Of course, you need both parents to do this reliably.

The second type of phasing, academic phasing, is still more of an unknown in terms of how it truly affects the accuracy of our genealogy matches. Ancestry has created a proprietary form of phasing optimized for large data bases and while we have seen the first generation of phased data, the jury is still out as to the success of this tool, in part, because we don’t have any tools like chromosome browsers and matrix matching tools to confirm the that the matches we have or lost were and are both genetic and genealogical matches.

Now that we understand how phasing works relative to matching, let’s talk about what an IBD and IBS match are, and why that’s important.

IBD vs IBS

When two people have a match on a autosomal DNA segment, it can either be identical by descent, IBD, or identical by state, IBS, although IBS really should be broken into multiple categories. In some cases, IBS can become IBD, but in the situation where the IBS match is actually false, it is simply not a valid match. Let’s talk about how to tell the difference.

Matches between any two people on a particular segment can be due to any of the following situations.

A valid IBD, meaning identical by descent, match where the segment has been passed from one specific ancestor to all of the people who match. That matching segment can be labeled and utilized as such. In these cases, we know, for example, that the segment is passed to the descendants of a specific ancestor or ancestral couple.
An IBS match, meaning identical by state, which is called that because we can’t yet identify the common ancestor, but there is one. So this is actually IBD but we can’t yet identify it as such by connecting it with an ancestral line. So this really isn’t IBS. With more matches, we may well be able to identify it with its contributing ancestor. As more people test and larger data bases and more sophisticated software become available, these matches will fall into place. Some people refer to any match they can’t identify as IBD as IBS.
An IBS match that is population based. These are often difficult to determine, because this is a segment that is found widely or within in a specific population. It is passed from your ancestors, but this segment may be found in a large part of the population they descend from. The key to determining these pileup areas is that you may find this same segment matching different proven lineages. I’ve found a couple of areas where I appear to have matches from my mother’s side of the family from different ancestors – so these areas are potentially IBS on a population level. That does not, however, make them completely irrelevant. In fact, this article speaks to how one genealogist noticed and worked with a group of 22 matches that appear to be IBS by population which are quite relevant to her genealogy.
An IBS match that is a false match, meaning the DNA segments that we receive from our father and mother just happen to align in a way that matches another person. Generally these are relatively easy to determine because the people you match won’t match each other. You also won’t tend to match other people with the same ancestral line, so they will tend to look like lone outliers on your match spreadsheets, but not always. I refer to these as IBS by chance, to distinguish them from IBS by population.

So, actually, there are three kinds of IBD and only one kind of IBS, which is by chance. This is because you do inherit DNA referred to as IBS because you don’t know which ancestor it is inherited from, and you do inherit IBS by population DNA from your ancestors, by descent. The only IBS that is actually inherited by state is a false match or IBS by chance. So, word to the wise – when someone tells you a match is IBS, ask what they mean and how they know.

Regarding IBS by chance, Felix Immanuel Chandrakumar (formerly Felix Chandrakumar) has been analyzing the probability of IBS matching. His interest was spurred because contrary to what had been expected, there are matches among living people to some of the ancient DNA results and at levels that, if interpreted today, would suggest a relationship in a genealogical timeframe. This means that these segments must be either IBS by population, meaning passed down within a population through a specific ancestor (and parent) to the living person, or they are IBS by chance and not relevant, although many of these matches have been phased against parents.

Felix’s article, “The true IBS noise range” discusses his findings that a true noise or false IBS segment cannot occur above the threshold of 150 SNPs at the 1MB threshold.

In addition, he generated a “noise file” which would allow people to see just how often they actually would match any segments down to 1cM and 100 SNPs just by chance. It is kit F999901 and surprisingly, not one person in the GedMatch data base matches at any segment.

The challenge of course is differentiating between these types of matches and then using that information to tell us something about our ancestry, either genealogically, meaning a specific ancestor, or ethnically, meaning that a segment of our DNA descends from a particular group of ancestors, like Acadians or Native Americans or Finns.

To do this, we need to map our chromosome segments to ancestors, but there are very few people actually mapping their chromosomes to ancestors. Why? Because it’s tedious and it certainly is not the “quick answer” many of us would like. Hopefully, the IBS and IBD guidelines below will help people better understand and categorize matches.

Guidelines for Determining IBS vs IBD

As mentioned previously, there are really 4 kinds of DNA segments. I’ve developed some guidelines for how to identify each type of match and attempted to quantify them below.

Segment Type	Characteristics – Definition	How to Identify
IBD – Identical by Descent	Can determine a common ancestor. Let’s say that we know that Mary, in our example, shares the ancestor Johann Michael Miller on my mother’s line. I label this segment IBD on my spreadsheet with the name of our common ancestor.	For genealogy matching of previously unknown cousins, at least three people match with a common segment and a common ancestor. In closer family, such as parents, grandparents, sibling and known close cousins, this three match criteria is not needed. Larger segments are much more likely to be IBD.
IBS that will be IBD	The segment is really IBD, but since we don’t know which ancestor contributed the segment, yet, it sometimes gets labeled it IBS. Let’s say this is Myrtle, and she matches us and others on the same segments, but we don’t know which ancestors contributed that segment. More genealogy work and/or more testers who know their pedigree charts will make determining the common ancestor more likely to occur.	Matches parents and/or multiple (sometimes close) known family members on the same segments. Sometimes the steps to identifying the common ancestor is to first identify a common surname or geography and pursue from that point, although multiple common surnames can occur that are not necessarily relevant. I have some people that I am genealogically related to on two different lines, but any one segment can only be contributed by one ancestral line.
IBS by population	These segments truly are IBD, but since they exist in a large population, you may see matches on these segments from multiple ancestors. Typically these are small because they have been passed within a population for a very long time, although based on the Anzick ancient DNA matches, they are not always small. Often, in population genetics, these would or could be called AIMS or Ancestry Informative Markers, meaning that they show up in a particular population at higher levels than elsewhere. Are these useful to genealogy? It depends on what you are looking for and the frequency at which they are found in any given population. They wouldn’t be terribly useful in terms of European genealogy, if you’re primarily European, but if you have minority admixture, finding one of these IBS by population segments would be extremely informative.	Indicated by areas where you find matches from multiple family lines on the same side of your family, on the same segment. These would be pileup areas. Alternatively, they can be segment areas where you notice a specific trend, like matches are primarily Acadian, or Finnish, etc. I label these segments, but I don’t discard them. IBS by population matches are generally, but not always, found in smaller segments, as shown by the ancient DNA matches.
IBS by chance	The example I used with Joe. False matches that match only by the luck of the draw in how the 2 strands of DNA was distributed in the two people who match.	When matching against both parents, IBS by chance can be discerned when a match matches you, but does not match either of your parents on that segment. If these segments are “larger,” 5 or 7 cM or with more than 500 or 700 SNPs, this could be due to a data read error or “no calls” in the parent’s file. You may want to check the original data file before disregarding the segment. If you don’t have both parents, but you do have triangulated cousins on both sides of your family on this same segment, you can still triangulate by determining if a match matches you and either set of cousins. If not, then the match is IBS by chance. Generally, I simply label these “IBS by chance” and leave them in the spreadsheet so I don’t confuse myself by coming across them again, but they could be discarded. The smaller the segment, the more likely it will be IBS by chance but all smaller segments are not IBS by chance.

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Chromosome Browser War

Posted on November 30, 2014 by Roberta Estes

There has been a lot of discussion lately, and I mean REALLY a lot, about chromosome browsers, the need or lack thereof, why, and what the information really means.

For the old timers in the field, we know the story, the reasons, and the backstory, but a lot of people don’t. Not only are they only getting pieces of the puzzle, they’re confused about why there even is a puzzle. I’ve been receiving very basic questions about this topic, so I thought I’d write an article about chromosome browsers, what they do for us, why we need them, how we use them and the three vendors, 23andMe, Ancestry and Family Tree DNA, who offer autosomal DNA products that provide a participant matching data base.

The Autosomal Goal

Autosomal DNA, which tests the part of your DNA that recombines between parents every generation, is utilized in genetic genealogy to do a couple of things.

To confirm your connection to a specific ancestor through matches to other descendants.
To break down genealogy brick walls.
Determine ethnicity percentages which is not the topic of this article.

The same methodology is used for items 1 and 2.

In essence, to confirm that you share a common ancestor with someone, you need to either:

Be a close relative – meaning you tested your mother and/or father and you match as expected. Or, you tested another known relative, like a first cousin, for example, and you also match as expected. These known relationships and matches become important in confirming or eliminating other matches and in mapping your own chromosomes to specific ancestors.
A triangulated match to at least two others who share the same distant ancestor. This happens when you match other people whose tree indicates that you share a common ancestor, but they are not previously known to you as family.

Triangulation is the only way you can prove that you do indeed share a common ancestor with someone not previously identified as family.

In essence, triangulation is the process by which you match people who match you genetically with common ancestors through their pedigree charts. I wrote about the process in this article “Triangulation for Autosomal DNA.”

To prove that you share a common ancestor with another individual, the DNA of three proven descendants of that common ancestor must match at the same location. I should add a little * to this and the small print would say, “ on relatively large segments.” That little * is rather controversial, and we’ll talk about that in a little bit. This leads us to the next step, which is if you’re a fourth person, and you match all three of those other people on that same segment, then you too share that common ancestor. This is the process by which adoptees and those who are searching for the identity of a parent work through their matches to work forward in time from common ancestors to, hopefully, identify candidates for individuals who could be their parents.

Why do we need to do this? Isn’t just matching our DNA and seeing a common ancestor in a pedigree chart with one person enough? No, it isn’t. I recently wrote about a situation where I had a match with someone and discovered that even though we didn’t know it, and still don’t know exactly how, we unquestionably share two different ancestral lines.

When you look at someone’s pedigree chart, you may see immediately that you share more than one ancestral line. Your shared DNA could come from either line, both lines, or neither line – meaning from an unidentified common ancestor. In genealogy parlance, those are known as brick walls!

Blaine Bettinger wrote about this scenario in his now classic article, “Everyone Has Two Family Trees – A Genealogical Tree and a Genetic Tree.”

Proving a Match

The only way to prove that you actually do share a genealogy relative with someone that is not a known family member is to triangulate. This means searching other matches with the same ancestral surname, preferably finding someone with the same proven ancestral tree, and confirming that the three of you not only share matching DNA, but all three share the same matching DNA segments. This means that you share the same ancestor.

Triangulation itself is a two-step process followed by a third step of mapping your own DNA so that you know where various segments came from. The first two triangulation steps are discovering that you match other people on a common segment(s) and then determining if the matches also match each other on those same segments.

Both Family Tree DNA and 23andMe, as vendors have provided ways to do most of this. www.gedmatch.com and www.dnagedcom.com both augment the vendor offerings. Ancestry provides no tools of this type – which is, of course, what has precipitated the chromosome browser war.

Let’s look at how the vendors products work in actual practice.

Family Tree DNA

1. Chromosome browser – do they match you?

Family Tree DNA makes it easy to see who you match in common with someone else in their matching tool, by utilizing the ICW crossed X icon.

In the above example, I am seeing who I match in common with my mother. Sure enough, our three known cousins are the closest matches, shown below.

You can then push up to 5 individuals through to the chromosome browser to see where they match the participant.

The following chromosome browser is an example of a 4 person match showing up on the Family Tree DNA chromosome browser.

This example shows known cousins matching. But this is exactly the same scenario you’re looking for when you are matching previously unknown cousins – the exact same technique.

In this example, I am the participant, so these matches are matches to me and my chromosome is the background chromosome displayed. I have switched from my mother’s side to known cousins on my father’s side.

The chromosome browser shows that these three cousins all match the person whose chromosomes are being shown (me, in this case), but it doesn’t tell you if they also match each other. With known cousins, it’s very unlikely (in my case) that someone would match me from my mother’s side, and someone from my father’s side, but when you’re working with unknown cousins, it’s certainly possible. If your parents are from the same core population, like Germans or an endogamous population, you may well have people who match you on both sides of your family. Simply put, you can’t assume they don’t.

It’s also possible that the match is a genuine genealogical match, but you don’t happen to match on the exact same segments, so the ancestor can’t yet be confirmed until more cousins sharing that same ancestral line are found who do match, and it’s possible that some segments could be IBS, identical by state, meaning matches by chance, especially small segments, below the match threshold.

2. Matrix – do they match each other?

Family Tree DNA also provides a tool called the Matrix where you can see if all of the people who match on the same segment, also match each other at some place on their DNA.

The Matrix tool measures the same level of DNA as the default chromosome browser, so in the situation I’m using for an example, there is no issue. However, if you drop the threshold of the match level, you may well, and in this case, you will, find matches well below the match threshold. They are shown as matches because they have at least one segment above the match threshold. If you don’t have at least one segment above the threshold, you’ll never see these smaller matches. Just to show you what I mean, this is the same four people, above, with the threshold lowered to 1cM. All those little confetti pieces of color are smaller matches.

At Family Tree DNA, the match threshold is about 7cM. Each of the vendors has a different threshold and a different way of calculating that threshold.

The only reason I mention this is because if you DON’T match with someone on the matrix, but you also show matches at smaller segments, understand that matrix is not reporting on those, so matrix matches are not negative proof, only positive indications – when you do match, both on the chromosome browser and utilizing the matrix tool.

What you do know at this point is that these individuals all match you on the same segments, and that they match each other someplace on their chromosomes, but what you don’t know is if they match each other on the same locations where they match you.

If you are lucky and your matches are cousins or experienced genetic genealogists and are willing to take a look at their accounts, they can tell you if they match the other people on the same segments where they match you – but that’s the only way to know unless they are willing to download their raw data file to GedMatch. At GedMatch, you can adjust the match thresholds to any level you wish and you can compare one-to-one kits to see where any two kits who have provided you with their kit number match each other.

3. Downloading data – mapping your chromosome.

The “download to Excel” function at Family Tree DNA, located just above the chromosome browser graphic, on the left, provides you with the matching data of the individuals shown on the chromosome browser with their actual segment data shown. (The download button on the right downloads all of your matches, not just the ones shown in the browser comparison.)

The spreadsheet below shows the downloaded data for these four individuals. You can see on chromosome 15 (yellow) there are three distinct segments that match (pink, yellow and blue,) which is exactly what is reflected on the graphic browser as well.

On the spreadsheet below, I’ve highlighted, in red, the segments which appeared on the original chromosome browser – so these are only the matches at or over the match threshold.

As you can see, there are 13 in total.

Smaller Segments

Up to this point, the process I’ve shared is widely accepted as the gold standard.

In the genetic genealogy community, there are very divergent opinions on how to treat segments below the match threshold, or below even 10cM. Some people “throw them away,” in essence, disregard them entirely. Before we look at a real life example, let’s talk about the challenges with small segments.

When smaller segments match, along with larger segments, I don’t delete them, throw them away, or disregard them. I believe that they are tools and each one carries a message for us. Those messages can be one of four things.

This is a valid IBD, meaning identical by descent, match where the segment has been passed from one specific ancestor to all of the people who match and can be utilized as such.
This is an IBS match, meaning identical by state, and is called that because we can’t yet identify the common ancestor, but there is one. So this is actually IBD but we can’t yet identify it as such. With more matches, we may well be able to identify it as IBD, but if we throw it away, we never get that chance. As larger data bases and more sophisticated software become available, these matches will fall into place.
This is an IBS match that is a false match, meaning the DNA segments that we receive from our father and mother just happen to align in a way that matches another person. Generally these are relatively easy to determine because the people you match won’t match each other. You also won’t tend to match other people with the same ancestral line, so they will tend to look like lone outliers on your match spreadsheets, but not always.
This is an IBS match that is population based. These are much more difficult to determine, because this is a segment that is found widely in a population. The key to determining these pileup areas, as discussed in the Ancestry article about their new phasing technique, if that you will find this same segment matching different proven lineages. This is the reason that Ancestry has implemented phasing – to identify and remove these match regions from your matches. Ancestry provided a graphic of my pileup areas, although they did not identify for me where on my chromosomes these pileup regions occurred. I do have some idea however, because I’ve found a couple of areas where I have matches from my mother’s side of the family from different ancestors – so these areas must be IBS on a population level. That does not, however, make them completely irrelevant.

The challenge, and problem, is where to make the cutoff when you’re eliminating match areas based on phased data. For example, I lost all of my Acadian matches at Ancestry. Of course, you would expect an endogamous population to share lots of the same DNA – and there are a huge number of Acadian descendants today – they are in fact a “population,” but those matches are (were) still useful to me.

I utilize Acadian matches from Family Tree DNA and 23andMe to label that part of my chromosome “Acadian” even if I can’t track it to a specific Acadian ancestor, yet. I do know from which of my mother’s ancestors it originated, her great-grandfather, who is her Acadian ancestor. Knowing that much is useful as well.

The same challenge exists for other endogamous groups – people with Jewish, Mennonite/Brethren/Amish, Native American and African American heritage searching for their mixed race roots arising from slavery. In fact, I’d go so far as to say that this problem exists for anyone looking for ancestors beyond the 5^th or 6^th generation, because segments inherited from those ancestors, if there are any, will probably be small and fall below the generally accepted match thresholds. The only way you will be able to find them, today, is the unlikely event that there is one larger segments, and it leads you on a search, like the case with Sarah Hickerson.

I want to be very clear – if you’re looking for only “sure thing” segments – then the larger the matching segment, the better the odds that it’s a sure thing, a positive, indisputable, noncontroversial match. However, if you’re looking for ancestors in the distant past, in the 5^th or 6^th generation or further, you’re not likely to find sure thing matches and you’ll have to work with smaller segments. It’s certainly preferable and easier to work with large matches, but it’s not always possible.

In the Ralph and Coop paper, The Geography of Recent Genetic Ancestry Across Europe, they indicated that people who matched on segments of 10cM or larger were more likely to have a common ancestor with in the past 500 years. Blocks of 4cM or larger were estimated to be from populations from 500-1500 years ago. However, we also know that there are indeed sticky segments that get passed intact from generation to generation, and also that some segments don’t get divided in a generation, they simply disappear and aren’t passed on at all. I wrote about this in my article titled, Generational Inheritance.

Another paper by Durand et al, Reducing pervasive false positive identical-by-descent segments detected by large-scale pedigree analysis, showed that 67% of the 2-4cM segments were false positives. Conversely, that also means that 33% of the 2-4cM segments were legitimate IBD segments.

Part of the disagreement within the genetic genealogy community is based on a difference in goals. People who are looking for the parents of adoptees are looking first and primarily as “sure thing” matches and the bigger the match segment, of course, the better because that means the people are related more closely in time. For them, smaller segments really are useless. However, for people who know their recent genealogy and are looking for those brick wall ancestors, several generations back in time, their only hope is utilizing those smaller segments. This not black and white but shades of grey. One size does not fit all. Nor is what we know today the end of the line. We learn every single day and many of our learning experiences are by working through our own unique genealogical situations – and sharing our discoveries.

On this next spreadsheet, you can see the smaller segments surrounding the larger segments – in other words, in the same match cluster – highlighted in green. These are the segments that would be discarded as invalid if you were drawing the line at the match threshold. Some people draw it even higher, at 10 cM. I’m not being critical of their methodology or saying they are wrong. It may well work best for them, but discarding small segments is not the only approach and other approaches do work, depending on the goals of the researcher. I want my 33% IBD segments, thank you very much.

All of the segments highlighted in purple match between at least three cousins. By checking the other cousins accounts, I can validate that they do all match each other as well, even though I can’t tell this through the Family Tree DNA matrix below the matching threshold. So, I’ve proven these are valid. We all received them from our common ancestor.

What about the white rows? Are those valid matches, from a common ancestor? We don’t have enough information to make that determination today.

Downloading my data, and confirming segments to this common ancestor allows me to map my own chromosomes. Now, I know that if someone matches me and any of these three cousins on chromosome 15, for example, between 33,335,760 and 58,455,135 – they are, whether they know it or not, descended from our common ancestral line.

In my opinion, I would think it a shame to discount or throw away all of these matches below 7cM, because you would be discounting 39 of your 52 total matches, or 75% of them. I would be more conservative in assigning my segments with only one cousin match to any ancestor, but I would certainly note the match and hope that if I added other cousins, that segment would be eventually proven as IBD.

I used positively known cousins in this example because there is no disputing the validity of these matches. They were known as cousins long before DNA testing.

Breaking Down Brick Walls

This is the same technique utilized to break down brick walls – and the more cousins you have tested, so that you can identify the maximum number of chromosome pieces of a particular ancestor – the better.

I used this same technique to identify Sarah Hickerson in my Thanksgiving Day article, utilizing these same cousins, plus several more.

Hey, just for fun, want to see what chromosome 15 looks like in this much larger sample???

In this case, we were trying to break down a brick wall. We needed to determine if Sarah Hickerson was the mother of Elijah Vannoy. All of the individuals in the left “Name” column are proven Vannoy cousins from Elijah, or in one case, William, from another child of Sarah Hickerson. The individuals in the right “Match” column are everyone in the cousin match group plus the people in green who are Hickerson/Higginson descendants. William, in green, is proven to descend from Sarah Hickerson and her husband, Daniel Vannoy.

The first part of chromosome 15 doesn’t overlap with the rest. Buster, David and I share another ancestral line as well, so the match in the non-red section of chromosome 15 may well be from that ancestral line. It becomes an obvious possibility, because none of the people who share the Vannoy/Hickerson/Higginson DNA are in that small match group.

All of the red colored cells do overlap with at least one other individual in that group and together they form a cluster. The yellow highlighted cells are the ones over the match threshold. The 6 Hickerson/Higginson descendants are scattered throughout this match group.

And yes, for those who are going to ask, there are many more Vannoy/Hickerson triangulated groups. This is just one of over 60 matching groups in total, some with matches well above the match threshold. But back to the chromosome browser wars!

23andMe

This example from 23andMe shows why it’s so very important to verify that your matches also match each other.

Blue and purple match segments are to two of the same cousins that I used in the comparison at Family Tree DNA, who are from my father’s side. Green is my first cousin from my mother’s side. Note that on chromosome 11, they both match me on a common segment. I know by working with them that they don’t match each other on that segment, so while they are both related to me, on chromosome 11, it’s not through the same ancestor. One is from my father’s side and one is from my mother’s side. If I hadn’t already known that, determining if they matched each other would be the acid test and would separate them into 2 groups.

23andMe provides you with a tool to see who your matches match that you match too. That’s a tongue twister.

In essence, you can select any individual, meaning you or anyone that you match, on the left hand side of this tool, and compare them to any 5 other people that you match. In my case above, I compared myself to my cousins, but if I want to know if my cousin on my mother’s side matches my two cousins on my father’s side, I simply select her name on the left and theirs on the right by using the drop down arrows.

I would show you the results, but it’s in essence a blank chromosome browser screen, because she doesn’t match either of them, anyplace, which tells me, if I didn’t already know, that these two matches are from different sides of my family.

However, in other situations, where I match my cousin Daryl, for example, as well as several other people on the same segment, I want to know how many of these people Daryl matches as well. I can enter Daryl’s name, with my name and their names in the group of 5, and compare. 23andMe facilitates the viewing or download of the results in a matrix as well, along with the segment data. You can also download your entire list of matches by requesting aggregated data through the link at the bottom of the screen above or the bottom of the chromosome display.

I find it cumbersome to enter each matches name in the search tool and then enter all of the other matches names as well. By utilizing the tools at www.dnagedcom.com, you can determine who your matches match as well, in common with you, in one spreadsheet. Here’s an example. Daryl in the chart below is my match, and this tool shows you who else she matches that I match as well, and the matching segments. This allows me to correlate my match with Gwen for example, to Daryl’s match to Gwen to see if they are on the same segments.

As you can see, Daryl and I both match Gwen on a common segment. On my own chromosome mapping spreadsheet, I match several other people as well at that location, at other vendors, but so far, we haven’t been able to find any common genealogy.

Ancestry.com

At Ancestry.com, I have exactly the opposite problem. I have lots of people I DNA match, and some with common genealogy, but no tools to prove the DNA match is to the common ancestor.

Hence, this is the crux of the chromosome browser wars. I’ve just showed you how and why we use chromosome browsers and tools to show if our matches match each other in addition to us and on which segments. I’ve also illustrated why. Neither 23andMe nor Family Tree DNA provides perfect tools, which is why we utilize both GedMatch and DNAGedcom, but they do provide tools. Ancestry provides no tools of this type.

At Ancestry, you have two kinds of genetic matches – ones without tree matches and ones with tree matches. Pedigree matching is a service that Ancestry provides that the other vendors don’t. Unfortunately, it also leads people to believe that because they match these people genetically and share a tree, that the tree shown is THE genetic match and it’s to the ancestor shown in the tree. In fact, if the tree is wrong, either your tree or their tree, and you match them genetically, you will show up as a pedigree match as well. Even if both pedigrees are right, that still doesn’t mean that your genetic match is through that ancestor.

How many bad trees are at Ancestry percentagewise? I don’t know, but it’s a constant complaint and there is absolutely nothing Ancestry can do about it. All they can do is utilize what they have, which is what their customers provide. And I’m glad they do. It does make the process of working through your matches much easier. It’s a starting point. DNA matches with trees that also match your pedigree are shown with Ancestry’s infamous shakey leaf.

In fact, in my Sarah Hickerson article, it was a shakey leaf match that initially clued me that there was something afoot – maybe. I had to shift to another platform (Family Tree DNA) to prove the match however, where I had tools and lots of known cousins.

At Ancestry, I now have about 3000 matches in total, and of those, I have 33 shakey leaves – or people with whom I also share an ancestor in our pedigree charts. A few of those are the same old known cousins, just as genealogy crazy as me, and they’ve tested at all 3 companies.

The fly in the ointment, right off the bat, is that I noticed in several of these matches that I ALSO share another ancestral line.

Now, the great news is that Ancestry shows you your surnames in common, and you can click on the surname and see the common individuals in both trees.

The bad news is that you have to notice and click to see that information, found in the lower left hand corner of this screen.

In this case, Cook is an entirely different line, not connected to the McKee line shown.

However, in this next case, we have the same individual entered in our software, but differently. It wasn’t close enough to connect as an ancestor, but close enough to note. It turns out that Sarah Cook is the mother of Fairwick Claxton, but her middle name was not Helloms, nor was her maiden name, although that is a long-standing misconception that was proven incorrect with her husband’s War of 1812 documents many years ago. Unfortunately, this misinformation is very widespread in trees on the internet.

Out of curiosity, and now I’m sorry I did this because it’s very disheartening – I looked to see what James Lee Claxton/Clarkson’s wife’s name was shown to be on the first page of Ancestry’s advanced search matches.

Despite extensive genealogical and DNA research, we don’t know who James Lee Claxton/Clarkson’s parents are, although we’ve disproven several possibilities, including the most popular candidate pre-DNA testing. However, James’ wife was positively Sarah Cook, as given by her, along with her father’s name, and by witnesses to their marriage provided when she applied for a War of 1812 pension and bounty land. I have the papers from the National Archives.

James Lee Claxton’s wife, Sara Cook is identified as follows in the first 50 Ancestry search entries.

Sarah Cook – 4

Incorrect entries:

Sarah Cook but with James’ parents listed – 3
Sarah Helloms Cook – 2, one with James’ parents
Sarah Hillhorns – 15
Sarah Cook Hitson – 13, some with various parents for James
No wife, but various parents listed for James – 12
No wife, no parents – 1

I’d much rather see no wife and no parents than incorrect information.

Judy Russell has expressed her concern about the effects of incorrect trees and DNA as well and we shared this concern with Ancestry during our meeting.

Ancestry themselves in their paper titled “Identifying groups of descendants using pedigrees and genetically inferred relationships in a large database” says, “”As with all analyses relating to DNA Circles™, tree quality is also an important caveat and limitation.” So Ancestry is aware, but they are trying to leverage and utilize one of their biggest assets, their trees.

This brings us to DNA Circles. I reviewed Ancestry’s new product release extensively in my Ancestry’s Better Mousetrap article. To recap briefly, Ancestry gathers your DNA matches together, and then looks for common ancestors in trees that are public using an intelligent ranking algorithm that takes into account:

The confidence that the match is due to recent genealogical history (versus a match due to older genealogical history or a false match entirely).
The confidence that the identified common recent ancestor represents the same person in both online pedigrees.
The confidence that the individuals have a match due to the shared ancestor in question as opposed to from another ancestor or from more distant genealogical history.

The key here is that Ancestry is looking for what they term “recent genealogical history.” In their paper they define this as 10 generations, but the beta version of DNA Circles only looks back 7 generations today. This was also reflected in their phasing paper, “Discovering IBD matches across a large, growing database.”

However, the unfortunate effect has been in many cases to eliminate matches, especially from endogamous groups. By way of example, I lost my Acadian matches in the Ancestry new product release. They would have been more than 7 generations back, and because they were endogamous, they may have “looked like” IBS segments, if IBS is defined at Ancestry as more than 7 or 10 generations back. Hopefully Ancestry will tweek this algorithm in future releases.

Ancestry, according to their paper, “Identifying groups of descendants using pedigrees and genetically inferred relationships in a large database,” then clusters these remaining matching individuals together in Circles based on their pedigree charts. You will match some of these people genetically, and some of them will not match you but will match each other. Again, according to the paper, “these confidence levels are calculated by the direct-line pedigree size, the number of shared ancestral couples and the generational depth of the shared MRCA couple.”

Ancestry notes that, “using the concordance of two independent pieces of information, meaning pedigree relationships and patterns of match sharing among a set of individuals, DNA Circles can serve as supporting evidence for documented pedigree lines.” Notice, Ancestry did NOT SAY proof. Nothing that Ancestry provides in their DNA product constitutes proof.

Ancestry continues by saying that Circles “opens the possibility for people to identify distant relatives with whom they do not share DNA directly but with whom they still have genetic evidence supporting the relationship.”

In other words, Ancestry is being very clear in this paper, which is provided on the DNA Circles page for anyone with Circles, that they are giving you a tool, not “the answer,” but one more piece of information that you can consider as evidence.

You can see in my Joel Vannoy circle that I match both of these people both genetically and on their tree.

We, in the genetic genealogy community, need proof. It certainly could be available, technically – because it is with other vendors and third party sites.

We need to be able to prove that our matches also match each other, and utilizing Ancestry’s tools, we can’t. We also can’t do this at Ancestry by utilizing third party tools, so we’re in essence, stuck.

We can either choose to believe, without substantiation, that we indeed share a common ancestor because we share DNA segments with them plus a pedigree chart from that common ancestor, or we can initiate a conversation with our match that leads to either or both of the following questions:

Have you or would you upload your raw data to GedMatch?
Have you or would you upload your raw data file to Family Tree DNA?

Let the begging begin!!!

The Problem

In a nutshell, the problem is that even if your Ancestry matches do reply and do upload their file to either Family Tree DNA or GedMatch or both, you are losing most of the potential information available, or that would be available, if Ancestry provided a chromosome browser and matrix type tool.

In other words, you’d have to convince all of your matches and then they would have to convince all of the matches in the circle that they match and you don’t to upload their files.

Given that, of the 44 private tree shakey leaf matches that I sent messages to about 2 weeks ago, asking only for them to tell me the identity of our common pedigree ancestor, so far 2 only of them have replied, the odds of getting an entire group of people to upload files is infinitesimal. You’d stand a better chance of winning the lottery.

One of the things Ancestry excels at is marketing.

If you’ve seen any of their ads, and they are everyplace, they focus on the “feel good” and they are certainly maximizing the warm fuzzy feelings at the holidays and missing those generations that have gone before us.

This is by no means a criticism, but it is why so many people do take the Ancestry DNA test. It’s advertised as easy and you’ll learn more about your family. And you do, no question – you learn about your ethnicity and you get a list of DNA matches, pedigree matches when possible and DNA Circles.

The list of what you don’t get is every bit as important, a chromosome browser and tools to see whether your matches also match each other. However, most of their customers will never know that.

Judging by the high percentage of inaccurate trees I found at Ancestry in my little experiment relative to the known and documented wife’s name of James Lee Claxton, which was 96%, based on just the first page of 50 search matches, it would appear that about 96% of Ancestry’s clientele are willing to believe something that someone else tells them without verification. I doubt that it matters whether that information is a tree or a DNA test where they are shown matches with common pedigree charts and circles. I don’t mean this to be critical of those people. We all began as novices and we need new people to become interested in both genealogy and DNA testing.

I suspect that most of Ancestry’s clients, especially new ones, simply don’t have a clue that there is a problem, let alone the magnitude and scope. How would they? They are just happy to find information about their ancestor. And as someone said to me once – “but there are so many of those trees (with a wrong wife’s name), how can they all be wrong?” Plus, the ads, at least some of them, certainly suggest that the DNA test grows your family tree for you.

The good news in all of this is that Ancestry’s widespread advertising has made DNA testing just part of the normal things that genealogists do. Their marketing expertise along with recent television programs have served to bring DNA testing into the limelight. The bad news is that if people test at Ancestry instead of at a vendor who provides tools, we, and they, lose the opportunity to utilize those results to their fullest potential. We, and they, lose any hope of proving an ancestor utilizing DNA. And let’s face it, DNA testing and genealogy is about collaboration. Having a DNA test that you don’t compare against others is pointless for genealogy purposes.

When a small group of bloggers and educators visited Ancestry in October, 2014, for what came to be called DNA Day, we discussed the chromosome browser and Ancestry’s plans for their new DNA Circles product, although it had not yet been named at that time. I wrote about that meeting, including the fact that we discussed the need for a chromosome browser ad nauseum. Needless to say, there was no agreement between the genetic genealogy community and the Ancestry folks.

When we discussed the situation with Ancestry they talked about privacy and those types of issues, which you can read about in detail in that article, but I suspect, strongly, that the real reason they aren’t keen on developing a chromosome browser lies in different areas.

Ancestry truly believes that people cannot understand and utilize a chromosome browser and the information it provides. They believe that people who do have access to chromosome browsers are interpreting the results incorrectly today.
They do not want to implement a complex feature for a small percentage of their users…the number bantered around informally was 5%…and I don’t know if that was an off-the-cuff number or based on market research. However, if you compare that number with the number of accurate versus inaccurate pedigree charts in my “James Claxton’s wife’s name” experiment, it’s very close…so I would say that the 5% number is probably close to accurate.
They do not want to increase their support burden trying to explain the results of a chromosome browser to the other 95%. Keep in mind the number of users you’re discussing. They said in their paper they had 500,000 DNA participants. I think it’s well over 700,000 today, and they clearly expect to hit 1 million in 2015. So if you utilize a range – 5% of their users are 25,000-50,000 and 95% of their users are 475,000-950,000.
Their clients have already paid their money for the test, as it is, and there is no financial incentive for Ancestry to invest in an add-on tool from which they generate no incremental revenue and do generate increased development and support costs. The only benefit to them is that we shut up!

So, the bottom line is that most of Ancestry’s clients don’t know or care about a chromosome browser. There are, however, a very noisy group of us who do.

Many of Ancestry’s clients who purchase the DNA test do so as an impulse purchase with very little, if any, understanding of what they are purchasing, what it can or will do for them, at Ancestry or anyplace else, for that matter.

Any serious genealogist who researched the autosomal testing products would not make Ancestry their only purchase, especially if they could only purchase one test. Many, if not most, serious genealogists have tested at all three companies in order to fish in different ponds and maximize their reach. I suspect that most of Ancestry’s customers are looking for simple and immediate answers, not tools and additional work.

The flip side of that, however, if that we are very aware of what we, the genetic genealogy industry needs, and why, and how frustratingly lacking Ancestry’s product is.

Company Focus

It’s easy for us as extremely passionate and focused consumers to forget that all three companies are for-profit corporations. Let’s take a brief look at their corporate focus, history and goals, because that tells a very big portion of the story. Every company is responsible first and foremost to their shareholders and owners to be profitable, as profitable as possible which means striking the perfect balance of investment and expenditure with frugality. In corporate America, everything has to be justified by ROI, or return on investment.

Family Tree DNA

Family Tree DNA was the first one of the companies to offer DNA testing and was formed in 1999 by Bennett Greenspan and Max Blankfeld, both still principles who run Family Tree DNA, now part of Gene by Gene, on a daily basis. Family Tree DNA’s focus is only on genetic genealogy and they have a wide variety of products that produce a spectrum of information including various Y DNA tests, mitochondrial, autosomal, and genetic traits. They are now the only commercial company to offer the Y STR and mitochondrial DNA tests, both very important tools for genetic genealogists, with a great deal of information to offer about our ancestors.

In April 2005, National Geographic’s Genographic project was announced in partnership with Family Tree DNA and IBM. The Genographic project, was scheduled to last for 5 years, but is now in its 9^th year. Family Tree DNA and National Geographic announced Geno 2.0 in July of 2012 with a newly designed chip that would test more than 12,000 locations on the Y chromosome, in addition to providing other information to participants.

The Genographic project provided a huge boost to genetic genealogy because it provided assurance of legitimacy and brought DNA testing into the living room of every family who subscribed to National Geographic magazine. Family Tree DNA’s partnership with National Geographic led to the tipping point where consumer DNA testing became mainstream.

In 2011 the founders expanded the company to include clinical genetics and a research arm by forming Gene by Gene. This allowed them, among other things, to bring their testing in house by expanding their laboratory facilities. They have continued to increase their product offerings to include sophisticated high end tests like the Big Y, introduced in 2013.

23andMe

23andMe is also privately held and began offering testing for medical and health information in November 2007, initially offering “estimates of predisposition for more than 90 traits ranging from baldness to blindness.” Their corporate focus has always been in the medical field, with aggregated customer data being studied by 23andMe and other researchers for various purposes.

In 2009, 23andMe began to offer the autosomal test for genealogists, the first company to provide this service. Even though, by today’s standards, it was very expensive, genetic genealogists flocked to take this test.

In 2013, after several years of back and forth with 23andMe ultimately failing to reply to the FDA, the FDA forced 23andMe to stop providing the medical results. Clients purchasing the 23andMe autosomal product since November of 2013 receive only ethnicity results and the genealogical matching services.

In 2014, 23andMe has been plagued by public relations issues and has not upgraded significantly nor provided additional tools for the genetic genealogy community, although they recently formed a liaison with My Heritage.

23andMe is clearly focused on genetics, but not primarily genetic genealogy, and their corporate focus during this last year in particular has been, I suspect, on how to survive, given the FDA action. If they steer clear of that landmine, I expect that we may see great things in the realm of personalized medicine from them in the future.

Genetic genealogy remains a way for them to attract people to increase their data base size for research purposes. Right now, until they can again begin providing health information, genetic genealogists are the only people purchasing the test, although 23andMe may have other revenue sources from the research end of the business

Ancestry.com

Ancestry.com is a privately held company. They were founded in the 1990s and have been through several ownership and organizational iterations, which you can read about in the wiki article about Ancestry.

During the last several years, Ancestry has purchased several other genealogy companies and is now the largest for-profit genealogy company in the world. That’s either wonderful or terrible, depending on your experiences and perspective.

Ancestry has had an on-again-off-again relationship with DNA testing since 2002, with more than one foray into DNA testing and subsequent withdrawal from DNA testing. If you are interested in the specifics, you can read about them in this article.

Ancestry’s goal, as it is with all companies, is profitability. However, they have given themselves a very large black eye in the genetic genealogy community by doing things that we consider to be civically irresponsible, like destroying the Y and mitochondrial DNA data bases. This still makes no sense, because while Ancestry spends money on one hand to acquire data bases and digitize existing records, on the other hand, they wiped out a data base containing tens of thousands of irreplaceable DNA records, which are genealogy records of a different type. This was discussed at DNA Day and the genetic genealogy community retains hope that Ancestry is reconsidering their decision.

Ancestry has been plagued by a history of missteps and mediocrity in their DNA products, beginning with their Y and mitochondrial DNA products and continuing with their autosomal product. Their first autosomal release included ethnicity results that gave many people very high percentages of Scandinavian heritage. Ancestry never acknowledged a problem and defended their product to the end…until the day when they announced an update titled….a whole new you. They are marketing geniuses. While many people found their updated product much more realistic, not everyone was happy. Judy Russell wrote a great summary of the situation.

It’s difficult, once a company has lost their credibility, for them to regain it.

I think Ancestry does a bang up job of what their primary corporate goal is….genealogy records and subscriptions for people to access those records. I’m a daily user. Today, with their acquisitions, it would be very difficult to be a serious genealogist without an Ancestry subscription….which is of course what their corporate goal has been.

Ancestry does an outstanding job of making everything look and appear easy. Their customer interface is intuitive and straightforward, for the most part. In fact, maybe they have made both genealogy and genetic genealogy look a little too easy. I say this tongue in cheek, full well knowing that the ease of use is how they attract so many people, and those are the same people who ultimately purchase the DNA tests – but the expectation of swabbing and the answer appearing is becoming a problem. I’m glad that Ancestry has brought DNA testing to so many people but this success makes tools like the chromosome browser/matrix that much more important – because there is so much genealogy information there just waiting to be revealed. I also feel that their level of success and visibility also visits upon them the responsibility for transparency and accuracy in setting expectations properly – from the beginning – with the ads. DNA testing does not “grow your tree” while you’re away.

I’m guessing Ancestry entered the DNA market again because they saw a way to sell an additional product, autosomal DNA testing, that would tie people’s trees together and provide customers with an additional tool, at an additional price, and give them yet another reason to remain subscribed every year. Nothing wrong with that either. For the owners, a very reasonable tactic to harness a captive data base whose ear you already have.

But Ancestry’s focus or priority is not now, and never has been, quality, nor genetic genealogy. Autosomal DNA testing is a tool for their clients, a revenue generation source for them, and that’s it. Again, not a criticism. Just the way it is.

In Summary

As I look at the corporate focus of the three players in this space, I see three companies who are indeed following their corporate focus and vision. That’s not a bad thing, unless the genetic genealogy community focus finds itself in conflict with the results of their corporate focus.

It’s no wonder that Family Tree DNA sponsors events like the International DNA Conference and works hand in hand with genealogists and project administrators. Their focus is and always has been genetic genealogy.

People do become very frustrated with Family Tree DNA from time to time, but just try to voice those frustrations to upper management at either 23andMe or Ancestry and see how far you get. My last helpdesk query to 23andMe submitted on October 24^th has yet to receive any reply. At Family Tree DNA, I e-mailed the project administrator liaison today, the Saturday after Thanksgiving, hoping for a response on Monday – but I received one just a couple hours later – on a holiday weekend.

In terms of the chromosome browser war – and that war is between the genetic genealogy community and Ancestry.com, I completely understand both positions.

The genetic genealogy community has been persistent, noisy, and united. Petitions have been created and signed and sent to Ancestry upper management. To my knowledge, confirmation of any communications surrounding this topic with the exception of Ancestry reaching out to the blogging and education community, has never been received.

This lack of acknowledgement and/or action on the issues at hand frustrates the community terribly and causes reams of rather pointed and very direct replies to Anna Swayne and other Ancestry employees who are charged with interfacing with the public. I actually feel sorry for Anna. She is a very nice person. If I were in her position, I’d certainly be looking for another job and letting someone else take the brunt of the dissatisfaction. You can read her articles here.

I also understand why Ancestry is doing what they are doing – meaning their decision to not create a chromosome browser/match matrix tool. It makes sense if you sit in their seat and now have to look at dealing with almost a million people who will wonder why they have to use a chromosome browser and or other tools when they expected their tree to grow while they were away.

I don’t like Ancestry’s position, even though I understand it, and I hope that we, as a community, can help justify the investment to Ancestry in some manner, because I fully believe that’s the only way we’ll ever get a chromosome browser/match matrix type tool. There has to be a financial benefit to Ancestry to invest the dollars and time into that development, as opposed to something else. It’s not like Ancestry has additional DNA products to sell to these people. The consumers have already spent their money on the only DNA product Ancestry offers, so there is no incentive there.

As long as Ancestry’s typical customer doesn’t know or care, I doubt that development of a chromosome browser will happen unless we, as a community, can, respectfully, be loud enough, long enough, like an irritating burr in their underwear that just won’t go away.

The Future

What we “know” and can do today with our genomes far surpasses what we could do or even dreamed we could do 10 years ago or even 5 or 2 years ago. We learn everyday.

Yes, there are a few warts and issues to iron out. I always hesitate to use words like “can’t,” “never” and “always” or to use other very strongly opinionated or inflexible words, because those words may well need to be eaten shortly.

There is so much more yet to be done, discovered and learned. We need to keep open minds and be willing to “unlearn” what we think we knew when new and better information comes along. That’s how scientific discovery works. We are on the frontier, the leading edge and yes, sometimes the bleeding edge. But what a wonderful place to be, to be able to contribute to discovery on a new frontier, our own genes and the keys to our ancestors held in our DNA.

______________________________________________________________

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

Posted on October 18, 2014 by Roberta Estes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Indeed, we do live in exciting times.

Honoring Anzick

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

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

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

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

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

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

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

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Disclosure

Thank you so much.

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Tenth Annual Family Tree DNA Conference Wrapup

Posted on October 15, 2014 by Roberta Estes

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

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

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

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

Resources

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

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

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

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

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

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

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

You can find my conference postings here:

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

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

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

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

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

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

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

The Mix

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

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

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

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

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

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

Collaboration

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

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

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

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

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

Autosomal DNA Results

Note the cool double helix light fixture behind the speakers.

Tim specifically mentioned two misconceptions which I run across constantly.

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

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

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

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

Tim included a great resource slide.

Tim has graciously made his entire presentation available for download.

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

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

Upload GEDCOM Files

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

Ethics

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

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

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

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

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

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

The SNP Tsunami

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

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

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

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

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

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

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

2007 was the same.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Utilizing the Big Y for Genealogy

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

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

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

Research and Development

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

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

Don’t Forget About Y Genealogy Research

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

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

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

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

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

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

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

Publications

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

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

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

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

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

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

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

Don’t Forget about Mitochondrial DNA Either

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

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

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

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

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

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

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

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

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

myOrigins

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

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

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

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

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

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

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

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

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

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

The Changing Landscape

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

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

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

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

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

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

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

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

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

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

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

Why now?

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

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

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

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

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

Michael Hammer

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

Testing, More Testing

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

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

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

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

Thank you

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

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

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DNA Day with Ancestry

Posted on October 8, 2014 by Roberta Estes

For quite some time now, the genetic genealogy community has been beating the living tar out of Ancestry.com for not listening, among other things. Well, I’m here to say, they are listening. Now, what I can’t say is how much they are hearing. The jury is out and we will see. However, we are hopeful.

Ancestry invited a few of the leaders in the genetic genealogy field to come and meet with them this week. They dedicated the resources of eighteen of their scientists and executives to this meeting and they spent the day with us, sharing information about the science underlying their upcoming product changes and having frank discussions with the group.

This was a very cordial, informative and I think, team-building, experience, but there was far from uniform agreement. There was a great deal of discussion which I think helps everyone understand the position and reasoning of the other parties involved. Like anything else, it’s not as simple as one might hope.

Another important aspect of these meeting is that they serve to put faces with names and humanize the other people involved.

I also found it encouraging that most of the people at Ancestry are genealogists and utilize their own tools.

Tim Sullivan, CEO of Ancestry stopped by and talked with us for a few minutes. He asked us what we wanted, why and if we had any questions for him. He told us about his own genealogy experiences. And, we discovered, he does read our blogs. Tim is very actively engaged as is Ken Chahine, Senior Vice President and General Manager DNA, who is in many of the photographs because he was sitting at the end of the screen and was with us for the entire day.

I will be covering different aspects of the content of these meetings as time moves forward and as Ancestry’s new software version is implemented, but for now, I wanted to update you on the two burning questions in the genetic genealogy community.

These, as you might guess, were also the most contentious aspects of the entire meeting.

Will We Receive a Chromosome Brower?

I want to share with you readers that there is absolutely no question that Ancestry heard the message that we need a chromosome browser, loud, clear and uniformly from us. Ancestry is equally as adamant, it appears, as we are, that we don’t need one.

So, the short answer is no.

The longer answer is probably not.

Judy Russell, in comments to her article, “when less is more,” which I strongly encourage you to read, says about the chromosome browser:

“In my personal opinion, speaking only for myself and based solely on my own perceptions of the attitudes of some folks at AncestryDNA and not on any specific representations by anyone else, my judgment is that we may get a chromosome browser at AncestryDNA when hell freezes over.”

This was also followed by a comment about pigs flying…..plus, she took all the good phrases…not much left for me to say.

I think this pretty well sums it up.

I do want to discuss why Ancestry does not feel a chromosome browser is warranted. This topic was discussed directly and indirectly several times throughout the day. These concerns listed below are not necessarily in priority order based on discussions, because I couldn’t really discern a priority.

1. Given that Ancestry will hit the million kit DNA mark sometime in the first quarter of 2015, they feel that very few, a small percentage, of those people would ever utilize, or understand the results of a chromosome browser. Given that, they don’t feel it is a good investment of their engineering time to invest in something that few people, or a small percentage of the whole, will utilize.

2. Since Ancestry did not begin utilizing chromosome browsing in the beginning, they are concerned about privacy issues having to do with now introducing the feature to people who did not expect to have that to begin with.

3. Ancestry is concerned about unexpectedly and unintentionally revealing health information. For example, let’s say that today, a particular SNP is included in their information and is not known to be medically relevant. Next year, someone discovers that a particular SNP on chromosome 7 is connected to the genetic propensity for erectile dysfunction. Remember, a genetic propensity does NOT mean you have or will get the particular disease. In this case, of course, that would not apply to women.

Ancestry’s concern is that since they would have already been displaying that match on chromosome 7 between several people for months/years, the cow is proverbially out of the barn and closing the door at that point it a bit late, if possible at all.

Of course, as we pointed out to Ancestry, that’s the entire point of having testers sign a release, and both Family Tree DNA and 23andMe both deal with the same issue.

4. Ancestry feels that a chromosome browser would provide information to people that they should not be drawing conclusions from, and they are.

For example, as they showed us, there are areas in each person’s chromosome and their matches chromosomes that are what they call “pile up” areas. These are areas that we would call IBS, identical by state as opposed to IBD, identical by descent. Some of these pileup areas are so old that they could potentially be considered AIMs, or Ancestrally Informative Markers that harken back to continents like Africa, Asia or Europe.

This slide shows Cathy Ball, VP Genomics and Bioinformatics, showing me my own pileup areas. The two screens are a TV screen to the right where the colors resolved much better, and the larger screen where the display was larger.

What this shows you is that on the chart at left, I have one area that has a very large number of pileups, probably about 800 matches (out of my 12,500 total matches), two areas that have 400 each, two that have about 200. On the chart at right, the top of the chart is 25 match segments, so you can see that most of my matches fall below that. Ancestry feels that the higher matched segments are less relevant because they match to so many people, that they aren’t really indicative of shared ancestry in a genealogical timeframe.

And no, they did not tell me which chromosome these pileup segments are found on, and I’m DYING to know so that I can relate that to my ancestral chromosome mapping….but no cigar. It’s so frustrating that they know, they have the info, our info, but they won’t share it with us. I’m not referring here to the slide and my pileup, but the lack of segment information in general. I don’t know how that’s any worse that allowing customers to infer that a shakey leaf tree match is equivalent to a DNA match…..

Everyone has these pileup areas, which also means that they show up on your chromosome browser as matches. Ancestry is concerned that you will see three people, whether from a common genealogy line or not, who match on one segment and you will presume that they are genealogically related, when perhaps they aren’t, because their match is IBS from a pileup area.

Clearly, those of us who work in this field daily deal with IBS issues routinely, but Ancestry is concerned about the general consumer who doesn’t.

I suggested that the chromosome browser could be even more useful if they had a way to show but “grey out” those pileup areas, so we would be aware that their confidence is low, and to highlight the areas where the rarest alleles match, because those matches are most likely to indicate true genealogical matches. That suggestion met with polite silence.

Roberta’s Opinion

I do agree that many people won’t utilize the chromosome browser, but many people won’t utilize many of their services. That doesn’t prevent Ancestry from providing those services for those who want to utilize them. I’m fine with Ancestry making the Chromosome Browser part of a subscription kit so only subscribers have access, just like many of their data bases.

Unfortunately, without a chromosome browser, we are left with nothing concrete to base any matches on, nor the ability to utilize that information in conjunction with chromosome segment information from other companies to map our segments to various ancestors. The problem of incorrect ancestor attribution remains and will remain present in their matches.

They are changing their matching algorithm and in some ways, it will be improved, but in one way, I am gravely concerned that it will be worse. Ancestry will begin weighting various factors in calculating the match strength, and one of those factors will be the number of trees that list a particular ancestor. If you’ve just had a coronary…so did we. I thought one of the genetic genealogists was going to have the big one right there – they turned so red in the face.

A second confidence weighting factor will be the amount of source information for a particular tree which Ancestry feels helps judge the quality of the tree. In a sense, I agree, but attaching source information, perhaps incorrectly, to the wrong family, or having the wrong ancestor you’ve just attached source information to, is still the same large problem. Clearly, quality is not a matter of quantity, but just as clearly Ancestry cannot look at each tree individually and render an opinion, so they have to develop some automated methodology if they are going down this path.

Ancestry is trying to find ways to improve their matching and predictions of common ancestry. As time moves forward, I’ll be covering these developments. As someone in the meeting said, first steps first.

But back to the chromosome browser, my gut reaction to this is, and this is my opinion alone, that they don’t want to invest the development effort into something that will make the user experience more complex and may increase their customer support staff load to support and explain matching on a chromosome browser. I don’t think they believe the genealogy community has the ability to utilize and understand this type of tool. Ancestry is a genealogy marketing company. They want the user’s experience to be pleasant, easy and fulfilling…not difficult and certainly not upsetting.

Our message did not waiver, we need a chromosome browser and “trust me” simply won’t work.

The Y DNA and mtDNA Data Base

When Ancestry sent the invitation to this meeting, I had to wonder if they really thought through the fact that this meeting would occur less than a week after they decommissioned their Y and mtDNA data base.

Did they really want a group of people that were mad as wet hens arriving to meet with them? I fully expected to receive an “un-invitation” after my article and before the meeting, but I didn’t.

Without going into nitty-gritty detail, Ancestry indicates that the data base that held those results was literally on its last leg and they did not want to invest any money into something they was not bringing in any revenue and for a product they were no longer selling. I do believe that data base was indeed in its death throes because after the denial of service attack in June, it was no longer searchable.

In the ensuing discussion, the genetic genealogy community provided a number of alternative scenarios both within and outside of Ancestry as a way to salvage the information in that database. Ancestry has agreed to take the matter under consideration internally and discuss the various options. They made no promises, but I personally find it very encouraging that they are willing to discuss the matter and reconsider.

I told them I’d like nothing more than to write a retraction article that says that Ancestry did not, after all, burn the DNA courthouse.

In the same vein, I asked if they had any plans to decommission the Sorenson data base at www.smgf.org and they indicated that they do not have any plans at this point to do that. Obviously, nothing is forever, and they could reconsider in the future but at least it appears that resource is safe for now and adding the Y and mtDNA records from Ancestry into that data base was one option discussed.

In Conclusion

I do feel this was a productive meeting. The scientific aspects of having a large data base to draw from are quite interesting and I’ll be sharing some those in upcoming articles. Some of the best conversations took place beside the proverbial “water cooler.” I am hopeful that we made progress, or at least thawed the ice a little on the issues so critical for the genetic genealogy community, but time will tell. In a way, I felt like this was a United Nations type of meeting where everyone leaves with a better understanding.

______________________________________________________________

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Ancestor Reconstruction

Posted on October 3, 2014 by Roberta Estes

No, this is not Jurassic Park and we’re not actually recreating or cloning our ancestors – just on paper.

Back in early 2012, I began to discuss the possibility of using chromosome mapping of descendants to virtually recreate ancestors.

In 2013, I wrote a white paper about how to do this, and circulated it among a group of scientists who I was hoping would take the ball and run, creating tools for genetic genealogists. So far, that hasn’t happened, but what has happened is that I’ve adapted a tool created by Kitty Cooper for something entirely different than its original purpose to do a “proof of concept.”

Kitty Cooper created the Ancestor Chromosome Mapper to allow people to map the DNA contributed by different ancestors on their chromosomes. It’s exciting to see your ancestors mapped out, in color, on your chromosomes.

I utilized Kitty’s tool, found here, to map the proven DNA of my ancestors, below, utilizing autosomal matching and triangulation, to create this ancestor map of my own chromosomes. As you can see there are still a lot of blank spaces.

After thinking about this a bit, I realized that I could do the same thing for my ancestors.

The chromosomes shown would be those of an individual ancestor, and the DNA mapped onto the chromosomes would be from the proven descendants that they inherited from that ancestor. Eventually, with enough descendants we could create a “virtual file” for that ancestor to represent themselves in autosomal matching. So, one day, I might create, or find created by someone else, a DNA “recreated” file for Abraham Estes, born in 1647 in Nonington, Kent, or for Henry Bolton, born about 1760 in England, or any of my other ancestors – all from the DNA of their descendants.

I decided a while back to take this concept for a test spin.

I wanted to see a visual of Joseph Preston Bolton’s DNA on his chromosomes, and who carries it today. I wrote about this in Joseph’s 52 Ancestors article.

Utilizing Kitty Cooper’s wonderful ancestor chromosome mapping tool, a little differently than she had in mind, I mapped Joseph’s DNA and the contributors are listed to the right of his chromosome. You can build a virtual ancestor from their descendants based on common matching segments, so long as they don’t share other ancestral lines as well. I have only utilized the proven, or triangulated DNA segments, where three people match on the same segment.

We have a couple more DNA testers that descended from Joseph Bolton’s father, Henry Bolton through children other than Joseph Preston Bolton. Adding these segments to the chromosome chart generated for Joseph Preston Bolton, we see the confirmed Henry Bolton segments below.

On the chart above, I’ve only used proven segments.

On the next chart I have not been able to “prove” all of the segments through triangulation (3 people), but if all of the provisional segments are indeed Bolton segments, then Henry’s chromosome map would have a few more colored segments. Clearly, we need a lot more people to test to create more color on Henry’s map, but still, it’s pretty amazing that we can recreate this much of Henry’s chromosome map from these few descendants.

There’s a lot of promise in this technique. Henry Bolton was married twice. By looking at the DNA the two groups of children, 21 in total, have in common, we know that their common DNA comes from Henry himself. DNA that is shared between only the groups descended from first wife, Catherine Chapman, but not from second wife, Nancy Mann, or vice versa, would be attributed to the wife of the couple. Since Henry was married twice, with enough testers, it would be possible to reconstruct, in part, at least some of the genome of both wives, in addition to Henry.

Now, think for a minute, a bit further out in time.

We don’t know who Nancy Mann’s parents are for sure, although we’ve done a lot of eliminating and we know, probably, who her father was, and likely who her grandfather and great-grandfather were….but certainty is not within grasp right now.

But, it will be in the future through ancestor reconstruction.

Let’s say that the descendants of John Mann, the immigrant, reconstruct his genome. He had 4 known sons and they had several children, so that would be possible. John, the immigrant, is believed to be Nancy’s great-grandfather through son John Jr.

Now, let’s say that some of those segments that we can attribute through Henry Bolton’s children, as described above, are attributable to Nancy Mann. The X chromosome match above is positively Nancy’s DNA. How do I know that? because it came through her son, Joseph Preston Bolton, and men don’t inherit an X chromosome from their father, only their mother. So today, 3 descendants carry that segment of Nancy Mann’s X chromosome.

Let’s say that one of the Nancy Mann’s proven DNA segments (not the X, because John didn’t give his X to his son John) matches smack dab in the middle of one of the proven “John Mann” segments. We’ve just proven that indeed, Nancy is related to John.

Think about the power of this for adoptees, for those who don’t know who their parent or parents are for other reasons, and for those of us who have dead end brick walls who are wives with no surnames. Who doesn’t have those?

We have the potential, within the foreseeable future, to create “ancestor libraries” that we can match to in order to identify our ancestors. Once the ancestor is reconstructed, kind of like reconstituting something dehydrated with water, we’ll be able to utilize their autosomal DNA file to make very interesting discoveries about them and their lives. For example, eye color – at GedMatch today there is an eye color predictor. There are several ethnicity admixture tools. Want to know if your ancestor was ethnically admixed? Virtually recreate them and find out.

Once recreated, we will be able to discover hair color, skin color and all of the other traits and medical conditions that we can today discover through the trait testing at Family Tree DNA and the genetic predispositions that Promethease reveals.

Yes, there will be challenges, like who creates those libraries, moderates any disputes and where are they archived for comparison….but those are details that can be worked out. Maybe that’s one of the new roles of project administrators or maybe we’ll have ancestor administrators.

Someday, it may be possible to construct an entire family tree from your DNA combined with proven genealogy trees – not by intensely laborious work like it’s done today, but with the click of a button.

And that someday is very likely within our lifetimes, and hopefully, shortly. The technology and techniques are here to do it today.

I surely hope one of the vendors implements this functionality, and soon, because, like all genealogists, I have a list of genealogy mysteries that need to be solved!!!

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Ancient DNA Matches – What Do They Mean?

Posted on September 25, 2014 by Roberta Estes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Q – What does this ancient match mean to me?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Well, guess what….so does Anzick.

Here are his matches to the Altai Neanderthal.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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That Unruly X….Chromosome That Is

Posted on January 23, 2014 by Roberta Estes

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Something is wrong with the X chromosome. More specifically, something is amiss with trying to use it, the way we normally use recombinant chromosomes for genealogy. In short, there’s a problem.

If you don’t understand how the X chromosome recombines and is passed from generation to generation, now would be a good time to read my article, “X Marks the Spot” about how this works. You’ll need this basic information to understand what I’m about to discuss.

The first hint of this “problem” is apparent in Jim Owston’s “Phasing the X Chromosome” article. Jim’s interest in phasing his X, or figuring out where it came from genealogically, was spurred by his lack of X matches with his brothers. This is noteworthy, because men don’t inherit any X from their father, so Jim’s failure to share much of his X with his brothers meant that he had inherited most of his X from just one of his mother’s parents, and his brothers inherited theirs from the other parent. Utilizing cousins, Jim was able to further phase his X, meaning to attribute portions to the various grandparents from whence it came. After doing this work, Jim said the following”

“Since I can only confirm the originating grandparent of 51% my X-DNA, I tend to believe (but cannot confirm at the present) that my X-chromosome may be an exact copy of my mother’s inherited X from her mother. If this is the case, I would not have inherited any X-DNA from my grandfather. This would also indicate that my brother Chuck’s X-DNA is 97% from our grandfather and only 3% from our grandmother. My brother John would then have 77% of his X-DNA from our grandfather and 23% from our grandmother.”

As a genetic genealogist, at the time Jim wrote this piece, I was most interested in the fact that he had phased or attributed the pieces of the X to specific ancestors and the process he used to do that. I found the very skewed inheritance “interesting” but basically attributed it to an anomaly. It now appears that this is not an anomaly. It was, instead the tip of the iceberg and we didn’t recognize it as such. Let’s look at what we would normally expect.

Recombination

The X chromosome does recombine when it can, or at least has the capacity to do so. This means that a female who receives an X from both her father and mother receives a recombined X from her mother, but receives an X that is not recombined from her father. That is because her father only receives one X, from his mother, so he has nothing to recombine with. In the mother, the X recombines “in the normal way” meaning that parts of both her mother’s and her father’s X are given to her children, or at least that opportunity exists. If you’re beginning to see some “weasel words” here or “hedge betting,” that’s because we’ve discovered that things aren’t always what they seem or could be.

The 50% Rule

In the statistical world of DNA, on the average, we believe that each generation receives roughly half of the DNA of the generations before them. We know that each child absolutely receives 50% of the DNA of both parents, but how the grandparents DNA is divided up into that 50% that goes to each offspring differs. It may not be 50%. I am in the process of doing a generational inheritance study, which I will publish soon, which discusses this as a whole.

However, let’s use the 50% rule here, because it’s all we have and it’s what we’ve been working with forever.

In a normal autosomal, meaning non-X, situation, every generation provides to the current generation the following approximate % of DNA:

Please note Blaine Bettinger’s X maternal inheritance chart percentages from his “More X-Chromosome Charts” article, and used with his kind permission in the X Marks the Spot article.

I’m enlarging the inheritance percentage portion so you can see it better.

Taking a look at these percentages, it becomes evident that we cannot utilize the normal predictive methods of saying that if we share a certain percentage of DNA with an individual, then we are most likely a specific relationship. This is because the percentage of X chromosome inherited varies based on the inheritance path, since men don’t receive an X from their fathers. Not only does this mean that you receive no X from many ancestors, you receive a different percentage of the X from your maternal grandmother, 25%, because your mother inherited an X from both of her parents, versus from your paternal grandmother, 50%, because your father inherited an X from only his mother.

The Genetic Kinship chart, below, from the ISOGG wiki, is the “Bible” that we use in terms of estimating relationships. It doesn’t work for the X.

Let’s look at the normal autosomal inheritance model as compared to the maternal X chart fan chart percentages, above, and similar calculations for the paternal side. Remember, the Maternal Only column applies only to men, because in the very first generation, men’s and women’s inheritance percentages diverge. Men receive 100% of their X from their mothers, while women receive 50% from each parent.

Recombination – The Next Problem

The genetic genealogy community has been hounding Family Tree DNA incessantly to add the X chromosome matching into their Family Finder matching calculations.

On January 2, 2014, they did exactly that. What’s that old saying, “Be careful what you ask for….” Well, we got it, but “it” doesn’t seem to be providing us with exactly what we expected.

First, there were many reports of women having many more matches than men. That’s to be expected at some level because women have so many more ancestors in the “mix,” especially when matching other women.

23andMe takes this unique mixture into consideration, or at least attempts to compensate for it at some level. I’m not sure if this is a good or bad thing or if it’s useful, truthfully. While their normal autosomal SNP matching threshold is 7cM and 700 matching SNPs within that segment, for X, their thresholds are:

Male matched to male – 1cM/200 SNPs
Male matched to female – 6cM/600 SNPs
Female matched to female – 6cM/1200 SNPs

Family Tree DNA does not use the X exclusively for matching. This means that if you match someone utilizing their normal autosomal matching criteria of approximately 7.7cM and 500 SNPs, and you match them on the X chromosome, they will report your X as matching. If you don’t match someone on any chromosome except the X, you will not be reported as a match.

The X matching criteria at Family Tree DNA is:

1cM/500 SNPs

However, matching isn’t all of the story.

The X appears to not recombine normally. By normally, I don’t mean something is medically wrong, I mean that it’s not what we are expecting to see in terms of the 50% rule. In essence, we would expect to see approximately half of the X of each parent, grandfather and grandmother, passed on to the child from the mother in the maternal line where recombination is a possibility. That appears to not be happening reliably. Not only is this not happening in the nice neat 50% number, the X chromosome seems to be often not recombining at all. If you think the percentages in the chart above threw a monkey wrench into genetic genealogy predictions, this information, if it holds up in a much larger test, in essence throws our predictive capability, at least as we know it today, out the window.

The X Doesn’t Recombine as Expected

In my generational study, I noticed that the X seemed not to be recombining. Then I remembered something that Matt Dexter said at the Family Tree DNA Conference in November 2013 in Houston. Matt has the benefit of having a full 3 generation pedigree chart where everyone has been tested, and he has 5 children, so he can clearly see who got the DNA from which of their grandparents.

I contacted Matt, and he provided me with his X chromosomal information about his family, giving me permission to share it with you. I have taken the liberty of reformatting it in a spreadsheet so that we can view various aspects of this data.

First, note that I have sorted these by grandchild. There are two females, who have the opportunity to inherit from 3 grandparents. The females inherited one copy of the X from their mother, who had two copies herself, and one copy of the X from her father who only had his mother’s copy. Therefore, the paternal grandfather is listed above, but with the note “cannot inherit.” This distinguishes this event from the circumstance with Grandson 1 where he could inherit some part of his maternal grandfather’s X, but did not.

For the three grandsons, I have listed all 4 grandparents and noted the paternal grandmother and grandfather as “cannot inherit.” This is of course because the grandsons don’t inherit an X from their father. Instead they inherit the Y, which is what makes them male.

According to the Rule of 50%, each child should receive approximately half of the DNA of each maternal grandparent that they can inherit from. I added the columns, % Inherited cM and % Inherited SNP to illustrate whether or not this number comes close to the 50% we would expect. The child MUST have a complete X chromosome which is comprised of 18092 SNPs and is 195.93cM in length, barring anomalies like read errors and such, which do periodically occur. In these columns, 1=100%, so in the Granddaughter 1 column of % Inherited cM, we see 85% for the maternal grandfather and about 15% for the maternal grandmother. That is hardly 50-50, and worse yet, it’s no place close to 50%.

Granddaughter 1 and 2 must inherit their paternal grandmother’s X intact, because there is nothing to recombine with.

Granddaughter 2 inherited even more unevenly, with about 90% and 10%, but in favor of the other grandparent. So, statistically speaking, it’s about 50% for each grandparent between the two grandchildren, but it is widely variant when looking at them individually.

Grandson 1, as mentioned, inherited his entire X from his maternal grandmother with absolutely no recombination.

Grandsons 2 and 3 fall much closer to the expected 50%.

The problem for most of us is that you need 3 or 4 consecutive generations to really see this happening, and most of us simply don’t have data that deep or robust.

A recent discussion on the DNA Genealogy Rootsweb mailing list revealed several more of these documented occurrences, among them, two separate examples where the X chromosome was unrecombined for 4 generations.

Robert Paine, a long-time genetic genealogy contributor and project administrator reported that in his family medical/history project, at 23andMe, 25% of his participants show no recombination on the X chromosome. That’s a staggering percentage. His project consists of 21 people in with 2 blood lines tested 5 generations deep and 2 bloodlines tested at 4 generations

One woman’s X matches her great-great-grandmother’s X exactly. That’s 4 separate inheritance events in a row where the X was not recombined at all.

The graphic below, provided by Robert, shows the chromosome browser at 23andMe where you can see the X matches exactly for all three participants being compared.

The screen shot is of the gg-granddaughter Evelyn being compared to her gg-grandmother, Shevy, Evelyn’s g-grandfather Rich and Evelyn’s grandmother Cyndi. 23andme only lets you compare 3 individuals at a time so Robert did not include Evelyn’s mother Shay, who is an exact match with Evelyn.

Where Are We?

So what does this mean to genetic genealogy? It certainly does not mean we should throw the baby out with the bath water. What it is, is an iceberg warning that there is more lurking beneath the surface. What and how big? I can’t tell you. I simply don’t know.

Here’s what I can tell you.

The X chromosome matching can tell you that you do share a common ancestor someplace back in time.

The amount of DNA shared is not a reliable predictor of how long ago you shared that ancestor.

The amount of DNA shared cannot predict your relationship with your match. In fact, even a very large match can be many generations removed.

The absence of an X match, even with someone closely related whom you should match does not disprove a descendant relationship/common ancestor.

The X appears to not recombine at a higher rate than previously thought, the previous expectation being that this would almost never happen.

The X, when it does recombine appears to do so in a manner not governed by the 50% rule. In fact, the 50% rule may not apply at all except as an average in large population studies, but may well be entirely irrelevant or even misleading to the understanding of X chromosome inheritance in genetic genealogy.

The X is still useful to genetic genealogists, just not in the same way that other autosomal data is utilized. The X is more of an auxiliary chromosome that can provide information in addition to your other matches because of its unique inheritance pattern.

Unfortunately, this discovery leaves us with more questions than answers. I found it incomprehensible that this phenomenon has never been studied in humans, or in animals, for that matter, at least not that I could find. What few references I did find indicated that the X seems to recombine with the same frequency as the other autosomes, which we are finding to be untrue.

What is needed is a comprehensive study of hundreds of X transmission events at least 3 generations deep.

As it turns out, we’re not the only ones confused by the behavior of the X chromosome. Just yesterday, the New York Times had an article about Seeing the X Chromosome in a New Light. It seems that either one copy of the X, or the other, is disabled cell by cell in the human body. If you are interested in this aspect of science, it’s a very interesting read. Indeed, our DNA continues to both amaze and amuse us.

A special thank you to Jim Owston, Matt Dexter, Blaine Bettinger and Robert Paine for sharing their information.

Additional sources:

Polymorphic Variation in Human Meiotic
Recombination (2007)
Vivian G. Cheung
University of Pennsylvania
http://repository.upenn.edu/cgi/viewcontent.cgi?article=1102&context=be_papers

A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome, Science October 2005, Myers et al
http://www.sciencemag.org/content/310/5746/321.full.pdf
Supplemental Material
http://www.sciencemag.org/content/suppl/2005/10/11/310.5746.321.DC1

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