Concepts – CentiMorgans, SNPs and Pickin’ Crab

In autosomal DNA testing, you’ll see the terms centiMorgans, represented as cM and SNPs, which stands for single nucleotide polymorphism, combined.

These are two terms that are used to discuss thresholds and measurements of matching amounts of autosomal DNA segments.

These two terms, relative to autosomal DNA, are two parts of a whole, kind of like the left and right hand.

CentiMorgans are units of recombination used to measure genetic distance. You can read a scientific definition here.

For our conceptual purposes, think of centiMorgans as lines on a football field. They represent distance.

football fabric 2

SNPs are locations that are compared to each other to see if mutations have occurred.  Think of them as addresses on a street where an expected value occurs. If values at that address are different, then they don’t match.  If they are the same, then they do match.  For autosomal DNA matching, we look for long runs of SNPs to match between two people to confirm a common ancestor.

Think of SNPs as blades of grass growing between the lines on the football field.  In some areas, especially in my yard, there will be many fewer blades of grass between those lines than there would be on either a well maintained football field, or maybe a manicured golf course.  You can think of the lighter green bands as sparse growth and darker green bands as dense growth.

If the distance between 2 marks on the football field is 5cM and there are 550 blades of grass growing there, you’ll be a match to another person if all of your blades of grass between those 2 lines match if the match threshold was 5cM and 500 SNPs.

So, for purposes of autosomal DNA, the combination of distance, centiMorgans, and the number of SNPs within that distance measurement determines if someone is considered a match to you. In other words, if the match is over the threshold as compared to your DNA, meaning the match is deemed to be relevant by the party setting the threshold.  Think of track and field hurdles.  To get to the end (match), you have to get over all of the hurdles!

hurdles

By Ragnar Singsaas – Exxon Mobil ÅF Golden League Bislett Games 2008, CC BY 2.0, https://commons.wikimedia.org/w/index.php?curid=5288962

For example, a threshold of 7 cM and 700 SNPs means that anyone who matches you OVER BOTH of these thresholds will be displayed as a match.  So centiMorgans and SNPs work together to assure valid matches.

Thresholds

These two numbers, cMs and SNPs, are used in conjunction with each other. Why?  Because the distribution of SNPs within cM boundaries is not uniform.  Some areas of the human genome have concentrations of SNPs and some areas are known as “SNP deserts.”  So distance alone is not the only relevant factor.  How many blades of grass growing between the lines matters.

Each of the vendors selects a default threshold that they feel will give you the best mix of not too many false positives, meaning matches that are identical by chance, and not too many false negatives, meaning people who do actually match you genealogically that are eliminated by small amounts of matching DNA. Unfortunately, there is no line in the sand, so no matter where the vendor sets that threshold, you’re probably going to miss something in either or both directions.  It’s the nature of the beast.

Company Min cMs Min SNPs Comment
Family Tree DNA 7cM for any one segment + 20cM total 500 After the initial match, you can view down to 1cM and 500 SNPs to people you match
23andMe 7cM 700
Ancestry 5cM after Timber and associated phasing routines Unknown Timber population based phasing removes matches they determine to be “too matchy” or population based
GedMatch User selectable – default is 7 User selectable – default is 700

As you might guess, there many opinions about the optimum threshold combinations to use – just about as many opinions as people!

These are important values, because the combined size of those matches to an individual allows you to roughly estimate the relationship range to the person you match.

As a general rule, the vendors do a relatively good job, with some exceptions that I’ve covered elsewhere and amount to beating a dead horse (Ancestry’s Timber, no chromosome browser). Of course, one of the big draws of GedMatch is that you can set your own cM and SNP matching thresholds.

Having said that, if you come from an endogamous population, you may want to raise your threshold to 10cM or even higher, depending on what you’re trying to accomplish

Effectively Using cMs and SNPs

Your personal goals have a lot to do with the thresholds you’ll want to select.

If you are new at genetic genealogy, you will first want to pursue your best matches, meaning the highest number of matching centiMorgans/SNPs, because they will be the low hanging fruit and the easiest matches to connect genealogically. Said another way, you’ll match your closer relatives on bigger chunks of DNA, so concentrate on those first.  Successes are encouraging and rewarding!

Your match to a second cousin, for example, will have a significant amount of shared DNA and second cousins share common great-grandparents – 2 of 8 people in that generation on your tree – so relatively easy to identity – as these things go.

The chart below shows the expected percentage of shared DNA in a given match pair, in this case, first and second cousins with a first cousin once removed thrown in for good measure. Also shown is the expected amount of shared centiMorgans for the given relationship, the average amount of shared DNA from a crowd sourced project titled The Shared cM Project by Blaine Bettinger and the range of shared DNA found in that same project.

A pedigree chart of my family members fitting those categories is shown below, plus the actual amount of shared cMs of DNA to the right.

shared cM table

The chart below shows my DNA matches to my first cousin once removed, Cheryl.

Since we do match at Family Tree DNA above the match threshold, I can view all of my matching segments to Cheryl down to 1cM and 500 SNPs.

Cheryl chart

Just as a matter of interest, I’ve color coded the cM segments:

  • >10 cM = green
  • 7-10 cM = yellow
  • <7 = red

This means that if these were the largest matching segments, you would or would not be able to see them at the various thresholds of 7 and 10 cM.

If the matching threshold is at the default of 7cM, the green and yellow segments would be displayed.

If the matching threshold was set at 10, only the green cM segments are going to be shown.

At Family Tree DNA, you can select various threshold display options when using the chromosome browser tool, but not for initial matching. In other words, you have to match at their default threshold before you can see your smaller segments or alter your threshold display.

Some people want to see all of their DNA that matches, and some only want to see the large and compelling pieces, those green segments.  Neither choice is wrong, simply a matter of personal preference and individual goals.

The “large and compelling” part of that statement brings me back to why you’re participating in genetic genealogy in the first place, those individual goals.  The larger segments are going to lead to common ancestors who are generally easier to find and identify, unless you have an unidentified parent or a misattributed parental event.

You would never start with smaller segments in terms of matching, but that does not mean those smaller segments are never useful.  In fact, after you’ve managed to analyze all of your low hanging fruit, and you’re ready to research or concentrate on those ugly brick walls, groupings of those smaller segments in descendants may just be your lifesaver.

Surviving Phasing

However, now I’m curious. How many of those smaller segments do stand up to the test of parental phasing, meaning they match both me and my parent?  If my match (Cheryl) matches both me and my parent, then Cheryl does not match me by chance on that segment so the match is genealogical in nature, the matching DNA proven to have descended to me from my mother.

Let’s see.

Cheryl Mom me chart

In order to phase my results with Cheryl against my mother, I copied Mother’s results into the same spreadsheet, above, color coding our rows so you can see them easier. “Cheryl matching Mom” rows are apricot and “Cheryl matching me” rows are yellow.

You can see that in some cases, like the first two rows, the two rows are identical which means I inherited all of Mom’s DNA in that segment and Cheryl inherited the same segment from her father, matching both Mom and me.

In other cases, I inherited part of Mom’s DNA on a particular segment.  I could also have inherited none of a particular segment.

In fact, of the 27 segments where I match Mom on any part of the segment, I match her on the entire segment 18 times, or 66.6% and on part of the segment 9 times, or 33.3%.

I left the color coding in the cM column the same as it was before, in my rows, to indicate small, medium and large segments. The small segments are red, which would be the most likely NOT to phase with my mother, in other words, the most likely to be Identical by Chance, not descent.  If Cheryl and I are Identical by Chance on these segments, it means that the reason I’m matching Cheryl is NOT because I inherited that chunk of DNA from mother. If Mom and I both match Cheryl, they Cheryl and I are Identical by Desent, meaning I inherited that piece of DNA from my mother, so the match is not because Cheryl’s DNA is randomly matching that of both of my parents.

In the spreadsheet below, I removed mother’s rows to eliminate clutter, but I color coded mine. The rows that show red in the CHR and SNP columns BOTH are rows that did NOT phase with my mother, meaning these matches were indeed identical to Cheryl by chance.  The rows that are red ONLY in the cM column (and not in the CHR column) are small segments that DID phase with my mother, so those are identical by descent (IBD).

Cheryl Me phased chart

Here’s the interesting part.

  • All of the large segments, 10cM and over passed phasing. They are legitimate IBD matches.
  • One of 2 of the medium cM matches passed phasing.
  • Of the 15 smaller segments, ranging in size from 1.38 cM to 6.14 cM, more than half, 8, passed phasing. Seven did not. The smallest segment to pass phasing was 1.38 cM. I suspect that part of the reason that the smaller cM segments are passing phasing is that the SNP threshold is held steady at 500 SNPs. In another (unpublished) study, dropping the SNP threshold below 500 results in a dramatic increase in matches (roughly fourfold) and a very small percentage of those matches phase with parents.

Small Segments Guidelines

There has been a lot of spirited debate about the usage, or not, of small segments, so I’m going to provide some guidelines.  Let me preface this by saying that none of this is worth getting your knickers in a knot, so please don’t.  If you don’t want to include or utilize small segments, then just don’t.

  • What is and is not a small segment can vary depending on who you are talking to and the context of the conversation.
  • Small segments CAN and do survive parental phasing, as shown above.
  • Small segments CAN be triangulated to a particular ancestor. Triangulated in this sense means that this segment is found in the descendants of a group of people (3 or more) proven to descend from the same ancestor AND who all match each other on the same segment.
  • Not all small segments can be triangulated to a common ancestor.  But then again, the same can be said for larger segments too.  It’s more difficult and unlikely to be successful with smaller segments unless you are starting with a group of people who descend from a common ancestor and are looking for “ancestral DNA.”
  • Small segments, even after triangulation, can be found matching a different lineage. This is an indicator that while the descendants of the first group share this DNA segment from a specific ancestor, it may also be prevalent in a population in general, which would cause the same segment to show up matching in a second lineage from the same region as well. I have an example where my Acadian line also matches a different German line on a particular segment – which really isn’t surprising given the geography and history of Germany and France..
  • Small segments without the benefit of other tools such as parental phasing, triangulation and match groups are, at this time, a waste of time genealogically. This may not always be the case.
  • Never start with small segments.
  • Never draw conclusions from small segments alone, meaning without corroborating evidence.
  • Use small segments only in context of a combination of parental phasing, triangulation and match groups.
  • Just because you match a group of people, out of context, on a segment (small or otherwise) doesn’t mean that you share a common ancestor. The smaller the segment, the more likely it is to be either IBC or IBP. Situations where the DNA is exactly the same from both parents, meaning everyone has all As in that location, for example, are called runs of homozygosity and the smaller the segment, the more likely you are to encounter ROH segments which appear as phased matches.  Yes, another cruel joke of nature.

As a proof point relative to how deceptive small segment matching out of context can be, I ran my kit against my friend who is unquestionably 100% Jewish. I have no Jewish ancestry.  At 7cM/700 SNPs we have no matches, at 3cM/300SNPs we have 7 matching segments.

Me to Jewish match

However, matching this individual to my phased parents, none of these segments match both me and either one of my phased parent. Phased parent kits, at GedMatch are kits reflecting the half of my parents DNA I received from that parent.  If you have one or both parents who have tested, you can create phased kits with instructions from this article.

Lowering the match threshold even further to 100 SNPs and 1cM, my Jewish friend and I match on a whopping 714 tiny matching segments, over 1100 cM total, but all very small pieces of DNA. Because of the absolute known 100% Jewish heritage of my friend, and my known non-Jewish heritage, these matches must be either IBC, identical by chance or perhaps some small segments of IBP, identical by population from a very long time ago when both of our ancestors lived in the Middle East, meaning thousands of years ago.  Bottom line, they are not genealogically relevant to either of us.  I repeated this same experiment with someone that is 100% Asian, with the same type of results.  You will match everyone at this threshold, including ancient DNA matches tens of thousands of years old.

The message here is that you can work from the “top down” with small segments, meaning in a known relationship situation like with my cousin and other relatives, but you cannot work from the bottom up with small segments as you have no way to differentiate the wheat from the chaff.

In the Crumley study, there are groups of small segments (greater than 3cM/300SNPs) that persist in multiple descendants of James Crumley born in 1712.  In this case, because you can separate the wheat from the chaff with more than 50 participants, others who triangulate with those small segments and match the group of Crumley descendants may well share a common ancestor at some point in time, especially if they can phase with their parents on those segments to prove the match is not IBC.

  • Remember, your match on any segment to one person can be IBD meaning you have identified the common ancestor, your match to another person on that same segment IBC, and yet to a third person, IBP where your match survives generational phasing, but you may never find the common ancestor due to the age of the segment or endogamy.
  • When utilizing small segments, I generally don’t drop the SNP threshold below 500, as the number of matches increases exponentially and the valid matches decrease proportionately as well. I’ll be publishing more on this shortly.
  • I do fully believe, within this set of cautionary criteria, that small segments can be useful. I also believe that small segments can be very easily misinterpreted. The use of matching segments has a lot to do with combining different pieces of evidence to build confidence in what the “match” is telling you. I wrote about the Autosomal DNA Matching Confidence Spectrum here.
  • Small segments should only be utilized after one has a good grasp of how genetic genealogy works and by utilizing the tools available to restrict those segments to genealogically descended DNA. In other words, small segments are for the advanced user. However, maintain those small segment groupings and triangulations in your spreadsheet, because when you have the level of experience needed to work with those small segments, they’ll be available for you to work with.  You may discover that most of your DNA triangulates by using large segments and you don’t need to utilize those small segments at all.
  • If you send me a list of matches from GedMatch with the cM set to 1 and the SNPs set to 100 and ask me what I think, I would simply to refer you to this article. But if I did reply, I would tell you that unless you have corroborating evidence, I think you’re wasting your time, but it’s your time and you’re welcome to do what you want with it. Life is about learning.
  • If you tell me you’ve drawn any conclusions from those types of matches (1cM and 100 SNPs), I’m going to be inconvincible without other tools such as genealogical proof,  parental phasing and triangulation groups that prove the segments to be valid to a specific ancestor for the people about whom you’re drawing conclusions. I might even suggest you look at the raw data in those segments to see if you’re dealing with runs of homozygosity.

Netting It Out

The net-net of this is that small segments can be useful, but it takes a lot more work because of the inherent questionable nature of small segment matches. This goes along with that old adage of “extraordinary claims require extraordinary evidence.”  Just be ready to roll up your shirt sleeves, because small segments are a lot more work!

Now having said all of that, I very much encourage continuing to triangulate your small segments and pay attention to them. You may notice patterns very relevant to your own genealogy, or you may learn that those patterns were somewhat deceptive – like IBD that turned into IBP.  Still useful and interesting, but perhaps not as originally intended.

Without continuing and ongoing research, we’ll never learn how to best utilize small segments nor develop the tools and techniques to sort the wheat from the chaff. Just be appropriately paranoid about conclusions based on small segments, especially small segments alone, and the smaller the segment, the more paranoid you should be!

There is a very big difference between working with small segments along with larger matching data and genealogy, which I encourage, and drawing conclusions based on small segment data alone and out of context, which I highly discourage.

Let’s hope that all of your matches come with large segments and matching ancestors in their trees!!!

Pickin’ Crab

You know, working with different cM levels and SNPs, especially as segments get smaller and more challenging, I’m reminded of “picking crab” at a good old North Carolina crab bake. You would never start out with a crab bake for breakfast.  You kind of have to work your way up to pickin’ crab – the same as small segments.  And you never pick crab alone. It’s a group activity, shared with friends and kin.  So is genetic genealogy.

You’ll need lessons, at first, in how to “pick crab” effectively. There’s a particular technique to it.  Friends teach friends.  You’ll find cousins you didn’t know you had, like Dawn in the brown shirt below, giving lessons to Anne.

Dawn lessons

A little practice and you’ll get it.

Just because it’s not easy doesn’t mean it’s not productive, especially when everyone works together!  And the results are “very good,” if you just have patience and work through the process.  If you decide that you “can’t pick crab,” then you’re right, you can’t pick crab, and you’ll just have to go hungry and miss out on all the fun!  Don’t let that happen.  Hint – sometimes the fun is in the pickin’!

Here’s hoping you can solve all of your brick walls with large cMs and large SNP counts, and if not, here’s hoping you enjoy “picking crab” with a group of friends and cousins and who will contribute to the ongoing research.

Pickin’ crab, or working on identifying difficult ancestors is always better when collaborating with others! Find cousins and fellow collaborators and enjoy!!! Genetic genealogy is not something you can do alone – it’s dependent on sharing.

crab pickin

Sometimes it’s as much about the friends and cousins you meet on the journey and the adventures along the way as it is about the answer at the end.

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Concepts – Identical by…Descent, State, Population and Chance

In genetic genealogy, what does it mean when someone says they are “identical by” something…and what are those various somethings?

In autosomal DNA, where your DNA on chromosomes 1-22 (and sometimes X) is compared to other people for matches of a size that indicates a genealogical relationship, you can actually match people in different ways, for different reasons.

But first, let’s make one thing perfectly clear. There is only one way to obtain your autosomal DNA – and that’s through your parents, 50% from each parent.  However, how much of their (and your) ancestor’s DNA you receive is not necessarily half of what they received from that ancestor.

If you receive ANY DNA from that ancestor, it MUST BE through your parents. There is no other way to inherit DNA.

Period.

No. Other. Way.

If you would like to read the Concepts article about inheritance and matching, click here. If you don’t understand autosomal DNA inheritance and matching concepts, you won’t be able to understand the rest of this article.

Identical by Descent (IBD)

When you match someone because you share DNA from a common ancestor, that is called Identical by Descent, or IBD. That’s what you want.  That’s a good thing, genealogically speaking.

Let’s take a look at how an IBD segment of DNA works. In the graphic below, the strand location is in the first column.  The next two pink columns are the two strands that your mother carries, one from her Mom and one from her Dad – and the values in each location from each parent.  Columns 4 and 5 are the two blue strands of DNA carried by your Dad, one from his Mom and one from his Dad.  The final two columns are what you inherited from both your mother and your father.  In this case, we made it easy and you simply inherited one of each of their strands entirely.  Yes, that does happen in some cases for a particular chromosome segment, but not all of the time.  Conceptually, for this example, it doesn’t matter.

Identical 1

Your Inheritance

In this example, you inherited strand 1 from your Mom, all As and strand 2 from Dad, all Gs. Your match, shown in the graphic below, matches you on all As, so also matches your mother.  This phenomenon is called parental phasing, which means we know it’s a legitimate match because the person matches both you and one of your parents.

For purposes of this conceptual discussion you must match on all 10 locations for this to be considered a matching segment. So in this case, your matching threshold is “10 locations.”

Identical 2

Your Match Matches You and Your Mother’s DNA – Identical by Descent

Now, understand that while I’ve shown “You” with your strands color coded so you can see who you received which pieces of DNA from – that’s not how your DNA really looks. There is no color coding in nature.  I’ve added color coding to make understanding these concepts easier.

This is how you and your parents DNA really look:

Identical 3

Notice that in your parents, their parent’s strands are mixed back and forth, so you really can’t tell which DNA came from whom.  It’s the same for you too.

What the matching software has to do is to look for a common letter between you and your match.

So, at location 1, you inherited an A and a G from your parents. Your match has an A and a T, so you and your match share a common A.  If you look at all of your matches locations, they share a common A with you on all of those locations.  It just so happens you received that A from your mother – but without your Mom to compare to – you have no way to know which parent that particular DNA value came from.  So, the best matching software can do is to tell you that indeed, you do match – on 10 locations in a row – so this is considered a match and will be reported as such on your match list.

Why you match is another matter altogether.

And, ahem….there is another way to match someone, aside from receiving ancestral DNA from your parents. I know, this is a bad joke isn’t it.  Yes, it is, but it’s real.

So, to summarize, there is no other way to obtain your DNA except 50% from one parent and 50% from the other.

However there are two ways to match someone:

  • Identical by Descent, IBD, meaning you match someone because you share the same DNA segment that you received from an ancestor through a parent, as shown above.
  • Identical by Chance, IBC, meaning that you match someone, but randomly – not by inheritance.  How the heck can that happen?

Let’s look at how that can happen.

Identical by Chance (IBC)

Because you receive a strand of DNA from each of your parents, but that DNA is all intermixed in you, you can possibly match someone else by virtue of the fact that they aren’t actually matching your ancestral DNA segment inherited from an ancestor, but by chance they are matching DNA that bounces back and forth between your parents’ DNA.

Identical 4

Your Match Matches Neither of your Parents’ Strands of DNA – Identical by Chance

In this example, you can see the that you inherited the same strands from your parents as in example 1 above, but your match is now matching you, not on your mother’s strand 1, all As, but on a combination of A from your mother and G from your father. Therefore, they don’t match either of your parents on this segment, because they are matching you by chance and not because you share a strand of DNA that you received from a common ancestor on this segment with your match.

This is easy to discern because while they match you, they won’t match either of your parents on that segment, because the match is not on an ancestral DNA segment, passed down from an ancestor. Using parental phasing, you compare your matches to your parents to see which “side” they fall on.  If they fall on neither parents’ side, then they are IBC or identical by chance.

Identical 5

Identical By Chance Identified Through Parental Phasing

In this example, you can see that you match all of these people. By using parental phasing, you can tell that you are identical by descent (IBD) to everyone except John, who matches neither of your parents, so your match to John is identical by chance (IBC).  We will talk more in an upcoming article about Parental Phasing.

If you don’t have your parents to compare to, and you match multiple people on the same segment, there should be 2 groups of people who all match each other on that segment – one group from your Mom’s side and one from your Dad’s side – even if you can’t identify your common ancestor. If there are people who don’t fit into either of those two groups, because they don’t match those group members, then the misfits are identical by chance.

Even if your parents are unavailable, this is a situation where testing other relatives helps, and the closer the better, because those relatives will also fall into those match groups and will help identify which group is from which side of your family, and which ancestral line.

In the example below, using the same people from the phased parent example above, we no longer have our parents to compare to, but we do have an aunt, Mom’s sister, and an uncle, Dad’s brother. By comparing those who match us to our close relatives – if everyone in the match group matches each other, then we know they are IBD and the come from Mom’s side of the family or Dad’s side of the family.

Identical 6

Identical By Chance Identified Through Close Family Match Groups

In general matching, meaning not on specific segments, just on your match list, if John and I match, but John doesn’t match mother’s sister, it could mean that John matches me on a different segment that my aunt didn’t inherit from my grandparents but that my mother did. So the match could be valid, even though he doesn’t match my aunt.

However, moving to the segment matching level, shown above, we can differentiate, at least for that segment.  This is yet another example of why segment analysis tools are so critically important.

If we only had one matching group, the green above, we would not be able to say that John was IBC on this segment, because John might be matching me on Dad’s side.

But in this case, we have proof points on both sides of this same segment, with two match groups, green from Mom and blue from Dad.  Mom’s side has a match group of 4+me (including her sister) who all match each other on this same segment, indicating that they all descend through my mother’s side of my tree.  On Dad’s side, we have his brother and two other people who match each other and me on those same segments.

Since John matches no one in either match group on either side, his match to me on this segment must be IBC.  You can read more about match groups and confidence here.

Identical by chance segments tend to be smaller segments, because the chances of matching more locations in a row by chance diminish as the number of locations increases.

Ok, so now you’ve got this – the two ways to match. Identical by descent (IBD) and identical by chance (IBC,) nature’s cruel joke.

So, what the heck are identical by state (IBS) and identical by population (IBP).

Good questions.

Identical by State (IBS)

Identical by state is really an archaic term now, but you’ll likely still run into it from time to time. Understand that genetic genealogy is still a really new field of discovery.  Initially, terms weren’t defined very well and have since evolved.  IBD was used to mean a match where you could find a common ancestral line.  IBS, or identical by state, was often used when one could not find the ancestral line.  What this implied was that the match was not genealogical in nature.  But that often wasn’t true.  Just because we can’t determine who the common ancestor is, doesn’t mean that common ancestor doesn’t exist.  After we have more matches, we may well figure out the common ancestor at a later time.

What are some reasons we might not be able to figure out who our common ancestor is?

  • There’s a NPE or undocumented adoption in one line or the other.
  • The pedigree chart of one or both people doesn’t go back far enough in time.
  • The pedigree chart of one or both people is incorrect.
  • Not enough people have tested to connect the dots between the DNA. For example, we may share a common surname, Dodson, but be unable to actually pinpoint which Dodson line/ancestor we share.
  • The match is identical by population (IBP) and not in a genealogical timeframe. We see this most often in highly endogamous populations.
  • The match is identical by chance (IBC) and there is no common ancestor.

The tendency in the past has been to assume that if you can’t find the ancestor, then the problem MUST be that the match is Identical by State. But the problem is that identical by state includes two categories that are mutually exclusive; Identical by Chance and Identical by Population.

Identical by chance means there is no common ancestor, as we illustrated above.

Identical by Population means there IS a common ancestor, and you did receive your DNA from that ancestor, but you may not be able to figure out who it was because it’s too far back in time and many people from that same population base share that DNA segment.

So, today, we don’t say IBS anymore, we say either IBD and if it’s not IBD then it’s either IBC or IBP, but not IBS. If someone says IBS, you need to ask and see if you can determine whether they mean, IBC or IBP, or if they are trying to say something else like “I can’t identify the common ancestor so it must be IBS.”

Identical by Population (IBP)

Identical by population means that a large portion of a population group shares a particular segment of DNA. Some people feel IBP segments are not useful and want all of these segments to be stripped away by population (or academic) based phasing software.

In some cases, if an individual is 100% Jewish, for example, they will have many IBP segments from within the highly endogamous Jewish population. They don’t have any other ancestral DNA segments from ancestors who aren’t Jewish to contrast against in their DNA, so their IBP segments are not useful to them, and are in fact, just in the opposite.  There are too many IBP segments and they are in the way – often referred to as “noise” because they are not genealogically useful, even though they are descended from an ancestor (IBD).  So, yes, IBP is a subset of IBD.

However, for someone who has the following genealogy, these same population based endogamous segments can be extremely useful and informative.

Identical 7

In this conceptual pedigree chart, the Jewish person married a non-Jewish person with deep colonial American ancestry. Their child “Colonial Jew” married someone who was mixed “Irish Asian.”  The person at the bottom, “me,” is not themselves endogamous but has several widely variant lines in their heritage including endogamous lines.

If I’m lucky enough to have an African population segment, that tells me very clearly which genealogical line that match is probably from. But if those IBP segments are removed, they can’t inform me in this situation.

Same with Jewish, or Asian, or Native American.

Let’s see how this might work in real matching.

Let’s say your mother’s A value is only found in African populations, and it’s found in very high proportions in African populations and much less frequently anyplace else in the world, except for where Africans settled.

Identical 8

Identical By Population Example Where Mother’s A Equals African

A few match outcomes are possible:

  1. You match with someone and you can discern a common ancestor or at least an ancestral line because you have only one African genealogical line – an ancestor in your mother’s line, like in the pedigree chart above.
  2. You match with someone and you cannot discern a common ancestor because many or all of your lines are African, similar to the Jewish example.
  3. You match with someone and you identify a common ancestor, but later a second genealogical line matches on that same segment because the segment is so common in the African population. This means you could have received that actual DNA segment from either ancestral line.
  4. Some DNA testing company runs academic or population based phasing software against your DNA and removes that segment entirely because they’ve decided that it occurs too frequently in a population to be useful. In this case, you won’t match that person at all.
  5. Some DNA testing company runs academic or population based phasing software against your DNA and removes that segment entirely because they’ve decided that particular segment in your results is “too matchy” so it must therefore be “invalid” and population based. This is often referred to as a “pile-up” and means that you have proportionally more matches on that segment than you do on other segments. If your “pile-up” segments are removed in this case, again, you won’t match at all. This is exactly what happened to my Acadian matches when Ancestry implemented their Timber phasing software, which removes pile-ups.

The graph below was provided to me at Ancestry DNA Day as an example of my own “pile-up” areas in my genome.

genome pileups

Ancestry with their Timber routine uses population phasing and removes your areas they deem “too matchy”? This helps Jewish and other heavily endogamous people by removing truly population based matches that are spurious and the contributing ancestor impossible to discern.  An endogamous individual could achieve much of the same effect by utilizing a higher matching threshold for their own matches, although that’s not an option at Ancestry.

However, for those of us who are not entirely endogamous, but who may have endogamous lines or lines from different parts of the world, population based phasing removes valuable informational segments and therefore, prevents valuable matches. When Ancestry ran Timber against my results, I lost all but one of my Acadian matches.  Yes, Acadians are heavily endogamous, but in my case, that line accounts for 1 of my 16 great-great-grandparents.  Believe me, if I had a tool to put all of my autosomal matches in one of 16 buckets, I would think it was a wonderful day!!!

16 gggrandparents

Because of endogamy, I actually carried MORE Acadian DNA that I would otherwise carry from a non-endogamous population – so yes, I am very matchy to my Acadian cousins, especially on smaller segments – or I was until Ancestry stripped all of that way.  Thankfully, I still have all of my matches at Family Tree DNA.

Why is endogamous DNA more matchy? Because endogamous populations only have the founders’ DNA and they just keep passing the same founder DNA around and around.

Ironically, another word for this kind of phasing is called “excess IBD” phasing. This means that “someone” decides unilaterally how much matching one “should” have and just chops the rest off at that threshold.  Clearly, that threshold for a fully Jewish person and me would be very different – and one size absolutely does NOT fit all.

I want to show you one more example of what population based phasing does. It chops the heart out of segments that would otherwise match.

People whose parents also test should match their parents on exactly 22 segments, one for each chromosome – because each child is a 100% match to their parents. If there is a read error or two (or three), then let’s say they could have as many as 25 matches, because some chromosomes are chopped in two because of a technical issue.  It occasionally happens.

At Ancestry, we’re seeing 80 to 120 matches for each parent/child pair, which means Timber is removing 58 to roughly 100 legitimate segments that you received from your parent.  One individual reported that they match one parent on 150 different segments, meaning that Ancestry removed 128 segments they decided are “too matchy” but are very clearly ancestral, or IBD, because all of your DNA must match your parents DNA on the strand they gave you.  However because of Timber’s removal of “too matchy” segments, the person no longer matches their parent on that removed segment – or on any of those 58 to 128 removed segments.  And remember, there is only one way to receive your DNA, so all of your DNA must match that of your parents.  You have no invalid matches to your parents DNA.  You can read more here.

Here’s a visual of what IBP phased matching does to you. Recall in our example that you need 10 contiguous matching locations to be considered a match.  I’m showing 20 locations in this example.

Identical 9

Normal Matching – No Population or Academic Phasing

In this first example, the DNA you inherited from your mother is a combination of T and A, where A=African. Notice that only part of what you inherited from your mother is the A this time.

In normal matching without IBP phasing, above, the matching threshold is still 10, but you match your match on a segment that totals 20 locations or units. Now it’s up to you to see if you can identify your common ancestor.

In the IBP phased example, below, your African DNA is removed as a result of population based phasing software. Your African DNA used to be where the red spot with no values is showing in the You 1 column.  Therefore, you still match on the Ts, but you only have a contiguous run of 7 Ts, then the 7 As phasing deleted, then 6 more matching Ts.  The problem is, of course, that instead of a nice matching segment of 20 units, above, you now have no match at all because you don’t have 10 matching locations in a row.  Of course, the same IBP phasing would apply to your mother, so your match would not match your mother either, which means that a valid parentally phased match is not reported.

Identical 10

Population Based Phased Matching Example Removing African

What’s worse, you’ll never have that opportunity to see if you can find your common ancestor, because you and your match will never be reported as a match. This is a lost opportunity.  In the first “normal matching” example, you may never BE able to find that common ancestor, but you have the opportunity to try.  In the second IBP phased matching example, you certainly won’t ever find your common ancestor because you’re not shown as a match.  When population based or academic phasing is involved, you’ll never know what you are missing.

This chopping phenomenon is not a rare occurrence with population based phasing. In fact, if you divide 100 removed segments by 22 chromosomes, there are approximately 4 artificial “chops” taken out of every one of your 22 chromosomes with each parent at Ancestry, and in some cases, more.  The person who now matches their parent on 150 segments has an average of 5.8 artifical phasing induced chops in each chromosome.  When Ancestry implemented Timber, many people lost between 80% and 90% of their total matches.  Mine went from 13,100 to 3,350, a loss of about 75%.  At least some of those were valid and we had identified common ancestral lines.

So, identical by population (IBP) doesn’t necessarily mean bad, unless you’re entirely endogamous. If you’re entirely endogamous, then IBP means challenging and can generally be overcome by looking at larger matching segments, which are less likely to be either IBP or IBC.

Identical by population can be very useful in someone not entirely endogamous in that it preserves ancestral DNA in a given population. In people who carry a combination of different endogamous lines, such as Jewish and Acadian, this phenomenon can actually be very useful, because it increases your chances of matching other individuals from that ancestral line – and being able to assign them appropriately.

Identical by What?

So, in summary, you are either identical because you received DNA from a common ancestor (IBD) or identical by chance (IBC) because nature is playing a mean joke on you and you match, literally, by chance because your match’s DNA is zigzagging back and forth between your parents’ DNA.  And by the way, you can match someone IBD on one segment and the same person IBC or IBP on others.

If you match someone but that person does not also match either of your parents, then it’s an IBC, identical by chance, match. Measuring a match against both yourself and your parents to determine if the match is IBC or IBD is called parental phasing.  We will have a Concepts article shortly about Parental Phasing, so stay tuned.

If you don’t have parents to match against, your matches on any segment should cleanly cluster into two matching groups where you match them and your matches also match each other on that same segment. One group for your mother’s side and one group for your father’s side.  Those who match you but don’t fall into one group or the other are identical by chance, like John in our example.  Of course, you won’t be able to sort these out until you have several matches on that segment.  This is also why testing all available upstream family members is so useful.

If you’re not IBC, you’re IBD meaning that you and your match received that DNA segment from a common ancestor, whether or not you can identify that ancestor.

Identical by population (IBP) is a type or subset of identical by descent (IBD) where many people from that same population group carry the same DNA segment. This is seen in its most pronounced fashion in heavily endogamous populations such as Ashkenazi Jews.

If you are from a highly endogamous population, you will have many IBP matches, generally on smaller segments that have been chopped up over time, and you will want to use a higher matching threshold, perhaps up to 10cM, for genealogical matching, or higher.

If you have endogamous lines in your tree, but are not entirely endogamous, IBP segments may actually be beneficial because you may be able to attribute matches to a specific line, even if not the specific ancestor in that line.

The smaller the segment, the more likely it is to be less useful to you, whether IBD or IBP – but that isn’t to say all small segments should be disregarded because they are assumed to be either IBC or not useful. That’s not the case.  Some are IBD and all IBD segments have the potential to be very useful.  Kitty Cooper just recently reported another wonderful success story using a 6cM triangulated segment.

If you’re highly endogamous, or only looking only for the low hanging fruit, which is more likely to be immediately rewarding, then work with only larger segment matches. They are less likely to be IBC or IBP and more likely to yield results more quickly.  I always begin with the largest matching segments, because not only are they easier to assign to an ancestor, but those matching people may also have smaller matching segments that I can tentatively (pending triangulation) attribute to that specific ancestor as well.

Here’s a handy-dandy cheat sheet if you’re having trouble remembering “Identical by What.”

Identical by Chart

Understand that working with genetic genealogy and autosomal DNA is much like panning for gold. You may get lucky and find a large nugget or two smiling at you from on top the pile, but the majority of your rewards will be as a result of hard work sifting and panning and accumulating those small golden flakes that aren’t immediately obvious and useful.  Cumulatively, they may well hold your family secrets and the keys to locks long ago frozen shut.

Here’s hoping all your matches are IBD!!!!!

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Autosomal DNA Matching Confidence Spectrum

Are you confused about DNA matches and what they mean…different kinds of matches…from different vendors and combined results between vendors.  Do you feel like lions and tigers and bears…oh my?  You’re not alone.

As the vendors add more tools, I’ve noticed recently that along with those tools has come a significant amount of confusion surrounding matches and what they mean.  Add to this issue confusion about the terminology being used within the industry to describe various kinds of matches.  Combined, we now have a verbiage or terminology issue and we have confusion regarding the actual matches and what they mean.  So, as people talk, what they mean, what they are trying to communicate and what they do say can be interpreted quite widely.  Is it any wonder so many people are confused?

I reached out within the community to others who I know are working with autosomal results on a daily basis and often engaged in pioneering research to see how they are categorizing these results and how they are referring to them.

I want to thank Jim Bartlett, Blaine Bettinger, Tim Janzen and David Pike (in surname alphabetical order) for their input and discussion about these topics.  I hope that this article goes a long way towards sorting through the various kinds of matches and what they can and do mean to genetic genealogists – and what they are being called.  To be clear, the article is mine and I have quoted them specifically when applicable.

But first, let’s talk about goals.

Goals

One thing that has become apparent over the past few months is that your goals may well affect how you interpret data.  For example, if you are an adoptee, you’re going to be looking first at your closest matches and your largest segments.  Distant matches and small segments are irrelevant at least until you work with the big pieces.  The theory of low hanging fruit, of course.

If your goal is to verify and generally validate your existing genealogy, you may be perfectly happy with Ancestry’s Circles.  Ancestry Circles aren’t proof, as many people think, but if you’re looking for low hanging fruit and “probably” versus “positively,” Ancestry Circles may be the answer for you.

If you didn’t stop reading after the last sentence, then I’m guessing that “probably” isn’t your style.

If your goal is to prove each ancestor and/or map their segments to your DNA, you’re not going to be at all happy with Ancestry’s lack of segment data – so your confidence and happiness level is going to be greatly different than someone who is just looking to find themselves in circles with other descendants of the same ancestor and go merrily on their way.

If you have already connected the dots on most of your ancestry for the past 4 or 5 generations, and you’re working primarily with colonial ancestors and those born before 1700, you may be profoundly interested in small segment data, while someone else decides to eliminate that same data on their spreadsheet to eliminate clutter.  One person’s clutter is another’s goldmine.

While, technically, the different types of tests and matches carry a different technical confidence level, your personal confidence ranking will be influenced by your own goals and by some secondary factors like how many other people match on a particular segment.

Let’s start by talking about the different kinds of matching.  I’ve been working with my Crumley line, so I’ll be utilizing examples from that project.

Individual Matching, Group Matching and Triangulation

There is a difference between individual matching, group matching and triangulation.  In fact, there is a whole spectrum of matching to be considered.

Individual Matching

Individual matching is when someone matches you.

confidence individual match

That’s great, but one match out of context generally isn’t worth much.  There’s that word, generally, because if there is one thing that is almost always true, it’s that there is an exception to every rule and that exception often has to do with context.  For example, if you’re looking for parents and siblings, then one match is all you need.

If this match happens to be to my first cousin, that alone confirms several things for me, assuming there is not a secondary relationship.  First, it confirms my relationship with my parent and my parent’s descent from their parents, since I couldn’t be matching my first cousin (at first cousin level) if all of the lines between me and the cousin weren’t intact.

confidence cousins

However, if the match is to someone I don’t know, and it’s not a close relative, like the 2nd to 4th cousins shown in the match above, then it’s meaningless without additional information.  Most of your matches will be more distant.  Let’s face it, you have a lot more distant cousins than close cousins.  Many ancestors, especially before about 1900, were indeed, prolific, at least by today’s standards.

So, at this point, your match list looks like this:

confidence match list

Bridget looks pretty lonely.  Let’s see what we can do about that.

Matching Additional People

The first question is “do you share a common ancestor with that individual?”  If yes, then that is a really big hint – but it’s not proof of anything – unless they are a close relative match like we discussed above.

Why isn’t a single match enough for proof?

You could be related to this person through more than one ancestral line – and that happens far more than I initially thought.  I did an analysis some time back and discovered that about 15% of the time, I can confirm a secondary genealogical line that is not related to the first line in my tree.  There were another 7% that were probable – meaning that I can’t identify a second common ancestor with certainty, but the surname and location is the same and a connection is likely.  Another 8% were from endogamous lines, like Acadians, so I’m sure there are multiple lines involved.  And of those matches (minus the Acadians), about 10% look to have 3 genealogical lines, not just two.  The message here – never assume.

When you find one match and identify one common genealogical line, you can’t assume that is how you are genetically related on the segment in question.

Ideally, at this point, you will find a third person who shares the common ancestor and their DNA matches, or triangulates, between you and your original match to prove the connection.  But, circumstances are not always ideal.

What is Triangualtion?

Triangulation on the continuum of confidence is the highest confidence level achievable, outside of close relative matching which is evident by itself without triangulation.

Triangulation is when you match two people who share a common ancestor and all three of you match each other on that same segment.  This means that segment descended to all three of you from that common ancestor.

This is what a match group would look like if Jerry matches both John and Bridget.

confidence example 1 match group

Example 1 – Match Group

The classic definition of triangulation is when three people, A, B and C all match each other on the same segment and share a known, identifiable common ancestor.  Above, we only have two.  We don’t know yet if John matches Bridget.

A matches B
A matches C
B matches C

This is what an exact triangulation group would look like between Jerry, John and Bridget.  Most triangulation matches aren’t exact, meaning the start and/or end segment might be different, but some are exact.

confidence example 2 triangulation group

Example 2 – Triangulation Group

It’s not always possible to prove all three.  Sometimes you can see that Jerry matches Bridget and Jerry matches John, but you have no access to John or Bridget’s kits to verify that they also match each other.  If you are at Family Tree DNA, you can run the ICW (in common with) tool to see if John and Bridget do match each other – but that tool does not confirm that they match on the same segment.

If the individuals involved have uploaded their kits to GedMatch, you have the ability to triangulate because you can see the kit numbers of your matches and you can then run them against each other to verify that they do indeed match each other as well.  Not everyone uploads their kits to GedMatch, so you may wind up with a hybrid combination of triangulated groups (like example 2, above) and matching groups (like example 1, above) on your own personal spreadsheet.

Matching groups (that are not triangulated) are referred to by different names within the community.  Tim Janzen refers to them as clusters of cousins, Blaine as pseudo triangulation and I have called them triangulation groups in the past if any three within the group are proven to be triangulated. Be careful when you’re discussing this, because matching groups are often misstated as triangulated groups.  You’ll want to clarify.

Creating a Match List

Sometimes triangulation options aren’t available to us.  For example, at Family Tree DNA, we can see who matches us, and we can see if they match each other utilizing the ICW tool, but we can’t see specifically where they match each other.  This is considered a match group.  This type of matching is also where a great deal of confusion is introduced because these people do match each other, but they are NOT (yet) triangulated.

What we know is that all of these people are on YOUR match list, but we don’t know that they are on each other’s match lists.  They could be matching you on different sides of your DNA or, if smaller segments, they might be IBC (identical by chance.)

You can run the ICW (in common with) tool at Family Tree DNA for every match you have.  The ICW tool is a good way to see who matches both people in question.  Hopefully, some of your matches will have uploaded trees and you can peruse for common ancestors.

The ICW tool is the little crossed arrows and it shows you who you and that person also match in common.

confidence match list ftdna

You can run the ICW tool in conjunction with the ancestral surname in question, showing only individuals who you have matches in common with who have the Crumley surname (for example) in their ancestral surname list.  This is a huge timesaver and narrows your scope of search immediately.  By clicking on the ICW tool for Ms. Bridget,  you see the list, below of those who match both the person whose account we are signed into and Ms. Bridget, below.

confidence icw ftdna

Another way to find common matches to any individual is to search by either the current surname or ancestral surnames.  The ancestral surname search checks the surnames entered by other participants and shows them in the results box.

In the example above, all of these individuals have Crumley listed in their surnames.  You can see that I’ve sorted by ancestral surname – as Crumley is in that search box.

Now, your match lists looks like this relative to the Crumley line.  Some people included trees and you can find your common ancestor on their tree, or through communications with them directly.  In other cases, no tree but the common surname appears in the surname match list.  You may want to note those results on your match list as well.

confidence match list 2

Of course, the next step is to compare these individuals in a matrix to see who matches who and the chromosome browser to see where they match you, which we’ll discuss momentarily.

Group Matching

The next type of matching is when you have a group of people who match each other, but not necessarily on the same segment of DNA.  These matching groups are very important, especially when you know there is a shared ancestor involved – but they don’t indicate that the people share the same segment, nor that all (or any) of their shared segments are from this particular ancestor.  Triangulation is the only thing that accomplishes proof positive.

This ICW matrix shows some of the Crumley participants who have tested and who matches whom.

confidence icw grid

You can display this grid by matching total cM or by known relationship (assuming the individuals have entered this information) or by predicted relationship range.  The total cMs shared is more important for me in evaluating how closely this person might be related to the other individual.

The Chromosome Browser

The chromosome browser at Family Tree DNA shows matches from the perspective of any one individual.  This means that the background display of the 22 Chromosomes (plus X) is the person all of the matches are comparing against. If you’re signed in to your account, then you are the black background chromosomes, and everyone is being compared against your DNA.  I’m only showing the first 6 chromosomes below.

confidence chromosome browser

You can see where up to 5 individuals match the person you’re comparing them to.  In this case, it looks like they may share a common segment on chromosome 2 among several descendants.  Of course, you’d need to check each of these individuals to insure that they match each other on this same segment to confirm that indeed, it did come from a common ancestor.  That’s triangulation.

When you see a grouping of matches of individuals known to descend from a common ancestor on the same chromosome, it’s very likely that you have a match group (cluster of cousins, pseudo triangulation group) and they will all match each other on that same segment if you have the opportunity to triangulate them, but it’s not absolute.

For example, below we have a reconstructed chromosome 8 of James Crumley, the common ancestor of a large group of people shown based on matches.  In other words, each colored segment represents a match between two people.  I have a lot more confidence in the matches shown with the arrows than the single or less frequent matches.

confidence chromosome 8 match group'

This pseudo triangulation is really very important, because it’s not just a match, and it’s not triangulation.  The more people you have that match you on this segment and that have the same ancestor, the more likely that this segment will triangulate.  This is also where much of the confusion is coming from, because matching groups of multiple descendants on the same segments almost always do triangulate so they have been being called triangulation groups, even when they have not all been triangulated to each other.  Very occasionally, you will find a group of several people with a common ancestor who triangulate to each other on this common segment, except one of a group doesn’t triangulate to one other, but otherwise, they all triangulate to others.

confidence triangulation issue

This situation has to be an error of some sort, because if all of these people match each other, including B, then B really must match D.  Our group discussed this, and Jim Bartlett pointed out that these problem matches are often near the vendor matching threshold (or your threshold if you’re using GedMatch) and if the threshold is lowered a bit, they continue to match.  They may also be a marginal match on the edge, so to speak or they may have a read error at a critical location in their kit.

What “in common with” matching does is to increase your confidence that these are indeed ancestral matches, a cousin cluster, but it’s not yet triangulation.

Ancestry Matches

Ancestry has added another level of matching into the mix.  The difference is, of course, that you can’t see any segment data at all, at Ancestry, so you don’t have anything other than the fact that you do match the other person and if you have a shakey leaf hint, you also share a common ancestor in your trees.

confidence ancestry matches

When three people match each other on any segment (meaning this does not infer a common segment match) and also share a common ancestor in a tree, they qualify to be a DNA Circle.  However, there is other criteria that is weighted and not every group of 3 individuals who match and share an ancestor becomes a DNA Circle.  However, many do and many Circles have significantly more than three individuals.

confidence Phoebe Crumley circle

This DNA Circle is for Phebe Crumley, one of my Crumley ancestors.  In this grouping, I match one close family group of 5 people, and one individual, Alyssa, all of whom share Phebe Crumley in their trees.  As luck would have it, the family group has also tested at Family Tree DNA and has downloaded their results to GedMatch, but as it stands here at Ancestry, with DNA Circle data only…the only thing I can do is to add them to my match list.

confidence match list 3

In case you’re wondering, the reason I only added three of the 5 family members of the Abija group to my match list is because two are children of one of the members and their Crumley DNA is represented through their parent.

While a small DNA Circle like Phebe Crumley’s can be incorrect, because the individuals can indeed be sharing the DNA of a different ancestor, a larger group gives you more confidence that the relationship to that group of people is actually through the common ancestor whose circle you are a member of.  In the example Circle shown below, I match 6 individuals out of a total of 21 individuals who are all interrelated and share Henry Bolton in their tree.

Confidence Henry Bolton circle

New Ancestor Discoveries

Ancestry introduced New Ancestor Discoveries (NADs) a few months ago.  This tool is, unfortunately, misnamed – and although this is a good concept for finding people whose DNA you share, but whose tree you don’t – it’s not mature yet.

The name causes people to misinterpret the “ancestors” given to them as genuinely theirs.  So far, I’ve had a total of 11 NADS and most have been easily proven false.

Here’s how NADs work.  Let’s say there is a DNA Circle, John Doe, of 3 people and you match two of them.  The assumption is that John Doe is also your ancestor because you share the DNA of his descendants.  This is a critically flawed assumption.  For example, in one case, my ancestors sister’s husband is shown as my “new ancestor discovery” because I share DNA with his descendants (through his wife, my ancestor’s sister.)  Like I said, not mature yet.

I have discussed this repeatedly, so let’s just suffice it to say for this discussion, that there is absolutely no confidence in NADs and they aren’t relevant.

Shared Matches

Ancestry recently added a Shared Matches function.

For each person that you match at Ancestry, that is a 4th cousin or closer and who has a high confidence match ranking, you can click on shared matches to see who you and they both match in common.

confidence ancestry shared matches

This does NOT mean you match these people through the same ancestor.  This does NOT mean you match them on the same segment.  I wrote about how I’ve used this tool, but without additional data, like segment data, you can’t do much more with this.

What I have done is to build a grid similar to the Family Tree DNA matrix where I’ve attempted to see who matches whom and if there is someone(s) within that group that I can identify as specifically descending from the same ancestor.  This is, unfortunately, extremely high maintenance for a very low return.  I might add someone to my match list if they matched a group (or circle) or people that match me, whose common ancestor I can clearly identify.

Shared Matches are the lowest item on the confidence chart – which is not to say they are useless.  They can provide hints that you can follow up on with more precise tools.

Let’s move to the highest confidence tool, triangulation groups.

Triangulation Groups

Of course, the next step, either at 23andMe, Family Tree DNA, through GedMatch, or some combination of each, is to compare the actual segments of the individuals involved.  This means, especially at Ancestry where you have no tools, that you need to develop a successful begging technique to convince your matches to download their data to GedMatch or Family Tree DNA, or both.  Most people don’t, but some will and that may be the someone you need.

You have three triangulation options:

  1. If you are working with the Family Inheritance Advanced at 23andMe, you can compare each of your matches with each other. I would still invite my matches to download to GedMatch so you can compare them with people who did not test at 23andMe.
  2. If you are working with a group of people at Family Tree DNA, you can ask them to run themselves against each other to see if they also match on the same segment that they both match you on. If you are a project administrator on a project where they are all members, you can do this cross-check matching yourself. You can also ask them to download their results to GedMatch.
  3. If your matches will download their results to GedMatch, you can run each individual against any other individual to confirm their common segment matches with you and with each other.

In reality, you will likely wind up with a mixture of matches on your match list and not everyone will upload to GedMatch.

Confirming that segments create a three way match when you share a common ancestor constitutes proof that you share that common ancestor and that particular DNA has been passed down from that ancestor to you.

confidence match list 4

I’ve built this confidence table relative to matches first found at Family Tree DNA, adding matches from Ancestry and following them to GedMatch.  Fortunately, the Abija group has tested at all 3 companies and also uploaded their results to GedMatch.  Some of my favorite cousins!

Spectrum of Confidence

Blaine Bettinger built this slide that sums up the tools and where they fall on the confidence range alone, without considerations of your goals and technical factors such as segment size.  Thanks Blaine for allowing me to share it here.

confidence level Blaine

These tools and techniques fall onto a spectrum of confidence, which I’ve tried to put into perspective, below.

confidence level highest to lowest

I really debated how to best show these.  Unfortunately, there is almost always some level of judgment involved. In some cases, like triangulation at the 3 vendors, the highest level is equivalent, but in other cases, like the medium range, it really is a spectrum from lowest to highest within that grouping.

Now, let’s take a look at our matches that we’ve added to our match list in confidence order.

confidence match list 5

As you would expect, those who triangulated with each other using some chromosome browser and share a common ancestor are the highest confidence matches – those 5 with a red Y.  These are followed by matches who match me and each other but not on the same segment (or at least we don’t know that), so they don’t triangulate, at least not yet.

I didn’t include any low confidence matches in this table, but of the lowest ones that are included, the shakey leaf matches at Ancestry that won’t answer inquiries and the matches at FTDNA who do share a common surname but didn’t download their information to be triangulated are the least confident of the group.  However, even those lower confidence matches on this chart are medium, meaning at Ancestry they are in a Circle and at FTDNA, they do match and share a common surname.  At Family Tree DNA, they may eventually fall into a triangulation group of other descendants who triangulate.

Caveats

As always, there are some gotchas.  As someone said in something I read recently, “autosomal DNA is messy.”

Endogamy

Endogamous populations are just a mess.  The problem is that literally, everyone is related to everyone, because the founder population DNA has just been passed around and around for generations with little or no new DNA being introduced.

Therefore, people who descend from endogamous populations often show to be much more closely related than they are in a genealogical timeframe.

Secondly, we have the issue pointed out by David Pike, and that is when you really don’t know where a particular segment came from, because the segment matches both the parents, or in some cases, multiple grandparents.  So, which grandparent did that actual segment that descended to the grandchild descend from?

For people who are from the same core population on both parent’s side, close matches are often your only “sure thing” and beyond that, hopefully you have your parents (at least one parent) available to match against, because that’s the only way of even beginning to sort into family groups.  This is known as phasing against your parents and while it’s a great tool for everyone to use – it’s essential to people who descend from endogamous groups. Endogamy makes genetic genealogy difficult.

In other cases, where you do have endogamy in your line, but only in one of your lines, endogamy can actually help you, because you will immediately know based on who those people match in addition to you (preferably on the same segment) which group they descend from.  I can’t tell you how many rows I have on my spreadsheet that are labeled with the word “Acadian,” “Brethren” and “Mennonite.”  I note the common ancestor we can find, but in reality, who knows which upstream ancestor in the endogamous population the DNA originated with.

Now, the bad news is that Ancestry runs a routine that removes DNA that they feel is too matchy in your results, and most of my Acadian matches disappeared when Ancestry implemented their form of population based phasing.

Identical by Population

There is sometimes a fine line between a match that’s from an ancestor one generation further back than you can go, and a match from generations ago via DNA found at a comparatively high percentage in a particular population.  You can’t tell the difference.  All you know is that you can’t assign that segment to an ancestor, and you may know it does phase against a parent, so it’s valid, meaning not IBC or identical by chance.

Yes, identical by population segment matching is a distinct problem with endogamy, but it can also be problematic with people from the same region of the world but not members of endogamous populations.  Endogamy is a term for the timeframe we’re familiar with.  We don’t know what happened before we know what happened.

From time to time, you’ll begin to see something “odd” happened where a group of segments that you already have triangulated to one ancestor will then begin to triangulate to a second ancestor.  I’m not talking about the normal two groups for every address – one from your Mom’s side and one from your Dad’s.  I’m talking, for example, when my Mom’s DNA in a particular area begins to triangulate to one ancestral group from Germany and one from France.  These clearly aren’t the same ancestors, and we know that one particular “spot” or segment range that I received from her DNA can only come from one ancestor.  But these segment matches look to be breaking that rule.

I created the example below to illustrate this phenomenon.  Notice that the top and bottom 3 all match nicely to me and to each other and share a common ancestor, although not the same common ancestor for the two groups.  However, the range significantly overlaps.  And then there is the match to Mary Ann in the middle whose common ancestor to me is unknown.

confidence IBP example

Generally, we see these on smaller segment groups, and this is indicative that you may be seeing an identical by population group.  Many people lump these IBP (identical by population) groups in with IBC, identical by chance, but they aren’t.  The difference is that the DNA in an IBP group truly is coming from your ancestors – it’s just that two distinct groups of ancestors have the same DNA because at some point, they shared a common ancestor.  This is the issue that “academic phasing” (as opposed to parental phasing) is trying to address.  This is what Ancestry calls “pileup areas” and attempts to weed out of your results.  It’s difficult to determine where the legitimate mathematical line is relative to genealogically useful matches versus ones that aren’t.  And as far as I’m concerned, knowing that my match is “European” or “Native” or “African” even if I can’t go any further is still useful.

Think about this, if every European has between 1 and 4% Neanderthal DNA from just a few Neanderthal individuals that lived more than 20,000 years ago in Europe – why wouldn’t we occasionally trip over some common DNA from long ago that found its way into two different family lines.

When I find these multiple groupings, which is actually relatively rare, I note them and just keep on matching and triangulating, although I don’t use these segments to draw any conclusions until a much larger triangulated segment match with an identified ancestor comes into play.  Confidence increases with larger segments.

This multiple grouping phenomenon is a hint of a story I don’t know – and may never know.  Just because I don’t quite know how to interpret it today doesn’t mean it isn’t valid.  In time, maybe its full story will be revealed.

ROH – Runs of Homozygosity

Autosomal DNA tests test someplace over 500,000 locations, depending on the vendor you select.  At each of those locations, you find a value of either T, A, C or G, representing a specific nucleotide.  Sometimes, you find runs of the same nucleotide, so you will find an entire group of all T, for example.  If either of your parents have all Ts in the same location, then you will match anyone with any combination of T and anything else.

confidence homozygosity example

In the example above, you can see that you inherited T from both your Mom and Dad.  Endogamy maybe?

Sally, although she will technically show as a match, doesn’t really “match” you.  It’s just a fluke that her DNA matches your DNA by hopping back and forth between her Mom’s and Dad’s DNA.  This is not a match my descent, but by chance, or IBC (identical by chance.)  There is no way for you to know this, except by also comparing your results to Sally’s parents – another example of parental phasing.  You won’t match Sally’s parents on this segment, so the segment is IBC.

Now let’s look at Joe.  Joe matches you legitimately, but you can’t tell by just looking at this whether Joe matches you on your Mom’s or Dad’s side.  Unfortunately, because no one’s DNA comes with a zipper or two sides of the street labeled Mom and Dad – the only way to determine how Joe matches you is to either phase against Joe’s parents or see who else Joe matches that you match, preferable on the same segment – in other words – create either a match or ICW group, or triangulation.

Segment Size

Everyone is in agreement about one thing.  Large segments are never IBC, identical by chance.  And I hate to use words like never, so today, interpret never to mean “not yet found.”  I’ve seen that large segment number be defined both 13cM and 15cM and “almost never” over 10cM.  There is currently discussion surrounding the X chromosome and false positives at about this threshold, but the jury is still out on this one.

Most medium segments hold true too.  Medium segment matches to multiple people with the same ancestors almost always hold true.  In fact, I don’t personally know of one that didn’t, but that isn’t to say it hasn’t happened.

By medium segments, most people say 7cM and above.  Some say 5cM and above with multiple matching individuals.

As the segment size decreases, the confidence level decreases too, but can be increased by either multiple matches on that segment from a common proven ancestor or, of course, triangulation.  Phasing against your parent also assures that the match is not IBD.  As you can see, there are tools and techniques to increase your confidence when dealing with small segments, and to eliminate IBC segments.

The issue of small segments, how and when they can be utilized is still unresolved.  Some people simply delete them.  I feel that is throwing the baby away with the bathwater and small segments that triangulate from a common ancestor and that don’t find themselves in the middle of a pileup region that is identical by population or that is known to be overly matchy (near the center of chromosome 6, for example) can be utilized.  In some cases, these segments are proven because that same small segment section is also proven against matches that are much larger in a few descendants.

Tim Janzen says that he is more inclined to look at the number of SNPs instead of the segment size, and his comfort number is 500 SNPs or above.

The flip side of this is, as David Pike mentioned, that the fewer locations you have in a row, the greater the chance that you can randomly match, or that you can have runs of heterozygosity.

No one in our discussion group felt that all small segments were useless, although the jury is still out in terms of consensus about what exactly defines a small segment and when they are legitimate and/or useful.  Everyone of us wants to work towards answers, because for those of us who are dealing with colonial ancestors and have already picked the available low hanging fruit, those tantalizing small segments may be all that is left of the ancestor we so desperately need to identify.

For example, I put together this chart detailing my matching DNA by generation. Interesting, I did a similar chart originally almost exactly three years ago and although it has seemed slow day by day, I made a lot of progress when a couple of brick walls fell, in particular, my Dutch wall thanks to Yvette Hoitink.

If you look at the green group of numbers, that is the amount of shared DNA to be expected at each level.  The number of shared cMs drops dramatically between the 5th and 6th generation from 13 cM which would be considered a reasonable matching level (according to the above discussion) at the 5th generation, and 3.32 cM at the 6th generation level, which is a small segment by anyone’s definition.

confidence segment size vs generation

The 6th generation was born roughly in 1760, and if you look to the white grouping to the right of the green group, you can see that my percentage of known ancestors is 84% in the 5th generation, 80% in the 6th generation, but drops quickly after that to 39, 22 and 3%, respectively.  So, the exact place where I need the most help is also the exact place where the expected amount of DNA drops from 13 to 3.32 cM.  This means, that if anyone ever wants to solve those genealogical puzzles in that timeframe utilizing genetic genealogy, we had better figure out how to utilize those small segments effectively – because it may well be all we have except for the occasional larger sticky segment that is passed intact from an ancestor many generations past.

From my perspective, it’s a crying shame that Ancestry gives us no segment data and it’s sad that 23andMe only gives us 5cM and above.  It’s a blessing that we can select our own threshold at GedMatch.  I’m extremely grateful that FTDNA shows us the small segment matches to 1cM and 500 SNPs if we also match on 20cM total and at least one segment over 7cM.  That’s a good compromise, because small segments are more likely to be legitimate if we have a legitimate match on a larger segment and a known ancestor.  We already discussed that the larger the matching segment, the more likely it is to be valid. I would like to see Family Tree DNA lower the matching threshold within projects.  Surname projects imply that a group of people will be expected to match, so I’d really like to be able to see those lower threshold matches.

I’m hopeful that Family Tree DNA will continue to provide small segment information to us.  People who don’t want to learn how to use or be bothered with small segments don’t have to.  Delete is perfectly legitimate option, but without the data, those of us who are interested in researching how to best utilize these segments, can’t.  And when we don’t have data to use, we all lose.  So, thank you Family Tree DNA.

Coming Full Circle

This discussion brings us full circle once again to goals.

Goals change over time.

My initial reason for testing, the first day an autosomal test could be ordered, was to see if my half-brother was my half-brother.  Obviously for that, I didn’t need matching to other people or triangulation.  The answer was either yes or no, we do match at the half-sibling level, or we don’t.

He wasn’t.  But by then, he was terminally ill, and I never told him.  It certainly explained why I wasn’t a transplant match for him.

My next goal, almost immediately, was to determine which if either my brother or I were the child of my father.  For that, we did need matching to other people, and preferably close cousins – the closer the better.  Autosomal DNA testing was new at that time, and I had to recruit cousins.  Bless those who took pity on me and tested, because I was truly desperate to know.

Suffice it to say that the wait was a roller coaster ride of emotion.

If I was not my father’s child, I had just done 30+ years of someone else’s genealogy – not a revelation I relished, at all.

I was my father’s child.  My brother wasn’t.  I was glad I never told him the first part, because I didn’t have to tell him this part either.

My goal at that point changed to more of a general interest nature as more cousins tested and we matched, verifying different lineages that has been unable to be verified by Y or mtDNA testing.

Then one day, something magical happened.

One of my Y lines, Marcus Younger, whose Y line is a result of a NPE, nonparental event, or said differently, an undocumented adoption, received amazing information.  The paternal Younger family line we believed Marcus descended from, he didn’t.  However, autosomal DNA confirmed that even though he is not the paternal child of that line, he is still autosomally related to that line, sharing a common ancestor – suggesting that he may have been born of a Younger female and given that surname, while carrying the Y DNA of his biological father, who remains unidentified.

Amazingly, the next day, a match popped up that matched me and another Younger relative.  This match descended not from the Younger line, but from Marcus Younger’s wife’s alleged surname family.  I suddenly realized that not only was autosomal DNA interesting for confirming your tree – it could also be used to break down long-standing brick walls.  That’s where I’ve been focused ever since.

That’s a very different goal from where I began, and my current goal utilizes the tools in a very different way than my earlier goals.  Confidence levels matter now, a great deal, where that first day, all I wanted was a yes or no.

Today, my goal, other than breaking down brick walls, is for genetic genealogy to become automated and much easier but without taking away our options or keeping us so “safe” that we have no tools (Ancestry).

The process that will allow us to refine genetic genealogy and group individuals and matches utilizing trees on our desktops will ultimately be the key to unraveling those distant connections.  The data is there, we just have to learn how to use it most effectively, and the key, other than software, is collaboration with many cousins.

Aside from science and technology, the other wonderful aspect of autosomal DNA testing is that is has the potential to unite and often, reunite families who didn’t even know they were families.  I’ve seen this over and over now and I still marvel at this miracle given to us by our ancestors – their DNA.

So, regardless of where you fall on the goals and matching confidence spectrum in terms of genetic genealogy, keep encouraging others to test and keep reaching out and sharing – because it takes a village to recreate an ancestor!  No one can do it alone, and the more people who test and share, the better all of our chances become to achieve whatever genetic genealogy goals we have.

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4 Generation Inheritance Study

I’ve recently had the opportunity to perform two, 4-generation, inheritance studies.

In both of these cases, we have the DNA of 4 generations: grandmother, parent, child and grandchild or grandchildren.  I’ll be using the second study because there are two great-grandchildren to compare.

Let me introduce you to the players.

4 gen pedigree

I wanted, with real data, to address some assertions and assumptions that I see being made periodically in the genetic genealogy community.  We need to know if these hold up to scrutiny, or not.  Besides that, it’s just fun to see what happens to DNA with 4 generations and 5 people to compare.

What kinds of information are we looking to confirm or refute in this study?

1 – That small segments don’t occur within a couple generations, meaning that that DNA can’t be or isn’t broken into small segments that quickly.

2 – That small segments can never be used genealogically and are not useful.

3 – That DNA is most of the time passed in 50% packages.  While this is true in the first generation, meaning a child does receive half of each parent’s DNA, they do not receive 25% of each grandparent’s DNA.

4 – That segments over a certain threshold, like 5 or 7 cM, are all reliable as IBD (identical by descent.)

5 – That segments under a certain threshold, like 5 or 7 cM are all unreliable and should never be used, in fact, cannot ever be used and should be discarded.

6 – That there is a rule that you cannot have more than two crossovers per chromosome.

All individuals tested at Family Tree DNA and we’ll be using the FTDNA chromosome browser for comparisons.

First, let’s look at the amount of expected DNA matching versus the actual amount of DNA matching, per generation.  The entire number of cM being measured is 6766.2, per the ISOGG Autosomal Statistics Wiki page.

Expected vs Actual Inheritance Chart

This chart compares the expected versus actual amount of DNA shared between person 1 and person 2,

Person 1 Person 2 Expected DNA Match cM/% Actual DNA Match
Grandmother Parent (grandmother’s child) 3383.1 / 50% 3384.03 / 50.01%
Grandmother Pink Child (grandmother’s grandchild) 1691.5 / 25% 1670.64 / 24.69%
Grandmother Blue Grandchild (grandmother’s great-grandchild) 845.775 / 12.5% 704.84 / 10.39%
Grandmother Green Grandchild (grandmother’s great-grandchild) 845.775 / 12.5% 842.64 / 12.45%

Chromosome Data

Now, let’s take a look at our chromosome data.  Keep in mind, everyone is being compared to the oldest generation – in this case – the great-grandmother’s DNA.

Legend

  • The background chromosome belongs to the great-grandmother of the youngest generation – meaning everyone is being compared to her.
  • Grandparent = orange – because the child receives 50% of each parent’s DNA, the orange child of the great-grandmother will match her DNA 100%.
  • Grandchild = pink – since the grandchild is being compared to the grandparent, and not their parent, we will see how much of the grandmother’s DNA the pink child received. The dark spaces are the “ghost image” of the grandfather’s DNA – identified by the lack of the grandmother’s DNA in that location.
  • Oldest great grandchild = blue
  • Youngest great grandchild = green

The two great grandchildren are full siblings.  None of the parents involved are related to each other or to other generational spouses.  This has been confirmed both by genealogy pedigree chart and by utilizing the tools at GedMatch for comparisons to each other as well as the “are your parents related” tool.

The first comparison, below, shows the 4 individuals compared to the great grandmother’s DNA at the Family Tree DNA with the match default set at 5cM

4 gen ftdna default

The image below, shows the same individuals after dropping the match criteria to 1cM.  Several small colored segments appear.

4 gen ftdna 1 cm

I downloaded all of the matching data for these individuals into a spreadsheet so that I could work with the actual chromosomal data.  I’m not boring you with that here, but I have used the raw matching data for the actual comparisons.

Crossover

Let’s talk about what a crossover is, because understanding crossovers are important

Crossover example 1 – A crossover is where you start/stop receiving DNA from one grandparent or the other.  This is easy to see if we look at chromosome 1.

4 gen crossover

In this example, the parent is orange and the child is pink but they are both being compared to the grandparent of the pink person, the mother of the orange person.

What this means is that while the orange person will always match the grey background chromosome of their mother, the pink person will only match their grandmother on the portion of the DNA they received from their mother that was from their grandmother.  The pink person received their grandfather’s DNA in some locations, and not their grandmother’s.  Where that transition happens is called a crossover and it is where the colored segment stops, as noted by the arrows above, and the back background begins, indicating no match to the grandmother.

You can see that the matches span the center of the chromosome where the grey area indicates there is no data being read.  There is also a second small grey area to the right of the center.  Ignore these grey areas.  They are in essence DNA deserts where there isn’t enough DNA to be read or useful.  Family Tree DNA (and other vendors) stitch the data on both sides together, so to speak, and matches on both sides of this area are considered to be contiguous matches.

You can see that the pink person has two crossover areas where they stopped receiving DNA from the mother’s mother (background chromosome being compared against) and instead started receiving DNA from the mother’s father.  How do we know that?  There only two people who contributed the orange parent’s DNA that the pink child inherited.  If the pink child did not inherit the orange parent’s Mom’s DNA on this segment, then the pink child had to have inherited the orange parent’s Dad’s DNA.

Crossover example 2 – A second kind of crossover is where you are still receiving DNA from the same parent, but from different ancestors on that parental line

I’ve created a chart to illustrate this phenomenon

The names in the charts at the bottom are the people who tested today.  All of these individuals are known cousins who are from my mother’s side.  The name at the top is the common ancestor of all of the testers.

In the first situation, in locations 1-5, Me, Charlie and David match.  None of the three of us match our cousin, Mary on those locations.  However, moving to locations 6-10, Me, Charlie and Mary match each other, but not David.  Looking at our pedigree charts, we can see that the cousins are matching on different ancestral lines.

4 gen generational crossover

Me, Charlie and David share a wife’s line, Sally (wife of John), that Mary does not share.  Me, Charlie and Mary share common DNA from George, a male further upstream in that line.  George’s son John married Sally.  Mary descends from George through a different child, which is why she does not match any of us on the segments we received from Sally, John’s wife.

Location Me Charlie David Mary
1 Sally Sally Sally No match
2 Sally Sally Sally No match
3 Sally Sally Sally No match
4 Sally Sally Sally No match
5 Sally Sally Sally No match
6 George George No match George
7 George George No match George
8 George George No match George
9 George George No match George
10 George George No match George

If you’re just looking at the question, “do Charlie and I match?” the answer would of course be yes, but until we look at a broader spectrum of cousins, we won’t know that our match is actually from two different people in the same descendancy line and that we have an ancestor crossover between locations 5 and 6.  However, we’re still receiving our DNA from the same parent, but which ancestor of that parent contributed the DNA has switched

How prevalent are crossovers?

Number of Crossover Events

These are all parent/child crossovers where the DNA donor switched.  We can only determine that this happened because we can compare generationally against the grey background great grandmother to the youngest generation

  • Orange parent to Pink child – 49
  • Pink child to Blue child – 47
  • Pink child to Green child – 39

The most segmented chromosome, chromosome 1, has 5 separate matching segments for the blue great grandchild (as compared to the great-grandmother), or 10 crossover events (because neither end was at the beginning or end, although start and end numbers are sometimes “fuzzy”).  You can see where a crossover event occurs when the DNA goes from matching to non-matching.

4 gen chr 1 crossovers

Results

I downloaded all of our matching data into a spreadsheet so that I can work with the segment matches individually.

Looking at the data, there are a few things that jump out immediately:

  • On chromosomes 4 and 14, the pink child received none of the orange grandmother’s DNA. That means that the pink child had to have received the grandfather’s DNA for all of chromosome 15. So, if anyone thinks that the 50% rule really works uniformly across generations – here’s concrete proof that it doesn’t. Furthermore, this occurred for an entire chromosome – twice out of 23 chromosomes, or 8.7% of the time.
  • On chromosome 11, the exact opposite happened. The pink child received all of the grandmother’s chromosome, but barely gave any to their blue child. The blue child received their mother’s DNA in that location. On chromosome 13, the pink child received almost all of the grandmother’s DNA.
  • Please note that while the averages of expected versus inherited DNA work out pretty closely, when averaging across all 23 chromosomes, as shown in the Expected vs Actual Inheritance Chart, the individual chromosomes and how much of which grandparent’s or great-grandparent’s DNA is inherited varies wildly from none to 100%.
  • There are several locations on 10 different chromosomes where the DNA has been passed generationally intact 2 or 3 times, without division.
  • Several small segments have been created within 3 transmission events.There are small green and blue segments on several different chromosomes which reflect very small amounts of the great grandmother’s DNA inherited by the green and blue great-grandchildren. This conclusively dismisses the theory that small segments aren’t ever created within a couple of generations.
  • Chromosome 10 is very choppy, including small blue and green grandchild segments that match the orange grandparent and the great-grandmother without having matches to the pink child. This means that those unconnected blue and green small segments are either identical by chance or there is a read issue with the pink person’s DNA on this chromosome.
  • There are a total of 31 small segments, meaning under 7cM. Of those, a total of 10 do not triangulate, meaning they match the grandmother but they do not match their parent.  The 7 pink segments appear to triangulate, but without another generation of transmission (like the blue and green great-grandchildren), or without the grandfather’s DNA, or without triangulation with a known relative on that segment, it’s impossible to tell for sure. Therefore, 14, or 45% are valid segments and do triangulate.
  • There are a total of 92 chromosomal transmission events that took place, meaning that 23 chromosomes got passed from the background person to their orange child, 23 from the orange child to their pink child, 23 from the pink child to the blue grandchild and 23 from the pink child to the green grandchild.
  • Furthermore, based on this limited study, at least 32.26% of the small segments do not triangulate and are not IBD, but are instead identical by chance.
  • In three instances, the exact DNA (from the great grandmother) was given to both the green and blue great grandchildren. In eight other events, the same DNA, without division, was given from a parent to one child.
  • There are several instances, on chromosomes 3, 4, 9, 14, 15, 16, 20, and 22 where the pink child passed none of their grandmother’s DNA to their child, even though they inherited the grandmother’s DNA.

Individual Chromosomes and Their Messages

I’d like to walk through several chromosomes and chat a little bit about what we’re seeing.

Chromosome 1

4 gen chr 1

First, I’d like to illustrate the difference between chromosome matches at the default level (the first chromosome, above) and at the 1cM level (the lower chromosome.)  At the lower match threshold, you will see additional small segment matches that are not shown at the higher threshold, noted by red arrows.

Let’s take a look at the messages held by our individual chromosomes.

On all of these chromosomes, you’ll see that the orange child matches thier mother, the background person being compared against, exactly, on every location that is measured.  Half of everyone’s DNA comes from their mother, so all of their DNA will match to her on any given chromosome.  Remember, we are only measuring matching DNA (half identical segments) – so the other half of the person’s DNA that matches their father is not shown.

I have left the orange segments in the graphics, even though they all match on the entire chromosome length, so you can see the continuity from generation to generation.  Pink is the orange person’s child, so you can see that the pink child inherited part of the DNA the orange person inherited from their mother, but not all.  The part that is black in the pink row, as compared to the orange segment, means that the pink child inherited that DNA from their grandfather at those locations – and not the grandmother being compared against

In one instance, on chromosome 1, the pink child gave their grandmother’s DNA to both of their children.  You can see that to the far left with the red arrow.

4 gen chr 1 grandmother transmission

You can also see that the blue grandchild only received a small part of their great grandmother’s DNA, but the green grandchild received a much larger segment.

In one area, the pink child clearly received their grandmother’s DNA, but didn’t give any of it to either the blue or green grandchild, shown below at the red arrow.  There is no blue or green matching the great-grandmother’s DNA.

4 gen chr 1 no transmission

To the right of the arrow, top, above, you can see where the pink child contributed their grandmother’s DNA to their blue child, but not to the green child.  The pink child contributed their other parent’s DNA in that instance, bottom, above, because their child does not match their orange mother – so that DNA had to come from the grandfather.

On the chromosome match that includes the smaller segments, below, you can see there are a total of 5 segments not shown with the higher threshold.

4 gen chr 1 small segments

The first two arrows, on the left, point to small segments shared by the blue and green grandchildren with their great-grandmother and their pink parent – so these triangulate and they are fine.

The third arrow, on the right hand side pointing to the green segment that does not match with the pink parent indicates a match that is identical by chance.  We’ll talk more about this in chromosome 3.

The fourth arrow, at the far right, shows a small segment of orange DNA that was passed to their pink child, but the pink child did not pass it on to either of their children.  This segment could be a legitimate segment by descent, but it could also be by chance.  We’ll talk about that more on chromosome 8.

Chromosome 2

4 gen chr 2

Chromosome 2 shows two small segments.  You can see that the pink child gave a significant portion of their grandmother’s DNA to the blue child, but only two small segments to the green child in that region, at the red arrows.  They do triangulate though, because they match their parents.  See how nicely the DNA stacks up between all of the generations.

Chromosome 3

4 gen chr 3

The pink child inherited very little of the grandmother’s DNA in this region.  Of the small amount the pink child did inherit, the pink child gave even less of it to their children.  One small piece to the green grandchild, shown at right, and none to the blue grandchild.

Why, then, is there a lonely blue segment on this comparison chromosome showing that the blue great-grandchild matches their orange grandmother and their great-grandmother, but not their pink parent?  This is the first example of an identical by chance segment (or a read error in the pink parent’s file).

4 gen chr 3 small seg

Three Kinds of DNA Match Segments

There are three kinds of DNA segment matches.

  1. Identical by descent (IBD) where you receive the segment from your ancestors and we can track it as far back up the tree as we have living people. This is the example where the small segment of the great-grandchildren (blue or green) match their parent (pink), their grandparent (orange) and their great-grandmother’s background chromosome being compared against.
  2. Identical by state (IBS) which sometimes is used to mean not identical by descent. What it actually means is that you can still match and receive the DNA from your ancestors, but the segment may be very prevalent in a specific community or ethnic group. An alternative explanation is that the DNA ‘state’ is so common that everyone in that area has it, so it’s virtually useless in identifying ancestors, because you can’t really tell which lines it came from. So IBS does triangulate, because it did come from a common ancestor, but you may match a large number of people at this location. Portions of chromosome 6 are known to fall into this category.  More often than not, I hear IBS used to indicate that there is a match, but the common ancestor isn’t known or hasn’t yet been identified.
  3. Identical by chance (IBC) is where a specific DNA combination is a match, but it’s not a match because it was handed down ancestrally, but simply by the luck of the draw.  Because everyone carries the DNA of both parents, sometimes people can match you by zigzagging back and forth between your father’s and mother’s DNA.  These matches aren’t ancestral, but just by luck or chance.  Shorter matches, meaning small segments, are much more likely to be identical by chance than longer matches. When you have both parents DNA, you can easily eliminate IBC segments because they won’t triangulate – as we have just demonstrated on chromosome 3.

You can read more about this here and here.

Chromosome 4

4 gen chr 4

Chromosome 4 is particularly interesting because the orange person matches their background mother, of course, but apparently their pink child inherited this entire chromosome from the pink person’s grandfather – because the pink person does not match their grandmother – there are no pink matching segments to the background grandmother.

Chromosome 5

On chromosome 5, the pink child matches the grandmother on almost the entire chromosome, except for a small part to the left of center.

4 gen chr 5

You may notice that there is a segment of blue that appears to extend beyond the pink bar at the left arrow – which would mean that the blue area matches the great-grandmother without matching the pink parent.  The segments on the chromosome map are not exactly to scale, and the beginnings and ends are sometimes what is referred to as fuzzy.  This means that they are not exact measurements but that they in essence the absence or presence of DNA in a bucket of a specific size.  If any part of your DNA is in that bucket, then your start or stop segment are the edges of that bucket.  In this case, the entire match is 47.51cM for the pink child and 49.82 for the blue grandchild, so the difference may or may not be relevant.

Although this actually is a small matching segment, or non-matching segment, you would never notice this if you were just looking at the blue grandchild matching to the great grandmother.  It’s only with the introduction of the parent’s pink DNA that you notice that the blue great grandchild’s DNA match with the great grandmother extends beyond that of the parent.

Chromosome 6

4 gen chr 6

Chromosome 6 is rather unremarkable except that the orange person seems to have had a read or file error of some sort.  The orange results are shown in two separate pieces, but we know that the orange person must match their mother 100%.  We know this issue is in the orange person’s file, because their pink child and both of the blue and green grandchildren match the background person, the orange persons’ mother, with no break in their DNA.

Chromosome 7

4 gen chr 7

Chromosome 7 shows another example of 5 generations matching with the stacking of orange, blue, green and pink against the background person’s chromosome, at right.  It also shows another example an identical by chance match, with the blue grandchild showing a match to their great-grandmother but no match to their pink parents, near the center at the red arrow.

Chromosome 8

4 gen chr 8

Chromosome 8 shows another example of the pink child having inherited a small segment of their grandmother’s DNA, but not passing it on to their children.

How do we know if this is a legitimate IBD segment, or if it something else?  Since the pink child will match their mother 100%, and they didn’t pass it on tho their children, how can we prove that the small pink segment where they match their grandmother is  IBD.

How could we prove this one way or the other?

First of all, it probably doesn’t matter, except as a matter of interest – or unless of course this one segment is THE one you need to identify that colonial ancestor.  If this was a normal match, we could just see if the match matched the child and the parent too, which would immediately phase the match against their parent – but we can’t do that when matching to a grandparent because the child will always match their parent 100%.

If you have the grandfather’s DNA at Family Tree DNA, you could compare the pink grandchild to their grandfather. On chromosome 8, the grandfather’s DNA in the pink row is identified by the dark grey – because it’s where the pink grandchild does not match their grandmother – so they must match their grandfather on that segment because their orange parent only had two pieces of DNA to give them, the piece from their mother or the piece from their father.

Therefore, if this is a valid segment, then you won’t see at match in the grandfather’s DNA on same portion of the segment.  If you see a match to both the grandmother and the grandfather, it’s likely that the small segment match to the grandmother is not identical by descent –  you but really don’t know for sure.

How could that be?  I asked David Pike that question and he pointed out that in one case, he discovered that the grandparents both shared the same DNA segment.  The child inherited it from one parent or the other, and passed it on to their child, but since the mother’s and father’s DNA was identical, there is no way to tell which grandparent the segment actually came from.  And in this case, the segment would match both grandparents.  That is a trait of endogamy and of IBS, or identical by population.  If you’re saying, BOO, HISS, about now, I totally understand.

After talking to David, I also realized that if your DNA at those locations just happens to be all homozygous, for example, all Ts, on both sides, for a run of SNPs in a row, and if your parents and grandparents have Ts in either location, you will match them…and anyone else who does too.

So here we have an example of a match that could be IBD if it truly is a small segment by descent and you don’t match the other grandparent at that location.  It could be IBC or IBS (by population) if you match both of your grandparents on this segment – but it might be IBD.  It’s IBD from one and IBC/IBS from the other – but which one is which?

However, since I don’t have the grandfather’s DNA at Family Tree DNA, my only other alternative is to move to GedMatch and create a phased kit for the grandfather by subtracting the grandmother’s DNA from her orange child, which will give me the DNA the orange child received from their father.  Then I can compare the pink grandchild to the grandfather’s phased kit – which is the father’s DNA that the orange child received.  This is fine, even if it is only half of the grandfather’s DNA – it s the half that the pink child’s mother received and passed a portion to the pink child.

I would suggest doing this entire exercise on either Family Tree DNA or on the GedMatch platform, and not jumping back and forth between the two.  The start and stop segments aren’t exactly the same, and sometimes the segments read differently, creating more segments at GedMatch than at FTDNA.  I’m not saying that is wrong, just that it isn’t consistent between the two platforms and when you are dealing with small segments, in particular, you need consistency.

Chromosome 9

4 gen chr 9

On chromosome 9, the pink child received little of the grandmother’s DNA, and gave none of it to their green child.  And yes, if you have a good eye the blue child’s right boundary is slightly beyond the their pink parents – so – you already know what that means.  Either a fuzzy boundary or a slight piece of DNA that happened to match with the great-grandmother identical by chance (IBC.)

Chromosome 10

4 gen chr 10

This chromosome is incredibly interesting because it’s comprised of all small segments.  In fact, this is the exact reason why you NEED to look at the 1cM range.  At the default setting, if there are no matches except the orange person to their mother.  It looks like none of the grandmother’s DNA was passed to the pink child, but in fact, may not be the case.  There are three segments passed to the pink child, although the pink child did not pass these on to either of their children.  See the discussion on segment 8 about how to tell for sure, if you need to.

The blue and green segments, since they do not match their pink parent are not IBD but are instead IBC.  The really interesting part of this is that in one case, the blue and green grandchildren’s DNA matches the orange grandmother on the same segments exactly, but does not match the pink parent.

How can this possible be, you ask, barring a file read issue?  Good question.  Remember, each child inherits half of their parent’s DNA.  In this case, both children apparently inherited the same DNA from both parents, but it wasn’t the orange DNA, but that of the pink child’s father.

It just happened, when the blue and green children’s DNA combined with that of their mother, it just happens to read as a match, for a small segment.  You can read about how this might happen in the article, “How Phasing Works and Determining IBD Versus IBS Matches.”

Unfortunately, all these comparisons can do is to tell us simply what does and does not match – they can’t tell us why.  Sometimes, based on other comparisons, like phasing and triangulation, we can figure out the “why” part of the puzzle – and sometimes, we can’t.

Chromosome 11

4 gen chr 11

On chromosome 11, the pink child inherited all of the grandmother’s DNA through their orange parent, but gave less than half to their green child and a small segment to the blue child.  The pink child gave the exact same segment in the center to both their blue and green children.

Chromosome 12

4 gen chr 12

On chromosome 12, the pink child inherited little of their grandmother’s DNA, but passed every bit of what they inherited to both of their children, shown by the nice stack at right.  The start and stop locations are exact between the three.

However, in addition, we have three small segments where the green and blue grandchildren match their orange grandmother without matching their pink parent – so those are IBC.

Chromosome 13

4 gen chr 13

The pink child inherited almost all of their grandmother’s entire chromosome, except for a very small bit at the far right end.  The pink child passed almost their entire chromosome 13 to their green child, but only a small amount to the blue child.

Chromosome 14

4 gen chr 14

This story is easy.  The pink child inherited their grandfather’s entire chromosome 14 because they do not match their grandmother’s DNA at all.

Chromosome 15

4 gen chr 15

This is a very “normal” chromosome.  The pink child inherited about half of their grandmother’s DNA and gave about half of what they inherited to their green child.  Of course, their blue child got left out altogether – but that looks to be a lot more “normal” than we once thought.

I am skipping chromosome 16-22, because they are more of what you’ve already seen and is, by now, quite familiar  Plus, you can take a look at the full chromosome comparison graphic and do your own analysis.

X Chromosome

The X chromosome is a bit different, and I’d like to take a look at that.

4 gen X

The X chromosome has special inheritance properties that other chromosomes don’t have.  In particular, women inherit an X just like they inherit their other chromosomes from 1-22 – one from Mom and one from Dad.  Men, however, only receive an X from their mother.  Therefore, there are relatives that you cannot inherit any X DNA from.  I wrote about this here and here along with examples and charts.

In this example, the inheritance path is such that it does not affect what can and cannot be inherited since we are comparing to a great-grandmother, but in other situations,  this would not be the case.

One last observation about the X chromosome.  I have found matching on the X to be particularly unreliable, and have found several situations, where, due to those special inheritance properties, we know beyond any doubt that the common ancestor on the X cannot be the same ancestor as has triangulated on the other chromosomes.  So word to the wise – be very vigilant and hesitant to draw conclusions from X matching.  I never utilize the X without corroborating autosomal matches and even then, I’m very reticent.

In Summary

On the average, we do inherit about half of our DNA from in each generation from each ancestral generation.  But the average and the actuality of what happens is two entirely different things.  Averages are made up of all of the outliers, and if you are one of those outliers, the average isn’t really relevant to you.  Kind of reminds me of “one size fits all” which really means “one size fits almost nobody well” and “everyone is some shade of unhappy.”

I wrote about generational inheritance and how it doesn’t always work the way we think, or expect.  It’s very important to pay close attention to your own DNA and not rely on averages unless you have absolutely no other choice – and only then understanding the averages are likely wrong in one direction or the other – but it’s the best we’ve got, under the circumstances.

So what can we apply to our genealogy from this little experiment.

  1. Some of the small segments across 4 generations are valid, meaning identical by descent or IBD.
  2. At least one third of the small segments aren’t valid and are identical by chance, or IBC.
  3. Without some form of triangulation or parental phasing, it’s impossible to tell which small segments are and are not valid, or identical by descent.
  4. Small segments are indeed formed within a 2 or 3 generation span, so they are not always a results of many generations of dividing.
  5. However, the further back in time your ancestor, the more likely that they will only be represented in your DNA by small segments, if any.
  6. Many small segments are valid and are not a result of IBC.  However, most are not and one needs to understand how to recognize signs of an IBC vs an IBD match.
  7. Disregarding small segments uniformly is like throwing away the only clues you may have to your most distant ancestors – which are likely your brick walls.
  8. The largest segment that was not valid was 3.14cM and 600 SNPs.
  9. The smallest valid segment was 1.25cM and 500 SNPs.

Getting the Most Out of Your DNA Experience

There is a lot more information available to us in our DNA results than is first apparent.  It takes a bit of digging and you need to understand how autosomal DNA works in order to ferret out those secrets.  Don’t discount or ignore evidence because it’s more difficult to use – meaning small segments.  The very piece or breadcrumb you need to solve a long-standing mystery may indeed be right there waiting for you.  Learn how to use your DNA information effectively and accurately – including those small segments.

You need to test every cousin you can find and convince to swab or spit.  It’s those cousin matches that help immensely with triangulation and confirming the validity of all DNA segments, matching them back to common ancestors.  You are building walkways or maybe pathways back in time, with your DNA as the steppingstones.  Genetic genealogy is not a one person endeavor.  It takes a village, hopefully of cousins willing to DNA test!

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Parent-Child Non-Matching Autosomal DNA Segments

Recently, I had the opportunity to compare 2 children’s autosomal DNA against both of their parents.  Since children obtain 50% of their DNA from each parent (except for the X chromosome in males), it stands to reason that all valid autosomal matches to these children not only will, but must match one parent or the other.  If not, then the match is not valid – in other words – it’s an identical match by chance.

If you remember, the definition of a match by chance, or IBC (identical by chance) is when someone matches a child but doesn’t match either parent.

This means that the DNA segments, or alleles, just happen to line up so that it reads as a match for the child, by zigzagging back and forth between the DNA of both parents, but it really isn’t a valid genealogical match.

You can read about how this works in my article, How Phasing Works and Determining IBD Versus IBS Matches and also in the article, One Chromosome, Two Sides, No Zipper.

The absolute best way to determine if a match is a valid match or not, valid meaning that the DNA was handed down by ancestors, not a match by chance, is to compare a child’s matches against both parents.  By doing that, we can quickly identify and isolate matches that aren’t real.

IBC

In the example above, you can see that Mom contributed all As to me and Dad contributed all Cs to me.  Joe has alternating As and Cs, so he is a match to me on every location.  However, he only matches my parents on half of their locations, so he is not a match to them, because it’s only chance that caused him to match me on those allele values in that order.

DNA matching programs have to take into consideration both allele values in their match routines, since you carry a value from your mother (A above) and a value from your father (C above), and they are not labeled as to which parent they come from.

Valid matches will also match one parent or the other.  After all, the child received all of their DNA from one parent or the other, so for someone to be a valid genealogical match a child, they must match a parent.

Some time back, when I was matching to my own mother’s DNA, I noticed that I matched her on about 40% of my matches, which left 60% to either be matches to my father or identical by chance.

Notice, I’m not talking about IBS, or identical by state, because that phrase is used to mean both identical by chance and identical by population.  Identical by population means that you did in fact inherit the DNA from an ancestor, but it’s either too far back in time to determine which ancestor, or that segment was present in a specific, probably endogamous population, and you could have inherited it from any number of ancestors.

So, identical by population is identical by descent, but we just can’t tell who we got received that DNA from.

  • IBC – identical by chance – not a valid match – you happen to match someone else on a particular segment, but it’s because the match software is jumping back and forth from your mother’s side to your father’s side.
  • IBD – Identical by descent – you share a common segment of DNA because you and another person(s) inherited that DNA segment from a common ancestor who you can identify
  • IBS – Identical by state – currently used to be both IBC and IBS, where IBS means that you did inherit this DNA from a common ancestor, but it’s so far back you can’t determine who, or that segment is so common within a particular population you could have inherited it from a number of people.

Now a 60-40 parental split is certainly possible, especially if one parent was from an endogamous population, which would mean more matches, or one parent was more recently immigrated from the old country, which would mean fewer matches.

However, without my father’s DNA, which is not available, we’ll never know.

Since that time, I have obtained access to 2 sets of child plus both parents DNA results, so I wanted to take a look at how IBD versus IBC stacked up.  These comparisons were done at Family Tree DNA.

Total Matches Non-Matching Either Parent Percent Non-Matching
Child 1 959 133 13.9
Child 2 1037 133 12.8

Based on other evidence I’ve seen, this percentage seems about right, but the amount of shared DNA and the largest segment size surprised me.  Keep in mind that the smallest possible segment size is 7cM which is Family Tree DNA’s lowest single segment threshold to be counted as a match (assuming you meet the 20cM total threshold first.)  If you match, they show you your matching DNA down to 1cM, but these tables are measurements by the 7cM matching criteria only.

In plain English, this means that in this case, 12% and 13% of these matches were identical by chance, or false matches.  These matches included people who shared up to 57cM of data and the largest block was 15cM.

Largest Shared cM Largest Longest Block
Child 1 46.87 14.38
Child 2 57.06 15.18

Could something else be causing this?  Certainly.  Some of these non-matches could be read errors in the files.  I’d certainly want to take a look at that if any of these became critical.  Another possibility could be that valid match segments are “stitched together” by IBC segments creating longer segments in the child.

An alternative to check validity would be to download the files to GedMatch and see if the pattern continues using the same match criteria.  Of course, testing at multiple labs and downloading the results to compare at GedMatch likely removes the issue of read errors in the first set of files.  And if you really, REALLY, want to know, you can look at the raw data files themselves.

Just so you know, this wasn’t an anomaly with just one high read.  Here are the highest 25 entries from Child 2, or about one fifth of her total mismatches.  Only a few were in the 3-5th cousin range.  None were closer.  Most were 4th or 5th to remote.

non-parent matching relationship range

If you want to do these comparisons yourself, they are easy to do if you have a child and both parents who have tested at Family Tree DNA.

On your Family Finder matches page, at the bottom, in the right corner, there is a button to download matches.

download button

I download the matches into separate spreadsheets for the child, mother and father.  I then color all of the rows pink in the mother’s results, and blue in the father’s results, then copy all three to a common spreadsheet.  You can then sort on the match name and this is what you’ll see.

non-match example

What you’re looking for is white (child) rows that don’t match either a blue row (father) or a pink row (mother.)  Don’t worry about pink or blue rows that don’t have matches. It’s normal for the DNA not to be passed to the child part of the time, so these are expected.

In this example, all white rows matched one parent or the other, except for Winnie Whines.  I colored this row red and added the Comment column where I entered the number of this non-matching entry.  When I’m finished comparing and coloring, then all I have to do is sort that column, bringing all of the nonmatching rows together.  I copied those nonmatching entries into a separate sheet so I could sort those alone and obtained the largest shared and longest segments.  To determine the percent, just divide the total number of nonmatches, in this case, 133, by the child’s total number of matches, in this case, 959, giving a non-parent-match percentage of 13.9%.

So, the take-home message is that not all small segment matches are genealogically irrelevant and not all larger segment matches are genealogically relevant.  Thank goodness we have tools and processes to begin to tell the difference.

So, if you don’t have both parents to compare to, and you’re wondering why you just can’t find a common ancestor with someone you match, the answer might be that they fall into your 12 or 13% that are IBC matches.

If you perform this little exercise, comparing a child to both parents, please feel free to post your results in the comments section along with any commentary about endogamous populations or special circumstances.  It really doesn’t take long, probably about an hour total, and the results are really interesting.  Plus, you’ll have eliminated all those irrelevant matches.

I’ll be writing more about this interesting experiment in coming days.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research