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!

37 thoughts on “4 Generation Inheritance Study

  1. I’m relatively new to DNA genealogy and I’m obviously not understanding something very critical. In your first browser diagram analysis you say that the orange daughter of the great grandmother (background) will always match her mother. But doesn’t she receive half of her DNA from her father? So why would she always match her mother 100% on any given chromosome?

    • Good question. Remember, a child has half of the parents’ DNA. You’re looking at this from the parent’s perspective – so your child’s DNA will always match yours 100%. They will also match the other parent 100%. Because they have half yours and half the father’s. Look at it this way. If you have an A and a B to give your child and your spouse has a C and a D. Your child gets the A and the D. Your child will always match your A and always match your husband’s D. In this diagram, you’re only comparing to one parent – the female great grandmother – so the orange child will always match her exactly.

    • June – one way to look at this is that we test 700,000 points. Your mother has two sets of chromosomes so she has two values for each of the 700,000 points. You got one of those two values (1/2) at each point. So you got 1/2 of your mother, and one of each of her 700,000 points. So when you are compared to your mother you will match at every point.

      • Thanks Roberta and Jim, for I had the same question as June.

        So Jim, does that mean when we test we get 2 results for every chromosome? And we can only match on one or the other with any person? (I am awaiting the results of my first test, so I am trying to learn in advance.)

      • You will have lots of people that match you on each chromosome. They should, eventually, cluster into two groups based on matching common ancestors. If you tested at Ancestry, you’ll have none of these tools. But you can upload your results to both Family Tree DNA and Gedmatch.

  2. Wow! You deserve a Metal of Honor from the genealogy community for putting this together.
    It is very valuable to those of us on our quest to learn and understand. Worthy of a power point presentation anywhere……You are the VERY greatest! We appreciate you.

  3. Isn’t it just as likely that the small pink segments on Chromosome 10 could be identical by chance instead of identical by descent? It is obvious for the blue and green segments to be IBC when they don’t match pink segments. However, those very small pink segments matching orange could have occurred randomly. Thank you.

    • I am afraid I have to agree with Connie. Until you show me a small pink segment that gets passed down, all those very small pink segments could be IBC. But maybe these were phased with the father so that is how you know they are IBD?

      But beautiful job Roberta, what a wonderful post. loving the details and the math, thank you.
      Kitty

      • I do have the other parent’s data at GedMatch and I will run that tomorrow for the pink segments. Too tired to think more about this tonight:)

  4. Bravo! Roberta. Real data to walk through the many possibilities and explain each one. It’s good to know that our experiences are very similar, and at the same time in different places. That is to say the averages tran to work out, AND the wide variation is usually there, too. It’s real examples like yours which indicate the kind of variation we can expect, and that it’s important to focus on our own jigsaw puzzle. Thanks for this blog post.

  5. Excellent analysis, Roberta! It was so interesting to see the comparisons chromosome by chromosome, and the explanations for the outcomes.

  6. Thanks for your very detailed analysis of the DNA results of this four generational family. I do, however, have a small quibble about your analysis of some of the small segments especially when you state that they triangulate and must be IBD. For example, on chr 2, for the green child if the two small segments are IBD that would imply that there were at least six crossovers events between the pink parent and the green child. While that maybe possible, it is certainly on the high side where I seem to remember that 2-4 crossovers is more reasonable for chr 2. Comparing the green child to their other parent (spouse of the pink parent) may show a match in that same region which would imply that it was IBC or IBS to the pink parent. Has there been any studies (two parent comparison to a child) to show that segments that small can be formed in a single generation? Thanks.

    • Part of the point of looking at this actual data is that the averages are not always what happens in reality. I do have the other parent’s DNA, but since the definition of IBD is that you match ancestral DNA, I did not compare it at that location. The green child will of course match the spouse of the pink parent because all children match their parents 100%.

      • I was incorrect when I suggested comparing the green child to the spouse of the pink parent for the reason you have pointed out. What I should have said was to compare the green child to the spouse of the orange grandparent. The two grandparents (orange + spouse) could be homozygous (identical) at those locations and thus the small segments appear to be IDB from the great-grandmother (and technically they could be called as such), but they could actually are part of a larger segment that was passed from the spouse of the orange grandparent via the pink parent. The issue is whether those segments support any conclusion about the frequencies of small segments being IDB (item 1 & 6 in your Summary) or whether small segments can be created within a single transmission (two generation span) (item 4). Without looking to see whether these small segments are part of larger segments inherited from another line (spouse of orange grandparent), you don’t know that they are from the great grandparent even it they show as a match.

      • Arthur, you raise a point that I recently asked about on Gedmatch but haven’t received an answer to. One of the data items reported by the File Diagnostics Utility is Heterozygosity index which in my case is 0.151432. If I’m following you correctly this indicates that all but 15% of my genes show the same allele from both parents, Is this typical or is my value more typical of an endogamous population? I’m mostly Ashkenazi and have been trying to figure our why my paternal 1st cousin seems to share so many significant (10 cM and more) segments with my maternal 1st cousin although there is no recent shared ancestry between the two family lines.

  7. This is very useful in getting used to “reading” DNA chromosone diagrams. Is the color scheme a standard? I was thinking, that if we used a known color progression (say, the rainbow progression of red, orange, yellow, green, blue, indigo, violet) we wouldn’t have to label the colors – we’d know that “red” is the oldest generation, orange the next, etc. and we’d know how many generations we were looking at based on how far we progressed.

      • Well… you have SOME control if you choose the order of the people from the Chromosome Browser page. So I would have put the Pink person right after the Orange parent. But no, a rainbow progression isn’t possible at FTDNA.

      • I suppose I could download the results to a Word or Excel document and replace the colors with the desired colors with Find/Replace

  8. Thanks for sharing this interesting four-generation study. It’s fascinating to see how the segments are passed on from one generation to the next, and to see the random nature of inheritance in practice.

    With regards to the smaller segments under 5 cMs I’m not aware of any study that has tested your hypothesis that triangulated segments are always going to be IBD. I think this is something that needs to be tested first before any conclusions can be drawn. Large triangulated segments are IBD by virtue of their size. We know, for example, that the majority of segments over 10 cMs are IBD, and virtually all segments over 15 cMs are IBD. Phasing is the gold standard for determining whether or not a segment is IBD. In a study by Durand et al using 2,952 father-mother-child trios, the authors found a false positive rate of over 67% for segments of 2-4 cMs in length and this was using phased data: http://mbe.oxfordjournals.org/content/early/2014/04/30/molbev.msu151.full.pdf. We also have the data from John Walden and Tim Janzen in the ISOGG Wiki. They used the GedMatch phasing engine where they found a similarly high false positive rate for these small segments. See: http://www.isogg.org/wiki/IBD.

    Has the mother of the two siblings been tested so that a comparison can be done between both parents and the two children? One of the difficulties of using data from siblings is that 25% of their shared DNA is fully identical (ie, they match on both the paternal and the maternal chromosomes. See: http://www.isogg.org/wiki/Fully_identical_region Has the grandfather been tested? Even if the mother and the grandfather aren’t available for testing it might still be worth doing the phasing with one parent at GedMatch to see how many of these small segments are discarded. Without doing the necessary phasing using both parents for each generation I don’t think it’s reasonable to make any claims about the inheritance of these problematical small segments.

  9. I think it’s terrific that you have access to four-generation data. You illustrate a lot of important points (e.g. the possibility of inheriting / not inheriting intact chromosomes from a grandparent). But… you are still hampered because you do not have access to phased data.

    You wrote “This conclusively dismisses the theory that small segments aren’t created within a couple of generations.” I agree that small segments CAN be created within a couple of generations. If a 20 cM segment does happen to be involved in a recombination event, the cross-over point could occur anywhere within the segment boundaries, perhaps creating an 18 cM and a 2 cM segment.

    But you haven’t demonstrated that the small segments in your case study are IBD, because you are limited to genotype data. For an example of how small segments can disappear with phased data, see my blog post

    http://www.thegeneticgenealogist.com/2015/03/30/guest-post-what-a-difference-a-phase-makes/

    My example might be even more dramatic if I had phased data for the other party.

    If you have data for some of the spouses, I’d be glad to assist you in phasing the data and creating a synthetic file to upload to FTDNA.

    • Hi Ann, Actually, you have just made my point. Small segments CAN be created and they ARE created. Certainly not all small segments are IBD – but some are and to dismiss all small segments as irrelevant and invalid is inaccurate. Yes, small segments need to be used with care, but that doesn’t mean they can’t be used. I’m not implying you’ve said this, but others have and it has become somewhat of an urban legend. Relative to phased data – I have some. I am in the process of uploading the files that weren’t at GedMatch to GedMatch. I would like to phase two kits and load the phased data back to FTDNA so that we can see the data in the same format. I will be in touch about that. Thank you.

  10. Wonderful! Thank you. Wish you would also explore “multiples” on one chromo of a match… “disconnected” goo, I presume… those can an up to a significant cM # sometimes… show well in FF chromo browser… show even better at GEDmatch w/ setting 300/3… I’ve had as many as 5 segments on one chromo w/ a match… up to 20+cM. It is my understanding the algorithms do not accommodate these.

  11. Pat Davis says he would like you to explore “multiples” on one chrome of a match. Along those lines, in a future article can you explain: It is my understanding that if 5 people overlap with me on a 10cM+ segment, and 4 of us match with a one-to-one comparison, we should find a Common Ancestor. But, how can the 5th person match me on the same 10cM+ segment, close to the same start and stop points, and match me with a DIFFERENT CA? Or, do I have it all wrong…….

    • Remember, you have two houses with the same address on the street of your DNA. One is your Mom’s address and one is your Dad’s address – but they are the same – so you will have people from both sides of your tree matching you at the same location. When you compare them to each other – they should cluster into two groups. A Mom’s group and a Dad’s group.

      • While that works most of the time the problem I keeping seeing is that those clusters sometimes include my cousins from both family lines so I can’t tell whether the segment reflects a direct inheritance from one of my parents or a historical segment passed through many generations of an endogamous population. Any suggestions for resolving that problem?

  12. Pingback: DNAeXplain Archives – Intermediate DNA Articles | DNAeXplained – Genetic Genealogy

  13. This is a very helpful “hands-on” explanation which must have taken you quite a lot of time to write. It is just what I (and probably lots of others) needed! THANK YOU. Just to be sure I am understanding correctly, I have this question. I share a solid (i.e. unbroken) 155 cM match on Chr7 with a first cousin. We share a paternal grandfather. A known descendant of this same grandfather’s mother matches a 45 cM block in the middle of the 155 cM segment. All three of us match each other. Can I assume my cousin and I inherited the entire 150 cM from our paternal grandfather?

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  15. Is it possible that exact match of Grand father’s and grand son’s DNA? How much percent did match in past history???
    Otherwise is there any record of perfect match of grandson and grandfather’s DNA??

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