This is the third article in a series about DNA Painter. To know DNA Painter is to love DNA Painter! Trust me!
The first two articles are:
- DNA Painter – Chromosome Sudoku for Genetic Genealogy Addicts
- DNAPainter – Mining Vendor Matches to Paint Your Chromosomes
The Chromosome Sudoku article introduces you to DNA Painter, it’s purpose and how to use the tool. The Mining Vendor Data article illustrates exactly how to find the segments you can paint from each of the main autosomal testing vendors and GedMatch.
This article is a leisurely tour through my colorful chromosome garden so that, together, we can see examples of how to utilize the information that chromosome painting unveils.
Chromosome painting can do amazing things: walk you back generations, show visual phasing…and reveal that there’s a mistake someplace, too.
If you’re not willing to be wrong and reconsider, this might not be the field for you😊
Chromosome painting automatically mathematically triangulates your DNA and in a much easier way than the old spreadsheet method. In fact, triangulation just happens, effortlessly IF you can determine which side is maternal and which side is paternal. Of course, you’ll always want to check to be sure that your matches also match each other. if not, then that’s an indication that maybe one or both are identical by chance.
The definition of triangulation in this context means:
- To find a common segment
- Of reasonable size (generally 7cM or over)
- That is confirmed to a common ancestor with at least two other individuals
- Who are not close family
Close family generally means parents, siblings, sometimes grandparents, although parents and grandparents can certainly be used to verify that the match is valid. The best triangulation situation is when you match those two other people through a second child, meaning siblings of your ancestor.
Different matches, depending on the circumstances, have a different level of value to you as a genealogist. In other words, some are more solid than others.
The X chromosome has special matching and triangulation rules, so we’ll talk about that when we get to that section.
Don’t think of chromosome painting as “doing” triangulation, because triangulation is a bonus of chromosome painting, and it just happens, automatically, so long as you can confirm that the segment is from either your maternal or paternal line.
What does triangulation look like in DNA Painter?
Here’s what my painted chromosome 15 looks like.
Here, I’ve drawn boxes around the areas that are triangulated. Actually, I made a small mistake and omitted one grey bar that’s also part of a second triangulation group. Can you spot it? Hint – look at the grey bars at far right in the overlapping triangulation group boxes where the red arrow is pointing. The box below should extend upwards to incorporate part of that top grey bar too.
Triangulation are those several segments piled up on top of each other. It means they match you at the same address on either the maternal or paternal chromosome. That’s good, but it’s not the same as an official “pileup area.”
Ok, so what’s a pileup area?
Certain locations in the human genome have been designated as pileup regions based on the fact that many people will match on these segments, not necessarily because they share a common relatively recent ancestor, but instead because a particular segment has a very high frequency in the general human population, or in the population of a specific region. Translated, this means that the segment might not be relevant to genealogy.
But before going too far with this discussion, it doesn’t mean that matches in pileup regions aren’t relevant to genealogy – just consider it a caution sign.
Aside from chromosome 6, which includes the HLA region, I’ve always been rather suspicious of pileup regions, because they don’t seem to hold true for me. You can view a chart that I assembled of the known pileup regions here.
DNA Painter generously includes pileup region warnings, in essence, along a chromosome bar at the top indicating “shared” or “both.”
Pileups regions are indicated by the grey hashed region at right. In my case, on chromosome 1, the pileup region isn’t piled up at all, on either the paternal (blue) chromosome or the maternal (pink) chromosome.
As you can see, I have exactly one match on the maternal side (green) and one (gold) on the paternal side (with a smidgen of a second grey match) as well, with both extending significantly beyond the pileup region. There is no reason to suspect that these gold and green matches aren’t valid.
If I saw many more matches in a pileup region than elsewhere, or many small matches, or DNA that was supposed to be from multiple ancestors not in the same line, then I’d have to question whether a pileup region was responsible.
DNA Painter provides you with the opportunity to see which of your ancestors’ segments stack. Stacking is a very important concept of DNA painting.
Before we talk about stacking, notice that the legend for which segments are color coded to specific ancestors is located at right. You can also click on the little grey box beside “Shared or Both,” at left, to show the match names beside the segments. This is very useful when trying to analyze the accuracy of the match.
I wish DNA Painter offered an option to paint the ancestor’s names beside the segments. Maybe in V2. It’s really difficult to complain about anything because this tool is both free and awesome.
I’m using Powerpoint to label this group of stacked matches for this example.
This is a situation where I know my pedigree chart really well, so I know immediately upon looking at this stacked segment group who this piece of DNA descends from.
Here’s my pedigree chart that corresponds to the stacked segment.
We attribute each DNA segment to a couple initially based on who we match. In this case, that’s William George Estes and Ollie Bolton, my grandparents. The DNA remains attributed to them until we have evidence of which individual person in the couple received that DNA from their ancestors and passed it on to their descendant.
Therefore, the pink people are the half of the couple who we now know (thanks to DNA Painter) did NOT contribute that DNA segment, because we can track the DNA directly through the yellow line until we’re once again to another genetic brick wall couple.
My father is listed at left, and the DNA path runs back to William Crumley the second and his unknown wife who is haplogroup H2a1, the yellow couple at far right. How cool is this? One of those ancestors (or a combined segment from both) has been passed intact to me today. This is not a trivial segment either at 23.3 cM. I would not expect a segment passed to 5th cousins to be that large, but it is!
Also, note that the grey segment of DNA from Lazarus Estes (1848-1918) and Elizabeth Vannoy (1847-1918) is sitting slightly to the left of the dark blue segment from William Crumley III, so part or all of the grey or blue segment may originate with a different ancestor. Perhaps we’ll know more when additional people test and match on this same segment.
I have one person who is related to me through two different lines. I need a way to determine which line (or both) our common DNA segment descends from.
Those two lines don’t converge, at least not that we know of.
Now, as I map additional people, I’ll watch this segment for a tie breaker match between the two ancestors. The gold is not a tie breaker because that’s my grandparents who are downstream of both the pink and blue ancestors.
23andMe does us the favor of painting our ethnicity segments and allowing us to download a file with those segments. Conversely, DNA Painter does us the favor of allowing us to paint that entire file at once.
I already know my two Native segments on chromosome 1 and 2 descend through my mother, because her DNA is Native in exactly the same location. In other words, in this case, my ethnicity segment does in fact phase to my mother, although that’s not always the case with ethnicity.
Multiple Acadian ancestors are also proven to be Native by both genealogical records and maternal and/or paternal haplogroups.
Therefore, I’ve painted my Native segments on my mother’s side in order to determine exactly from which ancestor(s) those Native segment descend.
Confirming Questionable Ancestors
One very long-standing mystery that seemed almost unsolvable was the identity of the parents of Elijah Vannoy (1784->1850). We know he was the son of one of 4 Vannoy brothers living in Wilkes County, NC. Two were eliminated by existing Bibles and other records, but the other two remained candidates in spite of sifting through every available record and resource. We were out of luck unless DNA came to the rescue. Y DNA confirmed that Elijah was descended from one of the Vannoy males, but didn’t shed light on which one.
I decided that the wives would be the key, since we knew the identity of all four wives, thankfully. Of course, that means we’d be using autosomal DNA to attempt to gather more information.
I entered one candidate couple at Ancestry as Elijah’s parents – the one I felt most likely based on tax records and other criteria – Daniel Vannoy and Sarah Hickerson. I also entered Sarah’s parents, Charles Hickerson (c 1725-<1793) and Mary Lytle.
I began getting matches to people who descend from Charles Hickerson and Mary Lytle through children other than Sarah.
The grey segment is from a descendant of Lazarus Estes & Elizabeth Vannoy. The salmon segments are from descendants of Charles Hickerson and Mary Lytle.
These segments aren’t small, 12.8 and 16.1 cM, so I’m fairly confident that these multiple segments in combination with the Elizabeth Vannoy segment do indeed descend from Charles Hickerson and Mary Lytle.
At Ancestry, I have 5 matches to Charles Hickerson and Mary Lytle through three of their children. However, only two of the individuals has transferred their results to either Family Tree DNA, MyHeritage or GedMatch where segment information is available to customers.
Finally, the thirty year old mystery is solved!
Shifting, Sliding, Offset or Staggered Segment Groups
Occasionally, you can prove an entire large segment by groups of shifting or sliding segments, sometimes referred as offset or staggered segments.
The entire bright pink region is inherited from Jacob Lentz (1783-1870) and Fredericka Reuhl (1788-1863.) However, it’s not proven by one individual but by a combination of 6 people whose segments don’t all overlap with each other. The top two do match very closely with me and each other, then the third spans the two groups. The bottom 3 and part of the middle segment match very closely as well.
I can conclude that the entire dark pink region from left to right descends from Jacob and Fredericka.
Two Matches – 7 Generations
The mustard match is to my grandparents (22cM), and the pink match is to George Dodson (1702-1770) and his wife (22cM) – 7 generations. These people also match each other.
Additional matches would make this evidence stronger, although a 22cM triangulated match is very significant alone. Future might also suggest ancestors further back in time.
First Chromosome Fully Mapped
I actually have chromosome 5 entirely mapped to confirmed ancestors. I’m so excited.
Uh Oh – Something’s Wrong
I found a stack that clearly indicates something is wrong. The question is, what?
The mustard represents my paternal grandparents, so these segments could have come through either of them, although on the pedigree chart below, we can see that this came through my grandfathers line..
There is only a small overlap with the magenta (Nicholas Speak 1782-1852 and Sarah Faires 1786-1865) and green (James Crumley 1711-1764 and Catherine c1712-c1790,) which could be by chance given that the Nicholas segment is 7.5 cM, so I’m leaving the magenta out of the analysis.
However, the rest of these segments overlap each other significantly, even though they are stepped or staggered.
As you can see from the colors on the pedigree chat, it’s impossible for the green segment to descend from the same ancestor as the purple segment. The purple and orange confirm that branch of the tree, but the red cannot be from the same ancestor or the same line as the green ancestor.
I suspect that the purple and orange line is correct, because there are 4 segments from different people with the same ancestral line.
This means that we have one of the following situations with the red and green segments:
- The smaller segments are incorrect, false positives, meaning matching by chance. The green segment is 14 cM, so quite large to match by chance. The red segment is 10 cM. Possible, but not probable.
- The segments are population-based matches, so appear in all 3 lines. Possible, technically, but also not probable due to the segment size.
- The segments are genuine matches, and one of the lines is also found in one of the other lines, upstream. This is possible, but this would have to be the case with both the red and green lines. To continue to weigh this possibility, I’ll be watching for similar situations with these same ancestors.
- Some combination of the above.
I need more matches on this segment for further clarity.
Visual Phasing – Crossovers
A crossover point is where the DNA on one side of a demarcation line is descended from one ancestor and the DNA on the other side is descended from another ancestor, represented by the pink and blue halves of the segment, below.
Crossovers occur when the DNA is combined from two different ancestors when it is passed to the child. In other words, a chunk of mom’s ancestors’ DNA is contributed by mom and a chunk of dad’s ancestors’ DNA is contributed as well. The seam between different ancestor’s DNA pieces is called a crossover.
In this example, the brown lines confirmed by several testers to be from Henry Bolton (c1759-1846) and Nancy Mann (c1780-1841) is shown with a very specific left starting point, all in a vertical line. It looks for all the world like this is a crossover point. The DNA to the left would have been contributed by another, as yet unidentified, ancestor.
The gold lines above are matches from more recent generations.
Naming Those Unnamed Acadians
My Acadian ancestry is hopelessly intertwined, but chromosome painting may in fact provide me with some prayer of unraveling this ball of twine. Eventually.
When I know that someone is Acadian, but I can’t tell which of many lines I connect through, I add them as “Acadian Undetermined.”
There’s a lot of Acadian DNA, because it’s an endogamous population and they just keep passing the same segments around and around in a very limited population.
On my maternal chromosome, all of the olive green is “Acadian Undetermined.” However, that blue segment in the stack is Rene de Forest (1670-1751) and Francoise Dugas (1678->1751).
In essence, this one match identified all of the DNA of the other people who are now simply a row in the Acadian Undetermined stack. Now I need to go back and peruse the trees of these individuals to determine if they descend form this line, or a common ancestor of this line, or if (some of) these matches are a matter of endogamy.
Endogamous matches can be population based, meaning that you do match each other, but it’s because you share so much of the same DNA because you have small pieces of many common ancestors – not because a particular segment comes from one specific ancestor. You can also share part of your DNA from Mom’s side and part from Dad’s side, because both of your parents descend from a common population and not because the entire segment comes from any particular ancestor.
On some long cold winter weekend, I’ll go through and map all of the trees of my Acadian matches to see what I can unravel. I just love matches with trees. You just can’t do something like this otherwise.
Of course, those Acadians (and other endogamous populations) can be tricky, no matter what, one click up from a needle in a haystack.
Acadian Endogamy Haystack on Steroids
At first, our haystack looks like we’ve solved the mystery of the identity of the stack. However, we soon discover that maybe things aren’t as neat and tidy as we think.
Of course, the olive green is Acadian Undetermined, but the three other colored segments are:
- Pink – Guillaume Blanchard (1650-1715/17) & Huguette Goujon (c1647-1717)
- Brown/Pink – Francois Broussard (c1653-1716) & Catherine Richard (c1663-1748)
- Coffee – Daniel Garceau (1707-1772) & Anne Doucet (1713-1791)
Looking at the pedigree chart, we find two of these couples in the same lineage, so all is good, until we find the third, pink, couple, at the bottom.
Clearly, this segment can’t be in two different lines at once, so we have a problem. Or do we?
Working the pink troublesome lines on back, we make a discovery.
We find a Blanchard line consisting of Guilluame Blanchard born circa 1590 and Huguette Poirier also born circa 1690.
Interesting. Let’s compare the Guillaume Blanchard and Huguette Goujon line. Is this the same couple, but with a different surname for her?
No, as it turns out, Guillaume Blanchard that married Huguette Goujon was the grandson of Guilluame Blanchard and Huguette Poirier. That haystack segment of DNA was passed down through two different lines, it appears, to converge in three descendants – me, the descendant of the pink segment couple and the descendant of the brown/burgundy segment couple. This segment reaches back in time to the birth of either Guilluame Blanchard or Huguette Poirier in 1590, someplace in France, rode over on the ship to Port Royal in the very early 1600s, probably before Jamestown was settled, and has been kicking around in my ancestors and their descendants ever since.
This 18 or so cM ancestral segment is buried someplace at Port Royal, Nova Scotia, but lives on in me and several other people through at least two divergent lines.
The X Chromsome
Several vendors don’t report the X chromosome segments. I do use X segments from those who do, but I utilize a different threshold because the SNP density is about half of that on the other chromosomes. In essence, you need a match twice as large to be equivalent to a match on another chromosome..
Generally, I don’t rely on segments below 10 for anyone, and I generally only use segments over 14cM and no less than 500 SNPs.
Having just said that, I have painted a few smaller segments, because I know that if they are inaccurate, they are very easy to delete. They can remain in speculative mode. The default for DNAPainter and that’s what I use.
The great thing about the X chromosome is that because of it’s special inheritance path, you can sometimes push these segments another 2 generations back in time.
Let’s use an X chromosome match in conjunction with my X fan chart printed through Charting Companion.
On the paternal X, I inherited the gold segment from the couple, William George Estes (1873-1971) & Ollie Bolton (1874-1955.) However, since my father didn’t inherit an X from William George Estes (because my father inherited the Y from his father,) that X segment has to be from Ollie Bolton, and therefore from her parents Joseph Bolton (1853-1920) and Margaret Claxton (1851-1920.)
The segment from Lazarus Estes (1848-1918) and Elizabeth Vannoy (1847-1918) that’s 14 cM is false. It can’t descend from that couple. Same for the 7.5 cM from Jotham Brown (c1740-c1799) & Phoebe unk (c1747-c1803.) That segment’s false too. The green 48 cM segment from Samuel Claxton (1827-1876) and Elizabeth Speak (1832-1907)? That segment’s good to go!
On my mother’s side, there’s a 7.8 cM Acadian Undetermined, which must be false, because Curtis Benjamin Lore (1856-1909) did not inherit an X chromosome from his Acadian father, Antoine Lore (1805-1862/67.) Therefore, my X chromosome has no Acadian at all. I never realized that before, and it makes my X chromosome MUCH easier.
How about that light green 33cM segment from Antoine Lore (1805-1862/67) & Rachel Hill (1814/15-1870/80)? That segment must come from Rachel Hill, so it’s pushed back another generation to Joseph Hill (1790-1871) and Nabby Hall (1792-1874.)
I love the X chromosome because when you find a male in the line, you automatically get bumped two more generations back to his mother’s parents. It’s like the X prize for genetic genealogy, pardon the pun!
Some adoptees are lucky and receive close matches immediately. Others, not so much and the search is a long process.
If you’re an adoptee trying to figure out how your matches connect together, use in-common-match groupings to cluster matches together, then paint them in groups. Utilize the overlapping segments in order to view their trees, looking for common surnames. Always start with the groups with the longest segments and the most matches. The larger the match, the more likely you are to be able to find a connection in a more recent generation. The more matches, the more likely you are to be able to spot a common surname (or two.)
Painting can speed this process significantly.
Much More Than Painting
I hope this tour through my colorful chromosomes has illustrated how much fun analysis can be. You’ll have so much fun that you won’t even realize you’re triangulating, phasing and all of those other difficult words.
If you have something you absolutely have to do, set an alarm – or you’ll forget all about it. Voice of experience here!
So, go and find some segments to paint so all of these exciting things can happen to you too!
How far back will you be able to identity a segment to a specific ancestor? How about a triangulated segment? An X segment?
Have fun!!! Don’t forget to eat!
PS – If you’d like to learn more about Phasing, Triangulation or hear my keynote speech, consider signing up for the Virtual DNA Conference June 21-24. I’ll be presenting on both of those topics. You can sign in anytime for the next year to listen to the sessions, not just during the conference days. The keynote will be recorded and available afterwards as well.
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Thank you so much.
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