6 Tips for Selecting DNA Matches to Paint in DNA Painter

DNA Painter is one of the coolest websites out there for genetic genealogy, offering an arsenal of tools to help genealogists visualize and understand their DNA matches through chromosome mapping. Let’s face it, there is tremendous aesthetic appeal in generating chromosome maps with neat little color-coded segments indicating specific chunks of DNA that can be traced back to a particular ancestor. But beyond just the aesthetics, it’s very useful to be able to predict how one must be related to an unknown DNA match, based on the location of the matching segment(s). In order to generate a useful chromosome map, however, there are decisions that must first be made about which matches to paint, so today I’d like to offer a few tips on how to do that, based on my own experience with using DNA Painter.

Getting Started with DNA Painter

DNA Painter is the brain child of Jonny Perl, a web developer and genealogist based in London, UK. He has created a very user-friendly site with a host of linked blog posts, webinars, videos, and instructions right on the site, making it easy for beginners to get started with chromosome mapping. Nonetheless, chromosome mapping isn’t exactly intuitive, and some thought is required to produce a good map. Therefore, there are some questions you should ask yourself before you begin.

What is My Goal?

For many of us, it’s inherently cool to be able to visualize a segment of DNA, lurking in nearly every cell of one’s body, and know that it was inherited from a particular ancestor who lived decades or centuries ago. If you’re content with knowing in a general way that your DNA was inherited from previous generations in your family, and you really don’t care about pinpointing a 46-centiMorgan segment on Chromosome 12 that you inherited from your great-great-great-grandfather, then maybe chromosome mapping isn’t your thing. But if you’d like to use a chromosome map to better understand your DNA match list, then your initial goal should be to create a map that identifies segments you inherited from each of your four grandparents.

On average, 25% of a person’s DNA was inherited from each of the four grandparents, but this number can vary a bit due to the randomness of genetic recombination. If you can identify on each chromosome the specific segments of DNA that were inherited from each grandparent, you can use this as a first step toward understanding unknown DNA matches.

Once you’ve established this goal, then you can decide which of your DNA matches to paint onto your chromosome map, based on the criterion of whether or not painting this match will bring you closer to your goal. The thing is, just because you can paint a match doesn’t mean you should paint it, as some of them will not be especially informative.

For example, if you have DNA test data from a parent, you could paint that on your chromosome map. But there’s no point in doing so, because you already know that you have inherited one of each of your 22 autosomes from your mother, and one from your father. By painting your DNA matches with a parent, all you’ve done is change the color of the canvas on which you’re painting your matches. Not sure what I mean by that? Figure 1 shows the blank canvas you start with, courtesy of DNA Painter.

Figure 1: Top portion of the page of a new, “unpainted” profile at DNA Painter, showing maternal (pink) and paternal (pale blue) copies of Chromosomes 1-10. If you were to scroll down the page, you would see the remaining chromosomes.

Now let’s say I’ve tested my mother, and I want to paint that DNA match onto my chromosome map. Figure 2 shows how that looks.

Figure 2: Top portion of the page showing Chromosomes 1-10 after I “paint” that blank canvas with segments of DNA shared between me and my mom.

You can see that all I’ve done here is to change those pink bars to lavender, which is not very informative. As a side note, you will see some regions on certain chromosomes where the lavender color does not “paint” all the way to the tip of the chromosome. That’s because those tips correspond to regions which exhibit a low density of single nucleotide polymorphisms (SNPs, or “snips”). Family Tree DNA does not test those SNP-poor regions, and since the segment data used in this map came from Family Tree DNA, we see those “unpainted” regions.

Similarly, some close matches, such as a full-blooded aunt or uncle, don’t help you identify the segments of DNA you inherited from each of your four grandparents. Why? A full-blooded aunt or uncle, let’s say on the paternal side, will have inherited a mix of DNA from your paternal grandparents, just as your father did. But painting these segments only tells you which bits of DNA were passed down from your grandparents to both the paternal aunt or uncle and to you. It doesn’t bring you any closer to knowing which paternal grandparent provided those segments. Additionally, painting DNA matches from a sibling onto your chromosome map isn’t particularly useful, because it only identifies segments that you both inherited from your parents. It doesn’t help you to assign those segments to either parent, or any grandparents.

Note that there are other great reasons for testing one’s siblings, and the data that comes from those tests can be very useful. For example, if you have data from three siblings, but none of their parents, you can do visual phasing, which will assign segments of DNA to each grandparent. Blaine Bettinger offers a 5-part tutorial on visual phasing here, and Andy and Devon Lee of Family History Fanatics offer a tutorial on visual phasing using only two siblings here. Note that visual phasing as described in these tutorials is not for the faint of heart; DNA Painter is much easier.

The best matches to paint are the ones with whom you share DNA from only one of your four grandparents, or those with whom you share DNA from generations earlier than that. Therefore, second cousins are ideal, as are any half first cousins you might have. Don’t despair, however, if you don’t have a huge selection of “ideal” matches to paint; you’ve just got to go with what you’ve got. My mom’s paternal grandfather, Joseph Zielinski, was the only one of the ten children in his family to marry and have children; all the rest died unmarried, before the age of 32. This means that every single one of Mom’s paternal second cousins is a match on her grandmother’s side. I have to go back at least one generation, to the level of 3C or more distant cousins, before I can hope to find any matches to her paternal grandfather’s family. Similarly, my paternal grandmother had only one sister who died at the age of 14, so my only paternal second cousins are on my grandfather’s side. If you know you come from a small family, it becomes even more important to research your family tree as thoroughly as you can, in the hope of identifying cousins from whom you can beg DNA samples.

Putting it all together, then, here is my list of tips for creating an ancestral chromosome map, focused on mapping your chromosomes to each of your four grandparents.

  1. Don’t paint willy-nilly. Think before you paint, and ask yourself if painting this match will bring you closer to your goal of identifying (at minimum) segments inherited from each of your four grandparents.
  2. Don’t paint matches to parents, full siblings, half siblings, or full aunts or uncles, as these will not help you identify segments inherited from each of your four grandparents. You can, of course, create separate profiles at DNA Painter for each person you test, and keep track of their DNA matches as well as your own. The ability to create multiple profiles for chromosome mapping is a benefit available with a subscription to DNA Painter; you can create one profile for free with a basic membership.
  3. Similarly, matches to first cousins, and first cousins X-times removed, will not help you identify which portions of your chromosomes were inherited from which grandparent. Full first cousins share both grandparents with you on either your maternal or paternal side. Therefore it’s not possible to identify the grandparent who contributed the DNA from any segments you share, so painting those matches is not informative.
  4. Try the Inferred Segment Generator for additional segments to map. This is a really neat tool that uses deductive reasoning to generate segments. I used it to generate segments from my maternal grandfather to paint onto my chromosome map. The principle here is simple: the chromosomes that I inherited from my mother must be a mixture of DNA she inherited from her mother, and DNA she inherited from her father. Since I was able to test my maternal grandmother before she passed away, I know precisely which segments I inherited from her. So, by deduction, I know that the remaining portions of my maternal chromosomes where I do not match Grandma, must have come from Grandpa.
  5. If there’s good evidence (e.g. through triangulation) to suggest that a segment was inherited from an earlier ancestor (great-grandparent, great-great-grandparent, etc.) by all means, paint it.
  6. If you have test data from a particular relative, additional test data from descendants of that relative will be less informative, so you may want to skip painting it. Figure 3 illustrates this. The blue bars represent DNA segments which I share with a documented third cousin (3C), and the red bars represent the DNA that I share with her daughter, my third cousin once removed (3C1R). I’ll definitely want to paint those blue segments onto my chromosome map at DNA Painter, because those segments represent DNA which I inherited from one of the great-great-grandparents that I have in common with that cousin. However, my 3C1R cannot inherit any DNA from our common ancestors unless it came through her parent (my 3C). The only exception to this would be in cases where her parents are related. So, the red bars will necessarily be fewer and shorter than the blue bars, and painting those segments of DNA onto my chromosome map will not provide any new information about regions of my own chromosomes that can be assigned to particular ancestral couples. Of course, you may choose to paint them anyway, if you just want to keep track of all of your DNA segment data this way, and you would definitely want to paint the matches to a 3C1R if you don’t have test data from your 3C.
Figure 3: Chromosome browser from Family Tree DNA, showing segments of DNA I share with one of my third cousins (blue) and her daughter (red).

At the end of the day, how you map your chromosomes is really a personal choice. Maybe you just want to create one heck of a colorful map, including data from your parents, siblings, aunts, uncles, and all your first cousins, and if that’s the case, then go for it! After some trial and error, I’ve found that this mapping strategy works best for me, because it focuses on quality of information, rather than quantity. Maybe it will help some of you, too. Happy mapping!

© Julie Roberts Szczepankiewicz 2021

5 thoughts on “6 Tips for Selecting DNA Matches to Paint in DNA Painter

  1. I’m a bit confused with your rule/point number 1. DNA Painter has ability to upload all matches and paint them over one profile. Isn’t it useful to have all the matches so when one will be figured out rest will fall into place? It does look messy, I’ll admit, but visually it gives a nice “grouping” of matches.

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  2. Are you referring to the cluster auto-painter function? You certainly can use that, if that helps you. I’ve been working with matches at 23&Me a lot lately, and it’s not an option there. However, with data from that site, it’s possible to paint ethnicity estimates onto one’s chromosome maps, and sometimes that can help to figure things out, too. Sometimes I find that less is more, when it comes to my chromosome map, but do whatever works for you!

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  3. I find it very useful to paint the segments I share with my aunt and uncle and half-brother, even though they don’t help me assign segments to a grandparent. It helps me get an overview of which matches’ segments overlap theirs, and then I can log into their profiles at FTDNA and check if they also match each other. If they do (or if they triangulate at MyHeritage), at least I know that those unknown matches are on my dad’s side and not on my mom’s.

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