DNA Painter

This is the second in my 3-part mini-series about using chromosome browsers in genetic genealogy.  You’ll find links to all my previous DNA posts [here].

My last post introduced chromosome browsers.  We looked at how to interpret the data revealed in the browser, how to use it for One-to-One or One-to-Many comparisons, and the importance of using this information in conjunction with documented trees.  We talked about the weakness of chromosome browsers, being that they are unable to distinguish between DNA from your maternal line and that from your paternal line.  MyHeritage have partly got round this by introducing a ‘Triangulation Tool’ which operates when using the chromosome browser in One-to-Many mode, highlighting when the matches being compared ‘triangulate’ – that is, when you and all the matches being compared are all descended from a common ancestor. 

What MyHeritage cannot tell you is which of your lines – maternal or paternal – this match is on.  You have to work that out yourself.  One other obvious issue – and this is by no means a weakness on the part of MyHeritage, but it is a drawback anyway – you can only use the Triangulation Tool on MyHeritage to compare segment data with people whose autosomal DNA was either tested with or has since been uploaded to MyHeritage.

DNA Painter is a third-party tool that helps you overcome these two difficulties.  It was created by Jonny Perl in 2017 and has gone from strength to strength.  It’s free to use provided you create only one profile.  If you want more than one profile, or if you want to use the advanced tools there is a charge.  I have seven profiles.

I cannot express enough how fantastic DNA Painter is.  For me, it’s right up there with seeing the Aurora Borealis.  I know that may sound excessive, but it’s true.

Briefly, the way DNA Painter works is this: when you’re comparing your DNA with another person’s using a chromosome browser you can download the segment data.  This data – whether it be from MyHeritage, FTDNA, 23andMe or GEDmatch – can then be uploaded to DNA Painter and ‘painted’ on your profile. Unlike a chromosome browser, DNA Painter has two lines for every chromosome – a paternal line and a maternal line so you can start to separate out your matches.  If you know which of your lines these segments are on – say, if you are painting a match with your maternal first cousin so you know this is on your maternal line – you can include this information, and these segments will be painted to your maternal copy of those chromosomes.

Blaine T Bettinger’s excellent video showing how to use DNA Painter was all I needed to get me started.  He covers how to paint segments, how to edit them, and other features (although there are more now than when this video was made in 2017).  I watched it through once, then again in short bursts alongside ‘painting’ my first segments, and after that it was all plain sailing.

So without further ado I’m going to suggest you watch this video. (The automatic start point is not right at the beginning – you’ll need to wind it back.)

Blaine T Bettinger: Mapping your Chromosomes with DNA Painter:

Just to be clear – you can’t use DNA Painter if your results are just on Ancestry.  You have to be able to see your results in a chromosome browser.  So if you tested with Ancestry you need to upload your data from there to MyHeritage or FTDNA or GEDmatch before you can use DNA Painter.

This is how my main profile on DNA Painter looks right now.  Click it to see a larger image:

Chromosome map from DNA Painter

The pale blue lines in the background represent the copy of each chromosome that I got from my father and the pale pink lines are for the copy I got from my mother.  By the time I found DNA Painter I had already confirmed a number of my matches on GEDmatch and MyHeritage. These were the ones I painted straight away. As these were known and confirmed matches I already knew our Most Recent Common Ancestor couple (MRCA) and I knew if the match sat on my maternal line or my paternal line so was able to paste them accordingly.  These known matches set the scene for anything else I paint.

More recently I allocated specific colours to each of my grandparents.  My paternal grandfather is shades of blue and my paternal grandmother yellow.  My maternal grandfather is green and my maternal grandmother red. You can see this on my profile: the blue and yellow shades are always on my paternal line, the green and red shades always on my maternal line.

Apart from my brother (he’s not on here; I made a separate profile for him) I have no matches at all closer than second cousin, so the nearest MRCAs for whom I have confirmed matches are at great grandparent level.  In my colour scheme the closer ancestors have a pale version of their allotted colour, and the further back generations have increasingly darker shades of that colour.  Again on my profile, look at the maternal line on chromosome 13.  You’ll see two long lines representing my great grandparents, and within them several shorter segments of darker green.  These darker segments are ancestors further back along these great grandparents’ lines whose DNA I’ve discovered because of matches with more distant cousins.  In fact these more distant matches have evidenced that the first long green segment on chromosome 13 is from my great grandfather, while the second long green segment is from his wife, my great grandmother. 

In every case I record the MRCA couple when I ‘paint’ the match, and these are shown in the table at the bottom right of the profile. 

If I have a segment already attributed to one of my copies of a chromosome – let’s say to my Dad’s paternal great grandparents and another match on that same segment comes along that seems to be from my Dad’s maternal line, then something is wrong.  While both of these relationships are consistent with my own paternal copy of that particular chromosome, it is not consistent with my Dad’s chromosome inheritance: one of these would be on his maternal copy and the other on his paternal.  He could not have passed on both of these copies to me on the same segment.

So – possibilities include:

  • I’ve made a mistake
  • My tree, or my match’s tree is wrong
  • There is a case of misattributed parentage (often referred to as an NPE – ‘non-paternity event’) somewhere along one of these lines in my own tree or my match’s tree
  • All of the above is absolutely in order but this person and I also match on my maternal line and that is where the segment is from
  • The segment is a piece of DNA belonging to a shared population group, such as Jewish or Irish

You make mistakes as you go but you can edit and change them very easily as new info comes in.

Here’s an example of a DNA match with a surprise and how I used DNA Painter to record it, changing my initial conclusions:

A and I matched at around 3rd to 4th cousin.  He was adopted but had found his birth mother and had an idea of who his father was.  Using my own tree and working back the tree of his suspected father I was able to confirm that we had MRCAs at 3xG grandparent level, making us 4th cousins.  The man A thought might be his father definitely was.  I added A to my list of confirmed matches and painted our segments to my profile.  Our match was on my paternal line, and painted yellow for my paternal grandmother’s ancestry.

After so many years of searching, A found it quite difficult to accept so easily that we had found his father, so I offered to work on three other close matches that triangulated with the two of us.  When A could see that other matches led to the same conclusion I thought he would be convinced.  The first two matches did indeed lead back to the same MRCA, and both of them were closer matches to A than they were to me – they are all descended from one of our 3xG grandparents’ sons, and I am descended from another.  A was happy: something shifted for him, and for the first time he really believed he knew his roots.  Then I moved on to the third of our common matches.  Starting with a small amount of information on this person’s online tree, I worked back until I found an overlap with A’s tree.  But it was confusing: A’s match with this person led up another of A’s lines – one that didn’t end with our confirmed 3xG grandparents.  It took a bit of working out (there was a lot of false information on census and marriage records and a nasty divorce) but eventually I was able to follow their common line… back to another set of my 2xG grandparents still on my paternal line, but this time my paternal grandfather.  A and I are cousins twice over: on both sides of my paternal line, both of these connections confirming different parts of A’s father’s line.  DNA Painter actually allowed me to record this information by keeping two of the segments yellow and changing the third segment we share to blue – it’s the pale blue segment you see on my paternal line towards the end of chromosome 12.  How amazing is that!

My main profile on DNA Painter is for confirmed matches only.  However, there are still a number of decent matches on MyHeritage, FTDNA and GEDmatch that I can’t place.  I didn’t want to lose sight of them, so I created a new profile for my mystery matches.  By comparing my mystery profile matches to other confirmed new matches from time to time, I’m able to narrow down our match, at the very least allocating some of them to either my paternal or maternal line or even moving them into my main profile.  More recently I decided to set up an Irish mystery matches profile which I hope in time will enable me to home in on distinct parishes or areas.

In the “Segment/Match Notes” I list how the match descends from the common ancestral couple, any relevant ID numbers, and anything else pertinent including other potential ancestral lines in common. This means that I list every generation beginning with the common ancestral couple and ending with the tester.

It occurs to me that chromosome mapping kind of turns it around so that it’s about mapping your DNA segments just as much as it is about proving your family tree.  I do know, though, that my chromosome map will never be complete.  My close family is too small.

******

It’s perfectly possible to make great DNA discoveries without even looking at a chromosome browser.  However, working with chromosome browsers and DNA Painter has done more than simply help me to sort out my matches.  It has helped me to visualise and better understand complex abstract information.  By viewing my matches in a chromosome browser I saw, for example, that the twenty-two chromosomes are all different lengths and numbered 1 to 22 broadly in that order of length.  I also saw and understood that the longer the segments, the closer the family connection.  Hence a lot of short segments indicates either that you are more distantly related, or you may simply share a lot of DNA as a result of being from an endogamous or close-knit community, going back centuries. I knew that the segments I was looking at came either from my mother or from my father, but it wasn’t until I started to use DNA Painter that I understand the maternal copy and paternal copy of each chromosome covers the full length of the chromosome.  Originally (because of the single grey line on the regular chromosome browser) I thought 50% of that line was from one parent and the other 50% from the other parent.

If you’re a visual person you too may find it easier and more enjoyable to work this way.  It is definitely more fun!

There is a DNA Painter User Group on Facebook with, at the time of writing, approaching 12,000 members, and there are very knowledgeable group members who will help with any questions. Jonny and Blaine are also on there.

*****

My DNA posts are intended as a beginners’ guide, building up the information in order, in bite-sized chunks.  Click [here] to see them all in the order of publication.

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