Inferred Chromosome Mapping using DNA Painter

A new tool has been added at DNA Painter: the Inferred Segments Generator. If you have a parent, sibling, half sibling or a descendant of a sibling whose DNA test results are on any of the sites displaying the chromosome browser, then you can make use of this new tool. Just a note though that it won’t be of use to you if your grandparents are related, or if they’re from a group with a high level of endogamy: you have to have grandparents whose lines are clearly distinct.

If you have no idea what a chromosome browser is, take a look at my previous post [here]. What you need to understand for inferred chromosome mapping is that we have two copies of each chromosome: the copy we inherited from our father and the other from our mother. DNA Painter is all about helping us to separate out which of those two copies any specific DNA match segment should sit on. However, homing in on any one of those copies, the DNA on either the mother’s or father’s copy is a random mix of what they inherited from their own mother and father, and this is why we talk about ‘segments’ – we will have a ‘chunk’ of DNA from our father that came from his own father’s side, followed by another chunk from his mother’s side, and so on. So at any specific place on our two copies (maternal and paternal) of any specific chromosome, we have inherited DNA from either our grandmother or our grandfather. A DNA match means we have inherited exactly the same segment as our DNA cousin, but precisely where the segment match begins and where it ends is where one of us – me or my DNA cousin – has switched at that point in our DNA inheritance from one grandparent to the other.

Inferred chromosome mapping is simply about using this understanding alongside our DNA results in comparison with those of our parent, sibling or nephew/niece. Let’s say my brother and I both match second cousin A on our maternal line. We know that this shared DNA comes from our mother’s paternal line. Now let’s say my brother’s shared segment with second cousin A on one segment is longer than mine. We can infer that here, the DNA I inherited from our mother has switched from my maternal grandfather to my maternal grandmother. Now, when I get a new match on those segments that I have been able to allocate through ‘inferred mapping’ to my maternal grandmother, it greatly reduces the parts of my tree I have to look at in my efforts to locate any new matches.

In the short video below, Jonny Perl, founder and creator of DNA Painter, explains all of the above with diagrams. He then explains what his new Inferred Segments Generator is and how you can use it for inferred chromosome mapping. I’ve been able to use it so far for just two matches my brother and I share – a second cousin and a second cousin once removed (both on the same line) – and I’ve been able to ‘infer’ and allocate 195 centiMorgans worth of segments.

For those of you who are into DNA for genealogy – may you be blessed with many, many centiMorgans of inferred DNA!

*****

For the next three months I have a very heavy workload and will be reducing my posts to one per month, the 1st of July, August and September. From October I’ll be returning to my usual pattern of two posts per month. Until next time, have a good June.

DNA Painter Ancestral Trees

Fan tree created using DNA Painter
DNA Painter fan tree

Today I have pretty things for you!
For ages I wanted to create a colourful fan tree. I had no idea how to go about doing that but suspected it would involve a lot of work, so I was particularly impressed when, a while back, Jonny Pearl introduced the facility to do this very quickly and easily on his DNA Painter site.

I wrote about DNA Painter earlier this year as part of my mini-series on using chromosome browsers as part of DNA research for genealogy. As explained in that previous post, DNA Painter is brilliant for mapping out your DNA segments, but in theory even if you don’t intend at this stage to use the main DNA functions, you could still get your own colourful fan just by uploading your tree to the site. You do this by downloading the GEDCOM file from your online tree or your own software or simply by inputting the information manually.

Once loaded, your tree will appear as a pedigree with each of the lines colour coded. The DNA Painter default palette uses pretty much the same colours I use on Ancestry to assign known DNA matches to each of my great grandparents’ lines, but here on DNA Painter the default paternal grandmother and maternal grandfather colours were the wrong way round for me. It was very easy to flip the colours. Editing and building the tree is very straightforward too. You can hover over any ancestor to edit their information, add their parents or delete them, and you can mark them as a genetic ancestor – someone who is a common ancestor confirmed not only by paper trail but also by DNA. Fly your cursor over any ancestor and then select View/Edit → Edit or Add Notes to change any information about them, including the colours used for them and their ancestors.

From this point you can go to the three options at the top left hand corner of the screen: TREE / FAN / TEXT. Tree is the default – the pedigree. Text is a handy pedigree list of all your ancestors, with dates and places of birth and death. However for me the fan is the most exciting part. It only goes to 10 generations and I have some lines further back than that, so they are not included. Already, though, you can see at a glance how well you’re doing and where you have gaps.

I’m sure the arrangement in the fan above is obvious, but in case it isn’t: from left to right, the colour blocks are pale blue for my paternal side and pink for maternal. Then I have blue for my paternal grandfather (with violet and blue for his ancestors); yellow for paternal grandmother (with orange and yellow for previous ancestors); green for maternal grandfather (with turquoise and green for his ancestors); and finally salmon pink for maternal grandmother, with deeper pink and browny pink for her ancestral lines.

For all versions of the fan tree shown in the images in this post, you can hover over any individual person’s ‘box’ to see their name, vital dates and their relationship to you. At the same time on the left of your screen you’ll see the lineage from that person to you. I couldn’t show this in these images because the screen shot process disables the hovering cursor.

You can also click on ‘Tree Completeness’ over at top right of the screen to get numbers and statistics of ancestors identified at each generational level. All the images in this post click for a bigger version, but you’ll definitely need to do that to see the info on this next image.

Screen grab of DNA Painter Ancestral Trees tool bar showing options for Tree view, DNA filters, Tree completeness and other options
DNA Painter Ancestral Trees toolbar

Moving along the toolbar options to ‘Dimensions’, these next two fan charts draw upon all the information you provided when you uploaded or built your tree. First, you can see all your ancestors colour-coded by the age at which they died.

Fan tree showing ancestors' ages at death
DNA Painter fan tree showing ancestors’ ages at death

Next, ancestors colour-coded by the century in which they were born.

Fan tree showing century of ancestors' births
DNA Painter fan tree showing century of ancestors’ births

So far all the charts shown relate simply to the detail of your family tree. However, if you also work with DNA, you can make use of all the following fan charts:

On the upper toolbar, select DNA Filters. The first option is Show Genetic Ancestors. Provided you have already marked which of your ancestors are proven as genetically linked (see above) you will now see how you’re doing in terms of corroborating your documented tree through DNA matching. This is mine.

Fan tree showing ancestors with genetic link proven by DNA
DNA Painter fan tree showing ancestors with genetic link proven by DNA

My first ever DNA post was about deep ancestral DNA testing: mitochondrial DNA and Y-chromosome DNA. To recap very quickly, everyone inherits mitochondrial DNA from their mother – but only daughters pass it on. This means everyone can be sure that they share the same mitochondrial haplogroup as their mother, their mother’s mother, and so on right back through time. That is illustrated by the following chart. (In fact I have only been able to trace this line back to 3xG grandmother, but even though I don’t know her name, I do know that my 4xG grandmother has the same mitochondrial as me.)

Fan tree showing mitochondrial DNA inheritance
DNA Painter fan tree showing mitochondrial DNA inheritance

Y-chromosome DNA works exactly the same way, but only males inherit it, and obviously therefore only fathers pass it on. So the Y-DNA inheritance path is an exact mirror image of the mitochondrial, following father’s father’s father’s father’s line right the way back. (The chart below showing this is for a man whose DNA I manage. Obviously I can’t get this information from my own DNA.)

Fan tree showing Y-chromosome DNA inheritance
DNA Painter fan tree showing Y-chromosome DNA inheritance

The second option in DNA Filters is Show X-DNA Path. At some point I’ll do a blogpost about X DNA. I haven’t done it so far because I don’t have many X matches to use as illustrations. If you already understand X-DNA inheritance patterns the meaning of the following two screenshots will already be clear, and when I do eventually write about this I’ll include them, since they illustrate perfectly the different inheritance patterns for females (the one immediately below)…

Fan tree showing X-DNA inheritance for females
DNA Painter fan tree showing X-DNA inheritance for females

… and males:

Fan tree showing X-DNA inheritance for males
DNA Painter fan tree showing X-DNA inheritance for males

Because of the dark colour used, it isn’t clear from these last two screen grabs that if you hover your cursor over the dark patch the intensity of colour reduces and you can see the individual ancestors’ names.

I don’t know about you, but I think all of this is pretty cool!