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Chromosome Mapping Inferred Chromosome Mapping

Interpreting inferred segments: a full aunt

An interesting DNA match to my mother-in-law Lynn* and her maternal aunt (Ann) appeared this week. In this article I’ll review how I interpreted their match with Tom alongside methods for interpreting inferred segments when working with a full aunt:

  • What can I infer about Lynn’s DNA from the segments her aunt Ann shares with Tom?

* Names of living people have been changed

The new match

Match to Tom in match list
Tom appeared as a new match last week

His name seemed familiar, and sure enough, Tom was already in my tree based on previous research. He is a half-second cousin to Ann and a half-second cousin once removed to her niece Lynn.

Ann’s maternal grandfather and Tom’s paternal grandmother were half-siblings, sharing a father, John Richards:

Tree showing how Tom connects to Ann and Lynn
Tree showing how Tom connects to Ann and Lynn

(If you find cousin relationships confusing, FindMyPast and MyHeritage have good explainer pages).

Reviewing the Shared cM Project tool, I can see that Tom’s 119cM match with Ann is almost exactly the average amount that two half-second cousins might expect to share.

The shared cM project tool tells me 119cM is reasonable for a half 2C
The shared cM project tool tells me 119cM is a typical number of cMs of DNA for a half 2C relationship

Shared segments

We also have access to the segment data, so I know the positions on the chromosome at which Ann matches Tom.

The segments of DNA that Tom shares with Ann
The segments of DNA that Tom shares with Ann

I do need to remember that there can be ambiguities with segment data, for example:

  • The precise reported start and end point for shared segments is slightly fuzzy for various reasons (for example, the companies only test certain SNPs)
  • Smaller segments can sometimes be not be real at all, based on weaving together a mixture of maternal and paternal DNA

However, my working assumption is that:

  • Each of these segments is genuine
  • Tom and Ann share each segment due to the known relationship via their common ancestor John Richards.

I’ll need to be particularly careful to review the smaller segments and compare them to existing matches.

Half-relatives have just one MRCA

As half-relatives, there’s just one ‘most recent common ancestor’ (MCRA) as opposed to a couple. Tom and Ann’s common ancestor John Richards was born about 1832 near Ebbw Vale in Wales.

Tom and Ann's ancestors were half-siblings, children of John Richards
Tom and Ann’s ancestors were half-siblings, children of John Richards

Ann is the granddaughter of John’s son William, while Tom is the grandson of William’s paternal half-sister Anna.

Any segments shared by Tom and Ann will have come from just one of John Richards’s parents: John Richards senior and his wife Sophia Jenkin.

John Richards's parents John Richards and Sophia Jenkin were the source of the segments Ann and Lynn share with Tom
John Richards’s parents John Richards and Sophia Jenkin were the source of the segments Ann and Lynn share with Tom

(Had Anna and William been full siblings, we would have had to have factored in their mother’s parents as possible sources as well)

Inferred chromosome mapping using an aunt

Frequent readers of this blog will know that I am very interested in the concept of inferred chromosome mapping. For more information on this technique, please read my blog articles in the inferred chromosome mapping section. Since I’m often asked how an aunt or uncle can be used, I’m presenting this example.

Lynn is one generation removed and not surprisingly shares slightly less DNA with Tom than Ann does: about 60cM:

The segments that Lynn shares with Tom
The segments that Lynn shares with Tom

Inferred chromosome mapping involves isolating the segments that someone definitely didn’t inherit from a certain relative. To do this I first need to download the segment data in numerical form as opposed to the pictures shown above.

Obtaining the segments

First of all, I download the segments as CSV files by clicking ‘Advanced Options’ above the chromosome browser on the match detail pages at MyHeritage for both Ann and Lynn.

(Different methods are used for 23andme, FTDNA and Gedmatch)

The 'advanced options' dropdown on the match detail page at MyHeritage
The ‘advanced options’ dropdown on the match detail page at MyHeritage

I can now use the Inferred segments generator at DNA Painter. This works as follows:

  • I paste the segments Lynn shares with Tom into the first box
  • I then paste the segments her aunt Ann shares with Tom into the second box and click ‘Generate Inferred Segments’
The inferred segments generator entry screen at DNA Painter
The inferred segments generator entry screen at DNA Painter

This then gives me the segments that Ann shares with Tom, but which Lynn does not:

The segments that Ann shares with Tom, but which Lynn does not
The segments that Ann shares with Tom, but which Lynn does not

Interpreting inferred segments

What can I say about these inferred segments? Let’s look at the tree again:

A tree showing segment inheritance
Tree showing how Ann and Lynn are related

These inferred segments refer to locations on Lynn’s chromosomes where Ann inherited DNA from William Gwynne, but Lynn did not. And that’s actually all I can immediately infer:

  • At these positions, Lynn did not inherit DNA from William Gwynne
  • I know this because the William Gwynne DNA available to be inherited by Ann and Lynn is from the same reference chromosomes: the paternal chromosomes of Esther Gwynne (Ann’s mother)
  • Since Lynn didn’t inherit these segments from William Gwynne, I can infer that she instead inherited DNA in these positions from some or all of Richard Foster, Jennet Llewellyn, and Mary Ann Williams, her other maternal great-grandparents
  • I can’t infer any more than this because as sisters, Ann and Lynn’s mother Deirdre might have inherited DNA from different grandparents in this position.

How can I use the inferred segments in Lynn’s chromosome map?

This information can definitely help me develop Lynn’s chromosome map, but I have to tread carefully due to what I referred to in a previous article as the full aunt/uncle exception.

When Lynn shares segments of DNA with a cousin, we can use a generic rule to help us assess which ancestors could have been the source of this DNA:

  • Each segment Lynn shares with a cousin will have been inherited from just one of the common ancestors’ parents

But in the case of Ann, Lynn’s full aunt, the situation is different because as full siblings, Ann and Deirdre, Lynn’s mother, will have shared several FIRs (fully identical regions). This means that some of the segments Lynn shares with Ann will span both the maternal and paternal copies of Ann’s chromosomes.

The segments that Lynn shares with Ann, shown within the context of Ann's chromosome map
The segments that Lynn shares with Ann, shown within the context of Ann’s chromosome map

Previewing the inferred segments

To investigate in more detail, I can preview the inferred segments by copying them from the Inferred Segments Generator and pasting them into the ‘Paint a match’ form within Lynn’s chromosome map. I lower the threshold to 6cM to ensure that I include all of the inferred segments.

(I would normally be wary of small segments, but since inferred segments are often smaller subsets of segments, I want to make sure I keep all of them.)

The 'Paint a match' form with the inferred segments pasted in
The ‘Paint a match’ form with the inferred segments pasted in

When I click ‘Preview these segments’, DNA Painter highlights these segments over the existing map. To help me focus on the relevant chromosomes, I can click ‘Maternal’ under the key to make sure I’m only looking at Lynn’s maternal chromosomes.

The key showing maternal chromosomes only are visible
The key showing maternal chromosomes only are visible

The inferred segments are on chromosomes 1, 9 and 17. The shaded vertical areas in the images below represent the inferred segments.

Inferred segments on chromosome 1

On chromosome 1, I have a clear indication of a recombination point to the right of the red segment where Lynn matches Tom:

  • It appears that this is a location on chromosome 1 where Lynn had a crossover, switching from
    • DNA from her maternal grandmother Esther Gwynne to
    • DNA from her maternal grandfather Thomas Foster
  • I can deduce this because Ann continues to share DNA with Tom in the shaded area to the right of the recombination point
An image showing inferred segments (grey) on chromosome 1
An image showing inferred segments (grey) on chromosome 1

As for the longer segment further along chromosome 1, I will put this in a group ‘Not William Gwynne’ until I can assign it more specifically.

Inferred segments on chromosome 9

An image showing inferred segments (grey) on chromosome 9
An image showing inferred segments (grey) on chromosome 9

On chromosome 9, there’s a small overlap between the inferred segment and the segment that Ann shares with Tom. I can’t really deduce anything from this:

  • The overlap is about 3cM and it could be that Lynn does match Tom here but it’s beneath the segment threshold
  • The shared segment here between Ann and Lynn may be on Ann’s paternal chromosome 9
  • I’ll therefore add both this and the other chromosome 9 inferred segment to the existing ‘Not William Gwynne’ group.

Inferred segments on chromosome 17

An image showing an inferred segment (grey) on chromosome 17
An image showing an inferred segment (grey) on chromosome 17

On chromosome 17 there’s just one huge inferred segment that covers a smaller segment that Lynn shares with Ann.

  • I can add this to the same ‘Not William Gwynne’ group
  • I can also move the smaller ‘Ann’ segment to a ‘Foster or Llewellyn’ group:
    • Since Ann matches Tom here on her maternal chromosome, her match to Lynn must be on her paternal Foster-Llewellyn side

Next steps

By using the inferred chromosome mapping technique, I have been able to narrow down the source of a few areas on Lynn’s maternal chromosomes. I’ve also identified a probable recombination point on chromosome 1.

Here are some ideas for what I could do next:

  • I could see if Lynn’s brother also shares any segments with Tom that Lynn doesn’t. If he does, then I can infer that Lynn inherited DNA at these positions from her maternal grandfather (for a primer on the logic behind this, you could try this article)
  • I could review the maternal matches who share DNA with Lynn at the same position where she matches Tom. Since I now know this DNA came from John Richards or Sophia Jenkin, this could help focus my efforts to identify these matches and find the connection.

I hope this was a useful summary. As always, all feedback is welcome!

Contact info: @dnapainter / jonny@dnapainter.com