Visual Phasing of Chromosome 1

If you have the possibility to test three full siblings, then the next great thing you could do with your DNA results, is to try out the Visual Phasing technique developed by Kathy Johnston. It allows you to map the segments of your chromosomes to your four grandparents (without having your parents tested) by comparing the recombination points of the three siblings. However, to figure out which of your grandparents a segment belongs to, you will still need additional cousin testing on several of your lines. Ideally multiple 2nd cousins on either side of your family, but more distant cousins have proved to be very valuable as well.

I do not have full siblings, but luckily both my mother and father do. I have tested my mother and my maternal uncle a few years ago and when I first read about Visual Phasing on Blaine Bettinger’s fantastic blog, I immediately knew what I was going to do next – get a DNA test for my maternal aunt, too!

After meticulously studying Blaine’s instructions along with Ann Raymont’s and rounding it all up by watching Lars Martin’s video on YouTube (you will find the links below) I just couldn’t wait to put my newly acquired skills into practice.

To my knowledge only English blog posts about implementing this methodology exist out there and I feel that many other foreign genealogists are missing out on something important here. So therefore, I’m going to explain the Visual Phasing of my mother’s and her sibling’s pairs of Chromosome 1 three times – in Russian and in German with the idea of introducing this superb method to a wider public and in English as a reference. (That’s how my idea for a multilingual blog on genetic genealogy was born.)

Chromosome 1 is one of the two largest chromosomes and is usually not recommended for beginners. In my case, however, it turned out to have the cousin matches that I needed to complete the mapping.

Your first step is to upload autosomal raw data files of the three siblings to GEDmatch (if you haven’t done so already) and then use the One-to-One tool to compare the chromosomes of each sibling to each other.

I find it easier to do Visual Phasing using Excel, but you are free to choose whatever works best for you. Capture and copy the images of each chromosome comparison using the Windows Snipping Tool and paste them to Excel.

Our next step is to identify all recombination events that have taken place on the chromosome pair of each sibling and assign them to a specific person involved in the crossing-over.

After looking at the GEDmatch table and the comparison of the chromosome pairs above, we see for example, that my aunt and uncle didn’t match each other on the first (red) bit of chromosome 1. It means that on both of their copies of the chromosome different DNA was received from different grandparents. Then we see that a recombination occurred as they began to share a half identical (yellow) segment, meaning that now on one of their chromosome copies, either maternal or paternal, the DNA was passed down from the same grandparent. Soon after, the next crossing-over occurred in one of the two as they now share a fully identical (green) segment, meaning that at that position on both the maternal and paternal copies of the chromosome the DNA came from the same two grandparents.

Here we have all recombination points in the three chromosome pairs at a glance:

Now, we need to make out the sibling involved in the crossing over. Here are the positions where a recombination occurred in my aunt’s chromosome pair:

By comparing my aunt vs. my uncle and then my aunt vs. my mother we see that a recombination has occurred at the same position in the beginning. Since my aunt is involved in both comparisons, this crossing-over will be assigned to her.

And in this image, the recombination positions belong to my mother:

 

At last the crossing-overs that occurred in my uncle:

 

For a better visualization, draw long vertical lines through all recombination points and label them. Don’t panic if the lines do not align perfectly, just place the line somewhere in the middle. The fuzzyness of the segment points has already been addressed in a blog post by Jim Bartlett (link is below).

 

Next step is to find out at what positions the crossing-overs occurred. One good way to do it is to use David Pike’s utility Search for Shared DNA Segments in Two Raw Data Files. After you have uploaded two raw unzipped files, you get a neatly arranged list of shared segments with their starting and ending points. First a list of fully identical segments shared between two individuals, followed by the list of half identical segments. The other way to do it is to use the data provided by the One-to-One tool, even though it is a bit more complicated. Blaine Bettinger did an excellent job explaining it and I will just follow his instructions.

By comparing my aunt and uncle via the One-to-One tool I get the following:

However, it only gives me the starting and endings points of their both half identical (yellow) segments. To figure out the starting and ending positions of the fully identical (green) segments, I need to check the full resolution box before the comparison.

The chromosome will be expanded and the positions marked. Unfortunately, the size of the chromosome has become too large now to fit properly onto one page, so we need to scroll to the right to find all starting and ending points. The following image compares my aunt’s and uncle’s first fully identical segment to its version in full resolution.

I will place the starting point of this fully identical segment at 30 and the ending point at 34. (We already learned that it is okay for the segment points to be a bit fuzzy.)

Let’s add all starting and ending points of all segments now, rounding the millions up.

 

And now the Visual Phasing can begin.

As you can see my mother and aunt share a fully identical segment between 115 and 156. Accordingly, neither one of them shares DNA with my uncle at that position. Therefore, we can already assign four colors to all their four grandparents – at this stage not knowing which color belongs to which grandparent, of course. What we do know is that pink and blue are complementary (either paternal or maternal) and so are purple and orange.

 

Now we can extend the segments to the next crossing-over points of each sibling. Well, in the case of my aunt we can’t – her segment lies between her two recombination points. My mother’s segments on the other hand can be extended to the left until her crossing-over at 17.5 and to the right until 183. My uncle’s segment can be extended to the left until 94 and to his recombination point on the right at 207.5.

 

Look at the area between 17.5 and 55 – my mother and aunt do not share any DNA here, so opposite colors will be assigned to my aunt. Furthermore, we can extend her segment to the left until her crossing-over point at 6. For the tiny region between 30 and 34 opposite colors will also be assigned to my uncle, since he doesn’t share DNA with my mother at this position, but a fully identical segment with my aunt instead.

 

It looks like I’m stuck, but not yet. I’m still able to extend my aunt’s segment to her crossing-over at 222, but I need to change one of her colors – at this point it doesn’t matter which one as the colors aren’t assigned to a specific grandparent yet. Why? Because in the region between 156 and 183 my aunt shares a half identical segment with her siblings, but a different one with each since they do not share any DNA at that position.

This allows me to fill out the area between 183-207.5 for my mother and then again 207.5-222 for my mother and uncle, because it’s fully identical to my aunt’s. Furthermore, I can extend my mother’s segment to the right until 238 and my uncle’s segment to the end.

 

Now I’m stuck.

Ideally you fill the chromosomes out entirely first and then turn to your matches and see whether they can help you separate your four ancestral lines. In my case, however, I need to start bringing my cousins in now.

Among the people who agreed to take a DNA test for me is E.A., my mother’s and her sibling’s maternal first cousin. E.A. and the Haas siblings therefore share maternal grandparents – maternal grandmother Ottilia Arnhold and maternal grandfather Heinrich Antoni. Let’s see whether E.A. can help to distinguish which of the Haas chromosome copies is maternal and which is paternal.

 

 

E.A. turned out to be an excellent match! Not only are we able to distinguish between the maternal and paternal chromosome copies now, thanks to E.A. we are also able to complete all three chromosome pairs of the Haas siblings!

Purple and orange colors are maternal, because E.A. matches both my mother and aunt (on the purple color) from 119.5 to 157 (156 – those fuzzy segments again) and then continues to match only my mother until 165.5, because my aunt switches to orange at 156 (157).

Furthermore, E.A. matches all three siblings between 6 and 14.5 and we know already that my aunt has orange between 6 and 17.5 at that position. Therefore, orange will also be assigned to my mother and uncle at 6 to 17.5  and then extended to the left end. In addition, my uncle’s segment will be extended to the right until his recombination point at 30. On their paternal copy at that position pink will be assigned to my mother and uncle.

 

My aunt doesn’t match her siblings on the tiny bit from the beginning to 6, so opposite colors will be assigned to her.

 

E.A. also matches all three Haas siblings between 67 and 94 and we already know that my mother has purple on her maternal copy of the chromosome at that region. My uncle will be assigned purple on his maternal copy of the chromosome and blue on the paternal one. In addition, his segment can be extended to the crossing-over on the left at 34. His chromosome pair is now completed!

 

 

E.A. matches my aunt at 238 to 244, but she doesn’t match my uncle, who has orange at that position, so it must be purple for my aunt. Furthermore, we can extend my aunt’s segment to the left to her recombination point at 222 and assign the pink color to my aunt’s paternal copy of the chromosome.

Opposite colors can be assigned to my mother from 238 to the end now, because she doesn’t share any DNA with my aunt at that position. We have completed my mother’s chromosome pair, too!

We see that my aunt and uncle share a fully identical segment between 55 and 94, so blue and purple will be assigned to my aunt at that area. Furthermore, we can extend her segment to her next recombination point at 106.

The tiny spot between 106 and 108 will be assigned blue and orange, because this region is fully identical to my uncle’s. Now only one last segment between 108 and 115 needs to be filled out and we turn to E.A. for help again. E.A. shares a purple segment at that position with my mother, but no segments with the other two Haas siblings. Hence orange will be assigned to my aunt on her maternal and pink on her paternal copy (she only shares a half identical segment with my uncle there). And voila – we have completed all three chromosome pairs now!

So now that we know that purple and orange are maternal and pink and blue are paternal, 2nd cousins can prove themselves very useful. N.B. happily agreed to take a DNA test for me (she even joked that at least her saliva will travel to the U.S, while she herself never has). Her paternal grandmother Margaretha Arnhold and my mother’s and her sibling’s maternal grandmother Ottilia Arnhold were sisters.

So, it looks like the purple color belongs to the Arnhold line. N.B. matches my mom and aunt on their fully identical segment at 114.5 -157 (115-156) and continues to match my mother to 165.5, while my aunt switches to the complementary color at that region. Thus, orange can be assigned to Antoni, the maternal grandfather’s line.

With regards to the Haas siblings’ paternal side, everything is a lot more complicated. My mother’s father grew up in an orphanage after being sent there as a toddler following his parents’ death and didn’t know anything about his biological relatives – not even the name of his mother. All he was told later was that the rest of his family emigrated to Canada and the United States at around the time of his birth. No names, no places. Who would have thought that a century later drops of saliva would be able to provide new information?

One of our family’s most interesting matches is the now deceased W. Schlegel, who agreed to test for his niece a few years ago while she was researching their Volga German ancestry. W. Schlegel’s ancestors emigrated to Canada from Pobochnoye, a Lutheran Volga German village and I immediately connected him to my grandfather. Pobochnoye was the mother colony of my grandfather’s birthplace (my maternal grandmother was from an entirely different part of the Volga river area and her portion of the family tree is well researched). What made W. Schlegel even more special was that he was a match on my maternal grandfather’s mothers side. Yes, my unknown great-grandmother. So how can I be so sure? It’s because W. Schlegel matched both my mother and my aunt on the X-Chromosome! The X-Chromosome my grandfather passed down to his daughters was inherited from his mother. (On W. Schlegel’s part, the X-Chromosome doesn’t come from his Schlegel side, but from his maternal Wagner side.)

Therefore, after comparing the segments W. Schlegel and the Haas siblings have in common, I can map DNA segments to their paternal grandmother (and by process of elimination to their paternal grandfather as well).

W. Schlegel matches my mother and aunt between 144 and 180 and shares no DNA with my uncle on this chromosome. Therefore, we can assign the pink color to their paternal grandmother – my maternal grandfather’s unknown mother. Accordingly, the complementary paternal color blue will be assigned to the Haas line.

We are done!

Conclusions:

Sometimes it is not possible to complete an entire chromosome by logic only, because multiple outcomes are possible. However, bringing in other family members still allows you to move forward. Visual Phasing can help you enormously in your research by providing valuable information about your ancestral composition, especially if you hit a brick wall due to adoption or lack of documentation. If you are adopted, but have three kids on your own, you can still use this methodology to learn which of your matches are maternal and which paternal.

This great technique allows you to prove a theory about a certain ancestral connection or dismiss it. Let’s imagine I had a cousin match with a large segment on chromosome 1 and a Haas ancestor in her tree. Naturally, I would be tempted to connect her immediately to my grandfather’s paternal side. However, after visually phasing my mother’s chromosome and learning that her paternal copy of chromosome 1 comes largely from her father’s mother’s side – thus shrinking my chances to have inherited a Haas segment to a minimum – I would now proceed more cautiously, considering the possibility of a different connection more open-mindedly.

Later this year I also plan to test my paternal aunts or uncles (my father has already tested) meaning that at some point in the future I will theoretically be able to assign the segments of my own chromosomes to all my 8 great-grandparents! Knowing which segments, I inherited from which of my ancestors, will help me to arrange my matches more accurately or sort them into new groups, which in turn may one day be the key to solving the mystery of our family. Or yours.

 

Sources used and further reading:

http://thegeneticgenealogist.com/wp-content/uploads/2016/11/Visual-Phasing-Bettinger.pdf

https://dnasleuth.wordpress.com/2016/05/13/chromosome-mapping-with-siblings-part-1/

https://dnasleuth.wordpress.com/2016/06/01/chromosome-mapping-with-siblings-part-2/

https://www.youtube.com/watch?v=neB4oFlwJHA&feature=youtu.be

https://dnagenealogy.tumblr.com/post/137722603308/the-use-of-crossover-lines-among-siblings-to

http://www.jmhartley.com/HBlog/?p=3046

https://genealogylady.net/2017/05/02/down-the-dna-rabbit-hole-visual-phasing-with-two-siblings/

https://segmentology.org/2015/05/30/fuzzy-data-fuzzy-segments-no-worry/

 

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