It all began when the data of one distant cousin messed everything up by not fitting into the visual phasing picture I’ve previously created for my father and his siblings. It ended with a discovery of a so-called hidden recombination (more than one actually!), a situation when your visual phasing results turn out to be entirely different from what they initially seemed due to very close crossover positions of two or more siblings.
I’ve read about hidden recombinations in the Visual phasing working group on Facebook before, but I’ve never come across one myself until recently, and I would like to share that discovery with you. But first, let me give you some background information about my paternal side of the family for the full picture.
My father’s family is of Russian ancestry including Native Siberian admixture, which is typical for long-established residents of Siberia, who settled there in the late 16th century, and occasionally intermarried with local populations. Despite having a large number of Russian and Finnish matches, all of my father’s genetic cousins are really distant, and neither their family trees nor mine go back far enough to find a MRCA.
Despite all the great tools out there, creating genetic networks for my paternal side turned out to be a rather difficult task, because nearly all of those distant cousins share less than 20cM between themselves and my father. And since no one of my father’s known relatives beyond the first cousin level has tested, I was not yet able to map any of my paternal chromosomes back to each of my great grandparents, let alone distant ancestors.
However, after comparing my father and his younger brother via the One-to-one X-DNA comparison tool at GEDmatch, I realized that thanks to the way the two of them matched, it was possible to sort their X-matches into two different groups, and then hopefully map the segments of both groups to a specific ancestor. (The original version read “segments of one group” referring to the ancestor who provided the unrecombinated copy of the X.)
According to this image my father and uncle P. share only one segment of about 28cM on the X-chromosome. This means that except for a stretch between 138.8Mb and 149.5Mb, both of my paternal grandmother’s X-chromosomes are represented in two of her sons.
One of my paternal grandmother’s two X-chromosomes is a unrecombinated copy she inherited from her father, which he in turn received from his mother, my great great grandmother Varvara Kachulina. Thus, Varvara’s DNA was represented to a large part in either my father’s or my uncle’s X-chromosome, meaning that there was a 50% chance for me to have inherited such a large portion of my great great grandmother’s DNA!
I got really excited at that thought, and immediately set out to look for my father’s and uncle’s X-matches in all databases. However, the first solid X-match I came across yielded a big surprise! Distant cousin Alexey matched my father (and me), two of his siblings and his aunt on the X-chromosome with the cM amount varying between 21cM and 48cM. The thing that struck me right away, however, were the positions of the DNA segments they shared – they just didn’t seem to make any sense!
Here is the 23andme X-chromosome comparison between distant cousin Alexey and my great aunt, uncle, aunt and father:
According to the One-to-one X-DNA comparison my father and uncle didn’t share any DNA until 138.8Mb. According to the 23andme comparison, however, Alexey shares two segments with each of them before 138.8Mb. Alexey, my father and my uncle all have only one X-chromosome, and logic tells me that person A can’t match person B and also person C, when B and C don’t match each other. And yet, I was presented with this data. Something was definitely amiss here!
VISUAL PHASING WITH DIFFERENT SIBLINGS PRODUCES DIFFERENT RESULTS
I’ve tested three of my father’s siblings for Visual phasing, but I initially preferred to work with my father and just two of them, and to use the segment data of the third sibling only when one or the other recombination position remained unclear. When I was phasing their chromosomes for the first time, I only used the data of my father, aunt L. and uncle P. (the LDP Visual phasing project).
Visual phasing of the X-chromosome is usually a lot easier than that of the autosomal chromosomes, and it’s often recommended for beginners, because you are working with the maternal copy only, and therefore, only two grandparents. I remember finishing it really quickly, and back then I didn’t see any reason to doubt the outcome.