Is this an example of crossover from the Y chromosome to the X chromosome?

+5 votes
I have a Danish family where the paternal grandfather P, the father F, the mother M and the daughter D all have tested. The relations are confirmed by autosomal results.  P, F and D all matches an American woman W with a segment of 17,14 cM for D, 20,47 cM  for F and 19,81 cM  for P on the same positions on Chromosome 16. M does not match W.  W ‘s great grandparents emigrated from Denmark in the 1880ies, but the connection has not been found. Besides the autosomal match D matches W with a 19,6 cM segment at chromosome X! The segment has the positions 1370495 – 8878959; the left end of the chromosome. Since neither the mother M’s or the father F’s X chromosomes matches W’s X chromosome I think there must have been a crossover from F’s Y chromosome to the X chromosome, he passed on to his daughter D. Correct?

If this is correct; how often does this happen and how often does the opposite happen? And can it be used to find the autosomal relations between the Danish family and the American woman?
in The Tree House by Ole Selmer G2G6 Mach 4 (43.5k points)
While it seems like a relatively large X Chr segment match, is it possible that the suggested X match between D and W is actually a false match, the result of the matching algorithm essentially zigzagging back and forth across the X Chromosomes that D inherited from both her father and mother, finding matching alleles with W, since neither parent appears to match W for any significant X Chr segment length?
Ole, a few words in a comment below about the pseudoautosomal regions. Those are the only areas where recombination between the X and Y happen. Under the (outdated) genome map version GRCh37/hg37 that all our testing and reporting companies still use, on the X-chromosome PAR1 starts at locus 60,001 and ends at 2,699,520. PAR2 starts at 154,931,044 and ends at 155,260,560.

That segment you found at 1,370,495 to 88,78,959 would be partially in PAR1, but only about 1.33Mbp of it. So the portion that could have been affected by recombination would be very small; using the sex-averaged values our testing/reporting companies give us, at most a fraction over 3cM.

What company is reporting that 19.6cM segment? If GEDmatch, they don't, to my knowledge, actively screen out any PAR SNPs they get from the uploaded raw data, but they don't do match reporting on them. If it's GEDmatch, my first-pass, starting position would be to assume that the segment on the X is functionally closer to 16cM to 17cM than 19.6.

Given the scenario you describe, I'd tend to think there is something amiss with that particular X-chromosome result, and especially so since the segment begins in the PAR. If it's on GEDmatch, can you try manually restricting the SNP density at comparison to 500, and then 700, to see what the outcome is? It's possible we could be seeing a false segment because a few small--and likely meaningless--ones are being "spliced" together because they're just barely within the mismatch threshold at the default floating 200-400 SNPs.

Since both parents are tested (same company at about the same time?), there should be no segment found in the daughter that isn't found in one of the parents.
Thanks Edison All 5 have tested at FTDNA, the Danish family 5 years apart and W before 2015. I will contact FTDNA and ask how they can explain the results. F and W are at Gedmatch and I will ask D to join Gedmatch, too.

I will keep you informed,
Ole, I really don't know enough about what's being seen at FTDNA to comment, but one factor that might come into play is that in April 2019 FTDNA switched from an augmented (meaning customized with some additional SNPs) Illumina OmniExpress v1.3 rev A1 chip to a similarly augmented Illumina Global Screening Array v2.0 rev A1 chip. I haven't investigated precisely what SNPs were programatically added to each FTDNA iteration (it could be up to a few tens of thousands, not more; difficult to analyze because FTDNA used unique, nonstandard, non-rsID naming for a thousand or so SNPs), but in their default configurations those particular chips tested 178,760 of the same SNPs out of 659,748, the total that the GSA chip looked at; or 27.1% of the same SNPs. Between the different versions of the OmniExpress chips, there was a fairly high in-common rate, over 95%.

So autosomal tests at FTDNA prior to April 2019 should present consistent results from a high overlap of identical SNPs. Tests after April 2019 may suffer from that not-many-identical-SNPs syndrome that impacted GEDmatch and MyHeritage. And FTDNA had to modify their own matching/comparison algorithms to compensate for the lowered in-common SNPs between their earlier and later tests.

No help you your question, I know. Just an observation.

2 Answers

+5 votes

I have never heard of this before, but apparently it happens. It has to do with the pseudoautosomal regions on the X and Y chromosome:

"Normal male mammals have two copies of these genes: one in the pseudoautosomal region of their Y chromosome, the other in the corresponding portion of their X chromosome. Normal females also possess two copies of pseudoautosomal genes, as each of their two X chromosomes contains a pseudoautosomal region. Crossing over between the X and Y chromosomes is normally restricted to the pseudoautosomal regions; thus, pseudoautosomal genes exhibit an autosomal, rather than sex-linked, pattern of inheritance. So, females can inherit an allele originally present on the Y chromosome of their father."

by Mark Burch G2G6 Pilot (226k points)

Absolutely correct. There are two pseudoautosomal regions on the Y and X, and they're both very small...well, one small and one tiny. The PAR are the areas that allow the Y and the X to join and form one diploid chromosome in males; we'd be in a world of hurt as a species if that didn't happen. PAR1 is at at the very end of the short arm, or p arm, of the X and the Y, and it's right around 2.7 million base pairs. PAR2 is at the end of the long, or q, arms and is only about 330K base pairs.

To my knowledge there's been no recombination observed in female meiosis in PAR2. In PAR1, ranges reported have been .3cM to 1.55cM. For the male, the recombination activity is up to a possible 6cM on PAR2 and 4.33 to 20.48cM on PAR1.

All of our common microarray tests look at some SNPs in the PAR, but only because they contain about half as many coding genes as all the rest of the Y-chromosome's 54 million base pairs combined, about 30. For example, Ancestry's v2.0a looked at only 21 PAR SNPs; v2.0c at 32 SNPs; the Illumina GSA v3.0 chip looks at a good deal more, 879 SNPs.

The regions are really of no use for genealogy. The PAR SNPs are never used for match comparison or reporting (I say that, but I'm uncertain if 23andMe has made any changes there in the past two years). The Y-specific tests like the STR and SNP offerings from FTDNA and YSEQ never test any SNPs in the PAR.

Thanks both for the links. Now it is time to read.
+4 votes
I think the obvious is being overlooked here.  It is very likely that the American woman is related to this Danish family through more than one common ancestor.  This happens with distant cousins much more often than you might expect.  I see it nearly every day when I'm looking.  I recognize it instantly because I know my chromosomes well -- I know where different regions came from in my tree.  20 cM on X is nothing much -- it doesn't suggest anything close.  This is especially true if a family is from an old-world place with much endogamy.  Our matches are listed the basis of total cM or and number of chromosome segments; as a result, we bring the rarer matches with multiple common ancestors up higher on our lists, so that they aren't so rare.  

As for recombination with Y, yes, it happens, and no, that isn't what you're seeing.  If you compare sisters to each other, you will see evidence of it: differences at the end of their paternal X.  But it only involves the left tip, up to ~2.5 Mbp if I recall -- and that's all.  Y can't recombine normally with X out to 8 million as you describe.  Y doesn't have this region, can't exchange with it or transmit it.
by John Yates G2G2 (2.8k points)

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