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Dr_McNinja
11-04-2014, 06:22 PM
Through recombination or something? To my knowledge this is impossible but I'm unsure. I had a cousin turn up who matches me on 3 segments and matches my mother on 1.

From 23andMe's advanced inheritance tool:

Chromosome 2: 8.4 cM - only me and this cousin
Chromosome 5: 16.7 cM - both me and my mom match this cousin here, exact same spot/SNP range and cM
X Chromosome: 8.7 cM - only me and this cousin

My father and my mother were second cousins, so the segment on Chr 2 could very well have come from my dad (who is not tested on 23andMe). But how did I get that segment on the X? Perhaps a result of random chance, a "back mutation" version of genetic recombination whereby a segment that was too jumbled up in my mom came out correct for me? I wasn't aware the X in males underwent much genetic recombination.

EDIT: The cousin is a female

bored
11-04-2014, 07:06 PM
It's possible I think. There is a small pseudoautosomal region on sex chromosomes that is inherited via recombination just like other autosomal genes. Genes within this region are not sex linked.

Dr_McNinja
11-04-2014, 07:19 PM
Thanks, I didn't know that.

http://en.wikipedia.org/wiki/Pseudoautosomal_region

My overlap with the cousin is 115,000,000 to 121,000,000 on the X on 23andMe.

geebee
11-05-2014, 09:12 AM
Actually, there are at least two of these "pseudoautosomal regions", one at each end of the chromosome (whether the X or Y).

Men who have tested at 23andMe have long noticed that at the beginning and end of their X chromosome, two SNP values are reported at end position -- as if they had two X chromosomes. In fact, one of each of these values is actually from the Y chromosome.

Since 23andMe cannot tell which is from the X and which from the Y at these positions (which are within PAR1 and PAR2), they report them with the X. So the reported Y is actually a bit "shortened", in that it doesn't include the SNPs from PAR1 or PAR2 (at the beginning at end of the chromosome, respectively).

parasar
11-09-2014, 06:24 AM
For example in R1a1-Z93-L380 (WTY) , L380 is suspected to be from the X.
Thomas Krahn: "This is a fairly confusing marker because it is close to the Yp pseudoautosomal region and it probably recombines with the X chromosome more often than we like it."

Hector
11-11-2014, 11:26 AM
Even in the pseudo-autosomal region the portion of X a son gets would be from his paternal grandma, not his own mother.

P.S. So I thought but I found out that mitotic crossover occurs in human cells and when that happens a portion of the pseudo-autosomal region may be from his mother. Sorry for the wrong info.

tejus
02-06-2016, 10:13 AM
Pseudo-autosomal region the portion of X a son gets from hid paternal grandma not mother.

C J Wyatt III
02-06-2016, 03:08 PM
Through recombination or something? To my knowledge this is impossible but I'm unsure. I had a cousin turn up who matches me on 3 segments and matches my mother on 1.

From 23andMe's advanced inheritance tool:

Chromosome 2: 8.4 cM - only me and this cousin
Chromosome 5: 16.7 cM - both me and my mom match this cousin here, exact same spot/SNP range and cM
X Chromosome: 8.7 cM - only me and this cousin

My father and my mother were second cousins, so the segment on Chr 2 could very well have come from my dad (who is not tested on 23andMe). But how did I get that segment on the X? Perhaps a result of random chance, a "back mutation" version of genetic recombination whereby a segment that was too jumbled up in my mom came out correct for me? I wasn't aware the X in males underwent much genetic recombination.

EDIT: The cousin is a female

Someone please correct me if I have this wrong about X-recombination.

OK, you get your X-chromosome from your mother. This X would be a recombination of her two X-chromosomes. I do not know 23andMe's matching algorithm, but perhaps your mother's parents both have a distant common ancestor with the cousin. Maybe with recombination a match showed up with you on the X-chromosome that was not strong enough to show on either of your mother's X-chromosomes.

Jack

geebee
02-15-2016, 03:23 AM
"OK, you get your X-chromosome from your mother. This X would be a recombination of her two X-chromosomes."

The first part is true, but the second part isn't always true. That is, yes, a man's X chromosome came from his mother; but it only may be a recombination of her two X-chromosomes -- it does not have to be.

My brother Bernie and sister Kim appear to illustrate this. The two half a half identical match across their entire X chromosome. Since a brother and sister can only match on their maternal X chromosomes, each received an identical X from our mother. That, in turn, suggests either identical crossover points (unlikely), or no crossovers at all.

7782

The above is an X chromosome comparison from Family Inheritance Advanced. My sister Kim is compared to all five of her siblings. From top to bottom: Her brothers Bernie, Curt, and Gary (me); and her sisters Luci and CJ. As expected, she matches Luci and CJ across the entire X, because FIA doesn't distinguish between paternal and maternal chromosomes, but only shows the totality of matching across the chromosome. Bernie and Kim can only match on one X chromosome, however -- the maternal -- and they match on all of it.

Based on their DNA Relatives who share segments with them on the X, it seems likely that Bernie and Kim each received a copy of our maternal grandfather's X chromosome -- with nothing from our maternal grandmother. I match on most of this chromosome, but not on the centromere. So my X chromosome is a recombination from both maternal grandparents, as are the X chromosomes of all of my siblings except Bernie and Kim. (So two out of six of us appear to have received an unrecombined X.)

Incidentally, my daughter seems to have inherited at least seven unrecombined chromosomes from me -- in addition to the X. This can be seen in the fact that she has 0 matching with my father on chromosomes 7, 15, 17, 18, and 22; and she matches my father across all of chromosome 9.

7781

geebee
02-15-2016, 04:09 AM
Through recombination or something? To my knowledge this is impossible but I'm unsure. I had a cousin turn up who matches me on 3 segments and matches my mother on 1.

From 23andMe's advanced inheritance tool:

Chromosome 2: 8.4 cM - only me and this cousin
Chromosome 5: 16.7 cM - both me and my mom match this cousin here, exact same spot/SNP range and cM
X Chromosome: 8.7 cM - only me and this cousin

My father and my mother were second cousins, so the segment on Chr 2 could very well have come from my dad (who is not tested on 23andMe). But how did I get that segment on the X? Perhaps a result of random chance, a "back mutation" version of genetic recombination whereby a segment that was too jumbled up in my mom came out correct for me? I wasn't aware the X in males underwent much genetic recombination.

EDIT: The cousin is a female

As you may know, 23andMe's matching algorithm handles segment matches on the X differently, depending on the sexes of the parties. A male-male match requires the least number of both cM and total SNPs; a female-female match requires the greatest.

As a result, the X-matching between my youngest sister and my daughter doesn't look exactly like the matching between my sister and me. I show three matching segments with my sister, but my daughter shows only the two.

Here's how it stacks up in table view:

Gary-CJ (brother-sister)

(1) 9000000-41000000 / 50.6 cM / 4082 SNPs
(2) 53000000-71000000 / 6.8 cM / 846 SNPs
(3) 142000000-155000000 / 22.0 cM / 1614 SNPs

CJ-Kathryn (aunt-niece)

(1) 9000000-41000000 / 51.5 cM / 4139 SNPs
(3) 142000000-155000000 / 23.0 cM / 1653 SNPs

The middle segment is less than 7 cM, which I believe is the minimum for a female-female match on the X. I believe that the minimum for male-female may be 6 cM; and for male-male, 5 cM. So that's the reason it shows between my sister and me, but not my sister and daughter.

Peculiarly, my daughter is actually shown as having a longer match with my sister on the first segment, by 0.9 cM and 57 SNPs. I think this is probably an illusion, based purely on the fact that since each has two X chromosomes, there are more chances to find a match by pure coincidence. (And that's the reason, of course, for treating male-male, male-female, and female-female matches differently.)

What puzzles me is that the two matches shared by you and your cousin but not your mother and your cousin, are both above the female-female threshold I'm remembering. I'm wondering if there might be something like a couple of "no calls" for your mother in the two matching regions? Whatever it is, if the segments shared by just you and your cousins are "real", your mother should also share these segments with your mother. I doubt that the answer is anything like a "back mutation".

(It could be a matter of where the start-end points were calculated. They're not always as precise as you might expect.)

geebee
02-15-2016, 05:12 AM
Since I said my brother Bernie and sister Kim appear to have identical copies of their maternal X chromosome, both of them should match both me and my daughter in the same way.

In fact, Kim matches me from 1-41000000, for 65.6 cM and 5052 SNPs. Bernie also matches me from 1-41000000, for 65.6 cM and 5052 SNPs.

However, Kim reportedly matches my daughter from 1-41000000, but for 66.5 cM and 5108 SNPs. Bernie also matches my daughter from 1-41000000, but for only 65.6 cM and 5056 SNPs. Kim and Kathryn's slightly higher cM and matching SNPs is surely just a function of having more SNPs to make a match -- and the "extra" matching isn't real.

Kim and I also match from 71000000-155000000 on the X, for 96.3 cM and 7715 SNPs. For Bernie and me, the match is likewise from 71000000-155000000, and for 96.3 cM and 7715 SNPs.

For Kim and Kathryn, the second matching segment is from 69000000-155000000, for 97.4 cM and 7803 SNPs. This is over 1 cM longer, and nearly an addition hundred SNPs. However, Bernie and Kathryn's second matching segment is much closer to mine: from 71000000-155000000, for 96.4 cM and 7722 SNPs. Once again, Kim and Kathryn's "extra" matching SNPs are likely just coincidence, based on their having more SNPs to match to.

EDIT: I checked http://isogg.org/wiki/DNA_Relatives, and reportedly an X (female vs female) requires a minimum of 1200 SNPs and must be at least 6 cM in length. The length requirement is the same for a male vs female match, but only 600 SNPs are required. A male vs male match will be reported where there are as few as 200 SNPs, and a match length of only 1 cM.

But this is probably reasonable since both chromosomes are effectively phased where both parties are male.

Unfortunately, the OP's question still isn't answered. All I can say is that his cousin should show the same matches on the X with his mother that she shares with him, since they exceed the female vs female threshold.

I'd note, though, that's there's also an error tolerance that comes into play. The tolerance is "1 opposite homozygote per 300 SNPs". In addition, each set of opposite homozygotes can't be closer to any other by less than 300 SNPs.

I'm also not sure if there's any limit on how many "no calls" there can be in the match region.

AJL
03-24-2016, 02:00 PM
This just in:

http://www.genetics.org/content/early/2016/03/21/genetics.114.172692

crossover
03-24-2016, 07:12 PM
Through recombination or something? To my knowledge this is impossible but I'm unsure. I had a cousin turn up who matches me on 3 segments and matches my mother on 1.

From 23andMe's advanced inheritance tool:

Chromosome 2: 8.4 cM - only me and this cousin
Chromosome 5: 16.7 cM - both me and my mom match this cousin here, exact same spot/SNP range and cM
X Chromosome: 8.7 cM - only me and this cousin

My father and my mother were second cousins, so the segment on Chr 2 could very well have come from my dad (who is not tested on 23andMe). But how did I get that segment on the X? Perhaps a result of random chance, a "back mutation" version of genetic recombination whereby a segment that was too jumbled up in my mom came out correct for me? I wasn't aware the X in males underwent much genetic recombination.

EDIT: The cousin is a female

since your parents are second cousins they might share an x-chromosome segment