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Grossvater
04-09-2013, 02:57 AM
I am puzzled by my wife's mysterious X. I've been comparing her 23andMe results with Dr. McDonald's. Since her Dad was an Anglo with roots in Kentucky and her mom Mexican, it is very obvious what halves the rest of her 23 pairs come from. Here's the weird thing:

23andMe shows her mother's half of the X to look like an old sequence of telegraph code...dot, dash, dot dash between Native American and Iberian whilst her father's side is solidly Northern European (no surprise there).

Dr. McDonald's results show a different picture. My wife's mother's side is solidly Native American whilst a large chunk of her dad's is Middle Eastern with the rest Northern European.

Now Dr. McDonald shows that several large chunks of her MOTHER'S side are Middle Eastern which doesn't surprise since I have paper trails galore back to the Converso Jewish Conquistador families of Nuevo Leon. Her dad has no recorded Middle Eastern ancestry and I have a multiple paper trails on him going way back.

My question: Does the X chromosome recombine differently than the other pairs? Can one get more than half of the X chromosome from one parent over the other? Or in my wife's case, did she get most of her X from Texas?

Grossvater
04-15-2013, 02:00 PM
Bumpity bump...is this question too dumb to respond to?

geebee
04-15-2013, 04:26 PM
I do not claim to be an expert, but my understanding is that for a woman the X chromosome behaves pretty much the same as the autosomes.

Since your wife's mother is Mexican, one of those X chromosomes would be expected to probably be Spanish, Native American, or a combination of the two. Middle Eastern is also possible, as you say.

Doug McDonald doesn't do any phasing as far as I know. So I'm not sure how he would be able to distinguish the two sides. If you're referring to a chromosome painting, I think that's like the old Ancestry Painting -- whether a particular color is in the top or the bottom of a chromosome isn't meant to tell you which parent it's from.

Now, unless your wife's mother or father has also been tested at 23andMe, I'm not sure about the phasing there either. I think they do some sort of phasing, although I'm not sure how when neither parent is tested. So if that's the case, I don't know how much stock you can put in the precision of the results.

Where one parent has been tested, I'd be more confident about the results. If neither, the results might still be okay -- but a bit less solid, if you will.

Even though only one X shows in the painting, your wife has two as she does with all the autosomes. (You and I, being male, only have one X of course.) One X is entirely from her father, and one is from her mother. The one from her father is like the one for any other male -- only from his mother. The one from her mother can be from either her mother's mother, her mother's father, or both.

Grossvater
07-09-2014, 01:21 PM
I recently got a sharing request from a man who shares 47mb of my X chromosome. Yet he has no matching DNA anywhere else on the genome. Obviously, he is related to me from my mother's side of the family. Is it unusual to share such a big chunk of X but share no where else?

leonardo
07-09-2014, 02:19 PM
I recently got a sharing request from a man who shares 47mb of my X chromosome. Yet he has no matching DNA anywhere else on the genome. Obviously, he is related to me from my mother's side of the family. Is it unusual to share such a big chunk of X but share no where else?

I have a similar situation, 45cM with a male match. I think male-male matches on the x chromosome carry extra significance. Therefore, from what I understand, a match this large is real.

haleaton
07-09-2014, 05:49 PM
I have a dumb X question which I seem to not find the answer to easily, though I am sure it is out there. Females have two X Chromosomes, but one of them is inactivated in each cell and for all descendants of that cell. However this takes time after fertilization so initially some cells have the father's X and others the mother's X--the famous reason for calico coated cats being mostly female--the cells that produce their hair color are in the X chromosome.

My question is if it is currently feasible to extract and sequence two X chromosomes from a female sample using various sample for differing places? If not is it theoretically possible.

geebee
07-10-2014, 05:28 PM
Even fairly small X matches between two men are likely to be "real". Each only has one X chromosome, so only one chance to match at each position in the segment. That's why 23andMe allows a smaller threshold for male-male matches.

The question is more, what does a match mean in terms of relatedness? You are related, yes, but how closely? There is some indication that in addition to the fact that the X and Y chromosomes don't recombine (at least, outside of PAR1, PAR2, and (in some individuals) PAR3), the X doesn't always recombine with the other X.

That means that matches on the X might be generations more remote than for similar matches on other chromosomes. I think it also helps explain why a person might share a fairly large chunk on the X, but not elsewhere. There have -- effectively -- been more recombination events for the other chromosomes than for the X.

This would of course also be true for the Y, if it were used for matching purposes. (In a sense it is, when people compare haplogroups.) Since the Y recombines so little (almost not at all), matches should persist for a very long time.

In any case, I've become a bit more cautious about my earlier statement that "for a woman the X chromosome behaves pretty much the same as the autosomes". In theory it seems that this should be true; empirically, it seems this may not be the case. Or maybe the way to think about it is that even autosomes don't recombine all the time -- or they do, but with a sister chromatid, so that the recombined chromosome is identical to either the maternal or paternal copy. The difference is, the X does this on top of already having a more limited inheritance pathway.

geebee
07-10-2014, 05:33 PM
X-inactivation doesn't inactivate every gene on the X, but only some of them. Typically, genes on the X chromosome that have counterparts on the X (which is actually not a lot) don't get inactivated, but there are also other genes that don't get inactivated.

But I'm not sure whether, in any event, it would be possible to tell via sequencing alone, which X chromosome was inactivated and which was not. (As you say, it can be different for different cells in any case, even though it will be the same for their daughter cells.)

geebee
07-10-2014, 05:55 PM
"My question: Does the X chromosome recombine differently than the other pairs? Can one get more than half of the X chromosome from one parent over the other? Or in my wife's case, did she get most of her X from Texas?"

The direct answers are yes, yes if you're referring to grandparents, and possibly. The X your wife got from her father should be identical to the one he got from his mother. That could be half and half from each of her parents, but doesn't have to be. It could indeed be all from just one of your wife's father's mother's parents -- if you can follow that.

Same thing is true for your wife's mother. The one she got from her father should be identical to the one he got from his mother; the one she got from her mother may -- or may not -- have been recombined.

I noticed recently that 23andMe's "Family Inheritance" feature shows light blue sharing between my eldest brother and eldest sister on the X chromosome. Obviously, this can only be on our mother's X, since my brother got a Y from our father.

If both are identical on the X, it very likely means it escaped recombination -- since the odds of two recombinations being the same would be pretty small. [Or technically, it did recombine, but between sister (identical) chromatids.]

At this point, I haven't been able to figure out if it's from our maternal grandfather, or our maternal grandmother. If it's from our maternal grandmother, then it basically goes back to a great grandmother with no change. (Of course, there's a good chance it's a recombination of her two X chromosomes.)

The funny thing is, Ancestry Composition says it's 100% British and Irish. The trouble is, on either side it looks as if I would have to look back pretty far to find a British/Irish source on my mother's one of my mother's X paths. On one side, to a 4th great grandmother; and to a 5th great grandmother on the other.

Based on my paper trail, "French and German" would seem much more plausible.

haleaton
07-10-2014, 06:04 PM
X-inactivation doesn't inactivate every gene on the X, but only some of them. Typically, genes on the X chromosome that have counterparts on the X (which is actually not a lot) don't get inactivated, but there are also other genes that don't get inactivated.

But I'm not sure whether, in any event, it would be possible to tell via sequencing alone, which X chromosome was inactivated and which was not. (As you say, it can be different for different cells in any case, even though it will be the same for their daughter cells.)

Yes, Wikepedia says 25% of inactivated Genes can be expressed. Has a nice microscope pic show both X's. I have not studied this, but for a female sample is the inactivated X removed or is it a combination of whatever ever gets chopped into little pieces?

geebee
07-11-2014, 02:26 AM
I located a study which describes a method for "Molecular determination of X inactivation pattern correlates with phenotype in women with a structurally abnormal X chromosome", although unfortunately I only have access to the abstract.

http://www.ncbi.nlm.nih.gov/pubmed/11397327

In this case, there actually is a structural difference between the two X chromosomes. As to how that structural difference is determined, you might find this an interesting article: http://www.nature.com/scitable/topic/chromosomes-and-cytogenetics-7

I don't think they can determine, a priori, which X chromosome is inactivate, or be able to separate just that one from removal. It's actually only during meiosis that the two chromosomes are completely separated, anyway. Otherwise, the DNA is the nucleus is all condensed into a very compact little package.

So not only are the X chromosomes combined -- basically all of the DNA is. So both X chromosomes are part of what's "chopped into little pieces". I found a Wikipedia article that describes the process: http://en.wikipedia.org/wiki/DNA_extraction.

I don't know, but I would expect a similar process to be used at the beginning, even when scientists are only concerned with one chromosome -- the X. Different techniques would presumably be necessary to tell one X from the other, but clearly those techniques exist. However, as far as I can determine, extraction (of all nuclear DNA) comes first. (And, again, I don't see how it could be otherwise, since it starts out all wrapped up in a little ball.)

vettor
08-22-2014, 07:41 PM
Is it odd, that in my x chromosome painting in ftdna , I have zero cm's marked from any of my matches. maybe they are pure Y matches only.

the maternal line links I have state..........from the gulf of Bothnia around the 16th century