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Thread: Matching on X but not Autosomal?

  1. #11
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    Well, consider this:

    My niece Stephanie's results have just come back, and as expected she matches her father perfectly on her paternal X chromosome. Her father is the one who inherited our mother's paternal X chromosome without recombination.

    What this means is that the chromosome has passed from great grandfather to great granddaughter with no changes -- no segments have "decayed" from three generations previous. But even in the three generations before that, a great deal depends on which sexes were involved.

    Since my grandfather received his X chromosome from his mother, it could have been a recombination of the X chromosomes from both of his maternal grandparents. But it could as easily have included DNA from just one of them. In that case, it makes a difference whether it was from his grandmother or from his grandfather. If from his grandmother, then it could contain DNA from either or both of her parents; if from her father, then it could contain DNA only from her father's mother.

    In that last scenario, the person we're considering is my grandfather's maternal grandfather's mother -- or, my brother's and my 3rd great grandmother, and my niece's 4th great grandmother. This is someone who would have been six generations before my niece -- exactly the distance from which someone said it was "almost impossible" for a large segment to remain intact. To the contrary, it's quite possible that my niece could have inherited 100% of her paternal X chromosome from that person.

    Whether this is true for my niece or not, it is possible. And not just barely possible; it's actually likely that many people have a nearly intact X chromosome from that generational distance. Notice, I am not saying that a large percentage of people do, only that the number of people in this situation is probably large. (23andMe does, after all, have over a million customers.)

    EDIT:

    I'm still doing more conparisons involving my niece and other close relatives, but one thing I've noticed is that she does not match my father on any part of chromosome 17, but she matches both me and my daughter Kathryn across the full length of the chromosome.

    This tells me that my brother and I appear to have inherited identical copies of our maternal chromosome 17, which may mean that we both not only received unrecombined copies from our mother, but passed those copies on without recombination.

    Now if you're wondering how I figure the copies my brother and I received from our mother likely were not recombined, but came from just one grandparent; it's if we inherited recombined copies, they'd have to have exactly the same crossovers. It's more likely that they had no crossovers (or effectively, no crossovers).
    Last edited by geebee; 07-27-2017 at 06:11 PM.
    The short explanation of my ancestry is British-German-Catalan, but it actually includes smaller amounts of French, Irish, Swiss, Choctaw and probably Cherokee. My avatar picture is of my father, his father, and his father's father. The baby in the picture is my eldest brother.

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  3. #12
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    Quote Originally Posted by C J Wyatt III View Post
    OK, let's start with my assertion: "For a large and distant matching segment to be IBD is a near impossibility."

    The length of chromosomes in centiMorgans vary, but only five are greater than 200 cM's, so 200 cM will be a good number to use. If you go back six generations. the average decay rate would give you an expected 3.125 cM remaining from the original 200 cM. Of course you cannot expect that will be one segment, but why worry about that detail? if your match is on the same level as you, the person also ends up with an average of 3.125 cM remaining. The catch is, to be a matching segment, it has to line up perfectly with yours. Like I said, a big distant IBD matching segment is near impossible. Do these big segments we see come about from the parents sharing a common ancestor? What other explanations are there?

    Jack
    males can pass more autosomal dna from one of their grandparents than one on the other side of their tree. Women tend to pass it as 50% from one of their maternal grandparents & 50% from one of their paternal grandparents.
    this would have an effect on auDNA transmission.

    I don't pay much attention to X-matches, unless it is a male that is being matched which would be on his mother's side.
    BTW. did any one remember https://www.daysoftheyear.com/days/cousins-day/
    Last edited by dp; 07-27-2017 at 10:16 PM.
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    Saetro, geebee and anyone interested:

    If my hypothesis is correct, that big, distant matching segments are not IBD, but reconstructed from multiple paths to a common ancestor, then the arguments you used against me are flawed. You cannot disprove my hypothesis with an argument that is disproved by the hypothesis. We are at an impasse.

    One way to get beyond this impasse is if I can show that most of us share a common ancestor, not in ancient times but within recent times. This can easily be done by triangulating X-matches. Many females have around 10,000 X-matches on the GEDmatch 'X one-to-many' using default parameters of 500 SNP's and 7.0 cM minimum segment. I have seen some females with around 25,000 matches and even one with over 50,000. I did an analysis on the 10,000 example and found that on average, any place on the X-chromosome (only one 'X' assuming male common ancestor) has around 400 or more triangulations with the matches from the 'X one-to-many' list. Intuitively I think the overlapping would mean that everything points to just one common ancestor, but I recently undertook another analysis that deals with that overlap issue. I used a female with about 10,000 matches, and skipped over the few close and known relationships at the top. Each additional match I would compare with the segments derived from all of the previous ones to add segments in untouched areas and extend the previous segments which overlapped with the ones from the new match. If the overlap between two segments is more than a handful of SNP's, the common ancestor from both segments is almost certainly the same. After less than fifty tries, I had the whole 196 cM X-chromsome divided into four segments with just three small gaps. I was able to very quickly find the matches that closed the gaps and show that anywhere on the whole X-chromosome points to one common ancestor, with about 9900 matches to spare. I believe almost anyone who has enough matches would get similar results.

    At least one or two genetic genealogists will admit that there is a large source of common ancestry in the 18th Century that they have not been able to pinpoint. These X-DNA triangulations add tremendous support to that idea. The big problem is that the existence of this large amount of common ancestry undermines much of mainstream genetic genealogy thought, at least for distant matching.

    Jack Wyatt
    Last edited by C J Wyatt III; 07-28-2017 at 08:47 AM.

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    Very interesting; the X-chromosome seems to harbour more ancient segments; this thread increased my knowledge about crossing-overs in general; I am lucky to know all (paper) ancestors 9 generations back who could have contributed to my X-chomosome, being Dutch, Belgian and German people. Reading the above, that would generally not even be enough to establish a match, since it could be from medieval times.
    Ancestry (approx.):
    3/4 Dutch; 1/8 German+Belgian+French+English+Swiss; 1/16 Indonesian+Dutch Colonial; 3/64 Ashkenazi; 1/64 Sephardi.

  6. #15
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    Quote Originally Posted by C J Wyatt III View Post
    Saetro, geebee and anyone interested:

    If my hypothesis is correct, that big, distant matching segments are not IBD, but reconstructed from multiple paths to a common ancestor, then the arguments you used against me are flawed. You cannot disprove my hypothesis with an argument that is disproved by the hypothesis. We are at an impasse.

    One way to get beyond this impasse is if I can show that most of us share a common ancestor, not in ancient times but within recent times. This can easily be done by triangulating X-matches. Many females have around 10,000 X-matches on the GEDmatch 'X one-to-many' using default parameters of 500 SNP's and 7.0 cM minimum segment. I have seen some females with around 25,000 matches and even one with over 50,000. I did an analysis on the 10,000 example and found that on average, any place on the X-chromosome (only one 'X' assuming male common ancestor) has around 400 or more triangulations with the matches from the 'X one-to-many' list. Intuitively I think the overlapping would mean that everything points to just one common ancestor, but I recently undertook another analysis that deals with that overlap issue. I used a female with about 10,000 matches, and skipped over the few close and known relationships at the top. Each additional match I would compare with the segments derived from all of the previous ones to add segments in untouched areas and extend the previous segments which overlapped with the ones from the new match. If the overlap between two segments is more than a handful of SNP's, the common ancestor from both segments is almost certainly the same. After less than fifty tries, I had the whole 196 cM X-chromsome divided into four segments with just three small gaps. I was able to very quickly find the matches that closed the gaps and show that anywhere on the whole X-chromosome points to one common ancestor, with about 9900 matches to spare. I believe almost anyone who has enough matches would get similar results.

    At least one or two genetic genealogists will admit that there is a large source of common ancestry in the 18th Century that they have not been able to pinpoint. These X-DNA triangulations add tremendous support to that idea. The big problem is that the existence of this large amount of common ancestry undermines much of mainstream genetic genealogy thought, at least for distant matching.

    Jack Wyatt
    Jack,

    Did you not read the part when I showed that one of my brothers and a 2nd cousin share an 80 cM segment? Another sibling and this 2nd cousin share 57 cM on the same segment, and yet another sibling shares 67 cM on an entirely different chromosome. These siblings and our 2nd cousin do not have any relatives more recent than two 2nd great grandparents.

    Why, if a segment of this size can survive for three successive transmissions on each side is it so hard for you to believe that large segments could survive for three more transmissions, or longer? The number of pairs of is vast, so that there are many, many opportunities for wide variances from the "average". The average is merely the result of summing all individual segments and dividing by the number of individuals.

    In virtually every recombination event, multiple chromosomes are transmitted which have entirely escaped recombination. Most of the time, you might not expect the same chromosome to do so twice in a row, yet whether it does or not is believed to be essentially random.

    With enough transmissions, it is inevitable; with even more transmissions, there is no reason it can't happen a third time, or a fourth. This is very similar to tossing a coin and getting ten "heads" in a row. It does happen. In fact, once you have managed to toss "heads" ten times in a row, the odds of doing so an eleventh time are undiminished. It's still 50% for the next toss.
    Last edited by geebee; 07-28-2017 at 03:54 PM.
    The short explanation of my ancestry is British-German-Catalan, but it actually includes smaller amounts of French, Irish, Swiss, Choctaw and probably Cherokee. My avatar picture is of my father, his father, and his father's father. The baby in the picture is my eldest brother.

    GB

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    Quote Originally Posted by geebee View Post
    Jack,

    Did you not read the part when I showed that one of my brothers and a 2nd cousin share an 80 cM segment? Another sibling and this 2nd cousin share 57 cM on the same segment, and yet another sibling shares 67 cM on an entirely different chromosome. These siblings and our 2nd cousin do not have any relatives more recent than two 2nd great grandparents.

    Why, if a segment of this size can survive for three successive transmissions on each side is it so hard for you to believe that large segments could survive for three more transmissions, or longer? The number of pairs of is vast, so that there are many, many opportunities for wide variances from the "average". The average is merely the result of summing all individual segments and dividing by the number of individuals.

    In virtually every recombination event, multiple chromosomes are transmitted which have entirely escaped recombination. Most of the time, you might not expect the same chromosome to do so twice in a row, yet whether it does or not is believed to be essentially random.

    With enough transmissions, it is inevitable; with even more transmissions, there is no reason it can't happen a third time, or a fourth. This is very similar to tossing a coin and getting ten "heads" in a row. It does happen. In fact, once you have managed to toss "heads" ten times in a row, the odds of doing so an eleventh time are undiminished. It's still 50% for the next toss.
    and you completely brush off the X-chromosome analysis?

    I am not questioning your big segments. I am questioning whether they are IBD or reconstructed by multiple lines back to the common ancestor. Without being able to examine your data with the high resolution chromosme browser, I cannot make that determination. However I have seen plenty of big segments pop up that are not IBD.

    I thought second cousins share great grandparents.

    Jack

  8. #17
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    I should mention that my brother Curt -- the one who shares an 80 cM segment on chromosome 20 with our 2nd cousin -- shares a total of 238.5 cM on the autosomes and 38.5 cM on the X chromosome. This is a pretty typical matching percentage -- more or less "average", if you will -- with a 2nd cousin.

    The 80 cM, however, is hardly an averaged-sized segment for 2nd cousins. But that's because shared segments are not uniform. There can be immensely large segments -- potentially, as large as the entire chromosome -- or immensely small segments, perhaps of a smaller size than is detectable. Together, these may well "average" out, without any particularly segment having to be at the average.

    As I've mentioned in previous posts, I have five full siblings with results at 23andMe. My father has also tested there, as has my daughter; and now one my nieces -- my eldest brother's daughter -- also has results.

    Among six siblings, there is very a large number of pairs: 5+4+3+2+1, as a matter of fact, or 15. There are multiple instances in which pairs of us have not only inherited "unrecombined" autosomes, but even the same unrecombined autosome.

    For example, my eldest brother and I fully match on both copies of chromosome 16. We also match on one copy of chromosome 17, and nearly match on all of the second copy. Our daughters only match on 94.27 cM of chromosome 16, although this is still a great deal more than half of the chromosome.

    On chromosome 17, those their matching is essentially across the entire chromosome. Further, neither one of the girls matches her paternal grandfather at all on chromosome 17, which means this must be my brother's and my maternal copy of the chromosome.

    So my brother and I each inherited an identical maternal copy of chromosome 17, meaning that it either has identically-placed crossovers for both of us, or is a chromosome which (essentially) avoided recombination altogether. The latter is actually the more likely of the two possibilities.

    Now, if both girls received a copy of chromosome 17 that came from the same great grandparent -- one of my my brother's and my grandparents; I haven't yet tracked down which one, but I may be able to -- what are the odds of the same chromosome being passed on in full to a child in the next generation?

    Well, for each daughter the odds aren't any different than they were in any of the previous generations. This is how recombination works. It is reasonably likely that the chromosome will have one or more crossovers in the next generation, but is far from impossible that it won't. My daughter has no children, so obviously she hasn't passed on any chromosomes yet. However, my niece has five children, so she's had five different opportunities to pass on part or all of this chromosome.

    The point, though, is to make it very clear just how far an entire chromosome can be passed on intact. And if the chromosome has been passed on intact, then every segment on the chromosome has also been passed on without "decay".

    So, five times my niece passed a set of 23 chromosomes on to a child. This set obviously included chromosome 17. What are the odds that she failed to pass on any portion of her paternal copy? What are the odds that in at least one transmission, she didn't pass on a fairly substantial portion of that copy? If she did, it means that the child who received it would share a rather large chunk of DNA -- much larger than average -- with a 2nd great grandparent.

    Now, my siblings and I collectively only have ten children, and a slightly larger number of grandchildren. But if we'd all been as prolific as my parents -- who had six children by themselves -- or my father's parents, who had twelve; there would be very many cousins by now.

    My father's parents had over 30 grandchildren. But I have a 4th great grandfather who had 20 children himself -- although it was by four different mothers. The point, though, is potentially have many 5th cousins, and 4th, and 3rd. I don't know precisely how many 2nd cousins I have, but my maternal grandfather's parents had at least seven children in addition to him, and most of these had children of their own.

    Now, CJ Wyatt III proposes that very large segments cannot be from distant relatives, even though it's clear that even whole chromosomes are sometimes passed through multiple generations -- which means the "average decay rate" idea is misleading when applied to individual situations. Instead, he claims that what we're seeing is just the "piling up" of smaller segments from multiple shared ancestors.

    This would require that both cousins inherited essentially the same small segments from these more distant ancestors, and that those segments would happen to line up in such a way as to give the appearance of a larger match. This might be true for someone with very recent membership in a very endogamous population, but most of us aren't -- or at least, not recently.

    Like most people (all, eventually) my tree has experienced a certain amount of pedigree collapse. However, the closest ancestors I have who were at all related were my paternal grandmother's parents. They were 2nd cousins twice removed, and I have a pair of ancestors who are both 4th and 6th grandparents to me. Neither of these is a particularly close relationship, and while I have some cousins who appear to be related to me through these ancestors, none of them shares any especially large segments with me.

    At any rate, ancestry on my father's side has no bearing on my mother's side, since she is unlikely to be related to my father within a genealogical time frame. They are from Pennsylvania and Mississippi, respectively, and met when my father was in basic training at Keesler Air Force Base. They certainly do not share any DNA.

    My maternal grandparents aren't related, either. My grandmother's ancestry consists of three immigrants -- two from Minorca and one from Alsace-Lorraine -- and one grandparent whose ancestry was from southern Mississippi for many generations. Now, that grandparent had a fairly large number of ancestors who were related to each other; but the only relevance of this would be to cousins in this part of my family. And, yes, here I have cousins who are related to me by multiple paths. But guess what? None of the more distant cousins on this side shares any unexpectedly large segments with me. A few may share more than one smaller segment, but they don't seem to have all managed to "pile up" anywhere. Why not? Probably because to have large pile ups -- especially on both sides -- you still need recent multiple paths, not distant multiple paths.

    In my previous posts, I've made reference to a 2nd cousin. Here we are talking about recent common ancestor -- our great grandparents. But we don't have any more recent connection. Nor do our great parents themselves seem to be related, so whatever pedigree collapse might exist between the two of us, it's beyond that. Eventually, there is some. Many of my Sizemore, Asher, and Bowling cousins are related by several paths.

    But it's still irrelevant for me, because I don't have all those multiple paths in my recent ancestry. Having multiple distant paths can't result in large segments today, because they still need some mechanism for "lining up". The only thing multiple distant paths gets you is more chances for that ancestor to pass on any DNA at all -- but for distant ancestors, the odds of any DNA at all being shared with you is small to begin with. So they end up with several small chances.

    Jack is wanting to find an alternate mechanism for explaining large distant matches, because he's already concluded that it's virtually impossible for a large segment to remain intact for so long. But I've already showed how even a whole chromosome can be passed on intact over multiple generations. An alternate mechanism is not needed. The most likely mechanism is obvious, and it isn't what Jack suggests. It's simply the random working of recombination -- operating much like the coin tosses I mentioned.

    On average, the coin will be heads half the time and tails half the time, but this doesn't mean that in any given set of 100 tosses, it will always be 50 of each. It can be anywhere from 0 heads and 100 tails, to 100 heads and 0 tails. Given enough coin tosses, you will see all possible combinations eventually.
    Last edited by geebee; 07-28-2017 at 05:43 PM.
    The short explanation of my ancestry is British-German-Catalan, but it actually includes smaller amounts of French, Irish, Swiss, Choctaw and probably Cherokee. My avatar picture is of my father, his father, and his father's father. The baby in the picture is my eldest brother.

    GB

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  10. #18
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    Quote Originally Posted by C J Wyatt III View Post
    and you completely brush off the X-chromosome analysis?

    I am not questioning your big segments. I am questioning whether they are IBD or reconstructed by multiple lines back to the common ancestor. Without being able to examine your data with the high resolution chromosme browser, I cannot make that determination. However I have seen plenty of big segments pop up that are not IBD.

    I thought second cousins share great grandparents.

    Jack
    Yeah, you're right about 2nd cousins and great grandparents. I hate it when my fingers type without any input from my brain.

    There's really no opportunity for the kind of "reconstruction" you're talking about. Most people -- including me -- do not have pedigree collapse sooner than great grandparents. For that you'd have to have either parents or grandparents marrying 1st cousins.

    This actually is the case for some of my relatives, but smaller segments that somehow manage to "bunch up" on just one side aren't going to have a corresponding match unless the other person actually managed to inherit a very large segment from the same source.

    Take a look at this chart from "The Shared cM Project" managed by by Blaine Bettinger. It certainly doesn't disprove your hypothesis, but it shows how variable the amount of DNA passed on by ancestors is. This variability is not just the product of receiving more or fewer segments, but also receiving longer or shorter segments.

    Recombination is essentially random, and because of that you don't get nice and neat segment sizes. You talked about an "average decay rate" at some point, but averages aren't prescriptive. You can speak of average family size, and some families will indeed be average-sized. But others will be very small -- just one person, really -- while still others will be huge (into double digits).

    In genealogy, as you know, it's common to treat the average length of a generation as 30 years. But of course there will be times when someone is descending from a series of very young parents, or a series of very old parents. The same thing is true of recombination. You can have very large segments which stay very large over multiple generations. In an essentially random process, it is inevitable that this will happen sometimes -- just as it's inevitable that when you do lots of coin tosses, you'll sometimes get very long strings of all heads or all tails.

    The average may 50-50, but that has absolutely no effect on whatever happens on the next toss.

    EDIT:

    Here's a comparison between the genomes of my father Bern and two of his granddaughters. They are my daughter Kathryn, shown in purple; and my brother Bernie's daughter Stephanie, shown in orange.

    Attachment 18590

    The main thing I want to call attention to is just how rarely recombination has resulted in a chromosome being evenly split between the two grandparents. Some chromosomes are passed on with virtually no recombination, while others have just small amounts of DNA from one grandparent and large amounts from the other.

    The overall result may be that children show close to 25% of their DNA with each grandparent -- though that can vary pretty widely, too -- but they hardly do this through sharing half of each chromosome.

    And, just as with coin tosses, while it may be that most chromosomes will see an "evening out" over a long period of time, there are going to be instances in which the same chromosome ends up being passed down over several generations without having all that many crossovers, or crossovers which are simply near one end or the other.

    The net result is that any segments on such a chromosome will not experience any sort of "average decay rate", at least over a sufficient number of generations that some cousins will share large segments with each other.

    So the idea of large segments always being formed by some sort of "piling up" process is completely unnecessary to explain why people sometimes share larger-than-expected segments. It is possible that it could happen. I do not, however, believe it is the most parsimonious explanation.
    Last edited by geebee; 09-07-2017 at 05:57 AM.
    The short explanation of my ancestry is British-German-Catalan, but it actually includes smaller amounts of French, Irish, Swiss, Choctaw and probably Cherokee. My avatar picture is of my father, his father, and his father's father. The baby in the picture is my eldest brother.

    GB

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    Hi!
    I have 4 X matches with American persons all of them women, does that mean we have a common female ancestor?
    Knowing that I got my X chromosome from my mother, does that mean that my maternal grandmother is related to those 4 Americans?!
    I am really confused, any help is welcomed, thanks!
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    A thread where I explain how the Tunisian sample used by various gedmatch calcs is not representative of Tunisians:
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    Quote Originally Posted by kikkk View Post
    Hi!
    I have 4 X matches with American persons all of them women, does that mean we have a common female ancestor?
    Knowing that I got my X chromosome from my mother, does that mean that my maternal grandmother is related to those 4 Americans?!
    I am really confused, any help is welcomed, thanks!
    What are the sizes of the segments? I also have American/Latin American X matches on Gedmatch but they're all <10cM i.e. most likely IBS instead of really IBD.
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