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Author Topic: Pedigree collapse and my mother's X chromosomes  (Read 2161 times)
JimT
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« on: January 19, 2009, 11:01:08 PM »

My mother's parents were born about 3 miles (5 km) from each other on farms in neighboring parishes in Sweden.  It was a rural area where people rarely moved more than a few miles from where they were born and nearly everyone was related.  I've traced most of my mother's ancestral lines back to the 1680s, when record keeping began in Sweden.  All of my mother's lines were Swedish.  Most of her lines lived in the two parishes where her parents were born, Fjärås and Tölö.  All of the lines that could have contributed to her X chromosomes lived in those two parishes.

Pedigree collapse occurs when cousins marry.  (See http://tinyurl.com/8r5qt9)  My mother's parents were third cousins.  That means that one pair of her 3rd-great-grandparents were ancestors of both her father and her mother.  If you look at the women's 6-generation X chromosome inheritance chart on this page: http://tinyurl.com/7sw89s, that pair of her 3rd-great-grandparents are in boxes 42, 43, 52, and 53 in the chart.  Their names were Börge Andersson (b. 13 Nov 1720 Fjärås, Halland, Sweden) and Elin Andersdotter (b. 2 Sep 1728 Fjärås, Halland, Sweden).

A woman can inherit X chromosome DNA from 13 of her 32 3rd-great-grandparents.  She inherits, on the average, 12.5% of her X DNA from each of four 3rd-great-grandparents (boxes 42, 43, 45, and 53 in the chart), and smaller amounts of X DNA from up to nine other 3rd-great-grandparents.  One of my mother's 3rd-great-grandmothers, Elin Andersdotter, is in two of the positions in her family tree that each contribute 12.5%, so Elin could be expected to contribute about 25% of my mother's X DNA.  Of course, the percentages are approximate.  In theory, my mother could have gotten anywhere from 0% to 100% of her X DNA from Elin.  She is certainly much more likely to have gotten some of her X DNA from Elin than from any of her other 3rd-great-grandparents.

People generally have 32 3rd-great-grandparents.  My mother only has 30 due to pedigree collapse.  Her pedigree collapses even more in earlier generations.  Not only were my mother's parents third cousins, but her father's parents were third cousins, her mother's parents were third cousins, and her father's mother and mother's father were third cousins.  One pair of my mother's great-grandparents were second cousins.  As previously mentioned, Elin Andersdotter was my mother's 3rd-great-grandmother in two different lines.  Elin's brother Anders and sister Maria were also 3rd-great-grandparents of my mother.  Börge Andersson was a double 3rd-great-grandfather, and his brother Ingemar was another of my mother's 3rd-great-grandparents.  I could mention others who contributed to the pedigree collapse, but I think you get the idea.

People normally have 64 4th-great-grandparents.  My mother can have no more than 54.  People normally have 128 5th-great-grandparents.  My mother can have no more than 98.  I've found records of 30 of the possible 98.  The rest lived before record keeping began.  I'm quite certain that the number would be less than 98 if there were records of earlier generations.  Because of pedigree collapse, I would expect my mother's X chromosomes, and all of her autosomes to be more homozygous than chromosomes in other people.

My mother's X chromosomes could be considered Danish rather than Swedish.  The province of Halland, where her parents were born, was part of Denmark from ancient times until 1645.  My mother's ancestors were certainly there before Sweden acquired Halland.  My 7th-great-grandfather Sefwed Mansson was born in 1636.  There are no records that would tell where he was born, but in the 1680s, when record keeping began in Sweden, he was living on the farm where my grandfather was born. 

Jim Turner
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X chromosome 100% Halländsk (Danish before 1645; Swedish after 1645)
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« Reply #1 on: January 20, 2009, 12:11:46 AM »

You have an interesting ancestry, Jim. 

My own X chromosome is 50% Swedish (and 50% French), at least as estimated from my pedigree.  I have been following the recent Rootsweb discussions on Scandinavian DNA with great interest.  I have sizeable blocks of Asian DNA in my 23andMe ancestry painting, but I strongly suspect that it comes from Native American ancestry rather than any Asian influence in Sweden (I say that because I have examined the ancestry paintings of several other people with Swedish ancestry, and they do not tend to show any Asian blocks--though perhaps this would show up differently under DeCODEme's detection thresholds).  I am currently having my father tested, which should verify from which side of my family those Asian blocks originated.
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a.k.a., GhostX
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« Reply #2 on: January 20, 2009, 03:24:14 AM »

You have an interesting ancestry, Jim. 

My own X chromosome is 50% Swedish (and 50% French), at least as estimated from my pedigree.  I have been following the recent Rootsweb discussions on Scandinavian DNA with great interest.  I have sizeable blocks of Asian DNA in my 23andMe ancestry painting, but I strongly suspect that it comes from Native American ancestry rather than any Asian influence in Sweden (I say that because I have examined the ancestry paintings of several other people with Swedish ancestry, and they do not tend to show any Asian blocks--though perhaps this would show up differently under DeCODEme's detection thresholds).  I am currently having my father tested, which should verify from which side of my family those Asian blocks originated.
As I look into things more closely and talk to more people it is clear that Scandinavian ancestry is going to be "problematic" in terms of interpretation.  You are all aware of the well known case of Anders (100%) Norwegian and his various Asian matches including the large Monglian - Pima one.  A Swedish fellow I know whose ancestors all come from a small area in the far SW (near Halland) is, if I recall, 15% Native American so DNAPrint would not do the Euro2 testing on him.  Also in parts of Norway there is 8% haplogroup Q, which is Cental Asian.  These are just examples.  I know of a young fellow who is mostly Norwegian but has a gggg grandmother who was Sioux and he has about 2% Asian on 23andme.  Imposible to tell the source of the orange patches but the NA is a good bet.

You said that your X is 50% French and 50% Swedish GhostX, where does the Native American fit it?
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X-chromosome:  56.25% England; 12.5% Scotland; 12.5% Ireland; 12.5% Germany; 6.25% North America (Lower Mohawk, Six Nations)
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« Reply #3 on: January 20, 2009, 03:36:20 AM »

Yes, this pedigree collapse is probably quite common in certain locations.  In Ontario where I am from, until my grandmother "layed down the law", first cousin marriages were common.  Two of her grandparents were first cousins, and the generation before, one of the parties married a first cousin once removed.  This complicates things immensely for the autosomes where the same names keep appearing over and over.  However refering to Jim and Blaine's charts for the X inheritance, just by the positioning of the cousins on the chart, the lines all go to separate individuals at the 7th generation and no ancestor in common.  I would never have believed it without the chart at the ready.
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X-chromosome:  56.25% England; 12.5% Scotland; 12.5% Ireland; 12.5% Germany; 6.25% North America (Lower Mohawk, Six Nations)
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« Reply #4 on: January 20, 2009, 03:58:32 AM »

Quote

You said that your X is 50% French and 50% Swedish GhostX, where does the Native American fit it?


Woops, I think I just answered my own question.  You were speaking of the autosomes and of course the ancestors here include not only the 21 X line ones, but the other 107 on both the mother and father's side for a male.  Slight lapses every so often - quite "normal" in this field (even among the younger set I understand).
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X-chromosome:  56.25% England; 12.5% Scotland; 12.5% Ireland; 12.5% Germany; 6.25% North America (Lower Mohawk, Six Nations)
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« Reply #5 on: January 20, 2009, 02:16:52 PM »

Quote

You said that your X is 50% French and 50% Swedish GhostX, where does the Native American fit it?


Woops, I think I just answered my own question.  You were speaking of the autosomes and of course the ancestors here include not only the 21 X line ones, but the other 107 on both the mother and father's side for a male.  Slight lapses every so often - quite "normal" in this field (even among the younger set I understand).


Yeah, I probably shouldn't have juxtaposed my two sentences like that without specifying what I was referring to, but yes, my NA ancestry contribution  is autosomal.  Of course it could also be on my X chromosome, if the source of the NA blocks turns out to be from my mother's side of the family, in which case my 50/50% estimate (Swedish/French) for my X may turn out to be off.

I'll know when my father's test results come in!
« Last Edit: January 22, 2009, 03:05:07 PM by GhostX » Logged

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« Reply #6 on: January 21, 2009, 09:11:55 AM »

Because of pedigree collapse, I would expect my mother's X chromosomes, and all of her autosomes to be more homozygous than chromosomes in other people.

Would it be or would it just became more like a "freezer"?
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JimT
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« Reply #7 on: January 21, 2009, 11:14:58 PM »

Because of pedigree collapse, I would expect my mother's X chromosomes, and all of her autosomes to be more homozygous than chromosomes in other people.

Would it be or would it just became more like a "freezer"?

I don't understand what you are trying to say.
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Svaale
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« Reply #8 on: January 22, 2009, 05:57:43 AM »

Because of pedigree collapse, I would expect my mother's X chromosomes, and all of her autosomes to be more homozygous than chromosomes in other people.

Would it be or would it just became more like a "freezer"?

I don't understand what you are trying to say.

Maybe the result would not be homog. but just less recombined as very closely related blocks of x-chr will recombine with a practically identical one would not show up as a recombination event.
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JimT
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« Reply #9 on: January 22, 2009, 02:40:53 PM »

Because of pedigree collapse, I would expect my mother's X chromosomes, and all of her autosomes to be more homozygous than chromosomes in other people.

Would it be or would it just became more like a "freezer"?

I don't understand what you are trying to say.

Maybe the result would not be homog. but just less recombined as very closely related blocks of x-chr will recombine with a practically identical one would not show up as a recombination event.

I still don't understand.  What are "very closely related blocks of x-chr" if they are not mostly homozygous?
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« Reply #10 on: January 22, 2009, 02:46:01 PM »

I still don't understand.  What are "very closely related blocks of x-chr" if they are not mostly homozygous?

I try it to ask it another way then, do the pedigree collapse suggest that a single founder dominate the remaining descendants to you?
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geneticgenie
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« Reply #11 on: January 25, 2009, 03:46:42 PM »

I still don't understand.  What are "very closely related blocks of x-chr" if they are not mostly homozygous?

I try it to ask it another way then, do the pedigree collapse suggest that a single founder dominate the remaining descendants to you?

Pedigree collapse can cause the same markers to show up in multiple descendants;
but alternatively the SNPs we deal with could also be UEP (unique event polymorphisms)
that show up in millions of people and rarely ever change, so you would not be able
to tell the difference between pedigree collapse and sequences that just hardly ever
change until one race just happens to mate with another race and there is crossover
recombination.  So I think what Svaale is saying, people who are related thousands of years ago can also be homozygous.

That is why we need to test more variable regions, as in STR regions that mutate more
often.  We are working backwards here. The Y chromosome has all kinds of people
who have close STRs, so now the associated SNPs in their haplogroups and subclades
are being discovered through data-mining.  With the X chromosome, we are finding the UEP SNPs first; so now we need to find the associated STRs within the appropriate haploblocks. The challenge is to find an appropriate haploblock , then test for STRs, then be able to compare with a public or already published database. 

There are four problems that I see with the X that are not a problem with the Y:
1. The X has crossover recombination.
2. The X has associated genes that some people may not want divulged.
3. The X does not have a lot of research papers and “X”perts to help us.
4. Genealogists are not familiar with the X and have not embraced testing so far; so why spend the money if there is no immediate gratification?
Kathy J.

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Kathy J.
X Chromosomes: 75% English, 12.5% German, 6.25% Dutch, 3.125% Irish, 3.125% Scottish;
from Father's X: 43.75% English, 6.25% Dutch;
from Mother's X: 31.25% English, 12.5% German, 3.125% Irish, 3.125% Scottish
JimT
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« Reply #12 on: January 25, 2009, 10:33:57 PM »

I still don't understand.  What are "very closely related blocks of x-chr" if they are not mostly homozygous?

I try it to ask it another way then, do the pedigree collapse suggest that a single founder dominate the remaining descendants to you?

Not a single founder but a  smaller number of founders than most other people have.   Each generation of my mother's ancestors has fewer people who could have possibly contributed to her X than other people have.  And many of the people who could have contributed to her X are cousins who inherited parts of their X chromosomes from the same ancestors.
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JimT
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« Reply #13 on: January 25, 2009, 10:56:34 PM »

The fact is that some women have significantly more homozygous regions in their X chromosomes than others.  You can see it in the data in Ben Moscia's spreadsheet.  Because my mother has significantly fewer people who contributed to her X DNA than most other women, I would expect her X chromosomes to be more homozygous than most other women.  I didn't make any claims about whether that would be of any use in genealogy. 

You didn't mention one of the big differences between the X and Y chromosomes; the number of X SNPs tested by 23andMe is far greater than the number of Y SNPs tested.  We have already seen several cases of back mutations in Y SNPs in 23andMe results.  With the much larger number of X SNPs, we should have a greater possibility of seeing back mutations, and that would definitely be useful for studying deep ancestry and possibly for genealogy.  Of course, STR testing has its place too.


Pedigree collapse can cause the same markers to show up in multiple descendants;
but alternatively the SNPs we deal with could also be UEP (unique event polymorphisms)
that show up in millions of people and rarely ever change, so you would not be able
to tell the difference between pedigree collapse and sequences that just hardly ever
change until one race just happens to mate with another race and there is crossover
recombination.  So I think what Svaale is saying, people who are related thousands of years ago can also be homozygous.

That is why we need to test more variable regions, as in STR regions that mutate more
often.  We are working backwards here. The Y chromosome has all kinds of people
who have close STRs, so now the associated SNPs in their haplogroups and subclades
are being discovered through data-mining.  With the X chromosome, we are finding the UEP SNPs first; so now we need to find the associated STRs within the appropriate haploblocks. The challenge is to find an appropriate haploblock , then test for STRs, then be able to compare with a public or already published database. 

There are four problems that I see with the X that are not a problem with the Y:
1. The X has crossover recombination.
2. The X has associated genes that some people may not want divulged.
3. The X does not have a lot of research papers and “X”perts to help us.
4. Genealogists are not familiar with the X and have not embraced testing so far; so why spend the money if there is no immediate gratification?
Kathy J.


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