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Author Topic: "African X Block" Around Centromere: Mystery Solved  (Read 1961 times)
DKF
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« on: February 01, 2009, 11:20:55 PM »

Well, it is always a pleasant surprise when a genetic mystery has a clear and unequivocal solution.

As some of you will recall, I noted a very large olive colored haploblock in my decodeme browser that was labeled 100% African.  It is the largest block seen on any of my chromosomes, and if taken at face value I would have assumed that the region from about 55 to 65 Mb (10 Mb or so in length) came from an African ancestor.

After exploring the family tree that is represented on the X, I had found a possible candidate for the “mystery African”.  Still, there was no hard evidence at all.

Anders Palsen used both the program PLINK and an Excel formula to identify matching haploblocks in the HDGP-CEPH panel of 52 worldwide populations.  When the bar was set at 1 Mb and 100 SNPs (PLINK uses a selected reduced SNP set to identify haploblocks) the output showed zero matches to any Africans on the autosomes or the X.  None showed up in the more rigorous (direct) Excel approach.  However when the criteria was amended to encompass 1 Mb and 50 SNPs via PLINK about twice as many “matches” appeared. 

Now I had a 10 Mb match to one of the Africans in the dataset – which is probably what triggered decodeme’s algorithm, using another but similar program, to call the haploblock African.  But, there were also 6 matches of almost equal size to three Europeans and three from the Middle East.  It should be noted that among my friends at decodeme, who are likely all European in the X line, there were three with the same large olive colored block. 

So the bottom line is – no African ancestor within a genealogical time frame.  Not even 25 or 50,000 years ago.  It would appear that this match represents the legacy of a pre “Out of Africa” ancestor who lived in Africa, left descendants there, but also descendants among those who left sometime during or after the event circa 60,000 years ago where less than 1000 humans left African to become the founders of the rest of the world.  My ancestor must have gone via the Middle East to Europe but may not have left any descendants east of the Near East (Palestinians, Druze).

To see the data you can click on this URL:

http://davidkfaux.org/FAUX1MB50SNPX.bmp, making sure to also click on the little box at the lower right hand corner that appears and disappears (which will make the graph larger and easier to read).

Thanks to Anders for this revelation.  Now I must rule out having any African ancestors, which I had suspected perhaps via 18th Century England or Colonial USA.   Not only is there no genealogical support, there is nothing in the DNA that would give credence to this hypothesis.

David.
« Last Edit: February 02, 2009, 01:11:36 AM by DKF » Logged

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 #1 on: February 02, 2009, 12:50:16 AM »

Very interesting, David.  I went to look at your data file, but can't figure out what type of file it is, as it doesn't appear to have a filename extension.  My browser can't figure out what type of application to use to view it.
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DKF
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« Reply #2 on: February 02, 2009, 01:12:49 AM »

Very interesting, David.  I went to look at your data file, but can't figure out what type of file it is, as it doesn't appear to have a filename extension.  My browser can't figure out what type of application to use to view it.
It was a pdf file GhostX and opened automatically by my computer.  Hopefully the edited link above will work better for all.
David.
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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: February 02, 2009, 10:50:06 AM »

It was a pdf file GhostX and opened automatically by my computer.  Hopefully the edited link above will work better for all.
David.

Ah yes, that worked, thanks David. 

I assume that the Y-axis is showing X-chromosome position numbers (an unfortunate choice of words to say "Y-axis!").  What a fantastic way to show that data.  It sure puts that block located at the centromere in perspective, with respect to the various world populations.

I'll have to do something similar with my own X-chromosome one of these days.
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DKF
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« Reply #4 on: February 02, 2009, 03:22:02 PM »

It was a pdf file GhostX and opened automatically by my computer.  Hopefully the edited link above will work better for all.
David.

Ah yes, that worked, thanks David. 

I assume that the Y-axis is showing X-chromosome position numbers (an unfortunate choice of words to say "Y-axis!").  What a fantastic way to show that data.  It sure puts that block located at the centromere in perspective, with respect to the various world populations.

I'll have to do something similar with my own X-chromosome one of these days.
Yes, so 60 on the Y axis (ordinate) means position 60 Mb which is pretty well dead center in the centromere.

Anders said that this display is taken from one used typically for the stock market.  It just goes to show how creative and inventive some people can be.
« Last Edit: February 02, 2009, 03:25:43 PM by DKF » Logged

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: February 02, 2009, 04:56:00 PM »

It was a pdf file GhostX and opened automatically by my computer.  Hopefully the edited link above will work better for all.
David.

Ah yes, that worked, thanks David. 

I assume that the Y-axis is showing X-chromosome position numbers (an unfortunate choice of words to say "Y-axis!").  What a fantastic way to show that data.  It sure puts that block located at the centromere in perspective, with respect to the various world populations.

I'll have to do something similar with my own X-chromosome one of these days.
Yes, so 60 on the Y axis (ordinate) means position 60 Mb which is pretty well dead center in the centromere.

Anders said that this display is taken from one used typically for the stock market.  It just goes to show how creative and inventive some people can be.


Can you give us the range in terms of positions or SNPs?
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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
DKF
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« Reply #6 on: February 02, 2009, 10:07:22 PM »

Quote

Can you give us the range in terms of positions or SNPs?
Decodeme has me blocked in as "African" between positions 54 to 63 Mb, so more on the p (top) arm of the chromosome but definitely on both sides.  I have various amounts of sharing for a number of groups looking at the 52 reference individuals.  It appears that this block, in one form or another is seen worldwide, but with a finer analysis Africa, Middle East, and Europe.

It is so dramatic (a very distinctive block that is attributed to decodme to Africa) that this would have been a formula for going on some sort of wild goose chase after some non - existant (recent) African ancestors.
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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 #7 on: February 02, 2009, 10:58:14 PM »

David, I was studying that graph that you posted here earlier today, and it's clear from that plot that there is another haploblock candidate somewhere around position 105,000,000.  So I went back to Ben's spreadsheet and took a closer look, and sure enough, this is a block that I had flagged for closer study a few weeks ago, but I never got around to posting it on the project's results spreadsheet because the region includes too many genes.

Anyway, I managed to isolate a portion of it that's in an intergenic region (bracketed on both sides by genes), and it's a rather interesting block.  It's got a very low recombination rate overall, yet there is nevertheless obviously evidence of recombination, as there are several distinct types within the block.

I just posted it on the results page.  It's the last block on the page, between position numbers 105,197,873 and 105,712,333.  I took the liberty of posting your results there (as I'm sure you would have wanted me to), along with my own, as well as the anonymous members of Ben's spreadsheet:

http://www.worldfamilies.net/geo/xdna/results
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« Reply #8 on: February 14, 2009, 05:17:47 PM »

I wonder if these huge centromere blocks in the future could be used for something, I speculate in the future when much more dense SNP scanning is reality that it could be a interesting block for observing mutations only as recombination appears to be so rare.
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Seán MacGorman Powell
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« Reply #9 on: February 14, 2009, 09:00:14 PM »

I wonder if these huge centromere blocks in the future could be used for something, I speculate in the future when much more dense SNP scanning is reality that it could be a interesting block for observing mutations only as recombination appears to be so rare.

Yes I wonder about that too.  I also wonder if when this denser SNP scanning comes along, that some of what appear to be point mutations within some of these well-conserved haploblocks are actually going to turn out be more than just a single polymorphic nucleotide.  Some of the sequences in between the currently-sampled SNPs could have some interesting hidden things going on there.
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