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Archiver > GENEALOGY-DNA > 2006-11 > 1164757429


From: "brian quinn" <>
Subject: Re: [DNA] DNA] DYS437+R1a=Strange
Date: Wed, 29 Nov 2006 10:43:49 +1100
In-Reply-To: <mailman.27315.1164729013.22941.genealogy-dna@rootsweb.com>


Ken,

fromhttp://www.cstl.nist.gov/biotech/strbase/pub_pres/ButlerJFS_Y-STRduplica
tion.pdf

"TABLE 2-Physical location of 50 Y-STR markers on the Y-chromosome
based on a sequence search using the July 2003 Human Genome sequence
assembly (http://genome.ucsc.edu). Megabase (Mb) positions are rounded
to the nearest thousand base pair."

Hence, I guess they are close but separated by less than one thousand base
pair.


I see that approx 200 kb separate dys385b from dys461. I am not sure if
thousand base pairs has the same meaning as kb of dna. But expect so.

"Note that DYS437, DYS439, and DYS389I/II,
which are duplicated in the sample displayed in Figure 1, all occur
within 150 kb of one another and therefore more likely to be
duplicated together. This AZFa region of the Y-chromosome was
also noted by Bosch and Jobling (29) to be duplicated in some
individuals." Op cit

150kb is close to 200kb base pairs I presume means 200kb. So it would be
possible that 460,461 were duplicated as well. However as the article points
out sometimes there is a duplication but not mutation subsequently and the
testing company or scientist may not notice that the peak is twice or three
etc times as high as a single copy.

The other dys you mention don't seem close to the 4 dys that all duplicated
in one event.

Interestingly it says the AZFa region homologously recombine at the HERV
spots, which are like retroviruses. Maybe shows our retrovirus ancestor!

I notice that the three copies of P25(one slightly different) that defines
R1b itself is in the Giant Palindrome region. I was wondering where that is
on the y chromosome in relation to the dys things.

Brian quinn
------------------------------

Message: 3
Date: Tue, 28 Nov 2006 03:44:20 -0700
From: "Ken Nordtvedt" <>
Subject: Re: [DNA] DNA] DYS437+R1a=Strange
To: <>
Message-ID: <002601c712da$29294710$>
Content-Type: text/plain; format=flowed; charset="iso-8859-1";
reply-type=original

It appears that 460 and 461 are at the same location? If 461 is triplicated

and 460 is not, why? Is it that 460 has not had its triplicated copies
mutated to different lengths? But nevertheless, one should still see a
single 460 peak three times higher than normal?

My great grandfather's R1b has normal 11-14 at 385a,b, but unusual 438 and
YCAIIb; and uncommon but not rare 464a,b,c,d

His 461 is reported as 12-13-14 (DNAH convention) 461 seems not a faster
mutator than 460 or 385a,b

----- Original Message -----
From: "brian quinn" <>
To: <>
Sent: Tuesday, November 28, 2006 1:27 AM
Subject: Re: [DNA] DNA] DYS437+R1a=Strange


> Ken,
>
> Well looking at the mentioned paper
>
> DYS385 a 19.998
> DYS385 b 20.039
> DYS461 (A7.2) 20.247
> DYS460 (A7.1) 20.247
>
> The numbers are the megabase positions from the end of the p arm.
>
>
> The 385a/b are next door to dys 461.
>
> They didn't study dys 461 but the 385a/b has these alleles observed in
> many
> papers etc
>
> DYS385a/b 9,13,14 Sahoo et al. 2003 (28) (1 time)
> DYS385a/b 11,12,13 Kurihara et al. 2004 (13) (1 time)
> DYS385a/b 11,12,14 http://www.yhrd.org (1 time)
> DYS385a/b 11,14,15 http://www.yhrd.org (2 times)
> DYS385a/b 12,13,18,19 http://www.yhrd.org (1 time)
> DYS385a/b 12,13,19,20 http://www.yhrd.org (1 time)
> DYS385a/b 12,16,17 Kayser and Sajantila 2001 (11) (1 time)
> DYS385a/b 13,14,15 http://www.yhrd.org (3 times); AMG (1 time)
> DYS385a/b 13,14,18 AMG (1 time)
> DYS385a/b 13,18,19 http://www.yhrd.org (1 time)
> DYS385a/b 13,19,20 http://www.yhrd.org (1 time)
> DYS385a/b 14,16,17 http://www.yhrd.org (1 time)
> DYS385a/b 15,16,17 Butler et al. 2002 (12) (1 time)
>
>
> The duplication they observe is at
> DYS437 13.778
> DYS435 13.807
> DYS439 13.826
> DYS389 I/II 13.923
>
> They are closer together than 385a/b are to dys 461
>
> But maybe in the same region as the tri and quadriplications observed for
> 385a/b?
> Wonder what your ggrandfathers 385a/b are?




------------------------------

Message: 4
Date: Tue, 28 Nov 2006 06:31:06 -0500
From: "Steven Bird" <>
Subject: Re: [DNA] Translating Oppenheimer
To:
Message-ID: <>
Content-Type: text/plain; format=flowed

Bob and Dennis,

It is possible to estimate haplogroups on a very broad basis using only the
six markers provided, in some cases. By this I mean R1b, E3b, I, etc., not
I1a for example. Some are ambiguous, however. As far as I can tell, all of

Oppenheimer's data for E3b was based on Capelli's 2003 paper. He discusses
nothing about that group that he did not infer from C.'s dataset.

The clusters of E3b1 cannot be separated from the six allele values used by
Capelli. However, E3b2 and E3b3 can be distinguished from E3b1 with the
particular set used. That's better than nothing.

Steve Bird



>We have all been asking the same question, R1b, I1a and E3b and the answer
>is the data is public but the groupings are private.
>I, for one want to know what markers he used to separate his R1b-14, which
>he states clearly is Irish, into R1b-14a 14b and 14c.
>Apparently the data is often only 6 markers ... hardly enough to separate
>the clusters, one would think.
>
>

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------------------------------

Message: 5
Date: Tue, 28 Nov 2006 08:52:14 -0500
From: "Dale E. Reddick" <>
Subject: [DNA] Two items from the new issue of the European Journal of
HumanGenetics.
To: ,
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Folks,

These seem to be possibly of some interest to list members.

Dale E. Reddick


The scale and nature of Viking settlement in Ireland from Y-chromosome
admixture analysis
Brian McEvoy, Claire Brady, Laoise T Moore and Daniel G Bradley
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ebN50Sn1nD0Hh40BGQY0EF
Article: http://ealerts.nature.com/cgi-bin24/DM/y/ebN50Sn1nD0Hh40BGQZ0EG


An utter refutation of the `Fundamental Theorem of the HapMap' by
Terwilliger and Hiekkalinna
Duncan C Thomas and Daniel O Stram
http://ealerts.nature.com/cgi-bin24/DM/y/ebN50Sn1nD0Hh40BGQJ0Ey







------------------------------

Message: 6
Date: Tue, 28 Nov 2006 06:45:52 -0800
From: "David Wilson" <>
Subject: Re: [DNA] Translating Oppenheimer
To: <>
Message-ID: <000001c712fb$ea293990$d34c2b3f@DW>
Content-Type: text/plain;charset="windows-1250"

I believe Oppenheimer had access to the Trinity College Dublin data set,
which runs to 17 markers and focuses on Ireland.

I'm a little nervous about his R1b-14 group. This must be the cluster that
includes haplogroup R1b1c7, which I have long thought is pretty ancient. If
Oppenheimer's root "Rory" group is to be associated with the R1b1c7 (M222+)
clade, then he seems to think the 14a, 14b and 14c groups derive from it.
This model seems to me not defensible. Alternatively, if he thinks "Rory" is
a generalized root Irish group, he must believe that what we know as R1b1c7
is associated with one of the subgroups he calls 14a, 14b and 14c. In that
case what we want to know is the identity of the other two.

Either way he seems to postulate a closer relationship between R1b1c7 and
the other Irish clusters than I think probable, but I'm certainly willing to
be persuaded otherwise if the data and the argument are ever systematically
presented.

David Wilson


On 11/27/2006 11:43:58 PM, Dennis Wright () wrote:
> We have all been asking the same question, R1b, I1a and E3b and the
> answer
> is the data is public but the groupings are private.
> I, for one want to know what markers he used to separate his R1b-14,
> which
> he states clearly is Irish, into R1b-14a 14b and 14c.
> Apparently the data is often only 6 markers ... hardly enough to separate
> the clusters, one would think.
> Sorry!
>
> Dennis Wright
> R1b1c Irish Type III
> Ysearch 6PWCD
> http://au.geocities.com/t120r61/Irish_Type_III.htm

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------------------------------

Message: 7
Date: Tue, 28 Nov 2006 09:38:46 -0600
From: "steven perkins" <>
Subject: Re: [DNA] Two items from the new issue of the European
Journal ofHuman Genetics.
To:
Message-ID:
<>
Content-Type: text/plain; charset=WINDOWS-1252; format=flowed

The abstract of the first article:

Article

European Journal of Human Genetics (2006) 14, 1288?1294.
doi:10.1038/sj.ejhg.5201709; published online 6 September 2006
The scale and nature of Viking settlement in Ireland from Y-chromosome
admixture analysis

Brian McEvoy1, Claire Brady1, Laoise T Moore1 and Daniel G Bradley1

1Smurfit Institute of Genetics, Trinity College, Dublin, Ireland

Correspondence: Professor D Bradley, Smurfit Institute of Genetics,
Trinity College, Dublin 2, Ireland. Tel: +353 1 608 1088; Fax: +353 1
679 8558; E-mail:

Received 22 December 2005; Revised 20 July 2006; Accepted 27 July
2006; Published online 6 September 2006.
Top of page
Abstract

The Vikings (or Norse) played a prominent role in Irish history but,
despite this, their genetic legacy in Ireland, which may provide
insights into the nature and scale of their immigration, is largely
unexplored. Irish surnames, some of which are thought to have Norse
roots, are paternally inherited in a similar manner to Y-chromosomes.
The correspondence of Scandinavian patrilineal ancestry in a cohort of
Irish men bearing surnames of putative Norse origin was examined using
both slow mutating unique event polymorphisms and relatively rapidly
changing short tandem repeat Y-chromosome markers. Irish and
Scandinavian admixture proportions were explored for both systems
using six different admixture estimators, allowing a parallel
investigation of the impact of method and marker type in Y-chromosome
admixture analysis. Admixture proportion estimates in the putative
Norse surname group were highly consistent and detected little trace
of Scandinavian ancestry. In addition, there is scant evidence of
Scandinavian Y-chromosome introgression in a general Irish population
sample. Although conclusions are largely dependent on the accurate
identification of Norse surnames, the findings are consistent with a
relatively small number of Norse settlers (and descendents) migrating
to Ireland during the Viking period (ca. AD 800?1200) suggesting that
Norse colonial settlements might have been largely composed of
indigenous Irish. This observation adds to previous genetic studies
that point to a flexible Viking settlement approach across North
Atlantic Europe.


On 11/28/06, Dale E. Reddick <> wrote:
> Hi Folks,
>
> These seem to be possibly of some interest to list members.
>
> Dale E. Reddick
>
>
> The scale and nature of Viking settlement in Ireland from Y-chromosome
admixture analysis
> Brian McEvoy, Claire Brady, Laoise T Moore and Daniel G Bradley
> Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ebN50Sn1nD0Hh40BGQY0EF
> Article: http://ealerts.nature.com/cgi-bin24/DM/y/ebN50Sn1nD0Hh40BGQZ0EG
>
>
> An utter refutation of the `Fundamental Theorem of the HapMap' by
Terwilliger and Hiekkalinna
> Duncan C Thomas and Daniel O Stram
> http://ealerts.nature.com/cgi-bin24/DM/y/ebN50Sn1nD0Hh40BGQJ0Ey
>
>
>
>
>
>
> -------------------------------
> To unsubscribe from the list, please send an email to
with the word 'unsubscribe' without the
quotes in the subject and the body of the message
>


--
Steven C. Perkins
http://stevencperkins.com/
Researching Indigenous Peoples' Rights
http://intelligent-internet.info/law/ipr2.html
Indigenous and Ethnic Minority Legal News
kttp://iemlnews.blogspot.com/
On-Line Journal of Genetics and Genealogy
http://jgg-online.blogspot.com/
Steven C. Perkins' Genealogy Page
http://stevencperkins.com/genealogy.html



------------------------------

Message: 8
Date: Tue, 28 Nov 2006 08:27:32 -0600
From: Rebekah <>
Subject: Re: [DNA] DYS437+R1a=Strange
To:
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Yes... But looking at the Qs it seems that once they decide to become
DYS437 = 15 they stay there. What is the effective mutation rate on
DYS437?

Ken Nordtvedt wrote:
> Yes, I suspect we'll find 14 in most any clade if your population is big
> enough. The question is if you have a clade with modal 14 how much 15 and

> 13 is there in that clade as well (in percent). In other words, some
clade
> had a founder thousands of years ago with 14 at DYS437. How many of his
> descendants today deviate from the 14, and which way do they deviate?
> Hardly any to 13 and some to 15 is the conjecture or observation.
>
> Ken
>

--
Regards,
Rebekah


"And they wonder why the maples
Can't be happy in their shade." Trees (Neil Peart from Rush)




------------------------------

Message: 9
Date: Tue, 28 Nov 2006 10:49:41 -0500
From: "ef_mckee" <>
Subject: Re: [DNA] Two items from the new issue of the European
JournalofHuman Genetics.
To: <>
Cc: Frank McGonigal <>
Message-ID: <000a01c71304$d1888310$>
Content-Type: text/plain; format=flowed; charset="Windows-1252";
reply-type=original

Every now and then I run across articles that would give one the impression
that the Norse influence on the history of Ireland was considerable. I
would like to see other viewpoints on the subject. I wonder whether the
Vikings might have spent a lot more time exploiting the area that now
encompasses Germany, Denmark, and other lands on conitnental Europe. I
dunno, jus' askin'. Has someone more knowledgeable of the history of
Ireland than I come to the same conclusions or to other conclusions?

Ed McKee

Ed McKee
----- Original Message -----
From: "steven perkins" <>
To: <>
Sent: Tuesday, November 28, 2006 10:38 AM
Subject: Re: [DNA] Two items from the new issue of the European Journal
ofHuman Genetics.


The abstract of the first article:

Article

European Journal of Human Genetics (2006) 14, 1288?1294.
doi:10.1038/sj.ejhg.5201709; published online 6 September 2006
The scale and nature of Viking settlement in Ireland from Y-chromosome
admixture analysis

Brian McEvoy1, Claire Brady1, Laoise T Moore1 and Daniel G Bradley1

1Smurfit Institute of Genetics, Trinity College, Dublin, Ireland

Correspondence: Professor D Bradley, Smurfit Institute of Genetics,
Trinity College, Dublin 2, Ireland. Tel: +353 1 608 1088; Fax: +353 1
679 8558; E-mail:

Received 22 December 2005; Revised 20 July 2006; Accepted 27 July
2006; Published online 6 September 2006.
Top of page
Abstract

The Vikings (or Norse) played a prominent role in Irish history but,
despite this, their genetic legacy in Ireland, which may provide
insights into the nature and scale of their immigration, is largely
unexplored. Irish surnames, some of which are thought to have Norse
roots, are paternally inherited in a similar manner to Y-chromosomes.
The correspondence of Scandinavian patrilineal ancestry in a cohort of
Irish men bearing surnames of putative Norse origin was examined using
both slow mutating unique event polymorphisms and relatively rapidly
changing short tandem repeat Y-chromosome markers. Irish and
Scandinavian admixture proportions were explored for both systems
using six different admixture estimators, allowing a parallel
investigation of the impact of method and marker type in Y-chromosome
admixture analysis. Admixture proportion estimates in the putative
Norse surname group were highly consistent and detected little trace
of Scandinavian ancestry. In addition, there is scant evidence of
Scandinavian Y-chromosome introgression in a general Irish population
sample. Although conclusions are largely dependent on the accurate
identification of Norse surnames, the findings are consistent with a
relatively small number of Norse settlers (and descendents) migrating
to Ireland during the Viking period (ca. AD 800?1200) suggesting that
Norse colonial settlements might have been largely composed of
indigenous Irish. This observation adds to previous genetic studies
that point to a flexible Viking settlement approach across North
Atlantic Europe.


On 11/28/06, Dale E. Reddick <> wrote:
> Hi Folks,
>
> These seem to be possibly of some interest to list members.
>
> Dale E. Reddick
>
>
> The scale and nature of Viking settlement in Ireland from Y-chromosome
> admixture analysis
> Brian McEvoy, Claire Brady, Laoise T Moore and Daniel G Bradley
> Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/ebN50Sn1nD0Hh40BGQY0EF
> Article: http://ealerts.nature.com/cgi-bin24/DM/y/ebN50Sn1nD0Hh40BGQZ0EG
>
>
> An utter refutation of the `Fundamental Theorem of the HapMap' by
> Terwilliger and Hiekkalinna
> Duncan C Thomas and Daniel O Stram
> http://ealerts.nature.com/cgi-bin24/DM/y/ebN50Sn1nD0Hh40BGQJ0Ey
>
>
>
>
>
>
> -------------------------------
> To unsubscribe from the list, please send an email to
> with the word 'unsubscribe' without the

> quotes in the subject and the body of the message
>


--
Steven C. Perkins
http://stevencperkins.com/
Researching Indigenous Peoples' Rights
http://intelligent-internet.info/law/ipr2.html
Indigenous and Ethnic Minority Legal News
kttp://iemlnews.blogspot.com/
On-Line Journal of Genetics and Genealogy
http://jgg-online.blogspot.com/
Steven C. Perkins' Genealogy Page
http://stevencperkins.com/genealogy.html


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