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Archiver > GENEALOGY-DNA > 2009-09 > 1254216441


From: Anders Pålsen <>
Subject: Re: [DNA] 23andMe and Proving Native Ancestry
Date: Tue, 29 Sep 2009 02:27:21 -0700 (PDT)
In-Reply-To: <ea3bd9560909280740y5a1cfc57h65d42089477e6347@mail.gmail.com>


David

It is of course best to have samples from the north-east than no samples from this area, but it the meantime under the assumption that this native american group cluster with other native american groups it should be possible to infer ancestry without the specific data for people with native american ancestry segment of the chromosomes from the north-east.

As far as I can see from my owm analysis and yours is that your specific Xibo segment is of native american origin with north-east asians as proxy in the analysis this is confirmed in the PLINK block match and your find of interesting start and end positions for the block together with the deCODEme's locus specific analysis suggesting "east-asian" origin as proxy of the same area of the chromosome. This double confirmation from different kind of methods is ensuring even only with east asians as proxy, but not "complete" as it may not capture everything in other cases for example the central-asian ancestry of native americans that may go for "european" in the deCODEme or 23andme analysis.

Actually our cases is very similar with an exception, my Pima-Mongol block have the same double confirmation, identified both in PLINK as East-Asian and Native American by block matching and in deCODEme's locus analysis of the same area as "East-Asian" but my block is much more frequent than yours in the areas sampled both in East-Asia and the Americas, somwehat smaller sizes of my block is observed among one central-asian, some mongolian, pima and even some maya's but I have no matches further south in America (maybe remnants of the Y-DNA C3 guys you mentioned and the that the most southern Na-Dene Kets family language Apache border the Pimas). Your block appear as you have said earlier to have currently escaped detection in the Americas because of no sampling of the north-east America where it may have been part of the main founders, but my case as a proxy for your case shows large segment matching with East-Asians vs Native Americans is reality, and
if there was a new wave of migration recently as you mention into Americas from north-east asia it may explain this, recent common ancestry may also give problems seperating north-east asians segments from native american segments by clustering.

So when it comes to the empty area above your Xibo block there is no PLINK matches to anyone in the HGDP but your deCODEme locus ancestry graph for this area suggest "european" origin for this area based on clustering of chunks of linked SNP that find it most similar to europeans, in this case it may be european but it may also be native american with european as proxy to "central-asia european" because of the lack of native american population data in deCODEme analysis. Here locus ancestry determination software may be able to infer the origin european like european or native american as in central-asia "european" by seperating the ambigious "european" part into european and native american by clustering, but currently as the deCODEme analysis stand now this area is labeled european and PLINK do not provide any clues with the current dataset.

Anders


--- Den man 2009-09-28 skrev David Faux <>:


> Anders,
>
> I will be very interested to see what type or software /
> algorithm can
> determine anwers to the matters below.  I have assumed
> that the only way to
> ascertain whether my Xibo - Yakut block is from my NA
> ancestor is to go
> about collecting samples from those who are band members of
> various First
> Nations groups residing in the region of the Great
> Lakes;  At the moment the
> block in question is infered to be NA since it is precisely
> the size
> expected based on paper genealogy - but the matches are to
> NE Asians (with
> the strongest genetic link to Native Americans).  The
> block also has a start
> point not seen in any Europeans, only a few East Asians,
> but a long list of
> Native Americans from HGDP-CEPH.  All this strongly
> suggests a NA connection
> but it only comes into focus at this point because it is
> consistent with
> predictions from standard genealogy of an X with 6.5% NA..
>
> There is now some discussion about the C3 group (Y-DNA)
> having arrived in
> the Central Plains much later (c. 8 k ybp) than the Q
> dominated initial
> group (c. 14 k ybp).
> The entire migration situation may be much more complicated
> or different
> than our conceptualizations to date.  It appears by
> the archaeological and
> morphological record that in North American the C3 group
> (e.g., Plano group)
> may have largely replaced the earlier group (e.g., Clovis
> group).  They
> likely brought autosomal and x sequences that are not today
> found in South
> America.  Hence the only way we are going to see them,
> if there was a
> founder effect involving a second migration that did not
> reach South
> America, is by collection of reference samples from North
> America.
>
> There is also the region flanking the Xibo block toward the
> telomeric area.
> As you know it is about 12 Mb and does not match any group,
> no matter how
> low you set the bar.  It would make sense that this is
> a rare block, due to
> a founder effect and like mtDNA X2a is perhaps only to be
> found in the Great
> Lakes region - not elsewhere in the Americas or in
> Asia.  If found in NA of
> the central regions of North America only, then as with the
> otherwise
> mysterious X2a, it is NA.  I don't see how one could
> "unearth" this data any
> other way than collecting reference samples from the few
> regions where it is
> likely to be found.
>
> Anyway, I have learned that you are developing an expertise
> in this area
> that leaves almost all of us "in the dust" (a pioneer
> blazing new paths and
> all that).  So I guess we will see what your analyses
> show and go from
> there.
>
> David K. Faux.
>
> On Mon, Sep 28, 2009 at 6:25 AM, Anders Pålsen <>
> wrote:


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