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From: "Alfred A. Aburto Jr." <>
Subject: Re: [DNA] Haplogroup N1 versus A2 versus D3
Date: Fri, 03 Feb 2006 21:15:01 -0800
References: <5110464.1139000955572.JavaMail.root@elwamui-royal.atl.sa.earthlink.net>
In-Reply-To: <5110464.1139000955572.JavaMail.root@elwamui-royal.atl.sa.earthlink.net>


Your post is interesting to me too because my aunt was recently
classified by the Genographic project as mtDNA Haplogroup A. The markers
where she had mutations different than the "CRS" in the HVS-1 region were:
16104T
16172C
16223T
16240G
16290T
16319A
16362C

When I checked literature sources I found that 16223T, 16290T, 16319A
and 16362C always lined up better with haplotype A than
Amerindian haplogroups B,C, or D. The other markers I don't see very
often or at all (like 16104T). What was interesting to me when I looked
more carefully at your post was that in addition to the 4 markers above
you have the mutation 16111T which I also found almost always in the
literature for haplogroup A. My aunt doesn't have that mutation though!
What was interesting to me was that you have more markers that I see for
haplogroup A than my aunt, yet she was classified A and you are N1.

The thing that is going on here, as Bonnie said, is that the mtDNA
haplogroups are defined by more than the mutations in the HVS-1 region.
For example there is another mutation called +663HaeIII which with HVS-1
mutations 16223T, 16290T, and 16319A are used to define haplogroup A. I
found a website that shows these relationships (old but it help me
understand how the mtDNA haplogroups are defined --- I'm new to all this
too): http://www.stats.gla.ac.uk/~vincent/founder2000/motif.html

In this reference you'll see that that N1 is defined by the mutation
+10237Hph1 and the HVS-1 mutation 16223T. The other HVS-1 mutations that
we have mean something of course in defining subclades, but I think more
work needs to be done to figure that all out.

I'm hoping that when the Genographic Project says we are N1 or A, that
they have actually checked those other mutations in that web page above
(+663HaeIII for example for A or +10237Hph1 for N1)! It is not stated
anywhere though, so I am not sure.

My paternal grandmother (my aunts mother) is from north-central Mexico.
Also my paternal grandfather is from Mexico too (Puebla area) and my
surname is Basque (I know this from records available in church
documents in Spain ... Basque Country). I'm a Y chromosome J2 though,
which is a bit odd for a Basque person. But I have found recently that
there is an area in Northern Spain, adjacent to Basque Country, where J2
is a fairely high percentage of the population (Galicia Spain, and
Cantabria Spain).
Al

> wrote:

>First, I'd like to apologize for starting a new thread. I had somehow deleted Bonnie Schrack's post from my email and didn't know how to respond so that my latest post automatically goes in the original thread.
>
>Second, I'd like to thank Bonnie very much for her help, as set out below. I intend to follow up with FTDNA.
>
>Third, my mother's side of the family probably is a mix of Basque, Native American, and Spanish/Mexican. Until the 1950s, when many moved to Los Angeles, almost all of them had lived in and around Las Vegas, New Mexico. My grandmother had a Basque maiden name (Ulibarri) and the family lore is that an ancestor was from that region. More family lore is that there is Apache in our past, perhaps through the unfortunate taking and adoption of Apache children during the 19th(?) century. And almost all of that side of my family has Spanish/Mexican surnames, like Silva, Romero, and Ortega. So, A or A2 seems like a good possibility to me.
>
>Finally, is it unusual to have 11 HVR-1 mutations?
>
>Thanks everyone.
>
>George
>
>----------------
>
>From: Bonnie Schrack <>
>Subject: Re: [DNA] Haplogroup N1 versus A2 versus D3
>Date: Fri, 03 Feb 2006 09:47:18 -0500
>
>Dear friend (we don't know your name),
>
>This is very interesting. The Genographic Project uses a limited amount
>of Coding Region testing, as well as the HVR testing, which you've
>reported the results of (above). The Coding Region mutations are the
>ones that actually determine which mtDNA haplogroup you belong to. We
>can often, but not always, tell which haplogroup a person is in, if they
>have HVR1 mutations typical of that group. But HVR1 mutations are not
>definitive, and there may be confusing overlap between the typical HVR1
>mutations found in different haplogroups.
>
>In the Genographic Project, they can't afford to test a large number of
>Coding Region sites, so people who are in one of the less common
>haplogroups may belong to a clade for which they don't test the Coding
>Region site which would define it.
>
>I checked an important paper on the N macrohaplogroup, Phylogeny of
>Mitochondrial DNA Macrohaplogroup N in India, Based on Complete
>Sequencing: Implications for the Peopling of South Asia, Am. J. Hum.
>Genet. 75:966–978, 2004, but the extensive phylogenetic tree diagrams
>did not show very many HVR1 mutations corresponding to haplogroup N1. I
>am interested in this haplogroup, since the one I belong to, haplogroup
>I, is now recognized to be a branch of N1.
>
>Probably he will answer your query before too long, but one of your best
>sources for more information may be Ian Logan and his mtDNA pages, here:
>http://www.ilbg18230.pwp.blueyonder.co.uk/mtdna.htm
>http://www.ilbg18230.pwp.blueyonder.co.uk/discussion/hap_N.htm
>http://www.ilbg18230.pwp.blueyonder.co.uk/discussion/hap_N_asian.htm
>
>The only way to be completely sure of where you fit in would be to have
>a full mtDNA sequence done, which is quite expensive. But in the
>meantime, there are a couple of other options:
>1) Upgrade to the mtDNA Plus test from FTDNA, to get your HVR2 sequence.
>This can be very important in pointing you to the correct haplogroup and
>clade.
>2) Once you have studied the papers and data on mtDNA, and have
>identified one or more clades that are the most likely candidates for
>you, find a key Coding Region mutation that defines the clade, and have
>Thomas Krahn of DNA-Fingerprint test that specific site in the Coding
>Region. He will test any 100 bases that you specify. Write to me for
>more information if interested.
>
>In the meantime, if I were you, I would write to FTDNA (who do the
>testing for the Genographic project), and strongly request to know the
>exact results of your Coding Region tests that were done on your sample
>(give them your ID number). It seems that currently, you do have good
>reason to question whether you belong in N1, A2, or another haplogroup.
>Don't be satisfied with a lower-level employee if they don't understand
>and answer your question; keep asking until you get an answer. Go to the
>top, if necessary.
>
>If you could tell us as much as you know about the geographic and ethnic
>origin of your maternal line, it would help to determine which of these
>haplogroups is most probable in your case.
>
>Best of luck in your research,
>
>Bonnie Schrack
>
>http://www.ancientrootsresearch.com/Hap-I/Hap-I-home.html
>
>

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