searching for L3

[Eryl08]

Hi,
I've found out that I'm L3 haplogroup and would like to know anything about what these sequences might mean:
16124C, 16166G, 161215G, 16223T, 16299G, 16325C, 16519C
Eryl

[lgmayka]

I presume you meant 16215G, not 161215G. In fact, I presume you are mitosearch user SH6B9.

As you already know, mitosearch doesn't show any matches for you. The worse news, judging from another L3, is that even if/when you get matches, they won't tell you much because the matching people don't know their original African countries of ancestry either. This appears to be an industrywide problem: a lack of African country-specific entries in genetic databases, that would enable you to find your African country of origin.

This is a genetic genealogy mailing list with some eminent professors and other researchers on it:

http://lists.rootsweb.com/index/other/DNA/GENEALOGY-DNA.html

I frankly suggest that you join this mailing list (at least temporarily), and post your DNA results to it. Make clear that the regular published databases simply do not have the African country-specific entries you need, and ask whether someone can somehow check the additional university databases that researchers obviously must be doing in order to publish their papers on African DNA.

[lgmayka]

I asked about L3 on the mailing list I mentioned earlier. Here are the responses so far:
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from [email protected]
The largest collection of African data is of course at African Ancestry, with
13,000+ records from the parts of African most involved in the slave trade.
Some of their data was gathered at their own expense, and they keep the data
proprietary and charge a premium price to amortize that cost. If a person has
mtDNA results from another company, African Ancestry will check their database
for a fee of $200. [I have no quarrel with that, BTW -- after all, they took
the initiative and the risk to do that -- but I can't help but wonder if they
could get a bigger volume of business if they reduced the price.]

Otherwise, people will need to dig into the primary literature and see if
they spot samples idential or similar to their own. Google Scholar
http://scholar.google.com is a good place to search, perhaps with a search strategy like
this

african mtdna L3

Some citations will have free full-text online. For example, Salas "The
Making of the African mtDNA Landscape" (using 2847 samples covering the entire
continent) is available at

http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=385086&blobtype=pdf

However, one should be cautious about over-interpreting a match. I rather
suspect African mtDNA haplotypes would be like European haplotypes: if a
haplotype is common, it will be found in many different locations, and if a haplotype
is rare, the location where *your* ancestors came from may not have enough
samples for it to show up. For example, my mtDNA haplotype is not too common, but
it is found among the Basques and in Finland -- but my ancestors may never
have lived in either of those places.

Another resource might be the African-American genealogy website
http://afrigeneas.com. I typed L3 into their search engine, and there are a number of
posts.

Ann Turner
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from [email protected]
Just to add a brief comment about L3 to what Ann has said.

The Haplogroup L3 can be split into 6 subgroups - by
using coding region mutations.

For example by determining:
L3b - using 3450
L3d - using 921
L3e - using 2352
L3f - using 15944d
L3h - using 4388
L3i - using 7645

If we do learn by looking at other Haplogroups, I suggest that most conclusions based on HVR1 & 2 mutations alone do not give reliable answers.

Clearly having the whole mtDNA genome tested (the MEGA test)
is expensive, but it is very important when advising on origins of persons in Haplogroup L3 to know the subgroup.

Perhaps over the next couple of years we will learn if the Genographic samples are being tested for their subgroups.

Ian

(More about all this on www.brookingsociety.org.uk/mtdna.htm )
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from [email protected]
To add to what has been said here and by Ann Turner....

www.argusbio.com has a full length mtDNA genome sequencing special for $399.

http://www.argusbio.com/store/product_info.php?products_id=29

But the African Ancestry analysis might be cheaper.

Another alternative would be:

1. Use mitosearch, the mtDNA concordance, and published papers to develop you best estimate of your haplogroup and seeing where the HVR1 & HVR2 sequences and haplogroups are found..
2. Develop a strategy of testing for your sub-group based on Step 1. -- Most likely, followed by second most likely, etc.
3. Have DNA-FP test "any 100 bp" to determine your subhaplogroup ($93.00 undiscounted). That is suppose you conclude in Step 1 that you are most likely L3d. DNA-FP could then test 900-999 for you. If you were correct, you have only spent the cost for this test. If not, you could test your second likeliest estimate.
At the 50% discount level, 100 base pairs would be
Isolation 70.68
1st 100 bp of your choice 93.00
Total 163.68
50% off 81.84
5% off that 77.75 [all the batches I coordinate get this discount]
kit 2.48 [not eligible for discount]

Any subsequent 100 base pairs at 50% off would add 44.18 to the 77.75. You can order one in one batch and the next when you get the results, or send in your strategy and pay only for the ones they end up testing.

This is something you will want to do only if you have a pretty good idea what subgroups you are NOT. I don't know L3 well, but in some mtDNA haplogroups, the appearance of some HVR1 or HVR2 mutation (or the lack thereof) will eliminate a haplogroup. So you might keep that in mind as well.

I coordinate the DNA-FP batches if you want to go that route.

Anne

[lgmayka]

The bottom line here, I think, is that anyone of African-American ancestry who is looking for a simple, 1-stop shopping solution should probably consider

http://www.africanancestry.com/

This company specializes in African ancestry along both the patrilineal and matrilineal lines, and offers various deals and packages for individuals and families.

If you have already spent money (e.g., in the Genographic project) to find out that your haplogroup is L3, do not think that your money has been "wasted." Rather, for a small initial investment you have confirmed that your matrilineal ancestry is indeed African, and that the services of AfricanAncestry.com will indeed be helpful and appropriate for you. AfricanAncestry.com may even give you a discount on their pricing if you forward your results to them. They will still have to perform further tests to identify your subclade, and probably your HVR2 mutations, in order to match you with a specific African country or tribe; and of course, as one of the mailing list experts says, part of your payment is to take advantage of AfricanAncestry's proprietary research into African DNA.

[lgmayka]

Interestingly, AfricanAncestry.com seems to need only the HVR1 results. For $200 + $10 shipping, they can apparently take your HVR1 results (plus haplogroup designation?) and tell you what African country(ies) match.

http://www.africanancestry.com/ExistDataOrderForm.pdf

Nevertheless, they claim excellent accuracy:

http://www.africanancestry.com/05faq.htm

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Our results are quite accurate. For about 85% of the people we test we find identical matches in our database. For the remaining people, we find closely related lineages with greater than 95% confidence. Our database is the most comprehensive resource of African lineages available.
...
We cannot necessarily tell you the particular tribe with which you share genetic ancestry. However, we can tell you the present-day country of Africa with which your lineage shares genetic ancestry.
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[lgmayka]

By the way, have you already joined the L3 Project?

http://www.familytreedna.com/public/L3/

[vraatyah]

Hi,
I've found out that I'm L3 haplogroup and would like to know anything about what these sequences might mean:
16124C, 16166G, 161215G, 16223T, 16299G, 16325C, 16519C
Eryl

There are 2 published sequences that match your type, not exactly but closely enough:

SWGDAM, African-American
124-166-215-223
73-152-263-315.1C
(complete control region sequence)
1 sample of 1096

Graven 1995, Mandenka (Eastern Senegal)
124-166-215-223-325 (between 16007 and 16380)
73-152-263-309.1C-315.1C (between 61 and 389)
3 samples of 119

As to the more distant types (I mean "124-166-223 + something else" which falls into L3bd) they appeared in

1) Rando et al 1998 paper (Senegalese samples, including Wolof)
2) Jackson 2005 (Sierra-Leone)
3) Forensic dataset of the University of California (Sierra-Leone)
4) Coia 2004 (Cameroon)
5) Watson 1996 (Yoruba, Nigeria)
6) Plaza 2003, Rando 1998 (Berber groups of Morocco and Tunissia)

Some authors used to classify sequences with 166 as L3b (instead of L3d of more recent papers) and none published sufficient RFLP information.

Regards,
Valery

[Eryl08]

Thanks all,

Thanks all for the information.
I have limited resources therefore I probably won't be able to access AfricanAncestry.com services but I am interested in anything I can find from the results of my test. Indeed, I was tested by National Geographic genographic and it's good to hear that money wasn't wasted, since it was a family member who paid for my test.

This family member also believes from what she has read in the results that it's possible that my family origin would be west African and not east African. She says I would probably be from the Bantu tribe. Another family member says its a possibility of east Africa because of my hair and features that aren't quite like most African Americans.

This is all very hard to determine to me. The furthest in my family tree I can go back is to my great grandmother (who I met when I was a child), that was supposedly Indian descent and the physical traits were very much that.

I see this is going to be a tough one to tackle, next we are getting my nephew for my father's side. My father was very light skinned and brown eyed, and there's no clues to his family history beyond his mother and father who were both the same as him.

again, thanks
Eryl

[lgmayka]

Eryl, Valery's post mentions a pretty close match for you in Senegal (west Africa). Without further research or expense, perhaps that is the most likely hypothesis.

Good luck on your nephew's test.

[lgmayka]

By the way, in case you didn't already know this:

Your mtDNA test only looked at your mother's mother's mother's mother(...). Your nephew's test will look at his father's father's father's father(...).

[Eryl08]

mtdna

Yes, I knew that about one being from the mother's side and another from the father's. I'll aim in the direction of Senegal. Thanks for mentioning it.
Eryl

[37PZK]

L3f

Does Anybody Have Any Info On L3f? Thanks

[lgmayka]

As I mentioned in another thread, this has a little:

http://www.pubmedcentral.gov/articlerender.fcgi?artid=1182259

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A few haplogroup L3f types in America match those of eastern Africans—again, however, never uniquely; they are also shared by western Africans, southeastern Africans, or both. At the same time, several L3f types are shared uniquely by western Africans only. L3f is likely of eastern African origin (Salas et al. 2002), but the derived subhaplogroup L3f1 is also present in western Africa, and it is this component that is most commonly found in Americans.
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