Y-Haplogroup A Project- Background

Administrators

Background

Welcome to the Y-Haplogroup A DNA Project! All members of Y-haplogroup A are encouraged to join, and we welcome all whose haplogroup has been estimated as A, to learn where you fit in.

Haplogroup A is unique in that all other human haplogroups spring from its primal branches.  Corresponding with this status is the fact that it, and haplogroup B, are found in their greatest concentrations and diversity among the few peoples of Africa who have kept alive the original hunting and gathering way of life, practiced by our ancestors ever since the dawn of human history. 

The New Haplogroup A Phylogenetic Tree is Here!
 
After long labors, we have a new version of the phylogenetic tree for Haplogroup A. It incorporates many discoveries made over the past year, including those published in papers by Cruciani and Batini, as well as those made by our friend Thomas Krahn at the FTDNA lab in Houston. We have much to look forward to, as a great deal of testing is about to happen, which will generate many more discoveries. This tree will then be modified in accordance with those findings.

Far more SNPs have been discovered than can be firmly placed on the tree at this time. ISOGG needs to maintain rigorous standards, in order for our tree to be something everyone can rely upon, and that is what has earned it increasing respect around the world. Each SNP must be found positive in more than one person, and those positive must not be closely related. Otherwise, the SNP has the Under Investigation status, unless years have gone by without any sign of a second positive sample, in which case the SNP is labeled “private.” These are minimal standards, but they are not always easy to meet when we are dealing with rare clades. I ask for your help in finding and testing the samples we need to confirm as many SNPs as possible.

We have been extremely fortunate in having some outstandingly generous donors to this project, who have made it possible for two Walk Through the Y orders to have been placed in a short time.  Results for these are hoped for early this spring. Individual SNP orders are also being made for project members whose samples will help us clarify the structure and understand how their haplotypes are related to the others.

In addition, the University of Arizona scientists, Drs. Tatiana Karafet and Michael Hammer, with whom I've been corresponding, have donated four Haplogroup A samples to Thomas Krahn’s lab for WTY sequencing!  These represent the clades A0a-P114, A2a1a1-M114, A2a1a2-P28, and A2a1a3-P262.  Their WTY test results should make it possible for us to place many more SNPs on the tree, and give us much better data with which to compare the test results of our project members.

Without further ado, then, here is the new ISOGG HaplogroupA tree for 2012:
  • A0 - V152, V164, V166, V196

•              A0*

•             A0a - P114

  • A1 -  V168, V171, V174, V203, V238, V241, V250

•              A1*

•              A1a - M31, P82, V4, V14, V25 

•              A1b – V221, P108

•           A2 - V50,V82, V198, V224

o            A2*

o            A2a - M14, M23, M29/P3/PN3, M71, M135,M141, M206, M276/P247, M277/P248, MEH1, P4, P5, P36.1, Page71, Page87, Page95

•              A2a*

•              A2a1 - M6, M49/Page41, M196

▪             A2a1*

▪              A2a1a - M212

o            A2a1a*

o            A2a1a1 - M114

o            A2a1a2 - P28

o            A2a1a3 - P262

•             A3 - M32

o            A3*

o            A3a - M144, M190/Page35, M220, M305, P100,P289, Page50, Page10

•              A3a*

•              A3a1 – M51

▪              A3a1*

▪             A3a1a - P71, P102, P291

•              A3a2 – M13, M63, M127, M202, M219, Page53,Page77/V10

▪              A3a2*

▪              A3a2a -M118

•             BT – SRY10831.1, M42, M91, M94, M139, M299, P97, PK1, V29, V31, V59, V64, V187,V202, V235


Notes:  

  •    “A0” is being used to emphasize that this constitutes a haplogroup distinct from A1 and downstream clades, although for practical reasons, the letter A will still be used in its name, following the precedent of the addition of L0 and its subclades to the mtDNA phylogenetic tree.

  •    There is some uncertainty about the position of M14, M29/P3/PN3, M71, M135, M141, M206, M276/P247, M277/P248, MEH1, P4, P5, P36.1, Page71, Page87, and Page95, since although they have been considered  equivalent to M23 in the past, they have not yet been tested in the A2* sample in which V50, V82, etc, are derived and M23 is ancestral.

  •    The above nomenclature allows for the A1a, A2, and A3 clades to keep their present names, instead of A2 and A3 being renamed to A1b1 and A1b2. 

  •    BT is shown on this tree, though it is not considered to be a part of Haplogroup A, in order to make it clear that as a brother clade with A2 and A3, BT and all other haplogroups are downstream of A1b.


SNPs Under Investigation:

  •    L896 – This SNP was found by Thomas Krahn in kit N38376, which is negative for SRY10831.1, M42, M91, and P97 (in their new definition as BT SNPs), and negative for M23, M32, P82, V151, V168, V171, V221, and V50, thus excluding it from all known A clades.  A WTY for this kit is pending, which should clarify the position of L896.

  •    L600, L601, L602, L603, L604 – These SNPs were found in an A2* individual by Thomas Krahn.  They need to be tested in more A2 samples to determine where they belong in the tree.

  •    P305 was previously considered equivalent to P114, but it needs to be tested now to find out where it belongs in relation to the V-SNPs.

  •     V148, V149, V150, V151, V153, V154, V157, V158, V159, V161, V162, V165, V167, V169, V170, V172, V173, V176, V177, V181, V190, V195, V223, V225, V229, V233, V239 – These SNPs were found in an A0a-P114+ sample by Cruciani (2011). Forthcoming WTY results should help determine where they belong in the tree.

  •    V15, V26, V28, V30, V40, V48, V53, V57, V58, V63, V67, V191, V201, V204, V214, V215, V236 – These SNPs were found in an A1a-M31+ sample by Cruciani (2011). They need to be tested in more A1a samples to determine where they belong in the tree.

  •    Page110 is downstream of Page41, Page71, Page87, and Page95, but it needs to be tested to find out where it belongs in relation to the other A2 SNPs.  It may be private.

  •    V60, V61, V70, V72, V79, V80, V81, V180, V188, V192, V200, V218.1, V228, V242 – These SNPs were found in an A2a1a3-P262 sample by Cruciani (2011). They need to be tested in more A2 samples to determine where they belong in the tree.

  •    V97 – This SNP was found in an A2a1a1-M114 sample by Trombetta (2010). It needs to be tested in more A2 samples to determine where it belongs in the tree.

  •    V1, V51, V56, V66, V67, V155, V156, V160, V193, V194, V230, V243 – These SNPs were found in an A3a2-M13* sample by Cruciani (2011). They need to be tested in more A3 samples to determine where they belong in the tree.

  •    V89, V98, V123, V124 – These SNPs were found in an A3a2-M13* by Trombetta (2010).  They need to be tested in more A3 samples to determine where they belong in the tree.

  •    L411, L412, L414, L418, L419,  L420, L421, L422, L423, L424, L425, L426, L427, L428, L429, L430, L436, L437, L438, L439, L440, L441, L442 – These SNPs were found in an A3a2-M13 WTY participant. They need to be tested in more samples from A, B, and other haplogroups, to determine where they belong in the tree.


Private SNPs:

  •    M28 – found in a single A3-M32+ sample from Ethiopia
  •    M59 – found in the same sample from Ethiopia
  •    M171 – found in a single A3a2 (the former A3b2, positive for M13 or its equivalents) sample from Sudan.
                                *                                *                                *                                *                                *
Earlier updates:

Sponsored SNP-testing is underway!

A generous donor, Dr. Hamma Bachir Ahmed, has stepped forward to assist our project in sorting out some of the unique, unclassified haplotypes in our project, which will at the same time help to clarify the little-understood structure of the A haplogroup. His donation is making it possible to test three to five key SNPs in each of four project members, whom he has selected as likely to cover the widest range in the phylogenetic tree.  We envision several more project members being included, but we need others to step forward and contribute at least a little toward our goal of learning more about the way haplogroup A is organized, and where our most unusual and rare haplotypes fit into it.

Sponsored Testing Chart

Kit no.

Previous SNP results

New SNP results

Pending SNP results

Planned SNP orders

Funding Status

N14468

SRY10831.1-, M23-, M32-, P108-

 

P114, P82, P97, M91, V151

V221

Funded

181787

M23-, M32-, M42-, P108-, P82-, P97+, SRY10831.1-

M91+, L604+, V151-

P114

V221

Funded

N38376

(M42-, M23-,M32-, P108-, P97+

 

P114, P82, M91, V151

V221

Funded

A1a, TBA

(M31+, P108+)

 

 

M91, P97, V30, V151, V221

Funded

A2, TBA

(M23+)

 

 

M91, P97, V30, V151, P108, M32, V221

A3,TBA

(M32+)

 

 

P97, V30, V151

B, TBA

(M42+, M181+)

 

 

M91, P97, V30, V151, P108, M32, M23

                        *                       *                       *                       *                       *                       *                       *                       *

The A haplogroup has become the focus of lively discussion lately, as new research has shown that its diverse branches form the roots of the human family tree. The 2011 paper by Cruciani, A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa, estimates that the first communities of modern humans split into the two branches, A1b and A1a, about 142,000 years ago, with A1a being the father of all other haplogroups. All the other groups split from A1a about 108,000 years ago, according to this paper,while A2 and A3 split off from the rest of the world’s haplogroups about 105,000 years ago. Haplogroup B then split from the rest of the haplogroups about 75,000 years ago. Click here for a diagram of these branchings. There is much more to be said about the discoveries in this study, which will have implications for the entire human phylogenetic tree. Stay tuned!

Because of its tremendous age, great diversity and variance are found amongst the haplotypes of the branches and subclades of haplogroup A.

While some members, especially of A3b2, can be found outside of Africa, the great majority of haplogroup A members are either African, or members of the African diaspora who have only lived outside of Africa for a few hundred years.

There have been many new SNPs discovered in haplogroup A in the paper mentioned above, a good number through the WTY (see below) and a few also through direct-to-consumer Illumina chip testing. We hope to help build momentum for more of these SNPs to become available from FTDNA for testing, so that we can discover where any individual from the A haplogroup fits within the new branchings of the phylogenetic tree.

While some of our project members have had negative results for the previously known SNPs that defined clades A1, A2, and A3, we hope that when more new SNPs become available, we’ll see more positive results and consequently, more clarity about where project members belong in the tree. There may be a few previous SNP results that will need to be re-examined.

We very much hope to have one or more project members tested through the Walk Through the Y, a research project directed by Thomas Krahn of FTDNA’s Advanced Genomic Research lab, which seeks the discovery of new SNPs. One member of A3b2 has already participated, with numerous SNPs being found. We hope to find a member of A1b as the next participant, or someone who is A1* or A*. In the meantime, members of the project need to be tested for some of the newly discovered SNPs. Some of them are probably not unique to A3b2. They could help clarify the structure of the whole haplogroup, if we're lucky.

Bonnie Schrack, administrator of the J Haplogroup project, has volunteered to work for some time with the Haplogroup A project, since the project's first admin, Vincent Vizachero, won't have adequate time to devote to its future development. We encourage any Haplogroup A members who would like to take an active role in the project to contact us, so that we can benefit from your contributions. Please contact Bonnie with any ideas, suggestions, questions, or problems you may have.

Another database

There is a free public database provided by the Sorenson Molecular Genealogy Foundation, SMGF.org. They have traveled the world collecting donated samples. It so happens that they have a very large number of samples from Cameroon, one of the countries that happens to be relatively rich in haplogroup A members, as well as from Nigeria, Benin, Mali and Ghana. If project members would like to try some searches there, they may find some good and interesting matches. Please let Bonnie know of any matches you find. This information will be valuable to our research on the distribution of haplogroup A. Have fun!

General Fund

Current balance: $295.50

Type Amount Date Donor Note KitNum Donation Type
Credit $30.00 1/26/2012       Unknown
Debit $29.00 1/23/2012     N64496 Unknown
Debit $145.00 1/23/2012     N71150 Unknown
Credit $100.00 1/18/2012 Piorek and Swies SNPs (of "chromosomal Adam"?)   Unknown
Debit $125.50 1/13/2012     N64496 Unknown
Debit $99.00 1/10/2012     N15176 Unknown
Debit $750.00 1/9/2012     N14468 Unknown
Credit $80.00 1/9/2012 Peter S Leggett     Individual
Credit $50.00 1/9/2012 S. Molek, Tropie WTY N14468   Unknown
Credit $100.00 1/6/2012 Janik, Nowy Sacz WTY N14468   Unknown
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Project Stats

Statistic Type Count
Distinct mtDNA Haplogroups 16
Distinct Y-DNA Confirmed Haplogroups 7
Distinct Y-DNA Predicted Haplogroups 8
Family Finder 10
Maternal Ancestor Information 41
Maternal GEDCOMs Uploaded 6
mtDNA 25
mtDNA Full Sequence 6
mtDNA Plus 15
mtDNA Subgroups 0
Paternal Ancestor Information 60
Paternal GEDCOMs Uploaded 18
Predicted Y-DNA Haplogroups 48
Total Members 90
Unpredicted Y-DNA Haplogroups 1
Unreturned Kits 0
WTY 3
Y-DNA Deep Clade (After 2008) 14
Y-DNA Subgroups 17
Y-DNA111 13
Y-DNA12 85
Y-DNA25 71
Y-DNA37 69
Y-DNA67 47