Phylogeography of the human Y chromosome haplogroup E3a

[beyoku]

Phylogeography of the human Y chromosome Haplogroup E3a


F. Cruciani1, B. Trombetta1, D. Sellitto2, C. Nodale1, R. Scozzari1;
1Sapienza Università di Roma, Rome, Italy, 2Consiglio Nazionale delle Ricerche, Rome, Italy.

The Y chromosome specific biallelic marker DYS271 defines the most common haplogroup (E3a) currently found in sub-Saharan Africa. A sister clade, E3b (E-M215), is rare in sub-Saharan Africa, but very common in northern and eastern Africa. On the whole, these two clades represent more than 70% of the Y chromosomes of the African continent. A third clade belonging to E3 (E3c or E-M329) has been recently reported to be present only in eastern Africa, at low frequencies.

In this study we analyzed more than 1,600 Y chromosomes from 55 African populations, using both new and previously described biallelic markers, in order to refine the phylogeny and the geographic distribution of the E3a haplogroup.
The most common E-DYS271 sub-clades (E-DYS271*, E-M191, E-U209) showed a non uniform distribution across sub-Saharan Africa. Most of the E-DYS271 chromosomes found in northern and western Africa belong to the paragroup E-DYS271*, which is rare in central and southern Africa. In these latter regions, haplogroups E-M191 and E-U209 show similar frequency distributions and coalescence ages (13 and 11 kyr, respectively), suggesting their involvement in the same migratory event/s.

By the use of two new phylogenetically equivalent markers (V38 and V89), the earlier tripartite structure of E3 haplogroup was resolved in favor of a common ancestor for haplogroups E-DYS271 (formerly E3a) and E-M329 (formerly E3c). The new topology of the E3 haplogroup is suggestive of a relatively recent eastern African origin for the majority of the chromosomes presently found in sub-Saharan Africa.

I believe we can compare the two trees:

Revised E1b1.PNG

This New (old) paper was from the ESHG 2008 abstracts. We are in 2010 and this paper has not been released and these New markers "V38" and "V89" are MIA not to be found anywhere and not listed on ISOGG's snp list (wile Cruciani's other ) V series SNP's are.)

Cruciani in this paper separates "East Africa" from "Sub Saharan Africa" therefore When he is speaking for the "relatively recent "eastern African" origin for the majority of the chromosomes presently found in "Sub-Saharan Africa" it is easy to assume he is speaking of E-M2. This study also shows that E-m2 has a closer relationsship not with E-M215 but E-M329 which is quite rare:

(Somebody else can do the legwork )

Anyway, I am quite sure with some of the Horn African E1b1* reaching levels at almost 20% some if it could be this "V28" and "V89" marker. Also some of the West African E1b1* is probably of this marker.

This New study sampled 55 African populations, his older study with the similar title:
"Phylogeography of the human Y chromosome haplogroup E3b"
Sampled 28 African Populations, 22 of which were Sub Saharan.
Source

This study, plus Haplogroup IV = E-M2

32.1keita_tab02Af.gif

And this:
Egypt-Ydnastudy.jpg

=
Migration Map of Haplogroup E1b1a.jpg

Any thoughts?

[Aware_Dog]

Good stuff. I wish you can get the whole paper. Also, I don't see, in your phylogenetic diagram above how E1b1c (E-M329) and E1b1a (E-M2) can have a 'sisterly' relationship when a common SNP has NOT YET been found that binds the two together. Or has it been found and I'm not just aware of it?
The common bond between E1b1*, E1b1a, E1b1b and E1b1c is E-PN2 AFAIK.

[beyoku]

Good stuff. I wish you can get the whole paper. Also, I don't see, in your phylogenetic diagram above how E1b1c (E-M329) and E1b1a (E-M2) can have a 'sisterly' relationship when a common SNP has NOT YET been found that binds the two together. Or has it been found and I'm not just aware of it?
The common bond between E1b1*, E1b1a, E1b1b and E1b1c is E-PN2 AFAIK.

I sort of went on this:

By the use of two new phylogenetically equivalent markers (V38 and V89), the earlier tripartite structure of E3 haplogroup was resolved in favor of a common ancestor for haplogroups E-DYS271 (formerly E3a) and E-M329 (formerly E3c)

Tripartite (I assmed knew what the word was but looked it up anyway)

Tripartite (adj) : Composed of or divided into three parts.

E3a, E3b, E3c = that earlier "Tripartite". Since he says it was resolved "in favor" of something else, a "common ancestor" of 2 of these markers (E-M2 and E-M329) I can only assume that (V38 and V89) is the common ancestor of E-M2 and E-M329 (Why else would he bring it up in making that conclusion?).

E-PN2* = E1b1* = E3*

So that leaves us with :

E > PN2 > M215 > M35 >
E > PN2 > V38/89 > M329
E > PN2 > V38/89 > M2

INSTEAD OF
E > PN2 > M215 > M35
E > PN2 > M2
E > PN2 > M329

wait.....am i confusing myself
********** Note: I revised that graphic myself. That is NOT from the study.

[Aware_Dog]

wait.....am i confusing myself
********** Note: I revised that graphic myself. That is NOT from the study.

No, I understand well what you are saying now after re-reading it, it makes sense as does the graphic. I just can't find these SNP's (V38 and V89) on ISOGG tho. Also, if this was true it would mean that the the common ancestor to E-M329 and E-M2 would be sisterly to E1b1b and thus ISOGG should have already alpha-neumerically renamed this common ancestor to E1b1a and the formerly E1b1a should have been renamed to E1b1a1 and E1b1c should have been renamed to E1b1a2, but it's been two years since this has been found and they haven't done so yet, strange, very strange....

[Ezana]

No, I understand well what you are saying now after re-reading it, it makes sense as does the graphic. I just can't find these SNP's (V38 and V89) on ISOGG tho. Also, if this was true it would mean that the the common ancestor to E-M329 and E-M2 would be sisterly to E1b1b and thus ISOGG should have already alpha-neumerically renamed this common ancestor to E1b1a and the formerly E1b1a should have been renamed to E1b1a1 and E1b1c should have been renamed to E1b1a2, but it's been two years since this has been found and they haven't done so yet, strange, very strange....

ISOGG doesn't do the renaming, do they? It was my understanding that they adopt the earliest naming of a mutation (or renaming) from a peer-reviewed study, a la Karafet et al. 2008.

[Aware_Dog]

ISOGG doesn't do the renaming, do they? It was my understanding that they adopt the earliest naming of a mutation (or renaming) from a peer-reviewed study, a la Karafet et al. 2008.

Good point, they may not directly rename them but these new SNP discoveries should have at least been communicated to the ISOGG Y-DNA Working group and included in the SNP index here, at the very least, considering that there have been Newer SNP's found after 2008 that are already reflected like M434-Underhill et al (2009) , V88 -Cruciani et al (2010), etc....

[beyoku]

This is a study I would pay to see. I am not sure why it doesn't exist. Emailed the author : No luck.

[Aware_Dog]

lol, Beyoku this is good homework you have given here.

I can't make heads or tails of this, for one, the Abstract of the presentation is for real and listed in the ESHG website:

http://www.abstractsonline.com/viewer/SearchResults.asp

Abstract


I can only think of 3 possibilities here:

1) A new peer-reviewed paper is in the works and hasn't been published yet with this putative topology of E1b1??

2) The statement "By the use of two new phylogenetically equivalent markers (V38 and V89), the earlier tripartite structure of E3 haplogroup was resolved in favor of a common ancestor for haplogroups E-DYS271 (formerly E3a) and E-M329 (formerly E3c)." indeed does not leave much ambiguity in its interpretation other than directly not stating that the earlier "tripartite" Structure was resolved into a "bipartite" one or maybe possibly one or a few Typos were made when printing the Mutation names ??

3) The entire Abstract submission is a hoax ??

[beyoku]

1) If this was the case though i would expect to see the abstract at your normal sites were abstracts and articles are found. While an abstract exist within the European Society of Human Genetics ( eshg2008@medacad.org -- anyone?), the real substance is somewhat "Vaporware" we can only find info on it from one place and that place ONLY : ESHG

2)..Cosign

3) I would hope not.