Haplogroups A branches: A2 A3

[TanTin]

Phylogenetic history

Prior to 2002, there were in academic literature at least seven naming systems for the Y-Chromosome Phylogenetic tree. This led to considerable confusion. In 2002, the major research groups came together and formed the Y-Chromosome Consortium (YCC). They published a joint paper that created a single new tree that all agreed to use. Later, a group of citizen scientists with an interest in population genetics and genetic genealogy formed a working group to create an amateur tree aiming at being above all timely. The table below brings together all of these works at the point of the landmark 2002 YCC Tree. This allows a researcher reviewing older published literature to quickly move between nomenclatures.

A major shift in the understanding of the Y-DNA tree came with the publication of (Cruciani 2011). While the SNP marker M91 had been regarded as a key to identifying haplogroup BT, it was realised that the region surrounding M91 was a mutational hotspot, which is prone to recurrent back-mutations. Moreover, the 8T stretch of Haplogroup A represented the ancestral state of M91, and the 9T of haplogroup BT a derived state, which arose following the insertion of 1T. This explained why subclades A1b and A1a, the deepest branches of Haplogroup A, both possessed the 8T stretch. Similarly, the P97 marker, which was also used to identify haplogroup A, possessed the ancestral state in haplogroup A, but a derived state in haplogroup BT.[10] Ultimately the tendency of M91 to back-mutate and (hence) its unreliability, led to M91 being discarded as a defining SNP by ISOGG in 2016.[52] Conversely, P97 has been retained as a defining marker of Haplogroup BT.

In the publication in 2015 Monica Karmin used these samples for Hg A:

No Assembly_ID Short_ID Population Haplogroup
1 GRC13292545 #N/A Mbo A00
2 GRC13292546 #N/A Mbo A00
3 GS000016204-ASM ISR07 Ethiopian-Jews A3
4 GS000035247-ASM CongPy6 Congo-Pygmies A2

In haplogroup A we keep the A00, A0, and A1 definitions according to (Cruciani et al. 2011;
Mendez et al. 2013). Following Table S5 scheme we define four subclades (A2-A5) in the A2’5
clade defined by L419 (Figure S14).

In V62 .anno file A2 and A3 are not used. There are : A00, A0, A1a, and A1b1 .


The known branches of haplogroup A are A00, A0, A1a, and A1b1;
these branches are only very distantly related, and are not more closely related to each other than they are to haplogroup BT.

[TanTin]

The main question is: do you think A2/A3 are the same haplogroup as A00 A1 ?
Or A2/A3 should be considered as a different haplogroup ? In the middle between A and B ?
I have my reasons to consider that A2 and A3 are in the same group, that should be considered as separated haplogroup..

However we don't have extra letters between A and B, so there is not much choice under this naming convention.

Why do I think this is a separate Haplogroup ?
- it is the level or the percentage of Chimp related snips , that are shared / or changed at that level..

In general, there is a huge gap between Hg A and Hg B..
During this gap, the percentage of Chimp snips is dropping sharply .
Let say: A00 are still keeping 947 of the 1700 Chimp snips.

In A2/ A3 individuals : we find only 450 of these 1700 Chimp snips.

in Hg B: there are only 257 or half of the above ... from the initial 1700 Chimp snips.

That means: A2/A3 are exactly in the middle between Hg A and Hg B..
They can't be considered neither A, neigher B.
May be we can use AB or something else ?

[kolompar]

Well haplogroup names are just for convenience, it's all a big tree and it's arbitrary which branches get a name. But I agree I would redo the whole thing objectively, cut the tree at somewhere like 40k BC number of SNPs and take the branches there. Still if a new branch gets discovered that messes it up.
A2 and A3 are both under A1b in the latest ISOGG naming if I understand right and that's your point. There shouldn't be differing number of Chimp SNPs unless branches had different rate of mutations. In this case it's probably just more derived SNPs covered from other haplogroups in 1240k.

[TanTin]

Hg A1b1  has a significant distance from A00. If we count this distance  as  a "number of shared snips with chimpanzee",  the A1b1  group is loosing half of the shared Chimp variants presented at A00.
This is a really big difference.
That means also  the time difference between A00 and A1b1  is important.
We may compare the distance A00 - A1b1  with the distance between Chimp and A00.
And the distance from A00 to B is near the same as between Chimp and A00.

And you may also notice that the decrease of the Chimp variants across the haplogroups is proportional by  2 . (Geometric progression * 1/2)

[kolompar]

But you're using 1240k for these calculations, right? There really shouldn't be a significant difference in chimp variants, all modern humans should be the same millions of years removed from chimp. (Unless maybe if they were selected for, but no, it's just 1240k having less A SNPs.)

[TanTin]

But you're using 1240k for these calculations, right? There really shouldn't be a significant difference in chimp variants, all modern humans should be the same millions of years removed from chimp. (Unless maybe if they were selected for, but no, it's just 1240k having less A SNPs.)

Here is the data:
link
(bed/bim/fam files )
It is 38k for Y chr.

[kolompar]

Ok but why do you think it's not simply differences in the coverage of each haplogroup's SNPs? Everything should descend from Y-Adam around 300k years ago, how would some haplogroups get more chimp SNPs since then? These are SNPs on the non-recombinant region of the Y chromosome.

[TanTin]

Ok but why do you think it's not simply differences in the coverage of each haplogroup's SNPs? Everything should descend from Y-Adam around 300k years ago, how would some haplogroups get more chimp SNPs since then? These are SNPs on the non-recombinant region of the Y chromosome.

The most ancient haplogroups will keep the highest number of chimp snps.
With the time some of these  chimp snps will mutate to non-chimp snps, and the opposite is also true: some non-chimp snps may revert back to  chimp snps.
You can use %  chimp snps to determine the Hg age.