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Passa
11-07-2015, 05:22 PM
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141510

It seems that the DE* cases found by such authors as Pour et al. back in 2013 are in fact M174+.

Passa
11-07-2015, 05:58 PM
If this is confirmed, I have already an hypothesis:

Premises

If these are indeed D cases, it means that there's no more real DE* cases left in Africa. While there's still a possibility for Tibetan DE* cases to be in fact M174+, there is a real Syrian DE(xM174,M96) left.

Hypothesis

1) DE* originated in West Eurasia
2) D* and E* both originated in West Eurasia (see high-D Ainu and their West Eurasian autosomal tendence)
3) Both of them migrated towards Africa and East Asia
4) D failed in Africa and survived only in small isolated pockets; E failed in East Eurasia. Today E dominates Africa and D is restricted to isolated/mountainous populations in East Asia and South Asia

Lank
11-07-2015, 08:34 PM
Now the question is, how come this study finds D-M147, when seperate studies have previously found DE* in Nigeria (http://www.genetics.org/content/165/1/229.full), Guinea-Bissau (http://www.biomedcentral.com/1471-2148/7/124), and the Carribean (http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22090/abstract), in addition to the African-Americans with DE* at 23andMe? What's more likely, that they are all wrong or that this study got something wrong?

Kale
11-09-2015, 06:09 PM
Now the question is, how come this study finds D-M147, when seperate studies have previously found DE* in Nigeria (http://www.genetics.org/content/165/1/229.full), Guinea-Bissau (http://www.biomedcentral.com/1471-2148/7/124), and the Carribean (http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22090/abstract), in addition to the African-Americans with DE* at 23andMe? What's more likely, that they are all wrong or that this study got something wrong?

Because most older papers don't test for D...they test for YAP+ (which is present in both D and E) and then various types of E.

Lank
11-09-2015, 07:27 PM
Because most older papers don't test for D...they test for YAP+ (which is present in both D and E) and then various types of E.
Wrong. I just checked the first study I linked that first reported DE* in Nigeria. They tested for D-M174.


The position of these 5 Nigerians on the Y chromosome tree has been confirmed by repeated typing for all the known UEP markers immediately above and below node a in Figure 1 (YAP, M145, M203, M174, M96, P29, and SRY4064) as well as for five additional UEP markers (92R7, M9, M20, 12f2, and SRY10831) as shown in Figure 1. The asterisk in DE* indicates that it is potentially, but not definitely, paraphyletic relative to one or both of groups D and E (Figure 2).

So they did test for D-M174 (as does 23andMe, which has assigned African-American samples to DE*). They make the caveat that these lineages may not be paraphyletic, which I would actually say they most likely are not.

We just need high-resolution testing to know exactly how they relate to D-M174 and E-M96, and if they may be closer to either of these. But they did test D-M174 and got a negative result, unlike this new study.

Megalophias
11-09-2015, 09:54 PM
This study genotyped a new Benin sample and did a meta-analysis of previous data from the literature. The only samples listed as D-M174 in the paper are half a dozen DE(xE) from Ansari Pour et al 2013, and I see nothing in the paper to suggest that they re-genotyped those samples.

I think they just mislabelled DE* as D-M174.

Passa
11-10-2015, 03:16 PM
This study genotyped a new Benin sample and did a meta-analysis of previous data from the literature. The only samples listed as D-M174 in the paper are half a dozen DE(xE) from Ansari Pour et al 2013, and I see nothing in the paper to suggest that they re-genotyped those samples.

I think they just mislabelled DE* as D-M174.

No. This is figure S6, showing the SNPs they tested in the 43 populations:

6610

Megalophias
11-10-2015, 04:44 PM
No. This is figure S6, showing the SNPs they tested in the 43 populations:

6610

Where does it say they *tested* those SNPs?

"In this study, we performed an up-to-date Y-chromosomal genotyping of four Beninese populations [populations D2-D5, n=120] which were sampled more than two decades ago. We compared the Y-SNP and Y-STR data of these samples with other Y-chromosomal data from the Bight of Benin and surrounding areas published in the literature (till July 2015). As each published study used its own Y-SNP panels based on different version of the Y-chromosomal phylogeny, we developed an extensive method to combine new and old Y-SNP data without losing information. Finally, we also analysed the Y-STR and Y-SNP data of the YRI HapMap sample to test its regional representativeness."

Passa
11-10-2015, 04:53 PM
Where does it say they *tested* those SNPs?

"In this study, we performed an up-to-date Y-chromosomal genotyping of four Beninese populations [populations D2-D5, n=120] which were sampled more than two decades ago. We compared the Y-SNP and Y-STR data of these samples with other Y-chromosomal data from the Bight of Benin and surrounding areas published in the literature (till July 2015). As each published study used its own Y-SNP panels based on different version of the Y-chromosomal phylogeny, we developed an extensive method to combine new and old Y-SNP data without losing information. Finally, we also analysed the Y-STR and Y-SNP data of the YRI HapMap sample to test its regional representativeness."

S6 Fig. Schematic representation of the phylogeny of Y-chromosomal subhaplogroups based on the binary markers which could be analysed for 43 West-African population samples given in S1 Table.

The nomenclature of the subhaplogroups is based on the terminal mutation that defines them, as proposed in van Oven et al. [40]. *Paragroups: Y-chromosomes not defined by any downstream-examined mutation.
doi:10.1371/journal.pone.0141510.s006
(TIF)

Megalophias
11-10-2015, 05:04 PM
S6 Fig. Schematic representation of the phylogeny of Y-chromosomal subhaplogroups based on the binary markers which could be analysed for 43 West-African population samples given in S1 Table.

The nomenclature of the subhaplogroups is based on the terminal mutation that defines them, as proposed in van Oven et al. [40]. *Paragroups: Y-chromosomes not defined by any downstream-examined mutation.
doi:10.1371/journal.pone.0141510.s006
(TIF)

It says "which could be analyzed", not "which we genotyped". Where does it say that they re-genotyped the samples from Ansari Pour et al? It only says that they did a *statistical analysis* of the samples from the literature.

"In this study, Y-chromosomal haplotypes from four Beninese populations were determined and a global meta-analysis with available Y-SNP and Y-STR data from populations along the Bight of Benin and surrounding areas was performed.... Fourth, Y-SNP data of 2198 individuals from 38 populations of Ghana, Benin, Nigeria and Cameroon were compared using the phylogeny presented in S5 Fig (see S6 Table for haplogroup frequencies).... Finally, the Y-SNP data for 2616 individuals from all 43 West-African populations in the collection were compared following the phylogeny of S6 Fig." There would be no need to do all these different phylogenies if they had tested all the samples using their own panel of SNPs.

ADW_1981
11-10-2015, 05:04 PM
If this is confirmed, I have already an hypothesis:

Premises

If these are indeed D cases, it means that there's no more real DE* cases left in Africa. While there's still a possibility for Tibetan DE* cases to be in fact M174+, there is a real Syrian DE(xM174,M96) left.

Hypothesis

1) DE* originated in West Eurasia
2) D* and E* both originated in West Eurasia (see high-D Ainu and their West Eurasian autosomal tendence)
3) Both of them migrated towards Africa and East Asia
4) D failed in Africa and survived only in small isolated pockets; E failed in East Eurasia. Today E dominates Africa and D is restricted to isolated/mountainous populations in East Asia and South Asia

I don't understand the motive of "back to Africa", why couldn't DE have split within Africa? Perhaps the Eastern Asian remnants of D-M174+ are the only ones who survived that particular OOA expansion?

Shaikorth
11-10-2015, 05:18 PM
If this is confirmed, I have already an hypothesis:

Premises

If these are indeed D cases, it means that there's no more real DE* cases left in Africa. While there's still a possibility for Tibetan DE* cases to be in fact M174+, there is a real Syrian DE(xM174,M96) left.

Hypothesis

1) DE* originated in West Eurasia
2) D* and E* both originated in West Eurasia (see high-D Ainu and their West Eurasian autosomal tendence)
3) Both of them migrated towards Africa and East Asia
4) D failed in Africa and survived only in small isolated pockets; E failed in East Eurasia. Today E dominates Africa and D is restricted to isolated/mountainous populations in East Asia and South Asia

Ainus didn't seem to have West Eurasian tendencies according to this (http://www.genetics.org/content/early/2015/10/20/genetics.115.178673.full.pdf+html). They're pretty much pure East Eurasian, though perhaps an old branch.

Megalophias
11-10-2015, 05:23 PM
Ainus didn't seem to have West Eurasian tendencies according to this (http://www.genetics.org/content/early/2015/10/20/genetics.115.178673.full.pdf+html). They're pretty much pure East Eurasian, though perhaps an old branch.
The Ainu did have a marginally greater affinity to West Eurasians in D stats:
D(Yoruba, Sardinian; Ainu, X)
Ami: -0.0035 -1.331
Atayal: -0.0043 -1.481
Dai: -0.0057 -2.305
Lahu: -0.0049 -1.907
Sherpa: -0.0031 -1.249

Consistent but not really significant.

Shaikorth
11-10-2015, 05:30 PM
The Ainu did have a marginally greater affinity to West Eurasians in D stats:
D(Yoruba, Sardinian; Ainu, X)
Ami: -0.0035 -1.331
Atayal: -0.0043 -1.481
Dai: -0.0057 -2.305
Lahu: -0.0049 -1.907
Sherpa: -0.0031 -1.249

Consistent but not really significant.

Was that in the supplements? I didn't have access to that, do you have a link? The usual threshold for significance is 3, so it makes sense they didn't mention it in the main paper.

Megalophias
11-10-2015, 05:42 PM
Was that in the supplements? I didn't have access to that, do you have a link? The usual threshold for significance is 3, so it makes sense they didn't mention it in the main paper.
I don't have it either, but someone posted a link to some of the supplementary info in the recent comments at Eurogenes.

Yeah, it is pretty borderline, it may not mean anything. There is no such pull toward MA-1 or Amerindians, so it doesn't seem to be ANE.

Shaikorth
11-10-2015, 06:19 PM
I don't have it either, but someone posted a link to some of the supplementary info in the recent comments at Eurogenes.

Yeah, it is pretty borderline, it may not mean anything. There is no such pull toward MA-1 or Amerindians, so it doesn't seem to be ANE.

Okay, found it. Ainu have statistically insignificant but consistent pull towards West Eurasians compared to Sherpa, but also towards Papuans who are more distant from West Eurasians than East Eurasians are. OTOH nothing towards Amerindians or Neanderthals/Denisovans. I would really like to see those stats with an ape outgroup instead of Yoruba to ascertain it is not related to African population history.

Farroukh
07-04-2019, 11:59 AM
Exciting New Y DNA Haplogroup D Discoveries! (https://dna-explained.com/2019/06/21/exciting-new-y-dna-haplogroup-d-discoveries/)


https://a.radikal.ru/a24/1907/19/d05135e0278a.jpg (https://radikal.ru)