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gihanga.rwanda
06-14-2019, 02:57 PM
A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans out of Africa

Abstract


Present-day humans outside Africa descend mainly from a single expansion out ∼50,000-70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we re-investigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y-chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000-100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300-81,000 years ago (latest date for FT lineage expansion outside Africa - earliest date for the D/D0 lineage split inside Africa), and most likely 50,300-59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.

https://www.genetics.org/content/early/2019/06/13/genetics.119.302368

I havenít had any time to read through the study but wanted to be the first one to post about it. Iosif Lazaridis has already tweeted about it.

thejkhan
06-14-2019, 04:47 PM
D0 might as well be a back migration to Africa from Levant along with E. There's a real DE* from Syria among ftdna customers -- one that diverged before D and E split.

Megalophias
06-14-2019, 05:17 PM
About bloody time!


D0 might as well be a back migration to Africa from Levant along with E. There's a real DE* from Syria among ftdna customers -- one that diverged before D and E split.
How do you know this? Has his Big Y been completed and the results made public?

Chad Rohlfsen
06-14-2019, 05:31 PM
At a minimum, they have Y-111

DE-M145

https://www.familytreedna.com/public/Lebanon-Syria-DNA/default.aspx?section=yresults

thejkhan
06-14-2019, 05:37 PM
About bloody time!


How do you know this? Has his Y-Full been completed and the results made public?

He has been previously tested for 4 mutations only (Big-Y pending) -- M145+, M203+, M174-, M96-

Being both M174- and M96-, he was assigned DE*.

On a second thought, I shouldn't assume his line diverged before D, E split. It could be a pre-D or a pre-E, with certain clade defining mutations missing (-ve).

gihanga.rwanda
06-14-2019, 05:45 PM
He has been previously tested for 4 mutations only (Big-Y pending) -- M145+, M203+, M174-, M96-

Being both M174- and M96-, he was assigned DE*.

On a second thought, I shouldn't assume his line diverged before D, E split. It could be a pre-D or a pre-E, with certain clade defining mutations missing (-ve).

His whole sequence would need to be analyzed. Syrians and other groups in the Levant can have minor West/Central African ancestry due to the slave trade and other historic events.

Megalophias
06-14-2019, 06:03 PM
On a second thought, I shouldn't assume his line diverged before D, E split. It could be a pre-D or a pre-E, with certain clade defining mutations missing (-ve).
Yes, D0 is also M174-, so the Syrian guy could be D0 as well, or not. His Big Y is being processed now, I believe.

Pylsteen
06-14-2019, 06:07 PM
We consider sharing of a single SNP as
a recurrent mutation in different lineages and interpret
the Nigerian chromosomes as lying on the D lineage,
diverging from other D chromosomes at 71,400 years
ago (Figure 1C), very soon after its divergence from E at
73,200 years ago
(...)
The three D0 chromosomes are distinguishable from one
another, and have a coalescence time of ~2,500 years
(Figure 1C), consistent with their collection from
different villages, languages, ethnic backgrounds, and
paternal birthplaces (Weale et al. 2003).


That's quite some time of wandering around..

TuaMan
06-14-2019, 06:17 PM
That's quite some time of wandering around..

Exactly why I don't think this really tells us much about where DE or CT formed. Hopefully these guys or some other group tests those Tibetan DEs some time soon.

ybmpark
06-14-2019, 06:27 PM
It will be funny if the few Chinese DE's turn out to be E0.

Megalophias
06-14-2019, 06:40 PM
It will be funny if the few Chinese DE's turn out to be E0.
I was just thinking that. :biggrin1:

But I'm not sure those Tibetan DE* are real. There were only a few, tested for only 1 SNP, and not found again in larger studies afterward, so could just be a false negative. (Unless someone knows of more recent finds I don't?)

K33
06-14-2019, 09:20 PM
(cross-post from discussion thread) From the paper: Haplogroup CT split keeps getting pushed back...now estimated at 101kya.

CT's split probably represents the latest that Basal Eurasian could have split from Basal African lineages, no?

https://i.imgur.com/u0ixDra.jpg?1

Lank
06-15-2019, 10:52 AM
Finally we can resolve those West African "DE*" lineages, which turn out to diverge fairly close to the DE root, albeit on the branch leading to D. So DE is now split between E, which is mainly African, and D/D0, which is African/Asian.

The recent TMRCA of the different West African D0 lineages is not surprising. Even the most important West African Y-DNA lineage, E-M2 (https://www.yfull.com/tree/E-M2/), has a ~14 kya YFull TMRCA. Other West-Central African lineages like E2b (https://www.yfull.com/tree/E-M98/) and E1a2 (https://www.yfull.com/tree/E-Z958/) are not that much older. What is clear is that West-Central Africans descend from some population(s) carrying divergent Y-DNA DE lineages. I would agree with the authors of this paper that the overall weight of the evidence indicates the original Y-DNA DE male lived somewhere in Africa, but we can't exclude the possibility that they may have ancestors who lived in the Middle East sometime in the 50-125 kya time interval.


I was just thinking that. :biggrin1:

But I'm not sure those Tibetan DE* are real. There were only a few, tested for only 1 SNP, and not found again in larger studies afterward, so could just be a false negative. (Unless someone knows of more recent finds I don't?)
The authors also raise this possibility:


Thus the combination of Y phylogenetic structure and dating of the out-of-Africa migration based on the 45,000-year-old Siberian fossil (Fu et al. 2014) favors the third scenario (Figure 2D) involving the migration out of C, D and FT between 50,300 years ago (lower bound of the FT diversification, Table S2) and 59,400 years ago (upper bound of the introgression; see Figure 3) which is in accordance with suggested models incorporating an African origin of the DE lineages (Underhill et al. 2001; Underhill and Roseman 2001). According to this interpretation, the reported Tibetan DE* chromosomes (Shi et al. 2008) would most likely represent back-mutations or genotyping errors at the one SNP used to define haplogroup D, but require further investigation.

It's a shame they did not sequence the "DE*" Tibetans. I'll see if YFull are able to add these D0 sequence to the YTree, it will be interesting to compare with the Syrian DE* when he is hopefully sequenced.

Kale
06-16-2019, 12:32 AM
(cross-post from discussion thread) From the paper: Haplogroup CT split keeps getting pushed back...now estimated at 101kya.

CT's split probably represents the latest that Basal Eurasian could have split from Basal African lineages, no?

That's not really a new result. See Karmin et al. 2015 (Figure 1)
https://www.ncbi.nlm.nih.gov/pmc/?term=25770088%5BPMID%5D&report=imagesdocsum

B and CT split at ~100kya
CF and DE split at ~73kya
C and F about 72kya
D and E about 69kya
Well within the intervals of the new study.

If Basal Eurasian exists, it hasn't left any super-basal lineages in it's descendant populations.
More likely to be chocked up as E or maybe G.

TuaMan
06-20-2019, 10:01 PM
If Basal Eurasian exists, it hasn't left any super-basal lineages in it's descendant populations.
More likely to be chocked up as E or maybe G.

I might have asked you this before, and sorry if I'm making you repeat yourself, but what's your take on Basal Eurasian as a whole? I know you're skeptical it's a real population, but I'm curious if you've fleshed out an alternative explanantion exactly.

alchemist223
06-21-2019, 03:18 AM
Apparently the DE* kit from Syria (130501) has been upgraded from DE-M145* to D-FT75. He tested positive for SNPs FT75 and F974.

Ebizur
06-21-2019, 10:44 AM
Apparently the DE* kit from Syria (130501) has been upgraded from DE-M145* to D-FT75. He tested positive for SNPs FT75 and F974.YFull has listed F974 as a marker of haplogroup D, but it appears to be a somewhat unreliable SNP.

According to ISOGG, FT75 has been observed in D2, but, again, I am unsure of this SNP's reliability.

EDIT: Apparently, the ISOGG 2019 spreadsheet for Haplogroup D has already been updated to reflect the results of the recently published paper about Nigerian D. Former D2, which has been observed in the Philippines, is now D1b, and former D1b, which has been observed mainly in Japan (and, marginally, also in Korea, Micronesia, China, and Timor), is now D1a2. Thus, all current indications point to a presence of D2-FT75 (aka D0-FT75) in Nigeria, Saudi Arabia, and Syria.

TuaMan
06-21-2019, 10:50 AM
Apparently the DE* kit from Syria (130501) has been upgraded from DE-M145* to D-FT75. He tested positive for SNPs FT75 and F974.

How does he relate to the overall D phylogeny? I see F974 is currently a defining SNP for D on yfull but not FT75.

EDIT: Reading the D0 paper again, and these Nigerian samples share 7 SNPs with regular D, whereas this Syrian only has 2 tentatively. So this would make the Syrian an even more diverged sample than D0 right? The plot thickens...

Megalophias
06-21-2019, 04:08 PM
The SNPs shared between D0 and D1'2 are CTS11804, CTS9692, CTS8111, CTS3946, CTS4030, CTS4031, and CTS7583. F974 is not included, don't know if negative or no call. I guess we'll need to wait for complete results before we know if they're even related.

thejkhan
06-21-2019, 06:04 PM
The Syrian guy's D lineage got some new members in ftdna - 2 Saudis assigned FT76 which is downstream to FT75 - https://www.familytreedna.com/public/y-dna-haplotree/D .

VytautusofAukstaitija
06-21-2019, 06:31 PM
That's not really a new result. See Karmin et al. 2015 (Figure 1)
https://www.ncbi.nlm.nih.gov/pmc/?term=25770088%5BPMID%5D&report=imagesdocsum

B and CT split at ~100kya
CF and DE split at ~73kya
C and F about 72kya
D and E about 69kya
Well within the intervals of the new study.

If Basal Eurasian exists, it hasn't left any super-basal lineages in it's descendant populations.
More likely to be chocked up as E or maybe G.

I think we should expect somewhere down the line or in that particular instance, that many populations for whom we have austosomal descendants have had their ydna completely washed out. And at some point the same may have happened to their mtdna lines as well. This can be similar to the processes that removed such mtdna and even ychromosomal neanderthal ancestry - but with different causes seemingly. So I don't think every population we see should be invalidated or not by whether they have any ydna or mtdna that can be in any way possibly derived from them in present day or any later populations. Not to mention what the seemingly infinite possibilities borne out of any hint of auDNA turnover. Their are too many possibilities to link ydna or mtdna with a specific population due to such autosomal turnover being very quick for human lineages, where original populations ancestral to those very lineages not being found anywhere in the autosome, and can take place in the space of 3,000 years or less. And We're speaking in the tens of thousands and up to 300,000, 100,000, 50,000, and 60,000. And seeing how unexpected our much more densely studied and predictable 10,000 year post-Neolithic window of aDNA findings are, I find myself expecting the most unexpected for anything concerning human ancestry at those ages. We're already speaking of superarchaics, whether A00 may from another parallel species, and Neanderthal mtdna and/or ydna being introgressed from more basal and more HSS lineages.

Which is why I ultimately only put my faith in ancient dna. But sometimes, as with the Ibermaurusians - it only serves to make things more confusing and muddied.

alchemist223
06-22-2019, 12:13 AM
Roberta Estes just posted a summary on these updates on her blog:

https://dna-explained.com/2019/06/21/exciting-new-y-dna-haplogroup-d-discoveries/

thejkhan
06-22-2019, 01:46 AM
Roberta Estes just posted a summary on these updates on her blog:

https://dna-explained.com/2019/06/21/exciting-new-y-dna-haplogroup-d-discoveries/

Some interesting stuff from the link you posted - just so everyone can understand the relation between the Syrian (ftdna), Saudis (ftdna) and the 3 Nigerians (Haber et al.):

31082

So the Syrian is "basal" (i.e. earlier split) to the lineage (D0a or D2a) that leads to the Saudis and Nigerians.

TuaMan
06-22-2019, 01:55 AM
Most interesting of all is that these samples are D2, which has hitherto only been found in the Philippines. Amazing how such a small, ancient lineage is found on nearly polar opposite corners of the world.

thejkhan
06-22-2019, 01:59 AM
Most interesting of all is that these samples are D2, which has hitherto only been found in the Philippines. Amazing how such a small, ancient lineage is found on nearly polar opposite corners of the world.

The Filipino D is M174+, so it should be reclassified as D1b.

TuaMan
06-22-2019, 02:05 AM
The Filipino D is M174+, so it should be reclassified as D1b.

Is he the YF03778 kit on YFull? Are there any other confirmed D2s?

thejkhan
06-22-2019, 02:10 AM
YF03778 kit on YFull

Yes he's the M174+ "D2" I was talking about. It's probably the same clade as the "D2" defined by isogg (https://isogg.org/tree/ISOGG_HapgrpD.html).

TuaMan
06-22-2019, 02:13 AM
Yes he is M174+ . It's probably the same clade as the "D2" defined by isogg (https://isogg.org/tree/ISOGG_HapgrpD.html).

Yes, but ISOGG has two separate subclades, D2a and D2b, so presumably they must have some other sample(s) than the guy already on YFull, no?

thejkhan
06-22-2019, 02:16 AM
Yes, but ISOGG has two separate subclades, D2a and D2b, so presumably they must have some other sample(s) than the guy already on YFull, no?

Yeah they are relying on other samples from some paper - but you can be sure those are also from Philippines - check the "geographic distribution" section in isogg site for D.

TuaMan
06-22-2019, 02:20 AM
Yeah they are relying on other samples from some paper - but you can be sure those are also from Philippines - check the "geographic distribution" section in isogg site for D.

So you're assuming the other D2 samples would fall under the same clade as the M174+ YFull guy? Is there any way we can get a hold of the samples from ISOGG?

thejkhan
06-22-2019, 02:24 AM
So you're assuming the other D2 samples would fall under the same clade as the M174+ YFull guy? Is there any way we can get a hold of the samples from ISOGG?

YFull has not defined a clade for him yet since they need two samples with common SNPs to define a new clade - so he remains M174* on YFull.

I am indeed assuming the YFull guy is more closely related to the Filipino samples that are assigned D2 by isogg than to all other D samples in YFull.

Kale
06-23-2019, 11:48 PM
If E = African and D = Asian wasn't confusing enough...
Now we have the first split in D within Africa?
Certainly an interesting puzzle. Would be so simple if DE = North Africa, CT = Eurasia.
But somehow Asians ended up with D1 (is that what it would be called now?) with no special autosomal connection to North Africa at all.
Then again C and F seem to have coexisted alongside each other amongst the ancestors of Eurasians from ~75-55kya.
Maybe pre-D1 made it into the initial Eurasian pool within that timeframe and was just unlucky enough to drift out of the group that split off to become West Eurasians?

Ebizur
06-24-2019, 11:12 AM
If E = African and D = Asian wasn't confusing enough...
Now we have the first split in D within Africa?
Certainly an interesting puzzle. Would be so simple if DE = North Africa, CT = Eurasia.
But somehow Asians ended up with D1 (is that what it would be called now?) with no special autosomal connection to North Africa at all.
Then again C and F seem to have coexisted alongside each other amongst the ancestors of Eurasians from ~75-55kya.
Maybe pre-D1 made it into the initial Eurasian pool within that timeframe and was just unlucky enough to drift out of the group that split off to become West Eurasians?According to information posted on Roberta Estes' blog, the phylogenetic structure of currently known members of D-FT75 is (Syrian [Nigerian Saudi]), i.e. the deepest split is between one branch that has been observed both in West Africa and in the Arabian Peninsula and another branch that has been observed only in the Levant.

Kale
06-26-2019, 03:51 AM
That makes it much less confusing! :P

Jm8
06-26-2019, 07:35 PM
This is interesting.
A plausible scenario seems to be that: DE may have originated in Africa as the paper suggests, seemingly likely East Africa (with E also originating/diverging there and staying and with one branch, E1b1b, later leaving for the Near East). And the D/D0 split could also have happened in (or near) East Africa, with D going east to Asia, and with some D0 moving deeper into Africa eventually to West Africa (e.g. Nigeria) and other D0 moving toward the Middle East (and with D0, as far as we know, dying out in regions in-between—leaving a few derived remnant lineages in both Africa and the Near East)—It seems that its (D0's) origin might likely have been in between the regions where it is now found (i.e. possibly originating in East Africa/northeast Africa, in between West Africa and the Middle East/West Asia—it is now found deep in Africa on the one hand, and in the Middle East near Africa on the other).

It also seems possible that the Middle Eastern D0, or some of the Middle Eastern D0 (especially the Saudi Arabian) could be the result of African gene flow into the Near East in more recent times (as was sometimes suggested for the proposed DE there), the Arab slave trade being one episode of this, and there is evidence of small amounts of African gene flow in much of the Middle East (some of it deriving from West/central Africa specifically, which is where some D0 is found). Some of the slaves brought to the Middle East came from the Bantu ethnic groups of Eastern Africa (Kenya, Tanzania, etc) who had ancestry ultimately originating from the Bantu homeland around Cameroon, not far from southeast Nigeria where the Nigerian D0 is found (which is, I believe, the Cross River region, not far from the Bantu homeland). D0 is, like DE, now very rare today both in Africa and Asia (likely once being more widespread but having largely died out/been mostly replaced by other haplogroups).

It would be great though to find ancient y-dna from the relevant periods in various parts of Africa and Eurasia, preferably mesolithic or earlier (however likely that may be). Hopefully, at the least, the purported Tibetan "DE" (and basal Filipino D) will be analyzed soon.

Jm8
07-04-2019, 10:16 PM
Edit: "...DE may have originated in Africa as the paper suggests, seemingly likely East Africa (with E also originating/diverging there and mostly staying in Africa—with one branch, E1b1b, later leaving for the Near East"

ataneojr1
07-04-2019, 10:53 PM
There is a Ydna D* in Yfull from the Philippines.

Nebro
12-13-2019, 03:51 PM
The Haplogroup J expansion in the near east destroyed the original Haplogroup E and D diversity.
this studies are severely lacking, only ancient dna can lead to the true story.

thejkhan
12-13-2019, 11:09 PM
The Haplogroup J expansion in the near east destroyed the original Haplogroup E and D diversity.

Your guess is probably valid for E. But D0 in Western Eurasia likely faced an earlier near extinction for whatever reason, much like C1a. I say that because it has not been found in any Near Eastern aDNA.