New study concentrating on E-M2 and E-M78

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eastara

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A new study has just come out "The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages"
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1393-5
It concentrates on several Y haplogroups common in Africa, from the Es on the M2 and M78 branches. I would not comment on the overall results relevant to African population, but just found interesting data in the Supplementary files. It seems new samples from Europe and the Balkan were sequenced, so we will have extra scientific data regarding those branches.

Regarding the African M2 branch, it is found only among Portuguese and not elsewhere in Europe.
Now for the M78, the most numerous is, of course V13. It is found with highest percent among Albanians with 33.82%, however the number of samples is small, 68 only. Second are Romanians with 26.67%, but again the number of samples is 30 only.
Bulgarians are 20.93%/129 samples, Macedonians 17.15%/99, Greek 11.32%/433, Hungarians 9.43%/106, etc.
Other branches under M78 on the Balkans are found mainly among Greeks - V12 and V65, One Bulgarian is V12 and one Macedonian V22. In other parts of Europe different branches under M78(xV13) are common only among South Italians and Spaniards.
 
Some interesting conclusions about R1b-V88. I think it's as was suspected.


" The presence of two nested R-V88 basal European clades can be related to the high frequencies of R-V88 internal lineages in the central Sahel assuming a movement from Europe toward the central Sahel across northern Africa. In turn, considering the trans-Saharan distribution and the “star-like” topology of the sub-clade R-V1589 (branch 233), it is likely that this lineage rapidly expanded in the lake Chad area between 5.73 and 5.25 kya and moved backward to northeastern Africa across the Saharan region "

"Outside Africa, both A3-M13 and R-V88 harbour sub-lineages geographically restricted to the island of Sardinia and both seem to indicate ancient trans-Mediterranean contacts. The phylogeography of A3-M13 suggests that the direction of the movement was from Africa to Sardinia, while R-V88 topology indicates a Europe-to-Africa migration. Indeed, our data suggest a European origin of R-V88 about 12.3 kya, considering both the presence of two Sardinian R-V88 basal clades (R-M18 and R-V35) and that the V88 marker arose in the R-M343 background, which in turn includes Near-Eastern/European lineages [52]. It is worth noting that the arrival of R-V88 in the Sahara seems to have occurred between 8.67 and 7.85 kya (considering as an upper limit the time estimates of the last node including a European-specific lineage, while the lower limit is the coalescence age of all the African-specific lineages), refining the time frame of the trans-Saharan migration proposed in previous studies [37, 56]. The route of R-V88 toward the lake Chad basin probably passed through northeastern Africa rather than Arabia, considering the absence of R-V88 in the Horn of Africa. Interestingly, both A3-M13 and R-V88 European sub-clades coalesced in ancient times (> 7.62 kya for A3-M13/V2742 and between 12.34 and 8.67 kya for R-V88/M18 and R-V88/V35) (Additional file 2: Figures S2 and S5). So it is possible that both clades were widespread in southern Europe, where they have been replaced by the Y haplogroups brought by the following recurrent migration waves from Asia [57]."

 
These data suggest that the presence in northern Africa of sub-Saharan patrilineages was not due to recent contacts but probably occurred in more ancient times, possibly during the Green Sahara period considering the coalescence ages of the clades. Our findings seem to be at odds with genome-wide studies [42, 43, 59, 60] reporting a recent relevant sub-Saharan genetic component in modern northern African populations, mainly attributed to the Arab slave trade. This apparent discrepancy between inferences based on Y chromosomal and autosomal data could be the consequence of a sex-biased sub-Saharan contribution to the northern African gene pool that occurred in historical times. Indeed, it is known that the trans-Saharan Arab slave trade involved twice as many servile women as men (almost the reverse of the Atlantic slave trade ratio). Moreover, few male slaves left descendants, whereas female slaves were imported in northern Africa as household servants and as concubines and their offspring were born free, thus contributing to the local gene pool [54, 61]. Thus, we suggest that the Arab slave trade mainly contributed to the mtDNA and autosomal gene pool of present-day northern Africans, whereas the paternal gene pool was mainly shaped by more ancient events. This hypothesis is in line with genome-wide data obtained from three ancient Egyptian mummies (dated between ~ 2.5 and 2 kya) showing a not negligible ancient sub-Saharan component (~ 6–10 %) [44]."

"The multifurcated structure of the E-M2 is suggestive of a first demographic expansion, which occurred about 10.5 kya, at the beginning of the last Green Sahara (Fig. 2; Additional file 2: Figure S4). After this initial expansion, we found that most of the trans-Saharan lineages within A3-M13, E-M2 and R-V88 radiated in a narrow time interval at 8–7 kya, suggestive of population expansions that may have occurred in the same time (Fig. 2; Additional file 2: Figures S3, S4 and S6). Interestingly, during roughly the same period, the Saharan populations adopted pastoralism, probably as an adaptive strategy against a short arid period [1, 62, 63]. So, the exploitation of pastoralism resources and the reestablishment of wetter conditions could have triggered the simultaneous population expansions observed here."
 
These results are fascinating! This suggests that we should (or maybe will) be finding more genetic connections between the northern and the southern coasts of the Mediterranean in ancient, pre-Neolithic times, and that R1b (V88 or otherwise) and even, at least regionally, A were a lot more common in Mesolithic Europe than we thought.
 
Angela said:
Some interesting conclusions about R1b-V88. I think it's as was suspected.


" The presence of two nested R-V88 basal European clades can be related to the high frequencies of R-V88 internal lineages in the central Sahel assuming a movement from Europe toward the central Sahel across northern Africa. In turn, considering the trans-Saharan distribution and the “star-like” topology of the sub-clade R-V1589 (branch 233), it is likely that this lineage rapidly expanded in the lake Chad area between 5.73 and 5.25 kya and moved backward to northeastern Africa across the Saharan region "

"Outside Africa, both A3-M13 and R-V88 harbour sub-lineages geographically restricted to the island of Sardinia and both seem to indicate ancient trans-Mediterranean contacts. The phylogeography of A3-M13 suggests that the direction of the movement was from Africa to Sardinia, while R-V88 topology indicates a Europe-to-Africa migration. Indeed, our data suggest a European origin of R-V88 about 12.3 kya, considering both the presence of two Sardinian R-V88 basal clades (R-M18 and R-V35) and that the V88 marker arose in the R-M343 background, which in turn includes Near-Eastern/European lineages [52]. It is worth noting that the arrival of R-V88 in the Sahara seems to have occurred between 8.67 and 7.85 kya (considering as an upper limit the time estimates of the last node including a European-specific lineage, while the lower limit is the coalescence age of all the African-specific lineages), refining the time frame of the trans-Saharan migration proposed in previous studies [37, 56]. The route of R-V88 toward the lake Chad basin probably passed through northeastern Africa rather than Arabia, considering the absence of R-V88 in the Horn of Africa. Interestingly, both A3-M13 and R-V88 European sub-clades coalesced in ancient times (> 7.62 kya for A3-M13/V2742 and between 12.34 and 8.67 kya for R-V88/M18 and R-V88/V35) (Additional file 2: Figures S2 and S5). So it is possible that both clades were widespread in southern Europe, where they have been replaced by the Y haplogroups brought by the following recurrent migration waves from Asia [57]."[FONT=&]

[/FONT]
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R1b-V88 indeed probably has a European origin, in the Iron Gate.
But I don't understand how they link the 12.3 ka origin with movements from Sardegna.
Mesolithic Sardegna was virtually uninhabited.
An arrival of R1b-V88 subclades in Sardegna with Cardium Ware 8 ka is possible.
But in the mean time R1b-V88 folks must have been roaming around elsewhere too.
Many Sardegnian genomes are known, that makes it easy, but that doesn't mean we always have to conclude for Sardegnian origins.
 
eastara said:
A new study has just come out "It is found with highest percent among Albanians with 33.82%, however the number of samples is small, 68 only. Second are Romanians with 26.67%, but again the number of samples is 30 only.
Bulgarians are 20.93%/129 samples, Macedonians 17.15%/99, Greek 11.32%/433, Hungarians 9.43%/106, etc.
Other branches under M78 on the Balkans are found mainly among Greeks - V12 and V65, One Bulgarian is V12 and one Macedonian V22.
Click to expand...

Where are you getting these numbers? The Eupedia haplogroup by countries page has different percentages.

Also, how can we get the new data from for each population?
 
bicicleur said:
R1b-V88 indeed probably has a European origin, in the Iron Gate.
But I don't understand how they link the 12.3 ka origin with movements from Sardegna.
Mesolithic Sardegna was virtually uninhabited.
An arrival of R1b-V88 subclades in Sardegna with Cardium Ware 8 ka is possible.
But in the mean time R1b-V88 folks must have been roaming around elsewhere too.
Many Sardegnian genomes are known, that makes it easy, but that doesn't mean we always have to conclude for Sardegnian origins.
Click to expand...

I didn't interpret the paper as saying that R1b-V88 originated or even was in Sardegna in the Mesolithic. It could have been picked up along the Cardial route, but isn't it also possible it arrived in the Chalcolithic with people from the Balkans?

I'm not so sure about this supposed movement of A3-M13 from North Africa to Sardegna either. It could have also come with the Neolithic.

It's just that because they've been so isolated, y lines that almost disappeared elsewhere survived in Sardegna.
 
Ownstyler said:
Where are you getting these numbers? The Eupedia haplogroup by countries page has different percentages.

Also, how can we get the new data from for each population?
Click to expand...

First, have in mind that Eupedia reports everything under E1b1b1, which is E-M35. This includes other branches under M78, not just V13, plus under M123, which are predominantly non European.

The data I was mentioning could be found in Additional file 1, Table S5.
It seems they had the full genomes by NGS in China of 104 Y chromosomes from their lab collection (77 of them belonging to the four trans-Saharan haplogroups), After identifying the SNPs of interest they further analysed samples from 7955 males from 145 worldwide populations (128 from our lab collection and 17 from the literature).
If somebody is interested to analyse the .bam files of the full Y genomes, they are available also on https://www.ebi.ac.uk/ena
 
Angela said:
Some interesting conclusions about R1b-V88. I think it's as was suspected.


" The presence of two nested R-V88 basal European clades can be related to the high frequencies of R-V88 internal lineages in the central Sahel assuming a movement from Europe toward the central Sahel across northern Africa. In turn, considering the trans-Saharan distribution and the “star-like” topology of the sub-clade R-V1589 (branch 233), it is likely that this lineage rapidly expanded in the lake Chad area between 5.73 and 5.25 kya and moved backward to northeastern Africa across the Saharan region "

"Outside Africa, both A3-M13 and R-V88 harbour sub-lineages geographically restricted to the island of Sardinia and both seem to indicate ancient trans-Mediterranean contacts. The phylogeography of A3-M13 suggests that the direction of the movement was from Africa to Sardinia, while R-V88 topology indicates a Europe-to-Africa migration. Indeed, our data suggest a European origin of R-V88 about 12.3 kya, considering both the presence of two Sardinian R-V88 basal clades (R-M18 and R-V35) and that the V88 marker arose in the R-M343 background, which in turn includes Near-Eastern/European lineages [52]. It is worth noting that the arrival of R-V88 in the Sahara seems to have occurred between 8.67 and 7.85 kya (considering as an upper limit the time estimates of the last node including a European-specific lineage, while the lower limit is the coalescence age of all the African-specific lineages), refining the time frame of the trans-Saharan migration proposed in previous studies [37, 56]. The route of R-V88 toward the lake Chad basin probably passed through northeastern Africa rather than Arabia, considering the absence of R-V88 in the Horn of Africa. Interestingly, both A3-M13 and R-V88 European sub-clades coalesced in ancient times (> 7.62 kya for A3-M13/V2742 and between 12.34 and 8.67 kya for R-V88/M18 and R-V88/V35) (Additional file 2: Figures S2 and S5). So it is possible that both clades were widespread in southern Europe, where they have been replaced by the Y haplogroups brought by the following recurrent migration waves from Asia [57]."
Click to expand...


fascinating :)
angela do you think haplogroup A is that old in sardinia ?
regards
Adam
 
kingjohn said:
fascinating :)
angela do you think haplogroup A is that old in sardinia ?
regards
Adam
[/B]
Click to expand...

The short answer is that I don't know. The long answer is that I'm not sure how you could determine when and how it arrived. I didn't comb through the supplement, but from this paragraph, the coalescence age is  >7.62 kya for A3-M13/V2742 .

So, could we be talking about 6,000 BC or around the time of the Neolithic? Could it have been very early in the Neolithic Near East and swept up in the migrations, and then straight to Sardegna, or even to the Balkans and then later to Sardegna in the Chalcolithic? I think that places like Sardegna can very easily shelter rare haplogroups that have drifted out of the gene pool in areas where there have been large scale migrations, as in the Middle East, for example, which was inundated with men with "J" lines.

I also didn't pore over the sources of the data. If the authors used the originally selected Sardinian samples from the isolated plateau, then I think it's probably no later than the Neolithic, or Chalcolithic at the most, because they're really a genetic isolate. Even the Romans couldn't absorb and assimilate them.
220px-Sardegna_Barbaria.png


If the samples were taken, and particularly this sample, from the southern coastal regions, then there are other possibilities. Sardegna was one of the few places in Italy, northwestern Sicily being the other, where the Carthaginians did have trading outposts and probably married or mated with some local women. Could it have come that late?

Although the studies indicate that the autosomal differences between the highlanders and the rest of the Sardinians are not significant, there are some, including ones indicating input from Yamnaya type people, and also some trace North African and even SSA. Y lines, of course, could very easily survive without any autosomal inpact at this point.

What I think is less plausible is that it has been there since the Mesolithic, having arrived directly from Africa. The signs of the Mesolithic there are not very robust. Even if it were, I think the populating of the island was predominantly from the Iberian and Italian peninsulas. That's been the consensus, I think. It's not impossible, as the currents from perhaps around Morocco might just allow it if the people were lucky, so I'd be willing to be persuaded.
 
i wonder what made the auther of this paper to decide that a3-m13 is
that old in sardinia
and not from Carthaginian for example ?
regards
adam

p.s
by the way e-m81 in sardinia could be linked to the punic Carthaginian rule of sardinia
 
kingjohn;532446[B said:
]i wonder what made the auther of this paper to decide that a3-m13 is
that old in sardinia
and not from Carthaginian for example [/B]?
regards
adam

p.s
by the way e-m81 in sardinia could be linked to the punic Carthaginian rule of sardinia
Click to expand...

Not to be pedantic, but there was no Punic/Carthaginian rule of the whole of Sardinia.

See:
https://en.wikipedia.org/wiki/History_of_Sardinia#Early_and_Classical_Antiquity

History_of_Sardinia
Carthaginian_Sardinia.JPG


As I mentioned above, no one, including the Romans, ever subjugated the Barbagia area from which most of the samples collected by Cavalli-Sforza come.

As to the bolded comment, I don't think they did. I interpreted their text to mean that the general direction of flow was from Africa to Europe, not specifically Africa to Sardinia in the Mesolithic.

Could you point me to the part of the text which leads you to believe that? Maybe I missed it.

However, I also don't know why you would single out the Carthaginian period, particularly if this sample came from the Barbagia. The Carthaginians had nothing to do with that area. Of course, as I said, I didn't check the geographical source of all the Sardinian samples. Knowing that would narrow the probabilities.
 
Here is Razib Khan's post on the paper. He focuses on the Chadic R1b...

https://www.gnxp.com/WordPress/2018...africa/?utm_source=dlvr.it&utm_medium=twitter

"There’s a lot of other Y lineages that are surveyed in this work, but in the supplements, the figure makes it clear that Sardinian R-V88 is basal to star-like African topologies. The implication here is that the African lineages derive from European ones."

The autosomal paper found Chad populations (though the one in question was not Chadic speaking) seem to share drift from Sardinians in particular. Looking at ancient genomes Early European Farmers seem to have been the primary donor population. Additionally, the coalescence of the African lineages seems to date to 5 to 6 thousand years before the present.


"Though not definitive, the association of Afro-Asiatic populations with R-V88 is strongly suggestive to me of the possibility that some western Near Eastern Farmers spoke Afro-Asiatic languages."

I'm not so sure of the latter.

Are they saying coalescence in the Neolithic, but it didn't expand to central Africa until the Bronze?
 
Angela said:
I didn't interpret the paper as saying that R1b-V88 originated or even was in Sardegna in the Mesolithic. It could have been picked up along the Cardial route, but isn't it also possible it arrived in the Chalcolithic with people from the Balkans?
I'm not so sure about this supposed movement of A3-M13 from North Africa to Sardegna either. It could have also come with the Neolithic.
It's just that because they've been so isolated, y lines that almost disappeared elsewhere survived in Sardegna.
Click to expand...
there is always this possibility too

attachment.php

View attachment 9737

that is the problem with studying modern population DNA - to many possibilities
 
bicicleur said:
there is always this possibility too

attachment.php

View attachment 9737

that is the problem with studying modern population DNA - to many possibilities
Click to expand...

Sorry, Bicicleur, it says invalid attachment.

As to your general point, I couldn't agree more. There are indeed a lot of possibilities if you're using yDna lines to try to figure out ancient migrations. That's why I'm leery of a lot of people's conclusions, and especially if they have an obvious agenda.

That's why it's become a sort of mantra with me that the real answers will only come with lots of ancient dna.

Perhaps that's why the authors of this paper kept it so general.
 
Angela said:
Not to be pedantic, but there was no Punic/Carthaginian rule of the whole of Sardinia.

See:
https://en.wikipedia.org/wiki/History_of_Sardinia#Early_and_Classical_Antiquity

History_of_Sardinia
Carthaginian_Sardinia.JPG


As I mentioned above, no one, including the Romans, ever subjugated the Barbagia area from which most of the samples collected by Cavalli-Sforza come.

As to the bolded comment, I don't think they did. I interpreted their text to mean that the general direction of flow was from Africa to Europe, not specifically Africa to Sardinia in the Mesolithic.

Could you point me to the part of the text which leads you to believe that? Maybe I missed it.

However, I also don't know why you would single out the Carthaginian period, particularly if this sample came from the Barbagia. The Carthaginians had nothing to do with that area. Of course, as I said, I didn't check the geographical source of all the Sardinian samples. Knowing that would narrow the probabilities.
Click to expand...

angela when they speak on 7.6ky that means that this certin branch of a3-m13 was in sardinia from 5600 bc this is neoliotic period
i never spoke about it as mesolithic one nor do they in the paper ......

i know there was punic carethegenian settlelmnts in the south and western part of the island

i thought the samples were taken from cagliary in south sardinia not barbagia {which as you mention is isolated area}
 
Angela said:
Sorry, Bicicleur, it says invalid attachment.

As to your general point, I couldn't agree more. There are indeed a lot of possibilities if you're using yDna lines to try to figure out ancient migrations. That's why I'm leery of a lot of people's conclusions, and especially if they have an obvious agenda.

That's why it's become a sort of mantra with me that the real answers will only come with lots of ancient dna.

Perhaps that's why the authors of this paper kept it so general.
Click to expand...

the map is about the obsidian trade, somewhere in the early neolithic

the authors didn't draw any solid conclusions, and yes, probably right so
I must admit though I did find it an interesting overview
but conclusions indeed can only be made with anciant DNA
 
kingjohn said:
angela when they speak on 7.6ky that means that this certin branch of a3-m13 was in sardinia from 5600 bc this is neoliotic period
i never spoke about it as mesolithic one nor do they in the paper ......

i know there was punic carethegenian settlelmnts in the south and western part of the island

i thought the samples were taken from cagliary in south sardinia not barbagia {which as you mention is isolated area}
Click to expand...

Well, regardless of where the sample was taken, then, the Carthaginians are irrelevant if it's dated to the Neolithic in Sardinia itself, yes?

The date of the earliest Neolithic in Sardinia, Cardial, is just around this time, so I suppose there could have been an overlap with any Mesolithic people who remained, but I think it's probably more likely this y line came with the Neolithic settlers, as I said initially.

If the E-M81 was from samples taken from Cagliari, then, yes, that line could be from Carthaginians, or maybe it was Saracen raiders from later in history. There are lots of possibilities. This is the problem with trying to use modern dna to assign "ethnicity" or a certain migration to the presence of certain y lines. Sometimes it's proven true, and sometimes it isn't.

Goodness, King John, you seem to have become infected with Azzurro's fascination with the Carthaginians. Well, I suppose if an Italian can so identify with the arch-enemy of Rome, it's possible. You'd have to identify with Titus to match that! :)

I certainly wouldn't take these minor y lines as necessarily having a direct correspondence with autosomal results. In the Dienekes K12 run, the Sardinians came out as 2.6% Northwest African. Yet, all he had were the samples generally from the Barbagia, so it's unlikely that had anything to do with any Carthaginians. At the same time, Otzi came out part NorthWest African too.

It just points out the limitations of Admixture runs based on modern clusters.

https://docs.google.com/spreadsheet...0SRE5L6ED2osPs9M/edit?hl=en_US&hl=en_US#gid=0

YtIUk8b.png
[/IMG]



Btw, I wasn't able to find info on where "particular samples" were taken. Could you point me to where you got that info?
 
Angela said:
Well, regardless of where the sample was taken, then, the Carthaginians are irrelevant if it's dated to the Neolithic in Sardinia itself, yes?

The date of the earliest Neolithic in Sardinia, Cardial, is just around this time, so I suppose there could have been an overlap with any Mesolithic people who remained, but I think it's probably more likely this y line came with the Neolithic settlers, as I said initially.

If the E-M81 was from samples taken from Cagliari, then, yes, that line could be from Carthaginians, or maybe it was Saracen raiders from later in history. There are lots of possibilities. This is the problem with trying to use modern dna to assign "ethnicity" or a certain migration to the presence of certain y lines. Sometimes it's proven true, and sometimes it isn't.

Goodness, King John, you seem to have become infected with Azzurro's fascination with the Carthaginians. Well, I suppose if an Italian can so identify with the arch-enemy of Rome, it's possible. You'd have to identify with Titus to match that! :)

I certainly wouldn't take these minor y lines as necessarily having a direct correspondence with autosomal results. In the Dienekes K12 run, the Sardinians came out as 2.6% Northwest African. Yet, all he had were the samples generally from the Barbagia, so it's unlikely that had anything to do with any Carthaginians. At the same time, Otzi came out part NorthWest African too.

It just points out the limitations of Admixture runs based on modern clusters.

https://docs.google.com/spreadsheet...0SRE5L6ED2osPs9M/edit?hl=en_US&hl=en_US#gid=0

YtIUk8b.png
[/IMG]



Btw, I wasn't able to find info on where "particular samples" were taken. Could you point me to where you got that info?
Click to expand...


azurro is a good man
he uploaded me and my family ftdna rqaw data to my heritage
and he didn't have to
i remmber is kind hourt :)
now to the subject i score 14% north central italian in gencove { yes i know this site is joke and use imoputation but still so maybe i do have some titus in me}

there was a research in sardinia who found 5.6% e-m81 thats not small % it was higher than e-m34 and e-m78-v13 in that specific study
unfortuntley i don't know from where trombolta took those samples .....
 
kingjohn said:
azurro is a good man
he uploaded me and my family ftdna rqaw data to my heritage
and he didn't have to
i remmber is kind hourt :)
now to the subject i score 14% north central italian in gencove { yes i know this site is joke and use imoputation but still so maybe i do have some titus in me}

there was a research in sardinia who found 5.6% e-m81 thats not small % it was higher than e-m34 and e-m78-v13 in that specific study
unfortuntley i don't know from where trombolta took those samples .....
Click to expand...

Gosh, KingJohn, no need to rush to man the ramparts; it just tickled my funny bone, that's all! It's a bit unusual, you'd have to admit. As I said, to equal it, you'd have to choose Titus as your avatar. :)

No, that isn't a small percentage, but that's one study, you say? I would think a lot of it is male mediated, so perhaps at the most half that in terms of autosomal inheritance?

This paper has a lot more samples, yes? What is the frequency they have for E-M81 island wide? I mean, they've got about 1500 samples, yes, so their number should be more accurate, I would think.
 
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