January 31, 2013

Y chromosome and mtDNA study of modern Middle Eastern populations (Badro et al. 2013)

I will just briefly comment on the occurrence of L3* mtDNA in the Near East. This is a critical haplogroup because of its age of ~70ky. If all L3* in the Near East represents African migrants, then only the M and N macrogroups appeared in Eurasia, and a good case can be made for a "late" OoA event.

On the other hand, it is quite possible that some of the L3* in the Near East does not represent recent admixture, but rather native forms of L3 with deep ancestry in the region. If that is the case, then the Near East will emerge as the origin of L3, with M, N representing Out-of-Near East-into-Eurasia founders, and the various L3*(xM, N) representing Out-of-Near East-into-Africa founders.

It is difficult to say at present what will turn out to be the case. Ancient DNA has the potential of resolving this issue, because if L3*(xM, N) in Eurasia is really recent (e.g., associated with Islamic/Arab dispersals spanning Africa and Eurasia), then it ought to be missing from the earliest genetic layers.

Also of interest the geographical distribution of Y-haplogroups; nothing much new here, but still useful as a reference:





PLoS ONE 8(1): e54616. doi:10.1371/journal.pone.0054616

Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations 

Danielle A. Badro et al.

The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

23 comments:

dok101 said...

Comparing the R1b modals for the ME populations from the study, plus the Assyrian modal for 393, 390, 19, 391, 439, 389i, 392, and 389ii.

TUR 12 24 14 11 12 13 13 29
JOR 12 24 14 10 12 13 13 29
LEB 12 24 14 10 13 13 13 28
PAL 12 25 14 10 12 13 13 29
SYR 12 24 14 10 12 13 13 30
ASY 12 24 14 10 12 14 13 30

Based on the record to date, one of the few possible links between Assyrian and Syrian DNA has been R-L23. Specifically, the R-L23 observed among the Alawites. I have speculated that this may be a remnant of Semitized Indo-Europeans (Hittites, Luwians, etc.) from the Early Iron Age. It is a fact that the Assyrians, and later the Babylonians, and then Persians absorbed northern Syria into their empires during the 1st millennium BCE. Recent archaeological discoveries are also of potential interest. Including Middle Assyrian horse and foal themed administrative seals, Late Hittite seals among Neo-Assyrian burials, and this:

January 30, 2013

"[D]iscovery that in the northwestern part of the empire there was a tradition of ‘cremation burials’, a practice not found in the Assyrian heartland."

http://www.cam.ac.uk/research/features/a-new-chapter-opens-in-the-study-of-the-assyrian-empire/

Dan Kalina said...

verified L2a1 HAS BEEN FOUND IN Syria THAT IS AT Least 10,000 YEARS OLD IN REMAINS, CLEARLY L is both rare in the Asian Arab Middle east (7%) And ancient being found in Northern Syria Over 10,000 years ago.

Unknown said...

more than 40% of H in mali ? 0_0 ,where did the sample come from ?

Dr Rob said...

"Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations "

haven't read it yet, but the ME has been somewhat of a blank spot.

As to its conclusions, Im hardly shocked. The geneto-sceptics would say, Im sure, that you didn't need "DNA evidence" to conclude such a common sense finding

Lank said...

As divergent L3 lineages are yet to be identified in Middle Eastern populations, there is no reason to suspect that Middle Eastern L3 lineages are particularly ancient. Kivisild 2004 compares Yemeni L lineages to sub-Saharan Africans, and the only "unique" lineages found belong to L6. But as that lineage is highly frequent in southern Ethiopia and its coalescence is dated to just 20 kya, it is unlikely that even L6 is particularly ancient in the Arabian peninsula.

It is of course possible that exceptions may be found in the future. However, the Middle East, and indeed all of West Eurasia, is lacking in diversity even for L3's daughter lineages, and the Y-DNA lineages for that matter. The highest Y-DNA and mtDNA diversity can instead be found in the southern parts of Eurasia (particularly Southeast Asia), rather than West Eurasia, which is the presumed source of the proto-Eurasians migrating out of Africa. Coupled with the fact that modern humans were unsuccessful in Europe and the Levant until about 40 kya, whereas a Southeast Asian AMH is dated to 46-63 kya, it appears that West Eurasia was not a major pit spot for early OOA humans. Rather, there was a rapid colonization of the southern parts of the Eurasia, and possibly a back migration (?) to Europe and the Levant. Alternatively, West Eurasians may be descendants of a very bottlenecked population that remained isolated in West Eurasia, and just hasn't been seen in the fossil record.

A "late", final OOA around 70 kya does sort of fit with the available evidence. The only problem is that the archaeology isn't quite there yet to prove or disprove such an event.

Paul Ó Duḃṫaiġ said...

They don't seem to have tested for Haplogroup J1, this probably explains the very high levels of F* especially among the Saudi's and Yemeni samples.

-Paul

AWood said...

Remember that one of the earliest Impressed Ware sites was Lebanon and that has a S Euro or SE Euro origin ultimately. The fact that the female lineages resemble European ones, and male lineages resemble more eastern ones tell me that the latter was an intrusive patriarchal culture from the east. This would make sense if you consider the number of eastern neolithic populations that began to dominate the Levant.

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raphael petit said...

The sample from Mali (n=21) was collected in Tuaregs (who are Berbers) near Gossi. Thats's why they have high percentage of West-Eurasian haplogroups (>50%). Their Y-Dna is 81% E1b1b.

http://www.nature.com/ejhg/journal/v18/n8/full/ejhg201021a.html

terryt said...

"verified L2a1 HAS BEEN FOUND IN Syria THAT IS AT Least 10,000 YEARS OLD IN REMAINS"

Ten thousand years is long after any postulated OoA. All it shows is that L2a1's presence in Arabia is not the result of recent slave trade. Traffic across the Red Sea was presumaby well established by that time.

"As divergent L3 lineages are yet to be identified in Middle Eastern populations, there is no reason to suspect that Middle Eastern L3 lineages are particularly ancient".

Yes. I've had many arguments with people who insist that any non-L# haplogroup in the Arabian Peninsula is a signal of the ancient OoA. It doesn't.

"it is unlikely that even L6 is particularly ancient in the Arabian peninsula".

And I've had the same arguments with the same people over that haplogroup. The argumant goes that L6's diversity is greatest in Arabia/Yemen. But it looks to me as though that diversity is the result of separate origins within Africa for L6a (Egypt) and L6b (Ethiopia).

"The highest Y-DNA and mtDNA diversity can instead be found in the southern parts of Eurasia (particularly Southeast Asia), rather than West Eurasia, which is the presumed source of the proto-Eurasians migrating out of Africa".

I suspect that the greater diversity in SE Asia is the result of increased aridity during the ice ages having driven people from the intermediate regions though.

"and possibly a back migration (?) to Europe and the Levant".

I'm certain of it. Y-DNA R and mt-DNA R certainly fit that scenario.

"Alternatively, West Eurasians may be descendants of a very bottlenecked population that remained isolated in West Eurasia"

I'm reasonably sure of that too. mt-DNAs such as X, N3, N1'5 and N2 look to have originated in SW Asia and later spread from there. And Y-DNAs G, F2 and IJK fit the same pattern. Neither group looks to have a Soutn Asian origin.

"The sample from Mali (n=21) was collected in Tuaregs (who are Berbers)"

Thanks for that explanation.

eurologist said...

"Alternatively, West Eurasians may be descendants of a very bottlenecked population that remained isolated in West Eurasia, and just hasn't been seen in the fossil record. "

For the most part - no; autosomal DNA does not show any additional bottleneck for Europe, at all. Also, the European - Asian split seems to have occurred after much of West Asia was no longer inhabitable (or was occupied by Neanderthals). Finally, most haplogroups also do not follow this picture. For y-DNA, some see IJ as a possible candidate.

However, I see G as back-migrated F, and IJ as back-migrated IJK. Of course, those as well as parts of H and LT were likely residing rather west / northwest in the subcontinent and apparently "peeled off" earlier from migrations into the Asian heartland. This is a repeated characteristic of F and its subgroups - C and D do not show this behavior.

terryt said...

"I see G as back-migrated F, and IJ as back-migrated IJK".

I see great difficulty in accepting that to be so for a couple of reasons. IJK breaks up perfectly in the manner we would expect of a haplogroup that moved from somewhere near Africa to somewhere near Australia. IJ in SW Asia, LT in South Asia and KMNOPS is SE Asia. Secondly it is difficult to make a case for G having coalesced in South Asia. Not present at all as far as I'm aware. And we have another basal F haplogroup, in the form of F3, which also appears to have no connection with South Asia. In other words both F and IJK haplogroups 'peeled off' during migrations from SW Asia to SE Asia via South Asia.

"C and D do not show this behavior".

Exactly. Their expansion is quite different.

"the European - Asian split seems to have occurred after much of West Asia was no longer inhabitable (or was occupied by Neanderthals)".

I agree that haplogroups derived from Y-DNA P look to have arrived in SW Asia via South Asia. So the 'European - Asian' split is probably more correctly a 'South Asian - East Asian' split.

eurologist said...

Terry,

To my knowledge, there is no evidence to connect IJ to SW Asia. There is some to connect it to Iran. And since the parent, F* is mostly found in India and China, all evidence indicates back-migration - with IJ* intermediate between the extant populations.

"it is difficult to make a case for G having coalesced in South Asia"

I did not say that. As the F3 you mention, it is most likely that G back-migrated from F in the subcontinent.

To me, the argument is more along the lines where and when the subcontinent was transparent to migrations, and where and when it mostly was not, during dry times. To me, everything (including paleo-climatic data) points to the NW being rather isolated to the S and E (with a few exceptions along the foothills of the Himalayas or perhaps north of that). I believe this had consequences regarding UP revolution expansion, and as to what haplogroups made it to Europe, and also regarding the ANI/ASI split.

terryt said...

"there is no evidence to connect IJ to SW Asia. There is some to connect it to Iran".

I guess it's a matter of definition. I limit myself to just the three terms SW Asia, S Asia and SE Asia to cover the whole region between Africa and Australia south of the Himalayas. Otherwise it gets too complicated. I agree that IJ looks more 'Iranian' than 'Levantine'. In fact J1 looks 'Arabian Peninsula', J2 looks 'Iranian/Anatolian, and I looks 'Danubian'. None look 'South Asian'.

"And since the parent, F* is mostly found in India and China, all evidence indicates back-migration"

I disagree. You're making the same mistake Maju insists on making. If we accept that humans moved from Africa to Australia we would expect to find a scatter of haplogroups along the route. That is exactly what we find. The fact F(xF1,F2,F3,F4) is not found west of India is more an indication of prolonged or severe drift outside that region than an indication of 'origin'. The basal F haplogroups G, IJ and F3 can hardly be convincingly placed in South Asia. There is no need at all to postulate 'back-migration'.

"To me, the argument is more along the lines where and when the subcontinent was transparent to migrations"

To me it is obvious that migration into or out of South Asia, either in the west or the east, has always been difficult. No great exchange of genes can be demonstrate except for members of Y-DNA MNOPS and mt-DNA R.

"To me, everything (including paleo-climatic data) points to the NW being rather isolated to the S and E (with a few exceptions along the foothills of the Himalayas or perhaps north of that)".

I agree that the main route through India to the east was north of the Ganges. The Ganges Delta, along with the jungle-clad mountains in Northeast India and beyond, have always been formidable barriers to human movement. Even mt-DNA M seems to separate into two groups: west and northeast of the Ganges. On the other hand mt-DNA R-derived haplogroups look to me to have basically spread up the Ganges from the Delta.

"I believe this had consequences regarding UP revolution expansion, and as to what haplogroups made it to Europe, and also regarding the ANI/ASI split".

I agree completely. In fact I believe Australia contains the key to the whole story.

eurologist said...

"If we accept that humans moved from Africa to Australia we would expect to find a scatter of haplogroups along the route."

Terry,

Well, there are E and DE, while C and D don't show any trace until India. And, realistically, SW Asia and much or W Asia were literally almost uninhabitable several times since ooA. And again, I am not claiming S Asia for the origin and residence of these halogroups - but the region of NW India and adjacent Pakistan. Iran and Afghanistan are out due to their then uninhabitable highlands and Neanderthal presence.

genetiker said...

50-45 ka - IJK evolves in Veddoids in India and spreads to Iran.

40-35 ka - IJ evolves in Veddoids in Iran and spreads west.

35-30 ka - J evolves in Veddoids in Arabia.

30-25 ka - I evolves in Cro-Magnoids in the Near East and spreads to Europe.

terryt said...

"there are E and DE"

I don't think this is a very good example of what we're looking for, a scatter of haplogroups along the route. E, D nor DE show a complete sequence all the way from somewhere near Africa to East Asia. On he other hand IJK does. In fact it seems to be the only haplogroup to do so although several mt-DNA N's may be relevant.

"while C and D don't show any trace until India".

C and D show virtually no trace IN India. Again, neither is an example of what we're trying to see.

"realistically, SW Asia and much or W Asia were literally almost uninhabitable several times since ooA".

That cannot be said of much of Anatolia and even parts of Iran such as valleys in the Zagros. And let's not forget the 'Perian oasis theory'.

"the region of NW India and adjacent Pakistan"

Any time SW Asia and much of W Asia were almost uninhabitable the same would be pretty much true of NW India and adjacent Pakistan.

"Iran and Afghanistan are out due to their then uninhabitable highlands and Neanderthal presence".

I don't think 'Neanderthal presence' necessarily precludes modern human presence. The evidence strongly indicates that Neanderthals did breed with modern humans somewhere.

"50-45 ka - IJK evolves in Veddoids in India and spreads to Iran".

On what grounds do you claim IJK evolved in India? I agree that derivatives of the K in that name moved into India but I and J are not really 'South Asian'. Just some downstream haplgroups are found there and are presumably more recent immigrants. I have no argument with the remainder of your current list.

Va_Highlander said...

@terryt: "And let's not forget the 'Perian oasis theory'."

Could you elaborate, please?

terryt said...

"Could you elaborate, please?"

http://dienekes.blogspot.co.nz/2010/12/persian-gulf-oasis-hypothesis.html

Dienekes has several other posts on the subject. Enter 'Persian Gulf oasis' in the search section of this blog.

eurologist said...

"Any time SW Asia and much of W Asia were almost uninhabitable the same would be pretty much true of NW India and adjacent Pakistan."

This is not so, because unlike almost all of SW Asia and much of W Asia, parts of NW India and adjacent Pakistan have reliable year-round water resources even in extreme arid times, and a somewhat benign climate even during the coldest times.

Va_Highlander said...

@terryt: Many thanks! I missed this yesterday.

terryt said...

The Thar Desert is far less inviting than is most of Iran, even today. That desert would have restricted movement into South Asia to the Punjab region of the upper Indus and Ganges Rivers. It would also have restricted movement from there south into Rajasthan and Madhya Pradesh. I agree that Y-DNA C has a presence in 'NW India and adjacent Pakistan'. But it also has a presence in SW Asia, and so could have entered South Asia from there some time after any 'original' OoA into India. But it is extremely difficult to make a case for either D or E, let alone DE, for ever having had a presence in that region.

terryt said...

Regarding Persian Gulf oasis this has recently come out of embargo:

http://www.sciencedirect.com/science/article/pii/S0002929711005453

It places the origin of mt-DNA N in that region.