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Saturday, November 16, 2013

mtDNA haplogroup U5a link between Eastern Europe and Iran


I'm reading a new paper at PLoS ONE on the mitochondrial DNA of Iranians. It's the first study to tackle the topic of Iranian maternal ancestry using complete mtDNA sequences. Here are a couple of quotes that caught my eye:

Between the third and second millennia BCE the Iranian Plateau became exposed to incursions of pastoral nomads from the Central Asian steppes, who brought the Indo-Iranian language of the Indo-European family, which eventually replaced Dravidian languages, perhaps by an elite-dominance model [13,17,20].

...

The U5a1a’g cluster itself (based on HVS1 sequence data) is concentrated in populations of the Pontic-Caspian steppe, extending from Romania, Ukraine, southern Russia and northwestern Kazakhstan to the Ural Mountains. The highest frequencies of the U5a1a’g were reported in the Volga-Ural region (5.3%), in particular in Bashkirs (4.3%) and Tatars (3.9%) [75], although the frequency varies from ,2.7% in Russians to ,1.5% in populations of the northern Caucasus [64,76–81]. It is worth mentioning that despite the low frequency of U5a1a’g haplotypes in Central Asian populations of Turkmens, Karakalpaks, Kazakhs and Uzbeks (,1.5% according to the data of [82], some haplotypes were common between Karakalpaks (haplotype marked by mutation at np 16293), Turkmens (by mutation at np 64) and Iranians. So, it seems likely that the sub-cluster U5a1g or its founder has arrived to Iran from Eastern Europe/southern Ural via the Caspian Sea coastal route.

Derenko M, Malyarchuk B, Bahmanimehr A, Denisova G, Perkova M, et al. (2013) Complete Mitochondrial DNA Diversity in Iranians. PLoS ONE 8(11): e80673. doi:10.1371/journal.pone.0080673


38 comments:

Kristiina said...

This is beside your point, but it is taken from the paper you are reading.

How do you understand the following:
Haplogroup H is the most frequent lineage in the Near East and Europe, but the coalescent age estimates for H in the Near East are significantly older than in Europe (23–28 kya versus 19–21 kya, respectively). It has been suggested earlier that the first expansions of the haplogroup H may have taken place in the northern part of the Near East and the southern Caucasus, where the oldest clades of haplogroup H are present. However, most of the Near Eastern/Caucasus and North African variants of haplogroup H started to expand after the LGM, between 18 and 10 kya. Certain sub-clades of haplogroup H are more prevalent in the Near East and the Caucasus (H1, H2a1, H4, H5, H6, H7, H13, H14, H15, H18, H20), and only several sub-clades (H6, H13, H14) coalesce to the pre-LGM period.

According to Soares, the oldest clades should be H6, H7, H13. H6a is most frequent in Iberia, Central Europe and southern Russia. H7 is most frequent in France, Balkans and Volga area. H13 is a near Eastern lineage. Do you think that H* may have arisen in Europe before the Ice Age and then receded near Caucasus when the Ice Age approached and from there started to spread in the Near East?

As for this discussion on mtDNA C in Europe, they say that “it is noteworthy that another eastern Eurasian-specific mtDNA lineage, C5c, characteristic of some European populations (Poles, Russians, Ukrainians, Belarusians, Romanians), has been also found in the Iranian gene pool. Moreover, the complete mtDNA genome phylogeny points to Iranian rather than South Siberian origin of the European specific branch C5c1 dated to around 10 kya.

Davidski said...

I'm going to wait for full mtDNA sequences from a wide variety of Iberian and Balkan foragers before I make up my mind what mtDNA H is exactly.

But I'd say that the mtDNA C in Europe comes from a few different sources, like contacts between Mesolithic European and Siberian foragers, and the movements of Kurgan groups, including the Scythians.

Maju said...

This seems to me quite more reasonable than the claims on U2 you made recently. U5, U4 and probably some of the H, V and maybe even I, may have arrived from Europe. However together they barely make up a 11%, what is about the highest possible percentage of European ancestry of Iranians, at least via mtDNA.

The study has some other highlights: in particular R2 ("sister" of JT) is resolved as of likely Iranian origin, what seems to suggest that R2'JT as a whole coalesced in West Asia, possibly Iran itself. Same for the rare N3.

Davidski said...

Yes, thanks for reminding me to include a link to my U2e blog entry.

Kristiina said...

As for hg H, most deep-rooted clades in Iran are H13, H15 and H14, in this order. All the rest looks sporadic. H15 seems not to be frequent in the Near East, while it is found in Northern Europe (excluding Scandinavia), so it may have a steppe origin. H13a2b is also found in Europe, including in Northern Finland. H13a2 seems to be frequent in Turkey as well. It is too old to be linked with the Indo-Europeans. H14 probably came to Iran from the Near East and Caucasus.

As Maju said, U4 haplotypes could have a European origin in Iran. Iranian subclades are U4b1a and U4b1b, U4a2a, U4c1a, and according to my papers, U4b1 and U4a2a are found in Russians, Slovaks, Poles and Belorussians. U4c1a has a more limited distribution in Western Slavs. I could not find U4 in Lalueza et al. paper on ancient Central Asian mtDNA, but there was one U* with mutation 311, and this mutation is present in Iranian U4b1b1. Instead, in ancient Kransnoyarsk samples, there is one U4 with 16356 and 16363 mutations and one with only 16356. The first two mutations are also found in Iranian U4b1a1a1. I wonder if the second one is U4a.

In Lalueza et al. paper there are two T’s with the same mutations as T2b in this Iranian mtDNA paper (16294, 16296, 16126).

Among the hunter gatherers from Gotland there were three U5a1a'g.

Davidski said...

Yes, I'd say that U2e, U4 and U5a all moved together from Europe to Central Asia during the Indo-Iranian expansions. It's just that U2e then experienced a founder effect and drift in the Kalash population. On this map, we could easily draw another arrow, like the one pointing to Central Europe, but make it point towards Asia.

http://img268.imageshack.us/img268/2310/wynh.png

Kristiina said...

Here you have a more detailed analysis of U4 subtypes:

Iranian U4a is not found in Slavs or in Volga area (old and divergent?)

Iranian U4a2a is close to
356 519 73 143 195 214 263 310 U4a2* R6II3 Russian

Iranian U4b (with mutation at 16319) is not found in Slavs or in Volga area (old and divergent?)

Iranian U4b1a1a1 is not found in Slavs, but a similar haplotype is found in Adyge, Italy, Tunisia:
U4b1a1 2083 8642 12297 15789 16362 (Ian Logan site)
In Bashkirs and Komi there is a haplotype with a mutation at 16362

Iranian U4b1a4 is not found in Slavs or in Volga

Iranian U4b1b1 (with 16311) is closest to
356 519 73 146 152 195 263 309iC 315iC U4b1 Sl212 Slovak

According to Ian Logan site, U4b1b is found in Europe, Slovakia, Georgia, Armenia

The most typical Ukrainian U4 is
U4_129-187-189-223-230-278-311-356

Iranian U4c1a could be close to
179 356 519 73 195 263 315iC U4c1 Sl182 Slovak
179 356 519 73 195 263 315iC U4c1 Kt123 Polish
179 356 519 73 195 263 315iC U4c1 Sv13 Belorussian

According to Ian Logan site
U4c1a T11009C is found in Hungary, North Europe, Slovakia, Belorussia, Poland, England, Ireland, Scotland, Netherlands

So also U4 may have different origins in Iran.

Maju said...

I keep seeing no reason for your attribution of European origin to U2. The lineage has been around since at least 30,000 years ago and its main distribution is too South-Central Asian to be of European origin.

IF you would at the very least provide a haplotype tree that could support your claim... but you bring nothing but speculation and blind faith to back your claim.

Davidski said...

I'm talking about U2e. It shows a pattern of a revival from Eastern Europe during the Indo-European timeframe.

barakobama said...

" the overwhelming majority of Iranian H13 mtDNAs clustered into sub-group H13a2 with a coalescence age estimated set as 14–16 kya."

I think that quote is important because the vast majority of European H13 is under H13a1. This means most Iranian H13a has been separate from most H13a in Europe for at least 14,000-16,000 years. I don't know that much about H13a in different regions of the middle east maybe H13a2 is more eastern. I doubt that H13a1 originated in Europe I am just guessing that it arrived in the Neolithic from the middle east but maybe not.

barakobama said...

"whereas the deeper HV2 clade shows the coalescence age estimates of 36–42 kya, closely matching with the timeframe of modern human arrival in the Near East"

I really don't understand why the age estimate of humans migrating out of Africa keeps getting younger. I think it is possible but unlikely that the family we all come from did not start in Africa. There are multiple modern human remains or some type of obvious modern human creation like a flute or statue in Europe that are dated as over 41,000 years old. mtDNA haplogroups M and N are exclusively non sub Saharan African. It goes N-R-RO-HV-HV2 why would they say that HV2 had just arrived from the first human migrations to the middle east?

barakobama said...

"The Iranian populations studied here and previously [11], [25], [26] exhibit similar mtDNA lineage composition and mainly consist of a western Eurasian component, accounting for about 90% of all samples, with a very limited contribution from eastern Eurasia, South Asia and Africa."

This makes a lot of sense because in Dodecade aust. DNA test globe13 Iranians have almost only west Eurasian groups. West Asian: 40-50%, Meditreaen: around 20%, Southwest Asian: 15-17%, North European: around 5%. They only had about 1-2% Siberian and 7% south Asian. I definitely think mtDNA haplogroups U, RO, HV, and JT which all have age estimates around 50,000 years old or more. Can be seen as very specifically west Eurasian aka Caucasian mtDNA haplogroups.

barakobama said...

"the majority of the Near Eastern U5 haplotypes belongs to the sub-cluster U5a1a’g"

Indo Iranian languages were spread in Asia by Europeans from Yamna culture in Russia-Ukraine area. I took all the mtDNA results from suspected Indo Iranian peoples in the bronze and iron age. I only counted their west Eurasian groups because the east Eurasian ones could be explained by inter marriage after migrating out of Russia. I also took any mtDNA samples from east Asian non Indo Iranian groups from that time that had typical haplogroups from Indo Iranians like T1 and U2e. I got 83 samples and 19% had U5 all with subclade found under U5 had U5a all with subclade found under U5a had U5a1. I think these Indo Europeans probably spread R1a1a1b2 Z93 in Asia and might at least partly be responsible for the U5a1a'g.

"The U5a1a’g cluster itself (based on HVS1 sequence data) is concentrated in populations of the Pontic-Caspian steppe, extending from Romania, Ukraine, southern Russia and northwestern Kazakhstan to the Ural Mountains. The highest frequencies of the U5a1a’g were reported in the Volga-Ural region (5.3%), in particular in Bashkirs (4.3%) and Tatars (3.9%) [75], although the frequency varies from ~2.7% in Russians to ~1.5% in populations of the northern Caucasus [64], [76]–[81]. It is worth mentioning that despite the low frequency of U5a1a’g haplotypes in Central Asian populations of Turkmens, Karakalpaks, Kazakhs and Uzbeks (~1.5% according to the data of [82], some haplotypes were common between Karakalpaks (haplotype marked by mutation at np 16293), Turkmens (by mutation at np 64) and Iranians. So, it seems likely that the sub-cluster U5a1g or its founder has arrived to Iran from Eastern Europe/southern Ural via the Caspian Sea coastal route."

The directions they say U5a1g migrated into Iran agrees with what I said about Indo Iranian languages. Are they basing it on that U5a1'g is most popular in the Pontiac Caspian steppe and that there are common haplotypes in Karakalpaks, Iranians, and Turkmens. When they say haplotype and it has a defining mutation that means it is a distinct lineage that exists in the ethnic groups they name right?

barakobama said...

"Another lineage potentially informative in revealing dispersals alongside the Eurasian steppe belt, extending from Manchuria to Europe, is haplogroup A4. Its rare sub-cluster A4h, with a specific HVS2 motif 97T-105-110del, revealed in Qashqais, has been observed earlier in Turkmens and Kazakhs [81], as well as in Buryats from southern Siberia [63]. Another A4 mtDNA lineage found in Qashqais, A4a1, has been registered previously in Central Asian Karakalpaks and Mongols, as well as in southern Siberian populations of Buryats and Altaians [63], [82]. It is noteworthy that another eastern Eurasian-specific mtDNA lineage, C5c, characteristic of some European populations (Poles, Russians, Ukrainians, Belarusians, Romanians), has been also found in the Iranian gene pool. Moreover, the complete mtDNA genome phylogeny points to Iranian rather than South Siberian origin of the European specific branch C5c1 dated to around 10 kya"

I totally agree that this shows inter marriage between Mongols in eastern Eurasia and Caucasians in western Eurasia. The C5c it seems they say has only been found in Iran and Europe or maybe they just didn't mention that it has been found in Mongoloids. They say C5c1 is specifically European but also say that it originated in Iran. Do they mean that it probably migrated from Iran to Europe and became C5c1? It is very surprising that this may mean a Mongoloid mtDNA haplogroup may have originated in Europe 10,000 years ago.

Davidski said...

It's not surprising, because mtDNA C shows up in Mesolithic, Neolithic and Bronze Age Russian and Ukrainian samples.

http://eurogenes.blogspot.com.au/2013/09/european-specific-mtdna-c-from.html

Nirjhar007 said...

You Drunk now?

Davidski said...

No, I'm at work.

Nirjhar007 said...

For how long?

barakobama said...

"According to Soares, the oldest clades should be H6, H7, H13. H6a is most frequent in Iberia, Central Europe and southern Russia. H7 is most frequent in France, Balkans and Volga area. H13 is a near Eastern lineage. Do you think that H* may have arisen in Europe before the Ice Age and then receded near Caucasus when the Ice Age approached and from there started to spread in the Near East?"

Haplogroups don't always originate where they are most popular today. I have heard from Maju and others of what they say is there are some pretty for sure H samples from Palaeolithic and Mesolithic European hunter gatherers.

http://forwhattheywereweare.blogspot.com/p/ancient-mtdna-maps-of-europe.html

If they are right or wrong it doesn't matter European Palaeolithic and Mesolithic mtDNA samples are overwhelmingly in haplogroup U all with subclades are under U5, U4, and U2(Mesolithic U2e).

http://www.ancestraljourneys.org/ancientdna.shtml

You can study the subclades and percentages yourself and see many subclades of U5 have been found. Looking at ancient DNA the Neolithic farmers have pretty modern European looking mtDNA, Even early Neolithic 7,000 year old samples show very specifically European J1c and H1b. But I have no idea how to explain that the vast majority of modern European mtDNA came out of the middle east just 9,000 years ago and was very developed 7,000 years ago. It makes the most sense to say mtDNA V, H1, and H3 originated in Europe but there is almost no for sure ancient DNA as evidence. If H1 originated in Europe I doubt that it spread before the Neolithic because of how many similar deep subclade percentages there are acroos Europe.

barakobama said...

"Among the hunter gatherers from Gotland there were three U5a1a'g."

I thought they were just reported as U5a or U5. Also more evidence U4b1 in Iran has a Europe origin is U4b1 was found in a about 8,600 year old hunter gatherer from the island of St. Forvar in the Baltic sea.

There is some info on its autosomal DNA

http://dienekes.blogspot.com/2013_09_01_archive.html

Kristiina said...

I think that Iranian U4c1a came from Europe (excluding Russia). Instead, U4b1a1a1 looks more West Asian and Mediterranean. According to Ian Logan site, U4b root type is found in Russia, but U4b1 must be old in Europe as it is found in 7000 years old site of Stora Förvar cave in Sweden. It might have spread to West Asia already in the Neolithic.

I think that Iranian U4a, like Kalash U4a, are old and divergent and not linked with the Indo-Aryans. By contrast, Iranian U4a2 is probably of Slavic origin.
It is interesting that U4a2b is found in Mari, in Sumerian Syria, 2900-2700 BC, 16223T, 16356C (http://www.ancestraljourneys.org/ancientdna.shtml). On Ian Logan site, there are 3 U4a2b’s: AY339550(Finland) Moilanen, EF222240 Grzybowski, EF222241 Grzybowski.

Kristiina said...

According to Ian Logan site, C5c1 is found in Poland, Asia, Uzbekistan. Upstream C5c is found in Tubalar and Teleut in Southern Siberia. On the Ian Logan site there is only one C5, and it is found in Nganasan.

Kristiina said...

All U5a cannot have moved together from Europe to Central Asia during the Indo-
Iranian expansions, as U5a is found in the Neolithic Shamanka II hunter-
gatherer cemetery, located at the southwestern tip of Lake Baikal, Siberia (c.
5800?4900 BCE). It is also found in the nearby Lokomotiv cemetary (5250-4000
BC), and among the Ust'Ida Early Bronze Age population (3800-2000 BCE).

U5a has also been found in the oldest Bronze Age burials of Baraba Steppe in Siberia, 4000-3000 BCE, and I do not think that they have anything to do with the Indo-Europeans, and the same goes for the ancient Russian Karelian burials.

Davidski said...

Is that Nganassan C5 a complete sequence?

Davidski said...

I just said there was a migration of Indo-European groups from Eastern Europe to Central and West Asia that had relatively high frequencies of U2e, U4 and U5a. I didn't mean that all of the U2e, U4 and U5 in Asia got there with the early Indo-Europeans.

Maju said...

"All U5a cannot have moved together from Europe to Central Asia during the Indo-Iranian expansions, as U5a is found in the Neolithic Shamanka II hunter-gatherer cemetery"...

Excellent point, Kristiina. It underlines that the Central Steppe was ethnically part of (Eastern) Europe even in Paleolithic times.

I find also quite interesting that, as you mentioned before, U4 existed in Iraq long before any Indoeuropean migrations, so, even if these lineages may have arrived to West Asia from Europe, it's possible that they did in extremely ancient times, maybe the Epipaleolithic or late Upper Paleolithic (Euro-like rock art of South Anatolia, possible Epigravettian influences in Zarzian).

Kristiina said...

Please judge yourself
C5 595.1C 16288
1. AY615359.1(Nganasan) Starikovskaya C5 02-JUN-2005 A73G A249- A263G 309.1C 309.2C 315.1C T489C 595.1C A750G A1438G 1718.1A A2706G A3397G T3552A A4715G A4769G C7028T C7196A G8584A A8701G A8860G T9233C T9540C A9545G A10398G C10400T T10873C G11719A G11914A C12705T A13263G T14318C C14766T T14783C G15043A G15301A A15326G A15487T C16148T C16223T T16288C T16298C C16327T T16519C

andrew said...

"who brought the Indo-Iranian language of the Indo-European family, which eventually replaced Dravidian languages, perhaps by an elite-dominance model"

The notion that the Dravidian languages were ever spoken in Iran, if that is what is implied by this quote, is very much outside the mainstream. Moreover, while there was clearly some IE replacement of Dravidian in South Asia, there is good reason to believe that the substrate language in some of South Asia which IE languages replaced was not Dravidian (particularly in NW South Asia).

vooruit said...

I also find it very weird that a mtDNA U5a1 and a mtDNA U2e have been found in Andhra Pradesh TRIBALS (Andhra Pradesh is rather south and above all EAST!)

http://www.biomedcentral.com/1471-2148/9/154

"The West Eurasian component

This component comprises the N haplogroups I and W, and the R haplogroups R0, H, T2 and U (xU2a,b,c) and is almost absent in the Tharus (only one H and one T2 mtDNAs from Chitwan). In contrast, it reaches a high frequency (25.0%) in New Delhi, where most of the haplogroups of this component are found, and is also common in Indians from Terai (12.5%) and Andhra Pradesh (10.3%). However, in spite of the similar frequencies, the two latter populations are remarkably different in their composition: Hgs I, U1 and T2 characterize the Terai Hindus, whereas Hgs U2e, U5a1 and U9a the Andhra Pradesh tribals."


It doesn't look like the result of an "indo-european" thing in this case either...

Davidski said...

It's hard to say what that means unless we see some full mtDNA genomes from India.

The problem is that many results coming out of Indian labs look really strange, and the samples aren't being shared, probably because there's a ban on exporting human DNA from India.

Maju said...

I for one do think that the Elamo-Dravidian theory has some potential. We know that Brahuis, who live near the Iranian border and speak Dravidian, are genetically near-identical to their Burusho neighbors (who seem to be mere Indo-Europeanized Brahuis) and not at all immigrants from anywhere in India. From this and other complementary data it's easy to conclude that IVC essentially spoke Dravidian and that Dravidian spread to the subcontinent with Neolithic. So at the very least South Asian Neolithic, beginning in Balochistan as far as we know, was a Dravidian phenomenon in the linguistic aspect.

This South Asian Neolithic, like the European one, has ultimate roots in West Asia, just that in different parts of that region. Logically the South Asian roots should be in Iran, where we know that a language "isolate" known as Elamite was spoken, language that has been proposed as relative of Dravidian.

Another thing is that in Kashmir, which is almost more Central Asia or a transitional region on its own right, other languages were spoken, much as in South Asia in general before the expansion of Dravidian (and SE Asian languages) first and IE later. But these were most likely peripheral phenomenons.

At most one can imagine that IVC could have been bilingual with Dravidian being spoken in the South and maybe something like Burusho in the North, but the Burusho geographical context is not central to IVC (actually it's well outside its archaeological area) and using it as reference is like trying to reach conclusions about the Sumerian civilization and language based on, say, Kartvelian.

Essentially IVC included: Balochistan, Sindh, both Punjabs and Gujarat, with some extension down the coast towards Mumbai - not Kashmir nor anywhere near the Himalayas.

Nirjhar007 said...

''I for one do think that the Elamo-Dravidian theory has some potential. We know that Brahuis, who live near the Iranian border and speak Dravidian, are genetically near-identical to their Burusho neighbors (who seem to be mere Indo-Europeanized Brahuis) and not at all immigrants from anywhere in India. From this and other complementary data it's easy to conclude that IVC essentially spoke Dravidian and that Dravidian spread to the subcontinent with Neolithic. So at the very least South Asian Neolithic, beginning in Balochistan as far as we know, was a Dravidian phenomenon in the linguistic aspect.''
Did you forget the New Indology Incident?
''This South Asian Neolithic, like the European one, has ultimate roots in West Asia, just that in different parts of that region. Logically the South Asian roots should be in Iran, where we know that a language "isolate" known as Elamite was spoken, language that has been proposed as relative of Dravidian.''
That is Baseless and just theoritical....
''At most one can imagine that IVC could have been bilingual with Dravidian being spoken in the South and maybe something like Burusho in the North, but the Burusho geographical context is not central to IVC (actually it's well outside its archaeological area) and using it as reference is like trying to reach conclusions about the Sumerian civilization and language based on, say, Kartvelian.''
On which basis we first start to think that IVC Was Drvidian?


Nirjhar007 said...

If U2e and others are also found in Tribal folks then your Card is more drained.....

Maju said...

"Did you forget the New Indology Incident?"

I can't forget what I never heard of to begin with. What's "new indology"?

"On which basis we first start to think that IVC Was Drvidian? "

The existence of Brahui people as mere variant of Baloch (i.e. not immigrants from the South) and the fact that Indo-Aryan is more recent, or at least the latest period in which IVC is shattered by (imported) violence.

It's a matter of common sense.

On which basis do you think that IVC was not Dravidian-speaking?

Maju said...

erratum: "or at least" should read "from at least".

Nirjhar007 said...

''I can't forget what I never heard of to begin with. What's "new indology"?
go to Google and search 'New Indology Maju'.....
Prove yourself in that blog it is easy to just say....
''On which basis do you think that IVC was not Dravidian-speaking?''
Because there is no basis for that to believe and go to the blog for Expert opinion....
I will reply on Saturday....
Good Day.

Maju said...

What I've read in your blog does not look really credible but rather sounds like religious fanaticism.

"It was the Aryans who discovered agriculture and initiated the agrarian revolution and a new mode of production. Earlier the Aryans were called Devas".

And what else?

"The Aryans were primarily agriculturists".

So that's why their nefarious caste dictatorship is based on warriors and priests, because they were all hard-working farmers, right? Nope: they were conqueror-exploiters.

Etc.

Nirjhar007 said...

Maju, You have serious communist issues......