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Friday, April 7, 2017

The story of mtDNA haplogroup U7


A very useful new paper on the origin and spread of mitochondrial (mtDNA) haplogroup U7 has just appeared at Scientific Reports.

It re-iterates some key points that I've made about this haplogroup; that it's a South Caspian-specific lineage and conspicuous by its absence from all Yamnaya samples sequenced to date. In fact, along with other South Caspian-specific lineages, such as U1, U3a, HV2 and HV0, it's missing from all Early Bronze Age steppe samples sequenced to date (see here).

This is surely a major problem for those positing that ancient populations from the South Caspian, in other words what is now mostly Iran, made a significant contribution to the formation of Early Bronze Age steppe pastoralist groups, including Yamnaya.

However, I'd say the paper's conclusion that U7 probably spread into Europe before the Early Bronze Age is a bit iffy. Based on the available ancient European mtDNA, it looks to me as if it mostly spread into Europe after the Early Bronze Age. So why are there European-specific U7 lineages, such as U7a19, seemingly with coalescent times dating to the Neolithic in Europe? Well, perhaps because after these lineages moved to Europe, they went extinct in the Near East? From the paper, emphasis is mine:

Abstract: Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region.

...

Compared to other subclades of hg U, both the phylogenetic structure and the ancestral origin of hg U7 are rather obscure. This haplogroup is characterized by generally low population frequencies and limited sequence diversity, despite a geographic distribution ranging from Europe to India [14,16,25,27,30,31,32,33]. Recently, it has been detected in skeletal remains from Southwest Iran [my note: that was U7a] dated ~six thousand years ago (kya) [34] as well as in remains from the Tarim Basin in Northwest China (3.5–4.0 kya) [35].

...

Another major episode of gene flow affecting the European gene pool appears to have occurred during the Late Neolithic and Early Bronze Age, from a source in the Pontic-Caspian Steppe region north of the Caucasus [3,54,66,72]. It has been suggested that this migration resulted in a further substantial shift in the genetic profile of Europeans and was a major vehicle for the movement of Indo-European languages to Europe [3,72], and likely also to South Asia54. Interestingly, the autosomal genetic component in Europeans considered to derive from the Steppe is almost fixed in two pre-Neolithic ancient genomes from the South Caucasus. This component is distributed eastwards towards South Asia as well54, where it mimics the distribution of U7 (Pearson’s r = 0.65, p = 0.01). Our time estimates for the expansion and differentiation of hg U7 in the Near East, Central Asia, South Asia, and Europe, however, predate these putative late Neolithic-early Bronze Age migrations and thereby rule them out as a major vehicle for the spread of U7 to Europe and South Asia. In this respect, it is also noteworthy that Yamnaya herders of the Steppe so far analysed (n = 43) show no traces of U7 [3,55,72,73] – and U7 is rarely found in this region today (Fig. 2).

...

The expansion time of hg U7 in the Near East, Central Asia and South Asia is more consistent with autosomal multi-locus estimates for the genetic separation of these regions during the Terminal Pleistocene74, suggesting a common demographic process, whose origin was unclear previously. Here, we show that the frequency and distribution of U7b lineages indicate an origin of this clade in the Near East, whilst for U7a these statistics cannot differentiate between South Asia and the Near East (including the Caucasus) as a possible homeland.



Sahakyan et al., Origin and spread of human mitochondrial DNA haplogroup U7, Scientific Reports 7, Article number: 46044 (2017), doi:10.1038/srep46044

See also...

Mitogenomes reveal post-Neolithic gene flow from the Near East to Tuscany

Big deal of 2016: the territory of present-day Iran cannot be the Indo-European homeland

129 comments:

Nirjhar007 said...

Thanks .

Aram said...

I didn't read it yet. But in one paper U7 was linked with Etruscans.

Here there are some Etruscans adna mtdna.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055519#pone.0055519.s008

The problem is that I am not familiar with their designations.

Aram said...

When all the genetic evidence obtained so far are taken together, it seems clear that the Etruscans cannot be regarded as ancestral of all modern-day Tuscans; however, almost all the studies agree that there is a proportion of their mtDNA pool that could be traced to somewhere in the Middle East, thus testifying to an ancient connection between both regions. While the age of the Middle Eastern founding U7b1 lineage [11] would fit well with Herodotus's theory, estimates based on mtDNA analysis in Ghirotto et al. [12] (and most recently also in Tassi et al. [13]) would indicate that this genetic link is too old and therefore consistent with the development of the Etruscan culture locally – and not directly mediated by migration from the Middle East.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105920#pone-0105920-g001


Italians have also an excess of affinity with Iran Chl. I think D stats will confirm this.

wagg said...

Aram: " in one paper U7 was linked with Etruscans."
--
Etruscans? Well, besides a mtDN U7 in Rostov Scythians (der Sarkissian et al, 2012 (IIRC)), U7 is also found in an old Norwegian Viking Burial (Holck, 2006), in a middle adges (Early christian period) Danish graves and in western Siberian peoples near the Urals (the Mansi IIRC) (for the two latter: http://www.ncbi.nlm.nih.gov/pubmed/15838837, I think), so... Norway, Denmark, Urals... I'm definitely not looking in the Etruscan direction.

Olympus Mons said...

Hummm... Can any one discern what do they mean by:
<¡>Interestingly, the autosomal genetic component in Europeans considered to derive from the Steppe is almost fixed in two pre-Neolithic ancient genomes from the South Caucasus

Davidski said...

They mean Yamnaya is up to 50% CHG. They just didn't express this too well, since CHG is not the autosomal genetic component in Europeans considered to derive from the Steppe; Yamnaya is actually that autosomal component, also known as Yamnaya-related or Steppe_EMBA.

Davidski said...

Etruscans? Well, besides a mtDN U7 in Rostov Scythians (der Sarkissian et al, 2012 (IIRC)), U7 is also found in an old Norwegian Viking Burial (Holck, 2006), in a middle adges (Early christian period) Danish graves and in western Siberian peoples near the Urals (the Mansi IIRC) (for the two latter: http://www.ncbi.nlm.nih.gov/pubmed/15838837, I think), so... Norway, Denmark, Urals... I'm definitely not looking in the Etruscan direction.

None of this contradicts the claim that U7 may have arrived in Italy with the Etruscans. I proposed this myself a couple of years ago...

http://eurogenes.blogspot.com.au/2015/03/mitogenomes-reveal-post-neolithic-gene.html

wagg said...

Davidski: "None of this contradicts the claim that U7 may have arrived in Italy with the Etruscans. I proposed this myself a couple of years ago..."
--
Well, it seems very unlikely to me. Scandinavians' aDNA, Uralic peoples... I find it hard to believe. but who knows...

Davidski said...

So you reckon the West Asian-specific U7a in Tuscany dated to after the Neolithic is more likely to be from Vikings or migrants from the Urals rather than the proto-Etruscans from, say, West Asia?

Roy King said...

Could U7 be the mtDNA analogue of Y chromosomal haplogroup J2? Both spread through the Mediterranean from a presumptive S Caucasus/West Iranian source and, likely, post-date the Neolithic yet predate the end of the EBA in Europe.

Jaydeep said...

This is another good paper to come out this year.

This paper again reiterates that the West Eurasian ancestry in South Asia split up from its West Asian counterpart at the end of LGM, likely around 15 kya.

This early split was first indicated by Metspalu et al in 2011 when they said that the the Caucasus group and the South Asian group (West Eurasian) had not admixed atleast since 12.5 kya.

Then last year we saw a paper by Sakshi Singh et al which argued that the ydna J2 in South Asia has its own unique history and cannot be associated with the Neolithic expansion from West Asia, since it appeared that the J2 presence in South Asia was older.

We also had Q3 paper by Balanovsky et al this year, which argued that the earliest split in Q3, Q3a'd & Q3e happened around 15 kya between South & West Asia.

Just a week or so ago, we had the Silva et al paper on Indian mtdna expansions, which argued for several pre-Neolithic expansions of Indian specific WE mtDNAs.

Now, we have this present paper which argues for the earliest split of U7 around 18 kya, also between West Asia & South Asia. In their own words,

"The expansion time of hg U7 in the Near East, Central Asia and South Asia is more consistent with autosomal multi-locus estimates for the genetic separation of these regions during the Terminal Pleistocene, suggesting a common demographic process, whose origin was unclear previously."

So the implication seems to be that, the CHG-ANI component had already split up between West Asia and South Asia by about 15 kya and therefore CHG is not ancestral to the ANI component in South Asia. It is not however not clear how Iran_Neolithic will fit in all of this.

The CHG-ANI split of around 15 kya seems to be associated with a demographic expansion whereby this component spread across South, Central & West Asia with the end of the LGM.

Lastly, I will again raise the issue of sample size. In this present study, about 33,000 samples were from Europe and around 16,000 from the Near East while from South Asia the no was 11,000. This is gross underrepresentation of South Asian diversity.

Europe which has a population of 750 million is represented by 33,000 samples and the Near East with a population of around 300 million has 16,000 samples but South Asia with a population of atleast 1.6 billion only has 11,000. This means the depth of sample coverage was about 6 times higher in Europe and Near East in comparison to South Asia. In such a scenario, how can we expect the diversity present in South Asia to be well-represented ?

Davidski said...

So the implication seems to be that, the CHG-ANI component had already split up between West Asia and South Asia by about 15 kya and therefore CHG is not ancestral to the ANI component in South Asia.

This doesn't make any sense, because CHG-related ancestry was carried to South Asia by Bronze Age steppe pastoralists.

ANI is a composite of Neolithic ancestry from Iran and EHG/CHG-related admixture from the steppe.

At this stage, without ancient DNA from South Asia, there is no direct evidence of West Eurasian ancestry in South Asia dating to before the Neolithic. Inferences from modern DNA cannot be assumed to be correct or even accurate, because they're based on too many assumptions.

batman said...

""Etruscans? Well, besides a mtDN U7 in Rostov Scythians (der Sarkissian et al, 2012 (IIRC)), U7 is also found in an old Norwegian Viking Burial (Holck, 2006), in a middle adges (Early christian period) Danish graves and in western Siberian peoples near the Urals (the Mansi IIRC) (for the two latter: http://www.ncbi.nlm.nih.gov/pubmed/15838837"

None of this contradicts the claim that U7 may have arrived in Italy with the Etruscans. I proposed this myself a couple of years ago..."

Agree. Moreover - it reactulizes what some etymologer proposed decades ago - about a connection between the etno-nymes of the aet-nic groups known as (a)Et-Ros-ki and Rhos/Rus-ki.

With the U7 there's yet again a possible connection between the Vendic/Russian area with the Vendic/Etruscan area.

The first one is already famous - as well as very well documented. Between the Venetic Bay at the top of the Adriatic Sea the first, venetian traders to be established were the Vendic traders that established the Venetian Bay as a harbour for export/import between the NE Europena mainland and the Mediterranean trading-circles.

Thus we re-actulize the connection between the Vindelici/Vennones/Wendi/Vends of the Amber-route with the Venedae/Veneje of NW Russia and Belo-Rus. The famous amber-route between the Venetian Bay and the Vistulan Veneti was well established no less than 6.000 years ago. As a highway for 5.000 years this Amber-route seem to have served as Europes major network for travel and trade throughout three successive periods - known as the Neolithic, the BA and the IA.

https://en.wikipedia.org/wiki/Vistula_Veneti

Annie Mouse said...

As I understand it, the evidence is that the Etruscans represent a population that is older in Italy than most Italians. They were culturally distinct from the Romans but not because THEY came from somewhere else. The links to the near East IMO just mean that they were part of the early Mediterranean continuum. Not specifically near eastern but Mediterranean.

It makes perfect sense that expanding near eastern U7 could flow into the Mediterranean spin cycle and arrive on the shores of northern Italy. It would be more odd if they hadn't.

khana said...

Interesting paper, my father is R1a-Z282/U7a3b.

Samuel Andrews said...

@Annie Mouse,

" Not specifically near eastern but Mediterranean."

There's CHG/Iran Neo-heavy ancestry in Italy. Lots of is from deep in the Middle East not the Mediterranean coast; Iran and Caucasus.

Plus this ancestry in modern Italy might be pretty significant; maybe 20-30% in the North and 50-60% in the South. To me that looks less like occasional contact with the Near East, that looks like a naval migration from the Near East. Basically imo everything is pointing towards a single pulse of migration.

Davidski said...

I can think of at least three CHG/Iran_N-related admixture pulses into Italy.

- EBA expansions from the steppes

- LBA expansions from the East Med

- Contacts with the Balkans and West Asia during the Roman period

Ryan said...

So how do we like U7 as associated with something like Iranian Chalcolithic? I think that would fit this decently well no?

Gioiello said...

@ Aram
"I didn't read it yet. But in one paper U7 was linked with Etruscans".
I wrote about that paper:
"How a theory is made: Etruscans, Italians and "elsewhere"

1
Let's take a young scholar who needs titles: Francesca Brisighelli (but what are doing here
a Cristian Capelli and others?).
The paper is "The Etruscan timeline: a recent Anatolian connection", EJHG (2009), 17, 693-6.
"We have analyzed a total of 258 Tuscan samples" (but what are doing here samples from Collevecchio,
Magliano Sabina, Monte Fiascone, Tarquinia, Tuscania and Vulci, which aren't in Tuscany but
in Latium, and, if they were searching for ancient Etruscans, why Collevecchio and Magliano
Sabina, which, as the name says, were in Sabine territory and not Etruscan?).
We know that, for being in line with what is expected from various Farfugliani and Cavallo Sforzesco,
we should demonstrate that Italians aren't Italians but came from elsewhere and that Etruscans too
came from there.
They were searching for "Near Eastern typical haplogroups (HV lineages that are non-H and non HV0,
R0a, U7 and U3)". After having scanned the samples for a few SNPs and a few selected ones for HVRI "only a
small fraction of them (about 10% of the total sample size) were finally confirmed to belong to the
mentioned haplogroups" (p. 694). Apart the fact that I have demonstrated that R0a, found from Arredi
and from me (my relative Fabrizio Federighi from Santa Maria a Monte (Pisa)), is very different
from the Middle Eastern ones in HVRI and II and it would be necessary an FGS to calculate the time
of separation, Miss Brisighelli let fall down all these "Middle Eastern" haplogroups and concentrate
her attention upon U7. In the sample she has found 11 U7: 9 from Elba Island (G17, G40, G5, G19, G30,
G39, G43, G49, G52) and 2 from Collevecchio (COL17 and COL23). The samples from Collevecchio are
very different from the Elba Island ones, in fact Collevecchio was Sabine and Elba Island was
Etruscan, and, being an island, probably has had many peoples from "elsewhere". But if young scholars
did know Geography (and History), in having found them it should have been anyway meaningful: U7 is present
in Italy overall and in different haplotypes. The Collevecchio samples, let down by the scholar, has HVRI
16309G 16318T 16519C (COL23), which are the typical "Eastern" (India and nearby) motives, but without HVRII
and the coding region we can't say how close they are (they could have a separation of thousands of
years), and 16093C 16309G 16318T 16519C (COL17), this too with the typical "Eastern" motives, but
16093C isn't documented in the "Eastern" samples we know (FTDNA, Mitosearch etc.), but is present in
Sicily (N12396), and also this should have been meaningful.
Brisighelli et alii, in examining the 7 Elba Island samples, have discovered a new "Etruscan" subclade
of U7a2 (U7a2a), with the mutations 16271 and 13395 plus other mutations: 16362 (and 1081) and 7394T.
Even though the bifurcation of U7a2 carries to samples with 6 or 7 mutations or back mutations, they
calculated the origin of the subclade U7a2a to 1.1+/- 0.1 kya / 2.3 +/- 0.4 kya, we could discuss about.

Then this is the demonstration that, at least a little part of Etruscan heritage (not more than 10% says
Miss Brisighelli), is linked to Asia Minor, as Herodotus said". [Posted: Mon Apr 09, 2012 4:35 pm, from www.eng.molgen.ord, but pergaps I posted thatalso beforeon www.worldfamilies.net]

TruthPrevails said...

All this is just waste of time, they are only trying to prove where the minute branches and leaves of the tree originated.

South Asia had 90% of the world population till 20,000 BC. And they started expanding out wards looking for more resources. Most of the admixture we see in old DNA is the result of co-habitation for a long period of time in the same place. Since no one has got hold of any ancient DNA from South Asia from any period all this speculation continues, which is good for the labs doing it as if they reveal everything in one go, then no one would be interested in funding their research further.

IBM with their extensive machine learning with the data from Nat Geo did a excellent autosomal analysis way back in 2011 and that big picture is not going to change.

https://www-03.ibm.com/press/us/en/pressrelease/35877.wss

Davidski said...

Ancient DNA has already debunked that model from Nat Geo as it pertains to Europe.

Rob said...

@ Truth

Do you have any physical evidence to support your notion?. I mean, we can do all the computer simulations in the world, but can you quote any site density studies ?

Gioiello said...

Of course the paper has many caveats about a "possible" origin of U7 in Middle East (but we know who funds these paper and which is the "ideology " beyond them). It would be as to say that hg Y I2 is older than I1 because the I1 survived have 4500 years as to YFull or 6000 for Ken Nordtvedt but their separation happened 22000 years ago. Without the aDNA no one may say where U7 came from, with the good peace of Roy King and Sanuel Andrews.

Gioiello said...

Also U6 was a "Northern African" haplogroup, except having found later it in Eastern Europe more than 30000 years ago. Ahahahahahahahahahh

Jaydeep said...

ANI is a composite of Neolithic ancestry from Iran and EHG/CHG-related admixture from the steppe.

That is just a convenient way of modelling West Eurasian ancestry made by Lazaridis et al. It is a guess work and not hard data. The ENA part is also modelled as part-Han & part-Onge in that. Should we assume that this means a migration of Han-like & Onge-like populations into South Asia from the East in different time-periods ? Obviously not. Moreover, the ASI split up from Onge around 26,000 YBP, still it is modelled based on Onge. As par as Han is concerned, its split from ASI would be perhaps of the order of 50,000 YBP. Hence, even the ASI ancestry was a guesswork by Lazaridis et al. The modelling of West Eurasian ancestry was based on modelling ASI as a patchwork of Onge-Han. Since the modelling of ASI itself is a guess, the WE ANI model of Iran_N & Steppe_EMBA is also a guesswork and does not represent any real evidence of migrations from West Asia and the Steppe.

At this stage, without ancient DNA from South Asia, there is no direct evidence of West Eurasian ancestry in South Asia dating to before the Neolithic. Inferences from modern DNA cannot be assumed to be correct or even accurate, because they're based on too many assumptions.

While nothing can replace the value of ancient DNA, as long as it is not published we have to make do with the next best thing. And that indicates that the West Eurasian ancestry in South Asia split up from its counterpart in West Asia around 15 kya or thereabouts. This is based on hard data and not some guesswork. To assume that all of West Eurasian ancestry split from West Asia in the Pliestocene but hid somewhere for thousands of years and only entered South Asia at the onset of Neolithic makes no sense.

It is increasingly evident from the papers cited in my earlier post, that the ANI ancestry in South Asia is present atleast from the Late Pliestocene. It would be more sensible if this fact is not continuously ignored.

TruthPrevails said...

@Rob

I don not know what evidence you are asking for. But let me give you an example, the admixture analysis which you do with limited sets shows which group is closer to which group based on autosomal DNA. However due to the limited capability of the softwares used it cannot point to the path of admixture. it can only show the end result for the groups involved as how close or far you are from the reference set.

However machine learning can uncover the admixture points and it did the admixture analysis for the whole world as it stands today and showed us how and where did this admixture happen, by showing us the path to the current modern distribution.

TruthPrevails said...

@Davidski aDNA is only a snapshot in time, you know it very well. And it will end up building upon the big picture shown. For the random aDNA found which is out of the path of the big picture it will be realized that no descendants of that line survived.

Davidski said...

@Jaydeep

As usual, you're ignoring the entirety of the evidence.

Who brought ancient European markers like R1a-Z93 and H2b to South Asia? Did they not come with the steppe ancestry that you're denying exists in South Asia?

Onge and Han are indeed modern proxies for indigenous South Asian ancestry. But they provide solid statistical fits when used in models with ancient groups from Iran and the steppe, which in all likelihood are close relatives of the people who settled in South Asia during the last few thousand years. So everything makes sense for the time being, and there's no indication this will change when ancient DNA from South Asia is published.

You can't keep ignoring reality. At some point you'll have to accept it.

Davidski said...

@TruthPrevails

aDNA is only a snapshot in time, you know it very well.

And you should know very well that we now have a lot of these snapshots in time, enough to say with confidence that the Nat Geo model, as it pertains to Europe, is a total flop.

Rob said...

@ Truth
Very simple- good old archaeological evidence with site numbers. If your assertion is correct , then it should be ample

Kristiina said...

When I look at the distribution of U7, the concentration of U7 in Western Siberia is of particular interest for me. I remember that Mansis carry a smaller amount of Yamna-related R1b-L23 and my first idea was to link both R1b-L23 and U7 in Mansis to Yamnaya influence. Then I checked the Excel file to get more detailed sub-clade information, and I see that Mansi U7 is U7a2b which is none of the deep India- or Iran-specific lineages. Instead, U7a2b is a smaller lineage with four branches: a Kurdish branch U7a2a, Mansi-Burusho branch U7a2b, Indian branch U7a2c and unnamed Burusho branch. It is significant that there is an old U7 branch stemming from West Asia and ending up in non-IE speaking Burusho and West Siberian Mansis.

As for Central Asian U7, I take note that Kirgiz U7 is U7a1a2 and closely related to a small Indian subclade with an older branch also present in Iran. Mongolian U7a3a1a1a1a and Bargut U7a3a1e are related to Iran NW branches. Kalmyk U7a3a1a1a2 is found in Jordania. Buryat U7 is U7a4c and the same haplotype is found in Turkish-speaking KaraNogays. U7a4 is distributed in Bedouins, Turkish and in an Iran Arabian.

Tajik and Afghan U7 haplotypes fall into U7a3b subclade, and they are relatively deep subclades with their own identity in a West Asian "family". Uzbek U7 is U7a10a and has a sister subclade in India. Also Tajik U7a11 has a sister subclade in India, but Tajiks also have a deep haplotype in this same broadly West Asian U7 cluster. It is important that Central Asians (Afghans, Tajiks, Uzbeks, Kazakhs) also have their own very deep U7 subclades that are unique to them and not found elsewhere! These include U7a12, U7a13, U7a14, U7a15. This means that they have their own identity outside of Iran and India.

There is also an interesting early Chinese branch of U7, i.e. U7a3a1. This subclade is outside of any modern West Asian population so it probably goes back to the first Bronze Age contacts between Western China and West Asia.

Simon_W said...

@ Gioiello
"Of course the paper has many caveats about a "possible" origin of U7 in Middle East (but we know who funds these paper and which is the "ideology " beyond them)."

A Jewish conspiracy? LOL. Even if you were correct and U7 was at home in Italy ~20'000 years ago, this wouldn't change the fact that modern Italians, including Tuscans, have plenty of post-Neolithic West Asian admixture. The autosomes speak for themselveves, you need to deblock your head.

Simon_W said...

And besides, as for your critique of Brisighelli et al., large parts of modern-day northern Latium used to belong to Etruria in antiquity. The border between Tuscany and modern Latium is arbitrary, a consequence of Medieval history, and has nothing to do with ethnic borders in antiquity. Rather it has to be observed that some towns in Tuscany have Roman origins rather than Etruscan ones, such as Florence (Florentia) and Siena (Saena Julia) for instance. Some towns in northern Latium have deep Etruscan roots, like Tarquinia (Etruscan Tarchna) and Cerveteri (Caisra).

TruthPrevails said...

North South East West of Indian Subcontinent harbors all know anthropological and race types. That kind of diversity it self should tell you where the origin was.

All other regions are simply founder effects, hence the proliferation of only one type in other regions.

Davidski said...

South Asians are simply more mixed and more recently mixed than most other Eurasians.

Grey said...

"Plus this ancestry in modern Italy might be pretty significant; maybe 20-30% in the North and 50-60% in the South. To me that looks less like occasional contact with the Near East, that looks like a naval migration from the Near East. Basically imo everything is pointing towards a single pulse of migration."

https://en.wikipedia.org/wiki/Magna_Graecia

http://www.madeinsouthitalytoday.com/assets/uploads/SouthernItaly/image680/a_MagnaGrecia650.jpg

Jaydeep said...

Who brought ancient European markers like R1a-Z93 and H2b to South Asia? Did they not come with the steppe ancestry that you're denying exists in South Asia?

Let us have a paper on H2b & R1a-z93, like the current one of U7, which does a fine scale phylogenetic resolution of these clades. Let us then see if South Asian R1a-Z93 & H2b looks to be derived from a steppe source or vice-versa. Based on modern day distribution, you cannot deny that R1a-Z93 is much more diverse in South Asia then it is on the steppe. Your claim is only based on R1a-Z93 turning up in aDNA from the steppe but unless we have aDNA from India or Pakistan, to argue that steppe is the source of South Asian R1a-Z93 is just prejudice.

--------

However, I do not deny co-ancestry between West Asians & South Asians on one hand and between South Asians & the steppe groups on the other that is of Early Bronze Age period. I fully agree when you say ...ancient groups from Iran and the steppe, which in all likelihood are close relatives of the people who settled in South Asia during the last few thousand years.

They are related but the ANI portion of South Asian ancestry was largely formed already during the Late Pliestocene when it separated from groups like the CHG. Groups like CHG and Iran_N serve as good proxies for the ANI ancestry of South Asia because they are closely related to the ancestral ANI . But they are certainly not ancestral to modern ANI in South Asia. You can prove me wrong if you can get a Mesolithic sample from North India or Pakistan which is ASI and not related to CHG/Iran_N and therefore not ancestral to modern ANI. Until then I have a valid case.

Jaydeep said...

I should add here that starting with the Early Bronze Age it is most likely that South Asians began moving out towards Eastern Iran and Central Asia. This is supported by the fact that Zebu cattle dominates both these regions and have been doing so since atleast 3,000 BC, and also about 10 % of the maternal ancestry of both Eastern Iranian and Central Asian consists of mtdna M subclades derived from South Asia.

Samuel Andrews said...

@Everyone,

An Anthrogencia user who went to a conference posted a tease about ancient Iberian DNA. A speaker said Neolithic Y DNA is G and I, Bronze age Y DNA is R1b. CHG-ancestry first appears in the Bronze age. During the presentation the speaker displayed how CHG ancestry existed in Yamnaya(R1b), Bronze age Ireland(R1b), and Bronze age Iberia(R1b).

Basically it looks like we finally have confirmation Steppe ancestry and R1b came together to Iberia.

Jaydeep said...

Kristina,

I appreciate your analysis. However, let us keep in mind that the West Asian origin of U7 is not certain. It may well have a South Asian origin.

The Steppe presence of U7a subclades suggests a clear evidence of movement from Central Asia into the steppe. The time period of this movement would be interesting.

As for China, the Xinjiang region is historically and geographically a part of Central Asia. Therefore an early presence of U7 in Xinjiang is very probable. We know from aDNA about the presence of U7 around 4000 YBP in the Xinjiang region. But it also had the Indian mtDNA lineage M5 in one of the samples. Interestingly M5 shows an outward expansion from South Asia around 4000 YBP and it has also been found among the ancient samples from Egypt.

Davidski said...

Your claim is only based on R1a-Z93 turning up in aDNA from the steppe but unless we have aDNA from India or Pakistan, to argue that steppe is the source of South Asian R1a-Z93 is just prejudice.

My claim is based on R1a-Z93 on the ancient European steppe, R1a-Z645 in Corded Ware, and both R1a and R1b in Northern European foragers.

It's all over. There's nothing to debate on the topic.

TruthPrevails said...

@jaydeep

you responses are scholarly with evidence, however I am afraid you are catering to the wrong audience with those responses.

TruthPrevails said...

My claim is based on R1a-Z93 on the ancient European steppe, R1a-Z645 in Corded Ware, and both R1a and R1b in Northern European foragers.

It's all over. There's nothing to debate on the topic.


@davidski

there is nothing to prove that they did not walk up to there from South Asia or neither did they carry a flag saying we are from here.

Davidski said...

Jaydeep's responses ignore reality.

I've learned a lot in the comments at this blog about how extreme the effect of bias can be on human cognitive ability thanks to some of you Indian guys.

Davidski said...

there is nothing to prove that they did not walk up to there from South Asia or neither did they carry a flag saying we are from here.

Right, there may have been waves of R1a, R1a-Z645 and R1a-Z93 from South Asia to Northern Europe, from the Mesolithic to the Bronze Age.

None of them showed any South Asian ancestry of course, but each somehow looked typically Northern European for their times.

So it just looks like South Asia was flooded by steppe herders carrying R1a-Z93. It's just all a big coincidence and misunderstanding.

Haha.

TruthPrevails said...

Why do you think so many people have a bias, and which is not based on reality.

And how differently would you categorize your bias/belief system which thinks everything that is found near the Euro zone belongs to you, without taking into consideration where did they arrive there from.

Davidski said...

My arguments are always based on what is generally considered to be the correct interpretation of the available data.

You guys are just plain crazy. You should see a shrink if you want to know why so many people have a bias not based on reality. He'll tell you after using you as a case study.

batman said...

Kristina,

Great compilation.

The skeleton from western Iran (Seb Gabi) is no more than 5.000 yrs old. Though, both this and the 4.000 years old U7 from the Tarim Basin are MINIMI-dates, rather than maximi. Which means U7 is still older in both Iran and Tarim. How much we still don't know...

The spread of U7 across ancient Eurasia had that obviously reached both western Russia and Scandianvia no later than BA/IA. Considering that the same spread have reached tropical areas we may have to presume that the daugthers of Ursula 7 was pretty popular, active and adaptive during the late Eurasian Mesolithic, already.

Thus we may compare the U7-distribution as a west-to-east paralell of the SE Asian mt-dna C, that voyaged west to reach Carelia and Oleni Ostrov, no later than 7.500 BP, some 4.000 years after the Younger Dryas mass-extinction. Which means that, teoretically, some early spin-offs of U7 could have reached China some 7.500 years ago, already. Perhaps along y-dna O. Alternatively Q.

You're obviously right about the close, continous connections between the dynasties of the Celtic and the Chineese Bronze Age. These connections are obviously far older though, spreading pottery no later than 9.000 yrs ago and agriculture no later than 7.500 yrs ago - between Uralia, Carelia (Sperring) and the old Bulgaria (Yamna). Which connects U7 to the early distribution of R1a/R1b, too, explaining its appearance in ancient DNA from western Russia and Scandinavia.

It seems obvious that the old, central waterway of central Eurasia - from Baltia to Uralia – have carried both men and women both ways since Early Neolithic.

It might be that the U7-spread confirms what the early distribution mt-dna C and Russian archaeology already have stated; An active and continous network of travel and trade along the Volga-Ural route were starting no later than 8.000 years ago - when the mesolithic pottery of Volga-Ural starts appearing along the rivers around the Baltic Ocean and the northern rivers of the Black Sea. As well as the rivers reaching the Persian bay and the Mediterranean Ocean.

The early ceramics of Iran shows the same basic motives as we find in the mesolithic idol from Shigir – as well as the first ceramics, whether CCC, PCW, TBK/LBK, CWC or BB. The same pits, fens, triangles, squares, zig-zags, fishbones, pillars, bows and arches seem to be the basic elements used on all of them, to express esthetic as well as symbolic qualities.

http://www.iranicaonline.org/uploads/files/Ceramics/v5f3a010_f6_300.jpg

The descendants of U7 did obviously reach the eastern shores of the Atlantic as well as the rivers reaching the Pacific no later than EBA. Besides the potmaking cultures between the Black Sea/Caspian Sea and the Persian bay - no less than 5.000 years ago.

Which may indicate that the roots of the Scandianvian as well as the Chinese circles of U7 are of similar age. Seems that the alledged 'first wave' of U7 was splitting in a set of western versus eastern clads already some 11.000 years ago, before a 'second wave' made them multiply across large areas, as the mesolithic pottery became traditional craftsmanship and household items during both eastern and western neolithics.

http://www.iranicaonline.org/articles/ceramics-iv

Davidski said...

@batman

Which connects U7 to the early distribution of R1a/R1b, too, explaining its appearance in ancient DNA from western Russia and Scandinavia.

Total bullshit.

There is no U7 in indigenous European forager groups carrying R1a/R1b. In fact, there's not a single instance of U7 in any ancient European DNA until the Iron Age (Rostov Scythians).

wagg said...

Davidski: "So you reckon the West Asian-specific U7a in Tuscany dated to after the Neolithic is more likely to be from Vikings or migrants from the Urals rather than the proto-Etruscans from, say, West Asia?"
--
No, of course not. The process would have been much earlier than Viking time anyway. let's be serious.
Wait, PROTO-ETRUSCANS? how much "proto-" ? :)
But anyway, _Etruscan_ offshoots settling in north Eurasia is as incredible for me.

I can't see why we should definitely exclude more ancient different processes anyway.
I'd go for it because I can't reconcile the distribution of U7a with a credible "recent" (say, Etruscan time) spreading, personallly.
But I'm not omniscient, so... I'll try to keep an open mind.


"There is no U7 in indigenous European forager groups carrying R1a/R1b. In fact, there's not a single instance of U7 in any ancient European DNA until the Iron Age"

That doesn't mean it wasn't there. Is your theory that all the diversity of aDNA in Europe has been revealed?
Where was Y-DNA I1? Where did it show up? If I'm not mistaken, it's stil missing in the the European aDNA. It's absent from the aDNA in the place where it's now quite sizable in the gene pool, while haplogroups that doesn't exist there anymore have been found majoritarily (specific I2a clades IIRC).

Let's wait a little more before having certitudes.

Davidski said...

See here...

Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran.

Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks.


http://eurogenes.blogspot.com.au/2015/03/mitogenomes-reveal-post-neolithic-gene.html

Gioiello said...

@ Davidski

From the paper you quoted:
"Therefore,while Brisighelli et al. [3] dated the arrival of theNear East U7a2a haplogroup (now known to as U7b1; Phylotree Build 16[10]) to the Isle of Elba about 2,300 y.a., and the studies of Achilli et al. [8] and Pellecchia et al. [9]agreed with a recent arrival of Near Easterners toTuscany (thus supporting the Herodotus theory), other studies (mainly based on the analysis of ancient DNA combined with demographic simulations) favored the proposition of a connection between Tuscans and the Near East in the Neolithic (that is, the moment in which gene flow was extensively occurring in Europe). The latter option would suggest that the Etruscan culture developed locally in Italy, and not as a consequence of the arrival of immigrants from Eastern Mediterranean regions".
1) In that time I didn't write on your blog, but very likely I break in pieces that paper elsewhere as I did with the paper of Brisighelli.
2) Antonio Salas has been in my mail list till a few months ago when he asked to be unsubscribed. The other only one was Richard Rocca, and you know that I defined him "a lackey of the criminal firm". Also Antonio Salas as mostly of the Iberian geneticists has his sponsors.
3) I'd need to take at hands all these matter again, for answering you, as Kristiina did above, but I'd need time.
4) You should know that it is a constant to backdate their theories from the Levantinists:
a) Once all came from Lebanon/Palestine, after from Caucasus but before from Lebanon/Palestine etc etc. Etruscans came from Asia Minor 3000 years ago, not demonstrated, thus they say that they came before from Iran! Only stupid people like xyyman may believe to that. b) Anyway this position was supported before from Barbujani, my Farfugliani, the notorious leftist as Cavallo Sforzesco, father of the Stanfordians, who, after having said that he too, wrote many years ago that the link with Asia Minor should be backdated to many thousands of years before, but not saying who was the source. I ask: from Anatolia to Italy or from Italy to Anatolia after the Younger Dryas?
5) Where did end the finding of mt hg. H32 in Natufians and Iranaians, that, if true, it had to have come from Italy or at least Western Europe?
6) We have to do only with bufoons!

Aram said...

Samuel

Can You please give the link on BA Iberia.

Alberto said...

@Aram

Unfortunately the guy who attended that talk doesn't seem to have payed much attention to details:

http://www.anthrogenica.com/showthread.php?5079-Irish-DNA-Atlas-Preliminary-Results&p=225462&viewfull=1#post225462

Maybe Olympus Mons should try to get in contact with Rui Martiniano to ask the dates of those samples from Portugal, around the Tagus. They had R1b and CHG admixture (probably Yamnaya-like, but maybe not), but the only periods mentioned are "Bronze Age" and "Neolithic", nothing about the Chalcolithic period which is the one decisive for OM's theory. The paper should be out soon, anyway (but who knows how soon is that).

Olympus Mons said...

@Alberto.
Will try to get hold of Rui.
Boarding now to Nice...so its going to be hard to pressure him.

Anyway I am, obviously,banned from Anthrogenica. Can you sum it up for us who do not have access?

And its annoying as hell the lack of precise periodic reference in Portugal, and spain for that matter. Something huge,gigantic, happened in Iberia around 3500Bc onwards. Population went from mere scattered people in caves to Porto torrao (20,000 plus people in one place) and still they refered vaguely as late neolithic embarking the all 4th milenia and sometimes late Neolithic as into 3rd milenia.it confuses everything. There was a before 3300 bc and a after that date. Until that is clear in every analisys they will be mixing things that shouldn't.

Olympus Mons said...

@alberto
Are you saying they are talking about samples from around tagus that had r1b and had CHG?
Because to me dates are important. If a I am right there was originally r1b (with earlier WHG) with some barcin and CHG arriving through north africa (merimde and el omari) with the rest of population fleeing the birth of the Sahara, that later became the bell beakers...

Davidski said...

Great story. You should write a fiction piece based on that.

Oh, wait...

Alberto said...

@OM

The guy does not give much details other than what I pointed above. He says that Neolithic samples from Iberia are similar to Neolithic samples from Ireland (the thread is about Irish DNA), and that Bronze Age samples from Iberia are similar to Bronze Age samples from Ireland. Then he mentions that those Iberian samples are from Portugal (Tagus), and that they have CHG admixture.

Just go into private mode in your browser and try the link to anthrogenica. That should probably work to read the thread.

Nirjhar007 said...

OM,

Looks like a decisive moment is coming soon .

Nirjhar007 said...

Alberto,

So it appears they have Steppe admixture !.

Olympus Mons said...

@davidski
Go get a fix of steppe drug somewhere and then comeback. It looks like its becoming real scarce the stuff "...and they came from the steppe".

Gioiello said...

@ Davidski

From the discussion about the thread you quoted above:
"And the date would suggest that this is related with Byzantine people leaving their decaying empire for Tuscany, where they eventually triggered the Renaissance".
A few scholars migrated to Tuscany for teaching Greek language would have given birth to the Rinascimento and influenced the Tuscan gene pool! An that by quoting the fake study of Hellenthal, whose dates (522 - 1222 AD) are long before the fall of Constantiple/Byzantium (1453). And this Simon_W was who pretended teaching me History! Have we to think that at Harvard and Stanford, beyond a worst genetics, they teach also the worst History? Simon_W shots bullshits as missiles, but let that their fleet go to Kim...
From now onward we haven't only xyyman...

Olympus Mons said...

At Nirjhar
Yes. But following Heydt paper and bearing in mimd he knows more than he can say,it looks like those iberians bell beakers are going to be r1b like hell.

Rob said...

@ Alberto

That person (Heber) generally knows what he's taking about. So if he says Bronze Age, I'd gather he means post 2200 BC. But who knows ..

Olympus Mons said...

@Nirjhar
So finding CHG now is steppe?! Since when?

Nirjhar007 said...

OM,

IINW , Irish samples had Steppe ADMIXTURE? . And as '' Neolithic samples from Iberia are similar to Neolithic samples from Ireland (the thread is about Irish DNA), and that Bronze Age samples from Iberia are similar to Bronze Age samples from Ireland. ''.


Which means Chalco Iberia perhaps didn't have R1b . Not certain yet but not a very favorable indication for you mate , I am sorry but your theory is in trouble (Apparently) .

Alberto said...

Yes, as I understand the Bronze Age reference should be correct and refer to after 2200 BC. And the CHG admixture should also refer to CHG+EHG (Yamnaya-like). But I was not there to check for myself, so we'll have to wait for the paper (or try to get those details from that researcher himself, if he's willing to answer those questions).

ANI EXCAVATOR said...

Jaydeep, you constantly misrepresent the results of Metspalu et al 2011. They uncovered nothing that rules out IE contribution to India from a European-like population. They never claim this in their paper.

Metspalu et al never state that South Asians and West Eurasians separated 12500 ya. They only said that the haplotype diversity measure they used is sensitive to migration and divergence up to 12500 ya, and their conclusions are valid up to that time.

You say that the haplotype diversity of South Asians is greater than in West Eurasians. In fact, the haplotype diversity of the south Asian Component is what they found to be the highest in South Asians. The diversity of the South Asian component is greater than for the West Asian component, which is in turn greater than the East European and Mediterranean components, but since West Eurasians other than Iranians and Central Asians do not have the South Asian component, this is a moot point. Furthermore this is entirely expected as the South Asian component has mixed affinities and South Asia has had higher population density.

In contrast to widespread light green ancestry, the dark green ancestry component, k6 is primarily restricted to the Indian subcontinent with modest presence in Central Asia and Iran. Haplotype diversity associated with dark green ancestry is greatest in the south of the Indian subcontinent, indicating that the alleles underlying it most likely arose there and spread northwards. It is notable that this ancestry component also exhibits greater haplotype diversity than European or Near Eastern components despite the fact that the Illumina genotyped markers were principally ascertained in a sample of European individuals.

Metspalu do not claim that the West Asian component associated with the Ganj Dareh type farmers arose in India and spread West.

If the k5 light green ancestry component (Figure 2B) originated from a recent gene flow event (for example by a demic diffusion model) with a single center of dispersal where the underlying alleles emerged, then one would expect different levels of associated haplotypic diversity to suggest the point of origin of the migration.... For alleles associated with k5, haplotype diversity is comparable among all studied populations across West Eurasia and the Indus basin (Figure S8).

In that supplement the most diverse haplotypes for the West Asian component is found in Caucasians and Iranians, followed by Brahui.

You further neglect this claim:
the Brahmin and Kshatriya from Uttar Pradesh stand out by being closer to Pakistani (FST = 0.006 on average) and West Eurasian populations (FST = 0.030) than to other Indian populations (average FSTs 0.017 and 0.046, respectively) from the same geographic area (Figures S1 and S11)

You conveniently leave out the fact that the component dominant in East Europe appears at a low level (5-15%) among all IE speakers in India, differentiating them from the Dravidians, and also peaks locally in Uttar Pradesh Brahmin, Kshatriya, Tamil Nadu Brahmin and High Caste Gujaratis. In line with their haplotype-based analysis, this component must have reached India within the last 12500 years, not before--likely much later than 12500 years ago.

https://imgpile.com/i/ZSPIo

Rami said...

Who brought U7 to Siberia???

Davidski said...

Who brought U7 to Siberia???

Probably Scythians or a similar Iron Age group.

batman said...

@ Davidski

""Which connects U7 to the early distribution of R1a/R1b, too, explaining its appearance in ancient DNA from western Russia and Scandinavia."

Total bullshit.

There is no U7 in indigenous European forager groups carrying R1a/R1b. In fact, there's not a single instance of U7 in any ancient European DNA until the Iron Age (Rostov Scythians)."

The Scytian U7 from Rostov belongs to the cathegory "ancient DNA".

I never claimed U7 to have spread among foragers. I just claimed that it could have. What's clear is that there actually exists one, from Rostov-on-Don, that belongs to an area and a time when R1a/R1b completely dominated the Scytian-Sarmatian areas.

Likewise, the U7 from Xiaohe (ca. 4.000 BP), had company of some R1a1a-highlanders, too. When the same signatories - U7 and R1a1a - are found together in IA Scandianvia we have to suspect that they both were involved in the spread of the slash-and-burn-agriculture, able to utilize an agricultural production in the boreal woodlands, the northern steppelands and the higher elevations of Eurasia.

Which, in turn, connects to the early pottery of the Volga-Kunda-Don-Bug-Ertebolle-cultures - from which the GA/TBK/BB-technocomplexes arise and thus the EBK/LBK/BB/COW/PWC/CWC/CCC/PW-cultures.

Since the 6.000 yrs old U7 from Iran also connects to a well-known culture pioneering agriculture and pottery in Mesopotamia, we might suspect that the U7 was part of that effort - both south and north of the Caucasian mountain-range.

Horsemaneure or not.

Davidski said...

Good post above from ANI EXCAVATOR.

Sounds like the ANI excavating is in reliable hands.

Davidski said...

@batman

I never claimed U7 to have spread among foragers. I just claimed that it could have. What's clear is that there actually exists one, from Rostov-on-Don, that belongs to an area and a time when R1a/R1b completely dominated the Scytian-Sarmatian areas.

Scythians also show other South Caspian mtDNA HGs, like HV2 and U1, which suggests that unlike East Euro foragers, Yamnaya, Srubnaya, and other older steppe groups, the Scythians actually had some maternal ancestry from Iran and surrounds.

They were highly mobile and their presence south of the Caspian is documented in historical literature, so I'm not surprised they carried U7, HV2, U1 and so on.

Davidski said...

@xyyman

Do not post any Afrocentric nonsense in the comments here. I will delete it as soon as I see it.

Gioiello said...

@ xyyman

If Davidski lets my post pass, this is the last time I write to you, because you have no idea what you speak about.

Etruscan is an agglutinative language, nothing to do with Afro-Asiatic ones:
culs "the door"
culs-l "of the door"
culs-cva "doors"
culs-cva-l "of the doors"

Al Bundy said...

Heber attended a talk and posted about it on Anthrogenica? He's definitely a bright guy but he supported John Koch's Celtic from the West theory which Koch has modified after the Haak and Allentoft papers come out.He seems to have latched onto the idea that CHG is crucial for the PIE debate so he might be overemphasing that element in his report.Not dissing him just saying,judging by his Anthrogenica posts he knows a lot about ancient Iberia and Ireland.

batman said...

Just note that the populations of western Russia, Estonia and Fenno-Scandia have old roots - as there were only two, known immigrations/spreads to these areas - unto modern time. The first known as "the pioneer-phase" when these areas were first populated after YD, the other as a consequence of the Holocene optimum (8.000-4.000 BP), when even higher elevations grew green, lush and tall - making slash-burn-agriculture possible across extraordinarily wide areas.

The spread of R1a is clearly connected to this quantum leap in population-growth across norther Eurasia. Just as the R1b-dynasty seems to be responsible for a similar and pretty contemporary growth in the lower, larger and milder plains of Eurasia, able to provide year-around grasslands for the larger bullhorns.

When we find Iron Age-samples from western Russia AND Scandinavia there is a certain possibility that also this clad have a pre-neolithic origin. The populations known to be "indigenous" to the mentioned areas where pretty 'completed' no later than LNE/BA.

Which is why one may suspect that U7, perhaps together with U5 and H/V, actually had something to do with the spread of agriculture OR pottery. Or both.

---

The 4.900 year old U7 from Iran may be of the same age and origin as the 4.000 yr old U7 from China. Moreover - the 2.500 yrs old sample from Rostov-on-Don and a 1.300 yrs old farming-woman from the Bay of Oslo may have a similar age, as independant clads.

Let's hope they find some more U7 - both extant and ancient. The few samples so far mapped are definitly hinting at some very intresting trends. "At least tentatively", to quote professor Kristiansen...

Davidski said...

@xyyman

Just deleted your post.

Nuragic and Etruscans are not Amazigh Africans. Do not claim nonsense or I will delete your posts.

Karl_K said...
This comment has been removed by the author.
Davidski said...

@xyyman

I am citing and referring to published SCIENTIFIC papers and you keep deleting it.

You don't understand the scientific papers you're quoting, and you're misrepresenting them.

Learn the basics before trying to post here again.

Karl_K said...
This comment has been removed by the author.
ak2014b said...

@Kristiina

Did you also look at that Palanichami et al 2015 paper that Davidski once blogged about, which has modern mtDNA samples from India and Bangladesh?
And Derenko et al 2013, which had modern mtDNA samples from Iran? I'm looking at the data in both the papers when going through your comment, and am adding in references to any pertinent samples.


"I see that Mansi U7 is U7a2b which is none of the deep India- or Iran-specific lineages. Instead, U7a2b is a smaller lineage with four branches: a Kurdish branch U7a2a, Mansi-Burusho branch U7a2b, Indian branch U7a2c and unnamed Burusho branch."

There's two U7a2 samples and one U7a2b from south and central India.
There's a U7a2a1 in a Kurd from Kermanshah in West Iran.


"As for Central Asian U7, I take note that Kirgiz U7 is U7a1a2 and closely related to a small Indian subclade with an older branch also present in Iran."

There's a U7a1* in a Persian from Fars Province in south Iran.
There's several instances of U7a1a in north and east India and Bangladesh.


"Buryat U7 is U7a4c and the same haplotype is found in Turkish-speaking KaraNogays. U7a4 is distributed in Bedouins, Turkish and in an Iran Arabian."

There's one modern sample of U7a4 and 2 of U7a4a from India.
There's one U7a4a sample in Iran, a Turkic speaking Qashqai from Fars in Iran's south. There's also one sample of U7a4a1 and 2 of U7a4a1a in Iran.


"There is also an interesting early Chinese branch of U7, i.e. U7a3a1. This subclade is outside of any modern West Asian population so it probably goes back to the first Bronze Age contacts between Western China and West Asia.

Tajik and Afghan U7 haplotypes fall into U7a3b subclade, and they are relatively deep subclades with their own identity in a West Asian "family".'

Mongolian U7a3a1a1a1a and Bargut U7a3a1e are related to Iran NW branches. Kalmyk U7a3a1a1a2 is found in Jordania."


The Chinese U7a3a1 could be from Iran, where it occurs. U7a3a1 doesn't occur in Indian and Bangladeshi samples, however U7a3a occurs in India, whereas it was not found among the Iranian samples.

In India, there's 3 instances of U7a3a, besides a handful of U7a3a3 samples, and quite a few of U7a3a2 and U7a3b1. In Bangladesh, there's further 2 samples of U7a3b1. There's a few U7a3b1a in Punjab in west India, as well as 1 sample of U7a3b1a in Gujarat and one in Uttar Pradesh in west and north India, respectively.

There's 2 x U7a3a1, 1 x U7a3a2 and 3 x U7a3b1 all in Kerman and Fars provinces in southeast and south Iran respectively. It may be connected or coincidence, but the only M5 subclades found by Derenko et al 2013 in modern Iran were from the same two regions, Kerman and Fars, and were comprised solely of M5a2a4 or downstream and one instance of M5a2a1a. So there is the possibility that the M5 subclades and U7a3a subclades were introduced into Iran together from further to its east.

Jaydeep said...

ANI EXCAVATOR,

I haven't misrepresented Metspalu et al but you've certainly done a fine job of misrepresenting me. So let me set the record straight.

They uncovered nothing that rules out IE contribution to India from a European-like population. They never claim this in their paper.

Where have I quoted Metspalu et al to support any such argument of mine ? Please show it. I am eager to know.

Metspalu et al never state that South Asians and West Eurasians separated 12500 ya. They only said that the haplotype diversity measure they used is sensitive to migration and divergence up to 12500 ya, and their conclusions are valid up to that time.

I have also not said that South Asians and West Eurasians separated 12,500 years ago. This is what I said..

This paper again reiterates that the West Eurasian ancestry in South Asia split up from its West Asian counterpart at the end of LGM, likely around 15 kya.

This early split was first indicated by Metspalu et al in 2011 when they said that the the Caucasus group and the South Asian group (West Eurasian) had not admixed atleast since 12.5 kya


Can you read the above ? Does it mean the same as what you accuse me of ?

The above statement of mine is not misrepresenting Metspalu et al because they say in their paper..

We found no regional diversity differences associated with k5 at K ¼ 8.
Thus, regardless of where this component was from (the Caucasus, Near East, Indus Valley, or Central Asia), its spread to other regions must have occurred well before our detection limits at 12,500 years. Accordingly, the introduction of k5 to South Asia cannot be explained by recent gene flow, such as the hypothetical Indo-Aryan migration.


Do you see any contradiction in my statement and the statement above by Metspalu et al ? Do enlighten me.

I did not say that South Asians separated from West Eurasians 12500 years ago. I said that the West Eurasian ancestry shared between the Caucasus/Iran and South Asia (k5 in Metspalu et al) is not of recent import in South Asia but is present there from before 12500 years ago. And this is what Metspalu et al say. Don't they ?

You say that the haplotype diversity of South Asians is greater than in West Eurasians. In fact, the haplotype diversity of the south Asian Component is what they found to be the highest in South Asians. The diversity of the South Asian component is greater than for the West Asian component, which is in turn greater than the East European and Mediterranean components, but since West Eurasians other than Iranians and Central Asians do not have the South Asian component, this is a moot point. Furthermore this is entirely expected as the South Asian component has mixed affinities and South Asia has had higher population density.

I never said anything regarding the above so it is irrelevant to the discussion. Don't create a strawman.

(continued...)

Gaspar said...

@ batman

Etruscans have origins in central Italy from Umbrian people. One needs to see where Umbrians originate from.

Wends are only associated with Veleti ( slav tribe ) of upper Vistula and have noting to to with Venedi of lower Vistula or Veneti from the adriatic.
check Veleti or wendish crusades.

Lower Vistula = next to baltic sea
Upper vistula = where Vistula river begins

Jaydeep said...

Metspalu do not claim that the West Asian component associated with the Ganj Dareh type farmers arose in India and spread West.

Neither did I. Please tell me where have you read my statement to such effect. I said something else - the assumption that this component originates in Iran or Caucasus and that it spread to South Asia during Neolithic is unwarranted. Its origin is not known and that is also what Metspalu et al say. Don't they ?

You further neglect this claim:
the Brahmin and Kshatriya from Uttar Pradesh stand out by being closer to Pakistani (FST = 0.006 on average) and West Eurasian populations (FST = 0.030) than to other Indian populations (average FSTs 0.017 and 0.046, respectively) from the same geographic area (Figures S1 and S11)


So ? Uttar Pradesh is close enough to Punjab & Haryana. The Brahmins and Kshatriyas probably have more western admixture from Punjab, Haryana and Pakistan. Why should it necessarily imply a migration from outside of South Asia ? Furthermore, it is most likely that the lower castes & tribes in places such as Uttar Pradesh received substantial East Eurasian admixture which the Brahmins and Kshatriyas stayed clear of. Read the recent paper on the Gond tribe in India.

You conveniently leave out the fact that the component dominant in East Europe appears at a low level (5-15%) among all IE speakers in India, differentiating them from the Dravidians, and also peaks locally in Uttar Pradesh Brahmin, Kshatriya, Tamil Nadu Brahmin and High Caste Gujaratis. In line with their haplotype-based analysis, this component must have reached India within the last 12500 years, not before--likely much later than 12500 years ago

This is the only sensible bit in your post. However I was not discussing this as you can see from above. This k4 European component is not necessarily East European because it dominates across Europe. Its presence in South Asia is patchy and in only trace quantity. It needs an explanation. But the presence of this component in trace quantities in South Asia is not an automatic proof of steppe migration into South Asia. Or is it ? It is present across Middle East & North Africa in larger proportion and has diversity equivalent to that in Europe, where the population is largely of non-IE speakers. How do you explain that ?

ak2014b said...

@batman
"The 4.900 year old U7 from Iran"

The Iran Chalcolithic sample was U7a (I believe) and was estimated to be from 4500-3500 BCE. So that would be between 6500 to 5500 years ago.

According to the Lazaridis et al 2016 supplementary information, the sample was labelled I1665 and was from Chalcolithic layer Mound A in Seh Gabi in Iran,

"No radiocarbon dates have been obtained on Mound A, and so we use archaeological dates for the Chalcolithic of 4500-3500 BCE."

Olympus Mons said...

@Alberto.
That is not what the comments in antrogenica shows....

Total confusion: Heber , heber did you mean ANE? No...CHG.
Than Heber saying Rui talked about south caucasus people taking the CHG up Kuban river to steppe (remember I was the guy saying that of the shulaveri up the kuban river and then taking Samara river?).
He says Rui also talked about Kura araxes and a south route of CHG into western europe, does he not? That does not reach eurogenes, does it?

ANI EXCAVATOR said...

Jaydeep, on 05/17/2016, you stated:

Coming to post-LGM population movements, it seems to me very likely that in comparison to the Neat East as well as Iran, South Asia would have been much more suitable as a vast LGM population refugium. So while during the LGM, most populations across the Northern hemisphere would have suffered bottlenecks, South Asia would have fared significantly better. Post-LGM, we can therefore envisage a scenario in which groups from South Asia began migrating Northward & Westward into sparsely inhabited regions, sensing better weather & vast empty spaces. This maybe how the CHG reached the Caucasus & the Iranian Mesolithic sample reached the Hotu cave South of the Caspian.

On June 3, 2016, you stated:
As I have pointed out earlier, Metspalu et al 2011 have already argued that the Caucasus & the Gedrosian components had already separated by 12500 BP. So the Gedrosian/CHG in South Asia is older than 12500 BP and is not a result of any movement from the Caucasus during the Holocene.

Then on June 5, 2016, you stated:
Here is my take. Zagros Neolithic is not the source of South Asian Neolithic. I think it's the other way around. During the LGM, South Asia probably was a vast refugium. After LGM, maybe groups started migrating westward - CHG & Zagros Neolithic being the examples of such early movements. While CHG may have moved before the advent of Neolithic, Zagros Neolithic perhaps moved later on at the start of Neolithic. Therefore it is probable that Zagros Neolithic was a western extension of South Asian Neolithic...


Metspalu have never found a haplotype-diversity based argument for movement from East to West. If anything, the most diverse haplotypes were found in Caucasians, Iranians, and Druze, not in South Asia.

It is present across Middle East & North Africa in larger proportion and has diversity equivalent to that in Europe, where the population is largely of non-IE speakers.

Twisting of facts again.
https://imgpile.com/i/ZaB1r

Alberto said...

@OM

Yes, as I clearly said from the beginning, he mentions CHG admixture. Apparently he means CHG+EHG (because he says they're like the Irish Bronze Age samples, which had CHG+EHG), but it's anyone's guess what he really meant.

Rui mentioned the migration of CHG to the steppe too. But that's nothing relevant to Iberia.

But no, this Herber doesn't say that Rui talked about a southern route of CHG into Western Europe. This is Herber's own "suspicion": "I suspect a southern route of CHG to Iberia either via Stelae route or Mediterranean."

Don't be paranoid. Details are scarce (no mention of chalcolithic, especially). Let's wait for the samples, or try to ask Rui directly about those details. If those samples turn out R1b and have only CHG admixture it's going to be a big thing. But for now I'd be cautious about that possibility.

Olympus Mons said...

@Alberto....got it.

batman said...

ak2014

Tx. 5.000 carbon-years is calibrated to "5.956-5.796 calBP".

Anyhow at the later half of the Neolithic, as the painted ceramics, heraldry and written languages spread around Crete, Egypt, Sumer and Indus.

Davidski said...

@Olympus Mons

Heber has a bit of a fixation with CHG. His report on Rui's talk reflects this, especially where he's trying to fill in the blanks.

But in fact, from what was actually said at the presentation, it's clear that a population originating on the Eastern European steppe, heavy in R1b, and basically identical to the steppe-admixed EHG-rich Rathlin samples, from Early Bronze Age Ireland, arrived in Iberia during the Bronze Age (not Chalcolithic).

This doesn't back up your theory. It contradicts it. There is no chance that these Bronze Age Iberians with R1b will show CHG admixture without EHG admixture, and no chance that they or their ancestors came to Iberia from North Africa.

Not sure why the penny hasn't dropped yet? Maybe you're suffering from the same condition as some of our Indian friends here, like Jaydeep, Balaji and Truth Prevails? Have you guys thought about getting together for therapy meetings? Apparently it's easier when you talk about it.

But I digress. Keep in mind also that Rui talked about Maykop and Kura-Araxes as potential sources of CHG-related admixture in Yamnaya (and I guess other Eneolithic/Early Bronze Age steppe groups), and not as populations that may have migrated to Iberia or even Europe.

However, let me make it clear that Rui was just speculating about Maykop and Kura-Araxes as potential sources of southern ancestry on the Eneolithic/Early Bronze Age steppe. I can assure you that it is still very much a mystery where this southern ancestry came from exactly.

Al Bundy said...

It is a mystery and that invites a lot of speculation,as in this is a smoking gun for whatever theory one already believes or hopes is true.Hopefully the upcoming papers will clear away the smoke and we'll see blue sky.

Davidski said...

Hopefully the upcoming papers will clear away the smoke and we'll see blue sky.

Not sure that they will. We might have to wait longer for a definitive answer.

But it won't matter much, if, for instance, we see more samples from Maykop, Kura-Araxes and Chalcolithic Iran and surrounds, and the uniparental markers still look wrong, with all sorts of weird stuff, like M and U7, that is found in the ancient Caucasians and Iranians, but missing in Yamnaya and close relatives.

At the same time, if Mesolithic, Neolithic and Eneolithic steppe samples show R1b-M269, R1b-L51 and R1b-Z2103, then it'll be practically over, without it being said outright.

Nirjhar007 said...

It can mean also ,that they have more CHG than EHG type, in that case perhaps EHG is negligible. We will have to wait .

Davidski said...

Not possible because they're like the Bronze Age samples from Ireland which have a lot of EHG.

Nirjhar007 said...

So four scenarios :

1. Typical Steppe like (CHG+EHG) + EEF .

2. (CHG heavy + EHG minor ) +EEF .

3. (CHG +WHG ) +EEF.

4. Not much EEF in all above sets .

I think no. 1 is very likely , we will see.

Al Bundy said...

To ultimately nail things down we need preYamnaya data,as far as the language is concerned.Evidence of steppe movement into Anatolia where the first PIE split took place.The migration of Yamnaya into Europe was massive according to the Haak paper and nothing since then at least that I've seen has changed that thinking.Anthony has speculated on what steppe groups went to Anatolia we don't know yet.

Nirjhar007 said...

At the moment we will get Mycenaean , expected this year . The Indian one , long awaited and perhaps more E European too .

There may be others too .

Nirjhar007 said...

Oh sorry Two Indian ones , oh yes.

Joerg Hensiek said...

you are aware of this new study?
"...showing that the paternal descendants of the Yamnaya still live in the Pontic steppe and that the ancient Yamnaya population was not an important source of paternal lineages in present-day West Europeans."

https://link.springer.com/article/10.1007/s00439-017-1770-2

Davidski said...

Sure am...

http://eurogenes.blogspot.com.au/2017/03/epic-fail.html

Gioiello said...

@ Joerg Hensiek

"you are aware of this new study?"

He knows that very well, because I am writing that long before the Balanovskij et al paper, also on his blog.

Matt said...

Though looking for a source for Iberian Bronze Age it's more the EHG:CHG ratio we will want to look at than looking for EHG without CHG.

Using a Fst PCoA model, fits for Armenia at: Chalcolithic - https://pastebin.com/FE9kaNre, EBA - https://pastebin.com/RLxepvG8, MLBA - https://pastebin.com/CmYCHBcJ.

They're all most substantially Anatolia_Neolithic in ancestry, but there is a good 14% (CA), 7% (EBA), 18% (MLBA) of EHG. CHG+Iran_N is at 32% (CA), 46% (EBA), 40% (MLBA).You would need quite a lot from any of them as a source to give a substantial quanity of either CHG or EHG!

For comparison: Iberia_CA - https://pastebin.com/j091ACwD, Central_MN - https://pastebin.com/mCf1mFW7, Jordan_EBA https://pastebin.com/acvxpvUT, Iran_Chalcolithic - https://pastebin.com/vV4YqFrW, Yamnaya_Kalmykia - https://pastebin.com/B2sSn6mQ

(European Bronze Agers - https://pastebin.com/EPsrWqP3. Yamnaya fraction implied by EHG level; Unetice - 58%, Bell Beaker - 50%, Corded Ware - 75%, Hungary_BA - 30%).

Karl_K said...

"you are aware of this new study?"

Does anyone here not have at least a google alert set to email the latest papers containing keywords of interest?

ak2014b said...

@batman

5.000 carbon-years is calibrated to "5.956-5.796 calBP".

Yes, the supplementary table 1 of the Lazaridis et al 2016 paper provides a calibrated date for the Iranian Chalcolithic U7a sample, ID I1665,

"3956-3796 calBCE (5070±30 BP)"

So the Iranian Chalcolithic individual with mtDNA U7a is indeed from around 6000-5800 years ago.


If the BP date they provide is the radiocarbon date, then I'm getting a calibrated date of 3877 ± 56 calBCE for this (3933-3821), which doesn't match Lazaridis et al's calibrated date. So I'm not sure how the "5070±30 BP" relates to their calBCE date. Perhaps I'm just using CalPal wrong.


@Nirjhar
Oh sorry Two Indian ones , oh yes.

Is the 2nd Indian paper, which you mention will be coming out this year too, also about aDNA? Or is it about modern DNA? Anthrogenica members had earlier mentioned that a new paper on Indian R1a diversity was in the works. That may be interesting, but not as interesting as more aDNA.

If the 2nd paper's about more aDNA, what region and period will the samples be from? The Himalayas, the Andamans, south or east, or more IVC? Upper Paleolithic, Mesolithic or early neolithic, or more from later periods?

mahaloeveryone said...

"Not sure why the penny hasn't dropped yet? Maybe you're suffering from the same condition as some of our Indian friends here, like Jaydeep, Balaji and Truth Prevails? Have you guys thought about getting together for therapy meetings? Apparently it's easier when you talk about it."

There's a good possibility these posters with opposing views are Indian, but just to differentiate, they are trying to logically prove a strand of Hindu-centric world view, there are Indians (and other Hindus) on this blog who agree with a lot of the findings you and others present Davidski. Just don't want this to be an a impression of a monolithic Indian position, when a lot of Indians, including those that are Hindu (the element I'm referring to are Hindutva who actively pursue a revisionist history but want to sound scientific about it) want the real truth, not the manipulated data that get presented to support a Hindutva position. That being said thank you all on this group for bringing together and discussing all this amazing data and findings that is illuminating the mysteries of the past and in my hope will bring people together in the joy of the discovery of the accurate academic findings of who our ancestors were.

Jaydeep said...

Let me just add a caveat to what you just said. No is disputing the findings. After all facts are facts. The difference is in the interpretation of facts. Most of the posters here are European. Though we have some wonderful unbiased people like Matt, Rob, Alberto & Frank, the others are quite Euro-centric. We do not have any aDNA from India but the insinuation of these Euro-centrists is that ancient demographic history of South Asia is already solved, there was a Bronze Age migration from steppe into South Asia and aDNA will prove it. As an Indian if you unquestioningly accept their view I have nothing to add. But so far there is only evidence of shared ancestry. This does not automatically mean a migration from the steppe into South Asia. Let us not allow these Westerners to bully us into accepting their version of our history. Standing firm against it does not make one biased. I hope you get the point.

Davidski said...

@Jaydeep

But so far there is only evidence of shared ancestry. This does not automatically mean a migration from the steppe into South Asia.

This is absolute nonsense.

The Y-DNA, mtDNA and genome-wide DNA indicate not only shared ancestry between Europeans and South Asians, but also major population movements from the Eastern European steppe into South Asia.

I've set out the evidence for this in multiple posts on my blogs in a way that should be easy to understand for most people with even a basic interest in population genetics and ancient DNA.

You refuse to accept this because you're in denial.

Karl_K said...
This comment has been removed by the author.
TruthPrevails said...

This is absolute nonsense.

The Y-DNA, mtDNA and genome-wide DNA indicate not only shared ancestry between Europeans and South Asians, but also major population movements from the Eastern European steppe into South Asia.

I've set out the evidence for this in multiple posts on my blogs in a way that should be easy to understand for most people with even a basic interest in population genetics and ancient DNA.

You refuse to accept this because you're in denial.


None of the aDNA found on the steppe is within close range of its TMRCA, so claiming some aDNA which is 1 to 3k years after its TMRCA without investigating aDNA from surrounding areas is simply wishful thinking. As of today with the existing data no body knows for sure, where the origin is, most studies are putting in a calculated guess.

This is almost like going all in on a full house hand in poker, without thinking there are more bigger hands above it.

TruthPrevails said...

On a lighter note: R and R1 is rooted in South Asia, so the way I see it is where ever the kids originated(R1a and R1b), some kids married WHG women and moved north and some kids married local women and stayed around. :)

Folker said...

TruthPrevails, are you sure that you understand correctly how genetics work? Because it is fairly clear that if a migration from South Asia to Eurasian Steppe or even Europe occured, you'll find some kind of specific admixture from South Asia into Europeans. This is not the case. But we find some specific European Admixture into South Asian, so the migration occured the other way: from the Eurasian Steppe to South Asia.

Karl_K said...

"On a lighter note: R and R1 is rooted in South Asia"

There is literally an ancient genome sequence with a pre-split R* haplotyoe from a location far from South Asia >20,000 years ago.

TruthPrevails said...

TruthPrevails, are you sure that you understand correctly how genetics work? Because it is fairly clear that if a migration from South Asia to Eurasian Steppe or even Europe occured, you'll find some kind of specific admixture from South Asia into Europeans. This is not the case. But we find some specific European Admixture into South Asian, so the migration occured the other way: from the Eurasian Steppe to South Asia.

You are comparing the modern admixture with aDNA. No one knows what the admixture level for South Asians was back in time without aDNA from there.

TruthPrevails said...

There is literally an ancient genome sequence with a pre-split R* haplotyoe from a location far from South Asia >20,000 years ago.

thats exactly the point, which proves folks from SouthAsia have in past been venturing out on the plains in central asia and eastern europe mutiple times, chasing food, as they must have found it much easier to hunt herbivores on the plains with clear line of sight.

ak2014b said...

I've noticed something peculiar looking through the Indian, Bangladesh and Iranian U7 samples from the Derenko et al 2013 and Palanichamy et al 2017 papers on modern Iranian mtDNA and on West-Eurasian mtDNA in India and Bangladesh, respectively.

There's many modern samples of basal U7 scattered throughout caste and tribe in India, though less in the east than the other 3 regions (and basal U7 is not found in the paper's samples from Bangladesh). If U7a3 subclades are counted as one group, then U7a3 is the frequent form of U7 in India, and basal U7 the 2nd most frequent.

However, in the modern Iranian samples from Derenko et al 2013, there's no U7 found at all.


There's 6 samples of U7a* in Iran. There's no U7a* in India or Bangladesh. Several instances of U7a occur in Indian samples, more in the north than in the west or other directions. U7a is however not documented by Derenko et al 2013 for Iran. Further, there are some instances of U7b and U7c in India and Bangladesh, and one sample of U7b* in Iran.

Even taking into account that the total Iranian sample size in Derenko et al 2015 is far lower than the Indian sample size in Palanichamy, the fact that U7a* turns up several times whereas U7 doesn't (nor U7a) is unexpected.

The Palanichamy et al 2015 paper referenced the Derenko et al 2013 paper, so the distinction between U7a* and U7a in these papers is real. However, there's no clarity on whether the U7a* instances in Iran are mostly individually different from each other, signifying a true paragroup, or whether they are mostly of the same type, being simply a branch distinct from U7a.

Though U7 didn't turn up in Iran Neolithic samples, the mtDNA of an Iranian Chalcolithic sample from the 6th millennium bc was U7a. It's unexpected that actual U7a appears to have left little, if any, trace in modern Iran (though some U7a* is present there), despite Iran Chalcolithic possibly making up a goodish part of modern Iranians, more so than in modern South Asians.

ak2014b said...

I'm further noticing that most of the mtDNA haplogroups found in Iran Neolithic and Chalcolithic aDNA have little or no presence in South Asia, whereas many are not insignificant in Iran. For example, I could find no X2 or any X listed among the West Eurasian mtDNA documented in modern Indians and Bangladeshis in Palanichamy et al 2015, whereas X2 was among the Iran Neolithic finds.

The mtDNA haplogroups found in ancient Iran samples in Lazaridis et al 2016 were documented in Supplementary Table S1 as

HV2 (in Mesolithic Hotu); R2, HV0f, J1c10, X2 (Neolithic); K1a12 (Late Neolithic); K1a12, H29, I1c, U3a'c, U7a.

And the Iranian Neolithic mtDNA in Broushaki et al 2016 consisted of
J1d6, 2 x R2, T2c

Of these, the HV2 found in Mesolithic Hotu occurs in modern India and Bangladesh samples, as well as HV2 subclades H2a, H2a1 and H2a2. HV is slightly more common than HV2 and also occurs in Bangladesh. But Iran Mesolithic is not considered a contributor to modern South Asia.

In contrast, most of the Neolithic Iranian mtDNA haplogroups don't occur in the mtDNA samples from modern India and Bangladesh, nor does the Late Neolithic (also Chalcolithic) Iranian K1a12. Neither X nor its subclades occur at all. J1c10 and HV0f don't occur either, with the J1c branch very rare and HV0 not present in any sample. And the only K1a is a solitary K1a1b2a sample.

R2 and T2c are the sole mtDNA haplogroups from Iran Neolithic that were found in the modern Indian (though not Bangladesh) samples, albeit in low frequency and in subclade forms, where R2 occurs as R2a, R2a4 and R2c1a, and T2c occurs in 3 samples as T2c2. But many more instances of basal T1 and T2 occur in the samples from India and Bangladesh.

Turning to Iran Chalcolithic, only the U7a found there (assuming it was not some U7a*) occurs in modern Indians, despite being apparently rare or perhaps even absent in modern Iranians. However, other Iran Chalcolithic mtDNA is rare or absent in the modern Indian and Bangladesh samples: there is no U3a'c, no H29 and K1a12a, and only 2 samples of I1c (as I1c1).

A larger sampling of Iran may be helpful. However, so far, all this makes me think that U7 in South Asia might not necessarily be from West Asia, because of the distinction in U7 lineages between modern South Asia and Iran, considering that the older lineage of basal U7 is not yet found in aDNA and not found in the modern Iran samples, but is found scattered in India and Bangladesh. Another reason is that none of the other Iranian Neolithic and Iran Chalcolithic mtDNA lineages managed to get a foothold in India and Bangladesh, whereas U7 and its subclades look to be the most common of the West Eurasian mtDNA haplogroups in India going by Table S3 of Palanichamy et al 2017.

I'd expect a greater survival of Iranian Neolithic lineages in South Asia if the Iranian Neolithic did contribute the earliest West Eurasian component in the region. Or is the West Eurasian contribution from the Iranian Neolithic only expected to be significant further northwest in South Asia (such as Pakistan), and in South Central Asia? Alternatively, is the Iran Neolithic West Eurasian input in modern South Asians supposed to have been due to a very male-heavy migration, while mtDNA lineages remained local?

Davidski said...

@ak2014b

But Iran Mesolithic is not considered a contributor to modern South Asia.

By whom?

Iran Hotu is very similar to Iran Neolithic and CHG, so how can it not be a plausible source of Neolithic ancestry in South Asia?

The reason it wasn't incorporated into the South Asian models in Lazaridis et al. is because it's a singleton Iran Mesolithic sample, of poor quality and with few markers.

I'd expect a greater survival of Iranian Neolithic lineages in South Asia if the Iranian Neolithic did contribute the earliest West Eurasian component in the region.

Seems to me like your expectations are rather arbitrary. There are obvious uniparental and genome-wide genetic links between all of the the ancient South Caspian samples and South Asians.

Folker said...

"You are comparing the modern admixture with aDNA. No one knows what the admixture level for South Asians was back in time without aDNA from there."

TruthPrevails, nobody needs to know what aDNA was in South Asia to fix the point, simply because that some components present in South Asians are absent in Europe, notably Iran_N (among other specific markers) is virtually absent in Northern Europeans even if they have the highest level of Steppe Admixture. And given than Steppe Admixture (or whatever you call it), is the common factor between Northern Europeans and South Asians, and that Iran_N predates other admixture in South Asia, there is a near impossibility for Steppe Admixture to come from South Asia, ipso facto. So the admixture came from the other way around.

ak2014b said...

The "H2a, H2a1 and H2a2" in my earlier comment should have been HV2a, HV2a1 and HV2a2.

@Davidski,

The reason it wasn't incorporated into the South Asian models in Lazaridis et al. is because it's a singleton Iran Mesolithic sample, of poor quality and with few markers.

Yes, that made sense and so that's what I had concluded after Lazaridis. But then I inferred that Iran Mesolithic was not considered a contributor, based on a combination of various different conclusions by people here and at anthrogenica that I took as gradually converging on limiting the possibility. Some of these different strands were,

Iran Hotu was considered different in several respects from Iran Neolithic, including something "ancient South Asian-derived ancestry" which looked like "Andamanese-related admixture". You reiterated a number of times that Iran Neolithic didn't have any ASI, which I took to mean that the Neolithic population in Iran would therefore have replaced the prior Mesolithic population, rather than being related to it (since an ASI-less population can't be derived from one which had some ASI or ASI-like constituent). You further also explained that there was no West Eurasian in South Asia until the Neolithic, and expressed several times that you already know that Mesolithic South Asia was just ASI with no West Eurasian, based on your advance knowledge of the results of upcoming aDNA publications. Here are some instances,

"According to the Basal-rich K7, Iran_Hotu packs more ANE and more of some other, perhaps Central Asian, stuff that often looks like Andamanese-related admixture.

This might be some sort of ancient South Asian-derived ancestry that has been floating around Iran and Central Asia since the Mesolithic.

My new test might be able to spot more differences between Iran_Hotu and Iran_Neolithic. We shall see soon."


"In fact, if anyone's still wondering whether Iran_Neolithic has any ASI from South Asia, just plot the Basal-rich cluster vs Dai and that'll give you an answer; a bit fat no."

"Nope, it's highly unlikely that we'll see any West Eurasian admixture in South Asia before the Neolithic. And certainly no R1a before the late Bronze Age."

Piecing together such summations of the current data, I therefore construed subsequent papers that continued to speak of Iran Neolithic and steppe as the source of all the West Eurasian in modern South Asia to mean that the earlier (pre steppe) WE in SA really did come from Iran Neolithic alone and not from Iran Mesolithic.

But since your present response further explains that "Iran Hotu is very similar to Iran Neolithic and CHG, so how can it not be a plausible source of Neolithic ancestry in South Asia?", does this mean you suspect that a population bearing an "Iran Mesolithic" component managed to survive into Iran's Neolithic period, still carrying over the ASI and extra ANE from the earlier era, while remaining somewhat distinct from the ASI-less Iran Neolithic groups? And do you think that both this ancient Iran population "persisting" from the Mesolithic and the ASI-less Iran Neolithic groups together contributed to South Asia since its Neolithic onwards?

ak2014b said...

"Seems to me like your expectations are rather arbitrary. There are obvious uniparental and genome-wide genetic links between all of the the ancient South Caspian samples and South Asians."

I've already gone through the mtDNA part of the uniparental markers. As I pointed out in previous comments, I could only make out a few proper correspondences between ancient Iranian mtDNA and the modern India and Bangladesh samples in the Palanichamy et al 2015 paper.

This is why I wondered whether perhaps a more northwestern part of South Asia, and further on into South Central Asia, might have been a greater recipient of the lineages found in ancient Iran. The only other alternative that I can think of was a male dominated dispersal into South Asia from Iran Neolithic, as I mentioned.

So now I'm following an idea you've provided, by looking at the other half of the uniparental markers, the Y. But this is not looking entirely satisfying either.

The Iran Neolithic Y-DNA lineages included pre-R2 and R2, but also J2b*, G2b, G2a1.
Iran Chalcolithic had G1a and J2a2.
Chris Rоttensteiner's analysis had Hotu Mesolithic as also likely J2a2.

Chris R found the Hotu sample negative for J2a1,

"Coverage is very low for terminal placement. It is likely that this sample is J2a2 since J2a1-CTS11251 and J2a2a-PF5073 are negative. Hopefully a better NextGenSequencing of this sample will be done in the future."

Chris Rоttensteiner further explained the Iran Neolithic J2b* is likely an extinct branch,

"Likely a fully developed J2b which is estimated by YFull YTree v4.06 with TMRCA 15800 ybp while AH2 is about 10000 years old. So likely a brother clade to J2b1-M205 and J2b2-Z575 which very likely got extinct since no other J2b-M12(xCTS560,Z620) modern result is known."


I'm splitting this comment in two, otherwise it's too long to go through.

ak2014b said...

For modern South Asian Y DNA, I'm looking at Figure 14 of the Supplementary Material of Poznik et al 2016, which uses 1000 Genomes.

The pre-R2 and R2 from Iran Neolithic can be used to explain R2 in modern South Asians. And there's a single G2b derived PJL sample in Lahore in Pakistan, matching with a G2b in Iran Neolithic. However, the rest of the Y lineages in ancient Iranian aDNA don't seem to have made (any) presence felt there,

South Asians seem to be J2a1 and J2b2. Whereas Iranian aDNA had J2a2 and an extinct branch J2b*.

Iran aDNA had G2a1, but the modern South Asian samples are under G2a2. (There's also one G2a sample in PJL)

A G1a was found in Iran Chalcolithic. There's however two G1 samples in modern South Asia.


All the J2 South Asian samples in Poznik et al 2016, using the current ISOGG tree to look up the SNPs:

M241 = J2b2, 3 samples in STU (Tamil), 2 x GIH (Gujarat), 1 PJL (Punjab), 2 x BEB (Bangladesh), 4 x ITU (Telugu)
L559 = J2a, 2 samples in PJL
M68 = J2a1c, 1 in PJL, 2 in STU
F4326 = J2a1, 6 in PJL, 3 in BEB, 2 in GIH, 2 in STU,
M322 = J2a1a, 1 in PJL
L25 = J2a1h2, 1 in PJL, 1 in STU, 1 in GIH.


All the G2 in South Asian samples in Poznik 2016:

L31 = G2a in 1 x PJL
P303 = G2a2b2a in 1 x PJL
L166 = G2a2a1a2a1a in 1 x PJL
M283 = G2b1a in 1 x PJL


The G1 in South Asians in Poznik et al 2016:
L833 = G1 in 2 x GIH

So other than the G2b1a instance in PJL, there's no real match between in terms of G and J between modern South Asia and Iran aDNA.


Chris Rottensteiner said,

While pre-Bronze ancient J2a1b so far was only found in Mesolithic Caucasus (Kotias Klde cave, Western Georgia, sample KK1) in Jones et al 2015 and Neolithic Anatolia (Barcın, Northwestern Turkey, sample I0708/BAR6/L11-439) in Mathieson et al 2015 the other J2a clade J2a2a has now been found In West Iran. It is my impression that more Mesolithic or older samples as well as from other places (Mesopotamia, South and East Iran, Afghanistan, Pakistan, India) are needed to reconstruct interesting hypotheses about the origin of J2a.

For J2b there is even more need for ancient DNA. The testing of deeper subclades for the two Neolithic Hungary J2’s in Szecsenyi-Nagy 2015 remains very interesting.



The uniparental Y marker match between ancient Iran and modern South Asia is with R2 and with G2b (one sample in PJL), not with the other Y Hgs in Iran aDNA.

Perhaps, excepting the correspondences with Y haplo R2 and with the rather few mtDNA instances already mentioned, only autosomal input from ancient Iran into South Asia remains at present? But the remaining west Eurasian lineages (Y and mtDNA) in modern South Asia can't all be explained exclusively by the steppe either.

Davidski said...

South Asians seem to be J2a1 and J2b2. Whereas Iranian aDNA had J2a2 and an extinct branch J2b*.

You're being very pedantic and unreasonable.

Considering the few samples that we have available from ancient Iran and the prevalence of strong founder effects in Y-chromosome lineages in ancient West Eurasian groups, the presence of J2a and J2b in both ancient Iran and modern-day South Asia is a smoking gun for population movements from ancient Iran to South Asia.

ak2014b said...

Your response has encouraged me to look up what's been said about the J in the aDNA samples so far. I can't say it's making the picture any clearer.

There's Anatolian Neolithic J2a from 6500-6200 BCE. However, Chris Rоttensteiner said

"Careful reanalysis of the ancient I0708 NW.Anatolia sample allowed to assess that Z6050, Z6052 are underived and therefore the ancient paragroup to date has no modern samples."

The Anatolian Neolithic J2a further seemed to be J2a1b, as indicated in this aforementioned statement by Chris R,

"While pre-Bronze ancient J2a1b so far was only found in Mesolithic Caucasus (Kotias Klde cave, Western Georgia, sample KK1) in Jones et al 2015 and Neolithic Anatolia (Barcın, Northwestern Turkey, sample I0708/BAR6/L11-439) in Mathieson et al 2015"

I think he's saying that both CHG Kotias and the AN sample were J2a1b.

In the Caucasus, the 13kya Satsurblia CHG was J1 and relative to extant J1b. Over at anthrogenica's discussion of "ancient J1b-F4306(xZS80) Satsurblia Late Upper Palaeolithic Caucasus", Chris R discussed the results of his analysing the Satsurblia sample,

Satsurblia is a full developed J (97 J-SNPs checked, 49 positive, 48 have no-calls), negative for J2 (21 SNPs checked, 12 negative, 9 no-calls) so I went on to do a quick check for J1.
J1 positive for: L255 (14937880 A->C), CTS426/PF4641/YSC307 (6745512 C->T), CTS10759 (22761824 G->A), CTS11188/PF4784 (22997977 G->T), CTS11636/PF4785 (23200045 T->C)
J1b positive for: CTS6101/PF3543 (16674560 G->A), F4306 (21492032 G->T), FGC20301/Y6337/ZS3624 (24468458 A->G), FGC20303/Y6336/ZS3620 (23650760 A->G),
J1b negative for: CTS3219/ZS80 (14738001 G->A),
So possibly this is
a) the ancestor (or a near relative of him) of all J1b-F4306 men
b) a split leading to an extinct J1b-F4306(xZS80) branch


In Supplementary Fig 14 of Poznik et al 2016, the 1000 genomes dataset for South Asians contained a J1a sample from Pakistan (the J-CTS5368 in the PJL data set), but not J1b or any other J1.

As mentioned, the 10kya Kotias Mesolithic CHG, also from Georgia, was J2a1b, just like the Anatolian Neolithic sample, as per Chris R. The Haplogroup J2 Tree page showed only Sardinians to be derived for J2a1b among modern populations, so no J2a1b on the page's South Asian samples either.

ak2014b said...

Among Iranian aDNA, Chris R found sample I1662 (4831-4612 calBCE) was J2a2 and that the Mesolithic Hotu J2a (9100-8600 BCE) sample was likely J2a2 too.

An interview with Jones and colleagues in 2015 contained

"The Caucasus hunter-gatherer genome showed a continued mixture with the ancestors of the early farmers in the Levant area, which Manica says makes sense given the relative proximity. This ends, however, around 25,000 years ago – just before the time of the last glacial maximum, or peak Ice Age.

At this point, Caucasus hunter-gatherer populations shrink as the genes homogenise, a sign of breeding between those with increasingly similar DNA. This doesn’t change for thousands of years as these populations remain in apparent isolation in the shelter of the mountains – possibly cut off from other major ancestral populations for as long as 15,000 years – until migrations began again as the Glacial Maximum recedes, and the Yamnaya culture ultimately emerges."


I think they're saying that CHG didn't admix with the world beyond the Caucasus between Satsurblia and Kotias, and since much before. On the other hand, Iran Mesolithic was J2a, likely J2a2, while Kotias was J2a1b. The Hotu sample's age range starts a little before Kotias' existence. This would mean J2a possibly already existed before CHG became isolated at 25 kya. Yet that may not fit J2a's TMRCA, which is around 18kya as mentioned at anthrogenica,

"J2a (J-M410), according to YFull has a TMRCA of 18100 ybp, and the branch formed 27800 ybp"
(The comment seems to have got Kotias's 10kya date mixed up with Satsurblia's 13kya)

So I think that either YFull's TMRCA for J2a is too conservative, or Jones et al's assumption that CHG was genetically isolated for 15k years from 25kya to 10kya isn't correct. Regardless, J2a was widespread in the Mesolithic, seen from the northern CHGs in Georgia, to the Hotu cave in Iran.

As concerns the J2a2 found in 2 ancient Iranian samples, The Haplogroup J2 Tree shows no South Asian samples off J2a2, confirming the lack of J2a2 in Poznik et al 2016's 1000 Genomes SA samples. However, J2a2 is found in samples of modern Irish, Armenians, Sardinians, Germans in The Haplogroup J2 Tree. So it's not that ancient Iran's J2a2 went extinct, it just seems to there in Europe rather than in modern South Asia.

The J2b* in Iran Neolithic AH2 sample (8205-7756 cal BCE) was likely an extinct branch as per Chris R. If you suspect that ancient Iran may be the source for all J2b, it would explain the J2b2 found in modern South Asia, as well as be the source of the J2b1 in Jordan EBA aDNA (2,400-2,200 calBCE) but also of the J2b subclades in Europe. The Haplogroup J2 Tree shows J2b1 is found in modern Sardinians, Ukrainians, Armenians, Hispanics and J2b2 is found in Circassians, Sardinians, Iberians and Tuscans. (Whereas J2b1 is not found in 1000 Genomes' modern SA samples.)

So far, even though Iran_N is to have contributed greatly to modern SA and to not have contributed directly to modern Europeans, the J2a2 and J2b first seen in ancient Iran samples (albeit with its particular J2b* extinct) is found to exist in modern European populations, yet only J2b2 occurs in modern SA samples. Has anyone looked at what other uniparental markers, which were first or exclusively found in ancient Iran so far, were found in Europe afterwards? mtDNA X, or X2, could be one of them, I believe.

ak2014b said...

You're being very pedantic and unreasonable.

It was the comments here that convinced me that we had enough samples. Even though R was so widespread since prehistoric times, such that it was found in 14kya Villabruna to Mesolithic Siberia and Russia, and Neolithic Iran, most here have argued that we know ancient Iranian aDNA didn't have R1, R1a or R1b because its aDNA samples only came up with R2. If the ancient Iranian samples we have are sufficient to come that conclusion, then they'd be sufficient to draw similar conclusions about specific J subclades, since J2a's TMRCA is over 18 kya and the aDNA J-derived samples found so far are all thousands of years younger than that. And these aDNA samples were found ranging from the Near Eastern agricultural populations since the Neolithic but also earlier Hunter Gatherers, allowing for a range of sources for J2 in modern SCA and SA. So I don't think I'm any more unreasonable or reasonable in my assumptions than any others commenting here.

It's further simply the case that the J2 subclades found in the present clutch of Iranian aDNA is insufficient to explain the different J2 branches in the modern South Asian samples, so that we can't yet draw a straight line from the one to the other.

And I'm not particularly pedantic in wondering about the holes remaining in reconstructing J2 phylogeny from ancient data, or how come South Asia is not explained by Iran Neolithic, when until a couple of days ago Iran N as the source for SA uniparental lineages seemed so promising to me. Consider that Chris R, on the Haplogroup J2 Research team, still thinks we need more samples to unravel the J2 and its extant subclades. He suggests we need more Mesolithic aDNA from unsampled regions of Iran, but also from unsampled areas like from Mesopotamia to even South Asia. I'd further be interested in looking for ancient J2a in regions he didn't mention too.

To be clear, I'm not suggesting that if not Iran, then Anatolia or Caucasus would have provided the J2 in SCA to SA, even though the specific subclades don't match there either. (Nor am I trying to argue that any of Iran or Anatolia or Caucasus were the PIE homeland with J2 as the PIE marker) I can't guess where the J2 was from, and my comments were not originally about J in specific, but about many other Y and mtDNA besides. I've simply noted that in terms of uniparental markers, the Iran Neolithic aDNA we have, and even Iran Mesolithic Hotu, still don't seem to account for much of the pre steppe West Eurasian lineages in large parts of South Asia, going by the modern samples, whereas this is what I had expected to find since the Broushaki and Lazaridis papers of 2016.

Davidski said...

The problem with looking for fairly deep modern Y-HG subclades in ancient populations is that only a small proportion of founders from the last couple of thousand years have made an impact on many modern populations. So looking for the precise ancestral lineages of these modern subclades in limited ancient DNA, especially as far back as the Neolithic, is usually a pointless exercise, and will be for many years.

But hey, we've also got genome-wide DNA. So why not try to correlate genome-wide DNA with broad Y-HG clades?

jv said...

Hi! I am trying to find out my friends MtDNA U1a4. I'm not finding much. I do see U1 was found in a Sarmatian grave. Is there any chance that this MtDNA U1a4 migrated to Europe after the Bronze Age? Perhaps during the Iron Age? She only has a couple of matches in the world BUT she has 5 daughters so that should change statistics!