mtDNAwiki on "Steppe folk" mtDNA and Indo-Iranian origins

Fascinating stuff from Samuel at mtDNAwiki. Emphasis is mine:

Steppe folk were people who resided in what are today Southern Russia and Eastern Ukraine between 6,000 and 4,000 years ago. They were very different from the Anatolian farmers I discussed earlier.

Ancient DNA shows that, between 3000 and 2000 BC, Steppe folk migrated en masse into Northern Europe, Central Asia and Siberia. Shortly afterwards, Steppe folk settled in South Europe, South Asia (India, Afghanistan, etc.), and Iran.

They contributed huge chunks of ancestry to countless modern ethnic groups. Modern-day Europeans are for the most part a two-way mixture between Steppe folk and European Neolithic farmers (who were mostly of Anatolian origin).

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As much as 33% of Tajik mtDNA really does derive from Eneolithic/Bronze Age Eastern Europe. No doubt about it. Yes, Tajiks are an exception, because they have a lot more Steppe mtDNA than essentially all other South Central Asians. However, significant frequencies of Steppe mtDNA exist in every population in this region. For example, the mtDNA in the Kalasha, a small ethnic group from the Hindu Kush, is mostly made up of founder effects involving Steppe mt-HGs U4a1, U4b1a4, U2e1h, and J2b1a. Each of these haplogroups has been found in remains from Eneolithic/Bronze Age Eastern Europe.

Typical European haplogroups such as U5a1a1, H2a1, T1a1, H5a1, H6a1, J1b1a1, J2b1a, H7b, etc. consistently pop up in every South Central Asian population. Realistically, none of these haplogroups are more than 10,000 years old. Indeed, all of them are likely to be less than 7,000 years old. The European-related mtDNA in South Central Asia isn’t derived from distant, Paleolithic shared ancestry between Europeans and Asians. It’s recent stuff from the Steppe.

For over a decade Y-haplogroup R1a-M417 perplexed many geneticists because it was the most common Y-haplogroup in two geographically very distant peoples; Balto-Slavs of Eastern Europe and Indo-Aryans of South Asia. But thanks to ancient DNA, it has now been confirmed that R1a-M417 is an European Steppe lineage which expanded both west and east from the Pontic-Caspian Steppe between 4,600 and 3,500 years ago.

Interestingly, I’ve found mtDNA haplogroups which correlate very well with R1a-M417; meaning that they either exist in South Asians & Eastern Europeans, or in South Asians & ancient Central and Eastern Europeans rich in R1a-M417, such as the Corded Ware and Srubnaya peoples.

J1c1b1a: Russia, Ukraine, Hungary, Romania, Denmark, UK, Spain, Tajik, India. Srubnaya (R1a-Z93), Corded Ware (R1a-M417).
H2a1a: Russia, Hungary=2, Finland, Britain, Ireland, France, Pathan, Tajik=16, Turkey, Siberia. Eneolithic Ukraine (R1a-M417), Bronze age Scotland, Unetice.
H5e1: Russia=2, Hungary, Greece, Tajik=3.
T1a1b: Russia=4, Poland=3, Hungary=2, Iran=2, Turkey, Tajik=4, India. Bronze age Latvia, Sycthian=2.
N1a1a1a1: Estonia=3, Finland=2, Italy, Turkmen, India=2. Sintashta, Sycthian, Sarmatian.
K2a5: Estonia, Ireland, Iran, Sindhi, Pathan, India. Corded Ware Germany, Corded Ware Sweden.
U4b2: Russia, Ukraine, Sweden, Spain, Burosho, Tajik, India.
U4b1a4: Kalash, Tajik, Iran, Siberia=3. Catacomb, Sycthian.
U2e1h: Kalash=3, Tajik=8, Siberia, Italy. Sintashta, Potapovka

The most important mt-HGs here are U2e1h, H2a1a, U4b1a4, T1a1b, and N1a1a1a1. They directly link modern Indo-Iranian speakers in Asia with Eneolithic/Bronze age Eastern Europeans generally considered by historical linguists and archaeologists to be Proto-Indo-European- or Proto-Indo-Iranian-speakers (i.e. Sintashta and Potapovka).

When I put all of this data together, and saw the undeniable links between modern-day Indo-Iranian speakers and Eneolithic/Bronze Age Eastern Europeans, I was amazed. The results confirmed to me, beyond any doubt, that the ancient migrations from the western Steppe deep into Asia long hypothesized by historical linguists and archaeologists did happen. Indo-Iranian languages really did originate in Eastern Europe, probably in what is now Ukraine, then took the long journey all the way to the Indian Subcontinent.

Case in point: ancient DNA sample I6561. That’s his lab ID, but he’s a man who died in what is now Ukraine ~5,500 years ago. He belonged to Y-HG R1a-M417 and mt-HG H2a1a. Today H2a1a is most common in the Tajik people of South Central Asia. The most common Y-HG in Tajiks, and many of their neighbors, such as Pashtuns, Kalasha, northern Indians, etc. is R1a-M417.

All of the evidence suggests that Mr. I6561 belonged to a PIE community whose descendants would go on to settle lands that stretch all the way from modern-day Norway to India. His people are important founders of countless modern ethnic groups; Russians, Czechs, Tajiks, Pashtuns, Indians, and so on. Oh yeah, and also the ancient Scythians, who dominated much of Asia around 500 BC, derived directly from his people. Pretty amazing.

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It’s been known for a while, via archaeological data, that Steppe folk traded with these farmers. But now, thanks to ancient DNA, it’s clear that they exchanged more than just goods. Enneolithic and Bronze Age genomes from what are now Ukraine, Romania, and Bulgaria show that the Steppe and farmer folks began mixing by at least 4400 BC.

Hence, when Steppe folk expanded both west and east, they took with them at least a little Anatolian admixture. This is also true for the Steppe folk who went to South Asia. Several of the mt-HGs that I labeled “Steppe” are in fact Anatolian mt-HGs that the Steppe folk acquired through admixture with farmer peoples before their mass migrations. These include mt-HGs H1b1, H5a1, H7b, J1c1b1a, J2b1a, N1a1a1a1, K1b1a1, HV6, and HV9.

It’s often said, in scientific literature as well as on various genetic blogs and forums, that the Steppe folk who moved into South Asia didn’t harbor any Anatolian ancestry. But my mtDNA data easily debunks this claim. South Asians do indeed carry some Anatolian-derived mtDNA which they, in all likelihood, acquired from their Steppe ancestors.

See also...

Another look at the genetic structure of Yamnaya

Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts

Descendants of ancient European (fair?) maidens in Central Asia's highlands

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

The Kho people: archaic Indo-Aryans

I've manged to get my hands on two Kho samples from Chitral, northern Pakistan, courtesy of Khana from the comments at this blog and someone named Sam Sloan. Here's what Wikipedia has to say about the Kho, who are Dardic-speakers and thus close linguistic relatives of the Kalasha people:

The Kho people are likely descendants of those who arrived in the region during the Indo-Aryan migration.[5] The Kho people formerly observed a form of ancient Hinduism;[6] during the Mongol invasion of India during the 1200s, many of the northern Kho converted to Islam.[7]

...

The Kho people speak the Khowar language, a member of the Dardic subgroup of the Indo-Aryan language family. The ethnologists Karl Jettmar and Lennart Edelberg noted, with respect to the Khowar language, that: "Khowar, in many respects [is] the most archaic of all modern Indian languages, retaining a great part of Sanskrit case inflexion, and retaining many words in a nearly Sanskritic form.”[9]

Moreover, Chitral is near Swat, which is the location of a Bronze Age cemetery that is generally presumed to be the oldest Indo-Iranian archaeological site in South Asia. It'll be interesting to compare the two Kho individuals to samples from this ancient burial ground if and when they're finally published (see here and here). Meantime, this is how they compare to the Kalasha from the HGDP dataset in several of my staple genome-wide analyses:

Overall, the qpGraph trees produce almost identical results for both the Kho and Kalasha. However, on the Kho tree, the drift path leading from C to Han is zero (i.e. no genetic drift), while on the Kalasha tree it's 18. That's a subtle, but perhaps important difference, because it suggests that the Kho and Kalasha have somewhat different types of East Eurasian admixture.

Indeed, in the West Eurasian and world Principal Component Analyses (PCA) the Kho pull more strongly towards the Bronze Age steppe and East Asia, respectively, compared to the Kalasha. This might mean that they've been less isolated genetically than the Kalasha since the initial Indo-Aryan settlement of what is now northern Pakistan.

I've also added the Kho to the Global 10 and Basal-rich K7 datasheets (see here and here, respectively). It might be possible to investigate in more detail the differences between the Kho and Kalasha by using this output to model their ancestry with nMonte (for instance, like here).

See also...

Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts

Descendants of ancient European (fair?) maidens in Central Asia's highlands

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Ancient mitogenomes reveal Central Asian (Hunnic?) admixture in Hungarian Conquerers (Neparáczki et al. 2018 preprint)

Over at bioRxiv at this LINK. The number of ancient mitogenomes in this preprint (102) is fairly impressive, but obviously there's only so much insight one can gain from maternally-inherited genetic markers when studying male-driven conquests like that of the Carpathian Basin by the early Hungarians. So yeah, let's wait and see how the conclusions in this preprint gel with the relevant ancient Y-chromosome and genome-wide data when it arrives. Below is the abstract. Emphasis is mine:

It has been widely accepted that the Finno-Ugric Hungarian language, originated from proto Uralic people, was brought into the Carpathian Basin by the Hungarian Conquerors. From the middle of the 19 th century this view prevailed against the deep-rooted Hungarian Hun tradition, maintained in folk memory as well as in Hungarian and foreign written medieval sources, which claimed that Hungarians were kinsfolk of the Huns. In order to shed light on the genetic origin of the Conquerors we sequenced 102 mitogenomes from early Conqueror cemeteries and compared them to sequences of all available databases. We applied novel population genetic algorithms, named Shared Haplogroup Distance and MITOMIX, to reveal past admixture of maternal lineages. Phylogenetic and population genetic analysis indicated that more than one third of the Conqueror maternal lineages were derived from Central-Inner Asia and their most probable ultimate sources were the Asian Huns. The rest of the lineages most likely originated from the Bronze Age Potapovka-Poltavka-Srubnaya cultures of the Pontic-Caspian steppe, which area was part of the later European Hun empire. Our data give support to the Hungarian Hun tradition and provides indirect evidence for the genetic connection between Asian and European Huns. Available data imply that the Conquerors did not have a major contribution to the gene pool of the Carpathian Basin, raising doubts about the Conqueror origin of Hungarian language.

Neparáczki et al., Mitogenomic data indicate admixture components of Asian Hun and Srubnaya origin in the Hungarian Conquerors, bioRxiv, Posted January 19, 2018, doi: https://doi.org/10.1101/250688

Another look at the genetic structure of Yamnaya

Yamnaya and other similar Eneolithic/Bronze Age herder groups from the Eurasian steppe were mostly a mixture of Eastern European Hunter-Gatherers (EHG) and Caucasus Hunter-Gatherers (CHG). But they also harbored minor ancestry from at least one, significantly more westerly, source that pulled them away from the EHG > CHG north/south genetic cline. This is easy to show with formal statistics (for instance, refer to the qpAdm output here) and illustrate with a decent Principal Component Analysis (PCA).

Over the past couple of years I've come to the conclusion that this minor westerly input probably came from the Carpathian Basin (modern-day Hungary) or somewhere nearby, like the Balkans (see here).

However, this inference was based on just a handful of Neolithic samples from the Carpathian Basin. Now, thanks to Lipson et al. 2017, I have genotype data from tens of individuals from several different Neolithic and Copper Age cultures from the region. So let's revisit the issue by plugging these new samples into qpAdm, and also using the very latest qpAdm methods as described in scientific literature (with Ethiopia_4500BP as the base pright sample to 15 other ancient pright groups and individuals).

Below are the results, best to worst, sorted by taildiff. For comparison, I ran extra models with ancient populations from other parts of Europe and also West Asia. It's interesting and, I'd say, important to note that the West Asian reference groups produce amongst the worst statistical fits (in bold text). What this suggests is that Yamnaya did not harbor extra West Asian ancestry on top of its CHG input. And, by the way, please note that I'm only using Yamnaya_Samara in these runs because I prefer UDG-treated, and thus higher quality, ancient samples.

CHG + EHG + Blatterhole_MN 0.465394061 > full output

CHG + EHG + Koros_HG 0.322245651 > full output

CHG + EHG + Germany_MN 0.321017025 > full output

CHG + EHG + Protoboleraz_LCA 0.315521424 > full output

CHG + EHG + Vinca_MN 0.292074267 > full output

CHG + EHG + Baden_LCA 0.255168297 > full output

CHG + EHG + Tisza_LN 0.246555616 > full output

CHG + EHG + ALPc_MN 0.220623346 > full output

CHG + EHG + Blatterhole_HG 0.219418173 > full output

CHG + EHG + Balaton_Lasinja_CA 0.211230222 > full output

CHG + EHG + Tiszapolgar_ECA 0.207527666 > full output

CHG + EHG + LBK_EN 0.182365613 > full output

CHG + EHG + TDLN 0.176675465 > full output

CHG + EHG + Koros_EN 0.15488361 > full output

CHG + EHG + Starcevo_EN 0.136365203 > full output

CHG + EHG + Armenia_EBA 0.127988891 > full output

CHG + EHG + Armenia_ChL 0.123057884 > full output

CHG + EHG + LBKT_MN 0.122780467 > full output

CHG + EHG + Tepecik_Ciftlik_N 0.110155019 > full output

CHG + EHG + Greece_N 0.105880232 > full output

CHG + EHG + Boncuklu_N 0.094240794 > full output

CHG + EHG + Anatolia_BA 0.069141519 > full output

CHG + EHG + Anatolia_ChL 0.067837662 > full output

...

CHG + EHG + Iran_ChL infeasible > full output

At the top of the list is Blatterhole_MN. Admittedly this is something of a surprise, considering the geographic distance between Blatterhole, Germany, and Samara, Russia. It's also an intriguing result because of the presence of Y-chromosome haplogroup R1b in both Blatterhole_MN and Yamnaya (see here).

However, this doesn't necessarily mean that Yamnaya harbors direct ancestry from Blatterhole_MN, or even any closely related group from North-Central Europe. Rather, Blatterhole_MN is simply the best proxy in this analysis for the non-CHG/EHG ancestry in Yamnaya, and the important question is why?

Considering also the presence at the top of the list of Koros_HG (which includes Hungary_HG I1507), Germany_MN and Vinca_MN, the likely answer is its high ratio of Western European Hunter-Gatherer (WHG) ancestry. Indeed, when I let qpAdm vary the WHG ratio, by dropping Blatterhole_MN and adding Koros_EN and Koros_HG in its place, I get an even better fit.

CHG + EHG + Koros_EN + Koros_HG 0.612772624 > full output

And for comparison...

CHG + EHG + LBK_EN + WHG 0.551431774 > full output

So is the missing piece of the Yamnaya puzzle a population with roughly equal ratios of Early Neolithic (EN) and WHG ancestries from the Carpathian Basin or surrounds? Quite possibly. But let's wait and see what happens when I add the ancient groups from the Balkans and North Pontic steppe from the forthcoming Mathieson et al. 2018 to this analysis.

Update 17/05/2018: My results have been confirmed in a new preprint from Harvard/Max Planck. See here: On the genetic prehistory of the Greater Caucasus (Wang et al. 2018 preprint).

See also...

What's Maykop (or Iran) got to do with it?

The Yamnaya outlier

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Genetic maps featuring 67 ancient genomes and more than 3,000 present-day individuals

I've got some eye candy for you guys as we wait for 2018 to really get going. Below are three Principal Component Analyses (PCA) plots, or genetic maps, based on the ancient diploid dataset from Martiniano et al. 2017 (described in more detail here). Click on the images to download hi-res PDFs of each plot. The relevant datasheets are available here.

The important thing about these PCA is that none of the samples in the analyses are missing more than 1% of the ~188K markers used to compute the PCs, which means that I didn't have to resort to any type of projection to get things right. In other words, the relationships between the samples that you see on these plots are direct.

PCA are easy to read. The main thing to keep in mind is that the results are dependent on the samples in the analysis. For instance, note that the Indians (Gujaratis and Brahmins) cluster rather close to some Europeans on the West Eurasian plot, but much further from them on the Eurasian/American plot. Why? Because the addition of hundreds of East Eurasian individuals to the latter plot highlights the significant East Eurasian-related admixture in the Indians, and pulls them away from the Europeans, who generally have much less of this type of ancestry.

It's interesting, I think, that all of the ancients from burial sites from within the borders of present-day Europe (discussed in an earlier blog post here), cluster with present-day Europeans, or at least closest to us. See anything else interesting? Feel free to share it in the comments below.

If you're having trouble spotting certain individuals and/or populations, type the relevant individual or population ID in the PDF search box and click enter. The PDF will initially show you a box where the samples of interest are located; click on the box, and the PDF will zoom into the boxed area and highlight these samples, like this:

See also...

Who's your (proto) daddy Western Europeans?