“Steppe ancestry” step by step: Khvalynsk, Sredni Stog, Repin, Yamna, Corded Ware

dzudzuana_pca-large

Wang et al. (2018) is obviously a game changer in many aspects. I have already written about the upcoming Yamna Hungary samples, about the new Steppe_Eneolithic and Caucasus Eneolithic keystones, and about the upcoming Greece Neolithic samples with steppe ancestry.

An interesting aspect of the paper, hidden among so many relevant details, is a clearer picture of how the so-called Yamnaya or steppe ancestry evolved from Samara hunter-gatherers to Yamna nomadic pastoralists, and how this ancestry appeared among Proto-Corded Ware populations.

anatolia-neolithic-steppe-eneolithic
Image modified from Wang et al. (2018). Marked are in orange: equivalent Steppe_Maykop ADMIXTURE; in red, approximate limit of Anatolia_Neolithic ancestry found in Yamna populations; in blue, Corded Ware-related groups. “Modelling results for the Steppe and Caucasus cluster. Admixture proportions based on (temporally and geographically) distal and proximal models, showing additional Anatolian farmer-related ancestry in Steppe groups as well as additional gene flow from the south in some of the Steppe groups as well as the Caucasus groups.”

Please note: arrows of “ancestry movement” in the following PCAs do not necessarily represent physical population movements, or even ethnolinguistic change. To avoid misinterpretations, I have depicted arrows with Y-DNA haplogroup migrations to represent the most likely true ethnolinguistic movements. Admixture graphics shown are from Wang et al. (2018), and also (the K12) from Mathieson et al. (2018).

1. Samara to Early Khvalynsk

The so-called steppe ancestry was born during the Khvalynsk expansion through the steppes, probably through exogamy of expanding elite clans (eventually all R1b-M269 lineages) originally of Samara_HG ancestry. The nearest group to the ANE-like ghost population with which Samara hunter-gatherers admixed is represented by the Steppe_Eneolithic / Steppe_Maykop cluster (from the Northern Caucasus Piedmont).

Steppe_Eneolithic samples, of R1b1 lineages, are probably expanded Khvalynsk peoples, showing thus a proximate ancestry of an Early Eneolithic ghost population of the Northern Caucasus. Steppe_Maykop samples represent a later replacement of this Steppe_Eneolithic population – and/or a similar population with further contribution of ANE-like ancestry – in the area some 1,000 years later.

PCA-caucasus-steppe-samara

This is what Steppe_Maykop looks like, different from Steppe_Eneolithic:

steppe-maykop-admixture

NOTE. This admixture shows how different Steppe_Maykop is from Steppe_Eneolithic, but in the different supervised ADMIXTURE graphics below Maykop_Eneolithic is roughly equivalent to Eneolithic_Steppe (see orange arrow in ADMIXTURE graphic above). This is useful for a simplified analysis, but actual differences between Khvalynsk, Sredni Stog, Afanasevo, Yamna and Corded Ware are probably underestimated in the analyses below, and will become clearer in the future when more ancestral hunter-gatherer populations are added to the analysis.

2. Early Khvalynsk expansion

We have direct data of Khvalynsk-Novodanilovka-like populations thanks to Khvalynsk and Steppe_Eneolithic samples (although I’ve used the latter above to represent the ghost Caucasus population with which Samara_HG admixed).

We also have indirect data. First, there is the PCA with outliers:

PCA-khvalynsk-steppe

Second, we have data from north Pontic Ukraine_Eneolithic samples (see next section).

Third, there is the continuity of late Repin / Afanasevo with Steppe_Eneolithic (see below).

3. Proto-Corded Ware expansion

It is unclear if R1a-M459 subclades were continuously in the steppe and resurged after the Khvalynsk expansion, or (the most likely option) they came from the forested region of the Upper Dnieper area, possibly from previous expansions there with hunter-gatherer pottery.

Supporting the latter is the millennia-long continuity of R1b-V88 and I2a2 subclades in the north Pontic Mesolithic, Neolithic, and Early Eneolithic Sredni Stog culture, until ca. 4500 BC (and even later, during the second half).

Only at the end of the Early Eneolithic with the disappearance of Novodanilovka (and beginning of the steppe ‘hiatus’ of Rassamakin) is R1a to be found in Ukraine again (after disappearing from the record some 2,000 years earlier), related to complex population movements in the north Pontic area.

NOTE. In the PCA, a tentative position of Novodanilovka closer to Anatolia_Neolithic / Dzudzuana ancestry is selected, based on the apparent cline formed by Ukraine_Eneolithic samples, and on the position and ancestry of Sredni Stog, Yamna, and Corded Ware later. A good alternative would be to place Novodanilovka still closer to the Balkan outliers (i.e. Suvorovo), and a source closer to EHG as the ancestry driven by the migration of R1a-M417.

PCA-sredni-stog-steppe

The first sample with steppe ancestry appears only after 4250 BC in the forest-steppe, centuries after the samples with steppe ancestry from the Northern Caucasus and the Balkans, which points to exogamy of expanding R1a-M417 lineages with the remnants of the Novodanilovka population.

steppe-ancestry-admixture-sredni-stog

4. Repin / Early Yamna expansion

We don’t have direct data on early Repin settlers. But we do have a very close representative: Afanasevo, a population we know comes directly from the Repin/late Khvalynsk expansion ca. 3500/3300 BC (just before the emergence of Early Yamna), and which shows fully Steppe_Eneolithic-like ancestry.

afanasevo-admixture

Compared to this eastern Repin expansion that gave Afanasevo, the late Repin expansion to the west ca. 3300 BC that gave rise to the Yamna culture was one of colonization, evidenced by the admixture with north Pontic (Sredni Stog-like) populations, no doubt through exogamy:

PCA-repin-yamna

This admixture is also found (in lesser proportion) in east Yamna groups, which supports the high mobility and exogamy practices among western and eastern Yamna clans, not only with locals:

yamnaya-admixture

5. Corded Ware

Corded Ware represents a quite homogeneous expansion of a late Sredni Stog population, compatible with the traditional location of Proto-Corded Ware peoples in the steppe-forest/forest zone of the Dnieper-Dniester region.

PCA-latvia-ln-steppe

We don’t have a comparison with Ukraine_Eneolithic or Corded Ware samples in Wang et al. (2018), but we do have proximate sources for Abashevo, when compared to the Poltavka population (with which it admixed in the Volga-Ural steppes): Sintashta, Potapovka, Srubna (with further Abashevo contribution), and Andronovo:

sintashta-poltavka-andronovo-admixture

The two CWC outliers from the Baltic show what I thought was an admixture with Yamna. However, given the previous mixture of Eneolithic_Steppe in north Pontic steppe-forest populations, this elevated “steppe ancestry” found in Baltic_LN (similar to west Yamna) seems rather an admixture of Baltic sub-Neolithic peoples with a north Pontic Eneolithic_Steppe-like population. Late Repin settlers also admixed with a similar population during its colonization of the north Pontic area, hence the Baltic_LN – west Yamna similarities.

NOTE. A direct admixture with west Yamna populations through exogamy by the ancestors of this Baltic population cannot be ruled out yet (without direct access to more samples), though, because of the contacts of Corded Ware with west Yamna settlers in the forest-steppe regions.

steppe-ancestry-admixture-latvia

A similar case is found in the Yamna outlier from Mednikarovo south of the Danube. It would be absurd to think that Yamna from the Balkans comes from Corded Ware (or vice versa), just because the former is closer in the PCA to the latter than other Yamna samples. The same error is also found e.g. in the Corded Ware → Bell Beaker theory, because of their proximity in the PCA and their shared “steppe ancestry”. All those theories have been proven already wrong.

NOTE. A similar fallacy is found in potential Sintashta→Mycenaean connections, where we should distinguish statistically that result from an East/West Yamna + Balkans_BA admixture. In fact, genetic links of Mycenaeans with west Yamna settlers prove this (there are some related analyses in Anthrogenica, but the site is down at this moment). To try to relate these two populations (separated more than 1,000 years before Sintashta) is like comparing ancient populations to modern ones, without the intermediate samples to trace the real anthropological trail of what is found…Pure numbers and wishful thinking.

Conclusion

Yamna and Corded Ware show a similar “steppe ancestry” due to convergence. I have said so many times (see e.g. here). This was clear long ago, just by looking at the Y-chromosome bottlenecks that differentiate them – and Tomenable noticed this difference in ADMIXTURE from the supplementary materials in Mathieson et al. (2017), well before Wang et al. (2018).

This different stock stems from (1) completely different ancestral populations + (2) different, long-lasting Y-chromosome bottlenecks. Their similarities come from the two neighbouring cultures admixing with similar populations.

If all this does not mean anything, and each lab was going to support some pre-selected archaeological theories from the 1960s or the 1980s, coupled with outdated linguistic models no matter what – Anthony’s model + Ringe’s glottochronological tree of the early 2000s in the Reich Lab; and worse, Kristiansen’s CWC-IE + Germano-Slavonic models of the 1940s in the Copenhagen group – , I have to repeat my question again:

What’s (so much published) ancient DNA useful for, exactly?

Related

Early Indo-Iranian formed mainly by R1b-Z2103 and R1a-Z93, Corded Ware out of Late PIE-speaking migrations

yamna-expansion-reich

The awaited, open access paper on Asian migrations is out: The Genomic Formation of South and Central Asia, by Narasimhan et al. bioRxiv (2018).

Abstract:

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

NOTE. The supplementary material seems to be full of errors right now, because it lists as R1b-M269 (and further subclades) samples that have been previously expressly said were xM269, so we will have to wait to see if there are big surprises here. So, for example, samples from Mal’ta (M269), Iron Gates (M269 and L51), and Latvia Mesolithic (L51), a Deriivka sample from 5230 BC (M269), Armenia_EBA (Z2103)…Also, the sample from Yuzhnyy Oleni Ostrov is R1a-M417 now.

EDIT (1 APR 2018): The main author has confirmed on Twitter that they have used a new Y Chr caller that calls haplogroups given the data provided, and depending on the coverage tried to provide a call to the lowest branch of the tree possible, so there are obviously a lot of mistakes – not just in the subclades of R. A revision of the paper is on its way, and soon more people will be able to work with the actual samples, since they say they are releasing them.

Nevertheless, since it is subclades (and not haplogroups) the apparent source of gross errors, for the moment it seems we can say with a great degree of confidence that:

  • New samples of East Yamna / Poltavka are of haplogroup R1b-L23.
  • Afanasevo is confirmed to be dominated by R1b-M269.
  • Sintashta, as I predicted could happen, shows a mixed R1b-L23/ R1a-Z645 society, compatible with my model of continuity of Proto-Indo-Iranian in the East Yamna admixture with late Corded Ware immigrants.

With lesser confidence in precise subclades, we find that:

  • A sample from Hajji Firuz in Iran ca. 5650 BC, of subclade R1b-Z2103, may confirm Mesolithic R1b-M269 lineages from the Caucasus as the source of CHG ancestry to Khvalynsk/Yamna, and be thus the reason why Reich wrote about a potential PIE homeland south of the Caucasus . (EDIT 11 APR 2018) The sample shows steppe ancestry, therefore the date is most likely incorrect, and a new radiocarbon dating is due. It is still interesting – depending on the precise subclade – for its potential relationship with IE migrations into the area.
  • New samples of East Yamna / Poltavka are of haplogroup R1b-Z2103.
  • Afanasevo migrants are mainly of haplogroup R1b-Z2103.
    • The Darra-e Kur sample, ca. 2655, of haplogroup R1b-L151, without a clear cultural adscription, may be the expected sign of Afanasevo migrants (Pre-Proto-Tocharian speakers) expanding a Northern Indo-European (in contrast with a Southern or Graeco-Aryan) dialect, in a region closely linked with the later desert mummies in the Tarim Basin. Its early presence there would speak in favour of a migration through the Inner Asian Mountain Corridor previous to the one caused by Andronovo migrants.
  • Sintashta shows a mixed R1b-Z2103 / R1a-Z93 society.
    • Later Indo-Iranian migrations are apparently dominated by R1a-Z2123, an early subclade of R1a-Z93, also found in Srubna.
    • R1b is also seen later in BMAC (ca. 1487 BC), although its subclade is not given.
  • There is also a sample of R1a-Z283 subclade in the eastern steppe (ca. 1600 BC). What may be interesting about it is that it could mark one of the subclades not responsible for the expansion of Balto-Slavic (or responsible for it with the expansion of Srubna, for those who support an Indo-Slavonic branch related Sintashta-Potapovka).
  • A sample of R1b-U106 subclade is found in Loebanr_IA ca. 950 BC, which – together with the sample of Darra-e Kur – is compatible with the presence of L51 in Yamna.

NOTE. Errors in haplogroups of previously published samples make every subclade of new samples from the supplementary table questionable, but all new samples (safe for the Darra_i_Kur one) were analysed and probably reported by the Reich Lab, and at least upper subclades in each haplogroup tree seem mostly coherent with what was expected. Also, the contribution of Iranian Farmer related (a population in turn contributing to Hajji Firuz) to Khvalynsk in their sketch of the genetic history may be a sign of the association of R1b-M269 lineages with CHG ancestry, although previous data on precise R1b subclades in the region contradict this. (EDIT 11 APR 2018) The sample of Hajji Firuz is most likely much younger than the published date, hence its younger subclade may be correct. No revision or comment on this matter has been published, though.

yamna-steppe-emba-mlba-cloud
Modeling results. (A) Admixture events originating from 7 “Distal” populations leading 538 to the formation of the modern Indian cloud shown geographically. Clines or 2-way mixtures of 539 ancestry are shown in rectangles, and clouds (3-way mixtures) are shown in ellipses.

Also, it seems that the Corded Ware culture appears now irrelevant for Late Proto-Indo-European migrations. Observe:

In the text, a consistent terminology of Yamnaya or Yamnaya-related Steppe pastoralists, discarding the relevance of previous migrations from the North Pontic steppe in spreading Late Indo-European:

Our results also shed light on the question of the origins of the subset of Indo-European languages spoken in India and Europe (45). It is striking that the great majority of Indo-European speakers today living in both Europe and South Asia harbor large fractions of ancestry related to Yamnaya Steppe pastoralists (corresponding genetically to the Steppe_EMBA cluster), suggesting that “Late Proto-Indo-European”—the language ancestral to all modern Indo- European languages—was the language of the Yamnaya (46). While ancient DNA studies have documented westward movements of peoples from the Steppe that plausibly spread this ancestry to Europe (5, 31), there has not been ancient DNA evidence of the chain 488 of transmission to South Asia. Our documentation of a large-scale genetic pressure from Steppe_MLBA groups in the 2nd millennium BCE provides a prime candidate, a finding that is consistent with archaeological evidence of connections between material culture in the Kazakh middle-to-late Bronze Age Steppe and early Vedic culture in India (46).

EDIT (1 APR 2018): I corrected this text and the word ‘official’ in the title, because more than rejecting the role of Corded Ware migrants in expanding Late PIE, they actually seem to keep considering Corded Ware migrants as continuing the western Yamna expansion in the Carpathian Basin, so no big ‘official’ change or retraction in this paper, just subtle movements out of their previous model.

yamna-migrations-indo-iranian
Modeling results.(B) A 540 schematic model of events originating from 7 “Distal” populations leading to the formation of 541 the modern Indian cline, shown chronologically. (C) Admixture proportions as estimated 542 using qpAdm for populations reflected in A and B.

NOTE. If they correct the haplogroups soon, I will update the information in this post. Unless there is a big surprise that merits a new one, of course.

EDIT (1 APR 2018): Multiple minor edits to the original post.

EDIT (2 APR 2018): While I and other simple-minded people were only looking to confirm our previous theories using Y-DNA haplogroups, and are content with wildly speculating over the consequences if some of those strange (probably wrong) ones were true, intelligent people are using their time for something useful, interpreting the results of the investigation as described in the paper, to offer a clearer picture of Indo-Iranian migrations for everyone:

Visit the beautiful interactive map with samples: with their location, PCA, ADMIXTURE and haplogroups (still with those originally given): https://public.tableau.com/profile/vagheesh#!/vizhome/TheGenomicFormationofSouthandCentralAsia/Fig_1

Featured image, from the article: “A Tale of Two Subcontinents. The prehistory of South Asia and Europe are parallel in both being impacted by two successive spreads, the first from the Near East after 7000 BCE bringing agriculturalists who mixed with local hunter-gatherers, and the second from the Steppe after 3000 BCE bringing people who spoke Indo-European languages and who mixed with those they encountered during their migratory movement. Mixtures of these mixed populations then produced the rough clines of ancestry present in both South Asia and in Europe today (albeit with more variable proportions of local hunter-gatherer-related ancestry in Europe than in India), which are (imperfectly) correlated to geography. The plot shows in contour lines the time of the expansion of Near Eastern agriculture. Human movements and mixtures, which also plausibly contributed to the spread of languages, are shown with arrows.”

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