On the Ukraine Eneolithic outlier I6561 from Alexandria

sredni-stog-eneolithic-late

Over the past week or so, since the publication of new Corded Ware samples in Narasimhan, Patterson et al. (2019) and after finding out that the R1a-M417 star-like phylogeny may have started ca. 3000 BC, I have been ruminating the relevance of contradictory data about the Ukraine_Eneolithic_o sample from Alexandria, its potential wrong radiocarbon date, and its implications for the Indo-European question.

How many other similar ‘controversial’ samples are there which we haven’t even considered? And what mechanisms are in place to control that the case of Hajji_Firuz_CA I2327 is not repeated?

Ukraine Eneolithic outlier I6561

It was not the first time that I (or many others) have alternatively questioned its subclade or its date, but the contradictory data seem to keep piling up. We can still explain all these discrepancies by assuming that the radiocarbon date is correct – seeing how it is a direct and newly reported lab analysis – because it is an isolated individual from a poorly sampled region, so he may actually be the first one to show features proper of later Corded Ware-related samples.

ukraine-eneolithic-from-caucasus
PCA of ancient Eurasian samples. An interpretation of the evolution of the Pontic-Caspian steppe populations in the Eneolithic. See full PCA.

The individual seems to be especially relevant for the Indo-European and Uralic homeland question. The last one to mention this sample in a publication was Anthony (2019), who considered it in common with two other Eneolithic samples from Dereivka to show how Anatolian farmer-related ancestry first appeared in the recently opened CHG mating network of the Pontic-Caspian steppes and forest-steppes during the Middle Eneolithic, after the expansion of Khvalynsk:

The currently oldest sample with Anatolian Farmer ancestry in the steppes in an individual at Aleksandriya, a Sredni Stog cemetery on the Donets in eastern Ukraine. Sredni Stog has often been discussed as a possible Yamnaya ancestor in Ukraine (Anthony 2007: 239- 254). The single published grave is dated about 4000 BC (4045–3974 calBC/ 5215±20 BP/ PSUAMS-2832) and shows 20% Anatolian Farmer ancestry and 80% Khvalynsk-type steppe ancestry (CHG&EHG). His Y-chromosome haplogroup was R1a-Z93, similar to the later Sintashta culture and to South Asian Indo-Aryans, and he is the earliest known sample to show the genetic adaptation to lactase persistence (I3910-T). Another pre-Yamnaya grave with Anatolian Farmer ancestry was analyzed from the Dnieper valley at Dereivka, dated 3600-3400 BC (grave 73, 3634–3377 calBC/ 4725±25 BP/ UCIAMS-186349). She also had 20% Anatolian Farmer ancestry, but she showed less CHG than Aleksandriya and more Dereivka-1 ancestry, not surprising for a Dnieper valley sample, but also showing that the old fifth-millennium-type EHG/WHG Dnieper ancestry survived into the fourth millennium BC in the Dnieper valley (Mathieson et al. 2018).

The main problem is that this sample has more than one inconsistent, anachronistic data compared to its reported precise radiocarbon date ca. 4045–3974 calBCE (5215±20BP, PSUAMS-2832). I summarized them on Twitter:

  • First known R1a-M417 sample, with subclade R1a-Y26 (Y2-), with formation date and TMRCA ca. 2750 BC (CI 95% ca. 3750–1950 BC), and proper of much later Steppe_MLBA bottlenecks. The closest available sample would be the Poltavka outlier of hg. R1a-Z94 (ca. 2700 BC), from a mixed cemetery that could belong to a later (likely Abashevo) layer; the closest related subclade is probably found in sample I12450 of Butkara_IA (ca. 800 BC).
  • NOTE. The formation date of upper clade R1a-Z93 is estimated ca. 3000 BC, with a CI 95% ca. 3550–2550 BC, suggesting that the actual TMRCA range for the subclade has most likely a lower maximum formation date than estimated with the available samples under Y3.

  • Ancestry and PCA cluster like Steppe_MLBA (see PCA below), different from neighbouring Sredni Stog samples of the roughly coetaneous Dereivka site (ca. 3600-3400 BC), and from a later Yamnaya sample from Dereivka (ca. 2800 BC), even more shifted toward WHG-related ancestry.
  • Allele for lactase persistence (I3910-T), found only much later among Bell Beakers, and still later in Sintashta and Steppe_MLBA samples. This suggests a strong selection in northern Europe and South Asia stemming from steppe-related (and not forest-steppe-related) peoples, postdating the age of massive Indo-European migrations.
  • Hajji Firuz Chalcolithic outlier

    My impression is that the Hajji_Firuz Chalcolithic outlier, initially dated ca. 5900-5500 BC, had much less reason to be questioned than this sample, since Pre-Yamnaya ancestry was (and apparently is still) believed by members of the Reich Lab to have come from south of the Caucasus, and to have arrived around that time or earlier to the North Caspian steppe, i.e. before the 5th millennium BC.

    The formation date of its initially reported haplogroup, R1b-Z2103, is ca. 4100 BC (CI 95% 4800-3500 BC), which seems also roughly compatible with that date and site – at least as compatible as R1a-Y3(xY2) is for ca. 4000 BC -, so it could have been interpreted as a migrant from the South Caspian region, potentially related to Proto-Anatolians, especially before the description of the Caucasus genetic barrier in Wang et al (2018). For some reason, though, the Hajji_Firuz sample was questioned, but this one didn’t even merited an interrogation mark.

    There was already a similar situation with two samples (RISE568 and RISE569) initially reported as belonging to Czech Corded Ware groups, that turned out to be Early Slavs ca. 3,000 years younger, in turn more closely related to Bell Beaker-derived cultures of Central-East Europe. It seems little has changed since that case.

    All in all, my guess is that genomic data of I6561 would have been a priori more compatible with a later period, during the expansion of East Corded Ware groups: at least Middle Dnieper culture, potentially Multi-Cordoned Ware culture, but most likely a Srubnaya-related one, given the most likely SNP mutation and TMRCA date, and the haplogroup variability found in the few samples available from that culture.

    ukraine-eneolithic-from-srubna
    PCA of ancient Eurasian samples. Marked I6561 sample within the cluster formed by Srubnaya samples. See full PCA.

    Compatibility checks

    I tried to start a thread on the possibility that the radiocarbon date was wrong, and IF it were, how likely it would be that formal stats could actually show this, or how could we automatically prevent ancestry magic fiascos.

    In other words: if this guy were a Srubnaya-related individual actually dated e.g. ca. 1700 BC, and someone would try to ‘prove’ – based on the current open source tools alone – that he was the ancestor of expanding peoples of the 4th and 3rd millennium BC (i.e. Balkan outliers, Yamnaya, Corded Ware, you name it), could these results be formally challenged?

    I was hoping for some original brainstorming where people would propose crazy, essentially impossible to understand statistical models, say plotting dozens of well-studied mutations of different geographically related ancient samples with their reported dates, to visually highlight samples that don’t exactly fit with such a feature-based time series analysis; I mean, the kind of theoretical models I wouldn’t even be able to follow after the first two tweets or so. I didn’t receive an answer like that, but still:

    I have nothing to add to these answers, because I agree that all contradictory data are circumstancial.

    The current absolute lack of this kind of validity checks for ancestry models is disappointing, though, and leaves the so-called outliers in a dangerous limbo between “potentially very interesting samples” and “potentially wrongly dated samples”. Radiocarbon date is thus – together with compatibility of population source in terms of archaeological cultures and their potential relationship – a necessary variable to take into account in any statistical design: an error in one of these variables means a catastrophic error in the whole model.

    Formal stats

    For example, in these qpAdm models, I assumed Srubnaya, Ukraine_Eneolithic_outlier, and Bulgaria_MLBA samples were roughly coetaneous and potentially related to the Srubnaya-SabatinovkaNoua cultural horizon, hence stemming from a source close to:

    1. Abashevo-like individuals (whose best proxy to date should be Poltavka_outlier I0432) potentially admixed with Poltavka-like herders; or
    2. Potapovka-like individuals potentially admixed with Catacomb-like peoples (whose best proxy until recently were probably Yamnaya_Kalmykia*).

    *To avoid adding more potential errors by merging different datasets, I have used only proxy samples available in the Reich Lab’s curated dataset of published ancient DNA.

    srubnaya-noua-sabatinovka-mlba
    Srubnaya and Noua-Sabatinovka cultural horizon during the MLBA. See full maps.

    Apart from the lack of more models for comparison (I’m not going to dedicate more time to this), the results can’t be interpreted without a proper sampling and context, either, because (1) Poltavka_o may actually be from a much later group closely related to Srubnaya; (2) Bulgaria_MLBA is only one sample; and (3) there are only two samples from Potapovka; so the models here presented are basically useless, as many similar models that have been tested looking just for a formal “best fit”.

    So feel free to chime in and contribute with ideas as to how to detect in the future whether a sample is ancestral to or derived from others. I will post here informative answers from Twitter, too, if there are any. I don’t think a discussion about the potentially wrong date in this specific sample is very useful, because this seems impossible to prove or disprove at this point. Just what tools or data would you use to at least try and assess whether samples are compatible with its reported date or not – preferably in some kind of automated sieve that takes dozens or hundreds of samples into account.

    On the bright side, there is so much more than formal stats to arrive to relevant inferences about prehistoric populations, their movements and languages. That’s why I6561 didn’t matter for the conclusion by Anthony (2019) that it was the R1b-rich Eneolithic Don-Volga-Caucasus region the most likely Indo-Anatolian and Late Proto-Indo-European homeland, due to the creation of a wide Eneolithic mating network with extended exogamy practices, where Y-chromosome bottlenecks seem to be one of the main genomic data to take into account from the Neolithic to the Middle Bronze Age.

    And that is the same reason why it doesn’t matter that much for the Proto-Indo-European or Uralic question for me, either.

    Related

Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations

pca-korea-japanese-han

Open access Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations, by Wang, Lu, Chung, and Xu, Hereditas (2018) 155:19.

Abstract (emphasis mine):

Background
Han Chinese, Japanese and Korean, the three major ethnic groups of East Asia, share many similarities in appearance, language and culture etc., but their genetic relationships, divergence times and subsequent genetic exchanges have not been well studied.

Results
We conducted a genome-wide study and evaluated the population structure of 182 Han Chinese, 90 Japanese and 100 Korean individuals, together with the data of 630 individuals representing 8 populations wordwide. Our analyses revealed that Han Chinese, Japanese and Korean populations have distinct genetic makeup and can be well distinguished based on either the genome wide data or a panel of ancestry informative markers (AIMs). Their genetic structure corresponds well to their geographical distributions, indicating geographical isolation played a critical role in driving population differentiation in East Asia. The most recent common ancestor of the three populations was dated back to 3000 ~ 3600 years ago. Our analyses also revealed substantial admixture within the three populations which occurred subsequent to initial splits, and distinct gene introgression from surrounding populations, of which northern ancestral component is dominant.

Conclusions
These estimations and findings facilitate to understanding population history and mechanism of human genetic diversity in East Asia, and have implications for both evolutionary and medical studies.

pca-phylogenetic-tree-east-asia
Population level phylogenetic Tree and Principal component analysis (PCA). (A) The maximum likelihood tree was constructed based on pair-wise FST matrix. And the marked number are bootstrap value; (B) The top two PCs of individuals representing six East Asian populations, mapped to their corresponding geographic locations (generated by R 2.15.2 and Microsoft Excel 2010)

Interesting excerpts:

It is obvious that the genetic difference among the three East Asian groups initially resulted from population divergence due to pre-historical or historical migrations. Subsequently, different geographical locations where the three populations are located, mainland of China, Korean Peninsular and Japanese archipelago, respectively, apparently facilitated population differentiation due to physical isolation and independent genetic drift. Our estimations of population divergence time among the three groups, 1.2~ 3.6 KYA, are largely consistent with known history of the three populations and those related. However, considering that recent admixture could have reduced genetic difference between populations, it is likely the divergence time was underestimated.

We detected substantial gene flow among the three populations and also from the surrounding populations. For example, based on our analysis with the F3 test, Korean received gene flow from Han Chinese and Japanese, and gene flow also happened between Han Chinese and Japanese (Additional file 12: Table S3). These gene flows are expected to have reduced the genetic differentiation between the three ethnic groups. On the other hand, we also detected considerable gene flow from surrounding populations to the three populations studied. For instance, an ancestral population represented by Ryukyuan have contributed greater to Japanese than to Han Chinese, while southern ethnic group like Dai have contributed more to continent populations than to island and peninsula populations. Contrary to the gene flow among the three populations, these gene flows from surrounding populations are expected to have increased genetic difference among the three populations if they occurred independently and from different source populations. According to our results, the major source of gene flow to the three ethnic groups were substantially different, for example, the major source of gene flow to Han Chinese was from southern ethnic groups, the major source of gene flow to Japanese was from southern islands, and the major source of gene flow to Korean were from both mainland and islands. Therefore, those gene flows might have significantly contributed to further genetic differentiation of the three populations.

The three populations have similar but not identical demographical history; they all experience a strong population expansion in the last 20,000 years. However, according to different geographic distribution, their effective population size and population expansion are different.

Although based on modern populations, the study is interesting in light of the potential implications for a Macro-Altaic proposal.

Related:

Indo-European demic diffusion model, 3rd edition

pca-yamna-corded-ware

I have just uploaded the working draft of the third version of the Indo-European demic diffusion model. Unlike the previous two versions, which were published as essays (fully developed papers), this new version adds more information on human admixture, and probably needs important corrections before a definitive edition can be published.

The third version is available right now on ResearchGate and Academia.edu. I will post the PDF at Academia Prisca, as soon as possible:

pca-map-yamna-corded-ware-bell-beaker
Map overlaid by PCA including Yamna, Corded Ware, Bell Beaker, and other samples

Feel free to comment on the paper here, or (preferably) in our forum.

A working version (needing some corrections) divided by sections, illustrated with up-to-date, high resolution maps, can be found (as always) at the official collaborative Wiki website indo-european.info.

Something is very wrong with models based on the so-called ‘steppe admixture’ – and archaeologists are catching up

steppe-admixture

Russian archaeologist Leo Klejn has published an article Discussion: Are the Origins of Indo-European Languages Explained by the Migration of the Yamnaya Culture to the West?, which includes the criticism received from Wolfgang Haak, Iosif Lazaridis, Nick Patterson, and David Reich (mainly on the genetic aspect), and from Kristian Kristiansen, Karl-Göran Sjögren, Morten Allentoft, Martin Sikora, and Eske Willerslev (mainly on the archaeological aspect).

I will not post details of Klejn’s model of North-South Proto-Indo-European expansion – which is explained in the article, and relies on the north-south cline of ‘steppe admixture’ in the modern European population -, since it is based on marginal anthropological methods and theories, including glottochronological dates, and archaeological theories from the Russian school (mainly Zalyzniak), which are obviously not mainstream in the field of Indo-European Studies, and (paradoxically) on the modern distribution of ‘steppe admixture’…

The most interesting aspects of the article are the reactions to the criticism, some of which can be used from the point of view of the Indo-European demic diffusion model, too. It is sad, however, that they didn’t choose to answer earlier to Heyd’s criticism (or to Heyd’s model, which is essentially also that of Mallory and Anthony), instead of just waiting for proponents of the least interesting models to react…

The answer by Haak et al.:

Klejn mischaracterizes our paper as claiming that practitioners of the Corded Ware culture spoke a language ancestral to all European Indo-European languages, including Greek and Celtic. This is incorrect: we never claim that the ancestor of Greek is the language spoken by people of the Corded Ware culture. In fact, we explicitly state that the expansion of steppe ancestry might account for only a subset of Indo-European languages in Europe. Klejn asserts that ‘a source in the north’ is a better candidate for the new ancestry manifested in the Corded Ware than the Yamnaya. While it is indeed the case that the present-day people with the greatest affinity to the Corded Ware are distributed in north-eastern Europe, a major part of the new ancestry of the Corded Ware derives from a population most closely related to Armenians (Haak et al., 2015) and hunter-gatherers from the Caucasus (Jones et al., 2015). This ancestry has not been detected in any European huntergatherers analysed to date (Lazaridis et al., 2014; Skoglund et al., 2014; Haak et al., 2015; Fu et al., 2016), but made up some fifty per cent of the ancestry of the Yamnaya. The fact that the Corded Ware traced some of its ancestry to the southern Caucasus makes a source in the north less parsimonious.

In our study, we did not speculate about the date of Proto-Indo-European and the locations of its speakers, as these questions are unresolved by our data, although we do think the genetic data impose constraints on what occurred. We are enthusiastic about the potential of genetics to contribute to a resolution of this longstanding issue, but this is likely to require DNA from multiple, as yet unsampled, ancient populations.

Klejn response to that:

Allegedly, I had accused the authors of tracing all Indo-European languages back to Yamnaya, whereas they did not trace all of them but only a portion! Well, I shall not reproach the authors for their ambiguous language: it remains the case that (beginning with the title of the first article) their qualifications are lost and their readers have understood them as presenting the solution to the whole question of the origins of Indo-European languages.

(…) they had in view not the Proto-Indo-European before the separation of the Hittites, but the language that was left after the separation. Yet, this was still the language ancestral to all the remaining Indo-European languages, and the followers of Sturtevan and Kluckhorst call only this language Proto-Indo-European (while they call the initial one Indo-Hittite). The majority of linguists (specialists in Indo-European languages) is now inclined to this view. True, the breakup of this younger language is several hundred years more recent (nearly a thousand years later according to some glottochronologies) than the separation of Anatolian languages, but it is still around a thousand years earlier than the birth of cultures derived from Yamnaya.
More than that, I analysed in my criticism both possibilities — the case for all Indo-European languages spreading from Yamnaya and the case for only some of them spreading from Yamnaya. In the latter case, it is argued that only the languages of the steppes, the Aryan (Indo- Iranian) are descended from Yamnaya, not the languages of northern Europe. Together with many scholars, I am in agreement with the last possibility. But, then, what sense can the proposed migration of the Yamnaya culture to the Baltic region have? It would bring the Indo-Iranian proto-language to that region! Yet, there are no traces of this language on the coasts of the Baltic!

My main concern is that, to my mind, one should not directly apply conclusions from genetics to events in the development of language because there is no direct and inevitable dependence between events in the life of languages, culture, and physical structure (both anthropological and genetic). They can coincide, but often they all follow divergent paths. In each case the supposed coincidence should be proved separately.

The authors’ third objection concerns the increase of the genetic similarity of European population with that of the Yamnaya culture. This increases in the north of Europe and is weak in the south, in the places adjacent to the Yamnaya area, i.e. in Hungary. This gradient is clearly expressed in the modern population, but was present already in the Bronze Age, and hence cannot be explained by shifts that occurred in the Early Iron Age and in medieval times. However, the supposed migration of the Yamnaya culture to the west and north should imply a gradient in just the opposite direction!

Regarding the arguments of Kristiansen and colleagues:

[They argue that] in two early burials of the Corded Ware culture (one in Germany, the other in Poland) some single attributes of Yamnaya origin have been found.

(…) if this is the full extent of Yamnaya infiltration into central Europe—two burials (one for each country) from several thousands (and from several hundreds of early burials)—then it hardly amounts to large-scale migration.

Quite recently we have witnessed the success of a group of geneticists from Stanford University and elsewhere (Poznik et al., 2016). They succeeded in revealing varieties of Y-chromosome connected with demographic expansions in the Bronze Age. Such expansion can give rise to migration. Among the variants connected with this expansion is R1b, and this haplogroup is typical for the Yamnaya culture. But what bad luck! This haplogroup connected with expansion is indicated by the clade L11, while the Yamnaya burials are associated with a different clade, Z2103, that is not marked by expansion. It is now time to think about how else the remarkable results reached by both teams of experienced and bright geneticists may be interpreted.

Regarding the work of Heyd,

(…) with regard to the barrow burials of the third millennium BC in the basin of the Danube, although they have been assigned to the Yamnaya culture, I would consider them as also belonging to
another, separate culture, perhaps a mixed culture: its burial custom is typical of the Yamnaya, but its pottery is absolutely not Yamnaya, but local Balkan with imports of distinctive corded beakers (Schnurbecher). I would not be surprised if
Y-chromosome haplogroups of this population were somewhat similar to those of the Yamnaya, while mitochondrial groups were indigenous. As yet, geneticists deal with great blocks of populations and prefer to match them to very large and generalized cultural blocks, while archaeology now analyses more concrete and smaller cultures, each of which had its own fate.

Iosif Lazaridis shares more thoughts on the discussion in his Twitter account:

As we mentioned in Haak, Lazaridis et al. (2015), the Yamnaya are the best proximate source for the new ancestry that first appears with the Corded Ware in central Europe, as it has the right mix of both ANE (related to Native Americans, MA1, and EHG), but also Armenian/Caucasus/Iran-like southern component of ancestry. The Yamnaya is a westward expansive culture that bears exactly the two new ancestral components (EHG + Caucasus/Iran/Armenian-like).
As for the Y-chromosome, it was already noted in Haak, Lazaridis et al. (2015) that the Yamnaya from Samara had Y-chromosomes which belonged to R-M269 but did not belong to the clade common in Western Europe (p. 46 of supplement). Also, not a single R1a in Yamnaya unlike Corded Ware (R1a-dominated). But Yamnaya samples = elite burials from eastern part of the Yamnaya range. Both R1a/R1b found in Eneolithic Samara and EHG, so in conclusion Yamnaya expansion still the best proximate source for the post-3,000 BCE population change in central Europe. And since 2015 steppe expansion detected elsewhere (Cassidy et al. 16, Martiniano et al. 17, Mittnik et al. 17, Mathieson et al. 17, Lazaridis et al. 2016 (South Asia) and …?…

I love the smell of new wording in the morning… viz. Yamnaya best proximate source for Corded Ware, Corded Ware might account for only a subset of Indo-European languages, Corded Ware representing Aryan languages (probably Klejn misinterprets what the authors mean, i.e. some kind of Indo-Slavonic or Germano-Balto-Slavic group)…

We shall expect more and more ambiguous rewording and more adjustments of previous conclusions as new papers and new criticisms appear.

Related:

Featured image from the article: Distribution of the ‘Yamnaya’ genetic component in the populations of Europe (data taken from Haak et al., 2015). The intensity of the colour corresponds to the contribution of this component in various modern populations