The concept of “Outlier” in Human Ancestry (II): Early Khvalynsk, Sredni Stog, West Yamna, Iron Age Bulgaria, Potapovka, Andronovo…

yamna-corded-ware-bell-beaker

I already wrote about the concept of outlier in Human Ancestry, so I am not going to repeat myself. This is just an update of “outliers” in recent studies, and their potential origins (here I will repeat some of the examples):

Early Khvalynsk: the three samples from the Samara region have quite different positions in PCA, from nearest to EHG (of Y-DNA haplogroup R1a) to nearest to ANE ancestry (of Y-DNA haplogroup Q). This could represent the initial consequences of the second wave of ANE ancestry – as found later in Yamna samples from a neighbouring region -, possibly brought then by Eurasian migrants related to haplogroup Q.
With only 3 samples, this is obviously just a tentative explanation of the finds. The samples can only be reasonably said to show an unstable time for the region in terms of admixture (i.e. probably migration), judging by the data on PCA.

Ukraine Eneolithic samples offer a curious example of how the concept of outlier can change radically: from the third version (May 30th) of the preprint paper of Mathieson et al. (2017), when the Ukraine Eneolithic sample with steppe ancestry (and clustering with central European samples) was the ‘outlier’, to the fourth version (September 19th), when two samples with steppe ancestry clustering close to Corded Ware samples were now the ‘normal’ ones (i.e. those representing Ukraine Eneolithic population), and the outlier was the one clustering closely with Ukraine Mesolithic samples…

pca-admixture-yamna
PCA and Admixture for south-eastern Europe. Image modified from Mathieson et al. (2017) – Third revision (May 30th), used in the 2nd edition of the Indo-European demic diffusion model.

This is one of the funny consequences of the wrong interpretation of the ‘yamnaya component’, that made geneticists believe at first that, out of two samples (!), the ‘outlier’ was the one with ‘yamnaya’ ancestry, because this component would have been brought by an eastern immigrant from early Khvalynsk…

This example offers yet another reason why precise anthropological context is necessary to offer the right interpretation of results. Within the Indo-European demic diffusion model – based mainly on Archaeology and Linguistics – , the sample with steppe ancestry was the most logical find in the region for a potential origin of the Corded Ware culture, and it was interpreted as such, well before the publication of the fourth version of Mathieson et al. (2017).

pca-south-east-europe
PCA of South-East European and other European samples. Image modified from Mathieson et al. (2017) – Fourth revision (September 19th), used in the 3rd edition of the Indo-European demic diffusion model.

West Yamna (to insist on the same question, the ‘yamnaya’ component): we have only four western Yamna samples, two of them showing Anatolian Neolithic ancestry (one of them, from Ukraine, with a strong ‘southern’ drift). On the other hand, Corded Ware migrants do not show this. So we could infer that their migrations were not coetaneous: whereas peoples of Corded Ware culture expanded ca. 3300 BC to the north – in the natural corridor to the Baltic that has been proposed for this culture in Archaeology for decades (and that is well represented by Ukraine Eneolithic samples) -, peoples of Yamna culture expanded to the west, replacing the Ukraine Eneolithic population (i.e. probably those of ‘Proto-Corded Ware culture’), and eventually mixing with Balkan populations of Anatolian Neolithic ancestry.

Potapovka, Andronovo, and Srubna: while Potapovka clusters closely to the steppe, and Andronovo (like Sintashta) clusters closely to Corded Ware (i.e. Ukraine Neolithic / Central-East European), both have certain ‘outliers’ in PCA: the former has one individual clustering closely to Corded Ware, and the latter to the steppe. Both ‘outliers’ fit well with the interpretation of the recent mixture of Corded Ware peoples with steppe populations, and they offer a different image for the evolution of populations of Potapovka and Sintashta-Petrovka, potentially influencing their language. The position of Srubna samples, nearer to Sintashta and Andronovo (but occupying the same territory as the previous Potapovka) offers the image of a late westward conquest from Corded Ware-related populations.

asia-early-bronze
Diachronic map of migrations ca. 2250-1750 BC

Iron Age Bulgaria: a sample of haplogroup R1a-z93, with more ‘yamnaya’ ancestry than any other previous sample from the Balkans. For some, it might mean continuity from an older time. However – as with the Corded Ware outlier from Esperstedt before it – it is more likely a recent migrant from the steppe. The most likely origin of this individual is therefore people from the steppe, i.e. either the Srubna culture or a related group. Its relatively close cluster in PCA to certain recent Slavic populations can be interpreted in light of the multiple back and forth migrations in the region: of steppe populations to the west (Srubna, Cimmerians, Scythians, Sarmatians,…), and of Slavic-speaking populations:

middle-bronze-age-middle-east
Diachronic map of Bronze Age migrations ca. 1750-1250 BC.

Well-defined outliers are, therefore, essential to understand a recent history of admixture. On the other hand, the very concept of “outlier” can be a dangerous tool – when the lack of enough samples makes their classification as as such unjustified -, leading to the wrong interpretations.

Related:

Globular Amphora not linked to Pontic steppe migrants – more data against Kristiansen’s Kurgan model of Indo-European expansion

eneolithic-steppe-cultures

New open access article, Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages, by Tassi et al. (2017).

Abstract:

It is unclear whether Indo-European languages in Europe spread from the Pontic steppes in the late Neolithic, or from Anatolia in the Early Neolithic. Under the former hypothesis, people of the Globular Amphorae culture (GAC) would be descended from Eastern ancestors, likely representing the Yamnaya culture. However, nuclear (six individuals typed for 597 573 SNPs) and mitochondrial (11 complete sequences) DNA from the GAC appear closer to those of earlier Neolithic groups than to the DNA of all other populations related to the Pontic steppe migration. Explicit comparisons of alternative demographic models via approximate Bayesian computation confirmed this pattern. These results are not in contrast to Late Neolithic gene flow from the Pontic steppes into Central Europe. However, they add nuance to this model, showing that the eastern affinities of the GAC in the archaeological record reflect cultural influences from other groups from the East, rather than the movement of people.

globular-amphora-pca-admixture
(a) Principal component analysis on genomic diversity in ancient and modern individuals. (b) K = 3,4 ADMIXTURE analysis based only on ancient variation. (a) Principal component analysis of 777 modern West Eurasian samples with 199 ancient samples. Only transversions considered in the PCA (to avoid confounding effects of post-mortem damage). We represented modern individuals as grey dots, and used coloured and labelled symbols to represent the ancient individuals. (b) Admixture plots at K = 3 and K = 4 of the analysis conducted only considering the ancient individuals. The full plot is shown in electronic supplementary material, figure S7. The ancient populations are sorted by a temporal scale from Pleistocene to Iron Age. The GAC samples of this study are displayed in the box on the right.

Excerpt, from the discussion:

In its classical formulation, the Kurgan hypothesis, i.e. a late Neolithic spread of proto-Indo-European languages from the Pontic steppes, regards the GAC people as largely descended from Late Neolithic ancestors from the East, most likely representing the Yamna culture; these populations then continued their Westward movement, giving rise to the later Corded Ware and Bell Beaker cultures. Gimbutas [23] suggested that the spread of Indo-European languages involved conflict, with eastern populations spreading their languages and customs to previously established European groups, which implies some degree of demographic change in the areas affected by the process. The genomic variation observed in GAC individuals from Kierzkowo, Poland, does not seem to agree with this view. Indeed, at the nuclear level, the GAC people show minor genetic affinities with the other populations related with the Kurgan Hypothesis, including the Yamna. On the contrary, they are similar to Early-Middle Neolithic populations, even geographically distant ones, from Iberia or Sweden. As already found for other Late Neolithic populations [18], in the GAC people’s genome there is a component related to those of much earlier hunting-gathering communities, probably a sign of admixture with them. At the nuclear level, there is a recognizable genealogical continuity from Yamna to Corded Ware. However, the view that the GAC people represented an intermediate phase in this large-scale migration finds no support in bi-dimensional representations of genome diversity (PCA and MDS), ADMIXTURE graphs, or in the set of estimated f3-statistics.

globular-amphora-hunter-gatherer-farmer-yamnaya
Scheme summarizing the five alternative models compared via ABC random forest. We generated by coalescent simulation mtDNA sequences under five models, differing as to the number of migration events considered. The coloured lines represent the ancient samples included in the analysis, namely Unetice (yellow line), Bell Beaker (purple line), Corded Ware (green line) and Globular Amphorae (red line) from Central Europe, Yamnaya (light blue line) and Srubnaya (brown line) from Eastern Europe. The arrows refer to the three waves of migration tested. Model NOMIG was the simplest one, in which the six populations did not have any genetic exchanges; models MIG1, MIG2 and MIG1, 2 differed from NOMIG in that they included the migration events number 1, 2 (from Eastern to Central Europe, respectively before and after the onset of the GAC), or both. Model MIG2, 3 represents a modification of MIG2 model also including a back migration from Central to Eastern Europe after the development of the Corded Ware culture.

Together with Globular Amphora culture samples from Mathieson et al. (2017), this suggests that Kristiansen’s Indo-European Corded Ware Theory is wrong, even in its latest revised models of 2017.

gimbutas-kurgan-indo-european
The background shading indicates the tree migratory waves proposed by Marija Gimbutas, and personally
checked by her in 1995. The symbols refer to the ancient populations considered in the ABC analysis

On the other hand, the article’s genetic finds have some interesting connections in terms of mtDNA phylogeography, but without a proper archaeological model it is difficult to explain them.

mtdna-yamnaya-gac-corded-ware-bell-beaker
Haplogroup frequencies were obtained for Early Neolithic (EN), Middle Neolithic (MN), Chalcolithic (CA), and Late Neolithic (LN). The color assigned to each haplogroup is represented on the lower right part of each plot. Haplogroup frequencies were plotted geographically using QGIS v2.14.

Text and images from the article under Creative Commons Attribution 4.0 license.

Discovered first via Bernard Sécher’s blog.

See also:

Human ancestry: how to work your own PCA, ADMIXTURE analyses for human evolutionary and genealogical studies

yamna-corded-ware-bell-beaker

I wrote two days ago in the post anouncing the revised version (October 2017) of the Indo-European demic diffusion model, about dumping the information I had on doing PCA and ADMIXTURE analyses as ‘drafts’, without reviewing them, in the new section of this website called Human Ancestry.

I had some time today to review them, and to correct gross mistakes in the texts, so that they might be more usable now

I began to work with free datasets to see if I could learn something more about results of recent Genetic research by working with the available free software. For the moment, I don’t see it necessary to continue working with samples myself, because there are many professionals in Bioinformatics doing an excellent job with their publications – much better than I could do -, and publishing results early (as pre-prints) and with free licenses, which allow us to reuse and modify their material. To work again with their samples seems most of the time like reinventing the wheel.

After all, my interpretation of Indo-European migrations does not depend on my own analysis of free datasets – or on genetic analysis, or on archaeological fieldwork, for that matter – but on the study of all anthropological questions involved. I am actually more interested in Linguistics, and – only marginally – in Archaeology, as is the field of Indo-European Studies in general.

I did find certain interesting aspects that I have commented in the model, though: especially by labelling all samples and reading about them carefully (usually in the supplementary notes of the published papers), you can observe certain patterns and derive some information that others might have missed. Such examples include the Corded Ware outlier from Esperstedt (see more on the Corded Ware migration), or the differences in the three samples from early Khvalynsk.

Now that most data published seem to keep supporting what I have suggested – regarding the more complex nature of the steppe component (so-called ‘yamnaya component‘), and also regarding the migration from Yamna to Bell Beaker, and a migration of a different population (and probably language) with Corded Ware – I don’t find it worthy to spend more of my quite limited time in these tasks.

However, if I need to work again with datasets, I will try to complete the drafts the best I can. Especially regarding F3 Statistics and qpGraph, which I didn’t even try. If you want to help improve the sections, you are welcome of course.

If I find time, I might be of help with your work. And even though modern genealogy does not interest me (for the moment), I guess it can also be relevant to obtain conclusions on more recent migrations, so if I can be of any help to any interesting work, I will do it too.

plot3d-yamna
Plot 3D of datasets Minoans and Mycenaeans + Scythians and Sarmatians, using the same colours as in the Indo-European demic diffusion model.

Related:

  • The concept of “outlier” in studies of Human Ancestry, and the Corded Ware outlier from Esperstedt
  • New Ukraine Eneolithic sample from late Sredni Stog, near homeland of the Corded Ware culture
  • The concept of “outlier” in studies of Human Ancestry, and the Corded Ware outlier from Esperstedt

    pca-yamna-corded-ware

    While writing the third version of the Indo-European demic diffusion model, I noticed that one Corded Ware sample (labelled I0104) clusters quite closely with steppe samples (i.e. Yamna, Afanasevo, and Potapovka). The other Corded Ware samples cluster, as expected, closely with east-central European samples, which include related cultures such as the Swedish Battle Axe, and later Sintashta, or Potapovka (cultures that are from the steppe proper, but are derived from Corded Ware).

    I also noticed after publishing the draft that I had used the wording “Corded Ware outlier” at least once. I certainly had that term in mind when developing the third version, but I did not intend to write it down formally. Nevertheless, I think it is the right name to use.

    pca-yamna-corded-ware
    PCA of dataset including Minoans and Mycenaeans, and Scythians and Sarmatians. The graphic has been arranged so that ancestries and samples are located in geographically friendly axes similar to north-south (Y), east-west(X). Symbols are used, in a simplified manner, in accordance with symbols for Y-DNA haplogroups used in the maps. Labels have been used for simplification of important components. Areas are drawn surrounding Yamna, Poltavka, Afanasevo, Corded Ware (including samples from Estonia, Battle Axe, and Poltavka outlier), and succeeding Sintashta and Potapovka cultures, as well as Bell Beaker. Corded Ware sample I0104, from Esperstedt, has also been labelled.

    Outlier in Statistics, as you can infer from the name, is a sample (more precisely an observation) that lies distant to others. It is a slippery concept in Human Evolutionary Biology, because it has no clear definition, and it is thus dependent on a certain degree of subjective evaluation. It seems to be mainly based on a combination of PCA and ADMIXTURE analyses, but should obviously be dependent on the number of samples available for a certain culture, and the regional distribution of the samples available.

    We have thus certain clear cases, like the Poltavka outlier, of R1a-M417 lineage, clustering close to Corded Ware (and Sintashta, and Potapovka) samples, but far from other R1b-L23 samples from Poltavka or Yamna cultures, from neighbouring regions in the steppe.

    We have also less clear observations, like Balkan Chalcolithic samples, which may or may not have been part of different cultural groups (say, related to the Suvorovo-Novodanilovka expansion, or not), which may justify their differences in ancestral components in ADMIXTURE, and in their position in PCA.

    And we have a Yamna sample from western Ukraine, which – unlike the other two available samples – clusters “to the south” of east Yamna samples. Taking into account the Yamna sample from Bulgaria, clustering closely with south-eastern European samples, could you really call this an outlier? Two outliers out of four western Yamna samples? Well, maybe. If you take east and west Yamna from the steppe as a whole, and exclude the Yamna sample from Bulgaria, of course you can. Whether that classification is useful, or actually hinders a proper interpretation of western Yamna samples, and of the “Yamna component” seen in them, is a different story…

    pca-yamna
    PCA for European samples of Mathieson et al. (2017)

    But what then about the Corded Ware male from Esperstedt, labelled I0104, dated ca. 2430 BC, which clusters among contemporaneous steppe (Poltavka) samples, and has the greatest proportion of ‘Yamna component’ in ADMIXTURE? After all, it is different in both respects from any other Corded Ware individual – including the oldest samples available, from Latvia (ca. 2885 BC) and Tiefbrunn (ca. 2755 BC).

    This sample is one of the direct links between the steppe and Corded Ware in late times, and has been the main reason for the confusion a lot of people seem to have about the “Yamna component” in Corded Ware, with some supporting a direct migration from one into the other, and a few even daring to say that “Corded Ware is indistinguishable from Yamna”(!?).

    His family members – all males of haplogroup R1a-M417 (like I0104 and most males from the Corded Ware culture) -, few generations later, show a decreased Yamna component, which clearly indicates that this individual’s admixture came directly from the steppe, and most likely from one or multiple female ancestors. That is compatible with the nomadic nature of the Corded Ware culture (and its known exogamy practices), which connected central Europe with the steppes, up to the North Caspian region.

    If labelling other samples as outliers may be interesting to improve the conclusions one can obtain from genetic research, labelling this sample is, in my opinion, essential, to avoid certain strong misconceptions about the origin of the Corded Ware culture.

    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.

    Palaeogenomic and biostatistical analysis of ancient DNA data from Mesolithic and Neolithic skeletal remains

    lepenski-vir-mesolithic-anatolia-neolithic

    PhD Thesis Palaeogenomic and biostatistical analysis of ancient DNA data from Mesolithic and Neolithic skeletal remains, by Zuzana Hofmanova (2017) at the University of Mainz.
    Abstract:

    Palaeogenomic data have illuminated several important periods of human past with surprising im- plications for our understanding of human evolution. One of the major changes in human prehistory was Neolithisation, the introduction of the farming lifestyle to human societies. Farming originated in the Fertile Crescent approximately 10,000 years BC and in Europe it was associated with a major population turnover. Ancient DNA from Anatolia, the presumed source area of the demic spread to Europe, and the Balkans, one of the first known contact zones between local hunter-gatherers and incoming farmers, was obtained from roughly contemporaneous human remains dated to ∼6 th millennium BC. This new unprecedented dataset comprised of 86 full mitogenomes, five whole genomes (7.1–3.7x coverage) and 20 high coverage (7.6–93.8x) genomic samples. The Aegean Neolithic pop- ulation, relatively homogeneous on both sides of the Aegean Sea, was positively proven to be a core zone for demic spread of farmers to Europe. The farmers were shown to migrate through the central Balkans and while the local sedentary hunter-gathers of Vlasac in the Danube Gorges seemed to be isolated from the farmers coming from the south, the individuals of the Aegean origin infiltrated the nearby hunter-gatherer community of Lepenski Vir. The intensity of infiltration increased over time and even though there was an impact of the Danubian hunter-gatherers on genetic variation of Neolithic central Europe, the Aegean ancestry dominated during the introduction of farming to the continent.

    Taking only admixture analyses using Yamna samples:

    This increased genetic affinity of Neolithic farmers to Danubians was observed for Neolithic Hungarians, LBK from central Europe and LBK Stuttgart sample. Some post-Neolithic samples also proved to share more drift with Danubians, again samples from Hungary (Bronze Age and Copper Age samples and also Yamnaya and samples with elevated Yamnaya ancestry (Early Bronze Age samples from Únětice, Bell Beaker samples, Late Neolithic Karlsdorf sample and Corded Ware samples).

    (…)

    The results of our ADMIXTURE analysis for the dataset including also Yamnaya samples are shown in Figure S1c. The cross-validation error was the lowest for K=2. Supervised and unsupervised analyses for K=3 are again highly concordant. Early Neolithic farmers again demonstrate almost no evidence of hunter-gatherer admixture, while it is observable in the Middle Neolithic farmers. However, much of the Late Neolithic hunter-gatherer ancestry from the previous analysis is replaced by Yamnaya ancestry. These results are consistent with the results of Haak et al. who demonstrated a resurgence of hunter-gatherer ancestry followed by the establishment of Eastern hunter-gatherer ancestry.

    Again, admixture results show that something in the simplistic Yamna -> Corded Ware model is off. It is still interesting to review admixture results of European Mesolithic and Late Neolithic genomic data in relation to the so-called steppe or yamna ancestry or component (most likely an eastern steppe / forest zone ancestry probably also present in the earlier Corded Ware horizons) and its interpretation…

    yamna-ancestry-europe
    Image composed by me, from two different images of the PhD Thesis. To the left: Supervised run of ADMIXTURE. The clusters to be supervised were chosen to best fit the presumed ancestral populations (for HG Motala and for farmers Bar8 and Bar31 and for later Eastern migration Yamnaya). To the Right: Unsupervised run of ADMIXTURE for the Anatolian genomic dataset with Yamnaya samples for K=8.

    Discovered via Généalogie génétique