Haplogroup R1b-M167/SRY2627 linked to Celts expanding with the Urnfield culture

bronze-age-late-urnfield

As you can see from my interest in the recently published Olalde et al. (2019) Iberia paper, once you accept that East Bell Beakers expanded North-West Indo-European, the most important question becomes how did its known dialects spread to their known historic areas.

We already had a good idea about the expansion of Celts, based on proto-historical accounts, fragmentary languages, and linguistic guesstimates, but the connection of Celtic with either Urnfield or slightly later Hallstatt/La Tène was always blurred, due to the lack of precise data on population movements.

The latest paper on Iberia is interesting for many details, such as:

  • The express dismissal of the newest pet theory based on the simplistic “steppe ancestry = IE”: the obsessive comparisons of Dutch Bell Beakers as the origin of basically anything that moves in Europe.
  • A discrete influx of North African ancestry in certain samples before the Moorish invasion (which was probably mediated by peoples of North African rather than Levantine admixture).
  • The finding of very Mycenaean-like Greek colonies of the 5th century (interestingly, under R1b lineages).
iberia-celts-romans
Modified from section of PCA of ancient samples by Olalde et al. (2019). “IE Iberia” refers to Pre-Celtic Indo-European languages of Iberia, such as Galaico-Lusitanian in the west (see more on Lusitanian), and a potentially Ligurian-related language in the North-East and southern France.

The paper is, however, of particular importance from the perspective of historical linguistics. It confirms that:

  • Celtic-speaking peoples expanded in Iberia likely during the Late Bronze Age – Early Iron Age (probably with the Urnfield culture, before 1000 BC) with North/Central European ancestry.

NOTE. The paper marks what are believed to be the boundaries of non-Indo-European languages during the Iron Age in later times, extrapolating that situation to the past. Mediterranean sites with Iberian traits (ca. 6th century on) were probably non-Indo-European-speaking tribes, but it is unclear what happened in the centuries before their sampling, and there are no clear boundaries. These incoming Celts from central Europe with the Urnfield culture makes it very likely that the Iberian expansion to the north happened later, incorporating thus this central European ancestry in the process. The southern (orientalizing, Tartessian) site of La Angorrilla shows incineration and influence from Phoenician settlers, and their actual language is also far from clear. The other investigated samples, with higher central European contribution, are from Celtiberian sites.

  • The slightly later arrival of (Phoenician, Greek and) Latin-speaking peoples into Iberia is marked by Central/Eastern Mediterranean and North African ancestry.
iberia-migrations-celts-romans
Expansion of different ancestry components in Iberia during Prehistory. Modified from Olalde et al. (2019) to include labels with populations expanding with each component.

While both confirm what was more or less already known about the oldest attested NWIE dialects, and further support the role of East Bell Beakers in expanding North-West Indo-European, the first part is interesting for two main reasons:

  1. Koch’s Celtic from the West hypothesis, which made a recent comeback with a renewed model based on “steppe ancestry”, is once again rejected in population genomics, as expected. At this point I doubt this will mean anything to the supporters of the theory (because you can propose as many “Celtic-over-Celtic” layers as you want), but if you are not obsessed with autochthonous continuity of Celtic languages in the Atlantic area we might begin to judge the most correct dialectal split (and thus classification) among those proposed to date, based on ancestry and haplogroup expansions.
  2. We believed in the 2000s that the expansion of haplogroup R1b-M167 (TMRCA ca. 1100 BC for YTree or 1700 BC for YFull) was coupled with the expansion of Iberians from the Pyrenees, in turn (thus) closely related to Basques. This non-IE presence has been contested with toponymic data in linguistics, and with the testing of many modern samples and the subsequent discovery of the widespread distribution of the subclade in western and northern Europe. Now it has become even more likely (lacking confirmation with aDNA) that this haplogroup expanded with Celts.

NOTE. Regarding R1b SNPs, YTree has more samples (and thus more SNPs) to work with estimates, due to its connection with FTDNA groups, so it is in principle more reliable (although estimates were calculated in 2017). Nevertheless, the methods to estimate the age of the MRCA are different between YTree and YFull.

df27-m167-z262-mcdonald
YTree estimations of TMRCA for R1b-Z262 (left) and R1b-M167 (right).

Why this is important has to do with the realization that Celts must have expanded explosively in all directions during the estimated range for Common Celtic (ca. 1500-1000 BC), and as such R1b-M167 is probably going to be one of the clear Y-DNA markers of the Celtic expansion, when it appears in the ancient DNA record, maybe in new SNP calls from samples of the Olalde et al. (2019) paper, or in future Urnfield/Hallstatt/La Tène papers.

Sister clades derived from R1b-Z262 (TMRCA ca. 1650 BC for YTree, or 2700 for YFull), although sharing a quite old origin, may have taken part in the same communities that expanded R1b-M167, likely from some point in central Europe, possibly as remnants of a previous (Tumulus culture?) central European expansion, as the sample SZ5 from Szólád (R1b-CTS1595) and the distribution of modern samples suggest.

r1b-df27-m167-sry2627
Left: Modern distribution of upstream clade L176.2 (YFull R1b-CTS4188); Right: Modern distribution of M167. Both include later expansions within Iberia (probably with the Crown of Aragon during the Reconquista). Contour maps of the derived allele frequencies of the SNPs analyzed in Solé-Morata et al. (2017).

The Celtic expansion might not have been a mass migration of peoples replacing all male lines of their controlled territories (as was common in the Neolithic and Chalcolithic), because of the Bronze Age dominant chiefdom-based system that relied on alliances, but it is becoming clear that Early Celts are also going to show the expansion of certain successful male lineages.

Oh, and you can say goodbye to the autochthonous “Vasconic = R1b-DF27” (latest heir of the “Vasconic = R1b-P312”) theory, too, if – for some strange reason – you hadn’t already.

EDIT (16 MAR) Just in case the wording is not clear: the fact that this haplogroup most likely expanded with Celts does not mean that its lineages didn’t become eventually incorporated into Iberian cultures and adopted non-IE languages: some of them probably did at some point, in some regions of northern Iberia, and most were certainly later incorporated to the Roman civilization and spoke Latin, then to the medieval kingdoms with their languages, and so on until the present day… Only those eventually associated with Iron Age Aquitanians may have retained their non-IE language, unless those lineages today associated with Basques were incorporated later to the Basque-speaking regions by expanding medieval kingdoms. A complex picture repeated everywhere in Europe: no haplogroup+language continuity in sight, anywhere.

NOTE: This here is currently the most likely interpretation of data based on estimations of mutations; it is not confirmed with ancient samples.

Related

Iberia: East Bell Beakers spread Indo-European languages; Celts expanded later

iberia-migrations-celts

New paper (behind paywall), The genomic history of the Iberian Peninsula over the past 8000 years, by Olalde et al. Science (2019).

NOTE. Access to article from Reich Lab: main paper and supplementary materials.

Abstract:

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non-Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.

Interesting excerpts:

From the Bronze Age (~2200–900 BCE), we increase the available dataset (6, 7, 17) from 7 to 60 individuals and show how ancestry from the Pontic-Caspian steppe (Steppe ancestry) appeared throughout Iberia in this period (Fig. 1, C and D), albeit with less impact in the south (table S13). The earliest evidence is in 14 individuals dated to ~2500–2000 BCE who coexisted with local people without Steppe ancestry (Fig. 2B). These groups lived in close proximity and admixed to form the Bronze Age population after 2000 BCE with ~40% ancestry from incoming groups (Fig. 2B and fig. S6).

Y-chromosome turnover was even more pronounced (Fig. 2B), as the lineages common in Copper Age Iberia (I2, G2, and H) were almost completely replaced by one lineage, R1b-M269. These patterns point to a higher contribution of incoming males than females, also supported by a lower proportion of nonlocal ancestry on the X-chromosome (table S14 and fig. S7), a paradigm that can be exemplified by a Bronze Age tomb from Castillejo del Bonete containing a male with Steppe ancestry and a female with ancestry similar to Copper Age Iberians.

iberian-adna

For the Iron Age, we document a consistent trend of increased ancestry related to Northern and Central European populations with respect to the preceding Bronze Age (Figs. 1, C and D, and 2B). The increase was 10 to 19% (95% confidence intervals given here and in the percentages that follow) in 15 individuals along the Mediterranean coast where non-Indo-European Iberian languages were spoken; 11 to 31% in two individuals at the Tartessian site of La Angorrilla in the southwest with uncertain language attribution; and 28 to 43% in three individuals at La Hoya in the north where Indo-European Celtiberian languages were likely spoken (fig. S6 and tables S11 and S12).

This trend documents gene flow into Iberia during the Late Bronze Age or Early Iron Age, possibly associated with the introduction of the Urnfield tradition (18). Unlike in Central or Northern Europe, where Steppe ancestry likely marked the introduction of Indo-European languages (12), our results indicate that, in Iberia, increases in Steppe ancestry were not always accompanied by switches to Indo-European languages.

I think it is obvious they are extrapolating the traditional (not that well-known) linguistic picture of Iberia during the Iron Age, believing in continuity of that picture (especially non-Indo-European languages) during the Urnfield period and earlier.

What this data shows is, as expected, the arrival of Celtic languages in Iberia after Bell Beakers and, by extension, in the rest of western Europe. Somewhat surprisingly, this may have happened during the Urnfield period, and not during the La Tène period.

Also important are the precise subclades:

We thus detect three Bronze Age males who belonged to DF27 (154, 155), confirming its presence in Bronze Age Iberia. The other Iberian Bronze Age males could belong to DF27 as well, but the extremely low recovery rate of this SNP in our dataset prevented us to study its true distribution. All the Iberian Bronze Age males with overlapping sequences at R1b-L21 were negative for this mutation. Therefore, we can rule out Britain as a plausible proximate origin since contemporaneous British males are derived for the L21 subtype.


New open access paper Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula, by Villalba-Mouco et al. Cell (2019):

BAL0051 could be assigned to haplogroup I1, while BAL003 carries the C1a1a haplogroup. To the limits of our typing resolution, EN/MN individuals CHA001, CHA003, ELT002 and ELT006 share haplogroup I2a1b, which was also reported for Loschbour [73] and Motala HG [13], and other LN and Chalcolithic individuals from Iberia [7, 9], as well as Neolithic Scotland, France, England [9], and Lithuania [14]. Both C1 and I1/ I2 are considered typical European HG lineages prior to the arrival of farming. Interestingly, CHA002 was assigned to haplogroup R1b-M343, which together with an EN individual from Cova de Els Trocs (R1b1a) confirms the presence of R1b in Western Europe prior to the expansion of steppe pastoralists that established a related male lineage in Bronze Age Europe [3, 6, 9, 13, 19]. The geographical vicinity and contemporaneity of these two sites led us to run genomic kinship analysis in order to rule out any first or second degree of relatedness. Early Neolithic individual FUC003 carries the Y haplogroup G2a2a1, commonly found in other EN males from Neolithic Anatolia [13], Starçevo, LBK Hungary [18], Impressa from Croatia and Serbia Neolithic [19] and Czech Neolithic [9], but also in MN Croatia [19] and Chalcolithic Iberia [9].

See also

Happy new year 2019…and enjoy our new books!

song-sheep-horses-header

Sorry for the last weeks of silence, I have been rather busy lately. I am having more projects going on, and (because of that) I also wanted to finish a project I have been working on for many months already.

I have therefore decided to publish a provisional version of the text, in the hope that it will be useful in the following months, when I won’t be able to update it as often as I would like to:

EDIT (20 JAN 2019): For those of you who are more comfortable reading in your native language, I have placed some links to automatic translations by Google Translate. They might work especially well for the texts of A Game of Clans & A Clash of Chiefs.

Don’t forget to check out the maps included in the supplementary materials: I have added Y-DNA, mtDNA, and ADMIXTURE data using GIS software. The PCA graphics are also important to follow the main text.

NOTE. Right now the files are only in my server. I will try to upload them to Academia.edu and Research Gate when I have time, I have uploaded them to Academia.edu and ResearchGate, in case the websites are too slow.

I would have preferred to wait for a thorough revision of the section on archaeology and the linguistic sections on Uralic, but I doubt I will have time when the reviews come, so it was either now or maybe next December…

I say so in the introduction, but it is evident that certain aspects of the book are tentative to say the least: the farther back we go from Late Proto-Indo-European, the less clear are many aspects. Also, linguistically I am not convinced about Eurasiatic or Nostratic, although they do have a certain interest when we try to offer a comprehensive view of the past, including ethnolinguistic identities.

I cannot be an expert in everything, and these books cover a lot. I am bound to publish many corrections as new information appears and more reviews are sent. For example, just days ago (before SNP calls of Wang et al. 2018 were published) some paragraphs implied that AME might have expanded Nostratic from the Middle East. Now it does not seem so, and I changed them just before uploading the text. That’s how tentative certain routes are, and how much all of this may change. And that only if we accept a Nostratic phylum…

NOTE. Since the first book I wrote was the linguistic one, and I have spent the last months updating the archaeology + genetics part, now many of you will probably understand 1) why I am so convinced about certain language relationships and 2) how I used many posts to clarify certain ideas and receive comments. Many posts offer probably a good timeline of what I worked with, and when.

A Song of Sheep and Horses (ASoSaH) reread

Edit (23 Jan 2019):

To be able to revise and update the text properly, I decided to start a series of posts on different aspects.

This is an updated list of the posts:

Acknowledgements

I did not add this section to the books, because they are still not ready for print, but I think this is due somewhere now. It is impossible to reference all who have directly or indirectly contributed to this, so this is a list of those I feel have played an important role.

I am indebted to the following people (which does not mean that they share my views, obviously):

First and foremost, to Fernando López-Menchero, for having the patience to review with detail many parts on Indo-European linguistics, knowing that I won’t accept many of his comments anyway. The additional information he offers is invaluable, but I didn’t want to turn this into a huge linguistic encyclopaedia with unending discussions of tiny details of each reconstructed word. I think it is already too big as it is.

I would not have thought about doing this if it were not for the interest of Wekwos (Xavier Delamarre) in publishing a full book about the Indo-European demic diffusion model (in the second half of 2017, I think). It was them who suggested that I extended the content, when all I had done until then was write an essay and draw some maps in my free time between depositing the PhD thesis and defending it.

Sadly, as much as I would like to publish a book with a professional publisher, I don’t think ancient DNA lends itself for the traditional format, so my requests (mainly to have free licenses and being able to review the text at will, as new genetic papers are published) were logically not acceptable. Also, the main aim of all volumes, especially the linguistic one, is the teaching of essentials of Late Proto-Indo-European and related languages, and this objective would be thwarted by selling each volume for $50-70 and only in printed format. I prefer a wider distribution.

At first I didn’t think much of this proposal, because I do not benefit from this kind of publications in my scientific field, but with time my interest in writing a whole, comprehensive book on the subject grew to the point where it was already an ongoing project, probably by the start of 2018.

I would not have been in contact with Wekwos if it were not for user Camulogène Rix at Anthrogenica, so thanks for that and for the interest in this work.

I would not have thought of writing this either if not for the spontaneous support (with an unexpected phone call!) of a professor of the Complutense University of Madrid, Ángel Gómez Moreno, who is interested in this subject – as is his wife, a professor of Classics more closely associated to Indo-European studies, and who helped me with a search for Indo-Europeanists.

EDIT (1 JAN 2019): I remembered that Karin Bojs sent me her book after reading the demic diffusion model. I may have also thought about writing a whole book back then, but mid-2017 is probably too early for the project.

Professor Kortlandt is still to review the text, but he contributed to both previous essays in some very interesting ways, so I hope he can help me improve the parts on Uralic, and maybe alternative accounts of expansion for Balto-Slavic, depending on the time depth that he would consider warranted according to the Temematic hypothesis.

The maps are evidently (for those who are interested in genetics) in part the result of the effort of the late Jean Manco: As you can see from the maps including Y-DNA and mtDNA samples, I have benefitted from her way of organising data and publishing it. Similarly, the work of Iain McDonald in assessing the potential migration routes of R1b and R1a in Europe with the help of detailed maps was behind my idea for the first maps, and consequently behind these, too.

I should thank all people responsible for the release of free datasets to work with, including the Reich and Jena labs, the Veeramah Lab, and also researchers from the Max Planck Institute or the Mainz Palaeogenetics group, who didn’t mind to share with me datasets to work with.

Readers of this blog with interesting comments have also been essential for the improvement of the texts. You can probably see some of your many contributions there. I may not answer many comments, because I am always busy (and sometimes I just don’t have anything interesting to say), but I try to read all of them.

EDIT (1 JAN 2019) I think I should mention at least Chetan, Egg, or Robert George; but then I would leave out old europe, Sgr Ganesh, or Tileman Ehlen; and if I include them I would leave out others…

Users of other sites, like Anthrogenica, whose particular points of view and deep knowledge of some very specific aspects are sometimes very useful. In particular, user Anglesqueville helped me to fix some issues with the merging of datasets to obtain the PCAs and ADMIXTURE, and prepared some individual samples to merge them.

Even without posting anything, Google Analytics keeps sending me messages about increasing user fidelity (returning users), and stats haven’t really changed (which probably means more people are reading old posts), so thank you for that.

I hope you enjoy the books.

Happy new year!

R1a-Z280 lineages in Srubna; and first Palaeo-Balkan R1b-Z2103?

herodotus-world-map

Scythian samples from the North Pontic area are far more complex than what could be seen at first glance. From the new Y-SNP calls we have now thanks to the publications at Molgen (see the spreadsheet) and in Anthrogenica threads, I think this is the basis to work with:

NOTE. I understand that writing a paper requires a lot of work, and probably statistical methods are the main interest of authors, editors, and reviewers. But it is difficult to comprehend how any user of open source tools can instantly offer a more complex assessment of the samples’ Y-SNP calls than professionals working on these samples for months. I think that, by now, it should be clear to everyone that Y-DNA is often as important (sometimes even more) than statistical tools to infer certain population movements, since admixture can change within few generations of male-biased migrations, whereas haplogroups can’t…

Srubna

Srubna-Andronovo samples are as homogeneous as they always were, dominated by R1a-Z645 subclades and CWC-related (steppe_MLBA) ancestry.

The appearance of one (possibly two) R-Z280 lineages in this mixed Srubna-Alakul region of the southern Urals and this early (1880-1690 BC, hence rather Pokrovka-Alakul) points to the admixture of R1a-Z93 and R1a-Z280 already in Abashevo, which also explains the wide distribution of both subclades in the forest zones of Central Asia.

If Abashevo is the cornerstone of the Indo-Iranian / Uralic community, as it seems, the genetic admixture would initially be quite similar, undergoing in the steppes a reduction to haplogroup R1a-Z93 (obviously not complete), at the same time as it expanded to the west with Pokrovka and Srubna, and to the east with Petrovka and Andronovo. To the north, similar reductions will probably be seen following the Seima-Turbino phenomenon.

NOTE. Another R1a-Z280 has been found in the recent sample from Bronze Age Poland (see spreadsheet). As it appears right now in ancient and modern DNA, there seems to be a different distribution between subclades:

  • R1a-Z280 (formed ca. 2900 BC, TMRCA ca. 2600 BC) appears mainly distributed today to the east, in the forest and steppe regions, with the most ‘successful’ expansions possibly related to the spread of Abashevo- and Battle Axe-related cultures (Indo-Iranian and Uralic alike).
  • R1a-M458 (formed ca. 2700, TMRCA ca. 2700 BC) appears mainly distributed to the north, from central Europe to the east – but not in the steppe in aDNA, with the most ‘successful’ expansions to the west.

M458 lineages seem thus to have expanded in the steppe in sizeable numbers only after the Iranian expansions (see a map of modern R1a distributions) i.e. possibly with the expansion of Slavs, which supports the model whereby cultures from central-east Europe (like Trzciniec and Lusatian), accompanied mainly by M458 lineages, were responsible for the expansion of Proto-Balto-Slavic (and later Proto-Slavic).

The finding of haplogroup R1a-Z93, among them one Z2123, is no surprise at this point after other similar Srubna samples. As I said, the early Srubna expansion is most likely responsible for the Szólád Bronze Age sample (ca. 2100-1700 BC), and for the Balkans BA sample (ca. 1750-1625 BC) from Merichleri, due to incursions along the central-east European steppe.

cheek-pieces
Map of decorated bone/antler bridle cheek-pieces and whip handle equivalents. They are often local translations that remained faithful to the originals (from data in Piggott, 1965; Kristiansen & Larsson, 2005; David, 2007). Image from Vandkilde (2014).

Cimmerians

Cimmerian samples from the west show signs of continuity with R1a-Z93 lineages. Nevertheless, the sample of haplogroup Q1a-Y558, together with the ‘Pre-Scythian’ sample of haplogroup N (of the Mezőcsát Culture) in Hungary ca. 980-830 BC, as well as their PCA, seem to depict an origin of these Pre-Scythian peoples in populations related to the eastern Central Asian steppes, too.

NOTE. I will write more on different movements (unrelated to Uralic expansions) from Central and East Asia to the west accompanied by Siberian ancestry and haplogroup N with the post of Ugric-Samoyedic expansions.

Scythians

The Scythian of Z2123 lineage ca. 375-203 BC from the Volga (in Mathieson et al. 2015), together with the sample scy193 from Glinoe (probably also R1a-Z2123), without a date, as well as their common Steppe_MLBA cluster, suggest that Scythians, too, were at first probably quite homogeneous as is common among pastoralist nomads, and came thus from the Central Asian steppes.

The reduction in haplogroup variability among East Iranian peoples seems supported by the three new Late Sarmatian samples of haplogroup R1a-Z2124.

Approximate location of Glinoe and Glinoe Sad (with Starosilya to the south, in Ukrainian territory):

This initial expansion of Scythians does not mean that one can dismiss the western samples as non-Scythians, though, because ‘Scythian’ is a cultural attribution, based on materials. Confirming the diversity among western Scythians, a session at the recent ISBA 8:

Genetic continuity in the western Eurasian Steppe broken not due to Scythian dominance, but rather at the transition to the Chernyakhov culture (Ostrogoths), by Järve et al.

The long-held archaeological view sees the Early Iron Age nomadic Scythians expanding west from their Altai region homeland across the Eurasian Steppe until they reached the Ponto-Caspian region north of the Black and Caspian Seas by around 2,900 BP. However, the migration theory has not found support from ancient DNA evidence, and it is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome results of 31 ancient Western and Eastern Scythians as well as samples pre- and postdating them that allow us to set the Scythians in a temporal context by comparing the Western Scythians to samples before and after within the Ponto-Caspian region. We detect no significant contribution of the Scythians to the Early Iron Age Ponto-Caspian gene pool, inferring instead a genetic continuity in the western Eurasian Steppe that persisted from at least 4,800–4,400 cal BP to 2,700–2,100 cal BP (based on our radiocarbon dated samples), i.e. from the Yamnaya through the Scythian period.

(…) Our results (…) support the hypothesis that the Scythian dominance was cultural rather than achieved through population replacement.

Detail of the slide with admixture of Scythian groups in Ukraine:

scythians-admixture

The findings of those 31 samples seem to support what Krzewińska et al. (2018) found in a tiny region of Moldavia-south-western Ukraine (Glinoi, Glinoi Sad, and Starosilya).

The question, then, is as follows: if Scythian dominance was “cultural rather than achieved through population replacement”…Where are the R1b-Z2103 from? One possibility, as I said in the previous post, is that they represent pockets of Iranian R1b lineages in the steppes descended from eastern Yamna, given that this haplogroup appears in modern populations from a wide region surrounding the steppes.

The other possibility, which is what some have proposed since the publication of the paper, is that they are related to Thracians, and thus to Palaeo-Balkan populations. About the previously published Thracian individuals in Sikora et al. (2014):

thracian-samples
Geographic origin of ancient samples and ADMIXTURE results. (A) Map of Europe indicating the discovery sites for each of the ancient samples used in this study. (B) Ancestral population clusters inferred using ADMIXTURE on the HGDP dataset, for k = 6 ancestral clusters. The width of the bars of the ancient samples was increased to aid visualization. https://doi.org/10.1371/journal.pgen.1004353.g001

For the Thracian individuals from Bulgaria, no clear pattern emerges. While P192-1 still shows the highest proportion of Sardinian ancestry, K8 more resembles the HG individuals, with a high fraction of Russian ancestry.

Despite their different geographic origins, both the Swedish farmer gok4 and the Thracian P192-1 closely resemble the Iceman in their relationship with Sardinians, making it unlikely that all three individuals were recent migrants from Sardinia. Furthermore, P192-1 is an Iron Age individual from well after the arrival of the first farmers in Southeastern Europe (more than 2,000 years after the Iceman and gok4), perhaps indicating genetic continuity with the early farmers in this region. The only non-HG individual not following this pattern is K8 from Bulgaria. Interestingly, this individual was excavated from an aristocratic inhumation burial containing rich grave goods, indicating a high social standing, as opposed to the other individual, who was found in a pit.

pca-thracians

The following are excerpts from A Companion to Ancient Thrace (2015), by Valeva, Nankov, and Graninger (emphasis mine):

Thracian settlements from the 6th c. BC on:

(…) urban centers were established in northeastern Thrace, whose development was linked to the growth of road and communication networks along with related economic and distributive functions. The early establishment of markets/emporia along the Danube took place toward the middle of the first millennium BCE (Irimia 2006, 250–253; Stoyanov in press). The abundant data for intensive trade discovered at the Getic village in Satu Nou on the right bank of the Danube provides another example of an emporion that developed along the main artery of communication toward the interior of Thrace (Conovici 2000, 75–76).

Undoubtedly the most prominent manifestation of centralization processes and stratification in the settlement system of Thrace arrives with the emergence of political capitals – the leading urban centers of various Thracian political formations.

getic-thracian
Image from Volf at Vol_Vlad LiveJournal.

Their relationships with Scythians and Greeks

The Scythian presence south of the Danube must be balanced with a Thracian presence north of the river. We have observed Getae there in Alexander’s day, settled and raising grain. For Strabo the coastlands from the Danube delta north as far as the river and Greek city of Tyras were the Desert of the Getae (7.3.14), notable for its poverty and tracklessness beyond the great river. He seems to suggest also that it was here that Lysimachus was taken alive by Dromichaetes, king of the Getae, whose famous homily on poverty and imperialism only makes sense on the steppe beyond the river (7.3.8; cf. Diod. 21.12; further on Getic possessions above the Danube, Paus. 1.9 with Delev 2000, 393, who seems rather too skeptical; on poverty, cf. Ballesteros Pastor 2003). This was the kind of discourse more familiarly found among Scythians, proud and blunt in the strength of their poverty. However, as Herodotus makes clear, simple pastoralism was not the whole story as one advanced round into Scythia. For he observes the agriculture practiced north and west of Olbia. These were the lands of the Alizones and the people he calls the Scythian Ploughmen, not least to distinguish them from the Royal Scythians east of Olbia, in whose outlook, he says, these agriculturalist Scythians were their inferiors, their slaves (Hdt. 4.20). The key point here is that, as we began to see with the Getan grain-fields of Alexander’s day, there was scope for Thracian agriculturalists to maintain their lifestyles if they moved north of the Danube, the steppe notwithstanding. It is true that it is movement in the other direction that tends to catch the eye, but there are indications in the literary tradition and, especially, in the archaeological record that there was also significant movement northward from Thrace across the Danube and the Desert of the Getae beyond it.

Greek literary sources were not much concerned with Thracian migration into Scythia, but we should observe the occasional indications of that process in very different texts and contexts. At the level of myth, it is to be remembered that Amazons were regularly considered to be of Thracian ethnicity from Archaic times onward and so are often depicted in Thracian dress in Greek art (Bothmer 1957; cf. Sparkes 1997): while they are most familiar on the south coast of the Black Sea, east of Sinope, they were also located on the north coast, especially east of the Don (the ancient Tanais). Herodotus reports an origin-story of the Sauromatians there, according to which this people had been created by the union of some Scythian warriors with Amazons captured on the south coast and then washed up on the coast of Scythia (4.110). While the story is unhistorical, it is not without importance. First, it reminds us that passage north from the Danube was not the only way that Thracians, Thracian influence, and Thracian culture might find their way into Scythia. There were many more and less circuitous routes, especially by sea, that could bring Thrace into Scythia. Secondly, the myth offered some ideological basis for the Sauromatian settlement in Thrace that Strabo records, for Sauromatians might claim a Thracian origin through their Amazon forebears. Finally, rather as we saw that Heracles could bring together some of the peoples of the region, we should also observe that Ares, whose earthly home was located in Thrace by a strong Greek and Roman tradition, seems also to have been a deity of special significance and special cult among the Scythians. So much was appropriate, especially from a Classical perspective, in associations between these two peoples, whose fame resided especially in their capacity for war.

skythen
Scythians: cultures and findings (ca. 7th-4th/3rd c. BC). Greek colonies marked with concentric circles.

This broad picture of cultural contact, interaction, and osmosis, beyond simple conflict, provides the context for a range of archaeological discoveries, which – if examined separately – may seem to offer no more than a scatter of peculiarities. Here we must acknowledge especially the pioneering work of Melyukova, who has done most to develop thinking on Thracian–Scythian interaction. As she pointed out, we have a good example of Thracian–Scythian osmosis as early as the mid-seventh century bce at Tsarev Brod in northeastern Bulgaria, where a warrior’s burial combines elements of Scythian and Thracian culture (Melyukova 1965). For, while the manner of his burial and many of the grave goods find parallels in Scythia and not Thrace, there are also goods which would be odd in a Scythian burial and more at home in a Thracian one of this period (notably a Hallstatt vessel, an iron knife, and a gold diadem). Also interesting in this regard are several stone figures found in the Dobrudja which resemble very closely figures of this kind (baby) known from Scythia (Melyukova 1965, 37–38). They range in date from perhaps the sixth to the third centuries bce, and presumably were used there – as in Scythia – to mark the burials of leading Scythians deposited in the area. Is this cultural osmosis? We should probably expect osmosis to occur in tandem with the movement of artefacts, so that only good contexts can really answer such questions from case to case. However, the broad pattern is indicated by a range of factors. Particularly notable in this regard is the observable development of a Thraco-Scythian form of what is more familiar as “Scythian animal style,” a term which – it must be understood – already embraces a range of types as we examine the different examples of the style across the great expanse from Siberia to the western Ukraine. As Melyukova observes, Thrace shows both items made in this style among Scythians and, more numerous and more interesting, a Thracian tendency to adapt that style to local tastes, with observable regional distinctions within Thrace itself. Among the Getae and Odrysians the adaptation seems to have been at its height from the later fifth century to the mid-third century (Melyukova 1965, 38; 1979).

The absence of local animal style in Bulgaria before the fifth century bce confirms that we have cultural influences and osmosis at work here, though that is not to say that Scythian tradition somehow dominated its Thracian counterpart, as has been claimed (pace Melyukova 1965, 39; contrast Kitov 1980 and 1984). Of particular interest here is the horse-gear (forehead-covers, cheek-pieces, bridle fittings, and so on) which is found extensively in Romania and Bulgaria as well as in Scythia, both in hoarded deposits and in burials. This exemplifies the development of a regional animal style, not least in silver and bronze, which problematizes the whole issue of the place(s) of its production. Accordingly, the regular designation as “Thracian” of horse-gear from the rich fourth century Scythian burial of Oguz in the Ukraine becomes at least awkward and questionable (further, Fialko 1995). And let us be clear that this is no minor matter, nor even part of a broader debate about the shared development of toreutics among Thracians and Scythians (e.g., Kitov 1980 and 1984). A finely equipped horse of fine quality was a strong statement and striking display of wealth and the power it implied

(…) while Thracian pottery appears at Olbia, Scythian pottery among Thracians is largely confined to the eastern limits of what should probably be regarded as Getic territory, namely the area close to the west of the Dniester, from the sixth century bce. Rather exceptional then is the Scythian pottery noted at Istros, which has been explained as a consequence of the Scythian pursuit of the withdrawing army of Darius and, possibly, a continued Scythian grip on the southern Danube in its aftermath (Melyukova 1965, 34). The archaeology seems to show us, therefore, that the elite Thracians and Scythians were more open to adaptation and acculturation than were their lesser brethren.

palaeo-balkan-languages
Paleo-Balkan languages in Eastern Europe between 5th and 1st century BC. From Wikipedia.

Conclusion

(…) we see distinct peoples and organizations, for example as Sitalces’ forces line up against the Scythians. Much more striking, however, against that general background, are the various ways in which the two peoples and their elites are seen to interact, connect, and share a cultural interface. We see also in Scyles’ story how the Greek cities on the coast of Thrace and Scythia played a significant role in the workings of relationships between the two peoples. It is not simply that these cities straddled the Danube, but also that they could collaborate – witness the honors for Autocles, ca. 300 bce (SEG 49.1051; Ochotnikov 2006) – and were implicated with the interactions of the much greater non-Greek powers around them. At the same time, we have seen the limited reality of familiar distinctions between settled Thracians and nomadic Scythians and the limited role of the Danube too in dividing Thrace and Scythia. The interactions of the two were not simply matters of dynastic politics and the occasional shared taste for artefacts like horse-gear, but were more profoundly rooted in the economic matrix across the region, so that “Scythian” nomadism might flourish in the Dobrudja and “Thracian-style” agriculture and settlement can be traced from Thrace across the Danube as far as Olbia. All of that offers scant justification for the Greek tendency to run together Thracians and Scythians as much the same phenomenon, not least as irrational, ferocious, and rather vulgar barbarians (e.g., Plato, Rep. 435b), because such notions were the result of ignorance and chauvinism. However, Herodotus did not share those faults to any degree, so that we may take his ready movement from Scythians to Thracians to be an indication of the importance of interaction between the two peoples whom he had encountered not only as slaves in the Aegean world, but as powerful forces in their own lands (e.g., Hdt. 4.74, where Thracian usage is suddenly brought into his account of Scythian hemp). Similarly, Thucydides, who quite without need breaks off his disquisition on the Odrysians to remark upon political disunity among the Scythians (Thuc. 2.97, a favorite theme: cf. Hdt. 4.81; Xen., Cyr. 1.1.4). As we have seen throughout this discussion, there were many reasons why Thracians might turn the thoughts of serious writers to Scythians and vice versa.

It seems, following Sikora et al. (2014), that Thracian ‘common’ populations would have more Anatolian Neolithic ancestry compared to more ‘steppe-like’ samples. But there were important differences even between the two nearby samples published from Bulgaria, which may account for the close interaction between Scythians and Thracians we see in Krzewińska et al. (2018), potentially reflected in the differences between the Central, Southern and the South-Central clusters (possibly related to different periods rather than peoples??).

If these R1b-Z2103 were descended from Thracian elites, this would be the first proof of Palaeo-Balkan populations showing mainly R1b-Z2103, as I expect. Their appearance together with haplogroup I2a2a1b1 (also found in Ukraine Neolithic and in the Yamna outlier from Bulgaria) seem to support this regional continuity, and thus a long-lasting cultural and ethnic border roughly around the Danube, similar to the one found in the northern Caucasus.

However, since these samples are some 2,500 years younger than the Yamna expansion to the south, and they are archaeologically Scythians, it is impossible to say. In any case, it would seem that the main expansion of R1a-Z645 lineages to the south of the Danube – and therefore those found among modern Greeks – was mediated by the Slavic expansions centuries later.

krzewinska-scythians-pca
Modified image from Krzewińska et al. (2018), with added Y-DNA haplogroups to each defined Scythian cluster and Sarmatians. Principal component analysis (PCA) plot visualizing 35 Bronze Age and Iron Age individuals presented in this study and in published ancient individuals in relation to modern reference panel from the Human Origins data set. See image with population references.

On the Northern cluster there is a sample of haplogroup R1b-P312 which, given its position on the PCA (apparently even more ‘modern Celtic’-like than the Hallstatt_Bylany sample from Damgaard et al. 2018), it seems that it could be the product of the previous eastward Hallstatt expansion…although potentially also from a recent one?:

Especially important in the archaeology of this interior is the large settlement at Nemirov in the wooded steppe of the western Ukraine, where there has been considerable excavation. This settlement’s origins evidently owe nothing significant to Greek influence, though the early east Greek pottery there (from ca. 650 bce onward: Vakhtina 2007) and what seems to be a Greek graffito hint at its connections with the Greeks of the coast, especially at Olbia, which lay at the estuary of the River Bug on whose middle course the site was located (Braund 2008). The main interest of the site for the present discussion, however, is its demonstrable participation in the broader Hallstatt culture to its west and south (especially Smirnova 2001). Once we consider Nemirov and the forest steppe in connection with Olbia and the other locations across the forest steppe and coastal zone, together with the less obvious movements across the steppe itself, we have a large picture of multiple connectivities in which Thrace bulks large.

scythian-peoples-balkans
Early Iron Age cultures of the Carpathian basin ca. 7-6th century BC, including steppe-related groups. Ďurkovič et al. (2018).

While the above description of clear-cut R1a-Steppe and R1b-Balkans is attractive (and probably more reliable than admixture found in scattered samples of unclear dates), the true ancient genetic picture is more complicated than that:

  • There is nothing in the material culture of the published western Scythians to distinguish the supposed Thracian elites.
  • We have the sample I0575, an Early Sarmatian from the southern Urals (one of the few available) of haplogroup R1b-Z2106, which supports the presence of R1b-Z2103 lineages among Eastern Iranian-speaking peoples.
  • We also have DA30, a Sarmatian of I2b lineage from the central steppes in Kazakhstan (ca. 47 BC – 24 AD).
  • Other Sarmatian samples of haplogroup R remain undefined.
  • There is R1a-Z93 in a late Sarmatian-Hun sample, which complicates the picture of late pastoralist nomads further.

Therefore, the possibility of hidden pockets of Iranian peoples of R1b-Z2103 (maybe also R1b-P312) lineages remains the best explanation, and should not be discarded simply because of the prevalent haplogroups among modern populations, or because of the different clusters found, or else we risk an obvious circular reasoning: “this sample is not (autosomically or in prevalent haplogroups) like those we already had from the steppe, ergo it is not from this or that steppe culture.” Hopefully, the upcoming paper by Järve et al. will help develop a clearer genetic transect of Iranian populations from the steppes.

All in all, the diversity among western Scythians represents probably one of the earliest difficult cases of acculturation to be studied with ancient DNA (obviously not the only one), since Scythians combine unclear archaeological data with limited and conflicting proto-historical accounts (also difficult to contrast with the wide confidence intervals of radiocarbon dates) with different evolving clusters and haplogroups – especially in border regions with strong and continued interactions of cultures and peoples.

With emerging complex cases like these during the Iron Age, I am happy to see that at least earlier expansions show clearer Y-DNA bottlenecks, or else genetics would only add more data to argue about potential cultural diffusion events, instead of solving questions about proto-language expansions once and for all…

Related

Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component

invasion-from-the-steppe-yamnaya

Good timing for the publication of two interesting papers, that a lot of people should read very carefully:

ADMIXTURE

Open access A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots, by Daniel J. Lawson, Lucy van Dorp & Daniel Falush, Nature Communications (2018).

Interesting excerpts (emphasis mine):

Experienced researchers, particularly those interested in population structure and historical inference, typically present STRUCTURE results alongside other methods that make different modelling assumptions. These include TreeMix, ADMIXTUREGRAPH, fineSTRUCTURE, GLOBETROTTER, f3 and D statistics, amongst many others. These models can be used both to probe whether assumptions of the model are likely to hold and to validate specific features of the results. Each also comes with its own pitfalls and difficulties of interpretation. It is not obvious that any single approach represents a direct replacement as a data summary tool. Here we build more directly on the results of STRUCTURE/ADMIXTURE by developing a new approach, badMIXTURE, to examine which features of the data are poorly fit by the model. Rather than intending to replace more specific or sophisticated analyses, we hope to encourage their use by making the limitations of the initial analysis clearer.

The default interpretation protocol

Most researchers are cautious but literal in their interpretation of STRUCTURE and ADMIXTURE results, as caricatured in Fig. 1, as it is difficult to interpret the results at all without making several of these assumptions. Here we use simulated and real data to illustrate how following this protocol can lead to inference of false histories, and how badMIXTURE can be used to examine model fit and avoid common pitfalls.

admixture-protocol
A protocol for interpreting admixture estimates, based on the assumption that the model underlying the inference is correct. If these assumptions are not validated, there is substantial danger of over-interpretation. The “Core protocol” describes the assumptions that are made by the admixture model itself (Protocol 1, 3, 4), and inference for estimating K (Protocol 2). The “Algorithm input” protocol describes choices that can further bias results, while the “Interpretation” protocol describes assumptions that can be made in interpreting the output that are not directly supported by model inference

Discussion

STRUCTURE and ADMIXTURE are popular because they give the user a broad-brush view of variation in genetic data, while allowing the possibility of zooming down on details about specific individuals or labelled groups. Unfortunately it is rarely the case that sampled data follows a simple history comprising a differentiation phase followed by a mixture phase, as assumed in an ADMIXTURE model and highlighted by case study 1. Naïve inferences based on this model (the Protocol of Fig. 1) can be misleading if sampling strategy or the inferred value of the number of populations K is inappropriate, or if recent bottlenecks or unobserved ancient structure appear in the data. It is therefore useful when interpreting the results obtained from real data to think of STRUCTURE and ADMIXTURE as algorithms that parsimoniously explain variation between individuals rather than as parametric models of divergence and admixture.

For example, if admixture events or genetic drift affect all members of the sample equally, then there is no variation between individuals for the model to explain. Non-African humans have a few percent Neanderthal ancestry, but this is invisible to STRUCTURE or ADMIXTURE since it does not result in differences in ancestry profiles between individuals. The same reasoning helps to explain why for most data sets—even in species such as humans where mixing is commonplace—each of the K populations is inferred by STRUCTURE/ADMIXTURE to have non-admixed representatives in the sample. If every individual in a group is in fact admixed, then (with some exceptions) the model simply shifts the allele frequencies of the inferred ancestral population to reflect the fraction of admixture that is shared by all individuals.

Several methods have been developed to estimate K, but for real data, the assumption that there is a true value is always incorrect; the question rather being whether the model is a good enough approximation to be practically useful. First, there may be close relatives in the sample which violates model assumptions. Second, there might be “isolation by distance”, meaning that there are no discrete populations at all. Third, population structure may be hierarchical, with subtle subdivisions nested within diverged groups. This kind of structure can be hard for the algorithms to detect and can lead to underestimation of K. Fourth, population structure may be fluid between historical epochs, with multiple events and structures leaving signals in the data. Many users examine the results of multiple K simultaneously but this makes interpretation more complex, especially because it makes it easier for users to find support for preconceptions about the data somewhere in the results.

In practice, the best that can be expected is that the algorithms choose the smallest number of ancestral populations that can explain the most salient variation in the data. Unless the demographic history of the sample is particularly simple, the value of K inferred according to any statistically sensible criterion is likely to be smaller than the number of distinct drift events that have practically impacted the sample. The algorithm uses variation in admixture proportions between individuals to approximately mimic the effect of more than K distinct drift events without estimating ancestral populations corresponding to each one. In other words, an admixture model is almost always “wrong” (Assumption 2 of the Core protocol, Fig. 1) and should not be interpreted without examining whether this lack of fit matters for a given question.

admixture-pitfalls
Three scenarios that give indistinguishable ADMIXTURE results. a Simplified schematic of each simulation scenario. b Inferred ADMIXTURE plots at K= 11. c CHROMOPAINTER inferred painting palettes.

Because STRUCTURE/ADMIXTURE accounts for the most salient variation, results are greatly affected by sample size in common with other methods. Specifically, groups that contain fewer samples or have undergone little population-specific drift of their own are likely to be fit as mixes of multiple drifted groups, rather than assigned to their own ancestral population. Indeed, if an ancient sample is put into a data set of modern individuals, the ancient sample is typically represented as an admixture of the modern populations (e.g., ref. 28,29), which can happen even if the individual sample is older than the split date of the modern populations and thus cannot be admixed.

This paper was already available as a preprint in bioRxiv (first published in 2016) and it is incredible that it needed to wait all this time to be published. I found it weird how reviewers focused on the “tone” of the paper. I think it is great to see files from the peer review process published, but we need to know who these reviewers were, to understand their whiny remarks… A lot of geneticists out there need to develop a thick skin, or else we are going to see more and more delays based on a perceived incorrect tone towards the field, which seems a rather subjective reason to force researchers to correct a paper.

PCA of SNP data

Open access Effective principal components analysis of SNP data, by Gauch, Qian, Piepho, Zhou, & Chen, bioRxiv (2018).

Interesting excerpts:

A potential hindrance to our advice to upgrade from PCA graphs to PCA biplots is that the SNPs are often so numerous that they would obscure the Items if both were graphed together. One way to reduce clutter, which is used in several figures in this article, is to present a biplot in two side-by-side panels, one for Items and one for SNPs. Another stratagem is to focus on a manageable subset of SNPs of particular interest and show only them in a biplot in order to avoid obscuring the Items. A later section on causal exploration by current methods mentions several procedures for identifying particularly relevant SNPs.

One of several data transformations is ordinarily applied to SNP data prior to PCA computations, such as centering by SNPs. These transformations make a huge difference in the appearance of PCA graphs or biplots. A SNPs-by-Items data matrix constitutes a two-way factorial design, so analysis of variance (ANOVA) recognizes three sources of variation: SNP main effects, Item main effects, and SNP-by-Item (S×I) interaction effects. Double-Centered PCA (DC-PCA) removes both main effects in order to focus on the remaining S×I interaction effects. The resulting PCs are called interaction principal components (IPCs), and are denoted by IPC1, IPC2, and so on. By way of preview, a later section on PCA variants argues that DC-PCA is best for SNP data. Surprisingly, our literature survey did not encounter even a single analysis identified as DC-PCA.

The axes in PCA graphs or biplots are often scaled to obtain a convenient shape, but actually the axes should have the same scale for many reasons emphasized recently by Malik and Piepho [3]. However, our literature survey found a correct ratio of 1 in only 10% of the articles, a slightly faulty ratio of the larger scale over the shorter scale within 1.1 in 12%, and a substantially faulty ratio above 2 in 16% with the worst cases being ratios of 31 and 44. Especially when the scale along one PCA axis is stretched by a factor of 2 or more relative to the other axis, the relationships among various points or clusters of points are distorted and easily misinterpreted. Also, 7% of the articles failed to show the scale on one or both PCA axes, which leaves readers with an impressionistic graph that cannot be reproduced without effort. The contemporary literature on PCA of SNP data mostly violates the prohibition against stretching axes.

pca-how-to
DC-PCA biplot for oat data. The gradient in the CA-arranged matrix in Fig 13 is shown here for both lines and SNPs by the color scheme red, pink, black, light green, dark green.

The percentage of variation captured by each PC is often included in the axis labels of PCA graphs or biplots. In general this information is worth including, but there are two qualifications. First, these percentages need to be interpreted relative to the size of the data matrix because large datasets can capture a small percentage and yet still be effective. For example, for a large dataset with over 107,000 SNPs for over 6,000 persons, the first two components capture only 0.3693% and 0.117% of the variation, and yet the PCA graph shows clear structure (Fig 1A in [4]). Contrariwise, a PCA graph could capture a large percentage of the total variation, even 50% or more, but that would not guarantee that it will show evident structure in the data. Second, the interpretation of these percentages depends on exactly how the PCA analysis was conducted, as explained in a later section on PCA variants. Readers cannot meaningfully interpret the percentages of variation captured by PCA axes when authors fail to communicate which variant of PCA was used.

Conclusion

Five simple recommendations for effective PCA analysis of SNP data emerge from this investigation.

  1. Use the SNP coding 1 for the rare or minor allele and 0 for the common or major allele.
  2. Use DC-PCA; for any other PCA variant, examine its augmented ANOVA table.
  3. Report which SNP coding and PCA variant were selected, as required by contemporary standards in science for transparency and reproducibility, so that readers can interpret PCA results properly and reproduce PCA analyses reliably.
  4. Produce PCA biplots of both Items and SNPs, rather than merely PCA graphs of only Items, in order to display the joint structure of Items and SNPs and thereby to facilitate causal explanations. Be aware of the arch distortion when interpreting PCA graphs or biplots.
  5. Produce PCA biplots and graphs that have the same scale on every axis.

I read the referenced paper Biplots: Do Not Stretch Them!, by Malik and Piepho (2018), and even though it is not directly applicable to the most commonly available PCA graphs out there, it is a good reminder of the distorting effects of stretching. So for example quite recently in Krause-Kyora et al. (2018), where you can see Corded Ware and BBC samples from Central Europe clustering with samples from Yamna:

NOTE. This is related to a vertical distorsion (i.e. horizontal stretching), but possibly also to the addition of some distant outlier sample/s.

pca-cwc-yamna-bbc
Principal Component Analysis (PCA) of the human Karsdorf and Sorsum samples together with previously published ancient populations projected on 27 modern day West Eurasian populations (not shown) based on a set of 1.23 million SNPs (Mathieson et al., 2015). https://doi.org/10.7554/eLife.36666.006

The so-called ‘Yamnaya’ ancestry

Every time I read papers like these, I remember commenters who kept swearing that genetics was the ultimate science that would solve anthropological problems, where unscientific archaeology and linguistics could not. Well, it seems that, like radiocarbon analysis, these promising developing methods need still a lot of refinement to achieve something meaningful, and that they mean nothing without traditional linguistics and archaeology… But we already knew that.

Also, if this is happening in most peer-reviewed publications, made by professional geneticists, in journals of high impact factor, you can only wonder how many more errors and misinterpretations can be found in the obscure market of so many amateur geneticists out there. Because amateur geneticist is a commonly used misnomer for people who are not geneticists (since they don’t have the most basic education in genetics), and some of them are not even ‘amateurs’ (because they are selling the outputs of bioinformatic tools)… It’s like calling healers ‘amateur doctors’.

NOTE. While everyone involved in population genetics is interested in knowing the truth, and we all have our confirmation (and other kinds of) biases, for those who get paid to tell people what they want to hear, and who have sold lots of wrong interpretations already, the incentives of ‘being right’ – and thus getting involved in crooked and paranoid behaviour regarding different interpretations – are as strong as the money they can win or loose by promoting themselves and selling more ‘product’.

As a reminder of how badly these wrong interpretations of genetic results – and the influence of the so-called ‘amateurs’ – can reflect on research groups, yet another turn of the screw by the Copenhagen group, in the oral presentations at Languages and migrations in pre-historic Europe (7-12 Aug 2018), organized by the Copenhagen University. The common theme seems to be that Bell Beaker and thus R1b-L23 subclades do represent a direct expansion from Yamna now, as opposed to being derived from Corded Ware migrants, as they supported before.

NOTE. Yes, the “Yamna → Corded Ware → Únětice / Bell Beaker” migration model is still commonplace in the Copenhagen workgroup. Yes, in 2018. Guus Kroonen had already admitted they were wrong, and it was already changed in the graphic representation accompanying a recent interview to Willerslev. However, since there is still no official retraction by anyone, it seems that each member has to reject the previous model in their own way, and at their own pace. I don’t think we can expect anyone at this point to accept responsibility for their wrong statements.

So their lead archaeologist, Kristian Kristiansen, in The Indo-Europeanization of Europé (sic):

kristiansen-migrations
Kristiansen’s (2018) map of Indo-European migrations

I love the newly invented arrows of migration from Yamna to the north to distinguish among dialects attributed by them to CWC groups, and the intensive use of materials from Heyd’s publications in the presentation, which means they understand he was right – except for the fact that they are used to support a completely different theory, radically opposed to those defended in Heyd’s model

Now added to the Copenhagen’s unending proposals of language expansions, some pearls from the oral presentation:

  • Corded Ware north of the Carpathians of R1a lineages developed Germanic;
  • R1b borugh [?] Italo-Celtic;
  • the increase in steppe ancestry on north European Bell Beakers mean that they “were a continuation of the Yamnaya/Corded Ware expansion”;
  • Corded Ware groups [] stopped their expansion and took over the Bell Beaker package before migrating to England” [yep, it literally says that];
  • Italo-Celtic expanded to the UK and Iberia with Bell Beakers [I guess that included Lusitanian in Iberia, but not Messapian in Italy; or the opposite; or nothing like that, who knows];
  • 2nd millennium BC Bronze Age Atlantic trade systems expanded Proto-Celtic [yep, trade systems expanded the language]
  • 1st millennium BC expanded Gaulish with La Tène, including a “Gaulish version of Celtic to Ireland/UK” [hmmm, dat British Gaulish indeed].

You know, because, why the hell not? A logical, stable, consequential, no-nonsense approach to Indo-European migrations, as always.

Also, compare still more invented arrows of migrations, from Mikkel Nørtoft’s Introducing the Homeland Timeline Map, going against Kristiansen’s multiple arrows, and even against the own recent fantasy map series in showing Bell Beakers stem from Yamna instead of CWC (or not, you never truly know what arrows actually mean):

corded-ware-migrations
Nørtoft’s (2018) maps of Indo-European migrations.

I really, really loved that perennial arrow of migration from Volosovo, ca. 4000-800 BC (3000+ years, no less!), representing Uralic?, like that, without specifics – which is like saying, “somebody from the eastern forest zone, somehow, at some time, expanded something that was not Indo-European to Finland, and we couldn’t care less, except for the fact that they were certainly not R1a“.

This and Kristiansen’s arrows are the most comical invented migration routes of 2018; and that is saying something, given the dozens of similar maps that people publish in forums and blogs each week.

NOTE. You can read a more reasonable account of how haplogroup R1b-L51 and how R1-Z645 subclades expanded, and which dialects most likely expanded with them.

We don’t know where these scholars of the Danish workgroup stand at this moment, or if they ever had (or intended to have) a common position – beyond their persistent ideas of Yamnaya™ ancestral component = Indo-European and R1a must be Indo-European – , because each new publication changes some essential aspects without expressly stating so, and makes thus everything still messier.

It’s hard to accept that this is a series of presentations made by professional linguists, archaeologists, and geneticists, as stated by the official website, and still harder to imagine that they collaborate within the same professional workgroup, which includes experienced geneticists and academics.

I propose the following video to close future presentations introducing innovative ideas like those above, to help the audience find the appropriate mood:

Related

The future of the Reich Lab’s studies and interpretations of Late Indo-European migrations

yamna-corded-ware-bell-beaker-reich

Short report on advances in Genomics, and on the Reich Lab:

Some interesting details:

  • The Lab is impressive. I would never dream of having something like this at our university. I am really jealous of that working environment.
  • They are currently working on population transformations in Italy; I hope we can have at last Italic and Etruscan samples.
  • It is always worth it to repeat that we are all the source of multiple admixture events, many of them quite recent; and I liked the Star Wars simile.
  • Also, some names hinting at potential new samples?? Zajo-I, Chanchan, Gurulde?, Володарка (Ukraine – medieval?), Autodrom, Облевка, Кресты, Кудуксай (Ural region, palaeo-metal?), Золкут, etc.
reich-lab-samples
Ancient DNA sample bag?

On the bad aspect, they keep repeating the same “steppe ancestry” meme (in the featured image above, or the one below). I know this is the news report (i.e. science communication), not exactly the Reich Lab, but these maps didn’t appear out of the blue.

steppe-admixture-reich
Steppe ancestry distribution in Europe, according to PBS.

Interesting for future interpretations is the whiteboard behind David Reich’s back (apparently they like to keep relevant information on whiteboards…):

reich-indo-european-tree
Whiteboard behind David Reich’s back (at his office?).

It seems that while the Copenhagen group will still be bound (see here) by the Gimbutas/Kristiansen starting point, the Reich Lab will remain bound by Anthony’s selection of Ringe’s (2002) glottochronological model, and they will try to make genomic data fit in with it.

In fact, the whiteboard doesn’t even include Ringe’s link of Germanic with Italo-Celtic, which could maybe hint at Anthony’s recent change of heart? (i.e. Yamna Hungary -> Corded Ware). That would mean still less Linguistics (if glottochronology can be called that), and more Archaeology…

anthony-ringe-migration-model
Image from Anthony & Ringe (2015). “The Proto-Indo-European homeland, with migrations outward at about 4200 BCE (1), 3300 BCE (2), and 3000 BCE (3a and 3b). A tree diagram (inset) shows the pre-Germanic split as unresolved. Modified from Anthony (2013).”

I don’t know why university labs need to do this: To select the linguistic model preferred by a single archaeologist, which happens to be the lead archaeologist of the group, and then try to make genetic data agree again and again with that model. I guess it is a strategic question, and has to do with granting continued contacts with archaeological sites, and access to samples from them?

I understand none of them will try to learn ancient languages, too much work probably. But, wouldn’t it have been more scientifish, at least, to depart from, say, three or four reasonable potential linguistic models (that is, from Indo-Europeanists), and from there discuss the best potential fits for the current genomic data in each paper?

This is, for example, how the Heyd (archaeologist) + German/Spanish Indo-Europeanist schools would look like:

yamnaya-heyd-dunkel
Yamnaya expansion coupled with Meid’s (1975) description of three stages of Proto-Indo-European development (as interpreted by Adrados 1998) and depiction of Heyd’s proposal of Yamna expansion.

Wouldn’t you say it could have fitted the statistical and Y-DNA data seamlessly, in contrast to Gimbutas/Trager (i.e. Kristiansen today), or to Anthony/Ringe?

NOTE. I would say the mainstream German school follows Meid’s (1975) three-stage theory coupled with Dunkel’s (e.g. 1997) nomenclature. The Spanish school follows Adrados, who has repeated ad nauseam that he was the first to mention the three-stage theory in conferences and papers previous to and coincident with Meid’s proposal (see his latest JIES article, a paper available in Scribd). In any case, Spanish and German scholars have been working hand in hand in accepting and developing a general linguistic model similar to the one above.

Archaeological theories like those of Heyd or Mallory for Yamna and Bell Beaker (in contrast to Kristiansen or Anthony), and Prescott and Walderhaug for Bell Beaker and Germanic (contrasting with Kristiansen and Iversen) are compatible with this German/Spanish model.

The French school is non-existent on the homeland matter, Italian scholars seem to be behind even in the description of Anatolian as archaic (probably related to the general wish to have Latin as derived from Vergil’s Troy), Russian scholars are still working with Nostratic and Mesolithic expansions, and Leiden, as the leading IE publisher worldwide today, is full of very different ‘divos’, each with his own pet theory (some obviously agreeing with the German/Spanish model; and especially interesting is that some of them are strong supporters of an Indo-Uralic proto-language).

The English-speaking world, on the other hand, has seen the most varied models being either proposed or translated into its language, with the most popular ones being those publicized by archaeologists (Winfred P. Lehmann being one of the noteworthy exceptions), which may explain why for some people (archaeologists or geneticists) linguistics seems more like a game. It is to be assumed that these same people haven’t taken a look at the dozens of genetic papers published to date – and hundreds of archaeological papers using a bit of linguistics to support their models – , and how wrong they have all been in their interpretations, or else they would realize that genomics does (sadly) not really look like a serious discipline at all right now among most linguists, and among many archaeologists either…

Thus, instead of comparing the main theories on Proto-Indo-European (i.e. linguistics->archaeology->genetics), which would have offered the most stable framework to assess potential prehistoric ethnolinguistic identifications, they keep using a single, simplistic language tree liked by an archaeologist, and trying to fit genetic data to it, while also adapting archaeology to genetics, i.e. genetics->archaeology->linguistics; which, as you can imagine, is not going to convince any linguist.

Especially disappointing is that the world’s leading genetic lab still relies on a marginal proposal based on glottochronology, the homeopathy of linguistics… At least in that regard everyone should know better by now.

Also, they keep interacting with the wrong audience: instead of trying to engage linguists into the real homeland and dialectal quest, to keep Genomics a serious discipline among academics, they tend to discuss with politically- or racially-motivated people, which is probably also in line with strategic decisions.

In the example below, we see the main author of their recent paper on Indo-Iranian migrations seeking once again interaction, this time through “news” promoted by Hindu nationalist bigots, so that – even if that makes them look more neutral in the eyes of those who may allow access to Indian samples – , in the end, we see in genomics a fictitious revival of the “AIT vs. OIT debate” dead long ago in linguistics and archaeology (anywhere but in India).

Pretty disappointing to see these trends; so much effort and time invested in futile discussions and infinitely reworked doomed glottochronological or 19th-century models, when it is the fine-scale population structure of expanding Yamna peoples what we should be discussing now, and thus Late PIE dialectalisation with offshoots Afanasevo, East Bell Beaker, Balkan Bronze Age, and Sintashta/Potapovka; as well as Corded Ware evolution in Uralic-speaking territory.

EDIT (7 JUN 2018): Some parts of the text have been corrected or slightly modified.

Related:

On Latin, Turkic, and Celtic – likely stories of mixed societies and little genetic impact

celtic-europe-national-geographic

Recent article on The Conversation, The Roman dead: new techniques are revealing just how diverse Roman Britain was, about the paper (behind paywall) A Novel Investigation into Migrant and Local Health-Statuses in the Past: A Case Study from Roman Britain, by Redfern et al. Bioarchaeology International (2018), among others.

Interesting excerpts about Roman London:

We have discovered, for example, that one middle-aged woman from the southern Mediterranean has black African ancestry. She was buried in Southwark with pottery from Kent and a fourth century local coin – her burial expresses British connections, reflecting how people’s communities and lives can be remade by migration. The people burying her may have decided to reflect her life in the city by choosing local objects, but we can’t dismiss the possibility that she may have come to London as a slave.

The evidence for Roman Britain having a diverse population only continues to grow. Bioarchaeology offers a unique and independent perspective, one based upon the people themselves. It allows us to understand more about their life stories than ever before, but requires us to be increasingly nuanced in our understanding, recognising and respecting these people’s complexities.

We already have a more or less clear idea about how little the Roman conquest may have shaped the genetic map of Europe, Africa, or the Middle East, in contrast to other previous or later migrations or conquests.

Also, on the Turkic expansion, the recent paper of Damgaard et al. (Nature 2018) stated:

In the sixth century AD, the Hunnic Empire had been broken up and dispersed as the Turkic Khaganate assumed the military and political domination of the steppes22,23. Khaganates were steppe nomad political organizations that varied in size and became dominant during this period; they can be contrasted to the previous stateless organizations of the Iron Age24. The Turkic Khaganate was eventually replaced by a number of short-lived steppe cultures25 (…).

We find evidence that elite soldiers associated with the Turkic Khaganate are genetically closer to East Asians than are the preceding Huns of the Tian Shan mountains (Supplementary Information section 3.7). We also find that one Turkic Khaganate-period nomad was a genetic outlier with pronounced European ancestries, indicating the presence of ongoing contact with Europe (…).

turk-medieval-populations
Analyses of Turk- and Medieval-period population clusters. a, PCA of Tian Shan Hun, Turk, Kimak, Kipchack, Karakhanid and Golden Horde, including 28 individuals analysed at 242,406 autosomal SNP positions. b, Results for model-based clustering analysis at K = 7. Here we illustrate the admixture analyses with K = 7 as it approximately identifies the major component of relevance (Anatolian/ European farmer component, Caucasian ancestry, EHG-related ancestry and East Asian ancestry).”

These results suggest that Turkic cultural customs were imposed by an East Asian minority elite onto central steppe nomad populations, resulting in a small detectable increase in East Asian ancestry. However, we also find that steppe nomad ancestry in this period was extremely heterogeneous, with several individuals being genetically distributed at the extremes of the first principal component (Fig. 2) separating Eastern and Western descent. On the basis of this notable heterogeneity, we suggest that during the Medieval period steppe populations were exposed to gradual admixture from the east, while interacting with incoming West Eurasians. The strong variation is a direct window into ongoing admixture processes and the multi-ethnic cultural organization of this period.

We already knew that the expansion of the La Tène culture, associated with the expansion of Celtic languages throughout Europe, was probably not accompanied by massive migrations (from the IEDM, 3rd ed.):

The Mainz research project of bio-archaeometric identification of mobility has not proven to date a mass migration of Celtic peoples in central Europe ca. 4th-3rd centuries BC, i.e. precisely in a period where textual evidence informs of large migratory movements (Scheeres 2014). La Tène material culture points to far-reaching inter-regional contacts and cultural transfers (Burmeister 2016).

Also, from the latest paper on Y-chromosome bottleneck:

[The hypothesis of patrilineal kin group competition] has an added benefit in that it could explain the temporal placement of the bottleneck if competition between patrilineal kin groups was the main form of intergroup competition for a limited episode of time after the Neolithic transition. Anthropologists have repeatedly noted that the political salience of unilineal descent groups is greatest in societies of ‘intermediate social scale’ (Korotayev47 and its citations on p. 2), which tend to be post-Neolithic small-scale societies that are acephalous, i.e. without hierarchical institutions48. Corporate kin groups tend to be absent altogether among mobile hunter gatherers with few defensible resource sites or little property (Kelly49 pp. 64–73), or in societies utilizing relatively unoccupied and under-exploited resource landscapes (Earle and Johnson50 pp. 157–171). Once they emerge, complex societies, such as chiefdoms and states, tend to supervene the patrilineal kin group as the unit of intergroup competition, and while they may not eradicate them altogether as sub-polity-level social identities, warfare between such kin groups is suppressed very effectively51,52.These factors restrict the social phenomena responsible for the bottleneck to the period after the initial Neolithic but before the emergence of complex societies, which would place the bottleneck-generating mechanisms in the right period of time for each region of the Old World.

chalcolithic_late_Europe_Bell_Beaker
Diachronic map of Late Copper Age migrations including Classical Bell Beaker (east group) expansion from central Europe ca. 2600-2250 BC

However, I recently read in a forum for linguists that the expansion of East Bell Beakers overwhelmingly of R1b-L21 subclades in the British Isles “poses a problem”, in that it should be identified with a Celtic expansion earlier than traditionally assumed…

That interpretation would be in line with the simplistic maps we are seeing right now for Bell Beakers (see below for the Copenhagen group).

If anything, the results of Bell Beaker expansions (taken alone) would seem to support a model similar to Cunliffe & Koch‘s hypotheses of a rather early Celtic expansion into Great Britain and Iberia from the Atlantic.

invasion-from-the-steppe-yamnaya
Spread of Indo-European languages (by the Copenhagen group).

But it doesn’t. Mallory already explained why in Cunliffe & Koch’s series Celtic from the West: the Bell Beaker expansion is too early for that; even for Italo-Celtic. It should correspond to North-West Indo-European speakers.

Not every population movement that is genetically very significant needs to be significant for the languages attested much later in the region.

This should be obvious to everyone with the many examples we already have. One of the least controversial now would probably be the expansion of R1b-DF27, widespread in Iberia probably at roughly the same time as R1b-L21 was in Great Britain, and still pre-Roman Iberians showed a mix of non-Indo-European languages, non-Celtic languages (at least Galaico-Lusitanian), and also some (certain) Celtic languages. And modern Iberians speak Romance languages, without much genetic impact from the Romans, either…

It is well-established in Academia that the expansion of La Tène is culturally associated with the spread of Celtic languages in Europe, including the British Isles and Iberia. While modern maps of U152 distribution may correspond to the migration of early Celts (or Italo-Celtic speakers) with Urnfield/Hallstatt, the great Celtic expansion across Europe need not show a genetic influence greater than or even equal to that of previous prehistoric migrations.

post-bell-beaker-europe
Post-Bell-Beaker Europe, after ca. 2200 BC.

You can see in these de novo models the same kind of invented theoretical ‘problem’ (as Iosif Lazaridis puts it) that we have seen with the Corded Ware showing steppe ancestry, with Old Hittite samples not showing EHG ancestry, or with CHG ancestry appearing north of the Caucasus but no EHG to the south.

However you may want to explain all these errors in scientific terms (selection bias, under-coverage, over-coverage, faulty statistical methods, etc.), these interpretations were simply fruit of the lack of knowledge of the anthropological disciplines at play.

Let’s hope the future paper on Celtic expansion takes this into consideration.

Related:

Copenhagen group: Germanic and Balto-Slavic from Bell Beaker; Indo-Anatolian homeland in the Caucasus

invasion-from-the-steppe-yamnaya

Article of general knowledge in Der Spiegel, Invasion from the Steppe, with comments from Willerslev and Kristiansen, appeared roughly at the same time as the Damgaard et al. Nature (2018) and Science (2018) papers were published.

NOTE. You can read the article (in German) from Kristiansen’s Academia.edu account.

Excerpts translated from German (emphasis mine):

On the Y-DNA data

Particularly striking is the genetic signature from the steppe on the Y chromosome. From this the researchers conclude that the majority of migrants were males. Kristian Kristiansen, chief archaeologist in the Willerslev team, also has an idea of ​​how this could be explained: “Maybe it’s a rite of initiation, as it was spread among the steppe peoples,” he says.

The younger sons of the Yamnaya herders, who were excluded from the succession, had to seek their fortune on their own. As part of a solemn ritual, they threw themselves to wolves’ skins and then swarmed in warlike gangs to buy their own herds by cattle-stealing.

(…)

An ally that they seem to have brought from their homeland may also have contributed to the genetic success of the steppe people: Yersinia pestis, the plague bacterium. Its genes were found by researchers from the Max Planck Institute in Jena – and apparently it emerged exactly at the same time as the Yamnaya thrust began.

About the Hittites

(…) And yet now, where Asia and Europe meet geographically, there is no trace of the Yamnaya genes. The wander-loving people from the Pontic-Caspian steppe apparently found neither the way across the Balkans nor through the Caucasus mountains.

Now the researchers are puzzled: How can it be that a language goes on a walk, without the accompanying speakers coming along? Is it possible that the Indo-European seeped into Anatolia, much like the English language spread today without the need for Englishmen?

Archaeologist Kristiansen does not believe it. The researchers would find it hard to reconsider their theories, he says: “Especially the first chapter of the story has to be rewritten.”

He suspects that there was a predecessor of the Yamnaya culture, in which a kind of Proto-Proto-Indo-European was spoken. And he also has a suspicion, where this people could have drifted around: The Caucasus, says Kristiansen, was their homeland. But that remains unproven: “There’s another hole left,” he admits.

invasion-yamnaya-steppe
Spread of Indo-European languages

About the Botai

The study of [the Botai] genome revealed that it was genetically radically different from the members of the Yamnaya culture. The Botai, it seems, consistently avoided any contact with their neighbors – even though they must have crossed the territory of the Botai on their migratory waves.

Willerslev assumes that the art of keeping horses from the Yamnaya steppe nomads was adopted from these peoples, and then they developed it further. At some point, the Botai could then have itself become doomed by its groundbreaking innovation: While the descendants of the Yamnaya spread over half of Eurasia, the Botai disappeared without leaving a trace.

Even more interesting than the few words that set the Copenhagen group’s views for future papers (such as the expected Maykop samples with EHG ancestry) is the artistic sketch of the Indo-European migrations, probably advised by the group.

A simple map does not mean that all members of the Danish workgroup have changed their view completely, but I would say it is a great improvement over the previous “arrows of migration” (see here), and it is especially important that they show a more realistic picture of ancient migrations to general readers.

NOTE. Especially absurd is the identification of the ‘Celtic’ expansion with the first Bell Beakers in the British Isles (that idea is hold by few, such as Koch and Cunliffe in their “Celtic from the West” series). Also inexact, but not so worrying, are the identification of ‘Germanic’ in Germany/Únětice, or the spread of ‘Baltic’ and ‘Slavic’ directly to East Europe (i.e. I guess Mierzanowice/Nitra -> Trzciniec), which is probably driven by the need to assert a close connection with early Iranians and thus with their satemization trends.

Also, as we know now thanks to Narasimhan et al. (2018), there is no need to support that convoluted west arrow (representing CWC) from West Yamna to Central Europe, and then to East Yamna, since the Proto-Indo-Iranian community – represented by the Steppe MLBA cloud that later expanded Indo-Aryan and Iranian languages – has a more direct connection with the in situ admixture of Poltavka/Abashevo within the Volga-Ural region.

I think we can keep this from the article:

Their results, as well as those of the competition labs at Harvard University and Jena’s Max Planck Institute for the History of Humanity, leave no doubt: Yes, the legendary herdsmen in the Pontic-Caspian steppe really existed. They belonged to the so-called Yamnaya culture, and they spread, as linguists had predicted, in massive migrations towards Central Europe and India – a later triumph for linguists.

This can be added to a recent comment by de Barros Damgaard:

The project has been an extremely enriching and exciting process. We were able to direct many very different academic fields towards a single coherent approach. By asking the right questions, and keeping limitations of the data in mind, contextualizing, nuancing, and keeping dialogues open between scholars of radically different backgrounds and approaches, we have carved out a path for a new field of research. We have already seen too many papers come out in which models produced by geneticists working on their own have been accepted without vital input from other fields, and, at the other extreme, seen archaeologists opposing new studies built on archaeogenetic data, due to a lack of transparency between the fields.

Data on ancient DNA is astonishing for its ability to provide a fine-grained image of early human mobility, but it does stand on the shoulders of decades of work by scholars in other fields, from the time of excavation of human skeletons to interpreting the cultural, linguistic origins of the samples. This is how cold statistics are turned into history.

Related: