Ahead of the (Indo-European – Uralic) game: in theory and in numbers

yamnaya-expansion-bell-beaker

There is a good reason for hope, for those who look for a happy ending to the revolution of population genomics that is quickly turning into an involution led by beliefs and personal interests. This blog is apparently one of the the most read sites on Indo-European peoples, if not the most read one, and now on Uralic peoples, too.

I’ve been checking the analytics of our sites, and judging by the numbers of the English blog, Indo-European.eu (without the other languages) is quickly turning into the most visited one from Academia Prisca‘s sites on Indo-European languages, beyond Indo-European.info (and its parent sites in other languages), which host many popular files for download.

If we take into account file downloads (like images or PDFs), and not only what Google Analytics can record, Indo-European.eu has not more users than all other websites of Academia Prisca, but at this pace it will soon reach half the total visits, possibly before the end of 2019.

Overall, we have evolved from some 10,000 users/year in 2006 to ~300,000 active users/year and >1,000,000 page+file views/year in 2018 (impossible to say exactly without spending too much time on this task). Nothing out of the ordinary, I guess, and obviously numbers are not a quality index, but rather a hint at increasing popularity of the subject and of our work.

NOTE. The mean reading time is ~2:40 m, which I guess fits the length of most posts, and most visitors read a mean of ~2+ pages before leaving, with increasing reader fidelity over time.

indo-european-eu-analytics
Number of active users of indo-european.eu, according to Google Analytics since before the start of the new blog. Notice the peaks corresponding to the posts below (except the last one, corresponding to the publication of A Song of Sheep and Horses).

The most read posts of 2018, now that we can compare those from the last quarter, are as follows:

  1. – The series on the Corded Ware-Uralic theory, with a marked increase in readers, especially with the last three posts:
    1. Finno-Permic and the expansion of N-L392/Siberian ancestry,
    2. “Siberian ancestry” and Ugric-Samoyedic expansions, and
    3. Haplogroups R1a and N in Finno-Ugric and Samoyedic
  2. Haplogroup is not language, but R1b-L23 expansion was associated with Proto-Indo-Europeans
  3. The history of the simplistic ‘haplogroup R1a — Indo-European’ association
  4. On the origin of haplogroup R1b-L51 in late Repin / early Yamna settlers
  5. On the origin and spread of haplogroup R1a-Z645 from eastern Europe
  6. The Caucasus a genetic and cultural barrier; Yamna dominated by R1b-M269; Yamna settlers in Hungary cluster with Yamna
  7. Something is very wrong with models based on the so-called ‘Yamnaya admixture’ – and archaeologists are catching up (II)
  8. Olalde et al. and Mathieson et al. (Nature 2018): R1b-L23 dominates Bell Beaker and Yamna, R1a-M417 resurges in East-Central Europe during the Bronze Age
  9. Early Indo-Iranian formed mainly by R1b-Z2103 and R1a-Z93, Corded Ware out of Late PIE-speaking migrations
  10. “Steppe ancestry” step by step: Khvalynsk, Sredni Stog, Repin, Yamna, Corded Ware

NOTE. Of course, the most recent posts are the most visited ones right now, but that’s because of the constant increase in the number of visitors.

I think it is obvious what the greatest interest of readers has been in the past two years. You can see the pattern by looking at the most popular posts of 2017, when the blog took off again:

  1. Germanic–Balto-Slavic and Satem (‘Indo-Slavonic’) dialect revisionism by amateur geneticists, or why R1a lineages *must* have spoken Proto-Indo-European
  2. The renewed ‘Kurgan model’ of Kristian Kristiansen and the Danish school: “The Indo-European Corded Ware Theory”
  3. The new “Indo-European Corded Ware Theory” of David Anthony
  4. Correlation does not mean causation: the damage of the ‘Yamnaya ancestral component’, and the ‘Future American’ hypothesis
  5. The Aryan migration debate, the Out of India models, and the modern “indigenous Indo-Aryan” sectarianism

The most likely reason for the radical increase in this blog’s readership is very simple, then: people want to know what is really happening with the research on ancestral Indo-Europeans and Uralians, and other blogs and forums are not keeping up with that demand, being content with repeating the same ideas again and again (R1a-CWC-IE, R1b-BBC-Vasconic, and N-Comb Ware-Uralic), despite the growing contradictions. As you can imagine, once you have seen the Yamna -> Bell Beaker migration model of North-West Indo-European, with Corded Ware obviously representing Uralic, you can’t unsee it.

The online bullying, personal attacks, and similar childish attempts to silence those who want to talk about this theory elsewhere (while fringe theories like R1a/CHG-OIT, R1b-Vasconic, or the Anatolian/Armenian-CHG hypotheses, to name just a few, are openly discussed) has had, as could be expected, the opposite effect to what was intended. I guess you can say this blog and our projects have profited from the first relevant Streisand effect of population genomics, big time.

If this trend continues this year (and other bloggers’ or forum users’ faith in miracles is not likely to change), I suppose that after the Yamna Hungary samples are published (with the expected results) this blog is going to be the most read in 2020 by a great margin… I can only infer that this tension is also helping raise the interest in (and politicization of) the question, hence probably the overall number of active users and their participation in other blogs and forums is going to increase everywhere in 2019, too, as this debate becomes more and more heated.

So, what I infer from the most popular posts and the numbers is that people want criticism and controversy, and if you want blood you’ve got it. Here it is, my latest addition to the successful series criticizing the “Corded Ware/R1a–Indo-European” pet theories, a post I wrote two-three months ago, slightly updated with the newest comedy, and a sure success for 2019 (already added to the static pages of the menu):

The “Indo-European Corded Ware theory” doesn’t hold water

This is how I feel when I see spikes in visits with more and more returning users linked to my controversial posts 😉

Are you not entertained?! Are you not entertained?! Is this not why you are here?!

The genetic and cultural barrier of the Pontic-Caspian steppe – forest-steppe ecotone

steppe-forest-steppe-biomes

We know that the Caucasus Mountains formed a persistent prehistoric barrier to cultural and population movements. Nevertheless, an even more persistent frontier to population movements in Europe, especially since the Neolithic, is the Pontic-Caspian steppe – forest-steppe ecotone.

Like the Caucasus, this barrier could certainly be crossed, and peoples and cultures could permeate in both directions, but there have been no massive migrations through it. The main connection between both regions (steppe vs. forest-steppe/forest zone) was probably through its eastern part, through the Samara region in the Middle Volga.

The chances of population expansions crossing this natural barrier anywhere else seem quite limited, with a much less porous crossing region in the west, through the Dnieper-Dniester corridor.

A Persistent ecological and cultural frontier

It is very difficult to think about any culture that transgressed this persistent ecological and cultural frontier: many prehistoric and historical steppe pastoralists did appear eventually in the neighbouring forest-steppe areas during their expansions (e.g. Yamna, Scythians, or Turks), as did forest groups who permeated to the south (e.g. Comb Ware, GAC, or Abashevo), but their respective hold in foreign biomes was mostly temporary, because their cultures had to adapt to the new ecological environment. Most if not all groups originally from a different ecological niche eventually disappeared, subjected to renewed demographic pressure from neighbouring steppe or forest populations…

The Samara region in the Middle Volga may be pointed out as the true prehistoric link between forests and steppes (see David Anthony’s remarks), something reflected in its nature as a prehistoric sink in genetics. This strong forest – forest-steppe – steppe connection was seen in the Eurasian technocomplex, during the expansion of hunter-gatherer pottery, in the expansion of Abashevo peoples to the steppes (in one of the most striking cases of population admixture in the area), with Scythians (visible in the intense contacts with Ananyino), and with Turks (Volga Turks).

steppe-forest-steppe-europe
Simplified map of the distribution of steppes and forest-steppes (Pontic and Pannonian) and xeric grasslands in Eastern Central Europe (with adjoining East European ranges) with their regionalisation as used in the review (Northern—Pannonic—Pontic). Modified from Kajtoch et al. (2016).

Before the emergence of pastoralism, the cultural contacts of the Pontic region (i.e. forest-steppes) with the Baltic were intense. In fact, the connection of the north Pontic area with the Baltic through the Dnieper-Dniester corridor and the Podolian-Volhynian region is essential to understand the spread of peoples of post-Maglemosian and post-Swiderian cultures (to the south), hunter-gatherer pottery (to the north), TRB (to the south), Late Trypillian groups (north), GAC (south), or Comb Ware (south) (see here for Eneolithic movements), and finally steppe ancestry and R1a-Z645 with Corded Ware (north). After the complex interaction of TRB, Trypillia, GAC, and CWC during the expansion of late Repin, this traditional long-range connection is lost and only emerges sporadically, such as with the expansion of East Germanic tribes.

A barrier to steppe migrations into northern Europe

One may think that this barrier was more permeable, then, in the past. However, the frontier is between steppe and forest-steppe ecological niches, and this barrier evolved during prehistory due to climate changes. The problem is, before the drought that began ca. 4000 BC and increased until the Yamna expansion, the steppe territory in the north Pontic region was much smaller, merely a strip of coastal land, compared to its greater size ca. 3300 BC and later.

This – apart from the cultural and technological changes associated with nomadic pastoralism – justifies the traditional connection of the north Pontic forest-steppes to the north, broken precisely after the expansion of Khvalynsk, as the north Pontic area became gradually a steppe region. The strips of north Pontic and Azov steppes and Crimea seem to have had stronger connections to the Northern Caucasus and Northern Caspian steppes than with the neighbouring forest-steppe areas during the Upper Palaeolithic, Mesolithic, and Neolithic.

NOTE. We still don’t know the genetic nature of Mikhailovka or Ezero, steppe-related groups possibly derived from Novodanilovka and Suvorovo close to the Black Sea (which possibly include groups from the Pannonian plains), and how they compare to neighbouring typically forest-steppe cultures of the so-called late Sredni Stog groups, like Dereivka or partly Kvityana.

steppe-forest-steppe-migration-routes
Typical migration routes through European steppes and forest-steppes. Red line represents the persistent cultural and genetic barrier, with the latest evolution in steppe region represented by the shift from dashed line to the north. Arrows show the most common population movements. Modified from Kajtoch et al. (2016).

Despite the Pontic-Caspian steppes and forest-steppes neighbouring each other for ca. 2,000 km, peoples from forested and steppe areas had an obvious advantage in their own regions, most likely due to the specialization of their subsistence economy. While this is visible already in Palaeolithic and Mesolithic hunter-gatherers, the arrival of the Neolithic package in the Pontic-Caspian region incremented the difference between groups, by spreading specialized animal domestication. The appearance of nomadic pastoralism adapted to the steppe, eventually including the use of horses and carts, made the cultural barrier based on the economic know-how even stronger.

Even though groups could still adapt and permeate a different territory (from steppe to forest-steppe/forest and vice-versa), this required an important cultural change, to the extent that it is eventually complicated to distinguish these groups from neighbouring ones (like north-west Pontic Mesolithic or Neolithic groups and their interaction with the steppes, Trypillia-Usatovo, Scythians-Thracians, etc.). In fact, this steppe – forest-steppe barrier is also seen to the east of the Urals, with the distinct expansion of Andronovo and Seima-Turbino/Andronovo-like horizons, which seem to represent completely different ethnolinguistic groups.

As a result of this cultural and genetic barrier, like that formed by the Northern Caucasus:

1) No steppe pastoralist culture (which after the emergence of Khvalynsk means almost invariably horse-riding, chariot-using nomadic herders who could easily pasture their cows in the huge grasslands without direct access to water) has ever been successful in spreading to the north or north-west into northern Europe, until the Mongols. No forest culture has ever been successful in expanding to the steppes, either (except for the infiltration of Abashevo into Sintashta-Potapovka).

2) Corded Ware was not an exception: like hunter-gatherer pottery before it (and like previous population movements of TRB, late Trypillia, GAC, Comb Ware or Lublin-Volhynia settlers) their movements between the north Pontic area and central Europe happened through forest-steppe ecological niches due to their adaptation to them. There is no reason to support a direct connection of CWC with true steppe cultures.

3) The so-called “Steppe ancestry” permeated the steppe – forest-steppe ecotone for hundreds of years during the 5th and early 4th millennium BC, due to the complex interaction of different groups, and probably to the aridization trend that expanded steppe (and probably forest-steppe) to the north. Language, culture, and paternal lineages did not cross that frontier, though.

EDIT (4 FEB 2019): Wang et al. is out in Nature Communications. They deleted the Yamna Hungary samples and related analyses, but it’s interesting to see where exactly they think the trajectory of admixture of Yamna with European MN cultures fits best. This path could also be inferred long ago from the steppe connections shown by the Yamna Hungary -> Bell Beaker evolution and by early Balkan samples:

wang-yamna-connection
Prehistoric individuals projected onto a PCA of 84 modern-day West Eurasian populations (open symbols). Dashed arrows indicate trajectories of admixture: EHG—CHG (petrol), Yamnaya—Central European MN (pink), Steppe—Caucasus (green), and Iran Neolithic—Anatolian Neolithic (brown). Modified from the original, a red circle has been added to the Yamna-Central European MN admixture.

Related

ASoSaH Reread (II): Y-DNA haplogroups among Uralians (apart from R1a-M417)

corded-ware-yamna-ancestry

This is mainly a reread of from Book Two: A Game of Clans of the series A Song of Sheep and Horses: chapters iii.5. Early Indo-Europeans and Uralians, iv.3. Early Uralians, v.6. Late Uralians and vi.3. Disintegrating Uralians.

“Sredni Stog”

While the true source of R1a-M417 – the main haplogroup eventually associated with Corded Ware, and thus Uralic speakers – is still not known with precision, due to the lack of R1a-M198 in ancient samples, we already know that the Pontic-Caspian steppes were probably not it.

We have many samples from the north Pontic area since the Mesolithic compared to the Volga-Ural territory, and there is a clear prevalence of I2a-M223 lineages in the forest-steppe area, mixed with R1b-V88 (possibly a back-migration from south-eastern Europe).

R1a-M459 (xR1a-M198) lineages appear from the Mesolithic to the Chalcolithic scattered from the Baltic to the Caucasus, from the Dniester to Samara, in a situation similar to haplogroups Q1a-M25 and R1b-L754, which supports the idea that R1a, Q1a, and R1b expanded with ANE ancestry, possibly in different waves since the Epipalaeolithic, and formed the known ANE:EHG:WHG cline.

y-dna-khvalynsk
Y-DNA samples from Khvalynsk and neighbouring cultures. See full version.

The first confirmed R1a-M417 sample comes from Alexandria, roughly coinciding with the so-called steppe hiatus. Its emergence in the area of the previous “early Sredni Stog” groups (see the mess of the traditional interpretation of the north Pontic groups as “Sredni Stog”) and its later expansion with Corded Ware supports Kristiansen’s interpretation that Corded Ware emerged from the Dnieper-Dniester corridor, although samples from the area up to ca. 4000 BC, including the few Middle Eneolithic samples available, show continuity of hg. I2a-M223 and typical Ukraine Neolithic ancestry.

NOTE. The further subclade R1a-Z93 (Y26) reported for the sample from Alexandria seems too early, given the confidence interval for its formation (ca. 3500-2500 BC); even R1a-Z645 could be too early. Like the attribution of the R1b-L754 from Khvalynsk to R1b-V1636 (after being previously classifed as of Pre-V88 and M73 subclade), it seems reasonable to take these SNP calls with a pinch of salt: especially because Yleaf (designed to look for the furthest subclade possible) does not confirm for them any subclade beyond R1a-M417 and R1b-L754, respectively.

The sudden appearance of “steppe ancestry” in the region, with the high variability shown by Ukraine_Eneolithic samples, suggests that this is due to recent admixture of incoming foreign peoples (of Ukraine Neolithic / Comb Ware ancestry) with Novodanilovka settlers.

The most likely origin of this population, taking into account the most common population movements in the area since the Neolithic, is the infiltration of (mainly) hunter-gatherers from the forest areas. That would confirm the traditional interpretation of the origin of Uralic speakers in the forest zone, although the nature of Pontic-Caspian settlers as hunter-gatherers rather than herders make this identification today fully unnecessary (see here).

EDIT (3 FEB 2019): As for the most common guesstimates for Proto-Uralic, roughly coinciding with the expansion of this late Sredni Stog community (ca. 4000 BC), you can read the recent post by J. Pystynen in Freelance Reconstruction, Probing the roots of Samoyedic.

eneolithic-ukraine-corded-ware
Late Sredni Stog admixture shows variability proper of recent admixture of forest-steppe peoples with steppe-like population. See full version here.

NOTE. Although my initial simplistic interpretation (of early 2017) of Comb Ware peoples – traditionally identified as Uralic speakers – potentially showing steppe ancestry was probably wrong, it seems that peoples from the forest zone – related to Comb Ware or neighbouring groups like Lublyn-Volhynia – reached forest-steppe areas to the south and eventually expanded steppe ancestry into east-central Europe through the Volhynian Upland to the Polish Upland, during the late Trypillian disintegration (see a full account of the complex interactions of the Final Eneolithic).

The most interesting aspect of ascertaining the origin of R1a-M417, given its prevalence among Uralic speakers, is to precisely locate the origin of contacts between Late Proto-Indo-European and Proto-Uralic. Traditionally considered as the consequence of contacts between Middle and Upper Volga regions, the most recent archaeological research and data from ancient DNA samples has made it clear that it is Corded Ware the most likely vector of expansion of Uralic languages, hence these contacts of Indo-Europeans of the Volga-Ural region with Uralians have to be looked for in neighbours of the north Pontic area.

sredni-stog-repin-contacts
Sredni Stog – Repin contacts representing Uralic – Late Indo-European contacts were probably concentrated around the Don River.

My bet – rather obvious today – is that the Don River area is the source of the earliest borrowings of Late Uralic from Late Indo-European (i.e. post-Indo-Anatolian). The borrowing of the Late PIE word for ‘horse’ is particularly interesting in this regard. Later contacts (after the loss of the initial laryngeal) may be attributed to the traditionally depicted Corded Ware – Yamna contact zone in the Dnieper-Dniester area.

NOTE. While the finding of R1a-M417 populations neighbouring R1b-L23 in the Don-Volga interfluve would be great to confirm these contacts, I don’t know if the current pace of more and more published samples will continue. The information we have right now, in my opinion, suffices to support close contacts of neighbouring Indo-Europeans and Uralians in the Pontic-Caspian area during the Late Eneolithic.

Classical Corded Ware

After some complex movements of TRB, late Trypillia and GAC peoples, Corded Ware apparently emerged in central-east Europe, under the influence of different cultures and from a population that probably (at least partially) stemmed from the north Pontic forest-steppe area.

Single Grave and central Corded Ware groups – showing some of the earliest available dates (emerging likely ca. 3000/2900 BC) – are as varied in their haplogroups as it is expected from a sink (which does not in the least resemble the Volga-Ural population):

Interesting is the presence of R1b-L754 in Obłaczkowo, potentially of R1b-V88 subclade, as previously found in two Central European individuals from Blätterhole MN (ca. 3650 and 3200 BC), and in the Iron Gates and north Pontic areas.

Haplogroups I2a and G have also been reported in early samples, all potentially related to the supposed Corded Ware central-east European homeland, likely in southern Poland, a region naturally connected to the north Pontic forest-steppe area and to the expansion of Neolithic groups.

corded-ware-haplogroups
Y-DNA samples from early Corded Ware groups and neighbouring cultures. See full version.

The true bottlenecks under haplogroup R1a-Z645 seem to have happened only during the migration of Corded Ware to the east: to the north into the Battle Axe culture, mainly under R1a-Z282, and to the south into Middle Dnieper – Fatyanovo-Balanovo – Abashevo, probably eventually under R1a-Z93.

This separation is in line with their reported TMRCA, and supports the split of Finno-Permic from an eastern Uralic group (Ugric and Samoyedic), although still in contact through the Russian forest zone to allow for the spread of Indo-Iranian loans.

This bottleneck also supports in archaeology the expansion of a sort of unifying “Corded Ware A-horizon” spreading with people (disputed by Furholt), the disintegrating Uralians, and thus a source of further loanwords shared by all surviving Uralic languages.

Confirming this ‘concentrated’ Uralic expansion to the east is the presence of R1a-M417 (xR1a-Z645) lineages among early and late Single Grave groups in the west – which essentially disappeared after the Bell Beaker expansion – , as well as the presence of these subclades in modern Central and Western Europeans. Central European groups became thus integrated in post-Bell Beaker European EBA cultures, and their Uralic dialect likely disappeared without a trace.

NOTE. The fate of R1b-L51 lineages – linked to North-West Indo-Europeans undergoing a bottleneck in the Yamna Hungary -> Bell Beaker migration to the west – is thus similar to haplogroup R1a-Z645 – linked to the expansion of Late Uralians to the east – , hence proving the traditional interpretation of the language expansions as male-driven migrations. These are two of the most interesting genetic data we have to date to confirm previous language expansions and dialectal classifications.

It will be also interesting to see if known GAC and Corded Ware I2a-Y6098 subclades formed eventually part of the ancient Uralic groups in the east, apart from lineages which will no doubt appear among asbestos ware groups and probably hunter-gatherers from north-eastern Europe (see the recent study by Tambets et al. 2018).

Corded Ware ancestry marked the expansion of Uralians

Sadly, some brilliant minds decided in 2015 that the so-called “Yamnaya ancestry” (now more appropriately called “steppe ancestry”) should be associated to ‘Indo-Europeans’. This is causing the development of various new pet theories on the go, as more and more data contradicts this interpretation.

There is a clear long-lasting cultural, populational, and natural barrier between Yamna and Corded Ware: they are derived from different ancestral populations, which show clearly different ancestry and ancestry evolution (although they did converge to some extent), as well as different Y-DNA bottlenecks; they show different cultures, including those of preceding and succeeding groups, and evolved in different ecological niches. The only true steppe pastoralists who managed to dominate over grasslands extending from the Upper Danube to the Altai were Yamna peoples and their cultural successors.

corded-ware-yamna-pca
Corded Ware admixture proper of expanding late Sredni Stog-like populations from the forest-steppe. See full version here.

NOTE. You can also read two recent posts by FrankN in the blog aDNA era, with detailed information on the Pontic-Caspian cultures and the formation of “steppe ancestry” during the Palaeolithic, Mesolithic and Neolithic: How did CHG get into Steppe_EMBA? Part 1: LGM to Early Holocene and How did CHG get into Steppe_EMBA? Part 2: The Pottery Neolithic. Unlike your typical amateur blogger on genetics using few statistical comparisons coupled with ‘archaeolinguoracial mumbo jumbo’ to reach unscientific conclusions, these are obviously carefully redacted texts which deserve to be read.

I will not enter into the discussion of “steppe ancestry” and the mythical “Siberian ancestry” for this post, though. I will just repost the opinion of Volker Heyd – an archaeologist specialized in Yamna Hungary and Bell Beakers who is working with actual geneticists – on the early conclusions based on “steppe ancestry”:

[A]rchaeologist Volker Heyd at the University of Bristol, UK, disagreed, not with the conclusion that people moved west from the steppe, but with how their genetic signatures were conflated with complex cultural expressions. Corded Ware and Yamnaya burials are more different than they are similar, and there is evidence of cultural exchange, at least, between the Russian steppe and regions west that predate Yamnaya culture, he says. None of these facts negates the conclusions of the genetics papers, but they underscore the insufficiency of the articles in addressing the questions that archaeologists are interested in, he argued. “While I have no doubt they are basically right, it is the complexity of the past that is not reflected,” Heyd wrote, before issuing a call to arms. “Instead of letting geneticists determine the agenda and set the message, we should teach them about complexity in past human actions.

Related

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!

Spread of Y. pestis, earlier than previously thought, may have caused Neolithic decline

spread-yersinia-pestis

Open access Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline, by Rascovan et al. Cell (2018)

Abstract (emphasis mine):

Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.

spread-yersinia-trypillia
(A) Schematic representation of the trajectories and time periods (thousand years before present, kyr) of major known human migrations in Eurasia during the Neolithic and Bronze Age. The observed geographic distribution and divergence times of Y. pestis strains from the Gok2 and Bronze Age clades cannot be explained by the timings and routes of these human movements.
(B) Geographic distribution of the use of animal traction and wheeled transport across Neolithic and Bronze Age populations in Eurasia, which broadly expanded during the period of 5,500 and 5,000 BP. The expansion of these technological innovations overlaps the predicted period for the expansion of the basal Y. pestis strains.
(C) Timeline indicating the proposed key historical events that contributed to the emergence and spread of plague during the Neolithic.

We have evolved in the interpretation of the plague from 1) a Corded Ware-driven disease, to 2) a steppe disease that was spread by Yamna and Corded Ware, and now 3) a (potentially) Trypillia-driven disease that spread to the west earlier than Yamna and Corded Ware, but probably also later east and west with both.

At least it still seems that the plague and its demographic consequences were a good reason for the expansion of Indo-Europeans and Uralians into Europe, as we thought…

Featured image, from the paper: “The predicted model of early dispersion of Y. pestis during Neolithic and Bronze Age was built by integrating phylogenetic information of Y. pestis strains from this period (Figure 1E), their divergence times (Figure 3), the geographic locations, carbon dating and genotypes of the individuals, and the archaeological record. The model suggests that early Y. pestis strains likely emerged and spread from mega-settlements in Eastern Europe (built by the Trypillia Culture) into Europe and the Eurasian steppe, most likely through human interaction networks. This was facilitated by wheeled and animal-powered transports, which are schematized in the map with red lines with arrows pointing in both senses. Our model builds upon a previous model (Andrades Valtuena et al., 2017) that proposed the spread of plague to be associated with large-scale human migrations (blue line).

Related

Eastern pressure blade technology in west Scandinavia associated with WHG

New interesting preprint Ancient DNA from chewing gums connects material culture and genetics of Mesolithic hunter-gatherers in Scandinavia, by Kashuba et al. (2018).

Interesting excerpts (emphasis mine):

Mitochondrial genomes from all three individuals belong to the U5a2d haplogroup. (…) The mitochondrial U5a2d haplogroup is consistent with earlier published results for ancient individuals from Scandinavia, U5a being the most common within SHG. Of the 16 Mesolithic individuals from Scandinavia published prior to our study, seven belong to the U5a haplogroup, nine share the U2 and U4 haplogroups

We divided the SHG group into two groups: SHGa and SHGb (ancient individuals found in contemporary Norway and Sweden, respectively). We based this on both the geographical distribution and the previous studies demonstrating the close relation of SHGa to EHG group and SHGb to WHG group. To further explore the demography within the SHG group, we compared the ancestry of BLE individuals within SHGa and SHGb groups. This comparison revealed a high relative shared drift between BLE individuals and the SHGb group

scandinavia-hunter-gatherer-admixture
Admixture analysis showing the major mode for K=15. The figure represents 11 runs out of 20 replicates (Greedy algorithm ran with the Jaccard distance and a 0.97 similarity threshold)

The results from Huseby Kiev allow us to finally connect the SHG group with the eastern pressure blade technology. However, the higher genetic affinity between Huseby Kiev individuals and the WHG group challenges the earlier suggested tie between eastern technology and EHG genetics. Our results suggest either early cultural transmission, or a more complex course of events involving both non- and co-dependent cultural and genetic admixture.

huseby-kiev

Seeing how culture is indeed usually associated with the expansion of a certain population, especially at such an early date, I guess this similarity with WHG of incoming eastern peoples comes from an originally EHG population expanding into a mainly WHG area in the west (similar to what happens e.g. with Bell Beakers), or being replaced later by a WHG population which adopted the culture (similar to what happened with late Corded Ware populations in central-east Europe after the expansion of Bell Beakers).

Unlike later periods, it will always be difficult to judge such ancient population movements with few samples covering thousands of years… Probably specific Y-DNA haplogroups would help differentiate between both expanding populations from east and west.

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Biparental inheritance of mitochondrial DNA in humans

mtdna-inheritance-paternal

New paper Biparental Inheritance of Mitochondrial DNA in Humans, by Luo et al. PNAS (2018).

Interesting excerpts (emphasis mine):

Abstract

Although there has been considerable debate about whether paternal mitochondrial DNA (mtDNA) transmission may coexist with maternal transmission of mtDNA, it is generally believed that mitochondria and mtDNA are exclusively maternally inherited in humans. Here, we identified three unrelated multigeneration families with a high level of mtDNA heteroplasmy (ranging from 24 to 76%) in a total of 17 individuals. Heteroplasmy of mtDNA was independently examined by high-depth whole mtDNA sequencing analysis in our research laboratory and in two Clinical Laboratory Improvement Amendments and College of American Pathologists-accredited laboratories using multiple approaches. A comprehensive exploration of mtDNA segregation in these families shows biparental mtDNA transmission with an autosomal dominantlike inheritance mode. Our results suggest that, although the central dogma of maternal inheritance of mtDNA remains valid, there are some exceptional cases where paternal mtDNA could be passed to the offspring. Elucidating the molecular mechanism for this unusual mode of inheritance will provide new insights into how mtDNA is passed on from parent tooffspring and may even lead to the development of new avenues for the therapeutic treatment for pathogenic mtDNA transmission.

An example

Compared with Family A, a strikingly similar mtDNA transmission pattern was demonstrated in Families B and C. Taking Family B for illustration, II-3 having 29 heteroplasmic and seven homoplasmic variants should have inherited mtDNA from both his father (I-1, haplogroup of K1b2a) and his mother (I-10, haplogroup of H), who were supposed to possess 34 and nine homoplasmic variants, respectively. II-3 further transmitted his mtDNA that he inherited from I-1 to his son (III-2), who also inherited all of his mother’s mtDNA (II-30, carrying 34 variants and a haplogroup of T2a1a). However, III-2’s sister (III-1) and half-brother (III-5) only inherited the maternal mtDNA. Fresh blood sampling and repeated mtDNA sequencing in a second independent laboratory were also performed to rule out the possibility of sample mix-up for III-2 (III-2, column F-G and H-I). Additionally, these samples were further verified using Pacific Bio single molecular sequencing (see Materials and Methods) and by restriction fragment length polymorphism (RFLP) analysis of Family A, and these results were fully consistent with the previous sequencing.

mtdna-inheritance
Biparental mtDNA inheritance pattern shown in Family B. (A) Pedigree of Family B. The black filled symbols indicate the two family members (II-3 and III-2) showing biparental mtDNA transmission. The IDs of five family members tested by whole mtDNA sequencing analysis have been underlined in the pedigree. (B) Schematic of the mtDNA genotype defined by the homoplasmic and/or heteroplasmic variants aligned from the reference mitochondrial genome. Blue bars represent the genotype of paternally derived mtDNA, whereas purple-red and orange-red bars represent maternally derived mtDNA. Entries labeled (D) represent deduced mtDNA genotypes. (C) Summary of the haplogroup and mtDNA variant numbers in Family B.

A Resurgence of the Paternal Transmission Hypothesis

The results presented in this paper make a robust case for paternal transmission of mtDNA. Here, we report biparental mtDNA inheritance (either directly or indirectly) in 17 members in three multigeneration families. Thirteen of these individuals were identified directly by sequencing of the mitochondrial genome, whereas four could be inferred based on preexisting maternal heteroplasmy caused by biparental inheritance in the previous generation.

To further confirm these remarkable results and to exclude the possibility of sample mix-up and/or contamination, the whole mtDNA sequencing procedure was repeated independently in at least two different laboratories by different laboratory technicians with newly obtained blood samples. All results were reproducible, indicating no artifacts or contamination exist. More importantly, the multiple mtDNA variants that were paternally transmitted differ in both number and position among each of these three families as well as the related haplogroup (R0a1 in Family A, K1b2a in Family B, and K2b1a1a in Family C, respectively), providing two distinct forms of evidence supporting transmission of the paternal mtDNA.

Therefore, we have unequivocally demonstrated the existence of biparental mtDNA inheritance as evidenced by the high number and level of mtDNA heteroplasmy in these three unrelated multigeneration families. Most interestingly, the mixed haplogroups in these samples are very reminiscent of the mixed haplogroups found in the 20 studies that were dismissed by Bandelt et al. as due to contamination or sample mix-up. One is forced to wonder how many other instances of individuals with biparental mtDNA inheritance have been dismissed as technical errors, and whether Schwartz and Vissing’s original discovery has really been given the proper follow-up that it deserves. We suspect that these results will initiate a broader reassessment of the topic.

We propose that the paternal mtDNA transmission in these families should be accompanied by segregation of a mutation in one nuclear gene involved in paternal mitochondrial elimination and that there is a high probability that the gene in question operates through one of the pathways identified above.

If I have to be honest, I was stuck with the paternal transmission hypothesis which we were taught in class long ago. I didn’t know it was controversial or dismissed, I just thought it was really exceptional, and I never thought about learning more on the subject.

This paper proves it may be more complicated than that, especially for population genomics purposes, because biparental mtDNA transmission with autosomal dominant-like inheritance puts a serious barrier to a general, simplistic interpretation of mtDNA.

I don’t think it is a blow to all interpretations based on mtDNA, though, because the traditional interpretation should often work statistically. However, one has to be always very careful when saying “if it’s mtDNA from region X, it’s about female exogamy”, especially when samples are from neighbouring regions and similar periods.

The term “uniparental marker” for mtDNA is obviously misleading and shouldn’t be used, and many research papers and interpretations taking mtDNA as strictly uniparental should be taken with a pinch of salt.

Related

Genetic landscape and past admixture of modern Slovenians

slovenes-snp

Open access Genetic Landscape of Slovenians: Past Admixture and Natural Selection Pattern, by Maisano Delser et al. Front. Genet. (2018).

Interesting excerpts (emphasis mine):

Samples

Overall, 96 samples ranging from Slovenian littoral to Lower Styria were genotyped for 713,599 markers using the OmniExpress 24-V1 BeadChips (Figure 1), genetic data were obtained from Esko et al. (2013). After removing related individuals, 92 samples were left. The Slovenian dataset has been subsequently merged with the Human Origin dataset (Lazaridis et al., 2016) for a total of 2163 individuals.

Y chromosome

First, Y chromosome genetic diversity was assessed. A total of 52 Y chromosomes were analyzed for 195 SNPs. The majority of individuals (25, 48.1%) belong to the haplogroup R1a1a1a (R-M417) while the second major haplogroup is represented by R1b (R-M343) including 15 individuals (28.8%). Twelve samples are assigned to haplogroup I (I M170): five and two samples belong to haplogroup I2a (I L460) and I1 (I M253), respectively, while the remaining five samples did not have enough information to be further assigned.

pca-slovenes
PCA of Slovenian samples with European populations (Slovenian_HO_EU dataset). For details regarding the populations included, see Supplementary Table 1.

PCA

Considering the unbalanced sample size of the Slovenian population compared to the other populations included in the dataset, a subset of 20 Slovenian individuals randomly sampled was used.

All Slovenian samples group together with Hungarians, Czechs, and some Croatians (“Central-Eastern European” cluster) as also suggested by the PCA. All Basque individuals with few French and Spanish cluster together (“Basque” cluster) while a “Northern-European” cluster is made of the majority of French, English, Icelanders, Norwegians, and Orcadians. Five populations contributed to the “Eastern-European” cluster including Belarusians, Estonians, Lithuanians, Mordovians, and Russians. Western and South Europe is split into two cluster: the first (“Western European” cluster) includes all Spanish individuals, few French, and some Italians (North Italy) while the second (“Southern-European” cluster) groups Sicilians, Greeks, some Croatians, Romanians, and some Italians (North Italy).

Admixture Pattern and Migration

admixture-slovenians
Modified image, from the paper (Central-East Europeans marked). Unsupervised admixture analysis of Slovenians. Results for K = 5 are showed as it represents the lowest cross-validation error. Slovenian samples show an admixture pattern similar to the neighboring populations such as Croatians and Hungarians. The major ancestral components are: the blue one which is shared with Lithuanians and Russians, followed by the dark green one that is mostly present in Greek samples and the light blue which characterizes Orcadians and English. For population acronyms see Supplementary Table 1.

All Slovenian individuals share common pattern of genetic ancestry, as revealed by ADMIXTURE analysis. The three major ancestry components are the North East and North West European ones (light blue and dark blue, respectively, Figure 3), followed by a South European one (dark green, Figure 3). Contribution from the Sardinians and Basque are present in negligible amount. The admixture pattern of Slovenians mimics the one suggested by the neighboring Eastern European populations, but it is different from the pattern suggested by North Italian populations even though they are geographically close.

Using ALDER, the most significant admixture event was obtained with Russians and Sardinians as source populations and it happened 135 ± 9.31 generations ago (Z-score = 11.54). (…) When tested for multiple admixture events (MALDER), we obtained evidence for one admixture event 165.391 ± 17.1918 generations ago corresponding to ∼2620 BCE (CI: 3101–2139) considering a generation time of 28 years (Figure 4), with Kalmyk and Sardinians as sources.

We then modeled the Slovenian population as target of admixture of ancient individuals from Haak et al. (2015) while computing the f3(Ancient 1, Ancient 2, Slovenian) statistic. The most significant signal was obtained with Yamnaya and HungaryGamba_EN (Z-score = -10.66), followed by MA1 with LBK_EN (Z-score -9.7) and Yamnaya with Stuttgart (Z-score = -8.6) used as possible source populations (Supplementary Figure 5).

We found a significant signal of admixture by using both pairs as ancient sources. Specifically, for the pair Yamnaya and Hungary_EN the admixture event is dated at 134.38 ± 23.69 generations ago (Z-score = 5.26, p-value of 1.5e-07) while for Yamnaya and LBK_EN at 153.65 ± 22.19 generations ago (Z-score = 6.92, p-value 4.4e-12). Outgroup f3 with Yamnaya put Slovenian population close to Hungarians, Czechs, and English, indicating a similar shared drift between these population with the Steppe populations (Supplementary Figure 6).

admixture-events-slovenes
Admixture events identified with ALDER and MALDER. The gray dots represent significant admixture events detected with ALDER using Slovenians as target, the solid line represents the single admixture event detected using MALDER, dashed lines represent the confidence interval. Only the significant results after multiple testing correction are plotted. For ALDER results see Supplementary Table 5.

Not that any of this would come as a surprise, but:

  • R1a-M458 and some R1a-Z280 (xR1a-Z92) lineages (found among Slovenes) were associated with the Slavic expansion, likely with the Prague-Korchak culture, originally stemming probably from peoples of the Lusatian culture. Other R1a-Z280 lineages remained associated with Uralic peoples, and some became Slavicized only recently.
  • PCA keeps supporting the common cluster of certain West, South, and East Slavs in a “Central-Eastern European” cluster, distinct from the “North-Eastern European” cluster formed by modern Finno-Ugrians, as well as ancient Finno-Ugrians of north-eastern Europe who were only recently Slavicized.
  • Admixture supports the same ancient ‘western’ (a core West+South+East Slavic) cluster, and the admixture event with Yamna + Hungary_EN is logically a proxy for Yamna Hungary being at the core of ancestral Central-East population movements related to Bell Beakers in the mid- to late 3rd millennium.

The theory that East Slavs are at the core of the Slavic expansion makes no sense, in terms of archaeology (see Florin Curta’s dismissal of those recent eastern ‘Slavic’ finds, his commentary on 19th century Pan-Slavic crap, or his book on Slavic migrations), in terms of ancient DNA (the earliest Slavs sampled cluster with modern West Slavs, distant from the steppe cluster, unlike Finno-Ugrians), or in terms of modern DNA.

I don’t know where exactly this impulse for the theory of Russia being the cradle of Slavs comes from today (although there are some obvious political trends to revive 19th c. ideas), but it was always clear for everyone, including Russians, that East Slavs had migrated to the east and north and assimilated indigenous Finno-Ugrians, apart from Turkic-, Iranian-, and Caucasian-speaking peoples to the east. Genetics is only confirming what was clear from other disciplines long ago.

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