Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

danemark-medieval

Open access Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans, by Krause-Kyora et al., Nature Communications (2018)

Abstract:

Leprosy, a chronic infectious disease caused by Mycobacterium leprae (M. leprae), was very common in Europe till the 16th century. Here, we perform an ancient DNA study on medieval skeletons from Denmark that show lesions specific for lepromatous leprosy (LL). First, we test the remains for M. leprae DNA to confirm the infection status of the individuals and to assess the bacterial diversity. We assemble 10 complete M. leprae genomes that all differ from each other. Second, we evaluate whether the human leukocyte antigen allele DRB1*15:01, a strong LL susceptibility factor in modern populations, also predisposed medieval Europeans to the disease. The comparison of genotype data from 69 M. leprae DNA-positive LL cases with those from contemporary and medieval controls reveals a statistically significant association in both instances. In addition, we observe that DRB1*15:01 co-occurs with DQB1*06:02 on a haplotype that is a strong risk factor for inflammatory diseases today.

danes-leprosy-positive
Relationship of 53 medieval leprosy-positive Danes to contemporary Europeans. Principal component analysis plot for 53 medieval St. Jørgen individuals in relation to European population samples from the 1000 Genomes project. (CEU, Northern Europeans from Utah; GBR, British in England and Scotland; IBS, Iberian population in Spain; TSI, Tuscans in Italy; FIN, Finnish in Finland)

The study shows mtDNA haplogroups comparable to those of northern Europeans today, and findings in general indicate no major genome-wide changes in the Danish population structure in the past 1000 years.

The paper may be of interest for earlier migrations:

rs3135388-t-allele-frequency-leprosy

Discovered via Iain Mathieson:

Related:

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

yamna-expansion-reich

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

Abstract:

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

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

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

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

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

With lesser confidence in precise subclades, we find that:

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

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

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

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

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

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

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

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

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

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

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

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

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

Related:

David Reich on the influence of ancient DNA on Archaeology and Linguistics

An interesting interview has appeared on The Atlantic, Ancient DNA Is Rewriting Human (and Neanderthal) History, on the occasion of the publication of David Reich’s book Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past.

Some interesting excerpts (I have emphasized some of Reich’s words):

On the efficiency of the Reich Lab

Zhang: How much does it cost to process an ancient DNA sample right now?

Reich: In our hands, a successful sample costs less than $200. That’s only two or three times more than processing them on a present-day person. And maybe about one-third to one half of the samples we screen are successful at this point.

This is probably the most controversial assessment for the Twitterverse, since it puts the Reich Lab at the top of the publishing chain, but I don’t find this fact controversial; at all.

Anyone interested in doing genetic studies has free datasets, papers, and bioinformatic tools at hand – thanks to his lab, mostly – to develop new methods and publish papers. Such secondary works won’t probably be published in journals with the highest impact factor, but what can you do, welcome to the scientific world…

Also, by the looks of it, every single researcher involved in recovering an archaeological sample is included as co-author of the papers, so there is a clear benefit for ‘local’ researchers collaborating with the Lab. Therefore, these researchers and their institutions are responsible for whatever unfair situation might be created by their exchange.

On Archaeology’s reaction to Kossinna and Nazi ideas:

(…)
Zhang: You actually had German collaborators drop out of a study because of these exact concerns, right? One of them wrote, “We must(!) avoid … being compared with the so-called ‘siedlungsarchäologie Method’ from Gustaf Kossinna!”

Reich: Yeah, that’s right. I think one of the things the ancient DNA is showing is actually the Corded Ware culture does correspond coherently to a group of people. I think that was a very sensitive issue to some of our coauthors, and one of the coauthors resigned because he felt we were returning to that idea of migration in archaeology that pots are the same as people. There have been a fair number of other coauthors from different parts of continental Europe who shared this anxiety.

We responded to this by adding a lot of content to our papers to discuss these issues and contextualize them. Our results are actually almost diametrically opposite from what Kossina thought because these Corded Ware people come from the East, a place that Kossina would have despised as a source for them. But nevertheless it is true that there’s big population movements, and so I think what the DNA is doing is it’s forcing the hand of this discussion in archaeology, showing that in fact, major movements of people do occur. They are sometimes sharp and dramatic, and they involve large-scale population replacements over a relatively short period of time. We now can see that for the first time.

What the genetics is finding is often outside the range of what the archaeologists are discussing these days.

This is mostly true: Genomics offers a whole new dimension to assess exchanges among groups, and help thus select anthropological models of cultural diffusion. They offer another way of interpreting prehistoric cultural evolution and change, including the investigation of potential languages of these cultures, ways of change and replacement, etc.

Also, he acknowledges that there is a lot of content added to the papers in search for context – and thus avoid simplistic assumptions and conclusions – , so this is a reasonable way to look at the (often erroneous) cultural and linguistic context which accompany most genetic papers, and even the new methods being developed to assess samples.

On the other hand, the fact that many in Archaeology didn’t want to discuss migrations does not mean that it was not discussed at all, as he seems to suggest.

On how Genomics fits with traditional disciplines

Zhang: I think at one point in your book you actually describe ancient DNA researchers as the “barbarians” at the gates of the study of history.

Reich: Yeah.

Zhang: Does it feel that way? Have you gotten into arguments with archaeologists over your findings?

Reich: I think archaeologists and linguists find it frustrating that we’re not trained in the language of archaeology and all these sensitivities like about Kossinna. Yet we have this really powerful tool which is this way of looking at things nobody has been able to look at before.

The point I was trying to make there was that even if we’re not always able to articulate the context of our findings very well, this is very new information, and a serious scholar really needs to take this on board. It’s dangerous. Barbarians may not talk in an educated and learned way but they have access to weapons and ways of looking at things that other people haven’t looked to. And time and again we’ve learned in the past that ignoring barbarians is a dangerous thing to do.

I think this is also mostly true: many academics find it frustrating to read these papers, most of which lack a minimal understanding of the topics being discussed.

For example, you can’t pretend to derive meaningful conclusions about Proto-Indo-Europeans knowing nothing about their language and the potential cultures associated with them (and why they were associated with them in the first place)…

I also agree with him in that the study of ancient DNA is a very powerful tool. Everyone involved in Anthropology and Archaeology should be trained these days in Genomics – or, at least, they should have the opportunity to do so.

On the dangers of Genomics

Reich: (…) I know there are extremists who are interested in genealogy and genetics. But I think those are very marginal people, and there’s, of course, a concern they may impinge on the mainstream.

But if you actually take any serious look at this data, it just confounds every stereotype. It’s revealing that the differences among populations we see today are actually only a few thousand years old at most and that everybody is mixed. I think that if you pay any attention to this world, and have any degree of seriousness, then you can’t come out feeling affirmed in the racist view of the world. You have to be more open to immigration. You have to be more open to the mixing of different peoples. That’s your own history.

I guess David Reich does not frequent forums on human genetics linked to ethnolinguistic identification, or he would not think of ‘extremists’ as marginal people. Or else we have a different view of what defines an ‘extremist’…

Conclusion

I did not have the best of opinions about David Reich – or any other geneticist involved in publishing anthropological theories, for that matter. I have always had great respect for their scientific work, though.

If anything, this article shows that he knows his own (and his fellow geneticists’) limitations, and the dangers and limitations of Genomics as a whole, so I have more respect for him – and anyone involved with his Lab’s work – after reading this piece.

I would sum up his interview with his humbling sentence:

We should think we really don’t know what we’re talking about.

NOTE. Also on the occasion of the publication of his book, Nature has published the piece Sex, power and ancient DNA – Turi King hails David Reich’s thrilling account of mapping humans through time and place.

After buying Lalueza-Fox’s recent book ‘La forja genètica d’Europa’, I don’t really feel like buying another book on Genomics and migrations from a geneticist. If you have read Reich’s book, please share your impressions.

EDIT (19 MAR 2018): Razib Khan has written a ‘preview of a review‘ that he intends to publish on the National Review, and it seems the book might be worth it, after all.

EDIT (20 MAR 2018): The New York Times’ Carl Zimmer writes a review, David Reich Unearths Human History Etched in Bone. Seen first in Razib Khan’s Gene Expression blog.

Iberian prehistoric migrations in Genomics from Neolithic, Chalcolithic, and Bronze Age

iberia-neolithic-bronze-age

New open access paper Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia, by Valdiosera, Günther, Vera-Rodríguez, et al. PNAS (2018) published ahead of print.

Abstract (emphasis mine)

Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500–3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.

iberia-admixture
(A) f4 statistics testing affinities of prehistoric European farmers to either early Neolithic Iberians or central Europeans, restricting these reference populations to SNP-captured individuals to avoid technical artifacts driving the affinities. The boxplots in A show the distributions of all individual f4 statistics belonging to the respective groups. The signal is not sensitive to the choice of reference populations and is not driven by hunter-gatherer–related admixture (Datasets S4 and S5). (B) Estimates of ancestry proportions in different prehistoric Europeans as well as modern southwestern Europeans. Individuals from regions of Iberia were grouped together for the analysis in A and B to increase sample sizes per group and reduce noise

Conclusion:

We present a comprehensive biomolecular dataset spanning four millennia of prehistory across the whole Iberian Peninsula. Our results highlight the power of archaeogenomic studies focusing on specific regions and covering a temporal transect. The 4,000 y of prehistory in Iberia were shaped by major chronological changes but with little geographic substructure within the Peninsula. The subtle but clear genetic differences between early Neolithic Iberian farmers and early Neolithic central European farmers point toward two independent migrations, potentially originating from two slightly different source populations. These populations followed different routes, one along the Mediterranean coast, giving rise to early Neolithic Iberian farmers, and one via mainland Europe forming early Neolithic central European farmers. This directly links all Neolithic Iberians with the first migrants that arrived with the initial Mediterranean Neolithic wave of expansion. These Iberians mixed with local hunter-gatherers (but maintained farming/pastoral subsistence strategies, i.e., diet), leading to a recovery from the loss of genetic diversity emerging from the initial migration founder bottleneck. Only after the spread of Bell Beaker pottery did steppe-related ancestry arrive in Iberia, where it had smaller contributions to the population compared with the impact that it had in central Europe. This implies that the two prehistoric migrations causing major population turnovers in central Europe had differential effects at the southwestern edge of their distribution: The Neolithic migrations caused substantial changes in the Iberian gene pool (the introduction of agriculture by farmers) (6, 9, 11, 13, 24), whereas the impact of Bronze Age migrations (Yamnaya) was significantly smaller in Iberia than in north-central Europe (24). The post-Neolithic prehistory of Iberia is generally characterized by interactions between residents rather than by migrations from other parts of Europe, resulting in relative genetic continuity, while most other regions were subject to major genetic turnovers after the Neolithic (4, 6, 7, 9, 25, 48). Although Iberian populations represent the furthest wave of Neolithic expansion in the westernmost Mediterranean, the subsequent populations maintain a surprisingly high genetic legacy of the original pioneer farming migrants from the east compared with their central European counterparts. This counterintuitive result emphasizes the importance of in-depth diachronic studies in all parts of the continent.

Related:

North Pontic steppe Eneolithic cultures, and an alternative Indo-Slavonic model

I am not a fan of continuity theories – that much should be clear for anyone reading this blog. However, most of such proposals’ supremacist (or rather fear-of-inferiority) overtones don’t mean they have to be wrong. It just means that most of them, most of the time, most likely are.

While reading Tommenable’s comments, I thought about a potential alternative model, where one could a priori accept an identification of North Pontic cultures as ‘Indo-Slavonic’, which seems to be the Eastern European R1a continuist trend right now.

NOTE. To accept this model, one should first (not a posteriori) accept an Indo-Slavonic linguistic group on theoretical grounds, of course, and take the steppe ancestral component (and not archaeological data) as the most meaningful aspect to consider for language expansion and exchange (which we know is not the most intelligent approach to cultural or language change).

Thinking about how Genomics could challenge what mainstream Linguistics and Archaeology accepts, the only situation I can think of (using simplistic phylogeography) regarding late Khvalynsk-Sredni Stog contacts (until ca. 3300 BC) is:

  1. That the community of R1b-L51 lineages was in fact an isolated group , and not a western one – i.e. to the east within the Volga-Ural groups, or maybe to the south within the North Caucasian groups .
  2. That the R1b-Z2103 community was a huge one dominating over much of the steppe, from the Dnieper area to the Volga-Ural region (where we know they were).
  3. That R1a-M417 subclades (and especially subclade R1a-Z645) with steppe ancestry, as found in Corded Ware migrants,were only found in the North Pontic area (i.e. in Sredni Stog) during the fourth millennium (until at least 3300 BC, when Yamna substitutes it), and did not form other communities in the forest-steppe or Forest Zone (from where Corded Ware eventually expanded), as it is quite likely.
  4. That both the R1b-Z2103 and R1a-Z645 communities shared obvious genetic connections (whatever they were) around the Dnieper, that could justify a common, shared language.
eneolithic-steppe-cultures
Diachronic map of Eneolithic migrations in eastern Europe ca. 4000-3100 BC

Only then, if a widespread Graeco-Aryan-speaking community happened to be spread from west to east in the Pontic-Caspian steppe, with close contacts with North Pontic cultures, and having an isolated Northern Late PIE community somewhere different than West Yamna, it could leave for me a reasonable doubt of a cultural connection (maybe “Indo-Slavonic” in nature) of the North Pontic steppe. But then we would probably be stuck – yet again – with some sort of cultural diffusion event, impossible to demonstrate.

Since it is known (in Linguistics, and also in Y-DNA lineages, due to the early expansion of Z2103 subclades) that Graeco-Aryan groups separated early, this model would not be impossible.

Also a priori in favour of that model would be the early expansion of a (Northern IE-speaking) Pre-Tocharian population to the east. On the other hand, from an archaeological point of view, the group reaching Afanasevo seems to have expanded from Repin, just like the community expanding Yamna to the west of the Dnieper.

I really doubt there can be any serious discussion though, apart from amateur geneticists with a personal interest on this, because:

  • Graeco-Aryan is a Late PIE dialect, and Late PIE guesstimates are more recent than that.
  • Dialectal separation within a Late Proto-Indo-European language must have happened late, gradually, and in close contact, allowing for common innovations to spread through dialectal groups.
  • It does not make sense in terms of prehistoric cultures, since there is no direct connection or migration among steppe cultures but for the Novodanilovka and the Yamna expansions.
  • Indo-Slavonic is only supported by a handful of linguists, and not in the way or timing described in this model.

NOTE. You can read Kortlandt’s works in Academia.edu (also on his personal website) if you are really interested in knowing more about an Indo-Slavonic proposal, from an expert Balticist and Slavicist. However, if your intent is to demonstrate some ancient ethnic link of “your” people (whatever that means) to mythical Proto-Indo-Europeans, you would not need actual knowledge or sound theories to do that, so you can skip that part. Also, Kortlandt would probably support a later model of Indo-Slavonic expansion in the steppe, related to East Yamna, and later Sintashta, Srubna, etc…

migration-steppe-yamnaya
Migration Yamna -> Corded Ware -> Bell Beaker as claimed by articles published in Nature (2015). From materials of the UAB.

If you think about it, if most modern Slavs were mainly of R1b-L23 lineages instead of R1a-Z645 (a replacement which, as it is clear know, is the consequence of a simple resurge of previous lineages in East-Central Europe, coupled with a later gradual replacement through founder effects, so no big migration history here), and Finnic speakers were mainly of R1a-Z645 lineages (whose replacement by N1c lineages seems also the consequence of quite late consecutive founder effects), I doubt we would be having this reticence to accept sound anthropological models.

So, we are speculating here for the sake of an unnecessary, naïve compromise…Just hoping to find some common ground to move on, now that the picture is clearer for everyone.

NOTE. The change of narratives where certain languages must have accompanied R1a-Z645 and N1c lineages, but in alternative ways not previously described, is obviously unjustified, if linguistic and archaeological data tell a different story. As unjustified as it is to change Yamna for “Neolithic Steppe” as homeland of Late Indo-European, to fit it with the steppe ancestry concept

See also:

Reactionary views on new Yamna and Bell Beaker data, and the newest IECWT model

You might expect some rambling about bad journalism here, but I don’t have time to read so much garbage to analyze them all. We have seen already what they did with the “blackness” or “whiteness” of the Cheddar Man: no paper published, just some informal data, but too much sensationalism already.

Some people who supported far-fetched theories on Indo-European migrations or common European haplogroups are today sharing some weeping and gnashing of teeth around forums and blogs – although, to be fair, neither Olalde et al. (2018) nor Mathieson et al. (2018) actually gave any surprising new data that you couldn’t infer before… People are nevertheless in the middle of the five stages of grief (for whatever expectations they had for new samples), and acceptance will surely take some time.

They will be confronted with two options:

  1. Keep fighting for what they believed, however wrong it turns out to be – after all, we still see all kinds of autochthonous continuists out there, no matter how much data there is against their views. People want to be supporters of a West European origin of R1b-M269 linked to Vasconic languages, fans of R1b-M269 continuity in Central Europe, Uralic speakers who believe in hidden N1c communities in Mesolithic or Neolithic Eastern Europe, fans of the OIT and Indian origins of R1a-M417…
  2. Just accept what seems now clear, change their model, and go on.
wiik-modified
Modified from Wiik for the current autochthonous continuity fans: Vasconic-Uralic distribution and Indo-European folk distribution

For me, the second option sounds quite simple, since whatever happens – markers of Indo-European migration being R1a or R1b, Corded Ware or Bell Beaker, or bothour group’s aim for the past 15 years or so is to support a North-West Indo-European proto-language, so any of the most reasonable anthropological models are a priori compatible with that. My model of Indo-European demic diffusion fits best the most recent proto-language guesstimates, though.

However, I understand that if I had been buying or selling dreams – and I mean literally buying or selling fantasies of whiteness and Europeanness (hidden behind an idealized concept of “Indo-European”, and ancestral components disguised as populations), beginning with the ‘R1a-M417/CWC’ and ‘Yamnaya ancestry’ craze of the 2015 papers – , and I realized data didn’t support that money exchange, I would be frustrated, too.

There is a funny mental process going on here for some of these people, as far as I could read today. Let me review some history of the Indo-European question here before getting to the point:

  1. Firstly linguists reconstructed (and are still doing it) Proto-Indo-European and other ancestral Indo-European proto-languages.
  2. Then archaeologists tried to identify certain ancestral cultures with these actual communities with help from linguistic guesstimates and dialectal classifications,
  3. using anthropological models of migration or cultural diffusion.
  4. Then genetic data came to support one of these alternative anthropological models, if possible.

Now some (amateur) geneticists are apparently disregarding what “Indo-European” means, and why Yamna was considered the best candidate for the expansion of Late Indo-European languages, and question the very sciences of Linguistics and Archaeology as unreliable, instead of questioning their own false assumptions and wrong interpretations from genetic papers.

Really? Genomics (especially ancestral components) now defines what an Indo-European population, culture, and language is? If that is not a fallacy of circular reasoning, I wonder what is.

The modified IECWT model

The surprise today came from the quick reaction of one member of the IECWT workgroup, Guus Kroonen, in his draft Comments to Olalde et al. 2018., The Beaker phenomenon and the genomic, transformation of northwest Europe, Nature.

Allentoft Corded Ware
The IECWT workgroup’s so-called “Steppe model” until today, as presented in Haak et al. (2015).

He and – I can only guess – the whole IECWT workgroup finally rejected their characteristic Corded Ware -> Bell Beaker migration model – which they defended as “The steppe model” of Indo-European migration in Haak et al. 2015. They now defend a proposal similar to Anthony (2007).

Fan fact: Anthony changed his mind recently to partially support what Heyd said in 2007. While I did not dislike Anthony’s new model, I consider it wrong.

The Danish group – unsurprisingly – sticks nevertheless to the hypothesis of some kind of autochthonous Germanic in Scandinavia being defined by Corded Ware migrants and haplogroup R1a, and being somehow special and older among Proto-Indo-European dialects because of its non-Indo-European substrate – although in fact Kroonen’s original linguistic paper didn’t imply so.

While this new change of the workgroup’s model brings it closer to Heyd (2007), and parallels in that sense the adaptation process of Anthony (but always one step behind), what they are proposing right now seems not anymore a modified Kurgan model, as I described it: it is essentially The Kurgan model of Marija Gimbutas (1963), with Bell Beakers spreading a language ancestral to Italo-Celtic, and Corded Ware spreading some kind of mythical Germano-Balto-Slavic

I find it odd that he would not cite Gimbutas, Heyd – as Anthony recently did – , or the most recent paper of Mallory on the language expanded with Bell Beakers, but just the workgroup’s papers and other old ones, to present this “new” theory.

However simple and (obviously) rapidly drafted it was, following the publications in Nature, it does not seem right: They were first, they were right, acknowledge them. Period.

It is interesting how the wrong interpretations of the ‘Yamnaya ancestral component’ (you know, that bulletproof “Yamna R1a-R1b community” and Yamna->Corded Ware migration that never happened) is affecting everyone involved in Indo-European studies.

Related:

Germanic tribes during the Barbarian migrations show mainly R1b, also I lineages

antiquity-europe

New preprint at BioRxiv, Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics, by Amorim, Vai, Posth, et al. (2018)

Abstract (emphasis mine):

Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early Medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data was consistent with the proposed long-distance migration from Pannonia to Northern Italy.

Interesting excerpts:

Since the adults were almost all non-local, it is tempting to suggest that we may be observing the historically described fara during migration. Regardless, this group appears to be a unit organized around one high-status, kin-based group of predominantly males, but also incorporating other males that may have some common central/northern European descent. The relative lack of adult female representatives from Kindred SZ1, the diverse genetic and isotope signatures of the sampled women around the males and their rich graves goods suggests that they may have been acquired and incorporated into the unit during the process of migration (perhaps hinting at a patrilocal societal structure that has been shown to be prominent in Europe during earlier periods).

The remaining part of this community for which we have genomic data (N=7) is composed of individuals of mainly southern European genetic ancestry that are conspicuously lacking grave goods and occupy the southeastern part of the cemetery, with randomly oriented graves with straight walls. While the lack of grave goods does not necessarily imply that these individuals were of lower status, it does point to them belonging to a different social group. Interestingly, the strontium isotope data suggest that they may have migrated together with the warrior-based group from outside Szólád, but barriers to gene flow were largely been maintained.

longobards-pca-szolad-collegno
Genetic structure of Szólád and Collegno. (A) Procrustes Principal Component Analysis of modern and ancient European population (faded small dots are individuals, larger circle is median of individuals) along with samples from Szólád (filled circles), Collegno (filled stars), Bronze Age SZ1 (filled grey circle), second period CL36 (grey star), two Avar-period samples from Szólád (yellow circles), Anglo-Saxon period UK (orange circles) and 6th Century Bavaria (green circles). Szólád and Collegno samples are filled with colors based on estimated ancestry from ADMIXTURE. Blue circles with thick black edge = Kindred_SZ1 , blue stars with thick black edge = Kindred_CL1 , stars with thick green edge = Kindred_CL2 . NWE = northwest Europe, NE = modern north Europe, NEE = modern northeast Europe, CE =central Europe, EE = eastern Europe, WE =western Europe, SE = southern Europe, SEE = southeast Europe, HUN = modern Hungarian, HBr = Hungarian Bronze Age, Br = central, northern and eastern Europe Bronze age.

Evidence for Migrating Barbarians and “Longobards”

Our two cemeteries overlap chronologically with the historically documented migration of Longobards from Pannonia to Italy at the end of the 6th century. It is thus intriguing that we observe that central/northern European ancestry is dominant not only in Szólád, but also in Collegno. Based on modern genetic data we would not expect to see a preponderance of such ancestry in either Hungary or especially Northern Italy. While we do not yet know the general genomic background of Europe in these geographic regions just before the establishment of Szólád and Collegno, other Migration Period genomes from the UK and Germany show a fairly strong correlation with modern geography (while also possessing a similar central/northern European ancestry component to that found in Szólád and Collegno). Going further back in time, Late Bronze Age Hungarians show almost no resemblance to populations from modern central/northern Europe, especially compare to Bronze Age Germans and in particular Scandinavians, who, in contrast, show considerable overlap with our Szólád and Collegno central/northern ancestry samples. Coupled with the strontium isotope data, our paleogenomic analysis suggest that the earliest individuals of central/northern ancestry in Collegno were probably migrants while those with southern ancestry were local residents. Our results are thus consistent with an origin of barbarian groups such as the Longobards somewhere in Northern and Central Europe east of the Rhine and north of the Danube. Thus our results cannot reject the migration, its route, and settlement of “the Longobards” described in historical texts.

We note however that whether these people identified as “Longobard” or any other particular barbarian people is impossible to assess. Modern European genetic variation is generally highly structured by geography 22,32 , even at the level of individual villages 33 . It is, therefore, surprising to find significant diversity, even amongst individuals with central/northern ancestry, within small, individual Langobard cemeteries. Even amongst the two family groups of primarily central/northern ancestry, who may have formed the heart of such migration, there is clear evidence of admixture with individuals with more southern ancestry. If we are seeing evidence of movements of barbarians, there is no evidence that these were genetically homogenous groups of people.

longobards-admixture-szolad-collegno
Model-based ancestry estimates from Admixture for Szólád (B) and Collegno (C) using 1000 Genomes Project Eurasian and YRI populations to supervise analysis. Note that high contamination was identified in CL31 and is shown with a triangle in the (A) and overlaid with a pink hue in the (C).

From the supplementary material:

The haplogroups detected in the samples show a prevalence of R1b (55.3%), which is the most common sub-haplogroup in western Europe, with a peak in the Iberian Peninsula and in the British islands and a west-east gradient in central Europe. A consistent percentage of haplotypes belongs to the I haplogroup (26.4%), both in the I1a and, more abundantly, in I2a2 sub-haplogroups. They are particularly frequent in the northern Balkans with a westward gradient in central and western Europe, with some lineages belonging to I2a2a1b particularly common in the Germanic region.

germanic-tribes
Relative and absolute haplogroup frequencies: COL = Collegno; SZO = Szólád; CEU = Central European from Utah; FIN = Finnish; GBR = Britons; IBS = Iberians; SAR = Sardinians; TSI = Tuscans

Related:

“How Asian nomadic herders built new Bronze Age cultures”

I recently wrote about a good informal summary of genomic research in 2017 for geneticists.

I found a more professional review article, How Asian nomadic herders built new Bronze Age cultures, by Bruce Bower, appeared in Science News (25th Nov. 2017).

NOTE: I know, I know, the Pontic-Caspian steppe is in East Europe, not Asia, but what can you do about people’s misconceptions regarding European geography? After all, the division is a conventional one, there are not many landmarks to divide Eurasia…

It refers to Kristiansen’s model, which we already know supports the expansion of IE languages with the Corded Ware culture, and a later Corded Ware -> Bell Beaker migration. This is followed by many geneticists today as “The steppe model”.

Corded Ware culture emerged as a hybrid way of life that included crop cultivation, breeding of farm animals and some hunting and gathering, Kristiansen argues. Communal living structures and group graves of earlier European farmers were replaced by smaller structures suitable for families and single graves covered by earthen mounds. Yamnaya families had lived out of their wagons even before trekking to Europe. A shared emphasis on family life and burying the dead individually indicates that members of the Yamnaya and Corded Ware cultures kept possessions among close relatives, in Kristiansen’s view.

“The Yamnaya and the Corded Ware culture were unified by a new idea of transmitting property between related individuals and families,” Kristiansen says.

Yamnaya migrants must have spoken a fledgling version of Indo-European languages that later spread across Europe and parts of Asia, Kristiansen’s group contends. Anthony, a longtime Kristiansen collaborator, agrees. Reconstructed vocabularies for people of the Corded Ware culture include words related to wagons, wheels and horse breeding that could have come only from the Yamnaya, Anthony says.

As Indo-European languages spread, the Yamnaya’s genetic impact in Europe remained substantial, even after the disappearance of Corded Ware culture around 4,400 years ago, Reich’s team reported online May 9 at bioRxiv.org. About 50 percent of the ancestry of individuals from a later Bronze Age culture, dubbed the Bell Beaker culture for its pottery vessels shaped like an inverted bell, derived from Yamnaya stock. Such pottery spread across much of Europe starting nearly 4,770 years ago and disappeared by 3,800 years ago. Migrations of either people or ideas may have accounted for that dispersal.

NOTE. Anthony, as we know, has already changed his mind with the most recent data.

The author juxtaposes other opinions, to somehow balance the article:

Like many of his colleagues, archaeologist Volker Heyd of the University of Bristol in England was jolted by the 2015 reports of a close genetic link between Asian herders and a Bronze Age culture considered native to Europe. But, Heyd says, the story of ancient Yamnaya migrations is more complex than the rapid-change scenario sketched out by Kristiansen and Anthony.

No evidence exists that Yamnaya people rapidly developed practices typical of the Corded Ware culture in one part of Europe, Heyd argues in the April Antiquity. Cultural shifts in Europe around 5,000 years ago must have emerged from an extended series of small-scale dealings with Yamnaya and other pastoralists, which was then capped off by a large influx of steppe wagon travelers, he says.

For instance, individual graves and other signs of contact with the Yamnaya people and even earlier Asian pastoralists appear in Europe 1,000 to 2,000 years before DNA-transforming migrations occurred. Consider that the Yamnaya account for 5 percent of the ancestry of Ötzi the Iceman, who lived in southeastern Europe roughly 300 years before the Yamnaya’s big move (SN: 5/27/17, p. 13). Little is known about those earlier encounters.

Efforts to decipher ties between Yamnaya and Corded Ware culture are complicated by the fact that DNA is available from just a few people from each group, says Heyd, who is currently excavating Yamnaya graves in Hungary. Ancient DNA samples analyzed in the 2015 papers come from only a handful of Yamnaya and Corded Ware culture sites in a few parts of Europe and Russia.

Heyd suspects that Yamnaya travelers had even earlier contacts, perhaps by 5,400 years ago, with central and eastern Europeans known for making globe-shaped pots with small handles. Individuals from that culture, excavated at two sites in Poland and Ukraine, possess no Yamnaya genes, a team affiliated with Reich’s lab reported online May 9 at bioRxiv.org. But Heyd thinks mating between members of that European culture and Yamnaya migrants may have occurred a bit farther east, where cross-cultural contacts probably occurred at the boundary of European forests and Asian grasslands.

Other genetic clues point to a long history of Asian pastoralists crossing into parts of Europe. Small amounts of DNA from steppe herders, possibly the Yamnaya, appeared in three hunter-gatherer skeletons from southeastern Europe dating to as early as around 6,500 years ago.

It is always interesting to see how reports gradually evolve, including more and more doubts about the ‘Yamnaya component’, and how it may be correctly interpreted. Slow but steady wins the race.

Check out the full article.

Featured image: from the article, based on the 2015 papers and Kristiansen’s model.

See also: