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


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

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

Taking only admixture analyses using Yamna samples:

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


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

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

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

Discovered via Généalogie génétique

Another hint at the role of Corded Ware peoples in spreading Uralic languages into north-eastern Europe, found in mtDNA analysis of the Finnish population


Open article at Scientific Reports (Nature): Identification and analysis of mtDNA genomes attributed to Finns reveal long-stagnant demographic trends obscured in the total diversity, by Översti et al. (2017).

Of special interest is its depiction of Finland’s past as including the expansion of Corded Ware population of mtDNA U5b1b2 (and probably Y-DNA R1a-M417 subclades), most likely Uralic speakers of the Forest Zone, to the north of the Yamna culture (where Late Proto-Indo-European was spoken).

A later expansion of other subclades – particularly Y-DNA N1c -, was probably associated with the later western expansion of the Eurasian Seima-Turbino phenomenon, and its current prevalence in Finnish Y-DNA haplogroups might have been the consequence of the population decline ca. 1500 BC, and later Iron Age population bottleneck (with the population peak ca. 500 AD) described in the article.

That would more naturally explain the ‘cultural diffusion’ of Finnic languages into invading eastern N1c lineages, a diffusion which would have been in fact a long-term, quite gradual replacement of previously prevalent Y-DNA R1a subclades in the region, as supported by the prevalent “steppe” component in genome-wide ancestry of Finns.

Therefore, there were probably no sudden, strong population (and thus cultural) changes associated with the arrival of N1c lineages, like the ones seen with R1a (Corded Ware / Uralic) and R1b (Yamna / Proto-Indo-European) expansions in Europe.

How the Saami fit into this scheme is not yet obvious, though.


In Europe, modern mitochondrial diversity is relatively homogeneous and suggests an ubiquitous rapid population growth since the Neolithic revolution. Similar patterns also have been observed in mitochondrial control region data in Finland, which contrasts with the distinctive autosomal and Y-chromosomal diversity among Finns. A different picture emerges from the 843 whole mitochondrial genomes from modern Finns analyzed here. Up to one third of the subhaplogroups can be considered as Finn-characteristic, i.e. rather common in Finland but virtually absent or rare elsewhere in Europe. Bayesian phylogenetic analyses suggest that most of these attributed Finnish lineages date back to around 3,000–5,000 years, coinciding with the arrival of Corded Ware culture and agriculture into Finland. Bayesian estimation of past effective population sizes reveals two differing demographic histories: 1) the ‘local’ Finnish mtDNA haplotypes yielding small and dwindling size estimates for most of the past; and 2) the ‘immigrant’ haplotypes showing growth typical of most European populations. The results based on the local diversity are more in line with that known about Finns from other studies, e.g., Y-chromosome analyses and archaeology findings. The mitochondrial gene pool thus may contain signals of local population history that cannot be readily deduced from the total diversity.

From its results:

In general, there appears to be two loose and largely overlapping clusters among the Finn-characteristic haplogroups: the first between 1,000–2,000 ybp and the second around 3,300–5,500 ybp. The age of the older cluster coincides temporally with the arrival of the Corded-Ware culture and, notably, the spread of agriculture in Finland. The arrival and spread of agriculture, temporally corresponding with the age estimates for most of the haplogroups characteristic of Finns, might be a sign of population size increase enabled by the new mode of subsistence, resulting in reduced drift and accumulation of genetic diversity in the population.


Another insight in the past population sizes in Finland is based on radiocarbon-dated archaeological findings in different time periods. These analyses suggest two prehistoric population peaks in Finland, the Stone Age peak (c. 5,500 ybp) and the Metal Age peak (~1,500 ybp). Both of these peaks were followed by a population decline, which appears to have reached its ebb around 3,500 ybp. These developments are not distinguishable in the BSPs. However, these ages correspond well to the two haplogroup age clusters described above. The presumably less severe Iron Age population bottleneck seen in the archaeological data, 1,500–1,300 ybp, temporally coincides with the population size reduction visible for the Finn-characteristic subhaplogroups.


Discovered via Eurogenes.

My European Family: The First 54,000 years, by Karin Bojs


I have recently read the book My European Family: The First 54,000 years (2015), by Karin Bojs, a known Swedish scientific journalist, former science editor of the Dagens Nyheter.

My European Family: The First 54,000 Years
It is written in a fresh, dynamic style, and contains general introductory knowledge to Genetics, Archaeology, and their relation to language, and is written in a time of great change (2015) for the disciplines involved.

The book is informed, it shows a balanced exercise between responsible science journalism and entertaining content, and it is at times nuanced, going beyond the limits of popular science books. It is not written for scholars, although you might learn – as I did – interesting details about researchers and institutions of the anthropological disciplines involved. It contains, for example, interviews with known academics, which she uses to share details about their personalities and careers, which give – in my opinion – a much needed context to some of their publications.

Since I am clearly biased against some of the findings and research papers which are nevertheless considered mainstream in the field (like the identification of haplogroup R1a with the Proto-Indo-European expansion, or the concept of steppe admixture), I asked my wife (who knew almost nothing about genetics, or Indo-European studies) to read it and write a summary, if she liked it. She did. So much, that I have convinced her to read The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World (2007), by David Anthony.

Here is her summary of the book, translated from Spanish:

The book is divided in three main parts: The Hunters, The Farmers, and The Indo-Europeans, and each has in turn chapters which introduce and break down information in an entertaining way, mixing them with recounts of her interactions and personal genealogical quest.

Part one, The Hunters, offers intriguing accounts about the direct role music had in the development of the first civilizations, the first mtDNA analyses of dogs (Savolainen), and the discovery of the author’s Saami roots. Explanations about the first DNA studies and their value for archaeological studies are clear and comprehensible for any non-specialized reader. Interviews help give a close view of investigations, like that of Frederic Plassard’s in Les Combarelles cave.

Part two, The Farmers, begins with her travel to Cyprus, and arouses the interest of the reader with her description of the circular houses, her notes on the Basque language, the new papers and theories related to DNA analyses, the theory of the decision of cats to live with humans, the first beers, and the houses built over graves. Karin Bojs analyses the subgroup H1g1 of her grandmother Hilda, and how it belonged to the first migratory wave into Central Europe. This interest in her grandmother’s origins lead her to a conference in Pilsen about the first farmers in Europe, where she knows firsthand of the results of studies by János Jakucs, and studies of nuclear DNA. Later on she interviews Guido Brandt and Joachim Burguer, with whom she talks about haplogroups U, H, and J.

The chapter on Ötzi and the South Tyrol Museum of Archaeology (Bolzano) introduces the reader to the first prehistoric individual whose DNA was analysed, belonging to haplogroup G2a4, but also revealing other information on the Iceman, such as his lactose intolerance.

Part three, dealing with the origin of Indo-Europeans, begins with the difficulties that researchers have in locating the origin of horse domestication (which probably happened in western Kazakhstan, in the Russian steppe between the rivers Volga and Don). She mentions studies by David Anthony and on the Yamna culture, and its likely role in the diffusion of Proto-Indo-European. In an interview with Mallory in Belfast, she recalls the potential interest of far-right extremists in genetic studies (and early links of the Journal of Indo-European Studies to certain ideology), as well as controversial statements of Gimbutas, and her potentially biased vision as a refugee from communist Europe. During the interview, Mallory had a copy of the latest genetic paper sent to Nature Magazine by Haak et al., not yet published, for review, but he didn’t share it.

Then haplogroups R1a and R1b are introduced as the most common in Europe. She visits the Halle State Museum of Prehistory (where the Nebra sky disk is exhibited), and later Krakow, where she interviews Slawomir Kadrow, dealing with the potential creation of the Corded Ware culture from a mix of Funnelbeaker and Globular Amphorae cultures. New studies of ancient DNA samples, published in the meantime, are showing that admixture analyses between Yamna and Corded Ware correlate in about 75%.

In the following chapters there is a broad review of all studies published to date, as well as individuals studied in different parts of Europe, stressing the importance of ships for the expansion of R1b lineages (Hjortspring boat).

The concluding chapter is dedicated to vikings, and is used to demystify them as aggressive warmongers, sketching their relevance as founders of the Russian state.

To sum up, it is a highly documented book, written in a clear style, and is capable of awakening the reader’s interest in genetic and anthropological research. The author enthusiastically looks for new publications and information from researchers, but is at the same time critic with them, showing often her own personal reactions to new discoveries, all of which offers a complex personal dynamic often shared by the reader, engaged with her first-person account the full length of the book.

Mayte Batalla (July 2017)

DISCLAIMER: The author sent me a copy of the book (a translation into Spanish), so there is a potential conflict of interest in this review. She didn’t ask for a review, though, and it was my wife who did it.

The over-simplistic “Kossinian Model”: homogeneous peoples speaking a common language within clearly delimited cultures


There seems to be a growing trend to over-simplistic assumptions in archaeology and linguistics, led by amateur and professional geneticists alike, due to the recent (only partially deserved) popularity of Human Evolutionary Biology.

These studies are offering ancient DNA samples, whose Y-DNA and mtDNA haplogroups and admixture analyses are showing some new valuable information on ancient cultures and peoples. However, their authors are constantly giving uninformed conclusions.

I have read a good, simple description of the Kossinnian model in the book Balkan Dialogues (Routledge, 2017), which has been shared to be fully read online by co-editor Maria Ivanova.

Chapter 3, The transitions between Neolithic and Early Bronze Age in Greece, and the “Indo-European problem”, by Jean-Paul Demoule, offers a clear account of the difficulties found in tracing the arrival of Proto-Greek speakers to Greece or the “Coming of the Greeks”. The identifications of cultural breaks most commonly supported by academics as potentially signaling the arrival of Proto-Greeks are cited, including the Early Helladic III period ca. 2300 BC (with the diffusion of Mynian ware), or the Middle Helladic period ca. 2000 BC. The problem of finding a clear cultural break before the emergence of Mycenaean Greece (which obviously spoke an early Greek dialect) has led some to adopt a “Palaeolithic autochthonous theory” (Giannopoulos 2012), which offers still more problems than it solves.

Of interest is his reference to Kossina in light of the recent popularity in resorting to DNA to answer all problems. It is mandatory for the field of Indo-European studies – regardless of what renown labs and journals of high impact factor are publishing – to avoid carrying on “in the steps of race based cranial measurement which enjoyed its floruit in the 19th century before fading into oblivion.”

This is why, without denying the relationship between Indo-European languages, we need to question the validity of the overall model itself, which has shown itself to be over-simplistic in assuming the movement of permanent and long-lasting homogeneous “peoples”. More precisely, we have to criticize in details the “Kossinnian Model” underlying all those assumptions – “Kossinnian”, because of the German archaeologist Gustaf Kossina (1858–1931), well known for the famous sentence: “Cultural provinces, which are clearly delimited on the basis of archaeology, correspond in every era to specific peoples or tribes” (“Scharf umgrenzte archäologische Kultur-provinzen decken sich zu allen Zeiten mit ganz bestimmten Völkern und Völkerstämmen”). Four basic assumptions arise from this central idea:

  1. Changes in languages are due to population movements, usually involving conquest, and every migration implies a linguistic change.
  2. Archaeological “cultures” are homogenous ethnic groups, with defined frontiers, based on the model of 19th- and 20th-century nation-states and equally on the model of biological entities that reproduce by parthenogenesis.
  3. There is coincidence between language and material culture.
  4. Finally, languages are also homogenous biological entities which are autonomous and clearly delimited, and which can reproduce by parthenogenesis or by scissiparity.

Unfortunately, none of these points is self-evident and each can be countered by a number of historical examples (Demoule 2014: 553–592).

While I agree with the first part of the first statement attributed to the “Kossinnian model”, i.e. that languages are usually the product of population movements (either involving conquest or not), the other statements are obviously and demonstrably false, and are frequently assumed in comments, blog posts, forums, and even research articles – particularly in those based on genetic studies -, and this trend seems to be increasing lately.

Indo-European demic diffusion model, 2nd edition, revised and updated

It has been three months since I published the first paper on the Indo-European demic diffusion model.

In the meantime, important pre-print papers with samples of Bell Beaker and South-Eastern European cultures compel me to add new data in support of the model. I have taken this opportunity to revise the whole text in a new paper, Indo-European demic diffusion model, 2nd edition, and also some of the maps of Indo-European migrations, which are now hosted in this blog.

I have made changes to some of the old blogs I had, like this one, and I have merged two of them (from and in this domain,, to begin blogging about anthropological questions regarding Proto-Indo-Europeans and their language.

This blog was used years ago as my personal dialectic training site in English, mostly filled with controversial topics, and while I hope to keep some form of discussion, I want to turn it into a more pragmatic blog for news and reports on Indo-European studies. will be used as a collaborative Wiki website for this model to include supplementary information from published papers – such as results of individual and group’s admixture analyses, archaeological information of individual samples, and also mtDNA. To collaborate, users will have to request an account first (it will be a closed community), and those with important contributions will be added as authors of the following editions of the paper.

Indo-European Demic Diffusion – The expansion of Proto-Indo-Europeans potentially explained as the expansion of R1b subclades

I published an essay (or “dissertation”) some weeks ago, about what seems to me one of the most likely models of expansion of Indo-European-speaking peoples, based on Y-DNA haplogroups. Recently J.P. Mallory had proposed* (although he was not the first) that North-West Indo-European (the ancestor of Italo-Celtic and Germanic, and Balto-Slavic**) expanded with the Bell Beaker culture, a hypothesis that is supported by the most recent radiocarbon data (and subsequent proposal of an eastern origin of the pre-Bell Beaker culture, linked to the Yamna expansion, by Volker and Heyd). As I outline in the paper, ancient DNA samples and genetic data from modern populations seem to support this new model.

The still most prevalent model followed by archaeologists, based on Gimbutas’ theory, links the Corded Ware culture expansion to an expansion of the Yamna culture. Gimbutas linked the expansion of Bell Beaker to the expansion of certain Indo-European dialects through Vucedol, and Corded Ware was associated with the expansion of Germano-Balto-Slavic. Even though linguistics has changed its mainstream view of the dialectalization of Late Indo-European in the past half century, the archaeological community (those who supported the steppe expansion, at least) has remained strongly linked to Gimbutas, and more recently David Anthony has supported a similar model (with a phylogenetic model of Proto-Indo-European dialects by Don Ringe), by explaining a dual expansion into Corded Ware by Pre-Germanic (through a mixed Old European / IE Usatovo culture) and Pre-Balto-Slavic (through the Middle Dnieper culture), while eastern Bell Beakers expanded with Italo-Celtic dialects. While a strong cultural connection between Yamna and Corded Ware is currently undeniable, and admixture analyses show a connection between steppe and both Bell Beaker and Corded Ware samples, the actual relationship is today far less clear than it was 10 years ago (when we would simply connect Yamna with a R1a-dominated Corded Ware), and far more ancient samples from the steppe, steppe-forest, and forest zone are needed to extract any strong conclusions.

During this time I have received some comments on the paper, and have discovered some interesting sources for more information, like BioRxiv (for the newest pre-print papers on Genetics), and (for papers on Archaeology), both of which I can’t hardly recommend enough for anyone interested in these topics. From what I have experienced, Linguistics – which seemed to me a quite closed, strongly conservative community, due to my proposal of speaking a reconstructed Proto-Indo-European dialect as a common language today – has been more open with my model than some archaeological/genetic tandems, and linguists have shown a clearer grasp of all anthropological disciplines involved in Indo-European studies than others… My model remains a theory that I expect to develop further with more details and more genetic data, as they are published.

There are some interesting upcoming samples (mainly from Bell Beaker) by the Reich Lab – and today its publication seems nearer. While the interpretation seems to be in line with what has been said in previous similar publications, the most interesting data will most likely be the actual samples, apparently already showing a lack of steppe ancestry in Iberian Bell Beaker, and a clear invasion of Bell Beaker peoples (hence R1b?) in Great Britain. Hopefully some new samples of Yamna and Corded Ware might give us interesting information.

It is always to be remembered that, when talking about Indo-European peoples, what matters is linguistics: after, all, the peoples whose place and time we want to find are defined by their language, Indo-European. Archaeology might be able to date some cultural developments potentially linked with Indo-European-speaking peoples, and genetics might give support to the expansion of peoples (and thus maybe languages) accompanying such cultural expansions. Recent genetic developments are quite interesting, in that we might be able to place Late Indo-European and North-West Indo-European speakers in place and time, but it seems to me that some people are trying to answer the Urheimat problem the other way around.

* J.P. Mallory, ‘The Indo-Europeanization of Atlantic Europe’, in Celtic From the West 2: Rethinking the Bronze Age and the Arrival of Indo-European in Atlantic Europe, eds J. T. Koch and B. Cunliffe (Oxford, 2013), p.17-40

** It has been proposed that Balto-Slavic derived partially from North-West Indo-European, and partially from a different Late Indo-European language, although there are different models to explain the pidginization of this dialect