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

About the European Union’s arcane language: the EU does seem difficult for people to understand

Mark Mardell asks in his post Learn EU-speak:

Does the EU shroud itself in obscure language on purpose or does any work of detail produce its own arcane language? Of course it is not just the lingo: the EU does seem difficult for people to understand. What’s at the heart of the problem?

His answer on the radio (as those comments that can be read in his blog) will probably look for complex reasoning on the nature of the European Union as an elitist institution, distant from real people, on the “obscure language” (intentionally?) used by MEPs, on the need of that language to be obscured by legal terms, etc.

All that is great. You can talk a lot about the possible reasons why people would find too boring those Europarliament discussions where everyone speaks his own national language; possible reasons why important media (like the BBC) would never show debates on important issues, unless the MEP uses their national language; possible reasons why that doesn’t happen with national parliaments where everyone speaks a common language…

But the most probable answer is so obvious it doesn’t really make sense to ask. The initeresting question is do people actually want to pay the price for having a common Europe?

European Higher Education Area : The Bologna Process implementation

I have read lots of articles about the Bologna Process (Wikipedia) and its effects on the European Higher Education system and on the education of future generations.

Apart from the (still to see) economic and social benefits for students and for the European Education system as a whole, I have only a tiny comment to make about its actual implementation by the different universities I’ve studied in, due to the great time I’m having right now with the “European system-like homework” I am currently doing for one of my “European implemented” professors:

a. In the Universidad Carlos III de Madrid, as far as I was able to test the implementation of the new system in Laws and Management Bachellor Degrees, back in 2003-2005, it seemed to me that, instead of substituting one method for another, professors took advantage of the changes that had to be made to develop their own innovative teaching concepts and call them “European method”. In this sense, some old-style professors kept on giving their traditional lectures – specially those who had coplex subjects, like Econometrics, Macroeconomics, Private International Law, Penal Law, etc. -, while other easier subjects – like Marketing, Management, Commercial Law, History of Law, etc. – were given a newer impulse, implementing ‘practices’, ‘seminars’, ‘homework-hour-units’, and that kind of stuff. All in all, the difficult subjects remained as difficult as before, while professors of easy subjects took advantage of the system to force students to work more, to go to their lessons more (however unnecessary they were), to go to their offices for ‘European’ or ‘ECTS tutorials’ – I hope that’s the correct English name -, etc. Only some Departments with ‘core’ subjects, like the Administrative Law, the Law of Process and the International Management Departments, had begun to implement it at that time; even so, their final exam was still as difficult as always. For example:
– In History of Law we had to go to the professor’s office for the necessary ‘European tutorials’, to inform her about our ‘tutorized homeworks’, and to explain her how we wanted to make our public presentations – we had to discuss publicly, in groups of 7, against each other, and twice in that semester, what we thought about this or that part of history, and make a debate, choosing one position each (for or against): my group and I discussed about the Castilian King’s power in the 14th century and about the French Revolution. I’ve never worked more on a subject, and I’ve never felt more disappointed with just an ‘excellent’ mark instead of a ‘Honours’ one; that was the first and last serious ‘European work’ for me; that proved how unfair and arbitrary the new system made the teaching – or how the professors used the new system to make their subjects unfair and arbitrary…
– In Law of Process we had to make a video representing a 1-hour process in a fictitious court, that took away lots of hours of preparation from each of us – in which I rejected a ‘good’ role (judge or lawyer) and acted as a witness and as an expert (a doctor!), and still only counted 1 point (of 10) in the final marks – indeed I get almost nothing for my ‘work’ on that drama
– In Administrative Law, there were ‘homeworks’ for each 2 weeks and partial exams every 4 weeks, very detailed and tough work that, if correctly done, could help you avoid the final exam and do ‘just a final proof’, ie. the same difficult exam but without being able to obtain a ‘fail’ mark; I abandoned the ‘European system’ in the 3rd week, after receiving a 5.5 (over 10) for a 10-15 hour work on some stupid Administrative dispute involving the Comunidad de Madrid and the Canal de Isabel II public entity.
– Economic subjects like Marketing, Introduction to Management, Accountancy Analysis, etc. had all something in common: they were easy, they had some ‘homework’, at least a public presentation, and a lot of personal work including a normal final exam; they were all arbitrarily organized, and the marks very subjectively interpreted by the professors.

b. In the Universidad de Extremadura, Medicine and Surgery Degree, 2006-2008, I have been (and will be) testing the changes made, and the changes to come – until, supposedly, 2010, when the European system should be fully implemented – , and it’s more of the same strategy I saw before: professors of difficult, ‘core’ subjects – Biochemistry, Physics, Physiology, Pathology, etc. – are not implementing any change at all: practices are the same (in content and number) as always, lectures are given the traditional way, and final exams are as complete and as difficult as 15 years ago – and I know it because I have the exams of my generation and still older ones. Other subjects like Anatomy and Histology, as well as some very easy ones – namely Psychology, Psychophysiology, Endocrinology & Nutrition or Radiology, to name some – are implementing this super-dooper new method (or ‘methods’?) called “European system”, which means something different to each professor – something that might be summed up in do what you always wanted to do teaching your subject and never dared to -, and every student has to do it to pass – or even be able to make – the final exam.

I could talk about my personal experience with the worst subjects I’ve had these 2 years, but I prefer not to do it until I have completed, at least, the first 3 years or pregrade; I don’t want to make my professors’ demands still more arbitrary…

Just to name the most irritating (general) consequence of this “adaptation process”, I have to say I have worked – in the last 6 years – more hours in ‘practices’ and ‘seminars’ (to call it something) of subjects like Marketing, History of Law, Psychology and Histology, than in the other ones I was interested in, like International Law, Law of Process, Physiology or Pathology.

If my case is (just) similar to all those generations that have studied Law and Medicine in Spain in the last 6 years – and what has to come… -, I really hope people are beginning to change their real legal and medical problems for stupid ones, or we’ll have some problems explaining them why we can make great public presentations prepared in PowerPoint, or “integrate concepts” drawing ‘tutoized Posters’ with Photoshop, but we can’t help them before a Court of Law, or can’t correctly diagnose their illnesses…