Ancient DNA from the Balkans

This study has been for several months around but I have not discussed until now and is well worth a mention.

Ian Mathieson et al., The Genomic History Of Southeastern Europe. BioRXiv (pre-pub) 2017. doi:10.1101/135616

There is a lot of ancient autosomal DNA from the region but it basically says one thing: everything was almost exactly as expected from archaeology. The Karanovo-Gumelnita people, famed for inventing the Bronze Age a whole millenium earlier than anyone else, and nearby related cultures, were within the mainstream (Vasconic) Neolithic genetic grouping. This changed however with the kurgan invasion expressed primarily in the Ezero culture, which I've been told should be considered direct precursors of Thracians. But the change is not something radical: more genetic affinity with the steppe is visible than before and more generalized through all samples. 

Fig. 1-D - Supervised ADMIXTURE plot, modeling each ancient individual (one per row), as a mixture of
populations represented by clusters containing Anatolian Neolithic (grey), Yamnaya from Samara (yellow), EHG (pink) and WHG (green).  (click to expand)

Well, it is not exactly everything what is as expected, if we consider Polish Globular Amphorae culture, which I would have expected to be at least somewhat steppary, Indoeuropean, already but were not. Thus it seems I have to concede on this culture and its precursors being still part of the Vasconic Neolithic. This makes Indoeuropean penetration into Central-North Europe a much more sudden episode and one directly tied to Corded Ware culture and nothing else. It must have been perceived by its victims like a massive catastrophe, because it was a huge area which they conquered and to a large extent colonized in a very short span of time.

Lots of R1b in Epipaleolithic Balkans

Most interesting anyhow is the huge hoard of ancient Y-DNA R1b in the Iron Gates region (Lepenski Vir) before the Neolithic. This not only demonstrates, again, that this haplogroup is Paleoeuropean, at least in part, but, quite intriguingly makes earlier findings on modern data suggesting a possible origin or R1b-M269 in or near modern Serbia (Morelli 2010 and Myres 2010) at least somewhat plausible. However none of the Iron Gates R1b is described as R1b-M269 and in some cases it is excluded that it could be this sublineage. 

Thus the issue of the ultimate origins of this key lineage remains open, but let me underline that these Iron Gate individuals belonged to the WHG grouping, as did Villabruna (so far the oldest R1b carrier kown) and that they breach this way the assumed haplogroup homogeneity I2 conceived on merely Central and Northern European samples. Just as happened with mtDNA U haplogroup homogeneity when mtDNA H was detected by several independent studies of Iberian ancient DNA. It is normal to expect more diversity towards the south for several reasons but maybe the most critical of them is just average temperature, which makes the southern lands naturally more fertile (notably so for crops domesticated in the Middle East) and easier to inhabit. 

This trend was only broken in the Middle Ages when the heavy plough allowed the improved exploitation of deep Oceanic soils, being useless in the Mediterranean region of shallow soils however. It was only then when the center of European development moved from south to north, to Belgium specifically, where it remains till present day. So let's take Southern Europe a bit seriously, please.

Everything you wanted to know about Balcan and Carpathian Neolithic

Prolific researcher Esther Bamfy recently uploaded to her academia.edu page this most interesting publication, which, even if it is not "recent", has a load of information on the Neolithic of the Balcans, which is crucial to understand that of Europe in general.

Various authors. A SHORT WALK THROUGH THE BALKANS:THE FIRST FARMERS OF THE CARPATHIAN BASIN AND ADJACENT REGIONS. Proceedings of the Conference held at the Institute of Archaeology UCL on June 20th - 22nd, 2005. Freely available at academia.edu → LINK.

The collection is pretty much exhaustive but the paper that most caught my attention was the one by J.K. Koszlowski, titled "Western Anatolia, the Aegean Basin and the Balcans in the Neolithisation of Europe", which underlines that, contrary to pop culture ideas, often making headway into flawed genetic or linguistic studies, the first European Neolithic of Greece (Thessaly and Argolid) can't be related to Western Anatolia, where there was no such Neolithic yet but probably arrived, maybe via Cyprus, by sea.

This is coincident with what I wrote months ago at PPNB ancient mtDNA and its legacy.

But all 18 papers are very much worth reading anyhow, take a look. 

Ancient Thracians, Ötzi and the origins of modern Europeans (another point of view)

A recent study has sequenced the DNA of an ancient Thracian woman but, for some reason, instead of looking at her comparison with modern Bulgarians and such, they have written a study that mostly goes about Ötzi "the iceman" and has not a single Bulgarian sample.

Martin Sikora et al., Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe. PLoS Genetics 2014. Open access → LINK [doi:10.1371/journal.pgen.1004353]

Abstract

Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture.

Notice please that, as the authors acknowledge, the DNA of the second Thracian individual, K8 may be contaminated:

the DNA damage pattern of this individual does not appear to be typical of ancient samples (Table S4 in [15]), indicating a potentially higher level of modern DNA contamination.

This does not seem to dissuade them to use it in the analyses.

Figure 1. Geographic origin of ancient samples and ADMIXTURE results.
(A) Map of Europe indicating the discovery sites for each of the ancient samples used in this study. (B) Ancestral population clusters inferred using ADMIXTURE on the HGDP dataset, for k = 6 ancestral clusters. The width of the bars of the ancient samples was increased to aid visualization.

Notice that, instead of attempting to model moderns on ancients, as would seem logical from the viewpoint of purported ancestry but would be incomplete for lack of a sufficiently large ancient sample or allow the ancient samples to "float freely" in the analysis, the researchers decided to force them into modern parameters what is still valid, because it indicates greater or lesser affinity to the various studied modern populations (among which there's not a single Balcanic sample, oddly enough). 

We can see that:

• Epipaleolithic Iberian Braña 1 approximates the French structure but is somewhat "more Basque" than these. 
• Neolithic Pitted Ware semi-forager Ajv70 (Gotland) approximates the Orcadians very well.
• Neolithic Megalithic/Funnelbeaker Gok4 (Southern Sweden) approximates North Italians. 
• Chalcolithic North Italian Ötzi (Iceman) is close to Sardinians but not quite the same ("more Basque" again).
• Iron Age Thracian commoner P 192-1 approximates Tuscans.
• I would ignore princely Thracian K8 because of the aforementioned contamination issues.

For completeness, I'm including here also fig. S1, which includes runs 1-8 of ADMIXTURE:

Fig S1- ADMIXTURE results for HGDP. Panels show the results for ADMIXTURE runs for k = 2 to k = 8 ancestral clusters on the HGDP individuals, and the corresponding cluster proportions inferred for the ancient samples.

Notice (see fig. S7) that K=3-5 are quite poor fits and therefore both should be ignored as meaningless. From K=6 onwards the scores slightly improve for all the ancient samples, however it must be said that K=2 is in general the best fit form most European populations, being most of the improvement in error score due to better approximation to West Asian samples. 

In most cases Basques have the lowest or one of the lowest fitness scores (except at K=5, where Basques are portrayed as a Russian-Sardinian mix, what is clearly a confounding artifact). Sardinians also have very low error scores but only from K=5 onwards, when the Sardinian component becomes apparent. The Iceman has very low error scores for all K values, while the Thracian samples have the greater ones, maybe owing to the lack of Balcanic samples.

For me these error results suggest that ancients are fine being just "unspecific Europeans" (K=2 blue), while the low error score for Basques and Sardinians surely underline that these are about the only modern populations which can be explained as simple Paleolithic-Neolithic mix, without need of a third Indoeuropean extra ancestry.

They also projected the ancient samples onto PCA plots of modern European populations:

Fig S2 - PCA results for HGDP. Panels show the results for PCA on the HGDP individuals for subsets of SNPs with data in the respective ancient sample. Each point represents an individual, with plot symbol and color indicating population of origin. The position of the ancient samples was inferred by projecting onto the PC space calculated using the modern samples only.

For some odd reason the PCAs are different in each case, even if the samples are the same (only moderns used, ancients are "projected" and should not affect the result). I have no explanation for this issue and I reckon I'm tempted to write to the authors asking for this unexpected complexity, which seems product of the projection itself altering the graph.

Whatever the case, the projection of the ancient samples, follows in general terms the patterns noted above for the ADMIXTURE graph:

• La Braña 1 projects between French and Basques.
• Ajv70 projects onto Orcadians, tending also towards France.
• Ötzi projects between Sardinians and Italians.
• Gok 4 with North Italians but not far from Basques.
• P 192-1 doesn't seem too akin to any specific modern population, although some French, Basques and Tuscans do approximate her.

These results may be frustrating for those already too accustomed to the previous analysis of ancient autosomal DNA but we must not forget that, because of its huge size and complexity, autosomal DNA requires statistical analysis, which is highly susceptible to variations in sample strategy particularly, as well as to other not always well understood factors. Hence different points of view are generally complementary rather that outright contradictory.

Of some interest is also this TreeMix graph of modern populations and Ötzi:

Figure 3. Results of TreeMix analysis of the Iceman with 1000G/Sardinia.
Shown are maximum-likelihood trees and the matrices of pairwise residuals (inset) for a model allowing (A) m = 0 and (B) m = 3 mixture events. Large positive values in the residual matrix indicate a poor fit for the respective pair of populations. Edges representing mixture events are colored according to weight of the inferred edge.

It is notable the African low level admixture arrow at the root of the Euro-Mediterranean branch (the so-called "Basal Eurasian" element in Lazaridis 2013) and the East Asian component in Finns. Also sizable admixture from the West Eurasian root is apparent among Tuscans. Once these admixture axes are allowed for, the topology of the European tree changes significantly, showing a main split between Eastern Europeans (Finns) and Western/Southern ones.

Other similar trees are available in fig. S6.

No extra Neanderthal admixture in Ötzi

Contrary to some previous rough estimates, Ötzi does not appear to differ from other Europeans in Neanderthal ancestry at all. See figs. S9 and S10.

First ever bronze was smelt in the Balcans

It seems that West Asia is losing a bit of its relevance as the origin of nearly every development. Much as the first steel is now known to have been made in Central Africa several centuries before the Hittites (or not: see update below), the first bronze ("tin bronze" to be specific) seems now to have been made in the Balcanic peninsula, more than a thousand years before it was in Mesopotamia.

Miljana Radivojevíc et al. Tainted ores and the rise of tin bronzes in Eurasia, c. 6500 years ago. Antiquity 87 (2013). Freely accessible → LINK

Abstract

The earliest tin bronze artefacts in Eurasia are generally believed to have appeared in the Near East in the early third millennium BC. Here we present tin bronze artefacts that occur far from the Near East, and in a significantly earlier period. Excavations at Plocnik, a Vinca culture site in Serbia, recovered a piece of tin bronze foil from an occupation layer dated to the mid fifth millennium BC. The discovery prompted a reassessment of 14 insufficiently contextualised early tin bronze artefacts from the Balkans. They too were found to derive from the smelting of copper-tin ores. These tin bronzes extend the record of bronze making by c. 1500 years, and challenge the conventional narrative of Eurasian metallurgical development.

The specific well-dated finding is from Plocnik, Southern Serbia, however as we can see in the map below, most 5th millenium bronze sites are from Bulgaria.

This highlights the likely central role in this earliest bronze metallurgy of the Karanovo-Gumelnita culture (very likely a full-fledged state older than dynastic Egypt), which spanned most of Bulgaria, as well as some nearby regions by the south and the north. However the neighbor cultures of Gradesnica-Krivodol (NW Bulgaria and nearby Romanian areas) and Vinca (Serbia) were also involved.

The highest quality alloys (stannite bronzes) belong to this core area of Thrace (Karanovo, Smjadovo and Bereketska Mogila), as well as Southern Serbian sites (Plocnic and Lazareva) while a second category, "high tin fahlore", seems to concentrate along the Danube (Gomolava and Ruse). A "low tin fahlore" category is rarer and seems centered in the Gradesnica area.

For some reason, maybe the disruptive Indoeuropean invasions of the 4th millennium, this technology was apparently lost later on, only to be regained from a West Asian source (Troy) already in the 3rd millennium.

An interesting question is the source of tin, which was in many cases the mineral stannite. The authors suggests further research on isotopes but also consider ancient mines that could have been sources:

Stannite is present in the Bronze Age mines of Mushiston in Tajikistan (Weisgerber & Cierny 2002), Deh Hosein in Iran (Nezafati et al. 2006), the Bolkardăg mining district in Turkey (Yener & ̈Ozbal 1987), as well as in Iberia (Rovira & Montero 2003).

The West and Central Asian mines are often argued not to have been sizable enough to be a major source of tin in the Bronze Age proper but, considering that this is a very early and limited bout of advanced metallurgy, I guess that they are also possible sources.


Update (Jan 22): I must (partly) take back my initial comment on steel metallurgy being older in Niger than Turkey: while the discovery of Nigerien steel-making c. 1500 BCE stands, other recent findings in Turkey seem to push back steel metallurgy in Anatolia to c. 1800 BCE (instead of the c. 1300 BCE date accepted before). Thanks to Aeolius for making us aware of this important detail.


Note: thanks to the Stone Pages newsletter ArcheoNews for directing me to this most interesting study.

Y-DNA survey of Bulgaria

Filling in a blank in the Y-DNA mapping of Europe comes this new paper:

Sena Karachanak et al., Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0056779]

Abstract

To better define the structure and origin of the Bulgarian paternal gene pool, we have examined the Y-chromosome variation in 808 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within the most informative haplogroups. We found that the Y-chromosome gene pool in modern Bulgarians is primarily represented by Western Eurasian haplogroups with ~ 40% belonging to haplogroups E-V13 and I-M423, and 20% to R-M17. Haplogroups common in the Middle East (J and G) and in South Western Asia (R-L23*) occur at frequencies of 19% and 5%, respectively. Haplogroups C, N and Q, distinctive for Altaic and Central Asian Turkic-speaking populations, occur at the negligible frequency of only 1.5%. Principal Component analyses group Bulgarians with European populations, apart from Central Asian Turkic-speaking groups and South Western Asia populations. Within the country, the genetic variation is structured in Western, Central and Eastern Bulgaria indicating that the Balkan Mountains have been permeable to human movements. The lineage analysis provided the following interesting results: (i) R-L23* is present in Eastern Bulgaria since the post glacial period; (ii) haplogroup E-V13 has a Mesolithic age in Bulgaria from where it expanded after the arrival of farming; (iii) haplogroup J-M241 probably reflects the Neolithic westward expansion of farmers from the earliest sites along the Black Sea. On the whole, in light of the most recent historical studies, which indicate a substantial proto-Bulgarian input to the contemporary Bulgarian people, our data suggest that a common paternal ancestry between the proto-Bulgarians and the Altaic and Central Asian Turkic-speaking populations either did not exist or was negligible.

Surely the most informative material is the haplogroup list (fig. 2, organized by pre-1999 provinces, in order to be as accurate as possible with the locality of paternal ancestry):

See ISOGG for the most up-to-date standard nomenclature

I find notable that the most common haplogroup seems to be I (27.6%) in all main variants: I1 (4.3%), I2a1b (20.2%) and I2a2a (1.7%), plus 0.4% I*. The only important missing clade is Western Mediterranean I2a1a. It reinforces my notion of I originating in SE Europe, Eastern Balcans or Ukraine maybe. Feel free to correct me if you think you know better anyhow. 

The second most common lineage is haplogroup E1b1b1 (M35), most of which belongs to E1b1b1a1b-V13 (18.1%), belonging to a local Balcan structure (although it is ultimately African, of course). This paper claims an Epipaleolithic origin for this Balcanic cluster, although experiencing Neolithic expansion. Not really surprised about this, I must say.

The third most notable haplogroup is R1a1a (17.5%), an Eastern European and Northern South Asian lineage with some spread in Central Asia as well. The authors remain cautious on this lineage's origins and dates of spread in wait of further phylogenetic resolution.

Within R1b (10.7%) the authors mention the relatively high frequency of R1b1a2a* (L23) at 5.2%. There is still some research to make in understanding the possible roots of R1b1a2 (M269) and its first sublayer R1b1ba2a (L23) in the Balcans (where both are important, at least relative to the frequencies of R1b in general) and in West Asia, where the highest diversity seems to be in Iran. I'm recycling here for the purpose of comparison a map I drew in 2010 (based on Myres et al., see here):

Notice that the nomenclature is a bit obsolete and that marker M529 was mistyped as M259

Haplogroup J2 (10.7%) is also important, while the presence of J1 is minor (3.4%), both in reasonable accordance with what is found in nearby populations. The authors attribute a Neolithic origin to the expansion of subclade J2b2 (M241) in the Balcans.

Less important are G (4.8%) and T (1.6%). Minimal presence exists of E(xE1b1b1) (0.4%), Q (0.4%) and C (0.5%). This last seems to reject any significant retaining of the presumable Turkic ancestry of the Bulgarian ethnicity (the original Bulgars were Turkic speakers, somehow related to the Huns). 

Wanted: volunteer archaeologists to dig Europe's oldest civilization

Tell Yunatsite in Southern Bulgaria was an important settlement of the Chalcolithic, in the context of an advanced culture that was older than Egypt or Troy. The place was settled in the seventh millennium (Neolithic) and destroyed by invaders at the end of the fifth millennium (Chalcolithic, Indoeuropean invasions), briefly resettled only to be evicted once again and left empty for a whole millennium. Later it was reoccupied in the late Bronze Age (Thracians) and continuously inhabited until the Middle Ages (when it may have been evacuated in the context of Slavic invasions). 

In brief: a whole slice of European late prehistory (and a bit of history also). In the words of the researchers:

In the seventh millenium BC the Balkan Peninsula was a gate through which farming, animal husbandry and generally Neolithisation spread to Europe from Anatolia and the Near East. App. 1000 years later in the very beginning of the fifth millennium BC prehistoric population in Central and Eastern Balkans turned known metal-processing technologies into an industry for the first time in human history (The World oldest copper mines are found near Rudna glava, Serbia and Mechi kladenets/Ai bunar near Stara Zagora, Bulgaria). Archaeological evidence shows that in the fifth millennium BC these prehistoric cultures enjoyed a constant raise of population and wealth meanwhile experiencing social stratification due the intensive trade with metal products, salt and other goods with the rest of prehistoric Europe and Asia. These Balkan Copper age cultures had all characteristics of the first civilizations including: the very first urban settlements in Europe (Tell Yunatsite, Durankulak and Provadia in Bulgaria), dense network of settlements, “industrial” proportions of production of goods, esp. metal products and salt, developed trade, distinguished social and professional stratification, pictograms and characters interpreted by some scholars as the World’oldest script (Gradeshnitsa tablet for instance dates back to the sixth or early fifth millennium BC) as well as precious artifacts made of gold, pottery, bone and stone (the World oldest gold treasure found in the Varna Copper age necropolis). This very first civilization in Europe was Pre-Indo-European and emerged for not more a millennium covering large parts of the Balkans, NW Anatolia and Eastern Europe. It collapsed around the end of the fifth millennium under the pressure of both drastic climatic changes and invasion of Early Indo-Europeans. The period of study of this very first civilization in Europe has been quite short - about 40 years have passed, since the excavation of the Varna Copper age necropolis brought to light the first certain evidences about its existence. Nowadays scholars from all over the World are still discovering new facts and adding new data about the “lost” first civilization in Europe.

They are looking for volunteers with an interest in archaeology and decent health for the campaign of summer 2013. Participation provides credits for university students.

More information on the relevant Prehistory and the volunteer program at Balcan Heritage.

Claim oldest European 'city' in Bulgaria

From Pileta de Prehistoria

According to the Sophia Globe (h/t Pileta), the oldest ever city in Europe would have been located at Provadia (Varna province, Bulgaria).

The city is defined as such by medieval standards because it is a settlement surrounded by a wall, a very thick and solid one. However only a few hundred people (300-350) lived inside them, always according to Prof. Vassil Nikolov.

Nikolov attributes the city an age of 4700-4200 BCE, belonging to the context of Varna culture and related to the relatively well known Varna necropolis, probably the first princely burial of the continent.

However such an early age places the Provadia-Solnitsata city almost two millennia before any other known European city (Greek islands, Southern Iberia) and even 1500 years before Troy I, traditionally considered a major influence in the urbanization and Bronze Age of Europe.

Not even Egypt's civilization is nearly as old; in all the wider region only some fortified cities from the Levant and Mesopotamia are as old and, excluding Jericho (c. 6800 BCE), none is significantly older. Even the oldest known Sumerian city, Eridu, was built only a few centuries before this Bulgarian city.

For more details, read the abstract (PDF) of Nikolov's study (to be published?, where?)

Looking for more information on the matter I also stumbled upon this webpage by Dr. L. Nikolova, which discusses the Provadia settlement as a salt-exporting site, something that also seems to be the leit motif of Nikolov's abstract.

Discussion

I am not really surprised by these findings because it has been known for some time that the area of Bulgaria was a very old center of civilization, comparable in age to Egypt (or, as it seems to be the case now, even quite older), probably evolving state and aristocracy structures first of all in Europe. It was probably the wealth of this realm and its successors which baited the Indoeuropean nomads into invasion later on (economic relations with the Volga are attested as early as this time). 

The only thing that really puzzles me is the age because when I first learned on these matters the time-frame appeared to be a thousand years more recent, more in agreement with other urbanizing and social-complexity developments elsewhere in Europe (Aegean, Iberia), Western Anatolia (Troy) and also Africa (Egypt). But well... I have to accept the dates estimated by the researchers, I just wish I knew a bit more about how these have been produced.


Update (Oct 10): photos and considerations on burial styles

Terrae Antiquae[es] has now a very extensive photo-gallery, of which I borrowed the following:

I must say that unlike the Varna necropolis burial which I initially used to illustrate the news, the burials shown here appear to be of the classical Neolithic flexed style (the lower part may be missing but the size of the pit and lateral deposition strongly suggest that.

I'm not just inferring from that and another photo but it was actually the burial style of all Balcano-Danubian Neolithic peoples and even some "Danubianized" Indoeuropeans later on: flexed lateral burial, so it is what should be expected in this context.

The extended position is actually typical of Paleolithic Continuity peoples, and the use of ochre is specially documented in Eastern Europe: Dniepr-Don Neolithic and related groups like Pitted Ware and the Early Bronze culture of Ezero also in Bulgaria but thousands of years after these layers.

At the Varna museum site however they do explain that the burials in what was surely a royal or otherwise princely necropolis are of two kinds: (a) 99 burials (mostly men) are in extended position (Paleolithic tradition), while other 67 (many of them women) lay on their right side in flexed position (Neolithic tradition).

This could point (my best guess here) to early penetrations from the steppe (Dniepr-Don culture), comparable maybe to those we see around the Baltic (Pitted Ware), all however anticipating and maybe preparing the way for what is probably the true Indoeuropean penetration of the Kurgan wave of cultures, which in most cases would return to the flexed burials... now in kurgan (tumulus).

However in Bulgaria the period of Kurgan invasions culminates in the formation of Ezero culture, which is the only one retaining extended burial with ochre, by that time already vanishing in the steppe and the Baltic.