The Yassitepe challenge

This is about the only successful qpAdm model that I can find for the pair of Early Bronze Age (EBA) females from Yassitepe, Turkey, using a decent set of outgroups and markers. I wouldn't take it too literally, but it does suggest a potentially significant level of European ancestry, including some steppe ancestry, in these Yassitepe individuals.

TUR_Aegean_Yassitepe_EBA
AZE_Caucasus_lowlands_LN 0.565±0.054
ROU_N 0.387±0.041
RUS_Progress_En 0.048±0.022
P-value 0.103248
Full output

If anyone reading this can find a better, more convincing solution then I'd love to see it. Feel free to share it in the comments below.

Obviously, both of the Yassitepe samples are from the recent Lazaridis, Alpaslan-Roodenberg et al. paper. Their EBA dating suggests that they might be relevant to the debate over the origins of Anatolian speakers, such as the Hittites and Luwians.

See also...

Dear Iosif, about that ~2%

The precursor of the Trojans

The genomic formation of modern Balkan peoples (Olalde et al. 2021 preprint)

Over at bioRxiv at this LINK. This preprint deals with some very complex issues, so I can't say much about it until I have a good look at the relevant genotype data. However, for now, my impression is that the authors have oversimplified the genetic origins of most Balkan peoples.

For instance, they model the present-day Greek population as a two way mixture between ancient Greeks from a Greek colony in Iberia and present-day Mordovians. The Mordovians are basically a proxy for the Slavs who moved into the Balkans during the Medieval period.

However, the problem is that, strictly speaking, this isn't a historically plausible model, because Mordovians are actually a Uralic-speaking group from the Volga region with significant Siberian ancestry. Needless to say, it's extremely unlikely that anyone like them had an appreciable impact on the present-day Greek gene pool.

So instead I'd like to see the authors try three-way and four-way models with ancients from Mycenae, Anatolia and some places (well to the west of the Volga River) likely to have been inhabited by early Slavs.

Feel free to let me know what you think about this preprint in the comments below. Here's the abstract:

The Roman Empire expanded through the Mediterranean shores and brought human mobility and cosmopolitanism across this inland sea to an unprecedented scale. However, if this was also common at the Empire frontiers remains undetermined. The Balkans and Danube River were of strategic importance for the Romans acting as an East-West connection and as a defense line against “barbarian” tribes. We generated genome-wide data from 70 ancient individuals from present-day Serbia dated to the first millennium CE; including Viminacium, capital of Moesia Superior province. Our analyses reveal large scale-movements from Anatolia during Imperial rule, similar to the pattern observed in Rome, and cases of individual mobility from as far as East Africa. Between ∼250-500 CE, we detect gene-flow from Central/Northern Europe harboring admixtures of Iron Age steppe groups. Tenth-century CE individuals harbored North-Eastern European-related ancestry likely associated to Slavic-speakers, which contributed >20% of the ancestry of today’s Balkan people.

Olalde et al., Cosmopolitanism at the Roman Danubian Frontier, Slavic Migrations, and the Genomic Formation of Modern Balkan Peoples, bioRxiv, posted August 31, 2021, doi: https://doi.org/10.1101/2021.08.30.458211

See also...

A Greek tragedy

A Greek tragedy

I wasn't going to blog about the Clemente et al. "Aegean palatial civilizations" paper, because I think that it's a rather strange effort overall. But apparently a lot of people want to know my thoughts on the topic, so here goes.

If you download the relevant PDF file (here) and do a search for "Slav", you'll see that the word doesn't even appear in the bibliography. How is that possible, considering the massive impact that the Slavs had on the Balkans, including Greece, during the Middle Ages?

Indeed, here's a quote from page 12 of the PDF: "Present-day Greeks - who also carry Steppe-related ancestry - share ~90% of their ancestry with MBA northern Aegeans, suggesting continuity between the two time periods."

That's a very optimistic view. In fact, there's no evidence whatsoever in the paper that there's even 1% genetic continuity between present-day Greeks and any ancient Greek population, let alone the MBA northern Aegeans.

The genetic impact of Medieval Slavic migrations on most present-day Greek populations is easy to see. For instance, below are several linear models based on D-statistics of the form D(Outgroup,Test;Ancient1,Ancient2). You don't need a PhD in mathematics to understand them. The relevant data file is available here.

Note that most of the present-day Greek groups cluster together, and they also form fairly neat clines with the other Greeks, as well as Cypriots, other Balkan populations, including those speaking Slavic languages, and also the Slavic-speaking Ukrainians. On the other hand, they don't overlap with any of the ancient groups from Greece and surrounds, nor do they generally form obvious clines with them.

To me this suggests that most present-day Greeks harbor significant levels of Slavic ancestry and some sort of recent Cypriot-related ancestry, and in large part they're only coincidentally similar to ancient Aegeans, including those from the MBA (labeled Greece_Helladic_MBA in my graphs).

And let me assure you that no matter which ancient populations you run in such D-stats, you'll always see similar present-day Greek clusters and present-day Balkan clines.

Obviously, it's fair enough to assume that there's been some genetic continuity in the Aegean from the Iron Age, Bronze Age, and even the Copper Age and Neolithic era to the present-day. But the point I'm making is that no one has yet proved this, or even attempted to measure it properly.

See also...

Greek confirmation bias

Armenians vs Georgians

Armenians and Georgians are ethnic groups that live side by side in the south Caucasus, or Transcaucasia. By all accounts, they've both been there since prehistoric times and they're very similar in terms of overall genetic structure.

However, they speak languages from totally unrelated families: Indo-European and Kartvelian, respectively. How did this happen and might the answer lie in the small genetic differences that do exist between them?

To investigate this issue, I ran a series of qpAdm formal mixture models of present-day Armenians and Georgians using tens of ancient reference populations. To come up with as straightforward and meaningful results as possible, I constrained myself to two-way models. I then discarded the runs that produced "tail probs" under 0.1 and retained less than 400K SNPs. Only a handful of models passed muster, including these two:

Armenian
Mycenaeans_&_Empuries2 0.233±0.041
Kura-Araxes_Kaps 0.767±0.041
chisq 18.422
tail prob 0.142151
Full output

Georgian
Globular_Amphora 0.071±0.025
Kura-Araxes_Kaps 0.929±0.025
chisq 18.419
tail prob 0.142266
Full output

At the most basic level, the results suggest that both Armenians and Georgians are overwhelmingly derived from populations of Bronze Age Transcaucasia associated with the Kura-Araxes archeological culture, albeit with minor ancestries from somewhat different sources from the west. As far as I can see, when using more than 400K SNPs and a wide range and large number of outgroups (or right pops), neither Armenians nor Georgians can pass perfectly for any one ancient population in my dataset.

The best proxies for the minor but significant western ancestry in Armenians are Mycenaeans of the Bronze Age Aegean region and Greek colonists from Iron Age Iberia (Empuries2). Obviously, and perhaps importantly, these are both attested Indo-European-speaking groups. On the other hand, the very minor western ancestry in Georgians is best characterized as gene flow from Middle to Late Neolithic European farmers rich in indigenous European forager ancestry. It's practically impossible to say what language or languages these farmers spoke. How about something Kartvelian?

In any case, for me, the perplexing thing about present-day Armenians is that they harbor very little steppe ancestry. By and large, no more than a few per cent. Compare that to the currently available samples from what is now Armenia dating to the Middle to Late Bronze Age, which show ratios of steppe ancestry of up to 25%. For now, I'm guessing that what we're dealing with here is the classic bounce back of older ancestry layers that has been documented for different parts and periods of prehistoric Europe.

See also...

Early chariot drivers of Transcaucasia came from...

Catacomb > Armenia_MLBA

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

A Mycenaean and an Iron Age Iranian walk into a bar...

What do they have in common? The same type of Near Eastern ancestry? From Iran? Nope, that's a joke. Obviously, they share the same type of steppe ancestry. This probably has some very important linguistic implications.

The relevant Principal Component Analysis (PCA) datasheet is available here. Below are two pairs of formal mixture models that support my inferences from the PCA.

Mycenaean
Srubnaya_MLBA 0.266±0.029
Tepecik_Ciftlik_N 0.734±0.029
taildiff: 0.588000631
Full output

Mycenaean
Minoan_Lasithi 0.790±0.023
Srubnaya_MLBA 0.210±0.023
taildiff: 0.187709803
Full output

...

Turkmenistan_IA
Namazga_CA 0.528±0.040
Srubnaya_MLBA 0.472±0.040
taildiff: 0.561330411
Full output

Turkmenistan_IA
Dzharkutan1_BA 0.530±0.037
Srubnaya_MLBA 0.470±0.037
taildiff: 0.485083377
Full output

But seriously, what's the direct link between populations like Tepecik_Ciftlik_N/Minoan_Lasithi and Namazga_CA/Dzharkutan1_BA, except some exceedingly distant farmer ancestry from the Fertile Crescent?

See also...

An early Iranian, obviously

Graeco-Aryan parallels

Yamnaya isn't from Iran just like R1a isn't from India

Steppe admixture in Mycenaeans, lots of Caucasus admixture already in Minoans (Lazaridis et al. 2017)

Over at Nature at this LINK. Why is the presence of steppe admixture in Mycenaeans important? And why does it matter if the Minoans already had a lot of ancestry from the Caucasus or surrounds? Because Mycenaeans were Indo-Europeans and Minoans weren't. I'm still reading the paper and will update this entry regularly over the next few days. Below is the abstract and, in my opinion, a key quote. Emphasis is mine.

The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We have assembled genome-wide data from 19 ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. Here we show that Minoans and Mycenaeans were genetically similar, having at least three-quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean [1, 2], and most of the remainder from ancient populations related to those of the Caucasus [3] and Iran [4, 5]. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter–gatherers of eastern Europe and Siberia [6, 7, 8], introduced via a proximal source related to the inhabitants of either the Eurasian steppe [1, 6, 9] or Armenia [4, 9]. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the Early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.

...

The simulation framework also allows us to compare different models directly. Suppose that there are two models (Simulated1, Simulated2) and we wish to examine whether either of them is a better description of a population of interest (in this case, Mycenaeans). We test f4(Simulated1, Simulated2; Mycenaean, Chimp), which directly determines whether the observed Mycenaeans shares more alleles with one or the other of the two models. When we apply this intuition to the best models for the Mycenaeans (Extended Data Fig. 6), we observe that none of them clearly outperforms the others as there are no statistics with |Z|>3 (Table S2.28). However, we do notice that the model 79%Minoan_Lasithi+21%Europe_LNBA tends to share more drift with Mycenaeans (at the |Z|>2 level). Europe_LNBA is a diverse group of steppe-admixed Late Neolithic/Bronze Age individuals from mainland Europe, and we think that the further study of areas to the north of Greece might identify a surrogate for this admixture event – if, indeed, the Minoan_Lasithi+Europe_LNBA model represents the true history.

Lazaridis, Mittnik et al., Genetic origins of the Minoans and Mycenaeans, Nature, Published online 02 August 2017, doi:10.1038/nature23310

Update 03/08/2017: This is my own Principal Component Analysis (PCA) of the Minoan and Mycenaean samples, which are freely available at the Reich Lab website here. The Armenian angle for the eastern admixture in Mycenaeans looks forced. The trajectory of this admixture obviously runs from Northern or Eastern Europe to the Minoans. If it did arrive from Armenia, then realistically only via a heavily steppe-admixed population. Right click and open in a new tab to enlarge:

Update 05/08/2017: Much like Lazaridis et al., I ran a series to qpAdm analyses to find the best mixture model for the Mycenaeans. However, just to see what would happen, unlike Lazaridis et al., I didn't group any of the archaeological populations into larger clusters based on their genetic affinities. The three models below stood out from the rest in terms of their statistical fits.

Mycenaean
Minoan_Lasithi 0.786±0.049
Sintashta 0.214±0.049
taildiff: 0.96574059
chisq: 6.030
Full output

Mycenaean
Corded_Ware_Germany 0.210±0.043
Minoan_Lasithi 0.790±0.043
taildiff: 0.961238695
chisq: 6.198
Full output

Mycenaean
Minoan_Lasithi 0.791±0.043
Srubnaya 0.209±0.043
taildiff: 0.950419642
chisq: 6.558
Full output

So it's essentially the same outcome as the one obtained by Lazaridis et al., because Sintashta and Srubnaya are part of their Steppe_MLBA cluster, while Corded Ware is part of their Europe_LNBA cluster, and it's these clusters that, along with Minoan_Lasithi, provided their most successful mixture models for the Mycenaeans. But it's nice to see Sintashta at the top of my results, because it fits so well with the long postulated archaeological links between Sintashta and the Mycenaeans (for instance, see here).

By the way, here's what I said back in May when the Mathieson et al. 2017 preprint came out (see here). So things are falling into place rather nicely.

The same paper also includes the following individual from present-day Bulgaria dated to the start of the Late Bronze Age (LBA), which is roughly when the Mycenaeans appeared nearby in what is now Greece:

Bulgaria_MLBA I2163: Y-hg R1a1a1b2 mt-hg U5a2 1750-1625 calBCE

This guy is the most Yamnaya-like of all of the Balkan samples in Mathieson et al. 2017, and, as far as I can see based on his overall genome-wide results, probably indistinguishable from the contemporaneous Srubnaya people of the Pontic-Caspian steppe. He also belongs to Y-haplogroup R1a-Z93, which is a marker typical of Srubnaya and other closely related steppe groups such as Andronovo, Potapovka and Sintashta. So there's very little doubt that he's either a migrant or a recent descendant of migrants to the Balkans from the Pontic-Caspian steppe.

See also...

A Mycenaean and an Iron Age Iranian walk into a bar...

Main candidates for the precursors of the proto-Greeks in the ancient DNA record to date

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...