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

Looking forward to a post-Covid world

I was hoping that the Covid-19 pandemic wouldn't have an immediate impact on the publication of ancient DNA papers and new data, but considering how much things have slowed down in this respect, it seems that I was fooling myself.

So let's take a break until early next year, and then see what happens.

Trust me, we've got a lot to look forward to in the post-Covid-19 world. Based on what I've heard from various sources, here are some predictions about what we might see:

- the search for the Proto-Indo-European homeland will shift west to the North Pontic steppe

- on the other hand, the search for the Proto-Uralic homeland will move deep into Siberia

- the key role of the Single Grave (westernmost Corded Ware) culture in the population history of Western Europe will finally get some attention

- following on from the above, Y-haplogroup R1b-L51 will be revealed as a Single Grave marker

- the idea that the Pontic-Caspian steppe was colonized by migrants from Mesopotamia during the Bronze Age will be forgotten, and, ironically, we'll instead learn that there was a significant influx of steppe ancestry into ancient Mesopotamia

- Old Kingdom Egyptians will come out less Sub-Saharan African than present-day Egyptians.

I probably shouldn't blab everything out, so that's all you're getting from me for now. You'll just have to wait for the rest until next year, or perhaps even the year after that.

See also...

Domestic horses were introduced into Anatolia and Transcaucasia during the Bronze Age (Guimaraes et al. 2020)

Over at Science Advances at this LINK. This is a very important paper because it basically eliminates West Asia as the source of the modern domestic horse lineage, which leaves the Pontic-Caspian steppe in Eastern Europe as the only viable option.

It also corroborates the linguistic theory that the Proto-Indo-European homeland was located on the Pontic-Caspian steppe. That's because the horse is a key animal in the Proto-Indo-European pantheon, and it appears in Indo-European mythology in intricate roles. This suggests that the speakers of Proto-Indo-European weren't just familiar with the horse but also managed to domesticate it. From the paper:

Abstract: Despite the important roles that horses have played in human history, particularly in the spread of languages and cultures, and correspondingly intensive research on this topic, the origin of domestic horses remains elusive. Several domestication centers have been hypothesized, but most of these have been invalidated through recent paleogenetic studies. Anatolia is a region with an extended history of horse exploitation that has been considered a candidate for the origins of domestic horses but has never been subject to detailed investigation. Our paleogenetic study of pre- and protohistoric horses in Anatolia and the Caucasus, based on a diachronic sample from the early Neolithic to the Iron Age (~8000 to ~1000 BCE) that encompasses the presumed transition from wild to domestic horses (4000 to 3000 BCE), shows the rapid and large-scale introduction of domestic horses at the end of the third millennium BCE. Thus, our results argue strongly against autochthonous independent domestication of horses in Anatolia.

Guimaraes et al., Ancient DNA shows domestic horses were introduced in the southern Caucasus and Anatolia during the Bronze Age, Science Advances 16 Sep 2020: Vol. 6, no. 38, eabb0030, DOI: 10.1126/sciadv.abb0030

See also...

The precursor of the Trojans

Who remembers kum4 from Omrak et al. 2016? I'm pretty sure now that this individual packs a lot of ancestry from the Pontic-Caspian (PC) steppe.

If so, that's a big deal, because her Chalcolithic (or Late Neolithic?) burial was located at Kumtepe. That is, in the same part of Anatolia as the later settlement of Troy, which may have been founded by early Anatolian speakers from Eastern Europe (see here).

The qpAdm mixture models below, featuring kum4 and the likely older kum6, also from Kumtepe, are based on qpfstats output. qpfstats is a new program from the David Reich Lab specifically designed to help analyze low coverage ancients (see here). And kum4 is certainly that.

TUR_Kumtepe_N_kum4
RUS_Progress_En 0.383±0.114
TUR_Barcin_N 0.617±0.114
chisq 7.868
tail prob 0.247957
Full output

TUR_Kumtepe_N_kum4
IRN_Seh_Gabi_C 0.325±0.150
TUR_Barcin_N 0.675±0.150
chisq 14.736
tail prob 0.0224096
Full output

TUR_Kumtepe_N_kum6
RUS_Progress_En 0.121±0.042
TUR_Barcin_N 0.879±0.042
chisq 21.790
tail prob 0.00132149
Full output

TUR_Kumtepe_N_kum6
IRN_Seh_Gabi_C 0.283±0.059
TUR_Barcin_N 0.717±0.059
chisq 6.289
tail prob 0.391566
Full output

Indeed, kum4 and kum6 offer just ~10,000 and ~100,000 "valid SNPs", respectively (see here). However, if nothing else, the results are clearly not random.

For one, because they fit the expected pattern, with the likely older individual lacking ancestry from the PC steppe (her model with RUS_Progress_En shows a weak statistical fit). Moreover, the qpAdm mixture ratios align almost perfectly with the results in my Principal Component Analysis (PCA) of ancient West Eurasian genetic variation. Coincidence?

See also...

Perhaps a hint of things to come

Perhaps a hint of things to come

It's still a mystery how the Hittites and other Anatolian speakers ended up in the Near East. However, the leading theory is that their ancestors migrated from the steppes of Eastern Europe to western Anatolia via the Balkans sometime during the Copper Age.

Consider the qpAdm mixture models below, made possible thanks to some of the ancient samples published recently along with Skourtanioti et al. 2020. The key ancients are described in a text file available here.

TUR_Barcin_C
AZE_Caucasus_lowlands_LN 0.471±0.094
RUS_Vonyuchka_En 0.148±0.040
TUR_Barcin_N 0.381±0.069
chisq 12.874
tail prob 0.116261
Full output

TUR_Barcin_C
RUS_Vonyuchka_En 0.107±0.029
TUR_Buyukkaya_EC 0.893±0.029
chisq 12.107
tail prob 0.207331
Full output

I'd say it's quite clear now that TUR_Barcin_C harbors minor ancestry from the Pontic-Caspian (PC) steppe. The reason this isn't widely accepted yet is because demonstrating it convincingly hasn't been possible without a proximate Anatolian ancestry source for TUR_Barcin_C, precisely like TUR_Buyukkaya_EC.

Admittedly, though, the statistical fits in my models aren't all that great. I suspect the problem lies with RUS_Vonyuchka_En, which is likely to be a rather poor stand in for the people who brought steppe ancestry, and possibly early Anatolian speech, to western Anatolia.

So let's see what happens when I try a more proximate reference for the steppe ancestry in TUR_Barcin_C. How about Yamnaya_BGR, an individual of mixed Balkan and steppe origin from what is now Bulgaria?

TUR_Barcin_C
AZE_Caucasus_lowlands_LN 0.518±0.075
TUR_Barcin_N 0.203±0.056
Yamnaya_BGR 0.279±0.067
chisq 10.602
tail prob 0.225269
Full output

TUR_Barcin_C
TUR_Buyukkaya_EC 0.749±0.058
Yamnaya_BGR 0.251±0.058
chisq 9.687
tail prob 0.376414
Full output

That's a little better. Unfortunately, the problem now is that the models are anachronistic, because TUR_Barcin_C is about a thousand years older than Yamnaya_BGR. Clearly, we need more Copper Age samples from the western edge of the PC steppe, the eastern Balkans, and especially northwestern Anatolia.

The Principal Component Analysis (PCA) below effectively illustrates why my qpAdm models work. It was produced with Global25 data using the Vahaduo PCA tools freely available here. Note that TUR_Barcin_C is shifted away from the essentially perfect cline formed by AZE_Caucasus_lowlands_LN, TUR_Barcin_N and TUR_Buyukkaya_EC towards samples from ancient Eastern Europe, including Yamnaya_BGR.

See also...

Steppe invaders in the Bronze Age Balkans

Evidence of European ancestry in the Philistines

The abstract below has just appeared at the European Nucleotide Archive (see here), so I'm guessing that the relevant paper and accompanying ancient genome-wide data will be published within weeks if not days. Emphasis is mine:

The ancient Mediterranean port-city of Ashkelon, identified as “Philistine” during the Iron Age, underwent a dramatic cultural change between the Late Bronze- and the early Iron- Age. It has been long debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called “Sea Peoples”. Here, we report genome-wide data of ten Bronze- and Iron- Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European related admixture. Interestingly, this genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze- to Iron- Age transition in Ashkelon but did not leave a long-lasting genetic signature.

Update 4/7/2019: The paper is now available at Science Advances [LINK]. One of the Ashkelon ancients, who also shows a relatively high level of European ancestry, belongs to Y-Chromosome haplogroup R1 (probably R1b-M269). I've updated my Global25 datasheets with the new samples. Look for the Levant_ISR_Ashkelon prefix. Same links as always...

Global25 datasheet ancient scaled

Global25 pop averages ancient scaled

Global25 datasheet ancient

Global25 pop averages ancient

This is how they cluster in my Principal Component Analysis (PCA) of ancient West Eurasian genetic variation. The relevant datasheet is available here. Based on these results, it's tempting to think that the European ancestry in the Philistines may have been of Greek provenance. But keep in mind that this is just a two dimensional view and a simplification of reality. I'll have more to say about the ancestry of these individuals and the origins of the Philistines in future blog posts.

See also...

Five foot Philistines

How did steppe ancestry spread into the Biblical-era Levant?

Catacomb > Armenia_MLBA

It's now clear, thanks to ancient DNA, that Transcaucasia and surrounds were affected by multiple, and at times significant, population movements from Eastern Europe during the Chalcolithic and Bronze Age periods. Based on the ancient samples from what is now Armenia, I'd say that this process peaked during the Middle Bronze Age. But who exactly were the people who perhaps swarmed south of the Caucasus at this time?

The most likely suspects are the various groups that occupied the southernmost parts of the Pontic-Caspian steppe throughout the Bronze Age. They were associated with the so called Catacomb, Kubano-Tersk and Yamnaya archeological cultures. Below is a Principal Component Analysis (PCA) that compares samples from these cultures with those from Middle to Late Bronze Age Armenia (labeled Armenia_MLBA). The relevant datasheet is available here.

Note that Armenia_MLBA forms a cline that appears to be stretching out towards the Catacomb, Kubano-Tersk, Yamnaya and other Bronze Age steppe groups, and this suggests that it harbors significant and probably recent steppe-related ancestry. But PCA plots based on just two dimensions of genetic variation can be misleading at times, so let's check this out with some formal mixture models using qpAdm.

Armenia_MLBA
Catacomb 0.234±0.028
Kura-Araxes_Kaps 0.766±0.028
chisq 10.723
tail prob 0.826248
Full output

Armenia_MLBA
Kubano-Tersk 0.254±0.030
Kura-Araxes_Kaps 0.746±0.030
chisq 13.535
tail prob 0.633284
Full output

Armenia_MLBA
Kura-Araxes_Kaps 0.768±0.028
Yamnaya_Kalmykia 0.232±0.028
chisq 14.454
tail prob 0.564954
Full output

Armenia_MLBA
Kura-Araxes_Kaps 0.762±0.029
Yamnaya_Caucasus 0.238±0.029
chisq 15.916
tail prob 0.458816
Full output

All of these models are statistically very sound, and even though I ranked the results by "tail prob", there's nothing in the output that clearly points to any one of the southern steppe groups as the obvious source of the steppe-related ancestry in Armenia_MLBA. But, interestingly, Catacomb tops the ranking, and it probably also makes the most sense based simply on Carbon-14 chronology. So, for now, I'm going with Catacomb.

I didn't get a chance yet to investigate this issue in detail with the Global25. Does it contradict the results from my PCA and qpAdm analyses? If anyone reading this would like to take a close look that'd be great. Feel free to post your findings in the comments below. And if the answer is indeed Catacomb, then what language did these Catacomb-derived migrants, or perhaps invaders, speak? If not proto-Armenian then what?

By the way, please be aware that the Kubano-Tersk samples in my analyses are the same individuals as those featured in Wang et al. 2019 under the label "North Caucasus".

See also...

Early chariot drivers of Transcaucasia came from...

Likely Yamnaya incursion(s) into Northwestern Iran

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