Slavs have little, if any, Scytho-Sarmatian ancestry

Here's an abstract of a new study from the David Reich Lab about ancient Slavs, titled "Genetic identification of Slavs in Migration Period Europe using an IBD sharing graph". Emphasis is mine:

Popular methods of genetic analysis relying on allele frequencies such as PCA, ADMIXTURE and qpAdm are not suitable for distinguishing many populations that were important historical actors in the Migration Period Europe. For instance, differentiating Slavic, Germanic, and Celtic people is very difficult relying on these methods, but very helpful for archaeologists given a large proportion of graves with no inventory and frequent adoption of a different culture. To overcome these problems, we applied a method based on autosomal haplotypes. Imputation of missing genotypes and phasing was performed according to a protocol by Rubinacci et al. (2021), and IBD inference was done for ancient Eurasian individuals with data available at >600,000 1240K sites. IBD links for a subset of these individuals were represented as a graph, visualized with a force-directed layout algorithm, and clusters in this graph are inferred with the Leiden algorithm. One of the clusters in the IBD graph emerged that includes nearly all individuals in the dataset annotated archaeologically as “Slavic”. According to PCA a hypothesis for the origin of this population can be proposed: it was formed by admixture of a Baltic-related group with East Germanic people and Sarmatians or Scythians. The individuals belonging to the “Slavic” IBD sharing cluster form a chronological gradient on the PCA plot, with the earliest samples close to the Baltic LBA/EIA group. Later “Slavic” individuals are shifted to the right, closer to Central and Southern Europeans and probably reflecting further admixture of Slavs with local populations during the Migration Period.

Apparently this abstract is causing a bit of confusion online because of the mention of possible Sarmatian or Scythian ancestry in Slavs.

However, it's important to understand that the authors are referring to certain Slavic or even just Slavic-related individuals, usually from culturally heterogeneous frontier settlements deep in what is now Russia.

So yes, it's possible that some of these individuals carry Sarmatian, Scythian or other exotic eastern ancestry. But even if this is true, then obviously we can't extend this inference to all ancient and modern-day Slavs.

Indeed, below is a G25/Vahaduo Principal Component Analysis (PCA) that shows why modern-day Slavic speakers can't be linked genetically to Sarmatians or Scythians. To experience a more detailed version of the PCA paste the data here into the relevant field here.

As you can see, dear reader, most of the Slavs (Belarusians, Poles, Ukrainians and many Russians) cluster with the Irish near the western end of the plot.

Some Russians are shifted significantly east of them along the "Uralic cline" and, as a result, they cluster with various Uralic speakers such as Mordovians. That's because when Slavs migrated deep into what is now northern Russia they mixed with Uralic speakers who were there before them.

Most of the Sarmatians and Scythians form a cluster southeast of the Slavs and Irish because they carry significant levels of East Asian ancestry. This type of eastern ancestry is basically missing in modern-day Slavs (see here).

Several of the Scythians cluster among the Slavs and Irish, but that's because they're genetic outliers, whose existence, if anything, suggests that some Scythians had significant Slavic-related and/or Irish-related ancestry.

Now, even though most of the Slavs do cluster with the Irish in the above PCA plot, I strongly disagree with the authors of the abstract when they claim that "differentiating Slavic, Germanic, and Celtic people is very difficult" with PCA. It's actually pretty damn easy and I've been doing it successfully for many years. For instance, see here.

See also...

Wielbark Goths were overwhelmingly of Scandinavian origin

The Caucasus is a semipermeable barrier to gene flow

Dear Sandra, Wolfgang...a problem

In their recent paper, titled Early contact between late farming and pastoralist societies in southeastern Europe, Penske et al. make the following claim:

By contrast, Yamnaya Caucasus individuals from the southern steppe can be modelled as a two-way model of around 76% Steppe Eneolithic and 26% Caucasus Eneolithic/Maykop, confirming the findings of Lazaridis and colleagues 47. This two-way mix (40% + 60%, respectively) also provides a well-fit model (P = 0.09) for the Ozera outlier individual, consistent with the position in PCA and corroborating an influence from the Caucasus.

Err, nope.

The Ozera Yamnaya outlier, a female dated to 3096-2913 calBCE, is, in fact, a ~50/50 mix between standard Yamnaya and Late Maykop. It's a result that is totally unambiguous.

There are a number of ways to demonstrate this fact. For example, with the qpAdm software that was also used by Penske et al., except with different outgroups or right pops. Please note that in my dataset the Ozera outlier is labeled Ukraine_Ozera_EBA_Yamnaya_o.

right pops:
Cameroon_SMA
Levant_N
Iran_GanjDareh_N
Iran_C_SehGabi
Georgia_HG
Turkey_N
Serbia_IronGates_Mesolithic
Russia_WestSiberia_HG
Russia_Karelia_HG
Latvia_HG
Russia_Boisman_MN
Brazil_LapaDoSanto_9600BP

Ukraine_Ozera_EBA_Yamnaya_o
Russia_Caucasus_EneolithicMaykop 0.554±0.031
Russia_Steppe_Eneolithic 0.446±0.031
P-value 0.00109868 (FAIL)

Ukraine_Ozera_EBA_Yamnaya_o
Russia_LateMaykop 0.512±0.035
Russia_Samara_EBA_Yamnaya 0.488±0.035
P-value 0.462447 (PASS)

I can also do it with the Global25/Vahaduo method. And you, dear reader, can too, by putting the Target and Source Global25 coords from the text file here into the relevant fields here.

Target: Ukraine_Ozera_EBA_Yamnaya_o
Distance: 2.9292% / 0.02929202
50.6 Russia_Samara_EBA_Yamnaya
49.4 Russia_Caucasus_LateMaykop
0.0 Russia_Caucasus_EneolithicMaykop
0.0 Russia_Steppe_Eneolithic

Moreover, here's a self-explanatory Principal Component Analysis (PCA) plot that illustrates why my Late Maykop/Samara Yamnaya combo is much better than the reference populations used by Penske and colleagues. It was done with the PCA tools here.

I'm pointing this out for two main reasons. First of all, this is a fairly obvious mistake that should've been avoided, especially considering the level of expertise and experience among the authors (such as Wolfgang Haak and Johannes Krause).

Secondly, it's important to understand that the Ozera outlier comes out almost exactly 50% Samara Yamnaya because the standard Yamnaya genotype already existed well before she was alive, and thus she cannot be used to corroborate any sort of influence from the Caucasus in the formation of the mainstream Yamnaya population.

As for the Yamnaya Caucasus individuals, I don't know why Penske et al. attempted to model their ancestry as a group, because they don't form a coherent genetic cluster. RK1001 and ZO2002 are fairly similar to standard Yamnaya samples, while RK1007 and SA6010 resemble Eneolithic steppe samples from the Progress burial site. This is what happens when I try to reproduce the Penske et al. model with my outgroups.

Russia_Caucasus_EBA_Yamnaya
Russia_Caucasus_EneolithicMaykop 0.187±0.019
Russia_Steppe_Eneolithic 0.813±0.019
P-value 4.15842e-06 (HARD FAIL)

Oh, and Penske et al. modeled the ancestry of mainstream Yamnaya as a three-way mixture with Steppe Eneolithic, Caucasus Eneolithic/Maykop and Ukraine Neolithic (or Ukraine N). They succeeded, but with my outgroups it's another hard fail.

Russia_Samara_EBA_Yamnaya
Russia_Caucasus_EneolithicMaykop 0.177±0.017
Russia_Steppe_Eneolithic 0.706±0.026
Ukraine_N 0.116±0.014
P-value 4.73919e-07 (HARD FAIL)

Admittedly, proximal models aren't easy to get right. And if you throw enough outgroups into a model, a large proportion of plausible models will fail. But I'm somewhat taken aback by these poor statistical fits.

In my opinion, mainstream Yamnaya doesn't harbor any Caucasus ancestry that wasn't already present on the Pontic-Caspian steppe during the Eneolithic or even much earlier (see here). But ultimately this problem can only be solved with direct evidence from ancient DNA, so let's now wait patiently for the right samples.

Citation...

Penske et al., Early contact between late farming and pastoralist societies in southeastern Europe, Nature, https://doi.org/10.1038/s41586-023-06334-8

See also...

Understanding the Eneolithic steppe

My take on the Erfurt Jews

I had a quick look at the genotype data from the recent Waldman et al. preprint focusing on the ancestry of early Jews from Erfurt, Germany. My impression is that the genetic origins of these Jews are somewhat more complex than claimed in the manuscript.

Indeed, I'd say the Waldman et al. characterization of the Erfurt Jews as a three-way mixture between populations similar to present-day Lebanese, South Italians and Russians doesn't exactly reflect reality.

Unlike Waldman et al., I designed an ADMIXTURE analysis that separated East Asian ancestry into East Asian and Siberian clusters, and also included Mediterranean and North African clusters. The output is available in a spreadsheet HERE. Below is a bar graph based on some of the output.

Now, keeping in mind that ADMIXTURE is not a formal mixture test, and that it estimates ancestry proportions from inferred populations, as opposed to ancient groups that actually existed, here are some key observations:

- in terms of fine scale ancestry, the Erfurt Jews show enough variation to be divided into three or four clusters, as opposed to just two as per Waldman et al.

- some of the Erfurt Jews show excess "Mediterranean" ancestry, while others excess "North African" ancestry, and this cannot be explained with ancestral populations similar to Lebanese and/or South Italians, but rather with significant gene flow from the western Mediterranean and possibly North Africa

- several of the Erfurt Jews show relatively high levels of "East Asian" ancestry that cannot be explained by admixture from Russians, or even any Russian-like populations, because such populations almost lack this type of ancestry, and instead show significant "Siberian" admixture

- as far as I can see, there are no correlations between any of the observations above and the quality of the samples. That is, low coverage doesn't appear to be causing the aforementioned excess "Mediterranean", "North African" and/or "East Asian" ancestry proportions.

Investigating this in more detail with, say, formal statistics will take some time. But I was able to reproduce the results from the above ADMIXTURE run using several somewhat different datasets, so that's something.

It seems to me that Waldman et al. want a simple and elegant model to explain the data, which is understandable, but I do think they should at least expand their ADMIXTURE analysis to include "Siberian", "Mediterranean" and "North African" clusters, and go from there depending on what they find.

Citation...

Waldman et al., Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century, bioRxiv, posted May 16, 2022, doi: https://doi.org/10.1101/2022.05.13.491805

See also...

Mediterranean PCA update

Lousy intel

I don't like discussing current events and politics here, but it's impossible to ignore what is happening in Eastern Europe.

It's a tragedy and catastrophe for both Ukraine and Russia. It's also likely to have a negative impact on ancient DNA research, Indo-European studies, and thus also on this blog.

I'm seeing a lot of confusion online about why Russia invaded Ukraine, but I don't think it's very complicated.

After getting the better of the West in recent years, Russia finally overreached and made a massive tactical blunder, in large part because of lousy intel. More broadly, I also see this as the Soviet Union's dead cat bounce moment.

Russia will now have to reinvent itself, possibly as China's junior partner or even vassal state.

As for the "special military operation", Russia's initial plan was to achieve a quick, relatively bloodless victory, followed by a military parade in Kyiv. But obviously that's not going to happen.

Russia's back up plan, if we can call it that, seems to be to keep pushing into Ukraine at any cost, and hope that the Ukrainians finally tap out. But right now that looks like a long shot.

See also...

Matters of geography

Yamnaya people drank horse milk (Wilkin et al. 2021)

Over at Nature at this LINK. I'm guessing the claim that Yamnaya pastoralists lived in Scandinavia is a huge typo. Obviously, the authors are referring to the people of the Corded Ware culture (CWC). From the paper:

During the Early Bronze Age, populations of the western Eurasian steppe expanded across an immense area of northern Eurasia. Combined archaeological and genetic evidence supports widespread Early Bronze Age population movements out of the Pontic–Caspian steppe that resulted in gene flow across vast distances, linking populations of Yamnaya pastoralists in Scandinavia with pastoral populations (known as the Afanasievo) far to the east in the Altai Mountains1,2 and Mongolia3. Although some models hold that this expansion was the outcome of a newly mobile pastoral economy characterized by horse traction, bulk wagon transport4,5,6 and regular dietary dependence on meat and milk5, hard evidence for these economic features has not been found. Here we draw on proteomic analysis of dental calculus from individuals from the western Eurasian steppe to demonstrate a major transition in dairying at the start of the Bronze Age. The rapid onset of ubiquitous dairying at a point in time when steppe populations are known to have begun dispersing offers critical insight into a key catalyst of steppe mobility. The identification of horse milk proteins also indicates horse domestication by the Early Bronze Age, which provides support for its role in steppe dispersals. Our results point to a potential epicentre for horse domestication in the Pontic–Caspian steppe by the third millennium bc, and offer strong support for the notion that the novel exploitation of secondary animal products was a key driver of the expansions of Eurasian steppe pastoralists by the Early Bronze Age.

Wilkin, S., Ventresca Miller, A., Fernandes, R. et al. Dairying enabled Early Bronze Age Yamnaya steppe expansions. Nature (2021). https://doi.org/10.1038/s41586-021-03798-4

See also...

On the origin of the Corded Ware people

Viking world open analysis and discussion thread

Global25 and Celtic vs Germanic coordinates for most of the samples from the recent Margaryan et al. Viking paper are now available HERE and HERE, respectively. Look for the VK2020 prefix.

Feel free to put them through their paces and let me know what you find. Below are a couple of examples of what can be done with these coordinates using Vahaduo Global25 Views.

See also...

Viking invasion at bioRxiv

Commoner or elite?

Who were the people of the Nordic Bronze Age?

Don't believe everything you read in peer reviewed papers

Case in point, here's a quote from a recent paper at the Journal of Human Genetics (emphasis is mine):

The Mordovian and Csango samples have a moderate to slight orientation toward the Central-Asian and Siberian Turkic groups. This could suggest the more significant East Eurasian or Turkic ancestry of these populations, which should be further investigated. German samples are inhomogeneous, and some of the German samples also show this tendency, which can be the result of the recent 20th century Turkish immigration into Germany [42].

Nope, these German samples don't show anything even remotely resembling recent Turkish ancestry. The authors of the paper, Ádám, V., Bánfai, Z., Maász, A. et al., should've been able to figure this out, even with the standard analyses that they ran. Failing that, the peer reviewers at the Journal of Human Genetics should've noticed that the authors were confused.

Moreover, if the authors and peer reviewers actually bothered to take a closer look at metadata for these samples, which were sourced from the Estonian Biocentre, they'd see that they're not even from Germany. In fact, they represent self-reported ethnic Germans from Russia.

My own quick and dirty analysis of these individuals suggests that many of them harbor East Slavic and/or Volga Finnic ancestries. Indeed, only some of them can pass genetically for run of the mill Germans from Germany. The Principal Component Analysis (PCA) below is self-explanatory. It was plotted with the Vahaduo Custom PCA tools freely available here. The relevant PCA datasheet can be gotten here.

That's not to say, of course, that some Germans don't have recent Turkish ancestry, because an increasing number of Germans nowadays do, nor that people with German heritage in Russia shouldn't identify as Germans, because that's entirely their choice.

This blog post isn't about what it takes to be German, and this is not something that I ever want to discuss for obvious reasons. The point I'm making here is that the authors and peer reviewers of the said paper at the Journal of Human Genetics were sloppy and half-arsed in their approach. And, sadly, this isn't an isolated case in peer reviewed scientific literature dealing with human population genetics.

I feel that the Estonian Biocentre is also partly to blame for this cock up, due to its somewhat peculiar sampling and labelling strategies. For instance, its scientists rely solely on self-reported identity to establish the ethnic origins of their samples, and they apparently never remove genetic outliers from their datasets or even try to identify them.

Unfortunately, I fear that this relaxed approach will eventually lead to basic errors and even unusual conclusions in a number of so called peer reviewed papers.

I first raised this issue with the Estonian Biocentre about five years ago, when I noticed that some of the supposedly Polish individuals in its dataset were genetically more similar to various groups from northern Russia than to Poles from Poland. These individuals also showed significant Siberian ancestry, which was very unusual indeed. Where the hell did the Estonian Biocentre find Poles who resembled people from near the Arctic Circle, you might ask? Apparently in Estonia.

OK, I can imagine that sampling ethnic Poles from Estonia may have been easier for the Estonian Biocentre than sampling Poles from Poland. And Estonian Poles certainly make for interesting and useful data points. However, as you can see in the PCA below, some of these individuals (labeled Polish_Estonia by me) aren't representative of the native Polish population, and yet the Estonian Biocentre not only lumps them with their Poles from Poland, but even labels them with the word "Poland". The relevant PCA datasheet can be gotten here.

However, based on my communications with some of the scientists at the Estonian Biocentre, including head honcho Mait Mestpalu, it seems that nothing will ever change there in regards to this issue. Who knows, perhaps some day we'll see a paper based on Estonian Biocentre data in the Journal of Human Genetics claiming that Poles originated near the Arctic Circle? I wouldn't be shocked if that actually happened.

Citation...

Ádám, V., Bánfai, Z., Maász, A. et al. Investigating the genetic characteristics of the Csangos, a traditionally Hungarian speaking ethnic group residing in Romania. J Hum Genet (2020). https://doi.org/10.1038/s10038-020-0799-6

See also...

Like three peas in a pod

Fatyanovo males were rich in Y-haplogroup R1a-Z93 (Saag et al. 2020 preprint)

I'd say that thanks to this preprint we're now a lot closer to solving the mystery of the Sintashta people. Over at bioRxiv at this LINK. From the preprint:

Transition from the Stone to the Bronze Age in Central and Western Europe was a period of major population movements originating from the Ponto-Caspian Steppe. Here, we report new genome-wide sequence data from 28 individuals from the territory north of this source area - from the under-studied Western part of present-day Russia, including Stone Age hunter-gatherers (10,800-4,250 cal BC) and Bronze Age farmers from the Corded Ware complex called Fatyanovo Culture (2,900-2,050 cal BC). We show that Eastern hunter-gatherer ancestry was present in Northwestern Russia already from around 10,000 BC. Furthermore, we see a clear change in ancestry with the arrival of farming - the Fatyanovo Culture individuals were genetically similar to other Corded Ware cultures, carrying a mixture of Steppe and European early farmer ancestry and thus likely originating from a fast migration towards the northeast from somewhere in the vicinity of modern-day Ukraine, which is the closest area where these ancestries coexisted from around 3,000 BC.

...

Interestingly, in all individuals for which the chrY hg could be determined with more depth (n=6), it was R1a2-Z93 (Table 1, Supplementary Data 2), a lineage now spread in Central and South Asia, rather than the R1a1-Z283 lineage that is common in Europe [38,39].

Saag et al., Genetic ancestry changes in Stone to Bronze Age transition in the East European plain, BioRxiv, Posted July 03, 2020, doi: https://doi.org/10.1101/2020.07.02.184507

See also...

Like three peas in a pod

Like three peas in a pod

One of the most interesting questions still waiting to be answered by ancient DNA is where exactly did the ancestors of the present-day European and South Asian bearers of Y-haplogroup R1a part their ways? Indeed, the answer to this question is likely to be informative about the place and time of the split between the Balto-Slavic and Indo-Iranian language families.

I was doing some reading today and discovered that the peoples associated with the Bronze Age Fatyanovo-Balanovo and Unetice archeological cultures shared strikingly similar metalwork, despite being separated by well over two thousand kilometers of forest and steppe. Apparently, this similarity is especially pronounced in the metalwork of the Unetice culture from what is now Slovakia (see Ancient Metallurgy in the USSR: The Early Metal Age, page 136).

S11953 is currently the only sample from Slovakia associated with the Unetice culture (Sirak et al. 2020). There are no Fatyanovo-Balanovo samples available yet. However, as far as I can tell, I0432 from Samara, Russia, should be a decent stand in (Mathieson et al. 2015).

Of course, both S11953 and I0432 belong to Y-haplogroup R1a. Moreover, S11953 belongs to a typically Balto-Slavic subclade of R1a, while I0432 belongs to a closely related subclade that is dominant nowadays among the Indo-Iranian speakers of Asia.

S11953 is younger than I0432, but this doesn't necessarily mean that his ancestors arrived in East Central Europe from deep in Russia during the Bronze Age. Indeed, the opposite is more likely to be true. That is, I0432 is probably the recent decedent of migrants from somewhere near the North Carpathians, because he shows elevated European Neolithic farmer ancestry compared to earlier ancients from the Samara region (see here).

Below is a Principal Component Analysis (PCA) showing how S11953 and I0432 compare to each other in the context of ancient West Eurasian genetic variation. Obviously, they're sitting in the same part of the plot, which suggests that they harbor very similar ratios of ancient genetic components and probably share relatively recent ancestry. The relevant PCA datasheet is available here.

I've also highlighted myself, Davidski, on the plot. That's because I share the same Balto-Slavic-specific subclade of R1a with S11953 and, in terms of overall ancestry, I'm similar to both S11953 and I0432. Moreover, I'm the speaker of Polish, which is a Balto-Slavic language. What are the chances that we're dealing here with a remarkable string of coincidences? Indeed, was the North Carpathian region perhaps the homeland of the language ancestral to both Balto-Slavic and Indo-Iranian?

However, please note that there's nothing unusual or remarkable about my ancestry. The vast majority of people of Central, Eastern and Northern European origin - that is, mostly the speakers of Balto-Slavic, Germanic and Celtic languages - would also land in this part of the plot.

See also...

On the doorstep of India

Y-haplogroup R1a and mental health

The mystery of the Sintashta people

Best of 2008: Corded Ware DNA from Germany

One of the biggest hits of the year for this blogger was the discovery of Y-DNA haplogroup R1a among three Corded Ware skeletons from a burial site in Eulau, eastern Germany. It's an important result, because it links one of Europe's most dominant Y-haplogroups to a major Late Neolithic archeological complex.

All three individuals were confirmed to be paternally related via their shared Y-STR haplotype. Nevertheless, the outcome appears far from a random coincidence. Consider that in Europe today R1a shows its highest frequencies in Poland and Western Russia, which are both located in former Corded Ware territory, and where the Eulau R1a haplotype appears to have its closest modern matches. Moreover, the Corded Ware culture is often classified as an Indo-European culture by archeologists and linguists, while at the same time R1a has been posited as a marker of the early Indo-Europeans by some geneticists. Needless to say, I'm expecting R1a to be a common, and perhaps dominant marker among Corded Ware samples when more of them make it to the lab.

The consensus haplotype of the three individuals (based on most complete profile) gave two exact matches in in an European population sample of 11,213 haplotypes in a set of 100 populations (as of July 2008, Release ‘‘23’’ from 2008–01-15 14:44:25): one individual from Poland (1/939 from Gdansk) and one from Russia (1/48 from Tambov).

...

The Y haplotype was predicted using the Web-based program Haplotype Predictor (9). The three individuals of grave 99 belong to haplotype R1a, with a probability of 100% based on the Y-STR profile of individual 3 (10). To confirm haplogroup status, we further amplified an 85-bp fragment covering the Y-SNP marker SRY10831.2 characteristic for R1a (11). Primer sequences are given in Table S6. Sequences and sequenced clones from independent extract of all three individuals show the specific G to A transition identifying R1a (Fig. S5).

The mitochondrial DNA (mtDNA) lineages of the Eulau skeletons belonged to haplogroups K1b (3), X2 (2), H, I, K1a2, and U5b. Most of these maternal markers aren't particularly common in Europe today, and the overall result appears decidedly unusual compared to the mtDNA frequencies of modern European populations, largely because of the low frequency of H.

I'm quite certain this is at least partly due to the small sample size and presence of several related individuals skewing some of the frequencies. However, it's interesting to note that this pattern of discontinuity between mtDNA gene pools from different time periods has also been reported in other studies, some with larger samples, and focusing on different regions of Europe. So it might well be a signal of significant shifts in mtDNA frequencies during European prehistory and early history, possibly as a result of major migrations leading to significant population replacements.

Interestingly, one of the ancient K1b lineages most closely matched a haplotype shared by two modern Shugnans from Tajikistan. Exactly how the Corded Ware individual is related to these two Central Asians isn't clear yet, but Shugni is an Indo-Iranian language, so some kind of early Indo-European relationship is possible.

Citation...

Wolfgang Haak et al, Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age, PNAS, Published online before print November 17, 2008, doi:10.1073/pnas.0807592105