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Monday, March 25, 2024

High-resolution stuff


I just emailed this to the authors of High-resolution genomic ancestry reveals mobility in early medieval Europe, a new preprint at bioRxiv [LINK].

I appreciate that Polish population history is not the main focus of your preprint, and also that you're constrained by the lack of relevant and suitably high quality ancient genomes from East-Central and Eastern Europe. However, I must say that your analysis of the Medieval Polish population and resulting conclusions about Polish population history don't reflect reality.

Your Poland_Middle_Ages genomic cluster is made up of just six samples that don't fully represent the genetic complexity of the core population of Medieval Poland.

As a result, you classified PCA0148 as one of the Poland_Middle_Ages outliers, even though this sample isn't an outlier when analyzed within the context of the full set of published Polish Medieval genomes.

Moreover, PCA0148 is very similar to several Polish Viking Age samples that show Scandinavian-specific genome-wide and Y-chromosome haplotypes, and probably likewise shows some Scandinavian-related ancestry.

This is important to note when attempting to recapitulate Polish population history, because it suggests that Scandinavian-related ancestry played a formative role in the shaping of the core Polish Medieval genetic cluster.

Thus, you might be correct when you claim that the six samples in your Poland_Middle_Ages cluster don't show any "detectable" Scandinavian-related ancestry, but this doesn't necessarily mean that this type of ancestry isn't a key part of the post-Iron Age Polish population history.

Below is a self-explanatory Principal Component Analysis (PCA) plot that illustrates my points. Interestingly, Figure 3c in your preprint shows very similar outcomes in regards to the post-Iron Age Polish population history. But the style and scale of your figure makes it difficult to spot the subtle but likely genuine Northwest European-related genetic shifts shown by PCA0148, the Viking context samples and present-day Poles relative to the Poland_Middle_Ages cluster.

However, I'm also skeptical that your Poland_Middle_Ages cluster doesn't carry any detectable or even significant Scandinavian-related ancestry. That's because I suspect that there might be some technical issues with your analysis that are masking this type of ancestry in the Polish samples.

Your top mixture model for the Poland_Middle_Ages cluster is, in all likelihood, an extreme statistical abstraction of reality, rather than a close reflection of it. That's because, due to a combination of historical, geographical and genetic factors, neither Italy.Imperial(I).SG nor Lithuania.IronRoman.SG are realistic formative source populations for the Medieval Polish gene pool.

One of the reasons why you ended up with such a surprising result is probably the lack of suitable samples from East-Central and Eastern Europe, especially those associated with plausibly the earliest Slavic-speaking populations.

It's also possible that basing your mixture model on formal statistics played a key part.

Formal statistics-based mixture models are known to be biased towards outcomes involving mixture sources from the extremes of mixture clines. If your analysis is affected by this problem, then this would help to explain why you characterized the Poland_Middle_Ages cluster as simply a two-way mixture between a Middle Eastern-related group from Imperial Rome and a Baltic population with a very high cut of European hunter-gatherer ancestry.

I do note that on page 6 of your manuscript you consider the possibility that the Southern European-related signal in the Poland_Middle_Ages cluster might only be very distantly related to Italy.Imperial(I).SG, and that it may even have spread across Poland with early Slavic speakers. This is a great point, and I think it should be emphasized and expanded upon, because I suspect that the problem runs deeper than this.

For instance, if the early Slavic ancestors of Poles carried substantially more Southern European-related ancestry than Lithuania.IronRoman.SG, and this ancestry was, say, more Balkan-related than Italian-related, then this might radically change your modeling of the Poland_Middle_Ages cluster. That's because these early Slavs would be positioned in a very different genetic space than Lithuania.IronRoman.SG, which could potentially require a significant signal of Scandinavian-related ancestry to get a robust mixture model.

Finally, it might be useful to consider Isolation-by-Distance as a partial vector for the Italy.Imperial(I).SG-related signal in Medieval Poland.

The full set of published Polish Medieval genomes includes a number of outliers with obvious ancestry from Western Europe and the Balkans. These people probably don't represent any large-scale migrations into Poland, but rather the movements of individuals and small groups. Over time, such small-scale mobility may have had a fairly significant impact on the genetic character of the Polish population.

Update 26/03/2024: I sent another email to Speidel et al., this time in regards to their analysis of present-day Hungarians.

Your preprint also claims that present-day Hungarians are genetically similar to Scythians, and that this is consistent with the arrival of Magyars, Avars and other eastern groups in this part of Europe.

However, present-day Hungarians are overwhelmingly derived from Slavic and German peasants from near Hungary. This is not a controversial claim on my part; it's backed up by historical sources and a wide range of genetic analyses.

Hungarians still show some minor ancestry from Hungarian Conquerors (early Magyars), but this signal only reliably shows up in large surveys of Y-chromosome samples.

The Scythians that you used to model the ancestry of present-day Hungarians are of local, Pannonian origin, and they don't show any eastern nomad ancestry. So they're either acculturated Scythians, or, more likely, wrongly classified as Scythians by archeologists.

And since these so-called Scythians lack eastern nomad ancestry, the similarity between them and present-day Hungarians is not a sign of the impact from Avars, Hungarian Conquerors and the like, but rather a lack of significant input from such groups in present-day Hungarians.

Citation...

Speidel et al., High-resolution genomic ancestry reveals mobility in early medieval Europe, bioRxiv, Posted March 19, 2024, doi: https://doi.org/10.1101/2024.03.15.585102

See also...

Wielbark Goths were overwhelmingly of Scandinavian origin

Thursday, February 22, 2024

Berkeley, we have a problem


A new preprint at bioRxiv by Kerdoncuff et al. makes the following, somewhat surprising, claim:

One of the individuals, referred to Sarazm_EN_1 (I4290) described above that was discovered with shell bangles showing affiliation with South Asia, has significant amount AHG-related ancestry, while a model without AHG-related ancestry provides the best fit for Sarazm_EN_2 (I4210) (Table S4.5).

First of all, the authors are actually referring to sample ID I4910 not I4210.

The aforementioned table, based on qpAdm output, shows that I4290 has 15.9% AHG-related ancestry and basically no Anatolian farmer-related ancestry. It also shows that I4910 has no AHG-related ancestry but 17.9% Anatolian farmer-related ancestry.

AHG stands for Andaman hunter-gatherer. The authors are using it as a proxy for South Asian hunter-gatherer ancestry.

However, I've looked at I4290 and I4910 in great detail over the years using ADMIXTURE, Principal Component Analysis (PCA), and qpAdm. And I'm quite certain that they do not show any obvious, above noise level South Asian ancestry. Indeed, I'd say that if they do have some minor South Asian ancestry, then I4910 probably has more of it than I4290.

Kerdoncuff et al. used the following "right pops" or outgroups: Ethiopia_4500BP.SG, WEHG, EEHG, ESHG, Dai.DG, Russia_Ust_Ishim_HG.DG, Iran_Mesolithic_BeltCave and Israel_Natufian.

This means they mixed data that were generated in very different ways (DG, SG and capture) and included some poor quality samples. For instance, the highest coverage version of Iran_Mesolithic_BeltCave offers just ~50K SNPs.

Mixing different types of data and relying on low coverage samples, even in part, often has negative consequences when using qpAdm. So I suspect that the above mentioned mixture results for I4290 are skewed by a poor choice of outgroups.

When I run qpAdm I try to stick to one type of data and avoid low quality singletons in the outgroups. This is the best qpAdm model that I can find for Sarazm_EN:

right pops:
Cameroon_SMA
Morocco_Iberomaurusian
Israel_Natufian
Levant_N
Iran_GanjDareh_N
Turkey_N
Russia_Karelia_HG
Russia_WestSiberia_HG
Mongolia_North_N
Brazil_LapaDoSanto_9600BP

Sarazm_EN
Kazakhstan_Botai_Eneolithic 0.113±0.017
Turkmenistan_C_Geoksyur_subset 0.887±0.017
P-value 0.06392

Sarazm_EN_1 (I4290)
Kazakhstan_Botai_Eneolithic 0.129±0.021
Turkmenistan_C_Geoksyur_subset 0.871±0.021
P-value 0.11019

Sarazm_EN_2 (I4910)
Kazakhstan_Botai_Eneolithic 0.104±0.021
Turkmenistan_C_Geoksyur_subset 0.896±0.021
P-value 0.07427

Also...

Sarazm_EN
Andaman_hunter-gatherer -0.018±0.020
Kazakhstan_Botai_Eneolithic 0.123±0.019
Turkmenistan_C_Geoksyur_subset 0.895±0.020
P-value 0.0298403
(Infeasible model)

Please note that Turkmenistan_C_Geoksyur_subset is made up of just three relatively high quality individuals: I8504, I12483 and I12487. That's because it's not possible to model the ancestry of Sarazm_EN using the full Geoksyur set, probably due to subtle genetic substructures within the latter.

Below is a PCA plot that, more or less, reflects my qpAdm model. I4290 and I4910 are sitting right next to each other in a cluster of ancient Central and Western Asians, and it's actually I4910 that is shifted slightly towards the South Asian pole of the PCA. Indeed, I can confidently say that there's no way to design a PCA in which I4290 is shifted significantly towards South Asia relative to I4910.

Citation...

Kerdoncuff et al., 50,000 years of Evolutionary History of India: Insights from ∼2,700 Whole Genome Sequences, bioRxiv, posted February 20, 2024, doi: https://doi.org/10.1101/2024.02.15.580575

See also...

The Nalchik surprise

A comedy of errors

Monday, February 12, 2024

The Nalchik surprise


If, like Iosif Lazaridis, you subscribe to the idea that the Yamnaya people carry early Anatolian farmer-related admixture that spread into Eastern Europe via the Caucasus, then I've got great news for you.

We now have a human sample from the Eneolithic site of Nalchik in the North Caucasus, labeled NL122, that packs well over a quarter of this type of ancestry (see here). Below is a quick G25/Vahaduo model to illustrate the point (please note that Turkey_N = early Anatolian farmers).

Target: Nalchik_Eneolithic:NL122
Distance: 2.1934% / 0.02193447
60.8 Russia_Steppe_Eneolithic
26.2 Turkey_N
13.0 Georgia_Kotias

On the other hand, if, again like Iosif Lazaridis, you subscribe to the idea that the Indo-European language spread into Eastern Europe via the Caucasus in association with this early Anatolian farmer-related admixture, then I've got terrible news for you.

That's because NL122 is apparently dated to a whopping 5197-4850 BCE (see here). This dating might be somewhat bloated, possibly due to what's known as the reservoir effect, because the Nalchik archeological site is generally carbon dated to 4840–4820 BCE.

However, even with the younger dating, this would still mean that early Anatolian farmer-related ancestry arrived in the North Caucasus, and thus in Eastern Europe, around 4,800 BCE at the latest. That's surprisingly early, and just too early to be relevant to any sort of Indo-European expansion from a necessarily even earlier Proto-Indo-Anatolian homeland somewhere south of the Caucasus.

This means that NL122 effectively debunks Iosif Lazaridis' Indo-Anatolian hypothesis. Unless, that is, Iosif can provide evidence for a more convoluted scenario, in which there are at least two early Anatolian farmer-related expansions into Eastern Europe via the Caucasus, and the expansion relevant to the arrival of Indo-European speech came well after 5,000 BCE.

I haven't done any detailed analyses of NL122 with formal stats and qpAdm. But my G25/Vahaduo runs suggest that it might be possible to model the ancestry of the Yamnaya people with around 10% admixture from a population similar to NL122.

Target: Russia_Samara_EBA_Yamnaya
Distance: 3.4123% / 0.03412328
72.6 Russia_Progress_Eneolithic
18.2 Ukraine_N
9.2 Nalchik_Eneolithic

However, I don't subscribe to the idea that the Yamnaya people carry early Anatolian farmer-related admixture that spread into Eastern Europe via the Caucasus (on top of what is already found in Progress Eneolithic). Based on basic logic and a wide range of my own analyses, I believe that they acquired this type of ancestry from early European farmers, probably associated with the Trypillia culture. For instance...

Target: Russia_Samara_EBA_Yamnaya
Distance: 3.2481% / 0.03248061
80.2 Russia_Progress_Eneolithic
13.6 Ukraine_Neolithic
6.2 Ukraine_VertebaCave_MLTrypillia
0.0 Nalchik_Eneolithic

Another way to show this is with a Principal Component Analysis (PCA) that highlights a Yamnaya cline made up of the Yamnaya, Steppe Eneolithic and Ukraine Neolithic samples. As you can see, dear reader, there's no special relationship between the Yamnaya cline and Nalchik_Eneolithic. The Yamnaya samples, which are sitting near the eastern end of the Yamnaya cline, instead seem to show a subtle shift towards the Trypillian farmers.

Indeed, I also don't exactly understand the recent infatuation among many academics, especially Iosif Lazaridis and his colleagues, with trying to put the Proto-Indo-Anatolian homeland somewhere south of the Caucasus. Considering all of the available multidisciplinary data, I'd say it still makes perfect sense to put it in the Sredny Stog culture of the North Pontic steppe, in what is now Ukraine.

Please note that all of the G25 coordinates used in my models and the PCA are available HERE.

See also...

The Caucasus is a semipermeable barrier to gene flow

Saturday, January 13, 2024

Romans and Slavs in the Balkans (Olalde et al. 2023)


It's always amusing to see some random Jovan or Dimitar arguing online that Slavic speakers have been in the Balkans since at least the Neolithic.

Obviously, Slavic peoples only turned up in the Balkans during the early Middle Ages. It's just that their linguistic and genetic impact on the region was so profound that it may seem like they've been there forever.

A new paper at Cell by Olalde et al. makes this point well. See here.

That's not to say, however, that it's an ideal effort. The paper's qpAdm mixture models probably could've been more precise and realistic. Genes of the Ancients has a useful discussion on the topic here.

Interestingly, Olalde et al. admit that they can't detect much, if any, admixture from the Italian Peninsula in the Balkans, even in samples dating to the Roman period. And yet, this doesn't stop them from accepting that the Roman Empire had a massive cultural and demographic impact on the Balkans.

I also assume that, by extension, they don't deny that Latin was introduced into the Balkans from the Italian Peninsula.

That is, Latin spread into the Balkans without any noticeable genetic tracer dye, and it eventually gave rise to modern Romanian spoken by millions of people today in the eastern Balkans. This might be a useful data point to keep in mind when discussing the spread of Indo-European languages into Anatolia.

See also...

Dear Iosif, about that ~2%