Paleogenomics of Upper Paleolithic to Neolithic European hunter-gatherers

[Finn]

Genetic profile

"TRB North German Plain" was also sharp differentiated from the neighbours.

Gross

"TRB North German Plain": HG/ Ertebølle, 70%- EEF, 30%

Neighbours:

North: TRB Sweden: HG 25%-EEF 75%
East: TRB Poland: HG 20%- EEF 80%
South: Wartberg: HG 40%- EEF 60%

[Finn]

And my hunch is that this excess of HG in these TRB-North German Plain even left a phenotypic marker there.

As represented by Coon's Borreby (1939), on the North German Plain:



Although I total agree with Gerhardt (1969), about the Borreby type:

It is just a changing conglomerate of certain robust characteristics, a kind of clan identification, nothing more than that, it has no typogenetic meaning whatsoever.

Nevertheless this reconstruction of the affiliated 'WHG' Iron Gate head doesn't need much imagination I guess:



(and euhm look at the avatar hahahah

[Billyh]

I get the point about Basal Eurasian diversity, in your case, you are hypothesizing Crown Eurasians and a branch of Basal Eurasians separately mixed with Neanderthals. The former is ancestral to Eurasians today (as well as many ancients) and the latter is ancestral to Zlaty Kun. In this situation it should be possible to detect the differences in the profile of the Neanderthal ancestry in Crown Eurasians (both modern and ancient) vs the profile of the Neanderthal ancestry in Zlaty Kun. This is important because in the basic Crown Eurasian hypothesis, there is one Neanderthal admixture which defines all of the Crown Eurasians and so the descendants (including Zlaty Kun) should have a similar profile/range of profiles. In the alternate hypothesis you posited, there would be a non-Crown Eurasian group with Neanderthal admixture which is ancestral to Zlaty Kun and have a different profile which stands out from all Crown Eurasians. So there is an experiment which can be done to distinguish the 2 hypotheses. After the experiment is done, more complex hypotheses could be tested like if Zlaty is indeed non-Crown and say, for instance, the experimental result shows Zalty's Neanderthal profile comes similar to Crowns then could that be caused by Zlaty/Zlaty-like contribution back to Crown Eurasians? This could be the next step to the complexity of the experiment, but only after the first step is resolved.

I believe such an experiment could be possible, but it really depends. Think of modern populations. We can distinguish trace amounts of Han from trace amounts of Siberian decently well, so I would assume due to the time and geography of Neanderthal samples, that we would also be able to distinguish trace amounts of European Neanderthal from ME/CA Neanderthal. However, I have no similarity with the substructure of Neanderthals, if we have discovered any. And even if there is detectable subgroups, we don't know where ZK got neanderthal. So it is possible that ZK's neanderthal comes from a similar area as Crown's Neanderthal to the point where we couldn't distinguish them in small amounts.

However, I don't think Crown Eurasians are the product of just a single Neanderthal admixture event. I say this because IUP Euros (BK, Oase1) show a greater affinity to European Neanderthals than contemporary Eurasian groups do, and have more Neanderthal than East Eurasians. This implies some degree of introgression from European Neanderthals, and if these populations have modern descendants (which I believe they do) then that means not all Neanderthal in moderns comes from one mixture event.

[CopperAxe]

1. The fact is that there are no archeological signs of the migration of Butovo to the Baltic sea, and even more so to Sweden. Rather, on the contrary, the culture of Butovo was formed as a result of the interaction of the Swiderian culture that arrived and the local Ressetin culture.
2. For Latvia HG and Sweden HG f3 statistics is positive if model EHG+WHG is used, it is negative only if ANE+WHG is used.
3. There is no high dispersion among Sweden HG and Latvia HG. For example if it was recent mixing of EHG and WHG some of the samples could be more WHG-like, some more EHG-like. But this is not observed, the given populations are quite homogeneous. For example, in Denmark, most of the samples are similar to WHG, but some are more like Scandinavian HGs, showing some mixing.



It cannot be ruled out that ANE admixture was already present in the Paleolithic in Central Europe in the Hamburg and Lyngby cultures. In Gravettian times ANE samples have not yet been found in Eastern Europe, there was a Sungir/Kostenki/Vestonice cluster that stretched from Eastern to Central Europe. So, the ANE migration could be later and overlap the earlier population. And this migration could also reach Central Europe.

Günther 2018 proposed that the EHG side migrated into Scandinavia from the Northeast, citing the articles which discuss findings and the spread of pressure micro-blade tools across Scandinavia.

[Kunig]

1. The fact is that there are no archeological signs of the migration of Butovo to the Baltic sea, and even more so to Sweden. Rather, on the contrary, the culture of Butovo was formed as a result of the interaction of the Swiderian culture that arrived and the local Ressetin culture.
2. For Latvia HG and Sweden HG f3 statistics is positive if model EHG+WHG is used, it is negative only if ANE+WHG is used.
3. There is no high dispersion among Sweden HG and Latvia HG. For example if it was recent mixing of EHG and WHG some of the samples could be more WHG-like, some more EHG-like. But this is not observed, the given populations are quite homogeneous. For example, in Denmark, most of the samples are similar to WHG, but some are more like Scandinavian HGs, showing some mixing.



It cannot be ruled out that ANE admixture was already present in the Paleolithic in Central Europe in the Hamburg and Lyngby cultures. In Gravettian times ANE samples have not yet been found in Eastern Europe, there was a Sungir/Kostenki/Vestonice cluster that stretched from Eastern to Central Europe. So, the ANE migration could be later and overlap the earlier population. And this migration could also reach Central Europe.

The microblade technique is found right across the East Baltic and Scandinavia, so whilst the Butovo culture is indeed further inland, it is the vector for many of the techniques adapted by East Baltic HGs and the proximal source of EHG-related admixture.

SHG is indeed a more complex case, because there are no male ANE/ EHG uniparentals such as Yhg R1 or Q1, despite having higher % EHG. It seems to be female mediated and via northern groups such as Karelia / Peschanitsa

People rarely run admixture F3, F4s and qpADM are better.

You should note that micro-blades (~ archaeological proxy for ANE in Europe) are missing in Lyngby groups which used Ahrensburgian tanged-points, whilst the Hamburg culture was Magdalenian derived, so def. no ANE~

[Ryukendo]

I'm assuming you've read deeper into this subject than I. My understanding based on skimmed reading is that a sample with missing data in a region has it's nearby regions analyzed and compared to a set of references to determine the most likely values for the missing data, yes? In that case, the references are mostly going to be modern or at the very least much younger when samples of great age are analyzed. To that end how biased are the results going to be towards mutation/selection events that post-date the sample? Was there any sort of trial such as... take Ust-Ishim (who is superb coverage) > remove portions of the data > run the imputation program > compare results?

People do do this, its standard practice. The match rate used to be >99% already pre-2020 for aDNA with coverage >0.4, now its even better, and with increasing size and geographic diversity of modern biobanks/genome datasets its only going to get even better.

The trick here is to see that the gaps between snps are often very short, and so the haplotypes that cover the gap are extremely old and so only get shuffled around among populations and don't really "disappear" so to speak (i.e. drift to freq of 0 everywhere, or gain so many new mutations that the freq of the original haplotype is now 0. Most genetic drift occurs instead when haplotypes get replaced by other haplotypes, or you get a change in freq between them). So with larger and larger sizes of biobanks/genome datasets, sooner or later almost every single short haplotype at every single locus will be represented in the biobank/dataset (i.e., we have near-saturation). Yes, even Ust-Ishim haplotypes, he will have combinations of haplotypes that are low-frequency today and not strongly overrepresented among any given population today but he will not have haplotypes that are completely missing today.

Issues arise when the alleles in the ancient genome you are imputing are supposed to be rare ones, and indeed sites around snps with low minor allele frequency among moderns are always the ones that are the least properly imputed and are most biased toward the majority haplotype in the reference panel. As your reference dataset size increases though this problem progressively disappears. And if you are worried, you can always exclude the sites with lowest minor allele frequency/you detect the strongest bias toward the majority haplotype, and this still gives you a lot of data to work with.

Edit:
P.S. thinking about it, Ust-Ishim had recent Neanderthal ancestors and much higher Neanderthal ancestry and so may have Neanderthal haplotypes that are missing today, so this is a special case. But snps that fall in the Neanderthal segments that are missing today will have extremely low minor allele frequency in the reference panel and so will get purged in the quality control step, which is very common in imputation-based pipelines, and you end up only working with human segments from the Ust-Ishim genome.

[Ryukendo]

Here is what Allentoft specifically writes:




It is clear that Allentoft obviously does not deny the presence in the genetic profile of the Battle Axes of a part from European "farmers". His assertion relates to the provenance of this part. The confrontation with previous analyzes lies in the ability of tools based on allelic statistics (such as Admixture or qpAdm) to differentiate between Globular Amphora (Poland) and Scandinavian TRB (or related, such as Swedish megalithic) as sources. My own analyzes with qpAdm ask to decide between very close tail probs, and differences on the coefficients which are in the window of uncertainty. So while I have said, in other places, that I was troubled by Allentoft's assertions on this point, I never said he was wrong. I'm troubled, that's all. Furthermore, I don't know what you call a "basic sanity check". The problem seems to me precisely beyond the reach of "basic" tools, whatever they are.

edit: As for post #424 from Ryukendo, to be clear, I really agree that the new tools based on IBDs are an important, perhaps decisive step forward. These tools are, for the reasons he mentions, demanding tools, in terms of application constraints and precision of interpretation. But I don't see any tools other than them that can help decide between genetic sources that are very similar in terms of allelic statistics.

Anglesqueville, could you run this f4 stat for us as a favor?
F4 (Mbuti.SG, Swedish_Battle_Axe.SG; Sweden_Megalithic.SG, Poland_Globular_Amphora.SG)
(I'm assuming that there are .SG versions for these, since the middle two are Scandinavian and presumably come from Eske Willerslev's group? And Globular Amphora should have at least a few .SG individuals from Reich?)

Thanks if you can! In the rotating outgroup setup Kunig ran both qpAdms passed, so it seems like whatever preference existed it was not that one-sided, but this is just another way to confirm.

[Kunig]

Anyhow I guess we must take the complete picture, in the NW Single Grave Culture (range N Netherlands -Jutland), 'in the middle' on the Danish Isles/Northern Germany FBC with high HG, and in the NE Scania FBC with partly high EEF (Gokhem) and Battle Axe. To me this is kind of basic. And on subregional level there are differences too (like in North Dutch Drenthe with FBC Ostorf derived and incoming SGC).

Indeed, there are a lof of subtleties that only archaeology & uniparentals can tell us about. All fancy tests are limited in resolution in some way.

Is the fact that BAx in all likelihood derives most of its ancestry from local TRb than Polish GAC going to change the way we breathe ? No

But details matter, and scholars would do better to come up with less trivial models, no matter what topic

[Kunig]

Anglesqueville, could you run this f4 stat for us as a favor?
F4 (Mbuti.SG, Swedish_Battle_Axe.SG; Sweden_Megalithic.SG, Poland_Globular_Amphora.SG)
(I'm assuming that there are .SG versions for these, since the middle two are Scandinavian and presumably come from Eske Willerslev's group? And Globular Amphora should have at least a few .SG individuals from Reich?)

Thanks if you can! In the rotating outgroup setup Kunig ran both qpAdms passed, so it seems like whatever preference existed it was not that one-sided, but this is just another way to confirm.

To repeat, it isn't a one-shot answer. Iin this case, F4's show nothing overriding, because of too many confounding ancestries


Mbuti.DG SWE_BAC.SG SWE_Megalithic POL_Globular_Amphora -0.0000 0.002820 -0.002 36857 36858 696703



But for our friend learning about the East Baltic microblades, the answer is decisive


Mbuti.DG LVA_HG RUS_Karelia_HG RUS_AfontovaGora3 -0.0672 0.005349 -12.568 11298 12927 250390

[Ryukendo]

To repeat, it isn't a one-shot answer. Iin this case, F4's show nothing overriding, because of too many confounding ancestries


Mbuti.DG SWE_BAC.SG SWE_Megalithic POL_Globular_Amphora -0.0000 0.002820 -0.002 36857 36858 696703



But for our friend learning about the East Baltic microblades, the answer is decisive


Mbuti.DG LVA_HG RUS_Karelia_HG RUS_AfontovaGora3 -0.0672 0.005349 -12.568 11298 12927 250390

Reich v54.1_1240K_public
Admixtools qpfstats (allSNPs = YES) > qpAdm

right pops:
Russia_Ust_Ishim.DG
Cameroon_SMA.DG
Italy_North_Villabruna_HG
Czech_Vestonice16
Belgium_UP_GoyetQ116_1
Russia_MA1_HG.SG
Iran_GanjDareh_N
Kazakhstan_Botai_Eneolithic.SG
Russia_Kostenki14.SG
Ukraine_Mesolithic
Indian_GreatAndaman_100BP.SG
Russia_Arkhangelsk_Veretye_Mesolithic.SG
Israel_PPNB
Georgia_Kotias.SG
Turkey_N_I0707


pop: Sweden_BAC.SG hetrate: 0.061 valid snps: 1008191 samples: 3
pop: Estonia_CordedWare.SG hetrate: 0.072 valid snps: 992581 samples: 4
pop: Poland_Koszyce_GlobularAmphora.SG hetrate: 0.121 valid snps: 1060740 samples: 6
pop: Sweden_Ansarve_Megalithic.SG hetrate: 0.097 valid snps: 1058726 samples: 6


left pops:
Sweden_BAC.SG
Estonia_CordedWare.SG
Sweden_Ansarve_Megalithic.SG


best coefficients: 0.814 0.186
totmean: 0.814 0.186
boot mean: 0.814 0.186
std. errors: 0.039 0.039


fixed pat wt dof chisq tail prob
00 0 13 13.644 0.39935 0.814 0.186
01 1 14 32.852 0.0030258 1.000 0.000
10 1 14 397.262 0 0.000 1.000
best pat: 00 0.39935 - -
best pat: 01 0.0030258 chi(nested): 19.208 p-value for nested model: 1.1724e-05



left pops:
Sweden_BAC.SG
Estonia_CordedWare.SG
Poland_Koszyce_GlobularAmphora.SG


best coefficients: 0.816 0.184
totmean: 0.816 0.184
boot mean: 0.816 0.184
std. errors: 0.039 0.039


fixed pat wt dof chisq tail prob
00 0 13 13.972 0.375836 0.816 0.184
01 1 14 32.874 0.00300399 1.000 0.000
10 1 14 496.651 0 0.000 1.000
best pat: 00 0.375836 - -
best pat: 01 0.00300399 chi(nested): 18.902 p-value for nested model: 1.37592e-05

Its really striking that both analyses show basically the same proportions (+-4%) and almost no preference between the two even in a rotating outgroup setup. This can show that the incoming Battle Axe had EEF related to both GAC and local megalithics almost evenly, but really what it shows is that there is almost no drift that differentiates Swedish megalithics and GAC, nothing specific to each population that is shared with Battle Axe anyway that is detectable in qpAdm, such that the two models can be clearly distinguished in p-value (e.g. differ in p-value by more than 10^1-2).